Barcoding a quantified food web: crypsis, concepts, ecology and hypotheses.

PubMed

Smith, M Alex; Eveleigh, Eldon S; McCann, Kevin S; Merilo, Mark T; McCarthy, Peter C; Van Rooyen, Kathleen I

2011-01-01

The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana--SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD)--the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the "bird feeder effect") and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time.

Barcoding a Quantified Food Web: Crypsis, Concepts, Ecology and Hypotheses

PubMed Central

Smith, M. Alex; Eveleigh, Eldon S.; McCann, Kevin S.; Merilo, Mark T.; McCarthy, Peter C.; Van Rooyen, Kathleen I.

2011-01-01

The efficient and effective monitoring of individuals and populations is critically dependent on correct species identification. While this point may seem obvious, identifying the majority of the more than 100 natural enemies involved in the spruce budworm (Choristoneura fumiferana – SBW) food web remains a non-trivial endeavor. Insect parasitoids play a major role in the processes governing the population dynamics of SBW throughout eastern North America. However, these species are at the leading edge of the taxonomic impediment and integrating standardized identification capacity into existing field programs would provide clear benefits. We asked to what extent DNA barcoding the SBW food web would alter our understanding of the diversity and connectence of the food web and the frequency of generalists vs. specialists in different forest habitats. We DNA barcoded over 10% of the insects collected from the SBW food web in three New Brunswick forest plots from 1983 to 1993. For 30% of these specimens, we amplified at least one additional nuclear region. When the nodes of the food web were estimated based on barcode divergences (using molecular operational taxonomic units (MOTU) or phylogenetic diversity (PD) – the food web became much more diverse and connectence was reduced. We tested one measure of food web structure (the “bird feeder effect”) and found no difference compared to the morphologically based predictions. Many, but not all, of the presumably polyphagous parasitoids now appear to be morphologically-cryptic host-specialists. To our knowledge, this project is the first to barcode a food web in which interactions have already been well-documented and described in space, time and abundance. It is poised to be a system in which field-based methods permit the identification capacity required by forestry scientists. Food web barcoding provided an effective tool for the accurate identification of all species involved in the cascading effects of future budworm outbreaks. Integrating standardized barcodes within food webs may ultimately change the face of community ecology. This will be most poignantly felt in food webs that have not yet been quantified. Here, more accurate and precise connections will be within the grasp of any researcher for the first time. PMID:21754977

Genetic Variation of the Endangered Neotropical Catfish Steindachneridion scriptum (Siluriformes: Pimelodidae)

PubMed Central

Paixão, Rômulo V.; Ribolli, Josiane; Zaniboni-Filho, Evoy

2018-01-01

Steindachneridion scriptum is an important species as a resource for fisheries and aquaculture; it is currently threatened and has a reduced occurrence in South America. The damming of rivers, overfishing, and contamination of freshwater environments are the main impacts on the maintenance of this species. We accessed the genetic diversity and structure of S. scriptum using the DNA barcode and control region (D-loop) sequences of 43 individuals from the Upper Uruguay River Basin (UUR) and 10 sequences from the Upper Paraná River Basin (UPR), which were obtained from GenBank. S. scriptum from the UUR and the UPR were assigned in two distinct molecular operational taxonomic units (MOTUs) with higher inter-specific K2P distance than the optimum threshold (OT = 0.0079). The COI Intra-MOTU distances of S. scriptum specimens from the UUR ranged from 0.0000 to 0.0100. The control region indicated a high number of haplotypes and low nucleotide diversity, compatible with a new population in recent expansion process. Genetic structure was observed, with high differentiation between UUR and UPR basins, identified by BAPS, haplotype network, AMOVA (FST = 0.78, p < 0.05) and Mantel test. S. scriptum from the UUR showed a slight differentiation (FST = 0.068, p < 0.05), but not isolation-by-distance. Negative values of Tajima’s D and Fu’s Fs suggest recent demographic oscillations. The Bayesian skyline plot analysis indicated possible population expansion from beginning 2,500 years ago and a recent reduction in the population size. Low nucleotide diversity, spatial population structure, and the reduction of effective population size should be considered for the planning of strategies aimed at the conservation and rehabilitation of this important fisheries resource. PMID:29520295

[Reconsideration of the "conversion theory" from the primacy of the heart to the primacy of the blood--William Harvey's observation, logic and the construction of the exercitatio].

PubMed

Tsukisawa, M

1995-01-01

In De Motu Cordis, W. Harvey sometimes waxes lyrical on the primacy of the heart. In his another treatise, De Generatione, however, he insists on the primacy of the blood. The "conversion theory" explained this discrepancy with Harvey's conversion as caused by his discovery of the antiquity of the blood. But Whitterridge showed that Harvey had already described the antiquity of the blood in his earliest notebook, Prelectiones. As shown in this article, Harvey's observation was not a mere accidental discovery; based on the "classic questions", it was continuously and persistently conducted until he was assured of having seen the blood to exist prior to the pulse and movement to occur in the blood. While this crucial observation was not yet made in Prelectiones and De Motu Cordis, it was described as crucial evidence of the theory of the primacy of the blood in De Generatione, in which this new theory was introduced as an independent topic of the exercitatio. The topic of the order of the generation was a crucial issue in the theoretical medicine of Harvey's days. That is, the Aristotelian primacy of the heart had been seriously challenged by the Galenic tripartite theory which pursued the antiquity of three organs. Harvey's theory, or the primacy of the blood, seems to consists with Aristotle's premise, in that it asserts the existence of the only source of all functions in living animals. Harvey's theory, however, was confronted, on the other hand, with Aristotle's another inconsistency, namely, the issue of two definitions about anima. We must consider the construction and strategy of the exercitatio in Harvey's days to understand the exact meaning of the primacy of the heart in De Motu Cordis. In De Motu Cordis, Harvey did not use the primacy of the heart in a central part of the exercitatio, namely, in confirming his unprecedented theory, the circulation of the blood, but he settled this Aristotelian premise in a marginal part, namely, in ratiocinating the final cause of the circulation and supporting his new theory from the sidelines.

[Reconsideration of the "conversion theory" from the primacy of the heart to the primacy of the blood--William Harvey's observation, logic and the construction of the exercitatio].

PubMed

Tsukisawa, M

1995-01-01

In De motu cordis, W. Harvey sometimes waxes lyrical on the primacy of the heart. In his another treatise, De generatione, however, he insists on the primacy of the blood. The "conversion theory" explained this discrepancy with Harvey's conversion as caused by his discovery of the antiquity of the blood. But Whitterridge showed that Harvey had already described the antiquity of the blood in his earliest notebook, Prelectiones. As shown in this article, Harvey's observation was not a mere accidental discovery; based on the "classic questions", it was continuously and persistently conducted until he was assured of having seen the blood to exist prior to the pulse and movement to occur in the blood. While this crucial observation was not yet made in Prelectiones and De motu cordis, it was described as crucial evidence of the theory of the primacy of the blood in De generatione, in which this new theory was introduced as an independent topic of the exercitatio. The topic of the order of the generation was a crucial issue in the theoretical medicine of Harvey's days. That is, the Aristotelian primacy of the heart had been seriously challenged by the Galenic tripartite theory which pursued the antiquity of three organs. Harvey's theory, or the primacy of the blood, seems to consists with Aristotle's premise, in that it asserts the existance of the only source of all functions in living animals. Harvey's theory, however, was confronted, on the other hand, with Aristotle's another inconsistency, namely, the issue of two definitions about anima. We must consider the construction and strategy of the exercitatio in Harvey's days to understand the exact meaning of the primacy of the heart in De motu cordis. In De motu cordis, Harvey did not use the primacy of the heart in a central part of the exercitatio, namely, in confirming his unprecedented theory, the circulation of the blood, but he settled this Aristotelian premise in a marginal part, namely, in ratiocinating the final cause of the circulation and supporting his new theory from the sidelines.

Low-Cost Ultra-Wideband EM Sensor for UXO Detection and Classification

DTIC Science & Technology

2012-04-01

Mechanical System MOTU Mark of the Unicorn – a brand name for audio equipment MR Magneto-Resistance NIST National Institute of Standards and...magnetic surveys are able to detect ferrous bodies at a further distance than EMI measurements. Consequently , the magnetic anomaly is broader

The Long Decay Model of One-Dimensional Projectile Motion

ERIC Educational Resources Information Center

Lattery, Mark Joseph

2008-01-01

This article introduces a research study on student model formation and development in introductory mechanics. As a point of entry, I present a detailed analysis of the Long Decay Model of one-dimensional projectile motion. This model has been articulated by Galileo ("in De Motu") and by contemporary students. Implications for instruction are…

Localization in Multiple Source Environments: Localizing the Missing Source

DTIC Science & Technology

2007-02-01

volunteer listeners (3 males and 3 females, 19-24 years of age ), participated in the experiment. All had normal hearing (au- diometric thresholds < 15...were routed from a control computer to a Mark of the Unicorn digital-to-analog con- verter (MOTU 24 I/O), then through a bank of amplifiers (Crown Model

Anthropometric Relationships of Body and Body Segment Moments of Inertia

DTIC Science & Technology

1980-12-01

platform balanced on a knife edge ( Borelli , 1679). While weight, volume, center of mass and moments of inertia of the whole body can be measured in a...Segments, Paper No. 720964, SAE Transactions, Vol. 81, Sect. 4, pp. 2818-2833. Borelli , J. A., 1679, De Motu Animalium. Lugduni Batavorum. Braune, W

Taxonomic classification of world map units in crop producing areas of Argentina and Brazil with representative US soil series and major land resource areas in which they occur

NASA Technical Reports Server (NTRS)

Huckle, H. F. (Principal Investigator)

1980-01-01

The most probable current U.S. taxonomic classification of the soils estimated to dominate world soil map units (WSM)) in selected crop producing states of Argentina and Brazil are presented. Representative U.S. soil series the units are given. The map units occurring in each state are listed with areal extent and major U.S. land resource areas in which similar soils most probably occur. Soil series sampled in LARS Technical Report 111579 and major land resource areas in which they occur with corresponding similar WSM units at the taxonomic subgroup levels are given.

Reference independent species level profiling of the largest marine microbial ecosystem.

NASA Astrophysics Data System (ADS)

Mende, D. R.; DeLong, E.; Aylward, F.

2016-02-01

Marine microbes are of immense importance for the flux of matter and energy within the global oceans. Yet, the temporal variability of microbial communities in response to seasonal and environmental changes remains understudied. In addition, there is only a very limited understanding of the effects that changes within microbial communities at a certain depth have on the other microbes within the water column. Further, existing studies have mostly been limited by the lack of good reference databases. Here we present an reference independent analysis of a year long time series at 5 different water depth of the microbial communities at Station ALOHA, a sampling location representative of the largest contiguous ecosystem on earth, the North Pacific Subtropical Gyre (NPSG). Due to the lack the lack of closely related reference genomes most recent meta-genomic studies of marine microbial ecosystems have been limited to a coarse grained view at higher taxonomic levels. In order to gain a fine grained picture of the microbial communities and their dynamics within the NPSG, we extended the mOTU approach that has been successfully applied to the human microbiome to this marine ecosystem using more than 60 deeply sequenced metagenomic samples. This method allows for species level community profiling and diversity estimates, revealing seasonal shifts within the microbial communities. Additionally, we detected a number of microbes that respond to changes of different changing environmental conditions. We further surveyed the depth specificity of microbes at station ALOHA, showing species specific patterns of presence at different depths.

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.

Sound Localization in Multisource Environments

DTIC Science & Technology

2009-03-01

A total of 7 paid volunteer listeners (3 males and 4 females, 20-25 years of age ) par- ticipated in the experiment. All had normal hearing (i.e...effects of the loudspeaker frequency responses, and were then sent from an experimental control computer to a Mark of the Unicorn (MOTU 24 I/O) digital-to...after the overall multisource stimulus has been presented (the ’post-cue’ condition). 3.2 Methods 3.2.1 Listeners Eight listeners, ranging in age from

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.

Lineage-specific responses of microbial communities to environmental change.

PubMed

Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

2013-01-01

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

CONCORDANCE OF TAXONOMIC RICHNESS PATTERNS ACROSS MULTIPLE ASSEMBLAGES IN LAKES OF THE NORTHEASTERN UNITED STATES

EPA Science Inventory

We investigated the concordance of taxonomic richness patterns and their environmental correlates for assemblages of benthic macroinvertebrates, riparian birds, sedimentary diatoms, fish, planktonic crustaceans, and planktonic rotifers in 186 northeastern U.S. lakes. Taxon counts...

Florisitic summary of 'Manual of Vascular Plants of Northeastern United States and Adjacent Canada', second edition

USGS Publications Warehouse

Bennett, J.P.

1996-01-01

The second edition of the Manual of Vascular Plants of Northeastern United States and Adjacent Canada by Gleason and Cronquist (1991) is the most recent and up-to-date taxonomic treatment of the flora of that region. Since no floristic summary of the Manual was included in the publication, a computer analysis of the taxonomic data of the Manual was performed in order to generate a floristic summary. Totals of 4285 species, 1091 genera, and 191 families were tabulated. The largest genus was Carex, with 230 species; the largest family was the Asteraceae, with 528 species. Comparisons made with earlier floras of the same region indicated small declines on the order of 10% for these taxonomic groups.

Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Walsh, Stephen Joseph; Meador, Michael R.

1998-01-01

Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

International Code of Nomenclature for Algae, Fungi, and Plants

USDA-ARS?s Scientific Manuscript database

Science requires a precise, stable, and simple system of nomenclature used by scientists in all countries of the world, dealing on the one hand with the terms that denote the ranks of taxonomic groups, and on the other with the scientific names that are applied to the individual taxonomic units of a...

A Guide to the Common Diatoms at Water Pollution Surveillance System Stations.

ERIC Educational Resources Information Center

Weber, Cornelius I.

This guide was developed by the United States Environmental Protection Agency (EPA) as a taxonomic reference for the identification of diatoms. The taxonomic information included consists of a generic key to the common genera of diatoms, a section illustrating 164 diatom species representing 43 common genera found at the Water Pollution…

The reprint of a chapter of Nicolaus Copernicus' principal book by Heinrich Brucaeus, Rostock 1573 (German Title: Der Nachdruck eines Kapitels des Hauptwerkes von Nicolaus Copernicus durch Heinrich Brucaeus, Rostock 1573)

NASA Astrophysics Data System (ADS)

Hamel, Jürgen

The book "De motu primo libri tres" of the Rostock professor Heinrich Brucaeus (1530-1593), which appeared in 1573, contains an unmodified reprint of a section of Copernicus` principal work, first book, 14th chapter, exercise 3. This reprint, hitherto unnoticed, is of interest for the reception of Copernicus' work. This article reproduces the text and presents some research on Brucaeus, who was Tycho Brahe's teacher in Rostock. His biography and his scientific achievements are outlined.

International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code): Appendices II-VIII

USDA-ARS?s Scientific Manuscript database

Science requires a precise, stable, and simple system of nomenclature used by scientists in all countries of the world, dealing on the one hand with the terms that denote the ranks of taxonomic groups, and on the other with the scientific names that are applied to the individual taxonomic units of a...

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.

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

Rapid evolution in lekking grouse: Implications for taxonomic definitions

USGS Publications Warehouse

Oyler-McCance, Sara J.; St. John, Judy; Quinn, Thomas W.

2010-01-01

Species and subspecies delineations were traditionally defined by morphological and behavioral traits, as well as by plumage characteristics. Molecular genetic data have more recently been used to assess these classifications and, in many cases, to redefine them. The recent practice of utilizing molecular genetic data to examine taxonomic questions has led some to suggest that molecular genetic methods are more appropriate than traditional methods for addressing taxonomic uncertainty and management units. We compared the North American Tetraoninae—which have been defined using plumage, morphology, and behavior—and considered the effects of redefinition using only neutral molecular genetic data (mitochondrial control region and cytochrome oxidase subunit 1). Using the criterion of reciprocal monophyly, we failed to recognize the five species whose mating system is highly polygynous, with males displaying on leks. In lek-breeding species, sexual selection can act to influence morphological and behavioral traits at a rate much faster than can be tracked genetically. Thus, we suggest that at least for lek-breeding species, it is important to recognize the possibility that morphological and behavioral changes may occur at an accelerated rate compared with the processes that led to reciprocal monophyly of putatively neutral genetic markers. Therefore, it is particularly important to consider the possible disconnect between such lines of evidence when making taxonomic revisions and definitions of management units.

Motuporamine Derivatives as Antimicrobial Agents and Antibiotic Enhancers against Resistant Gram-Negative Bacteria.

PubMed

Borselli, Diane; Blanchet, Marine; Bolla, Jean-Michel; Muth, Aaron; Skruber, Kristen; Phanstiel, Otto; Brunel, Jean Michel

2017-02-01

Dihydromotuporamine C and its derivatives were evaluated for their in vitro antimicrobial activities and antibiotic enhancement properties against Gram-negative bacteria and clinical isolates. The mechanism of action of one of these derivatives, MOTU-N44, was investigated against Enterobacter aerogenes by using fluorescent dyes to evaluate outer-membrane depolarization and permeabilization. Its efficiency correlated with inhibition of dye transport, thus suggesting that these molecules inhibit drug transporters by de-energization of the efflux pump rather than by direct interaction of the molecule with the pump. This suggests that depowering the efflux pump provides another strategy to address antibiotic resistance. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Synopsis of proposals on botanical nomenclature – Shenzhen 2017: A review of the proposals concerning the International Code of Nomenclature for algae, fungi, and plants submitted to the XIX International Botanical Congress

USDA-ARS?s Scientific Manuscript database

Science requires a precise, stable, and simple system of nomenclature used by scientists in all countries of the world, dealing on the one hand with the terms that denote the ranks of taxonomic groups, and on the other with the scientific names that are applied to the individual taxonomic units of a...

Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

PubMed Central

Nilsson, R. Henrik; Taylor, Andy F. S.; Adams, Rachel I.; Baschien, Christiane; Johan Bengtsson-Palme; Cangren, Patrik; Coleine, Claudia; Heide-Marie Daniel; Glassman, Sydney I.; Hirooka, Yuuri; Irinyi, Laszlo; Reda Iršėnaitė; Pedro M. Martin-Sanchez; Meyer, Wieland; Seung-Yoon Oh; Jose Paulo Sampaio; Seifert, Keith A.; Sklenář, Frantisek; Dirk Stubbe; Suh, Sung-Oui; Summerbell, Richard; Svantesson, Sten; Martin Unterseher; Cobus M. Visagie; Weiss, Michael; Woudenberg, Joyce HC; Christian Wurzbacher; den Wyngaert, Silke Van; Yilmaz, Neriman; Andrey Yurkov; Kõljalg, Urmas; Abarenkov, Kessy

2018-01-01

Abstract Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment. PMID:29559822

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

PubMed

Schloss, Patrick D; Handelsman, Jo

2006-10-01

The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.

PubMed

Haig, Susan M; Beever, Erik A; Chambers, Steven M; Draheim, Hope M; Dugger, Bruce D; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B; Kesler, Dylan C; Knaus, Brian J; Lopes, Iara F; Loschl, Pete; Mullins, Thomas D; Sheffield, Lisa M

2006-12-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act

USGS Publications Warehouse

Beever, E.A.; Haig, S.M.; Chambers, Steven M.; Draheim, Hope M.; Dugger, Bruce D.; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B.; Kesler, Dylan C.; Knaus, Brian J.; Lopes, Iara F.; Loschl, Peter J.; Mullins, Thomas D.; Sheffield, Lisa M.

2006-01-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Gut microbiota in MS: possible influence of immunomodulators

PubMed Central

Cantarel, Brandi L.; Waubant, Emmanuelle; Chehoud, Christel; Kuczynski, Justin; DeSantis, Todd Z.; Warrington, Janet; Venkatesan, Arun; Fraser, Claire M.; Mowry, Ellen M.

2015-01-01

Objectives Differences in gut bacteria have been described in several autoimmune disorders. In this exploratory pilot study, we compared gut bacteria in multiple sclerosis patients and healthy controls and evaluated the influence of glatiramer acetate and vitamin D treatment on the microbiota. Methods Subjects were otherwise healthy white women with or without relapsing-remitting multiple sclerosis who were vitamin D insufficient. Multiple sclerosis patients were untreated or were receiving glatiramer acetate. Subjects collected stool at baseline and after 90 days of vitamin D3 (5,000 IU/day) supplementation. The abundance of operational taxonomic units was evaluated by hybridization of 16S rRNA to a DNA microarray. Results While there was overlap of gut bacterial communities, the abundance of some operational taxonomic units, including Faecalibacterium, was lower in multiple sclerosis patients. Glatiramer acetate-treated MS subjects showed differences in community composition compared to untreated subjects, including Bacteroidaceae, Faecalibacterium, Ruminococcus, Lactobacillaceae, Clostridium, and Other Clostridiales. Compared to the other groups, untreated multiple sclerosis subjects had an increase in the Akkermansia, Faecalibacterium, and Coprococcus genera after vitamin D supplementation. Conclusions While overall bacterial communities were similar, specific operational taxonomic units differed between healthy and multiple sclerosis subjects. Glatiramer acetate and vitamin D supplementation were associated with differences or changes in the microbiota. This study was exploratory, and larger studies are needed to confirm these preliminary results. PMID:25775034

Gut microbiota in multiple sclerosis: possible influence of immunomodulators.

PubMed

Cantarel, Brandi L; Waubant, Emmanuelle; Chehoud, Christel; Kuczynski, Justin; DeSantis, Todd Z; Warrington, Janet; Venkatesan, Arun; Fraser, Claire M; Mowry, Ellen M

2015-06-01

Differences in gut bacteria have been described in several autoimmune disorders. In this exploratory pilot study, we compared gut bacteria in patients with multiple sclerosis and healthy controls and evaluated the influence of glatiramer acetate and vitamin D treatment on the microbiota. Subjects were otherwise healthy white women with or without relapsing-remitting multiple sclerosis who were vitamin D insufficient. Patients with multiple sclerosis were untreated or were receiving glatiramer acetate. Subjects collected stool at baseline and after 90 days of vitamin D3 (5000 IU/d) supplementation. The abundance of operational taxonomic units was evaluated by hybridization of 16S rRNA to a DNA microarray. While there was overlap of gut bacterial communities, the abundance of some operational taxonomic units, including Faecalibacterium, was lower in patients with multiple sclerosis. Glatiramer acetate-treated patients with multiple sclerosis showed differences in community composition compared with untreated subjects, including Bacteroidaceae, Faecalibacterium, Ruminococcus, Lactobacillaceae, Clostridium, and other Clostridiales. Compared with the other groups, untreated patients with multiple sclerosis had an increase in the Akkermansia, Faecalibacterium, and Coprococcus genera after vitamin D supplementation. While overall bacterial communities were similar, specific operational taxonomic units differed between healthy controls and patients with multiple sclerosis. Glatiramer acetate and vitamin D supplementation were associated with differences or changes in the microbiota. This study was exploratory, and larger studies are needed to confirm these preliminary results.

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.

PubMed

Stevens, John R; Jones, Todd R; Lefevre, Michael; Ganesan, Balasubramanian; Weimer, Bart C

2017-01-01

Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree , a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons.

The role of taxonomy in species conservation.

PubMed Central

Mace, Georgina M

2004-01-01

Taxonomy and species conservation are often assumed to be completely interdependent activities. However, a shortage of taxonomic information and skills, and confusion over where the limits to 'species' should be set, both cause problems for conservationists. There is no simple solution because species lists used for conservation planning (e.g. threatened species, species richness estimates, species covered by legislation) are often also used to determine which units should be the focus of conservation actions; this despite the fact that the two processes have such different goals and information needs. Species conservation needs two kinds of taxonomic solution: (i) a set of practical rules to standardize the species units included on lists; and (ii) an approach to the units chosen for conservation recovery planning which recognizes the dynamic nature of natural systems and the differences from the units in listing processes that result. These solutions are well within our grasp but require a new kind of collaboration among conservation biologists, taxonomists and legislators, as well as an increased resource of taxonomists with relevant and high-quality skills. PMID:15253356

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

PubMed

Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

2015-05-19

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

PubMed Central

Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

2015-01-01

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project. PMID:25988396

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

PubMed Central

Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

2017-01-01

Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities. PMID:28327636

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.

The history of the USDA Nematode Collection and its database: valuable resources for taxonomic research and identification

USDA-ARS?s Scientific Manuscript database

The United States Department of Agriculture Nematode Collection continues to serve as one of the largest and most comprehensive nematode repositories in the world. Nematology research in the United States began in the late 1800’s, and for many years the collections of the USDA nematologists remained...

FROGS: Find, Rapidly, OTUs with Galaxy Solution.

PubMed

Escudié, Frédéric; Auer, Lucas; Bernard, Maria; Mariadassou, Mahendra; Cauquil, Laurent; Vidal, Katia; Maman, Sarah; Hernandez-Raquet, Guillermina; Combes, Sylvie; Pascal, Géraldine

2018-04-15

Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own. This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME. Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr. geraldine.pascal@inra.fr. Supplementary data are available at Bioinformatics online.

Considering the spatial-scale factor when modelling sustainable land management.

NASA Astrophysics Data System (ADS)

Bouma, Johan

2015-04-01

Considering the spatial-scale factor when modelling sustainable land management. J.Bouma Em.prof. soil science, Wageningen University, Netherlands. Modelling soil-plant processes is a necessity when exploring future effects of climate change and innovative soil management on agricultural productivity. Soil data are needed to run models and traditional soil maps and the associated databases (based on various soil Taxonomies ), have widely been applied to provide such data obtained at "representative" points in the field. Pedotransferfunctions (PTF)are used to feed simulation models, statistically relating soil survey data ( obtained at a given point in the landscape) to physical parameters for simulation, thus providing a link with soil functionality. Soil science has a basic problem: their object of study is invisible. Only point data are obtained by augering or in pits. Only occasionally roadcuts provide a better view. Extrapolating point to area data is essential for all applications and presents a basic problem for soil science, because mapping units on soil maps, named for a given soil type,may also contain other soil types and quantitative information about the composition of soil map units is usually not available. For detailed work at farm level ( 1:5000-1:10000), an alternative procedure is proposed. Based on a geostatistical analysis, onsite soil observations are made in a grid pattern with spacings based on a geostatistical analysis. Multi-year simulations are made for each point of the functional properties that are relevant for the case being studied, such as the moisture supply capacity, nitrate leaching etc. under standardized boundary conditions to allow comparisons. Functional spatial units are derived next by aggregating functional point data. These units, which have successfully functioned as the basis for precision agriculture, do not necessarily correspond with Taxonomic units but when they do the Taxonomic names should be noted . At lower landscape and watershed scale ( 1:25.000 -1:50000) digital soil mapping can provide soil data for small grids that can be used for modeling, again through pedotransferfunctions. There is a risk, however, that digital mapping results in an isolated series of projects that don't increase the knowledge base on soil functionality, e.g.linking Taxonomic names ( such as soil series) to functionality, allowing predictions of soil behavior at new sites where certain soil series occur. We therefore suggest that aside from collecting 13 soil characteristics for each grid, as occurs in digital soil mapping, also the Taxonomic name of the representative soil in the grid is recorded. At spatial scales of 1:50000 and smaller, use of Taxonomic names becomes ever more attractive because at such small scales relations between soil types and landscape features become more pronounced. But in all cases, selection of procedures should not be science-based but based on the type of questions being asked including their level of generalization. These questions are quite different at the different spatial-scale levels and so should be the procedures.

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.

Whartonacarus floridensis sp. nov. (Acari: Trombiculidae), with a taxonomic review and the first record of Whartonacarus chiggers in the continental United States.

PubMed

Mertins, James W; Hanson, Britta A; Corn, Joseph L

2009-11-01

Among several unusual species collected during surveillance of ectoparasites on wildlife hosts in the southeastern United States and Caribbean Region, the larvae of a new species of Whartonacarus were encountered in 2003 on a cattle egret, Bubulcus ibis (L.), in the Florida Keys. This is the first record for a member of Whartonacarus in the continental United States. The mite is described and named as Whartonacarus floridensis Mertins, and the possible significance of this discovery with respect to the "tropical bont tick," Amblyomma variegatum (F.), is discussed. A brief taxonomic review of Whartonacarus raises questions about the putative synonymy of Whartonacarus nativitatis (Hoffmann) and Whartonacarus thompsoni (Brennan) and suggests that Whartonacarus shiraii (Sasa et al.) may include two distinct taxa. Whartonacarus is redefined, and a revised key to the known taxa is provided. Toritrombicula oceanica Brennan & Amerson is placed in the genus Whartonacarus. Also, Whartonacarus palenquensis (Hoffman) is rejected as a member of this genus and placed in its own new genus, Longisetacarus Mertins.

Systematics and biogeography of Orconectes, subgenus Trisellescens, in the southeastern United States, a test of morphology-based classification

Treesearch

Christopher A. Taylor; Susan B. Adams; Guenter A. Schuster

2014-01-01

Diagnosable taxonomic units are fundamental to conservation biology and management of resources and the need for sound science in both fields is more pressing for aquatic ecosystems. Within freshwater crayfishes, the North American genus Orconectes is one of the most diverse in the World. Accurate assessments of species level relationships and species boundaries within...

Architectural mutation and leaf form, for the palmate series.

PubMed

White, D A

2005-07-21

Palmate leaf form occurs in both the ferns and angiosperms. The palmate leaf form, and its variants, is present in distantly separated clades within both ferns and angiosperms. There tend not to be intermediate forms which link these palmate leaves to other leaf forms within the taxonomic groups in question. The recurrence of homoplasious leaf forms in separate taxonomic groups could be a consequence of the algorithmic like mode of leaf growth. Leaves develop through the reiteration of modular units. It is probable that the homoplasious leaf forms in different taxa are derived independently through re-combinations of the parameters in the basic leaf form development algorithm.

Guidance for Determining the Acceptability of Environmental Fate Studies Conducted with Foreign Soils

EPA Pesticide Factsheets

International and U.S. soil taxonomical classification systems, distribution of soil orders in the United States, specific criteria to help scientists determine when foreign soils are representative of U.S. soils at intended pesticide use sites.

PATTERNS OF ENDEMISM OF THE EASTERN NORTH AMERICAN CAVE FAUNA

EPA Science Inventory

Over 250 species of obligate terrestrial cave-dwelling animals (troglobionts) are known from single caves in the eastern United States. We investigate their geographic distribution, especially in relation to other troglobionts. We relate these patterns to taxonomic group, oppor...

Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.)

PubMed Central

Mee, Jonathan A; Bernatchez, Louis; Reist, Jim D; Rogers, Sean M; Taylor, Eric B

2015-01-01

The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units. PMID:26029257

Exploring the utility of DNA barcoding in species delimitation of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae).

PubMed

Song, Chao; Wang, Qian; Zhang, Ruilei; Sun, Bingjiao; Wang, Xinhua

2016-02-16

In this study, we tested the utility of the mitochondrial gene cytochrome c oxidase subunit 1 (CO1) as the barcode region to deal with taxonomical problems of Polypedilum (Tripodura) non-biting midges (Diptera: Chironomidae). The 114 DNA barcodes representing 27 morphospecies are divided into 33 well separated clusters based on both Neighbor Joining and Maximum Likelihood methods. DNA barcodes revealed an 82% success rate in matching with morphospecies. The selected DNA barcode data support 37-64 operational taxonomic units (OTUs) based on the methods of Automatic Barcode Gap Discovery (ABGD) and Poisson Tree Process (PTP). Furthermore, a priori species based on consistent phenotypic variations were attested by molecular analysis, and a taxonomical misidentification of barcode sequences from GenBank was found. We could not observe a distinct barcode gap but an overlap ranged from 9-12%. Our results supported DNA barcoding as an ideal method to detect cryptic species, delimit sibling species, and associate different life stages in non-biting midges.

An Overview of Marine Biodiversity in United States Waters

PubMed Central

Fautin, Daphne; Dalton, Penelope; Incze, Lewis S.; Leong, Jo-Ann C.; Pautzke, Clarence; Rosenberg, Andrew; Sandifer, Paul; Sedberry, George; Tunnell, John W.; Abbott, Isabella; Brainard, Russell E.; Brodeur, Melissa; Eldredge, Lucius G.; Feldman, Michael; Moretzsohn, Fabio; Vroom, Peter S.; Wainstein, Michelle; Wolff, Nicholas

2010-01-01

Marine biodiversity of the United States (U.S.) is extensively documented, but data assembled by the United States National Committee for the Census of Marine Life demonstrate that even the most complete taxonomic inventories are based on records scattered in space and time. The best-known taxa are those of commercial importance. Body size is directly correlated with knowledge of a species, and knowledge also diminishes with distance from shore and depth. Measures of biodiversity other than species diversity, such as ecosystem and genetic diversity, are poorly documented. Threats to marine biodiversity in the U.S. are the same as those for most of the world: overexploitation of living resources; reduced water quality; coastal development; shipping; invasive species; rising temperature and concentrations of carbon dioxide in the surface ocean, and other changes that may be consequences of global change, including shifting currents; increased number and size of hypoxic or anoxic areas; and increased number and duration of harmful algal blooms. More information must be obtained through field and laboratory research and monitoring that involve innovative sampling techniques (such as genetics and acoustics), but data that already exist must be made accessible. And all data must have a temporal component so trends can be identified. As data are compiled, techniques must be developed to make certain that scales are compatible, to combine and reconcile data collected for various purposes with disparate gear, and to automate taxonomic changes. Information on biotic and abiotic elements of the environment must be interactively linked. Impediments to assembling existing data and collecting new data on marine biodiversity include logistical problems as well as shortages in finances and taxonomic expertise. PMID:20689852

An overview of marine biodiversity in United States waters

USGS Publications Warehouse

Fautin, Daphne G.; Delton, Penelope; Incze, Lewis S.; Leong, Jo-Ann C.; Pautzke, Clarence; Rosenberg, Andrew A.; Sandifer, Paul; Sedberry, George R.; Tunnell, John W.; Abbott, Isabella; Brainard, Russell E.; Brodeur, Melissa; Eldredge, Lucius G.; Feldman, Michael; Moretzsohn, Fabio; Vroom, Peter S.; Wainstein, Michelle; Wolff, Nicholas

2010-01-01

Marine biodiversity of the United States (U.S.) is extensively documented, but data assembled by the United States National Committee for the Census of Marine Life demonstrate that even the most complete taxonomic inventories are based on records scattered in space and time. The best-known taxa are those of commercial importance. Body size is directly correlated with knowledge of a species, and knowledge also diminishes with distance from shore and depth. Measures of biodiversity other than species diversity, such as ecosystem and genetic diversity, are poorly documented. Threats to marine biodiversity in the U.S. are the same as those for most of the world: overexploitation of living resources; reduced water quality; coastal development; shipping; invasive species; rising temperature and concentrations of carbon dioxide in the surface ocean, and other changes that may be consequences of global change, including shifting currents; increased number and size of hypoxic or anoxic areas; and increased number and duration of harmful algal blooms. More information must be obtained through field and laboratory research and monitoring that involve innovative sampling techniques (such as genetics and acoustics), but data that already exist must be made accessible. And all data must have a temporal component so trends can be identified. As data are compiled, techniques must be developed to make certain that scales are compatible, to combine and reconcile data collected for various purposes with disparate gear, and to automate taxonomic changes. Information on biotic and abiotic elements of the environment must be interactively linked. Impediments to assembling existing data and collecting new data on marine biodiversity include logistical problems as well as shortages in finances and taxonomic expertise.

Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

PubMed Central

Shanks, Orin C.; Newton, Ryan J.; Kelty, Catherine A.; Huse, Susan M.; Sogin, Mitchell L.

2013-01-01

Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States. PMID:23435885

An overview of marine biodiversity in United States waters.

PubMed

Fautin, Daphne; Dalton, Penelope; Incze, Lewis S; Leong, Jo-Ann C; Pautzke, Clarence; Rosenberg, Andrew; Sandifer, Paul; Sedberry, George; Tunnell, John W; Abbott, Isabella; Brainard, Russell E; Brodeur, Melissa; Eldredge, Lucius G; Feldman, Michael; Moretzsohn, Fabio; Vroom, Peter S; Wainstein, Michelle; Wolff, Nicholas

2010-08-02

Marine biodiversity of the United States (U.S.) is extensively documented, but data assembled by the United States National Committee for the Census of Marine Life demonstrate that even the most complete taxonomic inventories are based on records scattered in space and time. The best-known taxa are those of commercial importance. Body size is directly correlated with knowledge of a species, and knowledge also diminishes with distance from shore and depth. Measures of biodiversity other than species diversity, such as ecosystem and genetic diversity, are poorly documented. Threats to marine biodiversity in the U.S. are the same as those for most of the world: overexploitation of living resources; reduced water quality; coastal development; shipping; invasive species; rising temperature and concentrations of carbon dioxide in the surface ocean, and other changes that may be consequences of global change, including shifting currents; increased number and size of hypoxic or anoxic areas; and increased number and duration of harmful algal blooms. More information must be obtained through field and laboratory research and monitoring that involve innovative sampling techniques (such as genetics and acoustics), but data that already exist must be made accessible. And all data must have a temporal component so trends can be identified. As data are compiled, techniques must be developed to make certain that scales are compatible, to combine and reconcile data collected for various purposes with disparate gear, and to automate taxonomic changes. Information on biotic and abiotic elements of the environment must be interactively linked. Impediments to assembling existing data and collecting new data on marine biodiversity include logistical problems as well as shortages in finances and taxonomic expertise.

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.

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

Do DNA barcoding delimitation methods affect our view of stream biodiversity?

EPA Science Inventory

How we delimit molecular operational taxonomic units (MOTUs) is an important aspect in the use of DNA barcoding for bioassessment. Four delimitation methods were examined to gain an understanding of their relative strengths at organizing data from 5300 specimens collected during ...

Vertebrate species introductions in the United States and its territories

USGS Publications Warehouse

Witmer, Gary W.; Fuller, Pam L.

2011-01-01

At least 1,065 introduced vertebrate species have been introduced in the United States and its territories, including at least 86 mammalian, 127 avian, 179 reptilian/amphibian, and 673 fish species. Examples in each major taxonomic group include domestic cat, small Indian mongoose, red fox, goat, pig, rabbit, rats, house mouse, gray squirrel, nutria, starling, Indian common myna, red-vented bulbul, brown treesnake, red-eared slider, brown trout, tilapia, and grass carp. We briefly review some of these species and the types of damage they cause. We then review the basic types of methods used for control or eradication of each taxonomic group, including physical, chemical, biological, and cultural methods. We discuss some of the challenges in managing these species, including issues with the use of toxicants, land access, public attitudes, and monitoring difficulties. Finally, we list some ongoing research and future research needs, including improved detection methods, improved attractants, improved barriers, improved capture methods, fertility control, and risk assessment methods.

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

PubMed Central

Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

2014-01-01

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

Common and scientific names of aquatic invertebrates from the United States and Canada: Mollusks

USGS Publications Warehouse

Turgeon, D. D.; Quinn, J.F.; Bogan, A.E.; Coan, E. V.; Hochberg, F.G.; Lyons, W.G.; Mikkelsen, P. M.; Neves, R.J.; Roper, C. F. E.; Rosenberg, G.; Roth, B.; Scheltema, A.; Thompson, F.G.; Vecchione, M.; Williams, J.D.

1998-01-01

This edition of Common and Scientific Names of Invertebrates from the United States and Canada: Mollusks represents the efforts of 15 molluscan taxonomic specialists in compiling a comprehensive checklist of the mollusks found in North America and Canada and their vernacular names. Built upon the success of the first edition, the authors have updated the nomenclature to reflect recent phylogenetic analyses and have included more than 300 new species.

Short-term regeneration dynamics of Wyoming big sagebrush at two sites in northern Utah

USDA-ARS?s Scientific Manuscript database

The herbicide tebuthiuron has been used historically to control cover of Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis - complete taxonomic designation), a widespread shrub across the western United States, with the intent of increasing herbaceous plant cover. Although the tebuthiur...

Beyond botany to genetic resource preservation: the S. P. Vander Kloet Vaccinium L. collections

USDA-ARS?s Scientific Manuscript database

Dr. S. P. Vander Kloet, botanist, traveled the world examining and obtaining specimens to redefine infrageneric taxonomic units within Vaccinium L., family Ericaceae. Besides his botanical treatises, his legacy includes herbarium voucher specimens and ex situ genetic resource collections including a...

Teaching the Scientific Method: It's All in the Perspective

ERIC Educational Resources Information Center

Ayers, James M.; Ayers, Kathleen M.

2007-01-01

A three unit module of inquiry, including morphological comparison, cladogram construction, and data mining has been developed to teach students the nature of experimental science. Students generate angiosperm morphological data, form cladistic hypotheses, then mine taxonomic, bioinformatic and historical data from many sources to replicate and…

Leonhard Euler and the mechanics of rigid bodies

NASA Astrophysics Data System (ADS)

Marquina, J. E.; Marquina, M. L.; Marquina, V.; Hernández-Gómez, J. J.

2017-01-01

In this work we present the original ideas and the construction of the rigid bodies theory realised by Leonhard Euler between 1738 and 1775. The number of treatises written by Euler on this subject is enormous, including the most notorious Scientia Navalis (1749), Decouverte d’un noveau principe de mecanique (1752), Du mouvement de rotation des corps solides autour d’un axe variable (1765), Theoria motus corporum solidorum seu rigidorum (1765) and Nova methodus motu corporum rigidorum determinandi (1776), in which he developed the ideas of the instantaneous rotation axis, the so-called Euler equations and angles, the components of what is now known as the inertia tensor, the principal axes of inertia, and, finally, the generalisation of the translation and rotation movement equations for any system. Euler, the man who ‘put most of mechanics into its modern form’ (Truesdell 1968 Essays in the History of Mechanics (Berlin: Springer) p 106).

Introgression and dispersal among spotted owl (Strix occidentatlis) subspecies.

Treesearch

W.Chris Funk; Eric D. Forsman; Thomas D. Mullins; Susan M. Haig

2008-01-01

Population genetics plays an increasingly important role in the conservation and management of declining species, particularly for defining taxonomic units. Subspecies are recognized by several conservation organizations and countries and receive legal protection under the US Endangered Species Act (ESA). Two subspecies of spotted owls, northern (Strix...

Integrated bird conservation web site in the United States

Treesearch

Roxanne Bogart; Chris Eberly; Elizabeth Martin

2005-01-01

In working towards a vision of integrated bird conservation, scientists, conservationists, land managers, and administrators are faced with a variety of scientific, managerial, administrative, and logistical challenges and complexities. The broad scope of integrated bird conservation requires organizations to work together to conserve birds across taxonomic groups,...

Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi

PubMed Central

Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R. Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M.; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

2011-01-01

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi. PMID:21949797

Molecular Evidences of a Hidden Complex Scenario in Leporinus cf. friderici

PubMed Central

Silva-Santos, Rosane; Ramirez, Jorge L.; Galetti, Pedro M.; Freitas, Patrícia D.

2018-01-01

The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity. In this study, we performed phylogenetic analyses, based on three nuclear (recombination activating gene 1, RAG1, recombination activating gene 2, RAG2, and myosin heavy chain 6 cardiac muscle alpha gene, Myh6) and two mitochondrial (COI and Cytochrome b, Cytb) markers, in specimens morphologically similar to L. friderici and related species from different hydrographic basins in South America. Our phylogenetic tree identified four well-supported clades, which point out to the existence of taxonomic inconsistencies within this fish group. A clade named L. cf. friderici sensu stricto included eight Molecular Operational Taxonomic Units recently diversified in the Brazilian Shield basins. These results were also confirmed by a single-gene species delimitation analysis. It is suggested that this clade includes a species complex, characterizing taxonomic uncertainties. Another clade recovered only L. friderici from the Suriname rivers, validating this nominal species in its type locality. A third no-named clade, characterized by deeper species divergence, recovered five different nominal species interleaved with other undescribed forms previously also recognized as L. cf. friderici, indicating taxonomic errors. The fourth clade only included L. taeniatus. Our results showed a complex scenario involving the morphotype L. cf. friderici and allowed us to address aspects related to evolutionary diversification of this fish group and historical processes involved with, highlighting the importance of revealing hidden biodiversity for the taxonomy and conservationist action plans of these fish. PMID:29497440

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.

Identification of Rays through DNA Barcoding: An Application for Ecologists

PubMed Central

Cerutti-Pereyra, Florencia; Meekan, Mark G.; Wei, Nu-Wei V.; O'Shea, Owen; Bradshaw, Corey J. A.; Austin, Chris M.

2012-01-01

DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data. PMID:22701556

UniEuk: Time to Speak a Common Language in Protistology!

PubMed

Berney, Cédric; Ciuprina, Andreea; Bender, Sara; Brodie, Juliet; Edgcomb, Virginia; Kim, Eunsoo; Rajan, Jeena; Parfrey, Laura Wegener; Adl, Sina; Audic, Stéphane; Bass, David; Caron, David A; Cochrane, Guy; Czech, Lucas; Dunthorn, Micah; Geisen, Stefan; Glöckner, Frank Oliver; Mahé, Frédéric; Quast, Christian; Kaye, Jonathan Z; Simpson, Alastair G B; Stamatakis, Alexandros; Del Campo, Javier; Yilmaz, Pelin; de Vargas, Colomban

2017-05-01

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes. © 2017 The Author(s) Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists.

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

DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

PubMed Central

Kekkonen, Mari; Hebert, Paul D N

2014-01-01

The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies. PMID:24479435

Is polychaete family-level sufficient to assess impact on tropical estuarine gradients?

NASA Astrophysics Data System (ADS)

Nóbrega-Silva, Climélia; Patrício, Joana; Marques, João Carlos; Olímpio, Monalisa dos Santos; Farias, Jéssica Natyelle Barros; Molozzi, Joseline

2016-11-01

Regular, robust monitoring programs set up to assess the environmental conditions of aquatic systems often target different biological groups. And, of these, macroinvertebrate communities and particularly the class Polychaeta are frequently used. Identifying these organisms takes time, money and specialized expertise to ensure correct identification to the lowest possible taxonomic level. Identification errors can lead to an erroneous assessment. The concept of taxonomic sufficiency has been proposed both to minimize errors and to save time and money. This study tested the usefulness of this concept in tropical estuaries in northeast Brazil. We selected two transitional systems with different degrees of human impact due to different land uses and different conservation systems: the Mamanguape estuary, which is in an environmental conservation unit for sustainable use, and the highly impacted, urban Paraíba do Norte estuary. The results clearly showed that nutrient concentrations were markedly higher in the Paraíba do Norte estuary in the dry season and that the composition of the polychaete assemblages differed between the two estuaries as well as along the spatial gradient of each estuary. The use of either genus or family level led to equivalent representation in each system in terms of taxon richness and both the Margalef and Shannon-Wiener diversity indices. Both taxonomic levels described similar changes in the polychaete assemblage along the estuarine gradients. Based on our findings, the use of a coarser taxonomic level (i.e., family) is a good option when the aim is to implement a monitoring program in tropical estuaries with the polychaete assemblages as one of the target groups. This time-efficient taxonomic resolution can help improve sampling designs and allow long-term monitoring studies without losing much vital information.

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.

Biochemical evidence that Dendroctonus frontalis consists of two sibling species in Belize and Chiapas, Mexico

Treesearch

Brian T. Sullivan; Alicia Nino; Benjamin Moreno; Cavell Brownie; Jorge Macias-Samano; Stephen R. Clarke; Lawrence R. Kirkendall; Gerardo. and Zuniga

2012-01-01

Dendroctonus frontalis Zimmermann (Coleoptera: Curculionidae: Scolytinae) is a major economic pest of pines in the United States, Mexico, and Central America. We report biochemical investigations relevant to the taxonomic status and semiochemistry of two distinct morphotypes of D. frontalis recently detected in the Central American...

Taxonomic revision of true morels (Morchella) in Canada and the United States

USDA-ARS?s Scientific Manuscript database

Recent molecular phylogenetic studies by Taskin et al. (Fungal Genet. Biol. 47:672-682. 2010; Mycologia [in press]) and O'Donnell et al. (Fungal Genet. Biol. 48:252-265. 2011) revealed the existence of at least 50 species of Morchella worldwide and demonstrated a high degree of continental endemism ...

Pinus ponderosa: a taxonomic review with five subspecies in the United States

Treesearch

Robert Z. Callaham

2013-01-01

Various forms of Pinus ponderosa Douglas ex C. Lawson are found from British Columbia southward and eastward through 16 states and, perhaps, into Mexico. The status of many names previously associated with this species, but excluded here, has been clarified. Accumulated evidence based on variation in morphology and xylem monoterpenes,...

Constructing Domain-Specific Knowledge in Kindergarten: Relations among Knowledge, Intelligence, and Strategic Performance

ERIC Educational Resources Information Center

Alexander, Joyce M.; Johnson, Kathy E.; Leibham, Mary E.; DeBauge, Christiane

2005-01-01

Thirty kindergarten children from two classrooms participated in a 3-week curricular unit on dinosaurs designed to teach taxonomic relations and distinguishing features aligned with 15 dinosaur species. Both domain-specific learning and strategic performance on a Twenty Questions game were assessed twice throughout the curriculum, as well as…

Species using red-cockaded woodpecker cavities in eastern Texas

Treesearch

Richard N. Conner; D. Craig Rudolph; Daniel Saenz; Richard R. Schaefer

1997-01-01

Because of its ability to excavate cavities in living pines, the Red-cockaded Woodpecker (Picoides borealis) is a keystone species in the tire-disclimax, pine ecosystems of the southeastern United States. Many species representing multiple taxonomic classes are dependent on this woodpecker species for the cavities it creates. We examined the...

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

Treesearch

Alena K. Oliver; Shawn P. Brown; Mac A. Callaham; Ari Jumpponen

2015-01-01

Rare taxa overwhelm metabarcoding data generated using next-generation sequencing (NGS). Low frequency Operational Taxonomic Units (OTUs) may be artifacts generated by PCR-amplification errors resulting from polymerase mispairing. We analyzed two Internal Transcribed Spacer 2 (ITS2) MiSeq libraries generated with proofreading (ThermoScientific Phusion

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.

A new look at the Lake Superior biomass size spectrum

USGS Publications Warehouse

Yurista, Peder M.; Yule, Daniel L.; Balge, Matt; VanAlstine, Jon D.; Thompson, Jo A.; Gamble, Allison E.; Hrabik, Thomas R.; Kelly, John R.; Stockwell, Jason D.; Vinson, Mark

2014-01-01

We synthesized data from multiple sampling programs and years to describe the Lake Superior pelagic biomass size structure. Data consisted of Coulter counts for phytoplankton, optical plankton counts for zooplankton, and acoustic surveys for pelagic prey fish. The size spectrum was stable across two time periods separated by 5 years. The primary scaling or overall slope of the normalized biomass size spectra for the combined years was −1.113, consistent with a previous estimate for Lake Superior (−1.10). Periodic dome structures within the overall biomass size structure were fit to polynomial regressions based on the observed sub-domes within the classical taxonomic positions (algae, zooplankton, and fish). This interpretation of periodic dome delineation was aligned more closely with predator–prey size relationships that exist within the zooplankton (herbivorous, predacious) and fish (planktivorous, piscivorous) taxonomic positions. Domes were spaced approximately every 3.78 log10 units along the axis and with a decreasing peak magnitude of −4.1 log10 units. The relative position of the algal and herbivorous zooplankton domes predicted well the subsequent biomass domes for larger predatory zooplankton and planktivorous prey fish.

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

The New World whirligig beetles of the genus Dineutus Macleay, 1825 (Coleoptera, Gyrinidae, Gyrininae, Dineutini)

PubMed Central

Gustafson, Grey T.; Miller, Kelly B.

2015-01-01

Abstract All New World members of the whirligig beetle genus Dineutus Macleay, 1825 are treated. The New World Dineutus are found to be composed of 18 species and 6 subspecies: one species, Dineutus mexicanus Ochs, 1925, stat. n. is elevated from subspecies to species rank, and the subspecies Dineutus carolinus mutchleri Ochs, 1925, syn. n. is synonymized here with the typical form. Lectotypes are designated for Dineutus discolor Aubé, 1838, Dineutes metallicus Aubé, 1838, Dineutus solitarius Aubé, 1838, Dineutes analis Régimbart, 1883, and Gyrinus longimanus Olivier, 1795. Each taxonomic unit is provided with a taxonomic history, type locality, diagnosis, distribution, habitat information, and a discussion section. The aedeagus and male mesotarsal claws are illustrated, and dorsal and ventral habitus images of both sexes, for each species and subspecies are provided. General distribution maps are provided for all taxonimc units. A key to the genera of New World Gyrinidae, as well as all the New World Dineutus species is provided. General Dineutus anatomy as well as a clarification of homology and anatomical terms is included. PMID:25685002

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).

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

Let's rise up to unite taxonomy and technology.

PubMed

Bik, Holly M

2017-08-01

What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance.

First report of bacterial community from a Bat Guano using Illumina next-generation sequencing.

PubMed

De Mandal, Surajit; Zothansanga; Panda, Amritha Kumari; Bisht, Satpal Singh; Senthil Kumar, Nachimuthu

2015-06-01

V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave - Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units) comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach.

First report of bacterial community from a Bat Guano using Illumina next-generation sequencing

PubMed Central

De Mandal, Surajit; Zothansanga; Panda, Amritha Kumari; Bisht, Satpal Singh; Senthil Kumar, Nachimuthu

2015-01-01

V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave — Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units) comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach. PMID:26484190

Let’s rise up to unite taxonomy and technology

PubMed Central

2017-01-01

What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional “model” organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance. PMID:28820884

Winter-summer succession of unicellular eukaryotes in a meso-eutrophic coastal system.

PubMed

Christaki, Urania; Kormas, Konstantinos A; Genitsaris, Savvas; Georges, Clément; Sime-Ngando, Télesphore; Viscogliosi, Eric; Monchy, Sébastien

2014-01-01

The objective of this study was to explore the succession of planktonic unicellular eukaryotes by means of 18S rRNA gene tag pyrosequencing in the eastern English Channel (EEC) during the winter to summer transition. The 59 most representative (>0.1%, representing altogether 95% of total reads), unique operational taxonomic units (OTUs) from all samples belonged to 18 known high-level taxonomic groups and 1 unaffiliated clade. The five most abundant OTUs (69.2% of total reads) belonged to Dinophyceae, Cercozoa, Haptophyceae, marine alveolate group I, and Fungi. Cluster and network analysis between samples distinguished the winter, the pre-bloom, the Phaeocystis globosa bloom and the post-bloom early summer conditions. The OTUs-based network revealed that P. globosa showed a relatively low number of connections-most of them negative-with all other OTUs. Fungi were linked to all major taxonomic groups, except Dinophyceae. Cercozoa mostly co-occurred with the Fungi, the Bacillariophyceae and several of the miscellaneous OTUs. This study provided a more detailed exploration into the planktonic succession pattern of the EEC due to its increased depth of taxonomic sampling over previous efforts based on classical monitoring observations. Data analysis implied that the food web concept in a coastal system based on predator-prey (e.g. grazer-phytoplankton) relationships is just a part of the ecological picture; and those organisms exploiting a variety of strategies, such as saprotrophy and parasitism, are persistent and abundant members of the community.

Overview of the taxonomy of zooxanthellate Scleractinia.

PubMed

Veron, John

2013-11-01

Coral taxonomy has entered a historical phase where nomenclatorial uncertainty is rapidly increasing. The fundamental cause is mandatory adherence to historical monographs that lack essential information of all sorts, and also to type specimens, if they exist at all, that are commonly unrecognizable fragments or are uncharacteristic of the species they are believed to represent. Historical problems, including incorrect subsequent type species designations, also create uncertainty for many well-established genera. The advent of in situ studies in the 1970s revealed these issues; now molecular technology is again changing the taxonomic landscape. The competing methodologies involved must be seen in context if they are to avoid becoming an additional basis for continuing nomenclatorial instability. To prevent this happening, the International Commission on Zoological Nomenclature (ICZN) will need to focus on rules that consolidate well-established nomenclature and allow for the designation of new type specimens that are unambiguous, and which include both skeletal material and soft tissue for molecular study. Taxonomic and biogeographic findings have now become linked, with molecular methodologies providing the capacity to re-visit past taxonomic decisions, and to extend both taxonomy and biogeography into the realm of evolutionary theory. It is proposed that most species will ultimately be seen as operational taxonomic units that are human rather than natural constructs, which in consequence will always have fuzzy morphological, genetic, and distribution boundaries. The pathway ahead calls for the integration of morphological and molecular taxonomies, and for website delivery of information that crosses current discipline boundaries.

Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales

PubMed Central

Daza, Juan D.; Köhler, Jörn; Vences, Miguel; Glaw, Frank

2017-01-01

The gecko genus Geckolepis, endemic to Madagascar and the Comoro archipelago, is taxonomically challenging. One reason is its members ability to autotomize a large portion of their scales when grasped or touched, most likely to escape predation. Based on an integrative taxonomic approach including external morphology, morphometrics, genetics, pholidosis, and osteology, we here describe the first new species from this genus in 75 years: Geckolepis megalepis sp. nov. from the limestone karst of Ankarana in northern Madagascar. The new species has the largest known body scales of any gecko (both relatively and absolutely), which come off with exceptional ease. We provide a detailed description of the skeleton of the genus Geckolepis based on micro-Computed Tomography (micro-CT) analysis of the new species, the holotype of G. maculata, the recently resurrected G. humbloti, and a specimen belonging to an operational taxonomic unit (OTU) recently suggested to represent G. maculata. Geckolepis is characterized by highly mineralized, imbricated scales, paired frontals, and unfused subolfactory processes of the frontals, among other features. We identify diagnostic characters in the osteology of these geckos that help define our new species and show that the OTU assigned to G. maculata is probably not conspecific with it, leaving the taxonomic identity of this species unclear. We discuss possible reasons for the extremely enlarged scales of G. megalepis in the context of an anti-predator defence mechanism, and the future of Geckolepis taxonomy. PMID:28194313

77 FR 59357 - Endangered and Threatened Wildlife and Plants; 12-Month Finding on a Petition To List Spring...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-27

... bibliography of the descriptive and systematic literature'' published in volume 40 of the Journal of Research... Integrated Taxonomic Information System (ITIS). The ITIS is hosted by the United States Geological Survey... potential sites) for the Spring Mountains acastus checkerspot butterfly in 1999. During the 1999 surveys...

50 CFR 17.12 - Endangered and threatened plants.

Code of Federal Regulations, 2010 CFR

2010-10-01

... lower taxonomic units (see § 17.11(g) for examples). (h) The “List of Endangered and Threatened Plants... Eragrostis fosbergii Fosberg's love grass U.S.A. (HI) Poaceae E 591 17.99(i) NA Eremalche kernensis Kern... 619 NA NA Neostapfia colusana Colusa grass ......do Poaceae T 611 17.96(a) NA Neraudia angulata None U...

Zinc treatment increases the titre of 'Candidatus Liberibacter asiaticus' in huanglongbing-affected citrus plants while affecting the bacterial microbiomes

USDA-ARS?s Scientific Manuscript database

The bacterial microbiomes of citrus plants in response to ‘Candidatus Liberibacter asiaticus’ (Las)-infection and zinc treatments were deciphered by Phylochip-based metagenomics. The results indicated that 5,475 of over 50,000 known Operational Taxonomic Units (OTUs) in 52 phyla were detected in cit...

Anatomically preserved "strobili" and leaves from the Permian of China (Dorsalistachyaceae, fam. nov.) broaden knowledge of Noeggerathiales and constrain their possible taxonomic affinities.

PubMed

Wang, Shi-Jun; Bateman, Richard M; Spencer, Alan R T; Wang, Jun; Shao, Longyi; Hilton, Jason

2017-01-01

Noeggerathiales are an extinct group of heterosporous shrubs and trees that were widespread and diverse during the Pennsylvanian-Permian Epochs (323-252 Ma) but are of controversial taxonomic affinity. Groups proposed as close relatives include leptosporangiate ferns, sphenopsids, progymnosperms, or the extant eusporangiate fern Tmesipteris. Previously identified noeggerathialeans lacked anatomical preservation, limiting taxonomic comparisons to their external morphology and spore structure. We here document from the upper Permian of China the first anatomically preserved noeggerathialeans, which enhance the perceived distinctiveness of the group and better indicate its systematic affinity. We describe in detail the newly discovered, anatomically preserved heterosporous strobilus Dorsalistachya quadrisegmentorum, gen. et sp. nov., and redescribe its suspected foliar correlate, the pinnate leaf Plagiozamites oblongifolius. Plagiozamites possesses an omega (Ω)-shaped vascular trace and prominent cortical secretory cavities-a distinctive anatomical organization that is echoed in the newly discovered strobili. Dorsalistachya strobili bear highly dissected sporophylls alternately in two vertical rows, suggesting that they are homologs of leaf pinnae. If so, the "strobilus" is strictly a pseudostrobilus and consists of sporangium-bearing units that are one hierarchical level below true sporophylls. The "sporophylls" bear four microsporangia on the lower (abaxial) surface, occasionally interspersed with short longitudinal rows of megasporangia. A single functional megaspore develops within each winged megasporangium, suggesting adaptation for dispersal as a single unit. Dorsalistachya presents a unique combination of reproductive features that amply justifies establishment of a new family, Dorsalistachyaceae. Noeggerathiales represent a distinct taxonomic Order of free-sporing plants that most resembles early-divergent eusporangiate ferns and the more derived among the extinct progymnosperms. By the early Permian, noeggerathialeans had attained levels of reproductive sophistication similar to the most derived among the Paleozoic sphenophytes and lycophytes, but their heterosporous life history may have contributed to their extinction during the Triassic climatic aridification. © 2017 Wang et al. Published by the Botanical Society of America. This work is licensed under a Creative Commons Attribution License (CC-BY-NC).

Genetic evaluation of the evolutionary distinctness of a federally endangered butterfly, Lange's Metalmark.

PubMed

Proshek, Benjamin; Dupuis, Julian R; Engberg, Anna; Davenport, Ken; Opler, Paul A; Powell, Jerry A; Sperling, Felix A H

2015-04-25

The Mormon Metalmark (Apodemia mormo) species complex occurs as isolated and phenotypically variable colonies in dryland areas across western North America. Lange's Metalmark, A. m. langei, one of the 17 subspecies taxonomically recognized in the complex, is federally listed under the U.S. Endangered Species Act of 1973. Metalmark taxa have traditionally been described based on phenotypic and ecological characteristics, and it is unknown how well this nomenclature reflects their genetic and evolutionary distinctiveness. Genetic variation in six microsatellite loci and mitochondrial cytochrome oxidase subunit I sequence was used to assess the population structure of the A. mormo species complex across 69 localities, and to evaluate A. m. langei's qualifications as an Evolutionarily Significant Unit. We discovered substantial genetic divergence within the species complex, especially across the Continental Divide, with population genetic structure corresponding more closely with geographic proximity and local isolation than with taxonomic divisions originally based on wing color and pattern characters. Lange's Metalmark was as genetically divergent as several other locally isolated populations in California, and even the unique phenotype that warranted subspecific and conservation status is reminiscent of the morphological variation found in some other populations. This study is the first genetic treatment of the A. mormo complex across western North America and potentially provides a foundation for reassessing the taxonomy of the group. Furthermore, these results illustrate the utility of molecular markers to aid in demarcation of biological units below the species level. From a conservation point of view, Apodemia mormo langei's diagnostic taxonomic characteristics may, by themselves, not support its evolutionary significance, which has implications for its formal listing as an Endangered Species.

New data on the stem and leaf anatomy of two conifers from the Lower Cretaceous of the Araripe Basin, northeastern Brazil, and their taxonomic and paleoecological implications

PubMed Central

Batista, Maria Edenilce Peixoto; Silva, Delmira da Costa; Sales, Marcos A. F.; Sá, Artur A.; Saraiva, Antônio A. F.; Loiola, Maria Iracema Bezerra

2017-01-01

Pseudofrenelopsis and Brachyphyllum are two conifers that were part of the Lower Cretaceous (Aptian) taphoflora of the Crato Formation, Araripe Basin, northeastern Brazil. The former genus includes, so far, P. capillata and indeterminate species, whilst the latter is mainly represented by B. obesum, the most common plant megafossil recovered from that stratigraphic unit. Here, the stem and leaf anatomy of Pseudofrenelopsis sp. and B. obesum specimens is revisited, including the first report of some epidermal and vascular traits for both taxa from the Crato Formation. Along with its paleoecological significance, the new data suggest the presence of more than one Pseudofrenelopsis species in the Aptian taphoflora of the Araripe Basin and further support the taxonomic placement of B. obesum within Araucariaceae. PMID:28257466

Definition of Tenuipalpus sensu stricto (Acari, Tenuipalpidae), with redescription of Tenuipalpus caudatus (Dugès) and description of a new species from Costa Rica

USDA-ARS?s Scientific Manuscript database

We discuss the taxonomic history of the genus Tenuipalpus Donnadieu and re-describe Tenuipalpus caudatus (Dugès) (= T. palmatus Donnadieu) based on specimens from Portugal intercepted at the United States ports of entry, and references including photographic records of the neotype of T. caudatus. In...

Cellulolytic Bacteria in the Foregut of the Dromedary Camel (Camelus dromedarius)

PubMed Central

Samsudin, Anjas A.; Wright, André-Denis G.

2012-01-01

Foregut digesta from five feral dromedary camels were inoculated into three different enrichment media: cotton thread, filter paper, and neutral detergent fiber. A total of 283 16S rRNA gene sequences were assigned to 33 operational taxonomic units by using 99% species-level identity. LIBSHUFF revealed significant differences in the community composition across all three libraries. PMID:23042173

Cellulolytic bacteria in the foregut of the dromedary camel (Camelus dromedarius).

PubMed

Samsudin, Anjas A; Wright, André-Denis G; Al Jassim, Rafat

2012-12-01

Foregut digesta from five feral dromedary camels were inoculated into three different enrichment media: cotton thread, filter paper, and neutral detergent fiber. A total of 283 16S rRNA gene sequences were assigned to 33 operational taxonomic units by using 99% species-level identity. LIBSHUFF revealed significant differences in the community composition across all three libraries.

A catalog of the Coleoptera of America north of Mexico, family: curculionidae subfamily: Curculioninae

Treesearch

Lester P. Gibson

1985-01-01

The Coleoptera, or beetles, are represented in the world by about 220,000 described species, of which about 24,000 occur in the United States and Canada. A comprehensive taxonomic catalog of beetles for this area has not been available except the series of world-based "Coleopterorum Catalogus" volumes (1909-present, Junk, Berlin). The Leng "Catalogue of...

50 CFR 17.12 - Endangered and threatened plants.

Code of Federal Regulations, 2011 CFR

2011-10-01

... lower taxonomic units (see § 17.11(g) for examples). (h) The “List of Endangered and Threatened Plants...) Asteraceae T 181 17.96(a) NA Eragrostis fosbergii Fosberg's love grass U.S.A. (HI) Poaceae E 591 17.99(i) NA... Neostapfia colusana Colusa grass ......do Poaceae T 611 17.96(a) NA Neraudia angulata None U.S.A. (HI...

A mutualistic interaction between a fungivorous nematode and a fungus within the endophytic community of Bromus tectorum

Treesearch

Melissa A. Baynes; Danelle M. Russell; George Newcombe; Lynn K. Carta; Amy Y. Rossman; Adnan Ismaiel

2012-01-01

In its invaded range in western North America, Bromus tectorum (cheatgrass) can host more than 100 sequence-based, operational taxonomic units of endophytic fungi, of which an individual plant hosts a subset. Research suggests that the specific subset is determined by plant genotype, environment, dispersal of locally available endophytes, and mycorrhizal associates....

Incidence and taxonomic richness of mosquitoes in the diets of little brown and big brown bats

Treesearch

Amy K Wray; Michelle A Jusino; Mark T Banik; Jonathan M Palmer; Heather Kaarakka; J Paul White; Daniel L Lindner; Claudio Gratton; M Zachariah Peery

2018-01-01

Bats have been portrayed as important consumers of mosquitoes, but evidence supporting this claim is surprisingly scant. We collected the fecal material of 2 common North American bats at 22 sites in Wisconsin, United States and screened samples for mosquitoes using a recently improved molecular method for detecting arthropod DNA. Overall, we detected 17 discrete...

Conservation status of freshwater gastropods of Canada and the United States

USGS Publications Warehouse

Johnson, Paul D.; Bogan, Arthur E.; Brown, Kenneth M.; Burkhead, Noel M.; Cordeiro, James R.; Garner, Jeffrey T.; Hartfield, Paul D.; Lepitzki, Dwayne A.; Mackie, Gerry L.; Pip, Eva; Tarpley, Thomas A.; Tiemann, Jeremy S.; Whelan, Nathan V.; Strong, Ellen E.

2013-01-01

This is the first American Fisheries Society conservation assessment of freshwater gastropods (snails) from Canada and the United States by the Gastropod Subcommittee (Endangered Species Committee). This review covers 703 species representing 16 families and 93 genera, of which 67 species are considered extinct, or possibly extinct, 278 are endangered, 102 are threatened, 73 are vulnerable, 157 are currently stable, and 26 species have uncertain taxonomic status. Of the entire fauna, 74% of gastropods are imperiled (vulnerable, threatened, endangered) or extinct, which exceeds imperilment levels in fishes (39%) and crayfishes (48%) but is similar to that of mussels (72%). Comparison of modern to background extinction rates reveals that gastropods have the highest modern extinction rate yet observed, 9,539 times greater than background rates. Gastropods are highly susceptible to habitat loss and degradation, particularly narrow endemics restricted to a single spring or short stream reaches. Compilation of this review was hampered by a paucity of current distributional information and taxonomic uncertainties. Although research on several fronts including basic biology, physiology, conservation strategies, life history, and ecology are needed, systematics and curation of museum collections and databases coupled with comprehensive status surveys (geographic limits, threat identification) are priorities.

Influence of Peanut Cultivars and Environmental Conditions on the Diversity and Community Composition of Pod Rot Soil Fungi in China.

PubMed

Wang, Mian; Chen, Mingna; Yang, Zhen; Chen, Na; Chi, Xiaoyuan; Pan, Lijuan; Wang, Tong; Yu, Shanlin; Guo, Xingqi

2017-12-01

Peanut yield and quality are seriously affected by pod rot pathogens worldwide, especially in China in recent years. The goals of this study are to analyze the structure of fungal communities of peanut pod rot in soil in three peanut cultivars and the correlation of pod rot with environmental variables using 454 pyrosequencing. A total of 46,723 internal transcribed spacer high-quality sequences were obtained and grouped into 1,706 operational taxonomic units at the 97% similarity cut-off level. The coverage, rank abundance, and the Chao 1 and Shannon diversity indices of the operational taxonomic units were analyzed. Members of the phylum Ascomycota were dominant, such as Fusarium , Chaetomium , Alternaria , and Sordariomycetes , followed by Basidiomycota. The results of the heatmap and redundancy analysis revealed significant variation in the composition of the fungal community among the three cultivar samples. The environmental conditions in different peanut cultivars may also influence on the structure of the fungal community. The results of this study suggest that the causal agent of peanut pod rot may be more complex, and cultivars and environmental conditions are both important contributors to the community structure of peanut pod rot fungi.

Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level

PubMed Central

Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K. E.; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

2014-01-01

Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes. PMID:25352837

Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

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

Martin, Erika C.; Gido, Keith B.; Bello, Nora

Stream fish can regulate their environment through direct and indirect pathways, and the relative influence of communities with different taxonomic and functional richness on ecosystem properties likely depends on habitat structure. Given this complexity, it is not surprising that observational studies of how stream fish communities influence ecosystems have shown mixed results. In this study, we evaluated the effect of an observed gradient of taxonomic (zero, one, two or three species) and functional (zero, one or two groups) richness of fishes on several key ecosystem properties in experimental stream mesocosms. Our study simulated small (less than two metres wide) headwatermore » prairie streams with a succession of three pool-riffle structures (upstream, middle and downstream) per mesocosm. Additionally, ecosystem responses included chlorophyll a from floating algal mats and benthic algae, benthic organic matter, macroinvertebrates (all as mass per unit area), algal filament length and stream metabolism (photosynthesis and respiration rate). Ecosystem responses were analysed individually using general linear mixed models. Significant treatment (taxonomic and functional richness) by habitat (pools and riffles) interactions were found for all but one ecosystem response variable. After accounting for location (upstream, middle and downstream) effects, the presence of one or two grazers resulted in shorter mean algal filament lengths in pools compared to no-fish controls. These observations suggest grazers can maintain short algal filaments in pools, which may inhibit long filaments from reaching the surface. Accordingly, floating algal mats decreased in mid- and downstream locations in grazer treatment relative to no-fish controls. At the scale of the entire reach, gross primary productivity and respiration were greater in treatments with two grazer species compared to mixed grazer/insectivore or control treatments. Lastly, the distribution of stream resources across habitat types and locations within a reach can therefore be influenced by the taxonomic and functional composition of fishes in small prairie streams. Thus, disturbances that alter diversity of these systems might have unexpected ecosystem-level consequences.« less

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.

Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

DOE PAGES

Martin, Erika C.; Gido, Keith B.; Bello, Nora; ...

2016-04-06

Stream fish can regulate their environment through direct and indirect pathways, and the relative influence of communities with different taxonomic and functional richness on ecosystem properties likely depends on habitat structure. Given this complexity, it is not surprising that observational studies of how stream fish communities influence ecosystems have shown mixed results. In this study, we evaluated the effect of an observed gradient of taxonomic (zero, one, two or three species) and functional (zero, one or two groups) richness of fishes on several key ecosystem properties in experimental stream mesocosms. Our study simulated small (less than two metres wide) headwatermore » prairie streams with a succession of three pool-riffle structures (upstream, middle and downstream) per mesocosm. Additionally, ecosystem responses included chlorophyll a from floating algal mats and benthic algae, benthic organic matter, macroinvertebrates (all as mass per unit area), algal filament length and stream metabolism (photosynthesis and respiration rate). Ecosystem responses were analysed individually using general linear mixed models. Significant treatment (taxonomic and functional richness) by habitat (pools and riffles) interactions were found for all but one ecosystem response variable. After accounting for location (upstream, middle and downstream) effects, the presence of one or two grazers resulted in shorter mean algal filament lengths in pools compared to no-fish controls. These observations suggest grazers can maintain short algal filaments in pools, which may inhibit long filaments from reaching the surface. Accordingly, floating algal mats decreased in mid- and downstream locations in grazer treatment relative to no-fish controls. At the scale of the entire reach, gross primary productivity and respiration were greater in treatments with two grazer species compared to mixed grazer/insectivore or control treatments. Lastly, the distribution of stream resources across habitat types and locations within a reach can therefore be influenced by the taxonomic and functional composition of fishes in small prairie streams. Thus, disturbances that alter diversity of these systems might have unexpected ecosystem-level consequences.« less

From Microhabitat of Floral Nectar Up to Biogeographic Scale: Novel Insights on Neutral and Niche Bacterial Assemblies.

PubMed

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2017-07-01

Microbial model systems are very useful in addressing macro-ecological questions. Two major theories exist to date, to explain the community structure of organisms: (1) the dispersal (neutral) assembly theory which predicts that community similarity decreases with increasing geographic distance, independent of any environmental variables, and (2) the niche assembly theory which predicts that the communities' compositions are more homogeneous among sites characterized by similar environmental conditions. Our study system offered a unique opportunity to investigate the relative role of environmental conditions and spatial factors in shaping community composition. We explored the bacterial community composition (BCC) of Nicotiana glauca floral nectar using the Illumina MiSeq technique at three spatial scales (plants, site, and region) and two taxonomic levels. Floral nectar samples were collected from 69 N. glauca plants at 11 different sites along a 200-km transect in Israel, along three biogeographic regions. A distance decay of BCC was found among all plants throughout Israel, but such pattern was not found among either sites or biogeographical regions. The BCC was also governed by environmental conditions in all examined scales (from the plant up to the biogeographical region). We also found that taxonomic resolution (89 and 97% sequence identity for clustering operational taxonomic units) affected the results of these BCC analyses. Hence, our study revealed that the BCC in N. glauca floral nectar is shaped by both the environmental conditions and the distance between plants, depending on the sampling scale under examination as well as by taxonomic resolution.

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.

Taxonomic classification of soils using digital information from LANDSAT data. Huayllamarca and eucaliptus areas. M.S. Thesis - Bolivia Univ.

NASA Technical Reports Server (NTRS)

Quiroga, S. Q.

1977-01-01

The applicability of LANDSAT digital information to soil mapping is described. A compilation of all cartographic information and bibliography of the study area is made. LANDSAT MSS images on a scale of 1:250,000 are interpreted and a physiographic map with legend is prepared. The study area is inspected and a selection of the sample areas is made. A digital map of the different soil units is produced and the computer mapping units are checked against the soil units encountered in the field. The soil boundaries obtained by automatic mapping were not substantially changed by field work. The accuracy of the automatic mapping is rather high.

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

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...

[Altitudinal patterns of species richness and species range size of vascular plants in Xiaolong- shan Reserve of Qinling Mountain: a test of Rapoport' s rule].

PubMed

Zheng, Zhi; Gong, Da-Jie; Sun, Cheng-Xiang; Li, Xiao-Jun; Li, Wan-Jiang

2014-09-01

Altitudinal patterns of species richness and species range size and their underlying mechanisms have long been a key topic in biogeography and biodiversity research. Rapoport's rule stated that the species richness gradually declined with the increasing altitude, while the species ranges became larger. Using altitude-distribution database from Xiaolongshan Reverse, this study explored the altitudinal patterns of vascular plant species richness and species range in Qinling Xiaolongshan Reserve, and examined the relationships between species richness and their distributional middle points in altitudinal bands for different fauna, taxonomic units and growth forms and tested the Rapoport's rule by using Stevens' method, Pagel's method, mid-point method and cross-species method. The results showed that the species richness of vascular plants except small-range species showed a unimodal pattern along the altitude in Qinling Xiaolongshan Reserve and the highest proportion of small-range species was found at the lower altitudinal bands and at the higher altitudinal bands. Due to different assemblages and examining methods, the relationships between species distributing range sizes and the altitudes were different. Increasing taxonomic units was easier to support Rapoport's rule, which was related to niche differences that the different taxonomic units occupied. The mean species range size of angiosperms showed a unimodal pattern along the altitude, while those of the gymnosperms and pteridophytes were unclearly regular. The mean species range size of the climbers was wider with the increasing altitude, while that of the shrubs which could adapt to different environmental situations was not sensitive to the change of altitude. Pagel's method was easier to support the Rapoport's rule, and then was Steven's method. On the contrary, due to the mid-domain effect, the results of the test by using the mid-point method showed that the mean species range size varied in a unimodal pattern along the altitude, which didn't support the Rapoport's rule, and because of the scatter-spot impact, the explanatory power of the cross-species method was much lower.

Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States

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

Troia, Matthew J.; McManamay, Ryan A.

Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records frommore » the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). In this study, we aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. Lastly, this comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.« less

Filling in the GAPS: evaluating completeness and coverage of open-access biodiversity databases in the United States

DOE PAGES

Troia, Matthew J.; McManamay, Ryan A.

2016-06-12

Primary biodiversity data constitute observations of particular species at given points in time and space. Open-access electronic databases provide unprecedented access to these data, but their usefulness in characterizing species distributions and patterns in biodiversity depend on how complete species inventories are at a given survey location and how uniformly distributed survey locations are along dimensions of time, space, and environment. Our aim was to compare completeness and coverage among three open-access databases representing ten taxonomic groups (amphibians, birds, freshwater bivalves, crayfish, freshwater fish, fungi, insects, mammals, plants, and reptiles) in the contiguous United States. We compiled occurrence records frommore » the Global Biodiversity Information Facility (GBIF), the North American Breeding Bird Survey (BBS), and federally administered fish surveys (FFS). In this study, we aggregated occurrence records by 0.1° × 0.1° grid cells and computed three completeness metrics to classify each grid cell as well-surveyed or not. Next, we compared frequency distributions of surveyed grid cells to background environmental conditions in a GIS and performed Kolmogorov–Smirnov tests to quantify coverage through time, along two spatial gradients, and along eight environmental gradients. The three databases contributed >13.6 million reliable occurrence records distributed among >190,000 grid cells. The percent of well-surveyed grid cells was substantially lower for GBIF (5.2%) than for systematic surveys (BBS and FFS; 82.5%). Still, the large number of GBIF occurrence records produced at least 250 well-surveyed grid cells for six of nine taxonomic groups. Coverages of systematic surveys were less biased across spatial and environmental dimensions but were more biased in temporal coverage compared to GBIF data. GBIF coverages also varied among taxonomic groups, consistent with commonly recognized geographic, environmental, and institutional sampling biases. Lastly, this comprehensive assessment of biodiversity data across the contiguous United States provides a prioritization scheme to fill in the gaps by contributing existing occurrence records to the public domain and planning future surveys.« less

PESI - a taxonomic backbone for Europe.

PubMed

de Jong, Yde; Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D; Boegh, Phillip S; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M J C; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

2015-01-01

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

PESI - a taxonomic backbone for Europe

PubMed Central

Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

2015-01-01

Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

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.

Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus.

PubMed

Ouvrard, Pierre; Hicks, Damien M; Mouland, Molly; Nicholls, James A; Baldock, Katherine C R; Goddard, Mark A; Kunin, William E; Potts, Simon G; Thieme, Thomas; Veromann, Eve; Stone, Graham N

2016-12-01

Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.

Pyrosequencing analysis of free-living and attached bacterial communities in Meiliang Bay, Lake Taihu, a large eutrophic shallow lake in China.

PubMed

Tang, Xiangming; Li, Linlin; Shao, Keqiang; Wang, Boweng; Cai, Xianlei; Zhang, Lei; Chao, Jianying; Gao, Guang

2015-01-01

To elucidate the relationship between particle-attached (PA, ≥ 5.0 μm) and free-living (FL, 0.2-5.0 μm) bacterial communities, samplings were collected seasonally from November 2011 to August 2012 in Meiliang Bay, Lake Taihu, China. We used 454 pyrosequencing of 16S rRNA genes to study bacterial diversity and structure of PA and FL communities. The analysis rendered 37,985 highly qualified reads, subsequently assigned to 1755 operational taxonomic units (97% similarity) for the 8 samples. Although 27 high-level taxonomic groups were obtained, the 3 dominant phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) comprised about 75.9% and 82.4% of the PA and FL fractions, respectively. Overall, we found no significant differences between community types, as indicated by ANOSIM R statistics (R = 0.063, P > 0.05) and the Parsimony test (P = 0.222). Dynamics of bacterial communities were correlated with changes in concentrations of total suspended solids (TSS) and total phosphorus (TP). In summer, a significant taxonomic overlap in the 2 size fractions was observed when Cyanobacteria, a major contributor of TSS and TP, dominated in the water, highlighting the potential rapid exchange between PA and FL bacterial populations in large shallow eutrophic lakes.

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.

[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.

Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach.

PubMed

Xu, Lei; Wang, Lianggen; Ning, Jiajia; Li, Hong; Ji, Yingying; Du, Feiyan

2018-04-19

Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology. Here, by analysing the mitochondrial COI gene, we explore the taxa across the SCA using molecular tools for the first time. Our results show that sequence divergence among species varies within a large range, from 12.93% to 35.82%. Sixteen of the taxonomic units recovered by DNA taxonomy agree well with morphology, but Paraconchoecia oblonga, Conchoecia magna and Halocypris brevirostris split into two clades each, each of which contains cryptic species.

A Falsification of the Citation Impediment in the Taxonomic Literature

PubMed Central

Steiner, Florian M.; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.

2015-01-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009–2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could easily improve—if the community becomes aware that there is no citation impediment in taxonomy. PMID:25944475

A Falsification of the Citation Impediment in the Taxonomic Literature.

PubMed

Steiner, Florian M; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C

2015-09-01

Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009-2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could easily improve-if the community becomes aware that there is no citation impediment in taxonomy. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities

USGS Publications Warehouse

Kidd, Haack S.; Garchow, H.; Odelson, D.A.; Forney, L.J.; Klug, M.J.

1994-01-01

We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid 'signatures' in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI- FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.

A new methodology to assess antimicrobial resistance of bacteria in coastal waters; pilot study in a Mediterranean hydrosystem

NASA Astrophysics Data System (ADS)

Almakki, Ayad; Estèves, Kevin; Vanhove, Audrey S.; Mosser, Thomas; Aujoulat, Fabien; Marchandin, Hélène; Toubiana, Mylène; Monfort, Patrick; Jumas-Bilak, Estelle; Licznar-Fajardo, Patricia

2017-10-01

The global resistome of coastal waters has been less studied than that of other waters, including marine ones. Here we develop an original method for characterizing the antimicrobial resistance of bacterial communities in coastal waters. The method combines the determination of a new parameter, the community Inhibitory Concentration (c-IC) of antibiotics (ATBs), and the description of the taxonomic richness of the resistant bacteria. We test the method in a Mediterranean hydrosystem, in the Montpellier region, France. Three types of waters are analyzed: near coastal river waters (Lez), lagoon brackish waters (Mauguio), and lake freshwaters (Salagou). Bacterial communities are grown in vitro in various conditions of temperature, salinity, and ATB concentrations. From these experiments, we determine the concentrations of ATB that decrease the bacterial community abundance by 50% (c-IC50) and by 90% (c-IC90). In parallel, we determine the taxonomic repertory of the resistant growing bacteria communities (repertory of Operational Taxonomic Units [OTU]). Temperature and salinity influence the abundance of the cultivable bacteria in presence of ATBs and hence the c-ICs. Very low ATB concentrations can decrease the bacterial abundance significantly. Beside a few ubiquitous genera (Bacillus, Pseudomonas, Shewanella, Vibrio), most resistant OTUs are specific of a type of water. In brackish water, resistant OTUs are more diverse and their community structure less vulnerable to ATBs than those in freshwater. We anticipate that c-IC measurement combined with taxonomic description can be applied to any littoral region to characterize the resistant bacterial communities in the coastal waters. This would help us to evaluate the vulnerability of aquatic ecosystems to antimicrobial pressure.

Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

PubMed

Hesse, Cedar N; Torres-Cruz, Terry J; Tobias, Terri Billingsley; Al-Matruk, Maryam; Porras-Alfaro, Andrea; Kuske, Cheryl R

Soil fungal communities are responsible for carbon and nitrogen (N) cycling. The high complexity of the soil fungal community and the high proportion of taxonomically unidentifiable sequences confound ecological interpretations in field studies because physiological information is lacking for many organisms known only by their rRNA sequences. This situation forces experimental comparisons to be made at broader taxonomic racks where functions become difficult to infer. The objective of this study was to determine OTU (operational taxonomic units) level responses of the soil fungal community to N enrichment in a temperate pine forest experiment and to use the sequencing data to guide culture efforts of novel N-responsive fungal taxa. Replicate samples from four soil horizons (up to 10 cm depth) were obtained from ambient, enriched CO 2 and N-fertilization plots. Through a fungal large subunit rRNA gene (LSU) sequencing survey, we identified two novel fungal clades that were abundant in our soil sampling (representing up to 27% of the sequences in some samples) and responsive to changes in soil N. The two N-responsive taxa with no predicted taxonomic association were targeted for isolation and culturing from specific soil samples where their sequences were abundant. Representatives of both OTUs were successfully cultured using a filtration approach. One taxon (OTU6) was most closely related to Saccharomycotina; the second taxon (OTU69) was most closely related to Mucoromycotina. Both taxa likely represent novel species. This study shows how observation of specific OTUs level responses to altered N status in a large rRNA gene field survey provided the impetus to design targeted culture approaches for isolation of novel N-responsive fungal taxa.

Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

PubMed

Savic, Olivera; Savic, Andrej M; Kovic, Vanja

2017-01-01

We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

The fossil record of ecdysis, and trends in the moulting behaviour of trilobites.

PubMed

Daley, Allison C; Drage, Harriet B

2016-03-01

Ecdysis, the process of moulting an exoskeleton, is one of the key characters uniting arthropods, nematodes and a number of smaller phyla into Ecdysozoa. The arthropod fossil record, particularly trilobites, eurypterids and decapod crustaceans, yields information on moulting, although the current focus is predominantly descriptive and lacks a broader evolutionary perspective. We here review literature on the fossil record of ecdysis, synthesising research on the behaviour, evolutionary trends, and phylogenetic significance of moulting throughout the Phanerozoic. Approaches vary widely between taxonomic groups, but an overall theme uniting these works suggests that identifying moults in the palaeontological record must take into account the morphology, taphonomy and depositional environment of fossils. We also quantitatively analyse trends in trilobite ecdysis based on a newly generated database of published incidences of moulting behaviour. This preliminary work reveals significant taxonomic and temporal signal in the trilobite moulting fossil record, with free cheek moulting being prevalent across all Orders and throughout the Phanerozoic, and peaks of cephalic moulting in Phacopida during the Ordovician and rostral plate moulting in Redlichiida during the Cambrian. This study and a review of the literature suggest that it is feasible to extract large-scale evolutionary information from the fossil record of moulting. Copyright © 2015 Elsevier Ltd. All rights reserved.

Anaerobic Ammonium-Oxidizing Bacteria in Cow Manure Composting.

PubMed

Wang, Tingting; Cheng, Lijun; Zhang, Wenhao; Xu, Xiuhong; Meng, Qingxin; Sun, Xuewei; Liu, Huajing; Li, Hongtao; Sun, Yu

2017-07-28

Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the global nitrogen cycle, but their role in composting remains poorly understood. In the present study, the community structure, diversity, and abundance of anammox bacteria were analyzed using cloning and sequencing methods by targeting the 16S rRNA gene and the hydrazine oxidase gene ( hzo ) in samples isolated from compost produced from cow manure and rice straw. A total of 25 operational taxonomic units were classified based on 16S rRNA gene clone libraries, and 14 operational taxonomic units were classified based on hzo gene clone libraries. The phylogenetic tree analysis of the 16S rRNA gene and deduced HZO protein sequences from the corresponding encoding genes indicated that the majority of the obtained clones were related to the known anammox bacteria Candidatus "Brocadia," Candidatus "Kuenenia," and Candidatus "Scalindua." The abundances of anammox bacteria were determined by quantitative PCR, and between 2.13 × 10 5 and 1.15 × 10 6 16S rRNA gene copies per gram of compost were found. This study provides the first demonstration of the existence of anammox bacteria with limited diversity in cow manure composting.

Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units

PubMed Central

Schürch, Anita C.; Schipper, Debby; Bijl, Maarten A.; Dau, Jim; Beckmen, Kimberlee B.; Schapendonk, Claudia M. E.; Raj, V. Stalin; Osterhaus, Albert D. M. E.; Haagmans, Bart L.; Tryland, Morten; Smits, Saskia L.

2014-01-01

Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae. PMID:25140520

Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes.

PubMed

Vick-Majors, Trista J; Priscu, John C; Amaral-Zettler, Linda A

2014-04-01

High-latitude environments, such as the Antarctic McMurdo Dry Valley lakes, are subject to seasonally segregated light-dark cycles, which have important consequences for microbial diversity and function on an annual basis. Owing largely to the logistical difficulties of sampling polar environments during the darkness of winter, little is known about planktonic microbial community responses to the cessation of photosynthetic primary production during the austral sunset, which lingers from approximately February to April. Here, we hypothesized that changes in bacterial, archaeal and eukaryotic community structure, particularly shifts in favor of chemolithotrophs and mixotrophs, would manifest during the transition to polar night. Our work represents the first concurrent molecular characterization, using 454 pyrosequencing of hypervariable regions of the small-subunit ribosomal RNA gene, of bacterial, archaeal and eukaryotic communities in permanently ice-covered lakes Fryxell and Bonney, before and during the polar night transition. We found vertically stratified populations that varied at the community and/or operational taxonomic unit-level between lakes and seasons. Network analysis based on operational taxonomic unit level interactions revealed nonrandomly structured microbial communities organized into modules (groups of taxa) containing key metabolic potential capacities, including photoheterotrophy, mixotrophy and chemolithotrophy, which are likely to be differentially favored during the transition to polar night.

Isolation, Characterization, and Antibacterial Activity of Hard-to-Culture Actinobacteria from Cave Moonmilk Deposits.

PubMed

Adam, Delphine; Maciejewska, Marta; Naômé, Aymeric; Martinet, Loïc; Coppieters, Wouter; Karim, Latifa; Baurain, Denis; Rigali, Sébastien

2018-03-22

Cave moonmilk deposits host an abundant and diverse actinobacterial population that has a great potential for producing novel natural bioactive compounds. In our previous attempt to isolate culturable moonmilk-dwelling Actinobacteria, only Streptomyces species were recovered, whereas a metagenetic study of the same deposits revealed a complex actinobacterial community including 46 actinobacterial genera in addition to streptomycetes. In this work, we applied the rehydration-centrifugation method to lessen the occurrence of filamentous species and tested a series of strategies to achieve the isolation of hard-to-culture and rare Actinobacteria from the moonmilk deposits of the cave "Grotte des Collemboles". From the "tips and tricks" that were tested, separate autoclaving of the components of the International Streptomyces Project (ISP) medium number 5 (ISP5) medium, prolonged incubation time, and dilution of the moonmilk suspension were found to most effectively improve colony forming units. Taxonomic analyses of the 40 isolates revealed new representatives of the Agromyces , Amycolatopsis , Kocuria , Micrococcus , Micromonospora , Nocardia , and Rhodococcus species, as well as additional new streptomycetes. The applied methodologies allowed the isolation of strains associated with both the least and most abundant moonmilk-dwelling actinobacterial operational taxonomic units. Finally, bioactivity screenings revealed that some isolates displayed high antibacterial activities, and genome mining uncovered a strong potential for the production of natural compounds.

Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials

PubMed Central

Savic, Olivera; Savic, Andrej M.; Kovic, Vanja

2017-01-01

We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280–460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520–600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation. PMID:29236767

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

PubMed

Cornman, R Scott; Otto, Clint R V; Iwanowicz, Deborah; Pettis, Jeffery S

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available.

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci

PubMed Central

Cornman, R. Scott; Otto, Clint R. V.; Iwanowicz, Deborah; Pettis, Jeffery S.

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available. PMID:26700168

Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci

USGS Publications Warehouse

Cornman, Robert S.; Otto, Clint R.; Iwanowicz, Deborah; Pettis, Jeffery S

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available.

Comparative community structure of archaea in rumen of buffaloes and cattle.

PubMed

Paul, Shyam S; Dey, Avijit; Baro, Daoharu; Punia, Balbir S

2017-08-01

Detailed knowledge of the community structure of methanogens is essential for amelioration of methane emission from livestock species. Several studies have indicated that predominant methanogens of buffalo rumen are different from those in cattle. However, predominant genera of methanogens reported by individual studies varied primarily because of limited scope of sampling, sequencing of limited number of sequences and potential PCR bias in individual studies. In this study, the collective comparative diversity of methanogenic archaea in the rumen of cattle and buffaloes was examined by performing a meta-analysis of all the 16S rRNA (rrn) sequences deposited in GenBank. Ruminal methanogen sequences of buffalo were clustered into 900 species-level operational taxonomic units (OTUs), and ruminal methanogen sequences of cattle were clustered into 1522 species level OTUs. The number of species-level OTUs shared between cattle and buffaloes was 229 (10.4% of all OTUs), comprising 1746 sequences (27% of the total 6447 sequences). According to taxonomic classification by three different classifiers, Methanobrevibacter was found to be the most predominant genus both in cattle (69-71% of sequences) as well as buffaloes (65.1-68.9% of sequences). Percentage of Methanomicrobium was much higher (P < 0.05) in the case of buffalo (18%) than that of cattle (4.5%). On the other hand, percentages of Methanosphaera- and Methanomassiliicoccus-like methanogens were much higher (P < 0.05) in cattle than in buffaloes. This study indicated that there is a substantial difference in community structure of ruminal methanogens of cattle and buffaloes. The study has also indicated that the percent of species-level operational taxonomic units shared between cattle and buffalo is very low, and thus host species-specific methane mitigation strategies need to be developed for cattle and buffaloes. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage.

PubMed

Duniere, Lysiane; Xu, Shanwei; Long, Jin; Elekwachi, Chijioke; Wang, Yuxi; Turkington, Kelly; Forster, Robert; McAllister, Tim A

2017-03-03

Describing the microbial populations present in small grain silage and understanding their changes during ensiling is of interest for improving the nutrient value of these important forage crops. Barley, oat and triticale forages as well as an intercropped mixture of the 3 crops were harvested and ensiled in mini silos for a period of 90 days, followed by 14 days of aerobic exposure. Changes in fermentation characteristics and nutritive value were assessed in terminal silages and bacterial and fungal communities during ensiling and aerobic exposure were described using 16S and 18S rDNA sequencing, respectively. All small grain silages exhibited chemical traits that were associated with well ensiled forages, such as low pH value (4.09 ± 0.28) and high levels of lactic acid (59.8 ± 14.59 mg/g DM). The number of microbial core genome operational taxonomic units (OTUs) decreased with time of ensiling. Taxonomic bacterial community profiles were dominated by the Lactobacillales after fermentation, with a notable increase in Bacillales as a result of aerobic exposure. Diversity of the fungal core microbiome was shown to also be reduced during ensiling. Operational taxonomic units assigned to filamentous fungi were found in the core microbiome at ensiling and after aerobic exposure, whereas the Saccharomycetales were the dominate yeast population after 90 days of ensiling and aerobic exposure. Bacterial and fungal orders typically associated with silage spoilage were identified in the core microbiome after aerobic exposure. Next Generation Sequencing was successfully used to describe bacterial communities and the first record of fungal communities throughout the process of ensiling and utilization. Adequately describing the microbial ecology of silages could lead to improved ensiling practices and the selection of silage inoculants that act synergistically with the natural forage microbiome.

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

Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem.

PubMed

Ruiz-Pérez, Carlos A; Restrepo, Silvia; Zambrano, María Mercedes

2016-01-08

Microbial populations residing in close contact with plants can be found in the rhizosphere, in the phyllosphere as epiphytes on the surface, or inside plants as endophytes. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neotropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass, and young and mature leaves, the last two analyzed separately as endophytes and epiphytes. The taxonomic composition determined by performing sequencing of the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass, and the rhizosphere, with predominance of some phyla but only few shared operational taxonomic units (OTUs). Functional profiles predicted on the basis of taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacities based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds, or microorganisms relevant to industry or for remediation efforts. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem

PubMed Central

Restrepo, Silvia

2016-01-01

Microbial populations residing in close contact with plants can be found in the rhizosphere, in the phyllosphere as epiphytes on the surface, or inside plants as endophytes. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neotropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass, and young and mature leaves, the last two analyzed separately as endophytes and epiphytes. The taxonomic composition determined by performing sequencing of the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass, and the rhizosphere, with predominance of some phyla but only few shared operational taxonomic units (OTUs). Functional profiles predicted on the basis of taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacities based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds, or microorganisms relevant to industry or for remediation efforts. PMID:26746719

Charting taxonomic knowledge through ontologies and ranking algorithms

NASA Astrophysics Data System (ADS)

Huber, Robert; Klump, Jens

2009-04-01

Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute to the preservation our scientific heritage.

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.

Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

PubMed

Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping

2016-03-01

Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the observed values of correlations were significantly different from null expectations of random extinction. Our assessment of island bird assemblages validated the predictions of no distance effects and low beta diversity due to pervasive dispersal events among islands and also suggested that selective extinction drives taxonomic and functional alpha and beta diversities. The contrasting turnover and nestedness-resultant components of taxonomic and functional beta diversities demonstrate the importance of considering the multifaceted nature of biodiversity when examining community assembly. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site.

PubMed

Laroche, Olivier; Wood, Susanna A; Tremblay, Louis A; Ellis, Joanne I; Lejzerowicz, Franck; Pawlowski, Jan; Lear, Gavin; Atalah, Javier; Pochon, Xavier

2016-09-01

At present, environmental impacts from offshore oil and gas activities are partly determined by measuring changes in macrofauna diversity. Morphological identification of macrofauna is time-consuming, expensive and dependent on taxonomic expertise. In this study, we evaluated the applicability of using foraminiferal-specific metabarcoding for routine monitoring. Sediment samples were collected along distance gradients from two oil platforms off Taranaki (New Zealand) and their physico-chemical properties, foraminiferal environmental DNA/RNA, and macrofaunal composition analyzed. Macrofaunal and foraminiferal assemblages showed similar shifts along impact gradients, but responded differently to environmental perturbations. Macrofauna were affected by hypoxia, whereas sediment grain size appeared to drive shifts in foraminifera. We identified eight foraminiferal molecular operational taxonomic units that have potential to be used as bioindicator taxa. Our results show that metabarcoding represents an effective tool for assessing foraminiferal communities near offshore oil and gas platforms, and that it can be used to complement current monitoring techniques. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

An horizon scan of biogeography

PubMed Central

2014-01-01

The opportunity to reflect broadly on the accomplishments, prospects, and reach of a field may present itself relatively infrequently. Each biennial meeting of the International Biogeography Society showcases ideas solicited and developed largely during the preceding year, by individuals or teams from across the breadth of the discipline. Here, we highlight challenges, developments, and opportunities in biogeography from that biennial synthesis. We note the realized and potential impact of rapid data accumulation in several fields, a renaissance for inter-disciplinary research, the importance of recognizing the evolution–ecology continuum across spatial and temporal scales and at different taxonomic, phylogenetic and functional levels, and re-exploration of classical assumptions and hypotheses using new tools. However, advances are taxonomically and geographically biased, and key theoretical frameworks await tools to handle, or strategies to simplify, the biological complexity seen in empirical systems. Current threats to biodiversity require unprecedented integration of knowledge and development of predictive capacity that may enable biogeography to unite its descriptive and hypothetico-deductive branches and establish a greater role within and outside academia. PMID:24707348

Treetrimmer: a method for phylogenetic dataset size reduction.

PubMed

Maruyama, Shinichiro; Eveleigh, Robert J M; Archibald, John M

2013-04-12

With rapid advances in genome sequencing and bioinformatics, it is now possible to generate phylogenetic trees containing thousands of operational taxonomic units (OTUs) from a wide range of organisms. However, use of rigorous tree-building methods on such large datasets is prohibitive and manual 'pruning' of sequence alignments is time consuming and raises concerns over reproducibility. There is a need for bioinformatic tools with which to objectively carry out such pruning procedures. Here we present 'TreeTrimmer', a bioinformatics procedure that removes unnecessary redundancy in large phylogenetic datasets, alleviating the size effect on more rigorous downstream analyses. The method identifies and removes user-defined 'redundant' sequences, e.g., orthologous sequences from closely related organisms and 'recently' evolved lineage-specific paralogs. Representative OTUs are retained for more rigorous re-analysis. TreeTrimmer reduces the OTU density of phylogenetic trees without sacrificing taxonomic diversity while retaining the original tree topology, thereby speeding up downstream computer-intensive analyses, e.g., Bayesian and maximum likelihood tree reconstructions, in a reproducible fashion.

Sympatry in the Culicoides variipennis complex (Diptera: Ceratopogonidae): a taxonomic reassessment.

PubMed

Holbrook, F R; Tabachnick, W J; Schmidtmann, E T; McKinnon, C N; Bobian, R J; Grogan, W L

2000-01-01

We report sympatry among larval populations of the Culicoides variipennis complex in widespread and diverse aquatic habitats throughout the United States. Six sites in California, Nevada, New Mexico, and Texas were co-inhabited by C. v. occidentalis and C. v. sonorensis, whereas 8 sites in Florida, Georgia, Louisiana, Maryland, and Texas were co-occupied by C. v. sonorensis and C. v. variipennis. No intermediate forms were identified either electrophoretically or morphologically in adults reared from field-collected larvae and pupae. The absence of intergrades in zones of sympatry represents sufficient evidence to confirm species status for Culicoides variipennis (Coquillett) and Culicoides occidentalis Wirth & Jones, and to elevate Culicoides sonorensis to species rank (NEW STATUS). Culicoides v. albertensis Wirth & Jones is a synonym of C. sonorensis (NEW SYNONYMY); C. v. australis Wirth & Jones also is confirmed as a synonym of C. sonorensis. We also demonstrated a correlation between population taxonomic status as determined by electrophoresis and adult morphology.

Spatial patterns of cryptobenthic coral-reef fishes in the Red Sea

NASA Astrophysics Data System (ADS)

Coker, Darren J.; DiBattista, Joseph D.; Sinclair-Taylor, Tane H.; Berumen, Michael L.

2018-03-01

Surveys to document coral-reef fish assemblages are often limited to visually conspicuous species, thus excluding a significant proportion of the biodiversity. Through standardized collections of cryptobenthic reef fishes in the central and southern Red Sea, a total of 238 species and operational taxonomic units (OTUs) from 35 families were collected. Abundance and species richness increased by 60 and 30%, respectively, from north to south, and fish community composition differed between the two regions and with proximity to shore in the central region. Models suggest regional influences in fish communities, with latitudinal patterns influenced by key coral groups ( Acropora, Pocilloporidae) and variation in environmental parameters (chlorophyll a, sea surface temperature, salinity). This study illustrates the limited taxonomic resolution in this group and in this region, and the need to expand baseline data for this under-studied assemblage. To assist in advancing this initiative, we have produced a catalogue of specimens, archived photographs, and established a DNA sequence library based on cytochrome-c oxidase subunit-I barcodes for all OTUs.

Partial Knowledge of Word Meanings: Thematic and Taxonomic Representations

ERIC Educational Resources Information Center

Whitmore, Jeannette M.; Shore, Wendelyn J.; Smith, Peg Hull

2004-01-01

The type of information (taxonomic or thematic) available at different levels of knowledge was investigated. Following extensive norming to identify taxonomic and thematic associates of low-frequency nouns, participants determined if taxonomic or thematic associates were meaningfully related to target words at three levels of knowledge: target…

Swarm: robust and fast clustering method for amplicon-based studies.

PubMed

Mahé, Frédéric; Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2014-01-01

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.

Swarm: robust and fast clustering method for amplicon-based studies

PubMed Central

Rognes, Torbjørn; Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

2014-01-01

Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units. PMID:25276506

Sex differences in gut microbiota in patients with major depressive disorder.

PubMed

Chen, Jian-Jun; Zheng, Peng; Liu, Yi-Yun; Zhong, Xiao-Gang; Wang, Hai-Yang; Guo, Yu-Jie; Xie, Peng

2018-01-01

Our previous studies found that disturbances in gut microbiota might have a causative role in the onset of major depressive disorder (MDD). The aim of this study was to investigate whether there were sex differences in gut microbiota in patients with MDD. First-episode drug-naïve MDD patients and healthy controls were included. 16S rRNA gene sequences extracted from the fecal samples of the included subjects were analyzed. Principal-coordinate analysis and partial least squares-discriminant analysis were used to assess whether there were sex-specific gut microbiota. A random forest algorithm was used to identify the differential operational taxonomic units. Linear discriminant-analysis effect size was further used to identify the dominant sex-specific phylotypes responsible for the differences between MDD patients and healthy controls. In total, 57 and 74 differential operational taxonomic units responsible for separating female and male MDD patients from their healthy counterparts were identified. Compared with their healthy counterparts, increased Actinobacteria and decreased Bacteroidetes levels were found in female and male MDD patients, respectively. The most differentially abundant bacterial taxa in female and male MDD patients belonged to phyla Actinobacteria and Bacteroidia, respectively. Meanwhile, female and male MDD patients had different dominant phylotypes. These results demonstrated that there were sex differences in gut microbiota in patients with MDD. The suitability of Actinobacteria and Bacteroidia as the sex-specific biomarkers for diagnosing MDD should be further explored.

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

Bacterial communities associated with the ectoparasitic mites Varroa destructor and Tropilaelaps mercedesae of the honey bee (Apis mellifera).

PubMed

Pakwan, Chonthicha; Kaltenpoth, Martin; Weiss, Benjamin; Chantawannakul, Panuwan; Jun, Guo; Disayathanoowat, Terd

2017-12-01

Varroa and Tropilaelaps mites have been reported as serious ectoparasites of the honey bee (Apis mellifera). In this study, bacterial communities associated with Varroa destructor and Tropilaelaps mercedesae from northern Thailand were determined, using both culture-dependent and culture-independent approaches. Adult female mites were collected from apiaries in Chiang Mai and Lampang provinces. Culturable bacteria were isolated from individual mites. On average, we observed approximately 1340 and 1140 CFU/mite in Varroa and Tropilaelaps, respectively. All isolates were assigned to the genus Enterococcus. Six samples of genomic DNA from 30-50 mites were extracted and subjected to pyrosequencing of bacterial 16S rRNA amplicons. The resulting 81 717 sequences obtained from Varroa were grouped into 429 operational taxonomic units. The most abundant bacteria in Varroa mites belonged to the family Enterobacteriaceae, especially the genera Arsenophonus, Enterobacter and Proteus. For Tropilaelaps mites, 84 075 sequences were obtained and clustered into 166 operational taxonomic units, within which the family Enterococcaceae (particularly the genus Enterococcus) was predominant. Localization of bacteria in the mites using fluorescence in situ hybridization with two universal bacterial probes revealed that these bacteria were in the cecum of the mites. Taxon-specific Enterobacteriaceae and Arsenophonus probes also confirmed their localization in the cecum of Varroa. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Conservation genetics and species recovery

USGS Publications Warehouse

Pendleton, Ed; Vandergast, A.G.; King, T.L.

2008-01-01

Recent advances in molecular genetics have proven to be extremely useful in efforts to conserve imperiled species. Genetics data are used to identify appropriate units of management (e.g., populations, metapopulations), effective sizes of breeding populations, population mixing rates, and other variables. These data help managers make decisions about which populations to preserve, whether to move individuals from one site to another, how to breed species most effectively in captivity, and even, in some cases, what taxonomic classification is most appropriate. Many U.S. Geological Survey (USGS) Science Centers and Cooperative Fish and Wildlife Research Units have developed capabilities in genetics research. The two case studies that follow illustrate how USGS geneticists are assisting managers in recovering species on the brink.

A Taxonomic Search Engine: Federating taxonomic databases using web services

PubMed Central

Page, Roderic DM

2005-01-01

Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. Conclusion The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names. PMID:15757517

Machine learning for predicting soil classes in three semi-arid landscapes

USGS Publications Warehouse

Brungard, Colby W.; Boettinger, Janis L.; Duniway, Michael C.; Wills, Skye A.; Edwards, Thomas C.

2015-01-01

Mapping the spatial distribution of soil taxonomic classes is important for informing soil use and management decisions. Digital soil mapping (DSM) can quantitatively predict the spatial distribution of soil taxonomic classes. Key components of DSM are the method and the set of environmental covariates used to predict soil classes. Machine learning is a general term for a broad set of statistical modeling techniques. Many different machine learning models have been applied in the literature and there are different approaches for selecting covariates for DSM. However, there is little guidance as to which, if any, machine learning model and covariate set might be optimal for predicting soil classes across different landscapes. Our objective was to compare multiple machine learning models and covariate sets for predicting soil taxonomic classes at three geographically distinct areas in the semi-arid western United States of America (southern New Mexico, southwestern Utah, and northeastern Wyoming). All three areas were the focus of digital soil mapping studies. Sampling sites at each study area were selected using conditioned Latin hypercube sampling (cLHS). We compared models that had been used in other DSM studies, including clustering algorithms, discriminant analysis, multinomial logistic regression, neural networks, tree based methods, and support vector machine classifiers. Tested machine learning models were divided into three groups based on model complexity: simple, moderate, and complex. We also compared environmental covariates derived from digital elevation models and Landsat imagery that were divided into three different sets: 1) covariates selected a priori by soil scientists familiar with each area and used as input into cLHS, 2) the covariates in set 1 plus 113 additional covariates, and 3) covariates selected using recursive feature elimination. Overall, complex models were consistently more accurate than simple or moderately complex models. Random forests (RF) using covariates selected via recursive feature elimination was consistently the most accurate, or was among the most accurate, classifiers between study areas and between covariate sets within each study area. We recommend that for soil taxonomic class prediction, complex models and covariates selected by recursive feature elimination be used. Overall classification accuracy in each study area was largely dependent upon the number of soil taxonomic classes and the frequency distribution of pedon observations between taxonomic classes. Individual subgroup class accuracy was generally dependent upon the number of soil pedon observations in each taxonomic class. The number of soil classes is related to the inherent variability of a given area. The imbalance of soil pedon observations between classes is likely related to cLHS. Imbalanced frequency distributions of soil pedon observations between classes must be addressed to improve model accuracy. Solutions include increasing the number of soil pedon observations in classes with few observations or decreasing the number of classes. Spatial predictions using the most accurate models generally agree with expected soil–landscape relationships. Spatial prediction uncertainty was lowest in areas of relatively low relief for each study area.

A Framework for Inferring Taxonomic Class of Asteroids.

NASA Technical Reports Server (NTRS)

Dotson, J. L.; Mathias, D. L.

2017-01-01

Introduction: Taxonomic classification of asteroids based on their visible / near-infrared spectra or multi band photometry has proven to be a useful tool to infer other properties about asteroids. Meteorite analogs have been identified for several taxonomic classes, permitting detailed inference about asteroid composition. Trends have been identified between taxonomy and measured asteroid density. Thanks to NEOWise (Near-Earth-Object Wide-field Infrared Survey Explorer) and Spitzer (Spitzer Space Telescope), approximately twice as many asteroids have measured albedos than the number with taxonomic classifications. (If one only considers spectroscopically determined classifications, the ratio is greater than 40.) We present a Bayesian framework that provides probabilistic estimates of the taxonomic class of an asteroid based on its albedo. Although probabilistic estimates of taxonomic classes are not a replacement for spectroscopic or photometric determinations, they can be a useful tool for identifying objects for further study or for asteroid threat assessment models. Inputs and Framework: The framework relies upon two inputs: the expected fraction of each taxonomic class in the population and the albedo distribution of each class. Luckily, numerous authors have addressed both of these questions. For example, the taxonomic distribution by number, surface area and mass of the main belt has been estimated and a diameter limited estimate of fractional abundances of the near earth asteroid population was made. Similarly, the albedo distributions for taxonomic classes have been estimated for the combined main belt and NEA (Near Earth Asteroid) populations in different taxonomic systems and for the NEA population specifically. The framework utilizes a Bayesian inference appropriate for categorical data. The population fractions provide the prior while the albedo distributions allow calculation of the likelihood an albedo measurement is consistent with a given taxonomic class. These inputs allows calculation of the probability an asteroid with a specified albedo belongs to any given taxonomic class.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

PubMed

Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

2017-10-30

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot. The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

Knowledge Management in Taxonomy and Biostratigraphy using TaxonConcept Software

NASA Astrophysics Data System (ADS)

Klump, J.; Huber, R.; Goetz, S.

2005-12-01

The use of fossils to constrain age models for geological samples is not as straightforward as it might seem. Even though index fossils have been defined as biostratigraphic time markers ambiguity arises from the synonymous use of taxonomic names. Progress in our understanding of the origin of certain species have sometimes lead to substantial changes in the taxonomic classification of these organisms. TaxonConcept was created as part of the Stratigraphy.net initiative as a tool to manage taxonomic information and complex knowledge networks to help resolve taxonomic ambiguities in biostratigraphy. Its workflow is based on the principles of open nomenclature. Open nomenclature allows researchers to comment on the identification of a specimen which cannot exactly be determined and is frequently used in synonymy lists. The use of such synonymy lists in TaxonConcept allows to work with taxonomic classifications that are uncertain, or where several versions exist. Every single taxonomic entity in TaxonConcept is recorded with its relevant citations in the literature. This allows to manage information on taxonomy. The members of working groups using TaxonConcept can record their opinion on the taxonomic classification of each taxon in the framework of open nomenclature and annotate it in free text. This managed and structured collection of taxonomic opinions is an example of knowledge management. Taxonomic opinions are otherwise dispersed throughout the literature, if recorded at all, and are only available to the specialist. Assembled as a collection, they represent our knowledge on the taxonomy of a certain group of organisms. In the terminology of computer science, the semantic relationships between taxonomic terms are an ontology. Open nomenclature offers a formal framework that lends itself very well to describe the nature of the relations between taxonomic terms. The use of such synonymy lists in a taxonomic information system allows interesting search options, ranging from tracking name changes to the investigation of complex taxonomic topologies. In addition to its synonymy and literature management, TaxonConcept allows to store many other information categories such as textual descriptions (e.g. diagnoses and comments), images, bioevents and specimen and collection data. Ecological information is scheduled for a later stage of the project. Already now TaxonConcept is linked to taxon names in paleoenvironmental data of the World Data Center for Marine Environmental Sciences (WDC-MARE), interfaces to other databases are planned. WDC-MARE stores environmental, marine and geological research data and frequently uses taxon names in its parameters. By linking TaxonConcept and WDC-MARE, synonymous names can be included in queries, e.g. when researching for stable isotope data measured on microfossils. TaxonConcept is not a project on authoritative taxonomic information, but is a tool for taxonomic projects to use to find a taxonomic consensus, e.g. to define a taxonomic framework for biostratigraphic studies. Both, the project specific hierarchical classification of selected taxa, as well as a project specific selection of any other information categories is supported by TaxonConcept. The results of such a taxonomic consensus can be used to create Fossilium Catalogus style summaries in various output formats which can later be used to create online or print publications.

What Belongs in Your 15-Bean Soup? Using the Learning Cycle to Address Misconceptions about Construction of Taxonomic Keys

ERIC Educational Resources Information Center

Ross, Ann; Vanderspool, Staria

2004-01-01

Students can use seed characteristics to discriminate between the different kinds of legumes using taxonomic classification processes of sorting and ranking, followed by construction of taxonomic keys. The application of the Learning Cycle process to taxonomic principles, hierarchical classification, and construction of keys presents the…

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.

Microbial communities associated with ferromanganese nodules and the surrounding sediments

PubMed Central

Tully, Benjamin J.; Heidelberg, John F.

2013-01-01

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment. PMID:23805131

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.

Diving into the analysis of time-depth recorder and behavioural data records: A workshop summary

NASA Astrophysics Data System (ADS)

Womble, Jamie N.; Horning, Markus; Lea, Mary-Anne; Rehberg, Michael J.

2013-04-01

Directly observing the foraging behavior of animals in the marine environment can be extremely challenging, if not impossible, as such behavior often takes place beneath the surface of the ocean and in extremely remote areas. In lieu of directly observing foraging behavior, data from time-depth recorders and other types of behavioral data recording devices are commonly used to describe and quantify the behavior of fish, squid, seabirds, sea turtles, pinnipeds, and cetaceans. Often the definitions of actual behavioral units and analytical approaches may vary substantially which may influence results and limit our ability to compare behaviors of interest across taxonomic groups and geographic regions. A workshop was convened in association with the Fourth International Symposium on Bio-logging in Hobart, Tasmania on 8 March 2011, with the goal of providing a forum for the presentation, review, and discussion of various methods and approaches that are used to describe and analyze time-depth recorder and associated behavioral data records. The international meeting brought together 36 participants from 14 countries from a diversity of backgrounds including scientists from academia and government, graduate students, post-doctoral fellows, and developers of electronic tagging technology and analysis software. The specific objectives of the workshop were to host a series of invited presentations followed by discussion sessions focused on (1) identifying behavioral units and metrics that are suitable for empirical studies, (2) reviewing analytical approaches and techniques that can be used to objectively classify behavior, and (3) identifying cases when temporal autocorrelation structure is useful for identifying behaviors of interest. Outcomes of the workshop included highlighting the need to better define behavioral units and to devise more standardized processing and analytical techniques in order to ensure that results are comparable across studies and taxonomic groups.

Genomic diversity guides conservation strategies among rare terrestrial orchid species when taxonomy remains uncertain.

PubMed

Ahrens, Collin W; Supple, Megan A; Aitken, Nicola C; Cantrill, David J; Borevitz, Justin O; James, Elizabeth A

2017-06-01

Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia. Four putative species were sampled from a total of 16 populations in the Victorian Volcanic Plain (VVP) bioregion and one population of a sub-alpine outgroup in south-eastern Australia. Morphological measurements were taken in situ along with leaf material for genotyping by sequencing (GBS) and microsatellite analyses. Species could not be differentiated using morphological measurements. Microsatellite and GBS markers confirmed the outgroup as distinct, but only GBS markers provided resolution of population genetic structure. The nationally endangered Diuris basaltica was indistinguishable from two related species ( D. chryseopsis and D. behrii ), while the state-protected D. gregaria showed genomic differentiation. Genomic diversity identified among the four Diuris species suggests that conservation of this taxonomically complex group will be best served by considering them as one ESU rather than separately aligned with species as currently recognized. This approach will maximize evolutionary potential among all species during increased isolation and environmental change. The methods used here can be applied generally to conserve evolutionary processes for groups where taxonomic uncertainty hinders the use of species as conservation units. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Hitting the right target: taxonomic challenges for, and of, plant invasions

PubMed Central

Pyšek, Petr; Hulme, Philip E.; Meyerson, Laura A.; Smith, Gideon F.; Boatwright, James S.; Crouch, Neil R.; Figueiredo, Estrela; Foxcroft, Llewellyn C.; Jarošík, Vojtěch; Richardson, David M.; Suda, Jan; Wilson, John R. U.

2013-01-01

This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.

Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation

PubMed Central

Sangster, George

2009-01-01

The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation’. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950–2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress’. PMID:19520805

The Neural Bases of Taxonomic and Thematic Conceptual Relations: An MEG Study

PubMed Central

Lewis, Gwyneth A.; Poeppel, David; Murphy, Gregory L.

2015-01-01

Converging evidence from behavioral and neuroimaging studies of human concepts indicate distinct neural systems for taxonomic and thematic knowledge. A recent study of naming in aphasia found involvement of the anterior temporal lobe (ATL) during taxonomic (feature-based) processing, and involvement of the temporoparietal junction (TPJ) during thematic (function-based) processing. We conducted an online magnetoencephalography (MEG) study to examine the spatio-temporal nature of taxonomic and thematic relations. We measured participants’ brain responses to words preceded by either a taxonomically or thematically related item (e.g., cottage→castle, king→castle). In a separate experiment we collected relatedness ratings of the word pairs from participants. We examined effects of relatedness and relation type on activation in ATL and TPJ regions of interest (ROIs) using permutation t-tests to identify differences in ROI activation between conditions as well as single-trial correlational analyses to examine the millisecond-by-millisecond influence of the stimulus variables on the ROIs. Taxonomic relations strongly predicted ATL activation, and both kinds of relations influenced the TPJ. Our results further strengthen the view of the ATL's importance to taxonomic knowledge. Moreover, they provide a nuanced view of thematic relations as involving taxonomic knowledge. PMID:25582406

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.

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory; processing, taxonomy, and quality control of benthic macroinvertebrate samples

USGS Publications Warehouse

Moulton, Stephen R.; Carter, James L.; Grotheer, Scott A.; Cuffney, Thomas F.; Short, Terry M.

2000-01-01

Qualitative and quantitative methods to process benthic macroinvertebrate (BMI) samples have been developed and tested by the U.S. Geological Survey?s National Water Quality Laboratory Biological Group. The qualitative processing method is based on visually sorting a sample for up to 2 hours. Sorting focuses on attaining organisms that are likely to result in taxonomic identifications to lower taxonomic levels (for example, Genus or Species). Immature and damaged organisms are also sorted when they are likely to result in unique determinations. The sorted sample remnant is scanned briefly by a second person to determine if obvious taxa were missed. The quantitative processing method is based on a fixed-count approach that targets some minimum count, such as 100 or 300 organisms. Organisms are sorted from randomly selected 5.1- by 5.1-centimeter parts of a gridded subsampling frame. The sorted remnant from each sample is resorted by a second individual for at least 10 percent of the original sort time. A large-rare organism search is performed on the unsorted remnant to sort BMI taxa that were not likely represented in the sorted grids. After either qualitatively or quantitatively sorting the sample, BMIs are identified by using one of three different types of taxonomic assessment. The Standard Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol III and typically provides Genus- or Species-level taxonomic resolution. The Rapid Taxonomic Assessment is comparable to the U.S. Environmental Protection Agency Rapid Bioassessment Protocol II and provides Familylevel and higher taxonomic resolution. The Custom Taxonomic Assessment provides Species-level resolution whenever possible for groups identified to higher taxonomic levels by using the Standard Taxonomic Assessment. The consistent use of standardized designations and notes facilitates the interpretation of BMI data within and among water-quality studies. Taxonomic identifications are quality assured by verifying all referenced taxa and randomly reviewing 10 percent of the taxonomic identifications performed weekly by Biological Group taxonomists. Taxonomic errors discovered during this review are corrected. BMI data are reviewed for accuracy and completeness prior to release. BMI data are released phylogenetically in spreadsheet format and unprocessed abundances are corrected for laboratory and field subsampling when necessary.

Doctor, Teacher, and Stethoscope: Neural Representation of Different Types of Semantic Relations.

PubMed

Xu, Yangwen; Wang, Xiaosha; Wang, Xiaoying; Men, Weiwei; Gao, Jia-Hong; Bi, Yanchao

2018-03-28

Concepts can be related in many ways. They can belong to the same taxonomic category (e.g., "doctor" and "teacher," both in the category of people) or be associated with the same event context (e.g., "doctor" and "stethoscope," both associated with medical scenarios). How are these two major types of semantic relations coded in the brain? We constructed stimuli from three taxonomic categories (people, manmade objects, and locations) and three thematic categories (school, medicine, and sports) and investigated the neural representations of these two dimensions using representational similarity analyses in human participants (10 men and nine women). In specific regions of interest, the left anterior temporal lobe (ATL) and the left temporoparietal junction (TPJ), we found that, whereas both areas had significant effects of taxonomic information, the taxonomic relations had stronger effects in the ATL than in the TPJ ("doctor" and "teacher" closer in ATL neural activity), with the reverse being true for thematic relations ("doctor" and "stethoscope" closer in TPJ neural activity). A whole-brain searchlight analysis revealed that widely distributed regions, mainly in the left hemisphere, represented the taxonomic dimension. Interestingly, the significant effects of the thematic relations were only observed after the taxonomic differences were controlled for in the left TPJ, the right superior lateral occipital cortex, and other frontal, temporal, and parietal regions. In summary, taxonomic grouping is a primary organizational dimension across distributed brain regions, with thematic grouping further embedded within such taxonomic structures. SIGNIFICANCE STATEMENT How are concepts organized in the brain? It is well established that concepts belonging to the same taxonomic categories (e.g., "doctor" and "teacher") share neural representations in specific brain regions. How concepts are associated in other manners (e.g., "doctor" and "stethoscope," which are thematically related) remains poorly understood. We used representational similarity analyses to unravel the neural representations of these different types of semantic relations by testing the same set of words that could be differently grouped by taxonomic categories or by thematic categories. We found that widely distributed brain areas primarily represented taxonomic categories, with the thematic categories further embedded within the taxonomic structure. Copyright © 2018 the authors 0270-6474/18/383303-15$15.00/0.

Primary structure of the wall peptidoglycan of leprosy-derived corynebacteria.

PubMed Central

Janczura, E; Leyh-Bouille, M; Cocito, C; Ghuysen, J M

1981-01-01

The cell walls isolated from axenically grown leprosy-derived corynebacteria were submitted to various chemical and enzymatic degradations. The glycan strands of the wall peptidoglycan are essentially composed of N-acetylglycosaminyl-N-acetylmuramic acid disaccharide units. Small amounts of N-acetylglycosaminyl-N-glycolylmuramic acid (less than 10%) were also detected. The muramic acid residues of adjacent glycan strands are substituted by amidated tetrapeptide units which, in turn, are cross-linked through direct linkages extending between the C-terminal D-alanine residue of one tetrapeptide and the mesodiaminopimelic acid residue of another tetrapeptide. Such a structure is very similar to that of the wall peptidoglycan found in the taxonomically related microorganisms of the Corynebacterium, Mycobacterium, and Nocardia groups. PMID:7462160

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.

Cybertaxonomy to accomplish big things in aphid systematics.

PubMed

Favret, Colin

2014-06-01

Biodiversity sciences have progressed at such a pace that the taxonomic community has been unable to grow concomitantly to keep up with the influx of biological data. This "taxonomic impediment" has led some to suggest that taxonomy is no longer pertinent and to the development of methodologies that circumvent the taxonomic process. This article does not seek to argue for the importance of taxonomy but rather is a call to the aphid taxonomy community to rise to the challenge by dramatically increasing the volume and comprehensiveness of its output without sacrificing quality. Recent informatics technology allows us to mobilize the 2 most important aphid taxonomy resources: experts and specimens, both distributed globally. "Cyberspecimens," museum specimens digitally rendered at a resolution sufficient for remote identification, and open "cybertaxonomic" tools will allow the international aphid taxonomic community to carry out large, ambitious, projects. The global aphid cybertaxonomy proposed here will serve not only the ends of research aphidologists, but also provide a model for other taxonomic communities to adapt and adopt as we confront both the taxonomic impediment and the taxonomic naysayers. © 2013 Institute of Zoology, Chinese Academy of Sciences.

The natural history of Caroline Atoll, Southern Line Islands. Part I. History, physiography, botany, and isle descriptions

USGS Publications Warehouse

Kepler, A.K.; Kepler, C.B.

1994-01-01

conclusion: Lushly wooded Caroline Atoll, with the majority of its 39 islets (399 ha of land) either in near-pristine condition or having recovered remarkably from past disturbance, is one of the least spoiled atolls in the Pacific. Uninhabited, it harbors plant ecosystems and breeding seabirds (Pt. II) of national and international importance. Its marine and terrestrial ecosystems are prime outdoor ecological laboratories for research on geological processes including ground water, sea level changes, the dynamics of motu formation, fish poisoning, and numerous facets of ecology including plant succession and Pisonia growth rates. Caroline boasts prime coral reefs thickly studded with Tridacna clams, substantial numbers of coconut crabs, breeding sites for green turtles, wintering grounds for shorebirds including the rare Bristle-thighed Curlew, ancient Tuamotuan marae, and a crystalline, unpolluted lagoon. The variety, abundance, and quality of its flora and fauna qualify it for status as an officially recognized international preserve (Pt. II, Sect. G). Efforts toward its conservation have thus far been unsuccessful: in 1992 it was leased to a private French businessman who is currently fishing the reefs for commercial profit, as well as disturbing seabird, turtle and coconut crab populations.

The natural history of Caroline Atoll, Southern Line Islands. Part II. Seabirds, other terrestrial animals, and conservation

USGS Publications Warehouse

Kepler, C.B.; Kepler, A.K.; Ellis, D.H.

1994-01-01

conclusion: Lushly wooded Caroline Atoll, with the majority of its 39 islets (399 ha of land) either in near-pristine condition or having recovered remarkably from past disturbance, is one of the least spoiled atolls in the Pacific. Uninhabited, it harbors plant ecosystems and breeding seabirds (Pt. II) of national and international importance. Its marine and terrestrial ecosystems are prime outdoor ecological laboratories for research on geological processes including ground water, sea level changes, the dynamics of motu formation, fish poisoning, and numerous facets of ecology including plant succession and Pisonia growth rates. Caroline boasts prime coral reefs thickly studded with Tridacna clams, substantial numbers of coconut crabs, breeding sites for green turtles, wintering grounds for shorebirds including the rare Bristle-thighed Curlew, ancient Tuamotuan marae, and a crystalline, unpolluted lagoon. The variety, abundance, and quality of its flora and fauna qualify it for status as an officially recognized international preserve (Pt. II, Sect. G). Efforts toward its conservation have thus far been unsuccessful: in 1992 it was leased to a private French businessman who is currently fishing the reefs for commercial profit, as well as disturbing seabird, turtle and coconut crab populations.

Environmental and faunal change in the Jurassic Sundance Seaway, western United States: a stratigraphic palaeobiological approach

NASA Astrophysics Data System (ADS)

Danise, Silvia; Holland, Steven

2017-04-01

Understanding how regional ecosystems respond to sea level and environmental perturbations is a main challenge in palaeoecology. Here we use quantitative abundance estimates, integrated within a sequence stratigraphic and environmental framework, to reconstruct benthic community changes through the 13 myr history of the Jurassic Sundance Seaway in the western United States. Faunal censuses of macroinvertebrates were obtained from marine rocks of the Gypsum Spring, Sundance and Twin Creek formations at 44 localities in Wyoming, Montana and South Dakota. Fossils were identified to species wherever possible. Ordination of samples shows a main turnover event at the Middle-Upper Jurassic transition, which coincided with the shift from carbonate to siliciclastic depositional systems in the Seaway. This shift was probably initiated by the northward migration of the North American Plate, which moved the study area from subtropical latitudes, fostering an arid climate, into progressively more humid conditions, and possibly also by global cooling at this time. Turnover was not uniform across the onshore-offshore gradient, but was higher in offshore environments, in both carbonate and siliciclastic settings. Both the Jaccard and the Bray-Curtis similarity measures indicate that taxonomic similarity decreases from onshore to offshore in successive third-order depositional sequences, although similarity values are low for both onshore and offshore environments The higher resilience of onshore communities to third-order sea-level fluctuations and to the change from a carbonate to a siliciclastic system was driven by a few abundant eurytopic species that persisted from the opening to the closing of the Seaway and that were not restricted to single depositional environments or sequences. Lower stability in offshore facies was instead controlled by the presence of more volatile stenotopic species. Such increased onshore stability in community composition contrasts with the well-documented onshore increase in taxonomic turnover rates, and indicates the need for ecological studies to complement taxonomic studies of macroevolutionary events. This study also shows how a stratigraphic palaeobiological approach is essential for understanding the link between environmental and faunal gradients, and for understanding the long-term changes in these gradients over time that produce the local stratigraphical pattern of changes in community composition.

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.

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

PubMed Central

2014-01-01

Background The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning. PMID:24708438

Phylogenetic distribution of genes encoding β-glucuronidase activity in human colonic bacteria and the impact of diet on faecal glycosidase activities.

PubMed

McIntosh, Freda M; Maison, Nathalie; Holtrop, Grietje; Young, Pauline; Stevens, Valerie J; Ince, Jennifer; Johnstone, Alexandra M; Lobley, Gerald E; Flint, Harry J; Louis, Petra

2012-08-01

Bacterial β-glucuronidase in the human colon plays an important role in cleaving liver conjugates of dietary compounds and xenobiotics, while other glycosidase activities are involved in the conversion of dietary plant glycosides. Here we detected an increase in β-glucuronidase activity in faecal samples from obese volunteers following a high-protein moderate carbohydrate weight-loss diet, compared with a weight maintenance diet, but little or no changes were observed when the type of fermentable carbohydrate was varied. Other faecal glycosidase activities showed little or no change over a fivefold range of dietary NSP intake, although α-glucosidase increased on a resistant starch-enriched diet. Two distinct groups of gene, gus and BG, have been reported to encode β-glucuronidase activity among human colonic bacteria. Degenerate primers were designed against these genes. Overall, Firmicutes were found to account for 96% of amplified gus sequences, with three operational taxonomic units particularly abundant, whereas 59% of amplified BG sequences belonged to Bacteroidetes and 41% to Firmicutes. A similar distribution of operational taxonomic units was found in a published metagenome dataset involving a larger number of volunteers. Seven cultured isolates of human colonic bacteria that carried only the BG gene gave relatively low β-glucuronidase activity that was not induced by 4-nitrophenyl-β-D-glucuronide. By comparison, in three of five isolates that possessed only the gus gene, β-glucuronidase activity was induced. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

On the role, ecology, phylogeny, and structure of dual-family immunophilins.

PubMed

Barik, Sailen

2017-11-01

The novel class of dual-family immunophilins (henceforth abbreviated as DFI) represents naturally occurring chimera of classical FK506-binding protein (FKBP) and cyclophilin (CYN), connected by a flexible linker that may include a three-unit tetratricopeptide (TPR) repeat. Here, I report a comprehensive analysis of all current DFI sequences and their host organisms. DFIs are of two kinds: CFBP (cyclosporin- and FK506-binding protein) and FCBP (FK506- and cyclosporin-binding protein), found in eukaryotes. The CFBP type occurs in select bacteria that are mostly extremophiles, such as psychrophilic, thermophilic, halophilic, and sulfur-reducing. Essentially all DFI organisms are unicellular. I suggest that DFIs are specialized bifunctional chaperones that use their flexible interdomain linker to associate with large polypeptides or multisubunit megacomplexes to promote simultaneous folding or renaturation of two clients in proximity, essential in stressful and denaturing environments. Analysis of sequence homology and predicted 3D structures of the FKBP and CYN domains as well as the TPR linkers upheld the modular nature of the DFIs and revealed the uniqueness of their TPR domain. The CFBP and FCBP genes appear to have evolved in parallel pathways with no obvious single common ancestor. The occurrence of both types of DFI in multiple unrelated phylogenetic clades supported their selection in metabolic and environmental niche roles rather than a traditional taxonomic relationship. Nonetheless, organisms with these rare immunophilins may define an operational taxonomic unit (OTU) bound by the commonality of chaperone function.

Escherichia coli O157:H7 super-shedder and non-shedder feedlot steers harbour distinct fecal bacterial communities.

PubMed

Xu, Yong; Dugat-Bony, Eric; Zaheer, Rahat; Selinger, Lorna; Barbieri, Ruth; Munns, Krysty; McAllister, Tim A; Selinger, L Brent

2014-01-01

Escherichia coli O157:H7 is a major foodborne human pathogen causing disease worldwide. Cattle are a major reservoir for this pathogen and those that shed E. coli O157:H7 at >104 CFU/g feces have been termed "super-shedders". A rich microbial community inhabits the mammalian intestinal tract, but it is not known if the structure of this community differs between super-shedder cattle and their non-shedding pen mates. We hypothesized that the super-shedder state is a result of an intestinal dysbiosis of the microbial community and that a "normal" microbiota prevents E. coli O157:H7 from reaching super-shedding levels. To address this question, we applied 454 pyrosequencing of bacterial 16S rRNA genes to characterize fecal bacterial communities from 11 super-shedders and 11 contemporary pen mates negative for E. coli O157:H7. The dataset was analyzed by using five independent clustering methods to minimize potential biases and to increase confidence in the results. Our analyses collectively indicated significant variations in microbiome composition between super-shedding and non-shedding cattle. Super-shedders exhibited higher bacterial richness and diversity than non-shedders. Furthermore, seventy-two operational taxonomic units, mostly belonging to Firmicutes and Bacteroidetes phyla, were identified showing differential abundance between these two groups of cattle. The operational taxonomic unit affiliation provides new insight into bacterial populations that are present in feces arising from super-shedders of E. coli O157:H7.

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit.

PubMed

Hoefman, Sven; van der Ha, David; Boon, Nico; Vandamme, Peter; De Vos, Paul; Heylen, Kim

2014-04-04

The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

PubMed

Links, Matthew G; Chaban, Bonnie; Hemmingsen, Sean M; Muirhead, Kevin; Hill, Janet E

2013-08-15

Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.

[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.

Taxonomic minimalism.

PubMed

Beattle, A J; Oliver, I

1994-12-01

Biological surveys are in increasing demand while taxonomic resources continue to decline. How much formal taxonomy is required to get the job done? The answer depends on the kind of job but it is possible that taxonomic minimalism, especially (1) the use of higher taxonomic ranks, (2) the use of morphospecies rather than species (as identified by Latin binomials), and (3) the involvement of taxonomic specialists only for training and verification, may offer advantages for biodiversity assessment, environmental monitoring and ecological research. As such, formal taxonomy remains central to the process of biological inventory and survey but resources may be allocated more efficiently. For example, if formal Identification is not required, resources may be concentrated on replication and increasing sample sizes. Taxonomic minimalism may also facilitate the inclusion in these activities of important but neglected groups, especially among the invertebrates, and perhaps even microorganisms. Copyright © 1994. Published by Elsevier Ltd.

Application of DNA barcodes in wildlife conservation in Tropical East Asia.

PubMed

Wilson, John-James; Sing, Kong-Wah; Lee, Ping-Shin; Wee, Alison K S

2016-10-01

Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced. © 2016 Society for Conservation Biology.

Biogeographic patterns of bacterial microdiversity in Arctic deep-sea sediments (HAUSGARTEN, Fram Strait)

PubMed Central

Buttigieg, Pier Luigi; Ramette, Alban

2015-01-01

Marine bacteria colonizing deep-sea sediments beneath the Arctic ocean, a rapidly changing ecosystem, have been shown to exhibit significant biogeographic patterns along transects spanning tens of kilometers and across water depths of several thousand meters (Jacob et al., 2013). Jacob et al. (2013) adopted what has become a classical view of microbial diversity – based on operational taxonomic units clustered at the 97% sequence identity level of the 16S rRNA gene – and observed a very large microbial community replacement at the HAUSGARTEN Long Term Ecological Research station (Eastern Fram Strait). Here, we revisited these data using the oligotyping approach and aimed to obtain new insight into ecological and biogeographic patterns associated with bacterial microdiversity in marine sediments. We also assessed the level of concordance of these insights with previously obtained results. Variation in oligotype dispersal range, relative abundance, co-occurrence, and taxonomic identity were related to environmental parameters such as water depth, biomass, and sedimentary pigment concentration. This study assesses ecological implications of the new microdiversity-based technique using a well-characterized dataset of high relevance for global change biology. PMID:25601856

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

The nature of plant species.

PubMed

Rieseberg, Loren H; Wood, Troy E; Baack, Eric J

2006-03-23

Many botanists doubt the existence of plant species, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (> 80%), the correspondence of taxonomic species to these clusters is poor (< 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages.

Imagining Sisyphus happy: DNA barcoding and the unnamed majority.

PubMed

Blaxter, Mark

2016-09-05

The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on 'charismatic megabionts': larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

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

Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos) Shown with 16S rRNA Gene-Based Microbial Community Analysis

PubMed Central

Maeda, Isamu; Siddiki, Mohammad Shohel Rana; Nozawa-Takeda, Tsutomu; Tsukahara, Naoki; Tani, Yuri; Naito, Taki; Sugita, Shoei

2013-01-01

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms. PMID:24058905

Population abundance of potentially pathogenic organisms in intestinal microbiome of jungle crow (Corvus macrorhynchos) shown with 16S rRNA gene-based microbial community analysis.

PubMed

Maeda, Isamu; Siddiki, Mohammad Shohel Rana; Nozawa-Takeda, Tsutomu; Tsukahara, Naoki; Tani, Yuri; Naito, Taki; Sugita, Shoei

2013-01-01

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

FIRST RESULTS FROM THE RAPID-RESPONSE SPECTROPHOTOMETRIC CHARACTERIZATION OF NEAR-EARTH OBJECTS USING UKIRT

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

Mommert, M.; Trilling, D. E.; Petersen, E.

2016-04-15

Using the Wide Field Camera for the United Kingdom Infrared Telescope (UKIRT), we measure the near-infrared colors of near-Earth objects (NEOs) in order to put constraints on their taxonomic classifications. The rapid-response character of our observations allows us to observe NEOs when they are close to the Earth and bright. Here we present near-infrared color measurements of 86 NEOs, most of which were observed within a few days of their discovery, allowing us to characterize NEOs with diameters of only a few meters. Using machine-learning methods, we compare our measurements to existing asteroid spectral data and provide probabilistic taxonomic classificationsmore » for our targets. Our observations allow us to distinguish between S-complex, C/X-complex, D-type, and V-type asteroids. Our results suggest that the fraction of S-complex asteroids in the whole NEO population is lower than the fraction of ordinary chondrites in the meteorite fall statistics. Future data obtained with UKIRT will be used to investigate the significance of this discrepancy.« less

Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

PubMed

Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

2015-12-30

The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY. Copyright © 2015. Published by Elsevier Ltd.

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.

The rDNA Internal Transcribed Spacer Region as a Taxonomic Marker for Nematodes

PubMed Central

Powers, T. O.; Todd, T. C.; Burnell, A. M.; Murray, P. C. B.; Fleming, C. C.; Szalanski, A. L.; Adams, B. A.; Harris, T. S.

1997-01-01

The ITS region from a wide taxonomic range of nematodes, including secernentean and adenophorean taxa, and free-living, entomopathogenic, and plant-parasitic species, was evaluated as a taxonomic marker. Size of the amplified product aided in the initial determination of group membership, and also suggested groups that may require taxonomic reevaluation. Congeneric species often displayed identically sized ITS regions, but genera such as Pratylenchus and Tylenchorhynchus had species with large differences in size. ITS heterogeneity in individuals and populations was identified in several nematode taxa. PCR-RFLP of ITS1 is advocated as a method of taxonomic analysis in genera such as Helicotylenchus that contain numerous species with few diagnostic morphological characteristics. PMID:19274180

Taxa: An R package implementing data standards and methods for taxonomic data

PubMed Central

Foster, Zachary S.L.; Chamberlain, Scott; Grünwald, Niklaus J.

2018-01-01

The taxa R package provides a set of tools for defining and manipulating taxonomic data. The recent and widespread application of DNA sequencing to community composition studies is making large data sets with taxonomic information commonplace. However, compared to typical tabular data, this information is encoded in many different ways and the hierarchical nature of taxonomic classifications makes it difficult to work with. There are many R packages that use taxonomic data to varying degrees but there is currently no cross-package standard for how this information is encoded and manipulated. We developed the R package taxa to provide a robust and flexible solution to storing and manipulating taxonomic data in R and any application-specific information associated with it. Taxa provides parsers that can read common sources of taxonomic information (taxon IDs, sequence IDs, taxon names, and classifications) from nearly any format while preserving associated data. Once parsed, the taxonomic data and any associated data can be manipulated using a cohesive set of functions modeled after the popular R package dplyr. These functions take into account the hierarchical nature of taxa and can modify the taxonomy or associated data in such a way that both are kept in sync. Taxa is currently being used by the metacoder and taxize packages, which provide broadly useful functionality that we hope will speed adoption by users and developers. PMID:29707201

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.

Taxonomic chauvinism revisited: insight from parental care research.

PubMed

Stahlschmidt, Zachary R

2011-01-01

Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring) is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s) and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior) from 2001-2010 (n = 712) to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1) taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2) taxonomic citation bias, which is a proxy for the breadth of a given article-specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines--in fact, taxonomic bias may have increased. As in Bonnet et al. (2002), my results should not be interpreted as evidence of an 'ornithological Mafia' conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to guide future work.

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

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

Distinct progression of the deterioration of thematic and taxonomic links in natural and manufactured objects in Alzheimer's disease.

PubMed

Simoes Loureiro, Isabelle; Lefebvre, Laurent

2016-10-01

Taxonomic and thematic relationships are core elements of lexico-semantic networks. However, the weight of both links differs in semantic memory, with distinct support for natural and manufactured objects: natural objects tend to be more taxonomically identified while manufactured objects benefit more from the underlying thematic relationships. Alzheimer's disease (AD) causes early semantic memory impairment characterized by a category-specific deterioration, where natural objects are more sensitive to the disease than manufactured objects. However, relatively few studies have examined the progressive deterioration of specific thematic versus taxonomic relations in both categories of objects in AD. To better understand semantic memory disorganization in AD and analyze the potential interaction effect between the category (natural/manufactured), the condition (thematic/taxonomic) and AD, we will investigate the lexico-semantic network in 82 AD patients (divided into three groups depending on their global cognitive deterioration and their performance in a preliminary semantic knowledge questionnaire (mild (AD1), moderate (AD2) and advanced (AD3) stages of semantic knowledge alteration). The experimental protocol contains two tasks: an implicit semantic priming paradigm and an explicit card-sorting test that uses the same items, equally divided between natural and manufactured objects. Results show a distinct taxonomic and thematic evolution pattern with early taxonomic deterioration. Natural objects are also more vulnerable to the disease. Lastly, there is an interaction effect between the category and the condition in the priming task indicating that natural objects are more taxonomically organized and manufactured objects benefit more from both thematic and taxonomic organizations, reinforcing the idea of the robustness of this category. The theoretical accounts of these observations will be discussed in detail. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Neuroanatomical dissociation for taxonomic and thematic knowledge in the human brain

PubMed Central

Schwartz, Myrna F.; Kimberg, Daniel Y.; Walker, Grant M.; Brecher, Adelyn; Faseyitan, Olufunsho K.; Dell, Gary S.; Mirman, Daniel; Coslett, H. Branch

2011-01-01

It is thought that semantic memory represents taxonomic information differently from thematic information. This study investigated the neural basis for the taxonomic-thematic distinction in a unique way. We gathered picture-naming errors from 86 individuals with poststroke language impairment (aphasia). Error rates were determined separately for taxonomic errors (“pear” in response to apple) and thematic errors (“worm” in response to apple), and their shared variance was regressed out of each measure. With the segmented lesions normalized to a common template, we carried out voxel-based lesion-symptom mapping on each error type separately. We found that taxonomic errors localized to the left anterior temporal lobe and thematic errors localized to the left temporoparietal junction. This is an indication that the contribution of these regions to semantic memory cleaves along taxonomic-thematic lines. Our findings show that a distinction long recognized in the psychological sciences is grounded in the structure and function of the human brain. PMID:21540329

Automatic processing of semantic relations in fMRI: neural activation during semantic priming of taxonomic and thematic categories.

PubMed

Sachs, Olga; Weis, Susanne; Zellagui, Nadia; Huber, Walter; Zvyagintsev, Mikhail; Mathiak, Klaus; Kircher, Tilo

2008-07-07

Most current models of knowledge organization are based on hierarchical or taxonomic categories (animals, tools). Another important organizational pattern is thematic categorization, i.e. categories held together by external relations, a unifying scene or event (car and garage). The goal of this study was to compare the neural correlates of these categories under automatic processing conditions that minimize strategic influences. We used fMRI to examine neural correlates of semantic priming for category members with a short stimulus onset asynchrony (SOA) of 200 ms as subjects performed a lexical decision task. Four experimental conditions were compared: thematically related words (car-garage); taxonomically related (car-bus); unrelated (car-spoon); non-word trials (car-derf). We found faster reaction times for related than for unrelated prime-target pairs for both thematic and taxonomic categories. However, the size of the thematic priming effect was greater than that of the taxonomic. The imaging data showed signal changes for the taxonomic priming effects in the right precuneus, postcentral gyrus, middle frontal and superior frontal gyri and thematic priming effects in the right middle frontal gyrus and anterior cingulate. The contrast of neural priming effects showed larger signal changes in the right precuneus associated with the taxonomic but not with thematic priming response. We suggest that the greater involvement of precuneus in the processing of taxonomic relations indicates their reduced salience in the knowledge structure compared to more prominent thematic relations.

Designing Multimedia Games for Young Children's Taxonomic Concept Development

ERIC Educational Resources Information Center

Sung, Yao-Ting; Chang, Kuo-En; Lee, Meng-Da

2008-01-01

This study aimed to design and evaluate multimedia games which were based on the theories of children's development of taxonomic concepts. Factors that might affect children's classification skills, such as use of single physical characteristics of objects, competition between thematic and taxonomic relationships, difficulty in forming…

Preschool Children's Taxonomic Knowledge of Animal Species

ERIC Educational Resources Information Center

Allen, Michael

2015-01-01

Although taxonomic proficiency is a prerequisite for understanding ideas central to biology, previous research has established that learners frequently misclassify animals by not following the tenets of accepted taxonomic rubrics. This has immediate relevance with the recently revised English National Curriculum now requiring concepts of animal…

Guidelines for the processing and quality assurance of benthic invertebrate samples collected as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Cuffney, T.F.; Gurtz, M.E.; Meador, M.R.

1993-01-01

Benthic invertebrate samples are collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program. This is a perennial, multidisciplinary program that integrates biological, physical, and chemical indicators of water quality to evaluate status and trends and to develop an understanding of the factors controlling observed water quality. The Program examines water quality in 60 study units (coupled ground- and surface-water systems) that encompass most of the conterminous United States and parts of Alaska and Hawaii. Study-unit teams collect and process qualitative and semi-quantitative invertebrate samples according to standardized procedures. These samples are processed (elutriated and subsampled) in the field to produce as many as four sample components: large-rare, main-body, elutriate, and split. Each sample component is preserved in 10-percent formalin, and two components, large-rare and main-body, are sent to contract laboratories for further processing. The large-rare component is composed of large invertebrates that are removed from the sample matrix during field processing and placed in one or more containers. The main-body sample component consists of the remaining sample materials (sediment, detritus, and invertebrates) and is subsampled in the field to achieve a volume of 750 milliliters or less. The remaining two sample components, elutriate and split, are used for quality-assurance and quality-control purposes. Contract laboratories are used to identify and quantify invertebrates from the large-rare and main-body sample components according to the procedures and guidelines specified within this document. These guidelines allow the use of subsampling techniques to reduce the volume of sample material processed and to facilitate identifications. These processing procedures and techniques may be modified if the modifications provide equal or greater levels of accuracy and precision. The intent of sample processing is to determine the quantity of each taxon present in the semi-quantitative samples or to list the taxa present in qualitative samples. The processing guidelines provide standardized laboratory forms, sample labels, detailed sample processing flow charts, standardized format for electronic data, quality-assurance procedures and checks, sample tracking standards, and target levels for taxonomic determinations. The contract laboratory (1) is responsible for identifications and quantifications, (2) constructs reference collections, (3) provides data in hard copy and electronic forms, (4) follows specified quality-assurance and quality-control procedures, and (5) returns all processed and unprocessed portions of the samples. The U.S. Geological Survey's Quality Management Group maintains a Biological Quality-Assurance Unit, located at the National Water-Quality Laboratory, Arvada, Colorado, to oversee the use of contract laboratories and ensure the quality of data obtained from these laboratories according to the guidelines established in this document. This unit establishes contract specifications, reviews contractor performance (timeliness, accuracy, and consistency), enters data into the National Water Information System-II data base, maintains in-house reference collections, deposits voucher specimens in outside museums, and interacts with taxonomic experts within and outside the U.S. Geological Survey. This unit also modifies the existing sample processing and quality-assurance guidelines, establishes criteria and testing procedures for qualifying potential contract laboratories, identifies qualified taxonomic experts, and establishes voucher collections.

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.

A taxonomic wish-list for community ecology.

PubMed Central

Gotelli, Nicholas J

2004-01-01

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists. PMID:15253346

Identifying taxonomic and functional surrogates for spring biodiversity conservation.

PubMed

Jyväsjärvi, Jussi; Virtanen, Risto; Ilmonen, Jari; Paasivirta, Lauri; Muotka, Timo

2018-02-27

Surrogate approaches are widely used to estimate overall taxonomic diversity for conservation planning. Surrogate taxa are frequently selected based on rarity or charisma, whereas selection through statistical modeling has been applied rarely. We used boosted-regression-tree models (BRT) fitted to biological data from 165 springs to identify bryophyte and invertebrate surrogates for taxonomic and functional diversity of boreal springs. We focused on these 2 groups because they are well known and abundant in most boreal springs. The best indicators of taxonomic versus functional diversity differed. The bryophyte Bryum weigelii and the chironomid larva Paratrichocladius skirwithensis best indicated taxonomic diversity, whereas the isopod Asellus aquaticus and the chironomid Macropelopia spp. were the best surrogates of functional diversity. In a scoring algorithm for priority-site selection, taxonomic surrogates performed only slightly better than random selection for all spring-dwelling taxa, but they were very effective in representing spring specialists, providing a distinct improvement over random solutions. However, the surrogates for taxonomic diversity represented functional diversity poorly and vice versa. When combined with cross-taxon complementarity analyses, surrogate selection based on statistical modeling provides a promising approach for identifying groundwater-dependent ecosystems of special conservation value, a key requirement of the EU Water Framework Directive. © 2018 Society for Conservation Biology.

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

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

A global organism detection and monitoring system for non-native species

USGS Publications Warehouse

Graham, J.; Newman, G.; Jarnevich, C.; Shory, R.; Stohlgren, T.J.

2007-01-01

Harmful invasive non-native species are a significant threat to native species and ecosystems, and the costs associated with non-native species in the United States is estimated at over $120 Billion/year. While some local or regional databases exist for some taxonomic groups, there are no effective geographic databases designed to detect and monitor all species of non-native plants, animals, and pathogens. We developed a web-based solution called the Global Organism Detection and Monitoring (GODM) system to provide real-time data from a broad spectrum of users on the distribution and abundance of non-native species, including attributes of their habitats for predictive spatial modeling of current and potential distributions. The four major subsystems of GODM provide dynamic links between the organism data, web pages, spatial data, and modeling capabilities. The core survey database tables for recording invasive species survey data are organized into three categories: "Where, Who & When, and What." Organisms are identified with Taxonomic Serial Numbers from the Integrated Taxonomic Information System. To allow users to immediately see a map of their data combined with other user's data, a custom geographic information system (GIS) Internet solution was required. The GIS solution provides an unprecedented level of flexibility in database access, allowing users to display maps of invasive species distributions or abundances based on various criteria including taxonomic classification (i.e., phylum or division, order, class, family, genus, species, subspecies, and variety), a specific project, a range of dates, and a range of attributes (percent cover, age, height, sex, weight). This is a significant paradigm shift from "map servers" to true Internet-based GIS solutions. The remainder of the system was created with a mix of commercial products, open source software, and custom software. Custom GIS libraries were created where required for processing large datasets, accessing the operating system, and to use existing libraries in C++, R, and other languages to develop the tools to track harmful species in space and time. The GODM database and system are crucial for early detection and rapid containment of invasive species. ?? 2007 Elsevier B.V. All rights reserved.

Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities

PubMed Central

Zaheer, Rahat; Selinger, Lorna; Barbieri, Ruth; Munns, Krysty; McAllister, Tim A.; Selinger, L. Brent

2014-01-01

Escherichia coli O157:H7 is a major foodborne human pathogen causing disease worldwide. Cattle are a major reservoir for this pathogen and those that shed E. coli O157:H7 at >104 CFU/g feces have been termed “super-shedders”. A rich microbial community inhabits the mammalian intestinal tract, but it is not known if the structure of this community differs between super-shedder cattle and their non-shedding pen mates. We hypothesized that the super-shedder state is a result of an intestinal dysbiosis of the microbial community and that a “normal” microbiota prevents E. coli O157:H7 from reaching super-shedding levels. To address this question, we applied 454 pyrosequencing of bacterial 16S rRNA genes to characterize fecal bacterial communities from 11 super-shedders and 11 contemporary pen mates negative for E. coli O157:H7. The dataset was analyzed by using five independent clustering methods to minimize potential biases and to increase confidence in the results. Our analyses collectively indicated significant variations in microbiome composition between super-shedding and non-shedding cattle. Super-shedders exhibited higher bacterial richness and diversity than non-shedders. Furthermore, seventy-two operational taxonomic units, mostly belonging to Firmicutes and Bacteroidetes phyla, were identified showing differential abundance between these two groups of cattle. The operational taxonomic unit affiliation provides new insight into bacterial populations that are present in feces arising from super-shedders of E. coli O157:H7. PMID:24858731

Evidence of cellulose metabolism by the giant panda gut microbiome.

PubMed

Zhu, Lifeng; Wu, Qi; Dai, Jiayin; Zhang, Shanning; Wei, Fuwen

2011-10-25

The giant panda genome codes for all necessary enzymes associated with a carnivorous digestive system but lacks genes for enzymes needed to digest cellulose, the principal component of their bamboo diet. It has been posited that this iconic species must therefore possess microbial symbionts capable of metabolizing cellulose, but these symbionts have remained undetected. Here we examined 5,522 prokaryotic ribosomal RNA gene sequences in wild and captive giant panda fecal samples. We found lower species richness of the panda microbiome than of mammalian microbiomes for herbivores and nonherbivorous carnivores. We detected 13 operational taxonomic units closely related to Clostridium groups I and XIVa, both of which contain taxa known to digest cellulose. Seven of these 13 operational taxonomic units were unique to pandas compared with other mammals. Metagenomic analysis using ~37-Mbp contig sequences from gut microbes recovered putative genes coding two cellulose-digesting enzymes and one hemicellulose-digesting enzyme, cellulase, β-glucosidase, and xylan 1,4-β-xylosidase, in Clostridium group I. Comparing glycoside hydrolase profiles of pandas with those of herbivores and omnivores, we found a moderate abundance of oligosaccharide-degrading enzymes for pandas (36%), close to that for humans (37%), and the lowest abundance of cellulases and endohemicellulases (2%), which may reflect low digestibility of cellulose and hemicellulose in the panda's unique bamboo diet. The presence of putative cellulose-digesting microbes, in combination with adaptations related to feeding, physiology, and morphology, show that giant pandas have evolved a number of traits to overcome the anatomical and physiological challenge of digesting a diet high in fibrous matter.

Individual differences in the strength of taxonomic versus thematic relations

PubMed Central

Mirman, Daniel; Graziano, Kristen M.

2011-01-01

Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) based on shared features, or thematically (eating breakfast, taking a dog for a walk, etc.) based on participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a single spoken word, even when the listener is not required to perform any active task. The results further revealed that an individual’s relative activation of taxonomic relations compared to thematic relations predicts that individual’s tendency to favor taxonomic over thematic relations when asked to choose between them in a similarity judgment task. These results argue that individuals differ in the relative strengths of their taxonomic and thematic semantic knowledge and suggest that meaning information is organized in two parallel, complementary semantic systems. PMID:22201413

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.

Two Influential Primate Classifications Logically Aligned

PubMed Central

Franz, Nico M.; Pier, Naomi M.; Reeder, Deeann M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-01-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments—in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms. PMID:27009895

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

PubMed

Lu, Yang Young; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

2017-03-15

The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L 1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT. The software is available at https://github.com/younglululu/COCACOLA . fsun@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

PubMed Central

Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E

2012-01-01

Taxonomic classification of the thousands–millions of 16S rRNA gene sequences generated in microbiome studies is often achieved using a naïve Bayesian classifier (for example, the Ribosomal Database Project II (RDP) classifier), due to favorable trade-offs among automation, speed and accuracy. The resulting classification depends on the reference sequences and taxonomic hierarchy used to train the model; although the influence of primer sets and classification algorithms have been explored in detail, the influence of training set has not been characterized. We compared classification results obtained using three different publicly available databases as training sets, applied to five different bacterial 16S rRNA gene pyrosequencing data sets generated (from human body, mouse gut, python gut, soil and anaerobic digester samples). We observed numerous advantages to using the largest, most diverse training set available, that we constructed from the Greengenes (GG) bacterial/archaeal 16S rRNA gene sequence database and the latest GG taxonomy. Phylogenetic clusters of previously unclassified experimental sequences were identified with notable improvements (for example, 50% reduction in reads unclassified at the phylum level in mouse gut, soil and anaerobic digester samples), especially for phylotypes belonging to specific phyla (Tenericutes, Chloroflexi, Synergistetes and Candidate phyla TM6, TM7). Trimming the reference sequences to the primer region resulted in systematic improvements in classification depth, and greatest gains at higher confidence thresholds. Phylotypes unclassified at the genus level represented a greater proportion of the total community variation than classified operational taxonomic units in mouse gut and anaerobic digester samples, underscoring the need for greater diversity in existing reference databases. PMID:21716311

Exploring Genetic Divergence in a Species-Rich Insect Genus Using 2790 DNA Barcodes

PubMed Central

Lin, Xiaolong; Stur, Elisabeth; Ekrem, Torbjørn

2015-01-01

DNA barcoding using a fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) has proven to be successful for species-level identification in many animal groups. However, most studies have been focused on relatively small datasets or on large datasets of taxonomically high-ranked groups. We explore the quality of DNA barcodes to delimit species in the diverse chironomid genus Tanytarsus (Diptera: Chironomidae) by using different analytical tools. The genus Tanytarsus is the most species-rich taxon of tribe Tanytarsini (Diptera: Chironomidae) with more than 400 species worldwide, some of which can be notoriously difficult to identify to species-level using morphology. Our dataset, based on sequences generated from own material and publicly available data in BOLD, consist of 2790 DNA barcodes with a fragment length of at least 500 base pairs. A neighbor joining tree of this dataset comprises 131 well separated clusters representing 121 morphological species of Tanytarsus: 77 named, 16 unnamed and 28 unidentified theoretical species. For our geographically widespread dataset, DNA barcodes unambiguously discriminate 94.6% of the Tanytarsus species recognized through prior morphological study. Deep intraspecific divergences exist in some species complexes, and need further taxonomic studies using appropriate nuclear markers as well as morphological and ecological data to be resolved. The DNA barcodes cluster into 120–242 molecular operational taxonomic units (OTUs) depending on whether Objective Clustering, Automatic Barcode Gap Discovery (ABGD), Generalized Mixed Yule Coalescent model (GMYC), Poisson Tree Process (PTP), subjective evaluation of the neighbor joining tree or Barcode Index Numbers (BINs) are used. We suggest that a 4–5% threshold is appropriate to delineate species of Tanytarsus non-biting midges. PMID:26406595

A taxonomic review of the centipede genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae) in mainland Southeast Asia, with description of a new species from Laos

PubMed Central

Siriwut, Warut; Edgecombe, Gregory D.; Sutcharit, Chirasak; Tongkerd, Piyoros; Panha, Somsak

2016-01-01

Abstract The centipede genus Scolopendra in mainland Southeast Asia is reviewed taxonomically based on morphological characters, informed by a molecular phylogenetic analysis using sequences from three mitochondrial and nuclear genes (COI, 16S rRNA and 28S rRNA). Eight nominal species of Scolopendra, namely Scolopendra morsitans Linnaeus, 1758, Scolopendra subspinipes Leach, 1816, Scolopendra dehaani Brandt, 1840, Scolopendra multidens Newport, 1844, Scolopendra calcarata Porat, 1876, Scolopendra japonica Koch, 1878, Scolopendra pinguis Pocock, 1891, and Scolopendra dawydoffi Kronmüller, 2012, are redescribed together with some revision of type materials. Geographical variation in each species has been compiled with reference to samples that span their distribution ranges in Southeast Asia and some parts of neighbouring areas such as East Asia, the Indian Ocean, and Africa. Comparative study of traditional taxonomic characters from external morphology provides further information to distinguish some closely related species. Scolopendra cataracta Siriwut, Edgecombe & Panha, sp. n., is described from the southern part of Laos, with additional records in Thailand and Vietnam. The phylogenetic framework for Southeast Asian Scolopendra recognizes Scolopendra calcarata + Scolopendra pinguis, Scolopendra morsitans, and a Scolopendra subspinipes group that unites the other six species as the main clades. Within the Scolopendra subspinipes group, two monophyletic groups can be distinguished by having either slender or short, thick ultimate leg prefemora and different numbers of apical spines on the coxopleuron. Scolopendra arborea Lewis, 1982, is placed in subjective synonymy with Scolopendra dehaani. A survey of external morphology of the genital segments confirms its potential for improving species identification in Scolopendra. Some observations on biology and behaviour are recorded based on field surveys in this area. PMID:27408540

Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.

PubMed

Göker, Markus; García-Blázquez, Gema; Voglmayr, Hermann; Tellería, M Teresa; Martín, María P

2009-07-29

Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms. Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews. A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.

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

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.

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

PubMed Central

Göker, Markus; García-Blázquez, Gema; Voglmayr, Hermann; Tellería, M. Teresa; Martín, María P.

2009-01-01

Background Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms. Methodology Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews. Conclusions A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence. PMID:19641601

Flexible taxonomic assignment of ambiguous sequencing reads

PubMed Central

2011-01-01

Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results. PMID:21211059

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean.

PubMed

Tavares, Tallita Cruz Lopes; Normando, Leonardo Ribeiro Oliveira; de Vasconcelos, Ana Tereza Ribeiro; Gerber, Alexandra Lehmkuhl; Agnez-Lima, Lucymara Fassarella; Melo, Vânia Maria Maciel

2016-07-01

Maritime ports are anthropogenic interventions capable of causing serious alterations in coastal ecosystems. In this study, we examined the benthic microbial diversity and community structure under the influence of two maritime ports, Mucuripe (MUC) and Pecém (PEC), at Equatorial Atlantic Ocean in Northeast Brazil. Those seaports differ in architecture, time of functioning, cargo handling and contamination. The microbiomes from MUC and PEC were also compared in silico to 11 other globally distributed marine microbiomes. The comparative analysis of operational taxonomic units (OTUs) retrieved by PCR-DGGE showed that MUC presents greater richness and β diversity of Bacteria and Archaea than PEC. In line with these results, metagenomic analysis showed that MUC and PEC benthic microbial communities share the main common bacterial phyla found in coastal environments, although can be distinguish by greater abundance of Cyanobacteria in MUC and Deltaproteobacteria in PEC. Both ports differed in Archaea composition, being PEC port sediments dominated by Thaumarchaeota. The microbiomes showed little divergence in their potential metabolic pathways, although shifts on the microbial taxonomic signatures involved in nitrogen and sulphur metabolic pathways were observed. The comparative analysis of different benthic marine metagenomes from Brazil, Australia and Mexico grouped them by the geographic location rather than by the type of ecosystem, although at phylum level seaport sediments share a core microbiome constituted by Proteobacteria, Cyanobacteria, Actinobacteria, Tenericuteres, Firmicutes, Bacteriodetes and Euryarchaeota. Our results suggest that multiple physical and chemical factors acting on sediments as a result of at least 60years of port operation play a role in shaping the benthic microbial communities at taxonomic level, but not at functional level. Copyright © 2016 Elsevier B.V. All rights reserved.

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

PubMed Central

2013-01-01

Background Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. Results Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). Conclusion The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial communities. PMID:24451270

Polysemy and the Taxonomic Constraint: Children's Representation of Words That Label Multiple Kinds

ERIC Educational Resources Information Center

Srinivasan, Mahesh; Snedeker, Jesse

2014-01-01

How do children resolve the problem of indeterminacy when learning a new word? By one account, children adopt a "taxonomic assumption" and expect the word to denote only members of a particular taxonomic category. According to one version of this constraint, young children should represent polysemous words that label multiple kinds--for…

Scientific names of organisms: attribution, rights, and licensing

PubMed Central

2014-01-01

Background As biological disciplines extend into the ‘big data’ world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world. Findings The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts. Conclusions A ‘blue list’ identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed. PMID:24495358

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.

Delimiting species of Protaphorura (Collembola: Onychiuridae): integrative evidence based on morphology, DNA sequences and geography.

PubMed

Sun, Xin; Zhang, Feng; Ding, Yinhuan; Davies, Thomas W; Li, Yu; Wu, Donghui

2017-08-15

Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences. Twenty-two molecular putative species were consistently recovered across molecular and geographical analyses. Geographic criteria were was proved to be an efficient delimitation method for onychiurids. Further morphological examination, based on the combination of the number of pseudocelli, parapseudocelli and ventral mesothoracic chaetae, confirmed 18 taxa of 22 molecular units, with six of them described as new species. These characters were found to be of high taxonomical value. This study highlights the potential benefits of integrative taxonomy, particularly simultaneous use of molecular/geographical tools, as a powerful way of ascertaining the true diversity of the Onychiuridae. Our study also highlights that discovering new morphological characters remains central to achieving a full understanding of collembolan taxonomy.

Drinking Water Microbiome as a Screening Tool for ...

EPA Pesticide Factsheets

Many water utilities in the US using chloramine as disinfectant treatment in their distribution systems have experienced nitrification episodes, which detrimentally impact the water quality. A chloraminated drinking water distribution system (DWDS) simulator was operated through four successive operational schemes, including two stable events (SS) and an episode of nitrification (SF), followed by a ‘chlorine burn’ (SR) by switching disinfectant from chloramine to free chlorine. The current research investigated the viability of biological signatures as potential indicators of operational failure and predictors of nitrification in DWDS. For this purpose, we examined the bulk water (BW) bacterial microbiome of a chloraminated DWDS simulator operated through successive operational schemes, including an episode of nitrification. BW data was chosen because sampling of BW in a DWDS by water utility operators is relatively simpler and easier than collecting biofilm samples from underground pipes. The methodology applied a supervised classification machine learning approach (naïve Bayes algorithm) for developing predictive models for nitrification. Classification models were trained with biological datasets (Operational Taxonomic Unit [OTU] and genus-level taxonomic groups) generated using next generation high-throughput technology, and divided into two groups (i.e. binary) of positives and negatives (Failure and Stable, respectively). We also invest

Combining morphometrics with molecular taxonomy: how different are similar foliose keratose sponges from the Australian tropics?

PubMed

Abdul Wahab, M A; Fromont, J; Whalan, S; Webster, N; Andreakis, N

2014-04-01

Sponge taxonomy can be challenging as many groups exhibit extreme morphological plasticity induced by local environmental conditions. Foliose keratose sponges of the sub-family Phyllospongiinae (Dictyoceratida, Thorectidae: Strepsichordaia, Phyllospongia and Carteriospongia) are commonly found in intertidal and subtidal habitats of the Indo-Pacific. Lacking spicules, these sponges can be difficult to differentiate due to the lack of reliable morphological characters for species delineation. We use molecular phylogenies inferred from the nuclear Internal Transcribed Spacer 2 region (ITS2) and morphometrics (19 characters; 52 character states) to identify evolutionarily significant units (ESUs; sensu Moritz) within foliose Phyllosponginiids collected from seven geographic locations across tropical eastern and Western Australia. The ITS2 topology was congruent with the tree derived from Bayesian inference of discrete morphological characters supporting expected taxonomic relationships at the genus level and the identification of five ESUs. However, phylogenies inferred from the ITS2 marker revealed multiple sequence clusters, some of which were characterised by distinct morphological features and specific geographic ranges. Our results are discussed in light of taxonomic incongruences within this study, hidden sponge diversity and the role of vicariant events in influencing present day distribution patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

PubMed Central

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

2015-01-01

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

PubMed Central

Nilsson, R. Henrik; Kristiansson, Erik; Ryberg, Martin; Hallenberg, Nils; Larsson, Karl-Henrik

2008-01-01

The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra- and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3% threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names. PMID:19204817

The nature of plant species

PubMed Central

Rieseberg, Loren H.; Wood, Troy E.; Baack, Eric J.

2008-01-01

Many botanists doubt the existence of plant species1–5, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or ‘units of evolution’. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few ‘botanical horror stories’, such as dandelions, blackberries and oaks6,7. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (>80%), the correspondence of taxonomic species to these clusters is poor (<60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom8, plant species are more likely than animal species to represent reproductively independent lineages. PMID:16554818

Synthesis of phylogeny and taxonomy into a comprehensive tree of life.

PubMed

Hinchliff, Cody E; Smith, Stephen A; Allman, James F; Burleigh, J Gordon; Chaudhary, Ruchi; Coghill, Lyndon M; Crandall, Keith A; Deng, Jiabin; Drew, Bryan T; Gazis, Romina; Gude, Karl; Hibbett, David S; Katz, Laura A; Laughinghouse, H Dail; McTavish, Emily Jane; Midford, Peter E; Owen, Christopher L; Ree, Richard H; Rees, Jonathan A; Soltis, Douglas E; Williams, Tiffani; Cranston, Karen A

2015-10-13

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

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 fecal microbiome of ALS patients.

PubMed

Brenner, David; Hiergeist, Andreas; Adis, Carolin; Mayer, Benjamin; Gessner, André; Ludolph, Albert C; Weishaupt, Jochen H

2018-01-01

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative motor neuron disease accompanied by both systemic and central nervous system-specific inflammation as well as deregulated energy metabolism. These potential pathogenetic factors have recently been found to mutually interact with the gut microbiota, raising the hypothesis of a link between microbiome alterations and ALS pathogenesis. The aim of our study was to assess whether ALS is associated with an altered composition of the fecal microbiota. We compared the fecal microbiota of 25 ALS patients with 32 age- and gender-matched healthy persons using 16S rRNA gene sequencing analysis. Confounding factors and secondary disease effects on the microbiome were minimized by selection of patients without dysphagia, gastrostomy, noninvasive ventilation, or reduced body mass index. Comparing the 2 carefully matched groups, the diversity and the abundance of the bacterial taxa on the different taxonomic levels as well as PICRUSt-predicted metagenomes were almost indistinguishable. Significant differences between ALS patients and healthy controls were only observed with regard to the overall number of microbial species (operational taxonomic units) and in the abundance of uncultured Ruminococcaceae. Conclusively, ALS patients do not exhibit a substantial alteration of the gut microbiota composition. Copyright © 2017 Elsevier Inc. All rights reserved.

DNA barcoding commercially important aquatic invertebrates of Turkey.

PubMed

Keskin, Emre; Atar, Hasan Hüseyin

2013-08-01

DNA barcoding was used in order to identify aquatic invertebrates sampled from fisheries bycatch and discards. A total of 440 unique cytochrome c oxidase sub unit I (COI) barcodes were generated for 22 species from three important phyla (Arthropoda, Cnidaria, and Mollusca). All the species were sequenced and submitted to GenBank and Barcode of Life Database (BOLD) databases using 654 bp-long fragment of mitochondrial COI gene. Two of them (Pontastacus leptodactylus and Rapana bezoar) were first records of the species for the BOLD database and six of them (Carcinus aestuarii, Loligo vulgaris, Melicertus kerathurus, Nephrops norvegicus, Scyllarides latus, and Scyllarus arctus) were first standard (>648 bp) COI barcode records for the GenBank database. COI barcodes were analyzed for nucleotide composition, nucleotide pair frequencies, and Kimura's two-parameter genetic distance. Mean genetic distance among species was found increasing at higher taxonomic levels. Neighbor-joining trees generated were congruent with morphometric-based taxonomic classification. Findings of this study clearly demonstrate that DNA barcodes could be used as an efficient molecular tool in identification of not only target species from fisheries but also bycatch and discard species, and so it could provide us leverage for a better understanding in monitoring and management of fisheries and biodiversity.

Seasonal and geographical distribution of near-surface small photosynthetic eukaryotes in the western North Pacific determined by pyrosequencing of 18S rDNA.

PubMed

Kataoka, Takafumi; Yamaguchi, Haruyo; Sato, Mayumi; Watanabe, Tsuyoshi; Taniuchi, Yukiko; Kuwata, Akira; Kawachi, Masanobu

2017-02-01

In this study, we investigated the distribution of small photosynthetic eukaryotes in the near-surface layer of the western North Pacific at four stations, including two oceanic stations where the subarctic Oyashio and subtropical Kuroshio currents influence a transition region and the bay mouth and head of the Sendai Bay, from April 2012 to May 2013. Flow cytometry was applied to sort small photosynthetic eukaryotes (<5 μm), and high-throughput sequencing of 18S rDNA was performed. Our taxonomic analysis showed that 19/195 operational taxonomic units (OTUs) were frequently distributed among all sites. Composition analysis showed that the OTUs had characteristic patterns and were divided into four main groups. Two groups reflected the low-saline water and winter season, with the characteristic OTUs belonging to diatoms; Chaetoceros and Leptocylindrus were characteristic of low saline water, and two diatom genera (Minidiscus and Minutocellus) and Cryptomonadales-related OTUs were prevalent in the winter. Our results indicate that the community composition of small photosynthetic eukaryotes seasonally changes in a dynamic manner according to variations in water properties. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

PubMed

Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

2014-04-01

Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

Deaf and hard of hearing adolescents' processing of pictures and written words for taxonomic categories in a priming task of semantic categorization.

PubMed

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written words for those of superordinate level (category names), in a priming task of semantic categorization. Stimulus onset asynchrony (SOA) was manipulated. The adolescents were less aware of taxonomic relations and were more likely to show the advantage of pictures over written words than their hearing counterparts. Their processing of exemplar primes steadily deepened as SOA increased, reaching its deepest level when SOA was 237 ms. Their processing of category names seemed immune to changes in SOA, probably because of their fuzzy representations of taxonomic categories of superordinate level.

Using an integral-field unit spectrograph to study radical species in cometary coma

NASA Astrophysics Data System (ADS)

Lewis, Benjamin; Pierce, Donna M.; Vaughan, Charles M.; Cochran, Anita

2015-01-01

We have observed several comets using an integral-field unit spectrograph (the George and Cynthia Mitchell Spectrograph) on the 2.7m Harlan J. Smith telescope at McDonald Observatory. Full-coma spectroscopic images were obtained for various radical species (C2, C3, CN, NH2). Various coma enhancements were used to identify and characterize coma morphological features. The azimuthal average profiles and the Haser model were used to determine production rates and possible parent molecules. Here, we present the work completed to date, and we compare our results to other comet taxonomic surveys. This work was funded by the National Science Foundation Graduate K-12 (GK-12) STEM Fellows program (Award No. DGE-0947419), NASA's Planetary Atmospheres program (Award No. NNX14AH18G), and the Fund for Astrophysical Research, Inc.

Using an integral-field unit spectrograph to study radical species in cometary coma

NASA Astrophysics Data System (ADS)

Lewis, Benjamin; Pierce, Donna; Cochran, Anita; Vaughan, Charles

2014-11-01

We have observed several comets using an integral-field unit spectrograph (the George and Cynthia Mitchell Spectrograph) on the 2.7m Harlan J. Smith telescope at McDonald Observatory. Full-coma spectroscopic images were obtained for various radical species (C2, C3, CN, NH2). Various coma enhancements were used to identify and characterize coma morphological features. The azimuthal average profiles and the Haser model were used to determine production rates and possible parent molecules. Here, we present the work completed to date, and we compare our results to other comet taxonomic surveys. This work was funded by the National Science Foundation Graduate K-12 (GK-12) STEM Fellows program (Award No. DGE-0947419), NASA’s Planetary Atmospheres program (Award No. NNX14AH18G), and the Fund for Astrophysical Research, Inc.

Molluscan extinction patterns across the Cenomanian-Turonian stage boundary in the western interior of the United States

USGS Publications Warehouse

Elder, W.P.

1989-01-01

High-resolution stratigraphic analysis of 18 sections spanning the Cenomanian-Turonian Stage boundary in the western interior of the United States has allowed determination of the magnitude and pattern of molluscan extinction and disruption. Composite range data from all sections show that the faunal turnover across the stage boundary occurs in a series of narrow stratigraphic zones, defined by multiple first and last occurrences, separated by intervals displaying little or no taxonomic turnover. Two of the apparent extinction steps (bottom and top of the Neocardioceras juddii Zone) may be intercontinentally developed. The additional steps apparently reflect cyclic changes in water mass and substrate characteristics in the western interior basin produced in response to orbital forcing of climate. The most affected mollusks were those having intercontinental distributions. -Author

The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics

PubMed Central

Beng, Kingsly Chuo; Tomlinson, Kyle W.; Shen, Xian Hui; Surget-Groba, Yann; Hughes, Alice C.; Corlett, Richard T.; Slik, J. W. Ferry

2016-01-01

Metabarcoding potentially offers a rapid and cheap method of monitoring biodiversity, but real-world applications are few. We investigated its utility in studying patterns of litter arthropod diversity and composition in the tropics. We collected litter arthropods from 35 matched forest-plantation sites across Xishuangbanna, southwestern China. A new primer combination and the MiSeq platform were used to amplify and sequence a wide variety of litter arthropods using simulated and real-world communities. Quality filtered reads were clustered into 3,624 MOTUs at ≥97% similarity and the taxonomy of each MOTU was predicted. We compared diversity and compositional differences between forests and plantations (rubber and tea) for all MOTUs and for eight arthropod groups. We obtained ~100% detection rate after in silico sequencing six mock communities with known arthropod composition. Ordination showed that rubber, tea and forest communities formed distinct clusters. α-diversity declined significantly between forests and adjacent plantations for more arthropod groups in rubber than tea, and diversity of order Orthoptera increased significantly in tea. Turnover was higher in forests than plantations, but patterns differed among groups. Metabarcoding is useful for quantifying diversity patterns of arthropods under different land-uses and the MiSeq platform is effective for arthropod metabarcoding in the tropics. PMID:27112993

MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

PubMed

Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

2010-02-15

We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

PubMed Central

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

2012-01-01

The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

Taxonomic bias in biodiversity data and societal preferences.

PubMed

Troudet, Julien; Grandcolas, Philippe; Blin, Amandine; Vignes-Lebbe, Régine; Legendre, Frédéric

2017-08-22

Studying and protecting each and every living species on Earth is a major challenge of the 21 st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

Zooplankton taxonomic and size diversity in Mediterranean coastal lagoons (NE Iberian Peninsula): Influence of hydrology, nutrient composition, food resource availability and predation

NASA Astrophysics Data System (ADS)

Badosa, Anna; Boix, Dani; Brucet, Sandra; López-Flores, Rocío; Gascón, Stéphanie; Quintana, Xavier D.

2007-01-01

The influence of hydrology, nutrient composition, food resource availability and predation on zooplankton taxonomic and size diversity was analyzed in several shallow lagoons of a Mediterranean salt marsh (Baix Ter Wetlands, NE Iberian Peninsula). Taxonomic diversity correlated better with variables related to the trophic state, such as nutrient concentrations, whereas size diversity was more sensitive to fish predation. However, the fish predation influence on the size diversity was only significant when fishes reached high densities. Under low fish densities no predation effects were observed and the food resource availability (FR a) appeared to be more important in structuring the zooplankton community. Nevertheless, the two diversity indexes showed opposite responses to this factor. With increasing FR a the taxonomic diversity increased and the size diversity decreased. Neither taxonomic nor size diversity of the zooplankton community correlated with other physical or biotic factors such as hydrological variability or macroinvertebrate predation. The relationships found suggest that the size diversity is mainly related to biotic interactions, such as fish predation or inter/intraspecific competition, while the taxonomic diversity appears to be more sensitive to abiotic factors such as the nutrient composition.

Insights into discriminating environmental quality status using taxonomic distinctness based on a small species pool of ciliated protozoa in marine ecosystems.

PubMed

Jiang, Yong; Xu, Henglong; Warren, Alan

2014-01-15

The objective of this study was to determine the feasibility of developing a protocol for assessing marine water quality based on taxonomic relatedness within a small pool of planktonic ciliates. An annual dataset was compiled based on samples collected biweekly at five sites, with a gradient of environmental stress, during a 1-year cycle in Jiaozhou Bay, northern China. A total of 60 species, belonging to 17 genera 10 families, 5 orders and 2 classes of the phylum Ciliophora, were identified. Among five orders, Tintinnida showed a low variability mainly at species level whereas the other orders (especially Strombidiida and Choreotrichida, although with the exception of the genus Strombidium) represented a high variability at higher taxonomic ranks (e.g. family or order). Mantel analyses showed that spatial patterns of the ciliate assemblages, with tinitinnids and Strombidium spp. excluded, were significantly correlated with those of the total planktonic ciliate communities in terms of their response to environmental status. The average taxonomic distinctness (Δ(+)) based on the small species pool was significantly negatively correlated with the changes in concentrations of nutrients (P<0.05). Furthermore, the paired indices of Δ(+) and the variation in taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that it is possible to assess the status of marine water quality using the taxonomic relatedness within a small pool of planktonic ciliates. © 2013.

Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities

DTIC Science & Technology

2001-09-30

1 Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities Dr. Gary Hitchcock Marine Biology and... Fisheries Rosenstiel School of Marine and Atmospheric Science 4600 Rickenbacker Cswy. Miami, FL 3149 phone: (305) 361-4926 fax: (305) 361-4765...ghitchcock.html LONG-TERM GOALS The spatial distribution and taxonomic composition of phytoplankton communities are important determinants of the

Deaf and Hard of Hearing Adolescents' Processing of Pictures and Written Words for Taxonomic Categories in a Priming Task of Semantic Categorization

ERIC Educational Resources Information Center

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written…

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

PubMed Central

Diaz, Naryttza N; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W

2009-01-01

Background Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Results Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. Conclusion An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference set can be easily updated as newly sequenced genomes become available. Moreover, the method demonstrated to be competitive when compared to the most current classifier PhyloPythia and has the advantage that it can be locally installed and the reference set can be kept up-to-date. PMID:19210774

Two Influential Primate Classifications Logically Aligned.

PubMed

Franz, Nico M; Pier, Naomi M; Reeder, Deeann M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2016-07-01

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2-317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3-483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments-in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Digitising legacy zoological taxonomic literature: Processes, products and using the output

PubMed Central

Lyal, Christopher H. C.

2016-01-01

Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. A means to do this is through marking up content into XML, and the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. We now need to automate this process as far as possible. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying in its production the requirements of the Code, is fit for purpose in the future. PMID:26877659

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.

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean

USGS Publications Warehouse

Yasuhara, Moriaki; Stepanova, Anna; Okahashi, Hisayo; Cronin, Thomas M.; Brouwers, Elisabeth M.

2015-01-01

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean was conducted to reduce taxonomic uncertainty that will improve our understanding of species ecology, biogeography and relationship to faunas from other deep-sea regions. Fifteen genera and 40 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images, covering most of known deep-sea species in the central Arctic Ocean. Seven new species are described: Bythoceratina lomonosovensis n. sp., Cytheropteron parahamatum n. sp., Cytheropteron lanceae n. sp.,Cytheropteron irizukii n. sp., Pedicythere arctica n. sp., Cluthiawhatleyi n. sp., Krithe hunti n. sp. This study provides a robust taxonomic baseline for application to paleoceanographical reconstruction and biodiversity analyses in this climatically sensitive region.

Global hotspots and correlates of alien species richness across taxonomic groups

USGS Publications Warehouse

Dawson, Wayne; Moser, Dietmar; van Kleunen, Mark; Kreft, Holger; Pergl, Jan; Pysek, Petr; Weigelt, Patrick; Winter, Marten; Lenzner, Bernd; Blackburn, Tim M.; Dyer, Ellie; Cassey, Phillip; Scrivens, Sally-Louise; Economo, Evan P.; Guenard, Benoit; Capinha, Cesar; Seebens, Hanno; Garcia-Diaz, Pablo; Nentwig, Wolfgang; Garcia-Berthou, Emili; Casal, Christine; Mandrak, Nicholas E.; Fuller, Pam; Meyer, Carsten; Essl, Franz

2017-01-01

Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally.

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

PubMed Central

Lu, Hsiao-Pei; Yeh, Yi-Chun; Sastri, Akash R; Shiah, Fuh-Kwo; Gong, Gwo-Ching; Hsieh, Chih-hao

2016-01-01

We propose a method for detecting evolutionary forces underlying community assembly by quantifying the strength of community–environment relationships hierarchically along taxonomic ranks. This approach explores the potential role of phylogenetic conservatism on habitat preferences: wherein, phylogenetically related taxa are expected to exhibit similar environmental responses. Thus, when niches are conserved, broader taxonomic classification should not diminish the strength of community–environment relationships and may even yield stronger associations by summarizing occurrences and abundances of ecologically equivalent finely resolved taxa. In contrast, broader taxonomic classification should weaken community–environment relationships when niches are under great divergence (that is, by combining finer taxa with distinct environmental responses). Here, we quantified the strength of community–environment relationships using distance-based redundancy analysis, focusing on soil and seawater prokaryotic communities. We considered eight case studies (covering a variety of sampling scales and sequencing strategies) and found that the variation in community composition explained by environmental factors either increased or remained constant with broadening taxonomic resolution from species to order or even phylum level. These results support the niche conservatism hypothesis and indicate that broadening taxonomic resolution may strengthen niche-related signals by removing uncertainty in quantifying spatiotemporal distributions of finely resolved taxa, reinforcing the current notion of ecological coherence in deep prokaryotic branches. PMID:27177191

Damage to temporo-parietal cortex decreases incidental activation of thematic relations during spoken word comprehension

PubMed Central

Mirman, Daniel; Graziano, Kristen M.

2012-01-01

Both taxonomic and thematic semantic relations have been studied extensively in behavioral studies and there is an emerging consensus that the anterior temporal lobe plays a particularly important role in the representation and processing of taxonomic relations, but the neural basis of thematic semantics is less clear. We used eye tracking to examine incidental activation of taxonomic and thematic relations during spoken word comprehension in participants with aphasia. Three groups of participants were tested: neurologically intact control participants (N=14), individuals with aphasia resulting from lesions in left hemisphere BA 39 and surrounding temporo-parietal cortex regions (N=7), and individuals with the same degree of aphasia severity and semantic impairment and anterior left hemisphere lesions (primarily inferior frontal gyrus and anterior temporal lobe) that spared BA 39 (N=6). The posterior lesion group showed reduced and delayed activation of thematic relations, but not taxonomic relations. In contrast, the anterior lesion group exhibited longer-lasting activation of taxonomic relations and did not differ from control participants in terms of activation of thematic relations. These results suggest that taxonomic and thematic semantic knowledge are functionally and neuroanatomically distinct, with the temporo-parietal cortex playing a particularly important role in thematic semantics. PMID:22571932

Few Highly Abundant Operational Taxonomic Units Dominate within Rumen Methanogenic Archaeal Species in New Zealand Sheep and Cattle

PubMed Central

Seedorf, Henning; Kittelmann, Sandra

2014-01-01

Sequencing and analyses of 16S rRNA gene amplicons were performed to estimate the composition of the rumen methanogen community in 252 samples from eight cohorts of sheep and cattle, separated into 16 different sample groups by diet, and to determine which methanogens are most prominent in the rumens of farmed New Zealand ruminants. Methanobacteriales (relative abundance ± standard deviation, 89.6% ± 9.8%) and Methanomassiliicoccales (10.4% ± 9.8%) were the two major orders and contributed 99.98% (±0.1%) to the rumen methanogen communities in the samples. Sequences from Methanobacteriales were almost entirely from only four different species (or clades of very closely related species). Each was detectable in at least 89% of the samples. These four species or clades were the Methanobrevibacter gottschalkii clade and Methanobrevibacter ruminantium clade with a mean abundance of 42.4% (±19.5% standard deviation) and 32.9% (±18.8%), respectively, and Methanosphaera sp. ISO3-F5 (8.2% ± 6.7%) and Methanosphaera sp. group5 (5.6% ± 5.7%). These four species or clades appeared to be primarily represented by only one or, in one case, two dominant sequence types per species or clade when the sequences were grouped into operational taxonomic units (OTUs) at 99% sequence identity. The mean relative abundance of Methanomassiliicoccales in the samples was relatively low but exceeded 40% in some of the treatment groups. Animal feed affected the apparent methanogen community structure of both orders, as evident from differences in relative abundances of the major OTUs in animals under different feeding regimens. PMID:25416771

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase

PubMed Central

Abdelfattah, Ahmed; Wisniewski, Michael; Droby, Samir; Schena, Leonardo

2016-01-01

The fungal diversity in harvested apples from organic or conventional management practices was analyzed in different fruit locations (stem end, calyx end, peel, and wounded flesh) shortly after fruit purchase (T1) and after 2 weeks of storage (T5). A total of 5,760,162 high-quality fungal sequences were recovered and assigned to 8,504 Operational Taxonomic Units. Members of the phylum Ascomycota were dominant in all samples and accounted for 91.6% of the total number of detected sequences. This was followed by Basidiomycota (8%), Chytridiomycota (0.1%), and unidentified fungi (0.3%). Alpha and beta diversity analyses revealed the presence of significantly different fungal populations in the investigated fruit parts. Among detected fungi, the genus Penicillium prevailed in the peel and in the wounded flesh while Alternaria spp. prevailed in the calyx and stem end samples that included apple core tissues. Several taxonomic units that appear to be closely related to pathogenic fungi associated with secondary human infections were present in peel and wounds. Moreover, significantly different populations were revealed in organic and conventional apples and this result was consistent in all investigated fruit parts (calyx end, peel, stem end, and wounded flesh). Several unique taxa were exclusively detected in organic apples suggesting that management practices may have been a contributing factor in determining the taxa present. In contrast, little differences were revealed in the two assessment times (T1 and T5). Results of the present study represent an advancement of the current knowledge on the fungal microbiota in collected fruit tissues of apple. PMID:27766161

What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae).

PubMed

Korotkova, Nadja; Borsch, Thomas; Quandt, Dietmar; Taylor, Nigel P; Müller, Kai F; Barthlott, Wilhelm

2011-09-01

The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions. • We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions (trnK intron, matK, rbcL, rps3-rpl16, rpl16 intron, psbA-trnH, trnQ-rps16), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA-based species recognition based on operational taxonomic units (OTUs) defined beforehand. • The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis, Lepismium, Schlumbergera, Hatiora, and Rhipsalidopsis. The species-level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA-trnH and trnQ-rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA-trnH, rps3-rpl16, trnK intron, and trnQ-rps16 as a minimum possible marker length (ca. 1660 nt). • The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility.

Chironomus group classification according to the mapping of polytene chromosomes

NASA Astrophysics Data System (ADS)

Salleh, Syafinaz; Kutty, Ahmad Abas

2013-11-01

Chironomus is one of the important genera in Chironomidae family since they are widely diverse and abundance in aquatic ecosystem. Since Chironomus is very diverse, taxonomic work on this genus is very difficult and incomplete. Objective of this study is to form group classification of Chironomus according to the polytene chromosome mapping. The specific characteristics of polytene chromosomes in the salivary gland appeared to be particularly promising for taxonomic diagnosis of chironomid species. Chironomid larvae were collected from pristine sites at Sg. Langat and cultured in laboratory to reach fourth instar stage. The salivary glands were removed from larvae and chromosomes were stained with aceto orcein. Results showed that polytene chromosomes of Chironomus comprise of three long metacentric or submetacentric arms (BF, CD and AE arms) and one short acrocentric (G arm). In regards to nucleolar organizing region (NOR), Balbiani ring (BR), puffings and chromosome rearrangement, a number of four groups of different banding patterns were found. Two groups called as G group A and B have common NOR on arm BF and BR on arm G. However, group A has rearrangement pattern on arm CD and not in group B. This makes group B separated from group A. Another two groups called as groups C and D do not have common NOR on arm BF and also BR on arm G. Groups C and D were separated using arms G and arm AE. At arm G, only group C rearrangement pattern at unit 23c whereas group D was found to have large NOR at arm G and as well as arm AE, only group D has rearrangement pattern at unit 12c. This study indicates that chromosome arrangement could aid in revealing Chironomus diversity.

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase.

PubMed

Abdelfattah, Ahmed; Wisniewski, Michael; Droby, Samir; Schena, Leonardo

2016-01-01

The fungal diversity in harvested apples from organic or conventional management practices was analyzed in different fruit locations (stem end, calyx end, peel, and wounded flesh) shortly after fruit purchase (T1) and after 2 weeks of storage (T5). A total of 5,760,162 high-quality fungal sequences were recovered and assigned to 8,504 Operational Taxonomic Units. Members of the phylum Ascomycota were dominant in all samples and accounted for 91.6% of the total number of detected sequences. This was followed by Basidiomycota (8%), Chytridiomycota (0.1%), and unidentified fungi (0.3%). Alpha and beta diversity analyses revealed the presence of significantly different fungal populations in the investigated fruit parts. Among detected fungi, the genus Penicillium prevailed in the peel and in the wounded flesh while Alternaria spp. prevailed in the calyx and stem end samples that included apple core tissues. Several taxonomic units that appear to be closely related to pathogenic fungi associated with secondary human infections were present in peel and wounds. Moreover, significantly different populations were revealed in organic and conventional apples and this result was consistent in all investigated fruit parts (calyx end, peel, stem end, and wounded flesh). Several unique taxa were exclusively detected in organic apples suggesting that management practices may have been a contributing factor in determining the taxa present. In contrast, little differences were revealed in the two assessment times (T1 and T5). Results of the present study represent an advancement of the current knowledge on the fungal microbiota in collected fruit tissues of apple.

Interactions Between Stress and Sex in Microbial Responses Within the Microbiota-Gut-Brain Axis in a Mouse Model.

PubMed

Tsilimigras, Matthew C B; Gharaibeh, Raad Z; Sioda, Michael; Gray, Laura; Fodor, Anthony A; Lyte, Mark

2018-05-01

Animal models are frequently used to examine stress response, but experiments seldom include females. The connection between the microbiota-gut-brain axis and behavioral stress response is investigated here using a mixed-sex mouse cohort. CF-1 mice underwent alternating days of restraint and forced swim for 19 days (male n = 8, female n = 8) with matching numbers of control animals at which point the 16S rRNA genes of gut microbiota were sequenced. Mixed linear models accounting for stress status and sex with individuals nested in cage to control for cage effects evaluated these data. Murine behaviors in elevated plus-maze, open-field, and light/dark box were investigated. Community-level associations with sex, stress, and their interaction were significant. Males had higher microbial diversity than females (p = .025). Of the 638 operational taxonomic units detected in at least 25% of samples, 94 operational taxonomic units were significant: 31 (stress), 61 (sex), and 34 (sex-stress interaction). Twenty of the 39 behavioral measures were significant for stress, 3 for sex, and 6 for sex-stress. However, no significant associations between behavioral measures and specific microbes were detected. These data suggest sex influences stress response and the microbiota-gut-brain axis and that studies of behavior and the microbiome therefore benefit from consideration of how sex differences drive behavior and microbial community structure. Host stress resilience and absence of associations between stress-induced behaviors with specific microbes suggests that hypothalamic-pituitary-adrenal axis activation represents a threshold for microbial influence on host behavior. Future studies are needed in examining the intersection of sex, stress response, and the microbiota-gut-brain axis.

Cryptic Eimeria genotypes are common across the southern but not northern hemisphere.

PubMed

Clark, Emily L; Macdonald, Sarah E; Thenmozhi, V; Kundu, Krishnendu; Garg, Rajat; Kumar, Saroj; Ayoade, Simeon; Fornace, Kimberly M; Jatau, Isa Danladi; Moftah, Abdalgader; Nolan, Matthew J; Sudhakar, N R; Adebambo, A O; Lawal, I A; Álvarez Zapata, Ramón; Awuni, Joseph A; Chapman, H David; Karimuribo, Esron; Mugasa, Claire M; Namangala, Boniface; Rushton, Jonathan; Suo, Xun; Thangaraj, Kumarasamy; Srinivasa Rao, Arni S R; Tewari, Anup K; Banerjee, Partha S; Dhinakar Raj, G; Raman, M; Tomley, Fiona M; Blake, Damer P

2016-08-01

The phylum Apicomplexa includes parasites of medical, zoonotic and veterinary significance. Understanding the global distribution and genetic diversity of these protozoa is of fundamental importance for efficient, robust and long-lasting methods of control. Eimeria spp. cause intestinal coccidiosis in all major livestock animals and are the most important parasites of domestic chickens in terms of both economic impact and animal welfare. Despite having significant negative impacts on the efficiency of food production, many fundamental questions relating to the global distribution and genetic variation of Eimeria spp. remain largely unanswered. Here, we provide the broadest map yet of Eimeria occurrence for domestic chickens, confirming that all the known species (Eimeria acervulina, Eimeria brunetti, Eimeria maxima, Eimeria mitis, Eimeria necatrix, Eimeria praecox, Eimeria tenella) are present in all six continents where chickens are found (including 21 countries). Analysis of 248 internal transcribed spacer sequences derived from 17 countries provided evidence of possible allopatric diversity for species such as E. tenella (FST values ⩽0.34) but not E. acervulina and E. mitis, and highlighted a trend towards widespread genetic variance. We found that three genetic variants described previously only in Australia and southern Africa (operational taxonomic units x, y and z) have a wide distribution across the southern, but not the northern hemisphere. While the drivers for such a polarised distribution of these operational taxonomic unit genotypes remains unclear, the occurrence of genetically variant Eimeria may pose a risk to food security and animal welfare in Europe and North America should these parasites spread to the northern hemisphere. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

A case study for effects of operational taxonomic units from intracellular endoparasites and ciliates on the eukaryotic phylogeny: phylogenetic position of the haptophyta in analyses of multiple slowly evolving genes.

PubMed

Nozaki, Hisayoshi; Yang, Yi; Maruyama, Shinichiro; Suzaki, Toshinobu

2012-01-01

Recent multigene phylogenetic analyses have contributed much to our understanding of eukaryotic phylogeny. However, the phylogenetic positions of various lineages within the eukaryotes have remained unresolved or in conflict between different phylogenetic studies. These phylogenetic ambiguities might have resulted from mixtures or integration from various factors including limited taxon sampling, missing data in the alignment, saturations of rapidly evolving genes, mixed analyses of short- and long-branched operational taxonomic units (OTUs), intracellular endoparasite and ciliate OTUs with unusual substitution etc. In order to evaluate the effects from intracellular endoparasite and ciliate OTUs co-analyzed on the eukaryotic phylogeny and simplify the results, we here used two different sets of data matrices of multiple slowly evolving genes with small amounts of missing data and examined the phylogenetic position of the secondary photosynthetic chromalveolates Haptophyta, one of the most abundant groups of oceanic phytoplankton and significant primary producers. In both sets, a robust sister relationship between Haptophyta and SAR (stramenopiles, alveolates, rhizarians, or SA [stramenopiles and alveolates]) was resolved when intracellular endoparasite/ciliate OTUs were excluded, but not in their presence. Based on comparisons of character optimizations on a fixed tree (with a clade composed of haptophytes and SAR or SA), disruption of the monophyly between haptophytes and SAR (or SA) in the presence of intracellular endoparasite/ciliate OTUs can be considered to be a result of multiple evolutionary reversals of character positions that supported the synapomorphy of the haptophyte and SAR (or SA) clade in the absence of intracellular endoparasite/ciliate OTUs.

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

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.

A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda)

PubMed Central

Mateus, Octávio; Benson, Roger B.J.

2015-01-01

Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s from the Morrison Formation of North America. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, and Argentina, as well as possibly Spain, England, Georgia, Zimbabwe, and Asia. To date, the clade includes about 12 to 15 nominal species, some of them with questionable taxonomic status (e.g., ‘Diplodocus’ hayi or Dyslocosaurus polyonychius), and ranging in age from Late Jurassic to Early Cretaceous. However, intrageneric relationships of the iconic, multi-species genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which has been previously implemented for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. The analysis includes 81 operational taxonomic units, 49 of which belong to Diplodocidae. The set of OTUs includes all name-bearing type specimens previously proposed to belong to Diplodocidae, alongside a set of relatively complete referred specimens, which increase the amount of anatomically overlapping material. Non-diplodocid outgroups were selected to test the affinities of potential diplodocid specimens that have subsequently been suggested to belong outside the clade. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses of sauropod dinosaurs. Character states were figured and tables given in the case of numerical characters. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Two numerical approaches were used to increase reproducibility in our taxonomic delimitation of species and genera. This resulted in the proposal that some species previously included in well-known genera like Apatosaurus and Diplodocus are generically distinct. Of particular note is that the famous genus Brontosaurus is considered valid by our quantitative approach. Furthermore, “Diplodocus” hayi represents a unique genus, which will herein be called Galeamopus gen. nov. On the other hand, these numerical approaches imply synonymization of “Dinheirosaurus” from the Late Jurassic of Portugal with the Morrison Formation genus Supersaurus. Our use of a specimen-, rather than species-based approach increases knowledge of intraspecific and intrageneric variation in diplodocids, and the study demonstrates how specimen-based phylogenetic analysis is a valuable tool in sauropod taxonomy, and potentially in paleontology and taxonomy as a whole. PMID:25870766

An annotated key to the identification of commonly occurring and dominant genera of algae observed in the phytoplankton of the United States

USGS Publications Warehouse

Greeson, Phillip E.

1982-01-01

In early 1979, a retrieval was made for all phytoplankton data contained in the computerized data file of the U. S. Geological Survey. The retrieval revealed the analytical results of 17,959 samples collected and processed between October 1973 and October 1978. Of the approximately 500 genera of freshwater algae reported in the United States, the U.S. Geological Survey observed 321 genera in the phytoplankton. Fifty-two genera were considered to be commonly occurring and 42 genera were considered to be community dominants. The report lists, describes, and provides a detailed taxonomic key to the identification of 58 genera of algae considered either commonly occurring or dominant. Also included is a summary of environmental conditions under which each algal genus was observed, as well as a glossary and an extensive list of selected references.

Prevalence of Ingested Fish Hooks in Freshwater Turtles from Five Rivers in the Southeastern United States

PubMed Central

Steen, David A.; Hopkins, Brittney C.; Van Dyke, James U.; Hopkins, William A.

2014-01-01

Freshwater turtles may ingest baited fish hooks because many are opportunistic scavengers. Although the ingestion of fish hooks is known to be a source of mortality in multiple vertebrate groups, the prevalence of hook ingestion by freshwater turtles has not been well studied. We trapped turtles from five rivers in the southeastern United States and used radiographs to examine over 600 individuals of four species. Depending on the species, sex, and age class, 0–33% of turtles contained ingested fish hooks. For some species, larger turtles were more likely to contain a fish hook than smaller individuals. Freshwater turtle demography suggests that even small increases in adult mortality may lead to population declines. If our study areas are representative of other aquatic systems that receive fishing pressure, this work likely identifies a potential conflict between a widespread, common recreational activity (i.e., fishing) and an imperiled taxonomic group. PMID:24621919

Preface: Proceedings of the seventh international symposium on the biology and management of corigonid fishes

USGS Publications Warehouse

Todd, Thomas; Fleischer, Guy

2002-01-01

This volume is the proceedings of the Seventh International Symposium on the Biology and Management of Coregonid Fishes (ISBMCF). As in all six preceding symposia, the seventh meeting of the ISBMCF provided an international forum for the scientific review and discussion of the various taxonomic, biological, ecological, and management issues that surround this important group of Holarctic fishes. The collection of presentations for this conference was addressed in the following convened sessions: Genetics, Stocking, Fisheries, and Biology, as well as special sessions on Lake Baikal, Russia and Lake Femund, Norway. The conference comprised 53 oral and 58 poster presentations by scientists from Canada, the United Kingdom, France, Switzerland, Germany, Finland, Norway, Poland, Russia, and the United States. In total, there were 162 participants, including an unprecedented 18 scientists from Russia as the result of additional, concerted support.

Chironomidae of the southeastern United States: a checklist of species and notes on biology, distribution, and habitat

USGS Publications Warehouse

Hudson, Patrick L.; Lenat, David R.; Caldwell, Broughton A.; Smith, David

1990-01-01

We provide a current listing of the species of midges (Diptera:Chironomidae) in the southeastern United States (Alabama, Florida, Georgia, North Carolina, South Carolina, and Tennessee). This checklist should aid research on this group of insects, which have often proved useful in the assessment of water quality. We document each species' distribution and general habitat and provide the best taxonomic reference to facilitate the identification or description of species in that genus. Changes in nomenclature, unique ecological traits, bibliographic sources, or other items of information are summarized in a paragraph on each genus. Of the 10 sub-families currently recognized in the Chironomidae, 7 occur in the Southeast. The chironomid fauna of the six southeastern States now consist of 164 described genera and 479 described species. In addition we have listed 14 genera and 245 species that are tenatively noted as undescribed.

One perspective on spatial variability in geologic mapping

USGS Publications Warehouse

Markewich, H.W.; Cooper, S.C.

1991-01-01

This paper discusses some of the differences between geologic mapping and soil mapping, and how the resultant maps are interpreted. The role of spatial variability in geologic mapping is addressed only indirectly because in geologic mapping there have been few attempts at quantification of spatial differences. This is largely because geologic maps deal with temporal as well as spatial variability and consider time, age, and origin, as well as composition and geometry. Both soil scientists and geologists use spatial variability to delineate mappable units; however, the classification systems from which these mappable units are defined differ greatly. Mappable soil units are derived from systematic, well-defined, highly structured sets of taxonomic criteria; whereas mappable geologic units are based on a more arbitrary heirarchy of categories that integrate many features without strict values or definitions. Soil taxonomy is a sorting tool used to reduce heterogeneity between soil units. Thus at the series level, soils in any one series are relatively homogeneous because their range of properties is small and well-defined. Soil maps show the distribution of soils on the land surface. Within a map area, soils, which are often less than 2 m thick, show a direct correlation to topography and to active surface processes as well as to parent material.

Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

PubMed Central

Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

2014-01-01

Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

PubMed

Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

2015-10-01

The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.

Functional and Taxonomic Differentiation of Macrophyte Assemblages Across the Yangtze River Floodplain Under Human Impacts

PubMed Central

Zhang, Min; García Molinos, Jorge; Zhang, Xiaolin; Xu, Jun

2018-01-01

Human activities and the consequent extirpations of species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. One of the main gaps in the assessment of biodiversity change in freshwater ecosystems is our limited understanding regarding how taxonomic and functional facets of macrophyte assemblages respond to human impacts on regional scales. Here, we assess the temporal (before 1970s against after 2000s) changes in taxonomic and functional richness and compositional dissimilarities, partitioned into its turnover and nestedness components, of freshwater macrophyte assemblages across the floodplain lakes of the Yangtze River in China. We found that functional and taxonomic assemblage differentiation occurred simultaneously under increasing human impact, concomitant to a general decrease in functional and taxonomic richness. However, this effect weakened when the historical level of taxonomic dissimilarity among assemblages was high. Macrophyte species with large dispersal range and submersed life form were significantly more susceptible to extirpation. The impact of human activities on differentiation was complex but habitat loss and fishery intensity were consistently the main drivers of assemblage change in these lakes, whereas water quality (i.e., light pollution and nutrient enrichment) had weaker effects. Further, macrophyte taxonomic and functional differentiation was mainly driven by the nestedness component of dissimilarity, accounting for changes in assemblage composition related to changes in species richness independent of species replacement. This result, markedly different from previous studies on freshwater fish assemblages conducted in these lakes, represents a novel contribution toward achieving a more holistic understanding of how human impacts contribute to shape community assemblages in natural ecosystems. PMID:29636763

TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies.

PubMed

Collin, Rachel; Fredericq, Suzanne; Freshwater, D Wilson; Gilbert, Edward; Madrid, Maycol; Maslakova, Svetlana; Miglietta, Maria Pia; Rocha, Rosana M; Rodríguez, Estefanía; Thacker, Robert W

2016-01-01

Correctly identifying organisms is key to most biological research, and is especially critical in areas of biodiversity and conservation. Yet it remains one of the greatest challenges when studying all but the few well-established model systems. The challenge is in part due to the fact that most species have yet to be described, vanishing taxonomic expertise and the relative inaccessibility of taxonomic information. Furthermore, identification keys and other taxonomic resources are based on complex, taxon-specific vocabularies used to describe important morphological characters. Using these resources is made difficult by the fact that taxonomic documentation of the world's biodiversity is an international endeavour, and keys and field guides are not always available in the practitioner's native language. To address this challenge, we have developed a publicly available on-line illustrated multilingual glossary and translation tool for technical taxonomic terms using the Symbiota Software Project biodiversity platform. Illustrations, photographs and translations have been sourced from the global community of taxonomists working with marine invertebrates and seaweeds. These can be used as single-language illustrated glossaries or to make customized translation tables. The glossary has been launched with terms and illustrations of seaweeds, tunicates, sponges, hydrozoans, sea anemones, and nemerteans, and already includes translations into seven languages for some groups. Additional translations and development of terms for more taxa are underway, but the ultimate utility of this tool depends on active participation of the international taxonomic community.

Qualitative analysis of the vaginal microbiota of healthy cattle and cattle with genital-tract disease.

PubMed

Rodrigues, N F; Kästle, J; Coutinho, T J D; Amorim, A T; Campos, G B; Santos, V M; Marques, L M; Timenetsky, J; de Farias, S T

2015-06-12

The microbial community of the reproductive appara-tus, when known, can provide information about the health of the host. Metagenomics has been used to characterize and obtain genetic infor-mation about microbial communities in various environments and can relate certain diseases with changes in this community composition. In this study, samples of vaginal surface mucosal secretions were col-lected from five healthy cows and five cows that showed symptoms of reproductive disorders. Following high-throughput sequencing of the isolated microbial DNA, data were processed using the Mothur soft-ware to remove low-quality sequences and chimeras, and released to the Ribosomal Database Project for classification of operational taxo-nomic units (OTUs). Local BLASTn was performed and results were loaded into the MEGAN program for viewing profiles and taxonomic microbial attributes. The control profile comprised a total of 15 taxa, with Bacteroides, Enterobacteriaceae, and Victivallis comprising the highest representation of OTUs; the reproductive disorder-positive profile comprised 68 taxa, with Bacteroides, Enterobacteriaceae, His-tophilus, Victivallis, Alistipes, and Coriobacteriaceae being the taxa with the most OTU representation. A change was observed in both the community composition as well as in the microbial attributes of the profiles, suggesting that a relationship might exist between the patho-gen and representative taxa, reflecting the production of metabolites to disease progression.

Effect of Dietary Oxalate on the Gut Microbiota of the Mammalian Herbivore Neotoma albigula

PubMed Central

Oakeson, Kelly F.; Dale, Colin; Dearing, M. Denise

2016-01-01

Diet is one of the primary drivers that sculpts the form and function of the mammalian gut microbiota. However, the enormous taxonomic and metabolic diversity held within the gut microbiota makes it difficult to isolate specific diet-microbe interactions. The objective of the current study was to elucidate interactions between the gut microbiota of the mammalian herbivore Neotoma albigula and dietary oxalate, a plant secondary compound (PSC) degraded exclusively by the gut microbiota. We quantified oxalate degradation in N. albigula fed increasing amounts of oxalate over time and tracked the response of the fecal microbiota using high-throughput sequencing. The amount of oxalate degraded in vivo was linearly correlated with the amount of oxalate consumed. The addition of dietary oxalate was found to impact microbial species diversity by increasing the representation of certain taxa, some of which are known to be capable of degrading oxalate (e.g., Oxalobacter spp.). Furthermore, the relative abundances of 117 operational taxonomic units (OTU) exhibited a significant correlation with oxalate consumption. The results of this study indicate that dietary oxalate induces complex interactions within the gut microbiota that include an increase in the relative abundance of a community of bacteria that may contribute either directly or indirectly to oxalate degradation in mammalian herbivores. PMID:26896138

Fumonisin-Exposure Impairs Age-Related Ecological Succession of Bacterial Species in Weaned Pig Gut Microbiota.

PubMed

Mateos, Ivan; Combes, Sylvie; Pascal, Géraldine; Cauquil, Laurent; Barilly, Céline; Cossalter, Anne-Marie; Laffitte, Joëlle; Botti, Sara; Pinton, Philippe; Oswald, Isabelle P

2018-06-05

Pigs are highly affected by dietary mycotoxin contamination and particularly by fumonisin. The effects of fumonisin on pig intestinal health are well documented, but little is known regarding its impact on gut microbiota. We investigate the effects of the fumonisin (FB1, 12 mg/kg feed) on the fecal microbiota of piglets ( n = 6) after 0, 8, 15, 22, and 29 days of exposure. A control group of six piglets received a diet free of FB1. Bacterial community diversity, structure and taxonomic composition were carried out by V3⁻V4 16S rRNA gene sequencing. Exposure to FB1 decreases the diversity index, and shifts and constrains the structure and the composition of the bacterial community. This takes place as early as after 15 days of exposure and is at a maximum after 22 days of exposure. Compared to control, FB1 alters the ecological succession of fecal microbiota species toward higher levels of Lactobacillus and lower levels of the Lachnospiraceae and Veillonellaceae families, and particularly OTUs (Operational Taxonomic Units) of the genera Mitsuokella , Faecalibacterium and Roseburia . In conclusion, FB1 shifts and constrains age-related evolution of microbiota. The direct or indirect contribution of FB1 microbiota alteration in the global host response to FB1 toxicity remains to be investigated.

Impact of a vegan diet on the human salivary microbiota.

PubMed

Hansen, Tue H; Kern, Timo; Bak, Emilie G; Kashani, Alireza; Allin, Kristine H; Nielsen, Trine; Hansen, Torben; Pedersen, Oluf

2018-04-11

Little is known about the effect of long-term diet patterns on the composition and functional potential of the human salivary microbiota. In the present study, we sought to contribute to the ongoing elucidation of dietary effects on the oral microbial community by examining the diversity, composition and functional potential of the salivary microbiota in 160 healthy vegans and omnivores using 16S rRNA gene amplicon sequencing. We further sought to identify bacterial taxa in saliva associated with host inflammatory markers. We show that compositional differences in the salivary microbiota of vegans and omnivores is present at all taxonomic levels below phylum level and includes upper respiratory tract commensals (e.g. Neisseria subflava, Haemophilus parainfluenzae, and Rothia mucilaginosa) and species associated with periodontal disease (e.g. Campylobacter rectus and Porphyromonas endodontalis). Dietary intake of medium chain fatty acids, piscine mono- and polyunsaturated fatty acids, and dietary fibre was associated with bacterial diversity, community structure, as well as relative abundance of several species-level operational taxonomic units. Analysis of imputed genomic potential revealed several metabolic pathways differentially abundant in vegans and omnivores indicating possible effects of macro- and micro-nutrient intake. We also show that certain oral bacteria are associated with the systemic inflammatory state of the host.

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing.

PubMed

de Melo, Fabiana; do Nascimento, Cássio; Souza, Diogo Onofre; de Albuquerque, Rubens F

2017-06-01

To characterize the profile of microbial communities colonizing titanium implants with different surface treatments after exposure to the oral environment at the genus or higher taxonomic level. Sixteen titanium disks, machined or sandblasted large-grit and acid-etched (SLA), were mounted on removable intraoral splints worn by four patients. After 24 h of intraoral exposure, biofilm samples were collected from disks and supra/subgingival teeth areas. The 16S rDNA genes from each sample were amplified, sequenced with the Miseq Illumina instrument and analyzed. A total of 29 genera and seven more inclusive taxa, representing the phyla Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria and candidate division TM7 were identified in both titanium surfaces and teeth. No differences were found in relation to the operational taxonomic units (OTUs) and microbial diversity, assessed by Chao 1 and Shannon indices, when comparing SLA and machined titanium surfaces. Machined and SLA surfaces are colonized by similar numbers of prokaryotic OTUs after 24 h of exposure to the oral environment. Higher complexity of the titanium surface topography in the initial phase of biofilm maturation does not seem to significantly influence the colonizing microbiota. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Molecular Identification of Ectomycorrhizal Mycelium in Soil Horizons

PubMed Central

Landeweert, Renske; Leeflang, Paula; Kuyper, Thom W.; Hoffland, Ellis; Rosling, Anna; Wernars, Karel; Smit, Eric

2003-01-01

Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (≥99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had ≥98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil. PMID:12514012

First Record of Raillietina celebensis (Cestoda: Cyclophyllidea) in South America: Redescription and Phylogeny.

PubMed

de Oliveira Simões, Raquel; Simões, Susana Balmant Enrique; Luque, José Luis; Iñiguez, Alena Mayo; Júnior, Arnaldo Maldonado

2017-08-01

Raillietina celebensis is a cestode that parasitizes the small intestine of rats and humans. Here, we detail the morphology and morphometry of R. celebensis based on specimens collected from Rattus norvegicus in the municipality of São Gonçalo, state of Rio de Janeiro, Brazil, by light and confocal scanning laser microscopies and also report the results of molecular phylogenetic analyses to determine its relationships within the family Davaineidae. Analysis of the number and size of testes, number and shape of rostellar hooks, cirrus sac length, capsules and eggs per capsule, and morphology of the mature proglottid allowed concluding that the present specimens constitute a new record of R. celebensis in South America. Our genetic and phylogenetic analyses, based on the partial small subunit 18S rRNA gene, revealed R. celebensis to be in the family Davaineidae within the genus Raillietina, in agreement with the morphological taxonomy. Phylogenetic trees obtained by neighbor-joining and maximum likelihood methods demonstrated R. celebensis as a unique taxonomic unit, and also demonstrated some taxonomic inconsistences. The incorporation of Brazilian R. celebensis sequences derived from mammals in the phylogeny of davaineids is consistent with the assertion that neither Raillietina nor Fuhrmannetta can be supported as distinct genera.

Transfer to forest nurseries significantly affects mycorrhizal community composition of Asteropeia mcphersonii wildings.

PubMed

Henry, Charline; Raivoarisoa, Jeanne-Françoise; Razafimamonjy, Angélo; Ramanankierana, Heriniaina; Andrianaivomahefa, Paul; Ducousso, Marc; Selosse, Marc-André

2017-05-01

Mycorrhizal symbiosis is extremely important for tree growth, survival and resistance after transplantation particularly in Madagascar where deforestation is a major concern. The importance of mycorrhizal symbiosis is further increased when soil conditions at the planting site are limiting. To identify technical itineraries capable of improving ecological restoration in Madagascar, we needed to obtain native ectomycorrhizal (ECM) saplings with a wide diversity of ECM fungi. To this end, we transplanted ECM seedlings from the wild (wildlings) to a nursery. Using molecular characterisation of internal transcribed spacer (ITS) rDNA, we tested the effect of transplanting Asteropeia mcphersonii wildlings on ECM communities after 8 months of growth in the nursery. With or without the addition of soil from the site where the seedlings were sampled to the nursery substrate, we observed a dramatic change in the composition of fungal communities with a decrease in the ECM infection rate, a tremendous increase in the abundance of an operational taxonomic unit (OTU) taxonomically close to the order Trechisporales and the disappearance of all OTUs of Boletales. Transplanting to the nursery and/or to nursery conditions was shown to be incompatible with the survival and even less with the development in the nursery of most ECM fungi naturally associated with A. mcphersonii wildings.

Interactions in the microbiome: communities of organisms and communities of genes

PubMed Central

Boon, Eva; Meehan, Conor J; Whidden, Chris; Wong, Dennis H-J; Langille, Morgan GI; Beiko, Robert G

2014-01-01

A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term ‘community’ is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of ‘Who is there?’ and ‘What are they doing?’ to the mechanistically driven question of ‘How will they respond?’ PMID:23909933

Local environmental pollution strongly influences culturable bacterial aerosols at an urban aquatic superfund site.

PubMed

Dueker, M Elias; O'Mullan, Gregory D; Juhl, Andrew R; Weathers, Kathleen C; Uriarte, Maria

2012-10-16

In polluted environments, when microbial aerosols originate locally, species composition of the aerosols should reflect the polluted source. To test the connection between local environmental pollution and microbial aerosols near an urban waterfront, we characterized bacterial aerosols at Newtown Creek (NTC), a public waterway and Superfund site in a densely populated area of New York, NY, USA. Culturable bacterial aerosol fallout rate and surface water bacterial concentrations were at least an order of magnitude greater at NTC than at a neighboring, less polluted waterfront and a nonurban coastal site in Maine. The NTC culturable bacterial aerosol community was significantly different in taxonomic structure from previous urban and coastal aerosol studies, particularly in relative abundances of Actinobacteria and Proteobacteria. Twenty-four percent of the operational taxonomic units in the NTC overall (air + water) bacterial isolate library were most similar to bacterial 16S rRNA gene sequences previously described in terrestrial or aquatic environments contaminated with sewage, hydrocarbons, heavy metals, and other industrial waste. This study is the first to examine the community composition and local deposition of bacterial aerosols from an aquatic Superfund site. The findings have important implications for the use of aeration remediation in polluted aquatic environments and suggest a novel pathway of microbial exposure in densely populated urban communities containing contaminated soil and water.

Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis.

PubMed

Ofek-Lalzar, Maya; Gur, Yonatan; Ben-Moshe, Sapir; Sharon, Or; Kosman, Evsey; Mochli, Elad; Sharon, Amir

2016-10-01

Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides and Aegilops sharonensis, and compared it to an endophyte community from wheat (T. aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods. In total, 514 intergenic spacer region sequences from single cultures were analyzed. Categorization at 97% sequence similarity resulted in 67 operational taxonomic units (OTUs) that were evenly distributed between the different plant species. A narrow core community of Alternaria spp. was found in all samples, but each plant species also contained a significant portion of unique endophytes. The cultivation-independent analysis identified a larger number of OTUs than the cultivation method, half of which were singletons or doubletons. For OTUs with a relative abundance >0.5%, similar numbers were obtained by both methods. Collectively, our data show that wild grass relatives of wheat contain a wealth of taxonomically diverse fungal endophytes that are not found in modern wheat, some of which belong to taxa with known beneficial effects. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

What's in a name: the taxonomic status of human head and body lice.

PubMed

Light, Jessica E; Toups, Melissa A; Reed, David L

2008-06-01

Human head lice (Anoplura: Pediculidae: Pediculus) are pandemic, parasitizing countless school children worldwide due to the evolution of insecticide resistance, and human body (clothing) lice are responsible for the deaths of millions as a result of vectoring several deadly bacterial pathogens. Despite the obvious impact these lice have had on their human hosts, it is unclear whether head and body lice represent two morphological forms of a single species or two distinct species. To assess the taxonomic status of head and body lice, we provide a synthesis of publicly available molecular data in GenBank, and we compare phylogenetic and population genetic methods using the most diverse geographic and molecular sampling presently available. Our analyses find reticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate that head and body lice do not represent genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and body lice, we contend that no known species concept would recognize these louse morphotypes as separate species. We recommend recognizing head and body lice as morphotypes of a single species, Pediculus humanus, until compelling new data and analyses (preferably analyses of fast evolving nuclear markers in a coalescent framework) indicate otherwise.

Molecular characterization of viable Legionella spp. in cooling tower water samples by combined use of ethidium monoazide and PCR.

PubMed

Inoue, Hiroaki; Fujimura, Reiko; Agata, Kunio; Ohta, Hiroyuki

2015-01-01

Viable Legionella spp. in environmental water samples were characterized phylogenetically by a clone library analysis combining the use of ethidium monoazide and quantitative PCR. To examine the diversity of Legionella spp., six cooling tower water samples and three bath water samples were collected and analyzed. A total of 617 clones were analyzed for their 16S rRNA gene sequences and classified into 99 operational taxonomic units (OTUs). The majority of OTUs were not clustered with currently described Legionella spp., suggesting the wide diversity of not-yet-cultured Legionella groups harbored in cooling tower water environments.

Palaeoecology and sedimentology of the dysaerobic Bedford fauna (late Devonian), Ohio and Kentucky (USA)

USGS Publications Warehouse

Pashin, J.C.; Ettensohn, F.R.

1992-01-01

Oxygen-deficient biofacies models rely on lithologic and paleontologic attributes to identify distinctive biofacies interpreted to reflect levels of oxygenation in anaerobic, dysaerobic, and aerobic parts of a stratified water column. This study of the Bedford fauna from the Bedford Shale of Ohio and Kentucky and from adjacent black-shale units reports faunal distributions different from those predicted by the accepted models. This study suggests that, although oxygenation was an important factor that determined the taxonomic makeup of the fauna, bacterially mediated nutrient recycling and substrate characteristics were more important than oxygenation in determining faunal distribution in the dysaerobic zone. ?? 1992.

Bacterial communities in the phylloplane of Prunus species.

PubMed

Jo, Yeonhwa; Cho, Jin Kyong; Choi, Hoseong; Chu, Hyosub; Lian, Sen; Cho, Won Kyong

2015-04-01

Bacterial populations in the phylloplane of four different Prunus species were investigated by 16 S rRNA pyrosequencing. Bioinformatic analysis identified an average of 510 operational taxonomic units belonging to 159 genera in 76 families. The two genera, Sphingomonas and Methylobacterium, were dominant in the phylloplane of four Prunus species. Twenty three genera were commonly identified in the four Prunus species, indicating a high level of bacterial diversity dependent on the plant species. Our study based on 16 S rRNA sequencing reveals the complexity of bacterial diversity in the phylloplane of Prunus species in detail. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Characterization of Viable Legionella spp. in Cooling Tower Water Samples by Combined Use of Ethidium Monoazide and PCR

PubMed Central

Inoue, Hiroaki; Fujimura, Reiko; Agata, Kunio; Ohta, Hiroyuki

2015-01-01

Viable Legionella spp. in environmental water samples were characterized phylogenetically by a clone library analysis combining the use of ethidium monoazide and quantitative PCR. To examine the diversity of Legionella spp., six cooling tower water samples and three bath water samples were collected and analyzed. A total of 617 clones were analyzed for their 16S rRNA gene sequences and classified into 99 operational taxonomic units (OTUs). The majority of OTUs were not clustered with currently described Legionella spp., suggesting the wide diversity of not-yet-cultured Legionella groups harbored in cooling tower water environments. PMID:25736979

Contribution of PCR Denaturing Gradient Gel Electrophoresis Combined with Mixed Chromatogram Software Separation for Complex Urinary Sample Analysis.

PubMed

Kotásková, Iva; Mališová, Barbora; Obručová, Hana; Holá, Veronika; Peroutková, Tereza; Růžička, Filip; Freiberger, Tomáš

2017-01-01

Complex samples are a challenge for sequencing-based broad-range diagnostics. We analysed 19 urinary catheter, ureteral Double-J catheter, and urine samples using 3 methodological approaches. Out of the total 84 operational taxonomic units, 37, 61, and 88% were identified by culture, PCR-DGGE-SS (PCR denaturing gradient gel electrophoresis followed by Sanger sequencing), and PCR-DGGE-RM (PCR- DGGE combined with software chromatogram separation by RipSeq Mixed tool), respectively. The latter approach was shown to be an efficient tool to complement culture in complex sample assessment. © 2017 S. Karger AG, Basel.

United States Department of Agriculture-Agricultural Research Service research programs in biological control of plant diseases.

PubMed

Roberts, Daniel P; Lohrke, Scott M

2003-01-01

A number of USDA-ARS programs directed at overcoming impediments to the use of biocontrol agents on a commercial scale are described. These include improvements in screening techniques, taxonomic studies to identify beneficial strains more precisely, and studies on various aspects of the large-scale production of biocontrol agents. Another broad area of studies covers the ecological aspects of biocontrol agents-their interaction with the pathogen, with the plant and with other aspects of the environmental complex. Examples of these studies are given and their relevance to the further development and expansion of biocontrol agents is discussed.

Chinese deaf adolescents' free recall of taxonomic, slot-filler, and thematic categories.

PubMed

Li, Degao; Zhang, Jijia

2009-08-01

Four experiments were conducted to show that deaf adolescents tended to process information in different ways from hearing adolescents. Memorizing items sequentially shown on computer screens under the control of their articulators' movements, deaf adolescents tended to treat items that cohered as taxonomic, thematic, or slot-filler categories as isolated pieces of information. Having to perceive information by means of sign language, however, their achievements were not worse than those of hearing adolescents anymore, no matter whether the stimuli were presented as words or pictures. They could not only utilize categories relations to help memorize categories exemplars but were relatively better aware of slot-filler or thematic than taxonomic relations as well, suggesting that they had a relatively delayed development of taxonomic category representations in comparison with hearing adolescents.

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.

Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri

PubMed Central

TANIZAWA, Yasuhiro; KOBAYASHI, Hisami; KAMINUMA, Eli; SAKAMOTO, Mitsuo; OHKUMA, Moriya; NAKAMURA, Yasukazu; ARITA, Masanori; TOHNO, Masanori

2017-01-01

Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573T to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L. parakefiri in functional foods such as kefir grains. PMID:28748134

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy.

PubMed

Gao, Xiang; Lin, Huaiying; Revanna, Kashi; Dong, Qunfeng

2017-05-10

Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provide species-level classification, or their classification results are unreliable. The unreliable results are due to the limitations in the existing methods which either lack solid probabilistic-based criteria to evaluate the confidence of their taxonomic assignments, or use nucleotide k-mer frequency as the proxy for sequence similarity measurement. We have developed a method that shows significantly improved species-level classification results over existing methods. Our method calculates true sequence similarity between query sequences and database hits using pairwise sequence alignment. Taxonomic classifications are assigned from the species to the phylum levels based on the lowest common ancestors of multiple database hits for each query sequence, and further classification reliabilities are evaluated by bootstrap confidence scores. The novelty of our method is that the contribution of each database hit to the taxonomic assignment of the query sequence is weighted by a Bayesian posterior probability based upon the degree of sequence similarity of the database hit to the query sequence. Our method does not need any training datasets specific for different taxonomic groups. Instead only a reference database is required for aligning to the query sequences, making our method easily applicable for different regions of the 16S rRNA gene or other phylogenetic marker genes. Reliable species-level classification for 16S rRNA or other phylogenetic marker genes is critical for microbiome research. Our software shows significantly higher classification accuracy than the existing tools and we provide probabilistic-based confidence scores to evaluate the reliability of our taxonomic classification assignments based on multiple database matches to query sequences. Despite its higher computational costs, our method is still suitable for analyzing large-scale microbiome datasets for practical purposes. Furthermore, our method can be applied for taxonomic classification of any phylogenetic marker gene sequences. Our software, called BLCA, is freely available at https://github.com/qunfengdong/BLCA .

Application of DNA barcoding in biodiversity studies of shallow-water octocorals: molecular proxies agree with morphological estimates of species richness in Palau

NASA Astrophysics Data System (ADS)

McFadden, C. S.; Brown, A. S.; Brayton, C.; Hunt, C. B.; van Ofwegen, L. P.

2014-06-01

The application of DNA barcoding to anthozoan cnidarians has been hindered by their slow rates of mitochondrial gene evolution and the failure to identify alternative molecular markers that distinguish species reliably. Among octocorals, however, multilocus barcodes can distinguish up to 70 % of morphospecies, thereby facilitating the identification of species that are ecologically important but still very poorly known taxonomically. We tested the ability of these imperfect DNA barcodes to estimate species richness in a biodiversity survey of the shallow-water octocoral fauna of Palau using multilocus ( COI, mtMutS, 28S rDNA) sequences obtained from 305 specimens representing 38 genera of octocorals. Numbers and identities of species were estimated independently (1) by a taxonomic expert using morphological criteria and (2) by assigning sequences to molecular operational taxonomic units (MOTUs) using predefined genetic distance thresholds. Estimated numbers of MOTUs ranged from 73 to 128 depending on the barcode and distance threshold applied, bracketing the estimated number of 118 morphospecies. Concordance between morphospecies identifications and MOTUs ranged from 71 to 75 % and differed little among barcodes. For the speciose and ecologically dominant genus Sinularia, however, we were able to identify 95 % of specimens correctly simply by comparing mtMutS sequences and in situ photographs of colonies to an existing vouchered database. Because we lack a clear understanding of species boundaries in most of these taxa, numbers of morphospecies and MOTUs are both estimates of the true species diversity, and we cannot currently determine which is more accurate. Our results suggest, however, that the two methods provide comparable estimates of species richness for shallow-water Indo-Pacific octocorals. Use of molecular barcodes in biodiversity surveys will facilitate comparisons of species richness and composition among localities and over time, data that do not currently exist for any octocoral community.

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.

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean.

PubMed

Pagliosa, Paulo R; Doria, João G; Misturini, Dairana; Otegui, Mariana B P; Oortman, Mariana S; Weis, Wilson A; Faroni-Perez, Larisse; Alves, Alexandre P; Camargo, Maurício G; Amaral, A Cecília Z; Marques, Antonio C; Lana, Paulo C

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/.

Borrelia burgdorferi Sensu Lato Spirochetes in Wild Birds in Northwestern California: Associations with Ecological Factors, Bird Behavior and Tick Infestation

PubMed Central

Newman, Erica A.; Eisen, Lars; Eisen, Rebecca J.; Fedorova, Natalia; Hasty, Jeomhee M.; Vaughn, Charles; Lane, Robert S.

2015-01-01

Although Borrelia burgdorferi sensu lato (s.l.) are found in a great diversity of vertebrates, most studies in North America have focused on the role of mammals as spirochete reservoir hosts. We investigated the roles of birds as hosts for subadult Ixodes pacificus ticks and potential reservoirs of the Lyme disease spirochete B. burgdorferi sensu stricto (s.s.) in northwestern California. Overall, 623 birds representing 53 species yielded 284 I. pacificus larvae and nymphs. We used generalized linear models and zero-inflated negative binomial models to determine associations of bird behaviors, taxonomic relationships and infestation by I. pacificus with borrelial infection in the birds. Infection status in birds was best explained by taxonomic order, number of infesting nymphs, sampling year, and log-transformed average body weight. Presence and counts of larvae and nymphs could be predicted by ground- or bark-foraging behavior and contact with dense oak woodland. Molecular analysis yielded the first reported detection of Borrelia bissettii in birds. Moreover, our data suggest that the Golden-crowned Sparrow (Zonotrichia atricapilla), a non-resident species, could be an important reservoir for B. burgdorferi s.s. Of 12 individual birds (9 species) that carried B. burgdorferi s.l.-infected larvae, no birds carried the same genospecies of B. burgdorferi s.l. in their blood as were present in the infected larvae removed from them. Possible reasons for this discrepancy are discussed. Our study is the first to explicitly incorporate both taxonomic relationships and behaviors as predictor variables to identify putative avian reservoirs of B. burgdorferi s.l. Our findings underscore the importance of bird behavior to explain local tick infestation and Borrelia infection in these animals, and suggest the potential for bird-mediated geographic spread of vector ticks and spirochetes in the far-western United States. PMID:25714376

NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean

PubMed Central

Pagliosa, Paulo R.; Doria, João G.; Misturini, Dairana; Otegui, Mariana B. P.; Oortman, Mariana S.; Weis, Wilson A.; Faroni-Perez, Larisse; Alves, Alexandre P.; Camargo, Maurício G.; Amaral, A. Cecília Z.; Marques, Antonio C.; Lana, Paulo C.

2014-01-01

Networks can greatly advance data sharing attitudes by providing organized and useful data sets on marine biodiversity in a friendly and shared scientific environment. NONATObase, the interactive database on polychaetes presented herein, will provide new macroecological and taxonomic insights of the Southwestern Atlantic region. The database was developed by the NONATO network, a team of South American researchers, who integrated available information on polychaetes from between 5°N and 80°S in the Atlantic Ocean and near the Antarctic. The guiding principle of the database is to keep free and open access to data based on partnerships. Its architecture consists of a relational database integrated in the MySQL and PHP framework. Its web application allows access to the data from three different directions: species (qualitative data), abundance (quantitative data) and data set (reference data). The database has built-in functionality, such as the filter of data on user-defined taxonomic levels, characteristics of site, sample, sampler, and mesh size used. Considering that there are still many taxonomic issues related to poorly known regional fauna, a scientific committee was created to work out consistent solutions to current misidentifications and equivocal taxonomy status of some species. Expertise from this committee will be incorporated by NONATObase continually. The use of quantitative data was possible by standardization of a sample unit. All data, maps of distribution and references from a data set or a specified query can be visualized and exported to a commonly used data format in statistical analysis or reference manager software. The NONATO network has initialized with NONATObase, a valuable resource for marine ecologists and taxonomists. The database is expected to grow in functionality as it comes in useful, particularly regarding the challenges of dealing with molecular genetic data and tools to assess the effects of global environment change. Database URL: http://nonatobase.ufsc.br/ PMID:24573879

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.

Borrelia burgdorferi sensu lato spirochetes in wild birds in northwestern California: associations with ecological factors, bird behavior and tick infestation.

PubMed

Newman, Erica A; Eisen, Lars; Eisen, Rebecca J; Fedorova, Natalia; Hasty, Jeomhee M; Vaughn, Charles; Lane, Robert S

2015-01-01

Although Borrelia burgdorferi sensu lato (s.l.) are found in a great diversity of vertebrates, most studies in North America have focused on the role of mammals as spirochete reservoir hosts. We investigated the roles of birds as hosts for subadult Ixodes pacificus ticks and potential reservoirs of the Lyme disease spirochete B. burgdorferi sensu stricto (s.s.) in northwestern California. Overall, 623 birds representing 53 species yielded 284 I. pacificus larvae and nymphs. We used generalized linear models and zero-inflated negative binomial models to determine associations of bird behaviors, taxonomic relationships and infestation by I. pacificus with borrelial infection in the birds. Infection status in birds was best explained by taxonomic order, number of infesting nymphs, sampling year, and log-transformed average body weight. Presence and counts of larvae and nymphs could be predicted by ground- or bark-foraging behavior and contact with dense oak woodland. Molecular analysis yielded the first reported detection of Borrelia bissettii in birds. Moreover, our data suggest that the Golden-crowned Sparrow (Zonotrichia atricapilla), a non-resident species, could be an important reservoir for B. burgdorferi s.s. Of 12 individual birds (9 species) that carried B. burgdorferi s.l.-infected larvae, no birds carried the same genospecies of B. burgdorferi s.l. in their blood as were present in the infected larvae removed from them. Possible reasons for this discrepancy are discussed. Our study is the first to explicitly incorporate both taxonomic relationships and behaviors as predictor variables to identify putative avian reservoirs of B. burgdorferi s.l. Our findings underscore the importance of bird behavior to explain local tick infestation and Borrelia infection in these animals, and suggest the potential for bird-mediated geographic spread of vector ticks and spirochetes in the far-western United States.

A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates.

PubMed

Helbling, Damian E; Johnson, David R; Lee, Tae Kwon; Scheidegger, Andreas; Fenner, Kathrin

2015-03-01

The rates at which wastewater treatment plant (WWTP) microbial communities biotransform specific substrates can differ by orders of magnitude among WWTP communities. Differences in taxonomic compositions among WWTP communities may predict differences in the rates of some types of biotransformations. In this work, we present a novel framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. We selected ten WWTPs with substantial variation in their environmental and operational metrics and measured the in situ ammonia biotransformation rate constants in nine of them. We isolated total RNA from samples from each WWTP and analyzed 16S rRNA sequence reads. We then developed multivariate models between the measured abundances of specific bacterial 16S rRNA sequence reads and the ammonia biotransformation rate constants. We constructed model scenarios that systematically explored the effects of model regularization, model linearity and non-linearity, and aggregation of 16S rRNA sequences into operational taxonomic units (OTUs) as a function of sequence dissimilarity threshold (SDT). A large percentage (greater than 80%) of model scenarios resulted in well-performing and significant models at intermediate SDTs of 0.13-0.14 and 0.26. The 16S rRNA sequences consistently selected into the well-performing and significant models at those SDTs were classified as Nitrosomonas and Nitrospira groups. We then extend the framework by applying it to the biotransformation rate constants of ten micropollutants measured in batch reactors seeded with the ten WWTP communities. We identified phylogenetic groups that were robustly selected into all well-performing and significant models constructed with biotransformation rates of isoproturon, propachlor, ranitidine, and venlafaxine. These phylogenetic groups can be used as predictive biomarkers of WWTP microbial community activity towards these specific micropollutants. This work is an important step towards developing tools to predict biotransformation rates in WWTPs based on taxonomic composition. Copyright © 2014 Elsevier Ltd. All rights reserved.

Use of congeneric assessment to reveal the linked genetic histories of two threatened fishes in the Murray-Darling Basin, Australia.

PubMed

Adams, M; Wedderburn, S D; Unmack, P J; Hammer, M P; Johnson, J B

2011-08-01

The intensely regulated Murray-Darling Basin in southeastern Australia is the nation's most extensive and economically important river system, and it contains fragmented populations of numerous fish species. Among these is the Murray hardyhead (Craterocephalus fluviatilis), a species listed as endangered (International Union for Conservation of Nature Red List) in the mid-1990 s prior to its acute decline with the progression of a severe drought that began in 1997. We compared the genetic structure of Murray hardyhead with 4 congeneric species (Darling hardyhead[C. amniculus], Finke hardyhead[C. centralis], Lake Eyre hardyhead[C. eyresii], and unspecked hardyhead[C. stercusmuscarum]), selected on the basis of their taxonomic or biological similarity to Murray hardyhead, in order to affirm species boundaries and test for instances of introgressive hybridization, which may influence species ecology and conservation prospects. We used allozyme (52 loci) and mtDNA markers (1999 bp of ATPase and cytochrome b) to provide a comparative genetic assessment of 139 Murray hardyhead, which represented all extant and some recently extirpated populations, and 71 congeneric specimens from 12 populations. We confirmed that Murray hardyhead and Darling hardyhead are taxonomically distinct and identified a number of potential conservation units, defined with genetic criteria, in both species. We also found allozyme and mtDNA evidence of historic genetic exchange between these 2 allopatric species, apparently involving one population of each species at the geographic edge of the species' ranges, not in the most proximate populations sampled. Our results provide information on species boundaries and offer insight into the likely causes of high genetic diversity in certain populations, results which are already being used to guide national recovery planning and local action. Given the prevalence of incorrect taxonomies and introgression in many organismal groups, we believe these data point to the need to commence genetic investigations of any threatened species from an initially broad taxonomic focus. © 2011 Society for Conservation Biology.

Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.

PubMed

Cui, Hong; Xu, Dongfang; Chong, Steven S; Ramirez, Martin; Rodenhausen, Thomas; Macklin, James A; Ludäscher, Bertram; Morris, Robert A; Soto, Eduardo M; Koch, Nicolás Mongiardino

2016-11-17

Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study.

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

Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing.

PubMed

Endara, Lorena; Cui, Hong; Burleigh, J Gordon

2018-03-01

Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Our protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon-by-character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. The NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.

Seasonality, Dietary Overlap and the Role of Taxonomic Resolution in the Study of the Diet of Three Congeneric Fishes from a Tropical Bay

PubMed Central

Pombo, Maíra; Denadai, Márcia Regina; Turra, Alexander

2013-01-01

Not only seasonality but also taxonomic resolution of prey categories has been shown to affect diet studies. We analyzed the stomach contents of three sympatric species, Stellifer rastrifer, S. brasiliensis and S. stellifer, sampled monthly from August 2003 to October 2004 in Caraguatatuba Bay, southeastern Brazil. General characteristics and similarities among their diets were evaluated by considering high taxonomic ranks of all prey groups, and also the lower taxonomic ranks of the main prey groups. Dietary similarity was relatively high among species and low between seasons, and both evaluation criteria gave the equivalent results. The rare items, however, provided information about resource partition, and the species compositions of the most important groups were apparently good indicators of food availability. PMID:23405256

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

PubMed

Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

PubMed Central

Dröge, J.; Gregor, I.; McHardy, A. C.

2015-01-01

Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data. Availability and implementation: Taxator-tk source and binary program files are publicly available at http://algbio.cs.uni-duesseldorf.de/software/. Contact: Alice.McHardy@uni-duesseldorf.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388150

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.

Contrasting Semantic versus Inhibitory Processing in the Angular Gyrus: An fMRI Study.

PubMed

Lewis, Gwyneth A; Poeppel, David; Murphy, Gregory L

2018-06-06

Recent studies of semantic memory have focused on dissociating the neural bases of two foundational components of human thought: taxonomic categories, which group similar objects like dogs and seals based on features, and thematic categories, which group dissimilar objects like dogs and leashes based on events. While there is emerging consensus that taxonomic concepts are represented in the anterior temporal lobe, there is disagreement over whether thematic concepts are represented in the angular gyrus (AG). We previously found AG sensitivity to both kinds of concepts; however, some accounts suggest that such activity reflects inhibition of irrelevant information rather than thematic activation. To test these possibilities, an fMRI experiment investigated both types of conceptual relations in the AG during two semantic judgment tasks. Each task trained participants to give negative responses (inhibition) or positive responses (activation) to word pairs based on taxonomic and thematic criteria of relatedness. Results showed AG engagement during both negative judgments and thematic judgments, but not during positive judgments about taxonomic pairs. Together, the results suggest that activity in the AG reflects functions that include both thematic (but not taxonomic) processing and inhibiting irrelevant semantic information.

Typification and taxonomic status re-evaluation of 15 taxon names within the species complex Cymbella affinis/tumidula/turgidula (Cymbellaceae, Bacillariophyta)

PubMed Central

da Silva, Weliton José; Jahn, Regine; Ludwig, Thelma Alvim Veiga; Hinz, Friedel; Menezes, Mariângela

2015-01-01

Abstract Specimens belonging to the Cymbella affinis / Cymbella tumidula / Cymbella turgidula species complex have many taxonomic problems, due to their high morphological variability and lack of type designations. Fifteen taxon names of this complex, distributed in five species, were re-evaluated concerning their taxonomic status, and lectotypified based on original material. In addition to light microscopy, some material was analyzed by electron microscopy. Four new combinations are proposed in order to reposition infraspecific taxa. PMID:26312038

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.

Integrative analysis of environmental sequences using MEGAN4.

PubMed

Huson, Daniel H; Mitra, Suparna; Ruscheweyh, Hans-Joachim; Weber, Nico; Schuster, Stephan C

2011-09-01

A major challenge in the analysis of environmental sequences is data integration. The question is how to analyze different types of data in a unified approach, addressing both the taxonomic and functional aspects. To facilitate such analyses, we have substantially extended MEGAN, a widely used taxonomic analysis program. The new program, MEGAN4, provides an integrated approach to the taxonomic and functional analysis of metagenomic, metatranscriptomic, metaproteomic, and rRNA data. While taxonomic analysis is performed based on the NCBI taxonomy, functional analysis is performed using the SEED classification of subsystems and functional roles or the KEGG classification of pathways and enzymes. A number of examples illustrate how such analyses can be performed, and show that one can also import and compare classification results obtained using others' tools. MEGAN4 is freely available for academic purposes, and installers for all three major operating systems can be downloaded from www-ab.informatik.uni-tuebingen.de/software/megan.

Comparative SEM and LM foliar epidermal and palyno-morphological studies of Amaranthaceae and its taxonomic implications.

PubMed

Hussain, Amara Noor; Zafar, Muhammad; Ahmad, Mushtaq; Khan, Raees; Yaseen, Ghulam; Khan, Muhammad Saleem; Nazir, Abdul; Khan, Amir Muhammad; Shaheen, Shabnum

2018-05-01

Palynological features as well as comparative foliar epidermal using light and scanning electron microscope (SEM) of 17 species (10genera) of Amaranthaceae have been studied for its taxonomic significance. Different foliar and palynological micro-morphological characters were examined to explain their value in resolving the difficulty in identification. All species were amphistomatic but stomata on abaxial surface were more abundant. Taxonomically significant epidermal character including stomata type, trichomes (unicellular, multicellular, and capitate) and epidermal cells shapes (polygonal and irregular) were also observed. Pollens of this family are Polypantoporate, pores large, spheroidal, mesoporous region is sparsely to scabrate, densely psilate, and spinulose. All these characters can be active at species level for identification purpose. This study indicates that at different taxonomic levels, LM and SEM pollen and epidermal morphology is explanatory and significant to identify species and genera. © 2018 Wiley Periodicals, Inc.

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

An intercomparison of the taxonomic and size composition of tropical macrozooplankton and micronekton collected using three sampling gears

NASA Astrophysics Data System (ADS)

Kwong, Lian E.; Pakhomov, Evgeny A.; Suntsov, Andrey V.; Seki, Michael P.; Brodeur, Richard D.; Pakhomova, Larisa G.; Domokos, Réka

2018-05-01

A micronekton intercalibration experiment was conducted off the southwest coast of Oahu Island, Hawaii in October 2004. Day and night samples were collected in the epipelagic and mesopelagic zones using three micronekton sampling gears: the Cobb Trawl, the Isaacs-Kidd Midwater Trawl (IKMT), and the Hokkaido University Frame Trawl (HUFT). Taxonomic composition and contribution by main size groups to total catch varied among gear types. However, the three gears exhibited similar taxonomic composition for macrozooplankton and micronekton ranging from 20 to 100 mm length (MM20-100). The HUFT and IKMT captured more mesozooplankton and small MM20-100, while the Cobb trawl selected towards larger MM20-100 and nekton. Taxonomic composition was described and inter-compared among gears. The relative efficacy of the three gears was assessed, and size dependent intercalibration coefficients were developed for MM20-100.

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.

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.

Macrozooplankton biomass in a warm-core Gulf Stream ring: Time series changes in size structure, taxonomic composition, and vertical distribution

NASA Astrophysics Data System (ADS)

Davis, Cabell S.; Wiebe, Peter H.

1985-01-01

Macrozooplankton size structure and taxonomic composition in warm-core ring 82B was examined from a time series (March, April, June) of ring center MOCNESS (1 m) samples. Size distributions of 15 major taxonomic groups were determined from length measurements digitized from silhouette photographs of the samples. Silhouette digitization allows rapid quantification of Zooplankton size structure and taxonomic composition. Length/weight regressions, determined for each taxon, were used to partition the biomass (displacement volumes) of each sample among the major taxonomic groups. Zooplankton taxonomic composition and size structure varied with depth and appeared to coincide with the hydrographic structure of the ring. In March and April, within the thermostad region of the ring, smaller herbivorous/omnivorous Zooplankton, including copepods, crustacean larvae, and euphausiids, were dominant, whereas below this region, larger carnivores, such as medusae, ctenophores, fish, and decapods, dominated. Copepods were generally dominant in most samples above 500 m. Total macrozooplankton abundance and biomass increased between March and April, primarily because of increases in herbivorous taxa, including copepods, crustacean larvae, and larvaceans. A marked increase in total macrozooplankton abundance and biomass between April and June was characterized by an equally dramatic shift from smaller herbivores (1.0-3.0 mm) in April to large herbivores (5.0-6.0 mm) and carnivores (>15 mm) in June. Species identifications made directly from the samples suggest that changes in trophic structure resulted from seeding type immigration and subsequent in situ population growth of Slope Water zooplankton species.

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

PubMed Central

Franz, Nico M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

2015-01-01

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations. PMID:25700173

New Trends and Perspectives in the Evolution of Neurotransmitters in Microbial, Plant, and Animal Cells.

PubMed

Roshchina, Victoria V

2016-01-01

The evolutionary perspective on the universal roles of compounds known as neurotransmitters may help in the analysis of relations between all organisms in biocenosis-from microorganisms to plant and animals. This phenomenon, significant for chemosignaling and cellular endocrinology, has been important in human health and the ability to cause disease or immunity, because the "living environment" influences every organism in a biocenosis relationship (microorganism-microorganism, microorganism-plant, microorganism-animal, plant-animal, plant-plant and animal-animal). Non-nervous functions of neurotransmitters (rather "biomediators" on a cellular level) are considered in this review and ample consideration is given to similarities and differences that unite, as well as distinguish, taxonomical kingdoms.

Carbonate-Dissolving Bacteria from ‘Miliolite’, a Bioclastic Limestone, from Gopnath, Gujarat, Western India

PubMed Central

Subrahmanyam, Gangavarapu; Vaghela, Ravi; Bhatt, Nilesh Pinakinprasad; Archana, Gattupalli

2012-01-01

In the present investigation, the abundance and molecular phylogeny of part of the culturable bacterial population involved in the dissolution of “miliolite”, a bioclastic limestone, from Gopnath, India, was studied. Carbonate-dissolving bacteria were isolated, enumerated and screened for their ability to dissolve miliolite. Amplified ribosomal DNA restriction analysis (ARDRA) indicated 14 operational taxonomic units (OTUs) to be distributed in 5 different clades at a similarity coefficient of 0.85. Then, 16S rRNA sequence analysis helped to decipher that the majority of carbonate-dissolving bacteria were affiliated to phyla Firmicutes (Families Bacillaceae and Staphylococcaceae) and Actinobacteria (Family Promicromonosporaceae) indicating their role in miliolite weathering. PMID:22446314

Taxonomic relationships among Phenacomys voles as inferred by cytochrome b.

Treesearch

M. Renee Bellinger; Susan M. Haig; Eric D. Forsmann; Thomas D. Mullins

2005-01-01

Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. I. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial...

Taxonomic changes in Solanum section Petota

USDA-ARS?s Scientific Manuscript database

In 1990, the latest comprehensive taxonomic monograph of Solanum section Petota Dumort. recognized 236 species partitioned into 21 series. Of these, 227 were tuber-bearing and nine non-tuber-bearing. NSF-sponsored research has drastically altered knowledge of their species boundaries and interrelati...

Molecular evidence of Ebola Reston virus infection in Philippine bats.

PubMed

Jayme, Sarah I; Field, Hume E; de Jong, Carol; Olival, Kevin J; Marsh, Glenn; Tagtag, Anson M; Hughes, Tom; Bucad, Anthony C; Barr, Jennifer; Azul, Rachel R; Retes, Lilia M; Foord, Adam; Yu, Meng; Cruz, Magdalena S; Santos, Imelda J; Lim, Theresa Mundita S; Benigno, Carolyn C; Epstein, Jonathan H; Wang, Lin-Fa; Daszak, Peter; Newman, Scott H

2015-07-17

In 2008-09, evidence of Reston ebolavirus (RESTV) infection was found in domestic pigs and pig workers in the Philippines. With species of bats having been shown to be the cryptic reservoir of filoviruses elsewhere, the Philippine government, in conjunction with the Food and Agriculture Organization of the United Nations, assembled a multi-disciplinary and multi-institutional team to investigate Philippine bats as the possible reservoir of RESTV. The team undertook surveillance of bat populations at multiple locations during 2010 using both serology and molecular assays. A total of 464 bats from 21 species were sampled. We found both molecular and serologic evidence of RESTV infection in multiple bat species. RNA was detected with quantitative PCR (qPCR) in oropharyngeal swabs taken from Miniopterus schreibersii, with three samples yielding a product on conventional hemi-nested PCR whose sequences differed from a Philippine pig isolate by a single nucleotide. Uncorroborated qPCR detections may indicate RESTV nucleic acid in several additional bat species (M. australis, C. brachyotis and Ch. plicata). We also detected anti-RESTV antibodies in three bats (Acerodon jubatus) using both Western blot and ELISA. The findings suggest that ebolavirus infection is taxonomically widespread in Philippine bats, but the evident low prevalence and low viral load warrants expanded surveillance to elaborate the findings, and more broadly, to determine the taxonomic and geographic occurrence of ebolaviruses in bats in the region.

Characterization of throat microbial flora in smokers with or without COPD

PubMed Central

Diao, Wenqi; Shen, Ning; Du, Yipeng; Qian, Ke; He, Bei

2017-01-01

The study aimed to determine the relationship between throat microbiome and COPD. Sixty-five Chinese males (n=20, smokers without COPD; n=45 smokers with COPD) were included. Nonmetric multidimensional scaling indicated differences of microbiome between COPD and controls, but no difference was observed between COPD patients with differing degrees of lung function or disease severity. Rarefaction analyses suggested that operational taxonomic units (OTUs, species-level) richness decreased in COPD. The dominant taxa between COPD and controls were similar, but the proportions of taxonomic distribution were different. The dominant phyla were Bacteroidetes, Proteobacteria, Firmicutes and Fusobacteria. The dominant genera were Haemophilus, Leptotrichia, Porphyromonas, Fusobacterium, Veillonella, Streptococcus, Neisseria and Prevotella. Two dominant OTUs, otu3 (Veillonella_dispar) and otu4 (Streptococcus_unclassified), were identified. Otu3 and its father-level taxa, which were negatively correlated with predicted percent of forced expiratory volume in a second (FEV1%pred), were increased in COPD. By contrast, otu4 and its father-level taxa, which were positively correlated with FEV1%pred, were decreased in COPD. Otu4 also showed a slight potential as a COPD biomarker. To conclude, the throat microbiome was different between smokers with or without COPD, which is similar to findings from the lower respiratory tract. This study may strengthen our understanding of the relationship between microbiomes of different airway sites and COPD. PMID:28740374

A genetic fingerprint of Amphipoda from Icelandic waters – the baseline for further biodiversity and biogeography studies

PubMed Central

Jażdżewska, Anna M.; Corbari, Laure; Driskell, Amy; Frutos, Inmaculada; Havermans, Charlotte; Hendrycks, Ed; Hughes, Lauren; Lörz, Anne-Nina; Bente Stransky; Tandberg, Anne Helene S.; Vader, Wim; Brix, Saskia

2018-01-01

Abstract Amphipods constitute an abundant part of Icelandic deep-sea zoobenthos yet knowledge of the diversity of this fauna, particularly at the molecular level, is scarce. The present work aims to use molecular methods to investigate genetic variation of the Amphipoda sampled during two IceAGE collecting expeditions. The mitochondrial cytochrome oxidase subunit 1 (COI) of 167 individuals originally assigned to 75 morphospecies was analysed. These targeted morhospecies were readily identifiable by experts using light microscopy and representative of families where there is current ongoing taxonomic research. The study resulted in 81 Barcode Identity Numbers (BINs) (of which >90% were published for the first time), while Automatic Barcode Gap Discovery revealed the existence of 78 to 83 Molecular Operational Taxonomic Units (MOTUs). Six nominal species (Rhachotropis helleri, Arrhis phyllonyx, Deflexilodes tenuirostratus, Paroediceros propinquus, Metopa boeckii, Astyra abyssi) appeared to have a molecular variation higher than the 0.03 threshold of both p-distance and K2P usually used for amphipod species delineation. Conversely, two Oedicerotidae regarded as separate morphospecies clustered together with divergences in the order of intraspecific variation. The incongruence between the BINs associated with presently identified species and the publicly available data of the same taxa was observed in case of Paramphithoe hystrix and Amphilochus manudens. The findings from this research project highlight the necessity of supporting molecular studies with thorough morphology species analyses. PMID:29472762

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.

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.

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

PubMed Central

Chow, Cheryl-Emiliane T; Kim, Diane Y; Sachdeva, Rohan; Caron, David A; Fuhrman, Jed A

2014-01-01

Characterizing ecological relationships between viruses, bacteria and protists in the ocean are critical to understanding ecosystem function, yet these relationships are infrequently investigated together. We evaluated these relationships through microbial association network analysis of samples collected approximately monthly from March 2008 to January 2011 in the surface ocean (0–5 m) at the San Pedro Ocean Time series station. Bacterial, T4-like myoviral and protistan communities were described by Automated Ribosomal Intergenic Spacer Analysis and terminal restriction fragment length polymorphism of the gene encoding the major capsid protein (g23) and 18S ribosomal DNA, respectively. Concurrent shifts in community structure suggested similar timing of responses to environmental and biological parameters. We linked T4-like myoviral, bacterial and protistan operational taxonomic units by local similarity correlations, which were then visualized as association networks. Network links (correlations) potentially represent synergistic and antagonistic relationships such as viral lysis, grazing, competition or other interactions. We found that virus–bacteria relationships were more cross-linked than protist–bacteria relationships, suggestive of increased taxonomic specificity in virus–bacteria relationships. We also found that 80% of bacterial–protist and 74% of bacterial–viral correlations were positive, with the latter suggesting that at monthly and seasonal timescales, viruses may be following their hosts more often than controlling host abundance. PMID:24196323

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

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

The Identification of Cable Bacteria Attached to the Anode of a Benthic Microbial Fuel Cell: Evidence of Long Distance Extracellular Electron Transport to Electrodes

PubMed Central

Reimers, Clare E.; Li, Cheng; Graw, Michael F.; Schrader, Paul S.; Wolf, Michael

2017-01-01

Multicellular, filamentous, sulfur-oxidizing bacteria, known as cable bacteria, were discovered attached to fibers of a carbon brush electrode serving as an anode of a benthic microbial fuel cell (BMFC). The BMFC had been operated in a temperate estuarine environment for over a year before collecting anode samples for scanning electron microscopy and phylogenetic analyses. Individual filaments were attached by single terminus cells with networks of pilus-like nano-filaments radiating out from these cells, across the anode fiber surface, and between adjacent attachment locations. Current harvesting by the BMFC poised the anode at potentials of ~170–250 mV vs. SHE, and these surface potentials appear to have allowed the cable bacteria to use the anode as an electron acceptor in a completely anaerobic environment. A combination of catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) and 16S rRNA gene sequence analysis confirmed the phylogeny of the cable bacteria and showed that filaments often occurred in bundles and in close association with members of the genera Desulfuromonas. However, the Desulfobulbaceae Operational Taxonomic Units (OTUs) from the 16S sequencing did not cluster closely with other putative cable bacteria sequences suggesting that the taxonomic delineation of cable bacteria is far from complete. PMID:29114243

Plant diversity and plant identity influence Fusarium communities in soil.

PubMed

LeBlanc, Nicholas; Kinkel, Linda; Kistler, H Corby

2017-01-01

Fusarium communities play important functional roles in soil and in plants as pathogens, endophytes, and saprotrophs. This study tests how rhizosphere Fusarium communities may vary with plant species, changes in the diversity of the surrounding plant community, and soil physiochemical characteristics. Fusarium communities in soil associated with the roots of two perennial prairie plant species maintained as monocultures or growing within polyculture plant communities were characterized using targeted metagenomics. Amplicon libraries targeting the RPB2 locus were generated from rhizosphere soil DNAs and sequenced using pyrosequencing. Sequences were clustered into operational taxonomic units (OTUs) and assigned a taxonomy using the Evolutionary Placement Algorithm. Fusarium community composition was differentiated between monoculture and polyculture plant communities, and by plant species in monoculture, but not in polyculture. Taxonomic classification of the Fusarium OTUs showed a predominance of F. tricinctum and F. oxysporum as well of the presence of a clade previously only found in the Southern Hemisphere. Total Fusarium richness was not affected by changes in plant community richness or correlated with soil physiochemical characteristics. However, OTU richness within two predominant phylogenetic lineages within the genus was positively or negatively correlated with soil physiochemical characteristics among samples within each lineage. This work shows that plant species, plant community richness, and soil physiochemical characteristics may all influence the composition and richness of Fusarium communities in soil.

Identifying the key taxonomic categories that characterize microbial community diversity using full-scale classification: a case study of microbial communities in the sediments of Hangzhou Bay.

PubMed

Dai, Tianjiao; Zhang, Yan; Tang, Yushi; Bai, Yaohui; Tao, Yile; Huang, Bei; Wen, Donghui

2016-10-01

Coastal areas are land-sea transitional zones with complex natural and anthropogenic disturbances. Microorganisms in coastal sediments adapt to such disturbances both individually and as a community. The microbial community structure changes spatially and temporally under environmental stress. In this study, we investigated the microbial community structure in the sediments of Hangzhou Bay, a seriously polluted bay in China. In order to identify the roles and contribution of all microbial taxa, we set thresholds as 0.1% for rare taxa and 1% for abundant taxa, and classified all operational taxonomic units into six exclusive categories based on their abundance. The results showed that the key taxa in differentiating the communities are abundant taxa (AT), conditionally abundant taxa (CAT), and conditionally rare or abundant taxa (CRAT). A large population in conditionally rare taxa (CRT) made this category collectively significant in differentiating the communities. Both bacteria and archaea demonstrated a distance decay pattern of community similarity in the bay, and this pattern was strengthened by rare taxa, CRT and CRAT, but weakened by AT and CAT. This implied that the low abundance taxa were more deterministically distributed, while the high abundance taxa were more ubiquitously distributed. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Identification of Amazonian trees with DNA barcodes.

PubMed

Gonzalez, Mailyn Adriana; Baraloto, Christopher; Engel, Julien; Mori, Scott A; Pétronelli, Pascal; Riéra, Bernard; Roger, Aurélien; Thébaud, Christophe; Chave, Jérôme

2009-10-16

Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests. Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon. We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.

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

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.

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys

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

Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.

The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable regionmore » of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Altogether, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.« less

The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level.

PubMed

Cho, Yong-Joon; Yi, Hana; Chun, Jongsik; Cho, Sang-Nae; Daley, Charles L; Koh, Won-Jung; Shin, Sung Jae

2013-01-01

Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.

Bacterial diversity and community composition from seasurface to subseafloor.

PubMed

Walsh, Emily A; Kirkpatrick, John B; Rutherford, Scott D; Smith, David C; Sogin, Mitchell; D'Hondt, Steven

2016-04-01

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450,104 pyrotags representing 29,814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.

Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus).

PubMed

Liu, Hsiu-Ping; Hershler, Robert; Rossel, Christopher S

2015-01-01

Undescribed freshwater snails (Amnicolidae: Colligyrus) from the Mount Hood region (northwestern United States) identified as a new species (commonly known as the Columbia duskysnail) in grey literature have been provided federal protection under the "survey and manage" provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and Colligyrusgreggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI) and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with Colligyrusgreggi. The COI divergence between these broadly disjunct groups (2.1%) was somewhat larger than that within Colligyrusgreggi (1.0%) but considerably less than that among the three currently recognized species of Colligyrus (8.7-12.1%). Additionally we found that the Columbia duskysnail and Colligyrusgreggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis) and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with Colligyrusgreggi.

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.

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study.

PubMed

Nuy, Julia K; Lange, Anja; Beermann, Arne J; Jensen, Manfred; Elbrecht, Vasco; Röhl, Oliver; Peršoh, Derek; Begerow, Dominik; Leese, Florian; Boenigk, Jens

2018-08-15

Stream ecosystems are affected by multiple anthropogenic stressors worldwide. Even though effects of many single stressors are comparatively well studied, the effects of multiple stressors are difficult to predict. In particular bacteria and protists, which are responsible for the majority of ecosystem respiration and element flows, are infrequently studied with respect to multiple stressors responses. We conducted a stream mesocosm experiment to characterize the responses of single and multiple stressors on microbiota. Two functionally important stream habitats, leaf litter and benthic phototrophic rock biofilms, were exposed to three stressors in a full factorial design: fine sediment deposition, increased chloride concentration (salinization) and reduced flow velocity. We analyzed the microbial composition in the two habitat types of the mesocosms using an amplicon sequencing approach. Community analysis on different taxonomic levels as well as principle component analyses (PCoAs) based on realtive abundances of operational taxonomic units (OTUs) showed treatment specific shifts in the eukaryotic biofilm community. Analysis of variance (ANOVA) revealed that Bacillariophyta responded positively salinity and sediment increase, while the relative read abundance of chlorophyte taxa decreased. The combined effects of multiple stressors were mainly antagonistic. Therefore, the community composition in multiply stressed environments resembled the composition of the unstressed control community in terms of OTU occurrence and relative abundances. Copyright © 2018 The Authors. Published by Elsevier B.V. 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.

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys

DOE PAGES

Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.

2015-12-09

The inclusion of phylogenetic metrics in community ecology has provided insights into important ecological processes, particularly when combined with high-throughput sequencing methods; however, these approaches have not been widely used in studies of fungal communities relative to other microbial groups. Two obstacles have been considered: (1) the internal transcribed spacer (ITS) region has limited utility for constructing phylogenies and (2) most PCR primers that target the large subunit (LSU) ribosomal unit generate amplicons that exceed current limits of high-throughput sequencing platforms. We designed and tested a PCR primer (LR22R) to target approximately 300–400 bp region of the D2 hypervariable regionmore » of the fungal LSU for use with the Illumina MiSeq platform. Both in silico and empirical analyses showed that the LR22R–LR3 pair captured a broad range of fungal taxonomic groups with a small fraction of non-fungal groups. Phylogenetic placement of publically available LSU D2 sequences showed broad agreement with taxonomic classification. Comparisons of the LSU D2 and the ITS2 ribosomal regions from environmental samples and known communities showed similar discriminatory abilities of the two primer sets. Altogether, these findings show that the LR22R–LR3 primer pair has utility for phylogenetic analyses of fungal communities using high-throughput sequencing methods.« less

The impact of zinc oxide nanoparticles on the bacterial microbiome of activated sludge systems

NASA Astrophysics Data System (ADS)

Meli, K.; Kamika, I.; Keshri, J.; Momba, M. N. B.

2016-12-01

The expected growth in nanomaterial applications could result in increased amounts of nanoparticles entering municipal sewer systems, eventually ending up in wastewater treatment plants and therefore negatively affecting microbial populations and biological nutrient removal. The aim of this study was to ascertain the impact of zinc oxide nanoparticles (nZnO) on the bacterial microbiome of an activated sludge system. A metagenomic approach combined with the latest generation Illumina MiSeq platform and RDP pipeline tools were used to identify and classify the bacterial microbiome of the sludge. Results revealed a drastic decrease in the number of operational taxonomic units (OTUs) from 27 737 recovered in the nZnO-free sample to 23 743, 17 733, and 13 324 OTUs in wastewater samples exposed to various concentrations of nZnO (5, 10 and 100 mg/L nZnO, respectively). These represented 12 phyla, 21 classes, 30 orders, 54 families and 51 genera, completely identified at each taxonomic level in the control samples; 7-15-25-28-20 for wastewater samples exposed to 5 mg/L nZnO; 9-15-24-31-23 for those exposed to 10 mg/L and 7-11-19-26-17 for those exposed 100 mg/L nZnO. A large number of sequences could not be assigned to specific taxa, suggesting a possibility of novel species to be discovered.

Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms.

PubMed

Kim, Eunsoo; Sprung, Ben; Duhamel, Solange; Filardi, Christopher; Kyoon Shin, Mann

2016-12-01

The diversity of microbial eukaryotes was surveyed by environmental sequencing from tropical lagoon sites of the South Pacific, collected through the American Museum of Natural History (AMNH)'s Explore21 expedition to the Solomon Islands in September 2013. The sampled lagoons presented low nutrient concentrations typical of oligotrophic waters, but contained levels of chlorophyll a, a proxy for phytoplankton biomass, characteristic of meso- to eutrophic waters. Two 18S rDNA hypervariable sites, the V4 and V8-V9 regions, were amplified from the total of eight lagoon samples and sequenced on the MiSeq system. After assembly, clustering at 97% similarity, and removal of singletons and chimeras, a total of 2741 (V4) and 2606 (V8-V9) operational taxonomic units (OTUs) were identified. Taxonomic annotation of these reads, including phylogeny, was based on a combination of automated pipeline and manual inspection. About 18.4% (V4) and 13.8% (V8-V9) of the OTUs could not be assigned to any of the known eukaryotic groups. Of these, we focused on OTUs that were not divergent and possessed multiple sources of evidence for their existence. Phylogenetic analyses of these sequences revealed more than ten branches that might represent new deeply-branching lineages of microbial eukaryotes, currently without any cultured representatives or morphological information. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

Unbiased Taxonomic Annotation of Metagenomic Samples

PubMed Central

Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

2018-01-01

Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones.

PubMed

Moorhouse-Gann, Rosemary J; Dunn, Jenny C; de Vere, Natasha; Goder, Martine; Cole, Nik; Hipperson, Helen; Symondson, William O C

2018-06-04

DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187-387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.

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.

Indices of benthic community tolerance in contaminated Great Lakes sediments: Relations with sediment contaminant concentrations, sediment toxicity, and the sediment quality triad

USGS Publications Warehouse

Wildhaber, M.L.; Schmitt, C.J.

1998-01-01

We evaluated the toxic-units model developed by Wildhaber and Schmitt (1996) as a predictor of indices of mean tolerance to pollution (i.e., Lenat, 1993; Hilsenhoff, 1987) and other benthic community indices from Great Lakes sediments containing complex mixtures of environmental contaminants (e.g., polychlorinated biphenyls – PCBs, polycyclic aromatic hydrocarbons – PAHs, pesticides, chlorinated dioxins, and metals). Sediment toxic units were defined as the ratio of the estimated pore-water concentration of a contaminant to its chronic toxicity as estimated by U.S. Environmental Protection Agency Ambient Water Quality Criteria (AWQC) or other applicable standard. The total hazard of a sediment to aquatic life was assessed by summing toxic units for all contaminants quantified. Among the benthic community metrics evaluated, total toxic units were most closely correlated with Lenat's (1993) and Hilsenhoff's (1987) indices of community tolerance (TL and TH, respectively); toxic units accounted for 42% TL and 53% TH of variability in community tolerance as measured by Ponar grabs. In contrast, taxonomic richness and Shannon-Wiener diversity were not correlated (P > 0.05) with toxic units. Substitution of order- or family-level identifications for lowest possible (mostly genus- or species-) level identifications in the calculation of TL and TH indices weakened the relationships with toxic units. Tolerance values based on order- and family-level identifications of benthos for artificial substrate samples were more strongly correlated with toxic units than tolerance values for benthos from Ponar grabs. The ability of the toxic-units model to predict the other two components (i.e., laboratory-measured sediment toxicity and benthic community composition) of the Sediment Quality Triad (SQT) may obviate the need for the SQT in some situations.

Taxonomic and Biological Characterization of Steinernema rarum Found in the Southeastern United States

PubMed Central

Nguyen, Khuong B.; Shapiro-Ilan, David I.; Fuxa, James R.; Wood, Bruce W.; Bertolotti, Maria A.; Adams, Byron J.

2006-01-01

Two Steinernema isolates found in Louisiana and Mississippi were later identified as isolates of S. rarum. DNA sequences of ITS regions of the United States isolates are identical with sequences of Argentinean S. rarum strains Samiento and Noetinger and differ by two bases from the Arroyo Cabral isolate from Córdoba, Argentina. SEM observations revealed several new structures in the isolates from the US: female face views have a hexagonal-star perioral disc and eye-shaped lips; some females do not have cephalic papillae; lateral fields of infective juveniles are variable; there are two openings observed close to the posterior edge of the cloaca. Virulence of the US isolates to Anthonomus grandis, Diaprepes abbreviatus, Solenopsis invicta, Coptotermes formosanus, Agrotis ipsilon, Spodoptera frugiperda, and Trichoplusia ni and reproductive potential were evaluated in comparison with other heterorhabditid and steinernematid nematodes. Results such as particularly high virulence to S. frugiperda indicate that the biocontrol potential of the new S. rarum strains merits further study. PMID:19259427

Extremophiles in Household Water Heaters

NASA Astrophysics Data System (ADS)

Wilpiszeski, R.; House, C. H.

2016-12-01

A significant fraction of Earth's microbial diversity comes from species living in extreme environments, but natural extreme environments can be difficult to access. Manmade systems like household water heaters serve as an effective proxy for thermophilic environments that are otherwise difficult to sample directly. As such, we are investigating the biogeography, taxonomic distribution, and evolution of thermophiles growing in domestic water heaters. Citizen scientists collected hot tap water culture- and filter- samples from 101 homes across the United States. We recovered a single species of thermophilic heterotroph from culture samples inoculated from water heaters across the United States, Thermus scotoductus. Whole-genome sequencing was conducted to better understand the distribution and evolution of this single species. We have also sequenced hyper-variable regions of the 16S rRNA gene from whole-community filter samples to identify the broad diversity and distribution of microbial cells captured from each water heater. These results shed light on the processes that shape thermophilic populations and genomes at a spatial resolution that is difficult to access in naturally occurring extreme ecosystems.

Abundance and composition of juvenile corals reveals divergent trajectories for coral assemblages across the United Arab Emirates.

PubMed

Pratchett, Morgan S; Baird, Andrew H; Bauman, Andrew G; Burt, John A

2017-01-30

Marked shifts in the composition of coral assemblages are occurring at many locations, but it is unknown whether these are permanent shifts reinforced by patterns of population replenishment. This study examined the composition of juvenile coral assemblages across the United Arab Emirates (UAE). Densities of juvenile corals varied significantly among locations, but were highest where coral cover was highest. Juvenile coral assemblages within the Persian Gulf were dominated by Porites, while no Acropora were recorded. We expect therefore, continued declines in Acropora abundance, while observed dominance of Porites is likely to persist. In the Oman Sea, Pocillopora was the dominant juvenile coral, with Acropora and Stylophora also recorded. This study shows that taxonomic differences in replenishment are reinforcing temporal shifts in coral composition within the southern Persian Gulf, but not in the Oman Sea. Differences in environmental conditions and disturbance regimes likely explain the divergent responses between regions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Levels of genetic diversity and taxonomic status of Epinephelus species in United Arab Emirates fish markets.

PubMed

Ketchum, Remi N; Dieng, Mame M; Vaughan, Grace O; Burt, John A; Idaghdour, Youssef

2016-04-30

Understanding the patterns of genetic diversity of fish species is essential for marine conservation and management. This is particularly important in the Arabian Gulf where marine life is subject to extreme environmental conditions that could impact genetic diversity. Here we assess genetic diversity of the most commercially important fish in the United Arab Emirates; groupers (Epinephelus spp.). Sequencing of 973 bp mitochondrial DNA from 140 tissue samples collected in four main fish markets revealed 58 haplotypes clustered within three groups. Data analysis revealed the presence of three distinct Epinephelus species being marketed as one species (hammour): Epinephelus coioides, Epinephelus areolatus and Epinephelus bleekeri. We report species-specific genetic markers and demonstrate that all three species exhibit relatively low levels of genetic variation, reflecting the effect of overfishing and environmental pressures. In light of the genetic evidence presented here, conservation and management of groupers in the UAE warrant the implementation of species-specific measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Taxonomic Approach to the Gestalt Theory of Perls

ERIC Educational Resources Information Center

Raming, Henry E.; Frey, David H.

1974-01-01

This study applied content analysis and cluster analysis to the ideas of Fritz Perls to develop a taxonomy of Gestalt processes and goals. Summaries of the typal groups or clusters were written and the implications of taxonomic research in counseling discussed. (Author)

Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications

EPA Science Inventory

Species-level identifications are difficult or impossible for many larval aquatic macroinvertebrates. We described the taxonomic composition of macroinvertebrate communities from 5 coastal streams in 3 neighboring catchments in southern California. We compared taxonomic identific...

Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data

PubMed Central

Häser, Annette

2016-01-01

Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women. PMID:27957401

Investigating the effect of forestry on leaf-litter arthropods (Algonquin Park, Ontario, Canada)

PubMed Central

Boyd, Amanda; Chan, Amelia; Clout, Simonne; des Brisay, Paulson; Dolson, Sarah; Eagalle, Thanushi; Espinola, Sean; Fairweather, Aaron; Frank, Sydney; Fruetel, Christopher; Garrido Cortes, Cristina; Hall, James; Ho, Chris; Matczak, Eryk; McCubbin, Sandra; McPhee, Megan; Pare, Kate A.; Paris, Kelsie; Richard, Ellen; Roblin, Morgan; Russell, Cassandra; Snyder, Ryan; Trombley, Carolyn; Schmitt, Tyler; Vandermeer, Caitlin; Warne, Connor; Welch, Natasha; Xavier-Blower, Chelsie

2017-01-01

Arthropods are the most diverse taxonomic group of terrestrial eukaryotes and are sensitive to physical alterations in their environment such as those caused by forestry. With their enormous diversity and physical omnipresence, arthropods could be powerful indicators of the effects of disturbance following forestry. When arthropods have been used to measure the effects of disturbance, the total diversity of some groups is often found to increase following forestry. However, these findings are frequently derived using a coarse taxonomic grain (family or order) to accommodate for various taxonomic impediments (including cryptic diversity and poorly resourced taxonomists). Our intent with this work was to determine the diversity of arthropods in and around Algonquin Park, and how this diversity was influenced by disturbance (in this case, forestry within the past 25 years). We used DNA barcode-derived diversity estimates (Barcode Index Number (BIN) richness) to avoid taxonomic impediments and as a source of genetic information with which we could conduct phylogenetic estimates of diversity (PD). Diversity patterns elucidated with PD are often, but not always congruent with taxonomic estimates–and departures from these expectations can help clarify disturbance effects that are hidden from richness studies alone. We found that BIN richness and PD were greater in disturbed (forested) areas, however when we controlled for the expected relationship between PD and BIN richness, we found that cut sites contained less PD than expected and that this diversity was more phylogenetically clustered than would be predicted by taxonomic richness. While disturbance may cause an evident increase in diversity, this diversity may not reflect the full evolutionary history of the assemblage within that area and thus a subtle effect of disturbance can be found decades following forestry. PMID:28575022

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.

Combining Taxonomic and Functional Approaches to Unravel the Spatial Distribution of an Amazonian Butterfly Community.

PubMed

Graça, Márlon B; Morais, José W; Franklin, Elizabeth; Pequeno, Pedro A C L; Souza, Jorge L P; Bueno, Anderson Saldanha

2016-04-01

This study investigated the spatial distribution of an Amazonian fruit-feeding butterfly assemblage by linking species taxonomic and functional approaches. We hypothesized that: 1) vegetation richness (i.e., resources) and abundance of insectivorous birds (i.e., predators) should drive changes in butterfly taxonomic composition, 2) larval diet breadth should decrease with increase of plant species richness, 3) small-sized adults should be favored by higher abundance of birds, and 4) communities with eyespot markings should be able to exploit areas with higher predation pressure. Fruit-feeding butterflies were sampled with bait traps and insect nets across 25 km(2) of an Amazonian ombrophilous forest in Brazil. We measured larval diet breadth, adult body size, and wing marking of all butterflies. Our results showed that plant species richness explained most of the variation in butterfly taxonomic turnover. Also, community average diet breadth decreased with increase of plant species richness, which supports our expectations. In contrast, community average body size increased with the abundance of birds, refuting our hypothesis. We detected no influence of environmental gradients on the occurrence of species with eyespot markings. The association between butterfly taxonomic and functional composition points to a mediator role of the functional traits in the environmental filtering of butterflies. The incorporation of the functional approach into the analyses allowed for the detection of relationships that were not observed using a strictly taxonomic perspective and provided an extra insight into comprehending the potential adaptive strategies of butterflies. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

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 gut microbiota, bile acids and their correlation in primary sclerosing cholangitis associated with inflammatory bowel disease.

PubMed

Torres, J; Palmela, C; Brito, H; Bao, X; Ruiqi, H; Moura-Santos, P; Pereira da Silva, J; Oliveira, A; Vieira, C; Perez, K; Itzkowitz, S H; Colombel, J F; Humbert, L; Rainteau, D; Cravo, M; Rodrigues, C M; Hu, J

2018-02-01

Patients with primary sclerosing cholangitis associated with inflammatory bowel disease (PSC-IBD) have a very high risk of developing colorectal neoplasia. Alterations in the gut microbiota and/or gut bile acids could account for the increase in this risk. However, no studies have yet investigated the net result of cholestasis and a potentially altered bile acid pool interacting with a dysbiotic gut flora in the inflamed colon of PSC-IBD. The aim of this study was to compare the gut microbiota and stool bile acid profiles, as well as and their correlation in patients with PSC-IBD and inflammatory bowel disease alone. Thirty patients with extensive colitis (15 with concomitant primary sclerosing cholangitis) were prospectively recruited and fresh stool samples were collected. The microbiota composition in stool was profiled using bacterial 16S rRNA sequencing. Stool bile acids were assessed by high-performance liquid chromatography tandem mass spectrometry. The total stool bile acid pool was significantly reduced in PSC-IBD. Although no major differences were observed in the individual bile acid species in stool, their overall combination allowed a good separation between PSC-IBD and inflammatory bowel disease. Compared with inflammatory bowel disease alone, PSC-IBD patients demonstrated a different gut microbiota composition with enrichment in Ruminococcus and Fusobacterium genus compared with inflammatory bowel disease. At the operational taxonomic unit level major shifts were observed within the Firmicutes (73%) and Bacteroidetes phyla (17%). Specific microbiota-bile acid correlations were observed in PSC-IBD, where 12% of the operational taxonomic units strongly correlated with stool bile acids, compared with only 0.4% in non-PSC-IBD. Patients with PSC-IBD had distinct microbiota and microbiota-stool bile acid correlations as compared with inflammatory bowel disease. Whether these changes are associated with, or may predispose to, an increased risk of colorectal neoplasia needs to be further clarified.

Taxonomic and geographic patterns of decline for threatened and endangered species in the United States.

PubMed

Leidner, Allison K; Neel, Maile C

2011-08-01

Species listed under the U.S. Endangered Species Act (i.e., listed species) have declined to the point that the probability of their extinction is high. The decline of these species, however, may manifest itself in different ways, including reductions in geographic range, number of populations, or overall abundance. Understanding the pattern of decline can help managers assess extinction probability and define recovery objectives. Although quantitative data on changes in geographic range, number of populations, and abundance usually do not exist for listed species, more often qualitative data can be obtained. We used qualitative data in recovery plans for federally listed species to determine whether each listed species declined in range size, number of populations, or abundance relative to historical levels. We calculated the proportion of listed species in each state (or equivalent) that declined in each of those ways. Nearly all listed species declined in abundance, and range size or number of populations declined in approximately 80% of species for which those data were available. Patterns of decline, however, differed taxonomically and geographically. Declines in range were more common among vertebrates than plants, whereas population extirpations were more common among plants. Invertebrates had high incidence of range and population declines. Narrowly distributed plants and invertebrates may be subject to acute threats that may result in population extirpations, whereas vertebrates may be affected by chronic threats that reduce the extent and size of populations. Additionally, in the eastern United States and U.S. coastal areas, where the level of land conversion is high, a greater percentage of species' ranges declined and more populations were extirpated than in other areas. Species in the Southwest, especially plants, had fewer range and population declines than other areas. Such relations may help in the selection of species' recovery criteria. © 2011 Society for Conservation Biology.

The necessity of DNA taxonomy to reveal cryptic diversity and spatial distribution of meiofauna, with a focus on Nemertea.

PubMed

Leasi, Francesca; Norenburg, Jon L

2014-01-01

Meiofauna represent one of the most abundant and diverse communities in marine benthic ecosystems. However, an accurate assessment of diversity at the level of species has been and remains challenging for these microscopic organisms. Therefore, for many taxa, especially the soft body forms such as nemerteans, which often lack clear diagnostic morphological traits, DNA taxonomy is an effective means to assess species diversity. Morphological taxonomy of Nemertea is well documented as complicated by scarcity of unambiguous character states and compromised by diagnoses of a majority of species (and higher clades) being inadequate or based on ambiguous characters and character states. Therefore, recent studies have advocated for the primacy of molecular tools to solve the taxonomy of this group. DNA taxonomy uncovers possible hidden cryptic species, provides a coherent means to systematize taxa in definite clades, and also reveals possible biogeographic patterns. Here, we analyze diversity of nemertean species by considering the barcode region of the mitochondrial gene Cytochrome Oxidase subunit I (COI) and different species delineation approaches in order to infer evolutionarily significant units. In the aim to uncover actual diversity of meiofaunal nemerteans across different sites in Central America, COI sequences were obtained for specimens assigned here to the genera Cephalothrix, Ototyphlonemertes, and Tetrastemma-like worms, each commonly encountered in our sampling. Additional genetic, taxonomic, and geographic data of other specimens belonging to these genera were added from GenBank. Results are consistent across different DNA taxonomy approaches, and revealed (i) the presence of several hidden cryptic species and (ii) numerous potential misidentifications due to traditional taxonomy. (iii) We additionally test a possible biogeographic pattern of taxonomic units revealed by this study, and, except for a few cases, the putative species seem not to be widely distributed, in contrast to what traditional taxonomy would suggest for the recognized morphotypes.

Three operational taxonomic units of Eimeria are common in Nigerian chickens and may undermine effective molecular diagnosis of coccidiosis.

PubMed

Jatau, Isa D; Lawal, Idris A; Kwaga, Jacob K P; Tomley, Fiona M; Blake, Damer P; Nok, Andrew J

2016-06-04

Chicken is fast becoming the world's most consumed meat. As a consequence poultry health is more important now than ever before, with pathogens of chickens recognised as serious threats to food security. One such threat are Eimeria species parasites, protozoa which can cause the disease coccidiosis. Eimeria can compromise economic poultry production and chicken welfare, and have serious consequences for poor livestock keepers. Seven Eimeria species that infect chickens are recognised with a global enzootic distribution. More recently three cryptic Operational Taxonomic Units (OTUx, y and z) have been described in populations of Eimeria recovered from chickens in Australia. Two of the three OTUs have also been detected in sub-Saharan Africa, but their occurrence, pathology and the risk they pose is largely unknown. Nigeria has witnessed a dramatic expansion in poultry production and is now the largest poultry producer in Africa. Here, faecal samples collected from nine of 12 commercial chicken farms sampled in Kaduna state, Nigeria, were found to contain eimerian oocysts. After amplification by in vivo propagation all three cryptic OTU genotypes were detected using polymerase chain reaction (PCR), including OTUy for the first time outside of Australia. Comparison with a widely used, established Eimeria species-specific PCR assay revealed failure to detect the OTU genotypes. All three of the Eimeria OTU genotypes appear to be common in north-western Nigeria. The failure of a leading species-specific molecular assay to detect these genotypes indicates a risk of false negative Eimeria diagnosis when using molecular tools and suggests that the spatial occurrence of each OTU may be far wider than has been recognised. The risk posed by these novel genotypes is unknown, but it is clear that a better understanding of Eimeria occurrence is required together with the validation of effective diagnostics.

Microbiome Associated with Severe Caries in Canadian First Nations Children.

PubMed

Agnello, M; Marques, J; Cen, L; Mittermuller, B; Huang, A; Chaichanasakul Tran, N; Shi, W; He, X; Schroth, R J

2017-11-01

Young Indigenous children in North America suffer from a higher degree of severe early childhood caries (S-ECC) than the general population, leading to speculation that the etiology and characteristics of the disease may be distinct in this population. To address this knowledge gap, we conducted the first microbiome analysis of an Indigenous population using modern molecular techniques. We investigated the caries-associated microbiome among Canadian First Nations children with S-ECC. Thirty First Nations children <72 mo of age with S-ECC and 20 caries-free children were recruited in Winnipeg, Canada. Parents or caregivers completed a questionnaire on general and dental health, diet, and demographics. The plaque microbiome was investigated by sequencing the 16S rRNA gene. Sequences were clustered into operational taxonomic units and taxonomy assigned via the Human Oral Microbiome Database, then analyzed at the community level with alpha and beta diversity measures. Compared with those who were caries free, children with S-ECC came from households with lower income; they were more likely to live in First Nations communities and were more likely to be bottle-fed; and they were weaned from the bottle at a later age. The microbial communities of the S-ECC and caries-free groups did not differ in terms of species richness or phylogenetic diversity. Beta diversity analysis showed that the samples significantly clustered into groups based on caries status. Twenty-eight species-level operational taxonomic units were significantly different between the groups, including Veillonella HOT 780 and Porphyromonas HOT 284, which were 4.6- and 9-fold higher, respectively, in the S-ECC group, and Streptococcus gordonii and Streptococcus sanguinis, which were 5- and 2-fold higher, respectively, in the caries-free group. Extremely high levels of Streptococcus mutans were detected in the S-ECC group. Overall, First Nations children with S-ECC have a significantly different plaque microbiome than their caries-free counterparts, with the S-ECC group containing higher levels of known cariogenic organisms.

Candida Berkhout (1923)

USDA-ARS?s Scientific Manuscript database

This chapter describes the 314 species assigned to the genus Candida and is to be published in the Yeasts, A Taxonomic Study, 5th edition. Ascomycete yeasts that do not form ascosporic state are assigned to the genus Candida, which is a highly polyphyletic taxonomic form genus. Assigned species in...

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 ...

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.

Within-species patterns challenge our understanding of the leaf economics spectrum.

PubMed

Anderegg, Leander D L; Berner, Logan T; Badgley, Grayson; Sethi, Meera L; Law, Beverly E; HilleRisLambers, Janneke

2018-05-01

The utility of plant functional traits for predictive ecology relies on our ability to interpret trait variation across multiple taxonomic and ecological scales. Using extensive data sets of trait variation within species, across species and across communities, we analysed whether and at what scales leaf economics spectrum (LES) traits show predicted trait-trait covariation. We found that most variation in LES traits is often, but not universally, at high taxonomic levels (between families or genera in a family). However, we found that trait covariation shows distinct taxonomic scale dependence, with some trait correlations showing opposite signs within vs. across species. LES traits responded independently to environmental gradients within species, with few shared environmental responses across traits or across scales. We conclude that, at small taxonomic scales, plasticity may obscure or reverse the broad evolutionary linkages between leaf traits, meaning that variation in LES traits cannot always be interpreted as differences in resource use strategy. © 2018 John Wiley & Sons Ltd/CNRS.

A taxonomic index, with names of descriptive authorities of termite genera and species: An accompaniment to Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, Editors. 2011. Springer, Dordrecht. 576 pp.)

PubMed Central

Bignell, D. E.; Jones, D. T.

2014-01-01

Abstract Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, (Editors), Springer, Dordrecht, 576pp, ISBN 978-90-481-3976-7, e-ISBN 978-90-481-3977-4, DOI 10.1007/978-90-481-3977-4) was published in 2011. With the agreement of the publishers, we give a taxonomic index of the book comprising 494 termite entries, 103 entries of other multicellular animal species mentioned as associates or predators of termites, with 9 fungal, 60 protist, and 64 prokaryote identities, which are listed as termite symbionts ( sensu stricto ). In addition, we add descriptive authorities for living (and some fossil) termite genera and species. Higher taxonomic groupings for termites are indicated by 25 code numbers. Microorganisms (prokaryotes, protists, and fungi) are listed separately, using broad modern taxonomic affiliations from the contemporary literature of bacteriology, protozoology, and mycology. PMID:25368037

Taxonomic and Thematic Semantic Systems

PubMed Central

Mirman, Daniel; Landrigan, Jon-Frederick; Britt, Allison E.

2017-01-01

Object concepts are critical for nearly all aspects of human cognition, from perception tasks like object recognition, to understanding and producing language, to making meaningful actions. Concepts can have two very different kinds of relations: similarity relations based on shared features (e.g., dog – bear), which are called “taxonomic” relations, and contiguity relations based on co-occurrence in events or scenarios (e.g., dog – leash), which are called “thematic” relations. Here we report a systematic review of experimental psychology and cognitive neuroscience evidence of this distinction in the structure of semantic memory. We propose two principles that may drive the development of distinct taxonomic and thematic semantic systems: (1) differences between which features determine taxonomic vs. thematic relations and (2) differences in the processing required to extract taxonomic vs. thematic relations. This review brings together distinct threads of behavioral, computational, and neuroscience research on semantic memory in support of a functional and neural dissociation, and defines a framework for future studies of semantic memory. PMID:28333494

A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites.

PubMed

Côté, Nathalie M L; Daligault, Julien; Pruvost, Mélanie; Bennett, E Andrew; Gorgé, Olivier; Guimaraes, Silvia; Capelli, Nicolas; Le Bailly, Matthieu; Geigl, Eva-Maria; Grange, Thierry

2016-01-01

Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

PubMed

Manor, Ohad; Borenstein, Elhanan

2017-02-08

Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Analysis of composition-based metagenomic classification.

PubMed

Higashi, Susan; Barreto, André da Motta Salles; Cantão, Maurício Egidio; de Vasconcelos, Ana Tereza Ribeiro

2012-01-01

An essential step of a metagenomic study is the taxonomic classification, that is, the identification of the taxonomic lineage of the organisms in a given sample. The taxonomic classification process involves a series of decisions. Currently, in the context of metagenomics, such decisions are usually based on empirical studies that consider one specific type of classifier. In this study we propose a general framework for analyzing the impact that several decisions can have on the classification problem. Instead of focusing on any specific classifier, we define a generic score function that provides a measure of the difficulty of the classification task. Using this framework, we analyze the impact of the following parameters on the taxonomic classification problem: (i) the length of n-mers used to encode the metagenomic sequences, (ii) the similarity measure used to compare sequences, and (iii) the type of taxonomic classification, which can be conventional or hierarchical, depending on whether the classification process occurs in a single shot or in several steps according to the taxonomic tree. We defined a score function that measures the degree of separability of the taxonomic classes under a given configuration induced by the parameters above. We conducted an extensive computational experiment and found out that reasonable values for the parameters of interest could be (i) intermediate values of n, the length of the n-mers; (ii) any similarity measure, because all of them resulted in similar scores; and (iii) the hierarchical strategy, which performed better in all of the cases. As expected, short n-mers generate lower configuration scores because they give rise to frequency vectors that represent distinct sequences in a similar way. On the other hand, large values for n result in sparse frequency vectors that represent differently metagenomic fragments that are in fact similar, also leading to low configuration scores. Regarding the similarity measure, in contrast to our expectations, the variation of the measures did not change the configuration scores significantly. Finally, the hierarchical strategy was more effective than the conventional strategy, which suggests that, instead of using a single classifier, one should adopt multiple classifiers organized as a hierarchy.

The taxonomic implication of frontal tubercles in Polypedilum subgenera diagnoses, with re-description of Polypedilum isigabeceum Sasa & Suzuki (Diptera, Chironomidae).

PubMed

Yamamoto, Nao; Yamamoto, Masaru

2016-11-15

Polypedilum isigabeceum Sasa et Suzuki, 2000 was described as belonging to subgenus Polypedilum s. str. However, if we accept the conclusion of Sæther et al. (2010), the species might be placed into Kribionympha with P. unagiquartum Sasa, 1985 because of the presence of distinct frontal tubercles in the adult males. However, other taxonomic characters do not support their treatment. P. isigabeceum is re-described and reconfirmed to be assigned to the subgenus Polypedilum s. str. The taxonomic meaning of frontal tubercles is discussed for defining the subgeneric rankings within genus Polypedilum.

Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

EPA Science Inventory

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 feedin...

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...

CONCORDANCE OF TAXONOMIC COMPOSITION PATTERNS ACROSS MULTIPLE LAKE ASSEMBLAGES: EFFECTS OF SCALE, BODY SIZE, AND LAND USE

EPA Science Inventory

We assessed environmental gradients and the extent to which they induced concordant patterns of taxonomic composition among benthic macroinvertebrate, riparian bird, sedimentary diatom, fish, and pelagic zooplankton assemblages in 186 northeastern U.S.A. lakes. Human population ...

THE EFFECTS OF MACROINVERTEBRATE TAXONOMIC RESOLUTION IN LARGE LANDSCAPE BIOASSESSMENTS: AN EXAMPLE FROM THE MID-ATLANTIC HIGHLANDS, USA

EPA Science Inventory

The macroinvertebrate taxonomic resolution needed for detecting human impacts on stream ecosystems draws continued attention from stream ecologists. During late spring 1993-1995, the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP) sam...

Documenting taxonomic data quality for field fish identifications: a proposal for national surveys

EPA Science Inventory

The U.S. Environmental Protection Agency is in the midst of a multiyear series of natinal surveys of water resource conditions. Because communicating ecological condition is the primary objective of the surveys, quantitative biological indicators are key. Thus, if raw taxonomic d...

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...

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.

Contrasting responses of functional diversity to major losses in taxonomic diversity.

PubMed

Edie, Stewart M; Jablonski, David; Valentine, James W

2018-01-23

Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.

PubMed

Zhang, Ximei; Johnston, Eric R; Barberán, Albert; Ren, Yi; Lü, Xiaotao; Han, Xingguo

2017-10-01

Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity. © 2017 John Wiley & Sons Ltd.

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.

Thesis Abstract Morphological and phylogeographic analysis of Brazilian tortoises (Testudinidae).

PubMed

Silva, T L; Venancio, L P R; Bonini-Domingos, C R

2015-12-29

The discriminative potentials of biogeography, vocalization, morphology, cytogenetics, hemoglobin, and molecular profiling of cytochrome b as taxonomic techniques for differentiating Brazilian tortoises were evaluated in this study. In Brazil, two species of tortoises are described, Chelonoidis carbonarius and Chelonoidis denticulatus. However, in the present study, some animals that were initially recognized based on morphological characters and coloring did not correspond to the typical pattern of C. carbonarius; these animals were classified as morphotypes 1 and 2. It was proposed that these morphotypes are differentiated species, and they should not be considered as a single taxonomic unit with C. carbonarius. Tortoises analyzed were provided by the National Institute for Amazonian Research (INPA); the Emilio Goeldi Museum, PA; municipal zoos in São José do Rio Preto, SP, and Araçatuba, SP; and the Reginaldo Uvo Leone breeding farm for Wild and Exotic Animals, Tabapuã, SP. Based on the data obtained using biogeographic evaluation of specimens in the literature, it was found that C. carbonarius is distributed in the Northeast Region of Brazil, and no animal of this pattern was observed in the investigated collections. On the other hand, C. denticulatus is found in all the states of the Legal Amazonia. In addition, isolated individual records of this species exist in the Atlantic Forest in Espírito Santo and Rio de Janeiro and in the Midwest Region composed of the states of Goiás, Mato Grosso, and Mato Grosso do Sul. In the Northeast Region, C. denticulatus occurs in the State of Bahia. Morphotype 1 has a wider geographical distribution than C. carbonarius, possibly because of several distribution reports associated with C. carbonarius, indicating erroneous association of morphotype 1 as a single taxonomic unit with C. carbonarius. Morphotype 2 is found only in the states of Pará, Maranhão, and Piauí. These biogeographic data indicate that the distribution of C. carbonarius can partially be explained by the fact that all the morphotypes are considered as a single taxonomic unit. Behavioral aspects such as intraspecific communication may be as reliable as morphological or molecular data for inferring evolutionary relationships. Analysis of the physical characteristics of vocalization [fundamental frequency (Hz), interval between notes (s), duration of each note (s), and number of notes from each vocalization] between C. carbonarius and morphotype 1 revealed statistically significant differences in the interval between notes (s) (P = 0.0000); duration of each note (s) (P = 0.0000); frequency of notes (Hz) (P = 0.0009); and number of notes (P = 0.0002). The results of preference experiments using sound stimulus were inconclusive with respect to species-specific vocalization preference; only females of C. carbonarius showed intraspecific vocalization preference, indicating possible reproductive isolation mechanisms. To explore the presence of sexual dimorphism and morphological differences between C. denticulatus, C. carbonarius, and morphotype 1, descriptive statistics to analyze the data obtained for the investigated measures were used. Two sets of analysis were conducted - the first for each group, to compare the sexes; and the second for each sex, to compare the groups. To examine the interspecific variation in size and shape, a correlation matrix inprincipal component analysis was used. Next, I used factor analysis to rank the features showing >0.75 correlation in the differentiation between the sexes. The results were consistent with the hypothesis that morphotype 1 corresponds to a new species, because it differs from the species pattern in terms of morphology, coloring, and sexual dimorphism. The results of classical cytogenetic analysis - to differentiate C. denticulatus, C. carbonarius, and morphotype 1 - revealed no consistent data that would enable its use as a taxonomic parameter. Conventional Giemsa staining revealed a diploid chromosome number of 2n = 52 for all the evaluated groups. The patterns obtained using chromosomal banding techniques showed high similarity and low reproducibility. Moreover, the sensitivity and resolution were insufficient to enable differentiation between the three groups, implying the existence of conserved characteristics of the karyotype in Testudinidae. To establish a hemoglobin profile for C. denticulatus, C. carbonarius, and morphotype 1, and to visualize the hemoglobin fractions of each group, I conducted acid and alkaline electrophoreses. The results of high-performance liquid chromatography revealed percentage differences in the hemoglobin fractions. In addition, electrophoresis of the polypeptide chains under acid and alkaline pH conditions showed the globin composition of each fraction. The observed differences in the chromatographic profile between C. carbonarius and morphotype 1 with respect to C. denticulatus validated the technique as an additional method for elucidating taxonomic issues in Testudinidae. The similarities observed in the hemoglobin profiles of C. carbonarius and morphotype 1 suggest recent separation between these groups. Alignment of mitochondrial DNA cytochrome b fragments revealed a degree of homogeneity among the C. denticulatus samples and the sequences published in the literature, indicating low genetic variability of the mitochondrial DNA cytochrome b fragment for this species. In contrast, the sequences of the mitochondrial DNA cytochrome b fragments from C. carbonarius and morphotypes 1 and 2 differed from those available in the published literature databases, indicating a variable genetic structure. This may be because it does not consider taxonomic divisions within C. carbonarius. Phylogenetic analysis did not reveal an appropriate phylogenetic signal for differentiating C. carbonarius and morphotypes 1 and 2. However, this analysis did differentiate C. denticulatus, indicating that the separation of C. carbonarius and morphotypes 1 and 2 is more recent than the separation of C. denticulatus and C. carbonarius. Owing to the problems associated with the use of cytochrome b in phylogenetic analysis, the polytomy observed for C. carbonarius and morphotypes 1 and 2 does not exclude the hypothesis that these samples represent different species. It is possible that the inclusion of morphological, behavioral, and hemoglobin profile data in a mixed matrix with the molecular data would enable the separation of morphotypes 1 and 2 as monophyletic species. This analysis would require data regarding external groups, to facilitate a more robust phylogenetic analysis, thereby enabling greater taxonomic resolution. In view of the differences in the biogeographical pattern, vocalization, specific-sound preference, and morphology found in the present study, I propose that morphotype 1 should be considered a new species. Data regarding the conservation status of natural tortoise populations in Brazil should be reviewed, because of the intensive human pressure on this species. There are no private or public plans for the conservation or recovery of natural tortoise populations. Hence, it is very likely that these animals have a more endangered status than that reported in the literature.

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...

Phylogenetic relationships and taxonomic revision of Paranoplocephala Lühe, 1910 sensu lato (Cestoda, Cyclophyllidea, Anoplocephalidae)

USDA-ARS?s Scientific Manuscript database

An extensive phylogenetic analysis and genus-level taxonomic revision of Paranoplocephala Lühe, 1910 -like cestodes (Cyclophyllidea, Anoplocephalidae) are presented. The phylogenetic analysis is based on DNA sequences of two partial mitochondrial genes, i.e. cytochrome c oxidase subunit 1 (cox1) and...

Species delimitations in plants: lessons learned from potato taxonomy by a practicing taxonomist

USDA-ARS?s Scientific Manuscript database

Solanum section Petota has been the subject of intensive taxonomic work since the description of the cultivated potato in 1753. In total, there are 494 epithets for wild taxa and 626 epithets for cultivated taxa. Different taxonomists applied various taxonomic philosophies and species concepts to th...

40 CFR 725.12 - Identification of microorganisms for Inventory and other listing purposes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... for the purpose of taxonomic classification. Upon EPA's request to the submitter, data supporting the taxonomic designation must be provided to EPA. The genetic history of the recipient microorganism should be... distinguishing genotypic characteristics of a microorganism, such as the identity of the introduced genetic...

Collaborative Processes in Species Identification Using an Internet-Based Taxonomic Resource

ERIC Educational Resources Information Center

Kontkanen, Jani; Kärkkäinen, Sirpa; Dillon, Patrick; Hartikainen-Ahia, Anu; Åhlberg, Mauri

2016-01-01

Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are…

A Probabilistic Model of Cross-Categorization

ERIC Educational Resources Information Center

Shafto, Patrick; Kemp, Charles; Mansinghka, Vikash; Tenenbaum, Joshua B.

2011-01-01

Most natural domains can be represented in multiple ways: we can categorize foods in terms of their nutritional content or social role, animals in terms of their taxonomic groupings or their ecological niches, and musical instruments in terms of their taxonomic categories or social uses. Previous approaches to modeling human categorization have…

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...

A detailed taxonomy of Upper Cretaceous and lower Tertiary Crassatellidae in the Eastern United States; an example of the nature of extinction at the boundary

USGS Publications Warehouse

Wingard, G. Lynn

1993-01-01

Current theories on the causes of extinction at the CretaceousTertiary boundary have been based on previously published data; however, few workers have stopped to ask the question, 'How good is the basic data set?' To test the accuracy of the published record, a quantitative and qualitative analysis of the Crassatellidae (Mollusca, Bivalvia) of the Gulf and Mid-Atlantic Coastal Plains of the United States for the Upper Cretaceous and lower Tertiary was conducted. Thirty-eight species names and four generic names are used in publications for the Crassatellidae within the geographic and stratigraphic constraints of this analysis. Fourteen of the 38 species names are represented by statistically valid numbers of specimens and were tested by using canonical discriminant analysis. All 38 names, with the exception of 1 invalid name and 4 names for which no representative specimen could be located, were evaluated qualitatively. The results show that the published fossil record is highly inaccurate. Only 8 valid, recognizable species exist in the Crassatellidae within the limits of this study, 14 names are synonymized, and 11 names are represented by indeterminate molds or poorly preserved specimens. Three of the four genera are well founded; the fourth is based on the juvenile of another genus and therefore synonymized. This detailed taxonomic analysis of the Crassatellidae illustrates that the published fossil record is not reliable. Calculations of evolutionary and paleobiologic significance based on poorly defined, overly split fossil groups, such as the Crassatellidae, are biased in the following ways: Rates of evolution and extinction are higher, Faunal turnover at mass extinctions appears more catastrophic, Species diversity is high, Average species durations are shortened, and Geographic ranges are restricted. The data on the taxonomically standardized Crassatellidae show evolutionary rates one-quarter to one-half that of the published fossil record; faunal change at the Cretaceous-Tertiary boundary that was not catastrophic; a constant number of species on each side of the Cretaceous-Tertiary boundary; a decrease in abundance in the Tertiary; and lower species diversity, longer average species durations, and expanded geographic ranges. Similar detailed taxonomic studies need to be conducted on other groups of organisms to test the patterns illustrated for the Crassatellidae and to determine the extent and direction of the bias in the published fossil record. Answers to our questions about evolutionary change cannot be found in the literature but rather with the fossils themselves. Evolution and extinction occur within small populations of species groups, and it is only through detailed analysis of these groups that we can achieve an understanding of the causes and effects of evolution and extinction.

RESPONSE OF PHENOLIC METABOLISM INDUCED BY ALUMINIUM TOXICITY IN FAGOPYRUM ESCULENTUM MOENCH. PLANTS.

PubMed

Smirnov, O E; Kosyan, A M; Kosyk, O I; Taran, N Yu

2015-01-01

Buckwheat genus (Fagopyrum Mill.) is one of the aluminium tolerant taxonomic units of plants. The aim of the study was an evaluation of the aluminium (50 μM effect on phenolic accumulation in various parts of buckwheat plants (Fagopyrum esculentum Moench). Detection of increasing of total phenolic content, changes in flavonoid and anthocyanin content and phenylalanine ammonia-lyase activity (PAL) were revealed over a period of 10 days of exposure to aluminium. The most significant effects of aluminium treatment on phenolic compounds accumulation were total phenolic content increasing (by 27.2%) and PAL activity rising by 2.5 times observed in leaves tissues. Received data could be helpful to understand the aluminium tolerance principles and relationships of phenolic compounds to aluminium phytotoxicity.

Genetic relationships between blowflies (Calliphoridae) of forensic importance.

PubMed

Stevens, J; Wall, R

2001-08-15

Phylogenetic relationships among blowfly (Calliphoridae) species of forensic importance are explored using DNA sequence data from the large sub-unit (lsu, 28S) ribosomal RNA (rRNA) gene, the study includes representatives of a range of calliphorid species commonly encountered in forensic analysis in Britain and Europe. The data presented provide a basis to define molecular markers, including the identification of highly informative intra-sequence regions, which may be of use in the identification of larvae for forensic entomology. Phylogenetic analysis of the sequences also provides new insights into the different evolutionary patterns apparent within the family Calliphoridae which, additionally, can provide a measure of the degree of genetic variation likely to be encountered within taxonomic groups of differing forensic utility.

Uniting Tricholoma sulphureum and T. bufonium.

PubMed

Comandini, Ornella; Haug, Ingeborg; Rinaldi, Andrea C; Kuyper, Thomas W

2004-10-01

The taxonomic status and relationship of Tricholoma sulphureum and the similar T. bufonium were investigated using different sets of characters. These included morphological data on fruit bodies, ecological and chorological data, and analysis of the sequence data obtained for the ITS of basidiomes of different ecological and geographic origin. Moreover, the ectomycorrhizas formed by T. bufonium on Abies alba and Quercus sp. were characterised, and anatomical features compared with those of T. sulphureum mycorrhizas on coniferous and broad-leaved host trees. Our results revealed extensive ITS variation in members of the T. sulphureum group, but this variation was not correlated with morphology, ecology, or geographical distribution. We conclude that T. bufonium cannot be maintained as an autonomous taxon and should be treated as an infraspecific variant of T. sulphureum.

A movement ecology paradigm for unifying organismal movement research

PubMed Central

Nathan, Ran; Getz, Wayne M.; Revilla, Eloy; Holyoak, Marcel; Kadmon, Ronen; Saltz, David; Smouse, Peter E.

2008-01-01

Movement of individual organisms is fundamental to life, quilting our planet in a rich tapestry of phenomena with diverse implications for ecosystems and humans. Movement research is both plentiful and insightful, and recent methodological advances facilitate obtaining a detailed view of individual movement. Yet, we lack a general unifying paradigm, derived from first principles, which can place movement studies within a common context and advance the development of a mature scientific discipline. This introductory article to the Movement Ecology Special Feature proposes a paradigm that integrates conceptual, theoretical, methodological, and empirical frameworks for studying movement of all organisms, from microbes to trees to elephants. We introduce a conceptual framework depicting the interplay among four basic mechanistic components of organismal movement: the internal state (why move?), motion (how to move?), and navigation (when and where to move?) capacities of the individual and the external factors affecting movement. We demonstrate how the proposed framework aids the study of various taxa and movement types; promotes the formulation of hypotheses about movement; and complements existing biomechanical, cognitive, random, and optimality paradigms of movement. The proposed framework integrates eclectic research on movement into a structured paradigm and aims at providing a basis for hypothesis generation and a vehicle facilitating the understanding of the causes, mechanisms, and spatiotemporal patterns of movement and their role in various ecological and evolutionary processes. ”Now we must consider in general the common reason for moving with any movement whatever.“ (Aristotle, De Motu Animalium, 4th century B.C.) PMID:19060196

Annotated checklist of the recent and extinct pythons (Serpentes, Pythonidae), with notes on nomenclature, taxonomy, and distribution

PubMed Central

Schleip, Wulf D.; O’Shea, Mark

2010-01-01

Abstract McDiarmid et al. (1999) published the first part of their planned taxonomic catalog of the snakes of the world. Since then, several new python taxa have been described in both the scientific literature and non-peer-reviewed publications. This checklist evaluates the nomenclatural status of the names and discusses the taxonomic status of the new taxa, and aims to continue the work of McDiarmid et al. (1999) for the family Pythonidae, covering the period 1999 to 2010. Numerous new taxa are listed, and where appropriate recent synonymies are included and annotations are made. A checklist and a taxonomic identification key of valid taxa are provided. PMID:21594030

Distribution of taxonomic classes and the compositional structure of the asteroid belt

NASA Technical Reports Server (NTRS)

Gradie, Jonathan C.; Chapman, Clark R.; Tedesco, Edward F.

1989-01-01

This paper reviews previous studies on the distribution of the asteroid taxonomic classes and analyzes the techniques, results, and interpretations of these studies, with special attention given to the strong and weak points of these studies and the important caveat for their interpretation. It is concluded that, in spite of the differences in class definition, the rather ordered heliocentric distribution of the composition is real and must be due to either primordial, evolutionary, or dynamical processes, or to a combination of all three. In general, the distribution of asteroid taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner asteroid belt, and low-albedo asteroids prevalent in the outer belt and beyond.

At the Feet of the Fortress: Analysis of Inka Period (ca. AD 1430-1536) Archaeofaunal Assemblages from Residential Unit 1 (RU1), Pucara de Tilcara (Jujuy, Argentina)

PubMed Central

2016-01-01

This paper reports the results of a zooarchaeological analysis conducted on the occupation layer of a compound structure (Residential Unit 1) of the Pucara de Tilcara archaeological site (Jujuy Province, northwestern Argentina). Its occupation span extends between the 13th and 15th centuries AD, but evidence diagnostic of the Inka Period (AD 1430–1536) is predominant. Residential Unit 1 was a house-workshop that hosted specialized crafts like metallurgy and lapidary during the Inka Period. It was proposed in previous works that artisans living at Pucara de Tilcara were provisioned with agropastoral products by the Inka administration. This paper aims to test that hypothesis against the zooarchaeological evidence of Residential Unit 1. Three variables were used as proxies for state-sponsored distribution: taxonomic diversity (family and species ranks), and skeletal and age profiles of the predominant zoological family (Camelidae) in the assemblage. The results show a high degree of continuity with the regional record, characterized by a herding-hunting strategy focused on domestic and wild species of Camelidae and a mixed mortality pattern. The skeletal profile shows a strong and negative correlation with the desiccation potential of elements, which could be indicative of local production of chalona. Overall, faunal evidence does not show any sign of centralized distribution. PMID:27732648

Expanding the World of Marine Bacterial and Archaeal Clades

PubMed Central

Yilmaz, Pelin; Yarza, Pablo; Rapp, Josephine Z.; Glöckner, Frank O.

2016-01-01

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies. PMID:26779174

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.

Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet

PubMed Central

Meyer, Christopher P.; Mills, Suzanne C.

2015-01-01

Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators’ diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction. PMID:26137428

Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet.

PubMed

Leray, Matthieu; Meyer, Christopher P; Mills, Suzanne C

2015-01-01

Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction.

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.

Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp

USDA-ARS?s Scientific Manuscript database

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 up...

The identity of three South American “smiliine” treehoppers (Hemiptera: Membracidae) and related taxonomic changes, including description of a new genus in Thuridini

USDA-ARS?s Scientific Manuscript database

Based on examination of holotype or interpretation of original descriptions, four taxonomic changes are proposed for South American species erroneously placed in the tribe Smiliini: Flynnia, n. gen. (Thuridini) and F. fascipennis (Funkhouser), n. comb. from Bolivia; Antianthe atromarginata (Goding),...

Spectrophotometry of Artemisia tridentata to quantitatively determine subspecies

Treesearch

Bryce A. Richardson; Alicia A. Boyd; Tanner Tobiasson; Matthew J. Germino

2018-01-01

Ecological restoration is predicated on our abilities to discern plant taxa. Taxonomic identification is a first step in ensuring that plants are appropriately adapted to the site. An example of the need to identify taxonomic differences comes from big sagebrush (Artemisia tridentata). This species is composed of three predominant subspecies occupying distinct...

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...

Generic Language Facilitates Children's Cross-Classification

ERIC Educational Resources Information Center

Nguyen, Simone P.; Gelman, A.

2012-01-01

Four studies examined the role of generic language in facilitating 4- and 5-year-old children's ability to cross-classify. Participants were asked to classify an item into a familiar (taxonomic or script) category, then cross-classify it into a novel (script or taxonomic) category with the help of a clue expressed in either generic or specific…

Taxonomic Knowledge of Children with and without Cochlear Implants

ERIC Educational Resources Information Center

Lund, Emily; Dinsmoor, Jessica

2016-01-01

Purpose: The purpose of this study was to compare the taxonomic vocabulary knowledge and organization of children with cochlear implants to (a) children with normal hearing matched for age, and (b) children matched for vocabulary development. Method: Ten children with cochlear implants, 10 age-matched children with normal hearing, and 10…

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...

Revision of the taxonomic status of Aphis floridanae Tissot (Hemiptera:Aphididae) using morphological and molecular insight

USDA-ARS?s Scientific Manuscript database

Three Aphis species are involved in this study. Aphis floridanae Tissot, 1933 and A. nasturtii Kaltenbach, 1843 are currently treated as synonym, and A. impatientis Thomas, 1878 has a valid taxonomic status. Morphological and cytochrome oxidase 1 (Cox1) data show that Aphis floridanae is not synonym...

Phylogenetic analyses of mtDNA sequences corroborate taxonomic designations based on cuticular hydrocarbons in subterranean termites

Treesearch

Kirsten A. Copren; Lori J. Nelson; Edward L. Vargo; Michael I. Haverty

2005-01-01

Cuticular hydrocarbons (CHCs) are valuable characters for the analysis of cryptic insect species with few discernible morphological characters. Yet, their use in insect systematics, speciWcally in subterranean termites in the genus Reticulitermes (Isoptera: Rhinotermitidae), remains controversial. In this paper, we show that taxonomic designations...

Further elucidation of the taxonomic relationships and geographic distribution of Escobaria sneedii var. sneedii, E. sneedii var. leei, and E. guadalupensis (Cactaceae)

Treesearch

Marc A. Baker

2007-01-01

Individuals of E. sneedii var. sneedii were found to occur in greater abundance within the Guadalupe Mountains than was previously recorded. No additional populations morphologically intermediate between E. guadalupensis and E. sneedii were found. Taxonomic affiliation and geographic...

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae)

PubMed Central

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G.

2018-01-01

Abstract Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera, which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised. PMID:29416412

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae).

PubMed

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G

2018-01-01

Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera , which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised.

Rich in vitamin C or just a convenient snack? Multiple-category reasoning with cross-classified foods.

PubMed

Hayes, Brett K; Kurniawan, Hendy; Newell, Ben R

2011-01-01

Two studies examined multiple category reasoning in property induction with cross-classified foods. Pilot tests identified foods that were more typical of a taxonomic category (e.g., "fruit"; termed 'taxonomic primary') or a script based category (e.g., "snack foods"; termed 'script primary'). They also confirmed that taxonomic categories were perceived as more coherent than script categories. In Experiment 1 participants completed an induction task in which information from multiple categories could be searched and combined to generate a property prediction about a target food. Multiple categories were more often consulted and used in prediction for script primary than for taxonomic primary foods. Experiment 2 replicated this finding across a range of property types but found that multiple category reasoning was reduced in the presence of a concurrent cognitive load. Property type affected which categories were consulted first and how information from multiple categories was weighted. The results show that multiple categories are more likely to be used for property predictions about cross-classified objects when an object is primarily associated with a category that has low coherence.

A taxonomic index, with names of descriptive authorities of termite genera and species: an accompaniment to Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, Editors. 2011. Springer, Dordrecht. 576 pp.).

PubMed

Bignell, D E; Jones, D T

2014-01-01

Biology of Termites: A Modern Synthesis (Bignell DE, Roisin Y, Lo N, (Editors), Springer, Dordrecht, 576pp, ISBN 978-90-481-3976-7, e-ISBN 978-90-481-3977-4, DOI 10.1007/978-90-481-3977-4) was published in 2011. With the agreement of the publishers, we give a taxonomic index of the book comprising 494 termite entries, 103 entries of other multicellular animal species mentioned as associates or predators of termites, with 9 fungal, 60 protist, and 64 prokaryote identities, which are listed as termite symbionts (sensu stricto). In addition, we add descriptive authorities for living (and some fossil) termite genera and species. Higher taxonomic groupings for termites are indicated by 25 code numbers. Microorganisms (prokaryotes, protists, and fungi) are listed separately, using broad modern taxonomic affiliations from the contemporary literature of bacteriology, protozoology, and mycology. This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.

Inductive reasoning about causally transmitted properties.

PubMed

Shafto, Patrick; Kemp, Charles; Bonawitz, Elizabeth Baraff; Coley, John D; Tenenbaum, Joshua B

2008-11-01

Different intuitive theories constrain and guide inferences in different contexts. Formalizing simple intuitive theories as probabilistic processes operating over structured representations, we present a new computational model of category-based induction about causally transmitted properties. A first experiment demonstrates undergraduates' context-sensitive use of taxonomic and food web knowledge to guide reasoning about causal transmission and shows good qualitative agreement between model predictions and human inferences. A second experiment demonstrates strong quantitative and qualitative fits to inferences about a more complex artificial food web. A third experiment investigates human reasoning about complex novel food webs where species have known taxonomic relations. Results demonstrate a double-dissociation between the predictions of our causal model and a related taxonomic model [Kemp, C., & Tenenbaum, J. B. (2003). Learning domain structures. In Proceedings of the 25th annual conference of the cognitive science society]: the causal model predicts human inferences about diseases but not genes, while the taxonomic model predicts human inferences about genes but not diseases. We contrast our framework with previous models of category-based induction and previous formal instantiations of intuitive theories, and outline challenges in developing a complete model of context-sensitive reasoning.

Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals

PubMed Central

Raia, P.; Carotenuto, F.; Passaro, F.; Piras, P.; Fulgione, D.; Werdelin, L.; Saarinen, J.; Fortelius, M.

2013-01-01

A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation. PMID:23173207

Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

PubMed

Alsop, Eric B; Raymond, Jason

2013-01-01

Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses) for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

PubMed Central

van Hazel, Ilke; Santini, Francesco; Müller, Johannes; Chang, Belinda SW

2006-01-01

Background Vertebrate SWS1 visual pigments mediate visual transduction in response to light at short wavelengths. Due to their importance in vision, SWS1 genes have been isolated from a surprisingly wide range of vertebrates, including lampreys, teleosts, amphibians, reptiles, birds, and mammals. The SWS1 genes exhibit many of the characteristics of genes typically targeted for phylogenetic analyses. This study investigates both the utility of SWS1 as a marker for inferring vertebrate phylogenetic relationships, and the characteristics of the gene that contribute to its phylogenetic utility. Results Phylogenetic analyses of vertebrate SWS1 genes produced topologies that were remarkably congruent with generally accepted hypotheses of vertebrate evolution at both higher and lower taxonomic levels. The few exceptions were generally associated with areas of poor taxonomic sampling, or relationships that have been difficult to resolve using other molecular markers. The SWS1 data set was characterized by a substantial amount of among-site rate variation, and a relatively unskewed substitution rate matrix, even when the data were partitioned into different codon sites and individual taxonomic groups. Although there were nucleotide biases in some groups at third positions, these biases were not convergent across different taxonomic groups. Conclusion Our results suggest that SWS1 may be a good marker for vertebrate phylogenetics due to the variable yet consistent patterns of sequence evolution exhibited across fairly wide taxonomic groups. This may result from constraints imposed by the functional role of SWS1 pigments in visual transduction. PMID:17107620

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

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.

First insight into the faecal microbiota of the high Arctic muskoxen (Ovibos moschatus)

PubMed Central

Bockwoldt, Mathias; Hagen, Live H.; Pope, Phillip B.; Sundset, Monica A.

2016-01-01

The faecal microbiota of muskoxen (n=3) pasturing on Ryøya (69° 33′ N 18° 43′ E), Norway, in late September was characterized using high-throughput sequencing of partial 16S rRNA gene regions. A total of 16 209 high-quality sequence reads from bacterial domains and 19 462 from archaea were generated. Preliminary taxonomic classifications of 806 bacterial operational taxonomic units (OTUs) resulted in 53.7–59.3 % of the total sequences being without designations beyond the family level. Firmicutes (70.7–81.1 % of the total sequences) and Bacteroidetes (16.8–25.3 %) constituted the two major bacterial phyla, with uncharacterized members within the family Ruminococcaceae (28.9–40.9 %) as the major phylotype. Multiple-library comparisons between muskoxen and other ruminants indicated a higher similarity for muskoxen faeces and reindeer caecum (P>0.05) and some samples from cattle faeces. The archaeal sequences clustered into 37 OTUs, with dominating phylotypes affiliated to the methane-producing genus Methanobrevibacter (80–92 % of the total sequences). UniFrac analysis demonstrated heterogeneity between muskoxen archaeal libraries and those from reindeer and roe deer (P=1.0e-02, Bonferroni corrected), but not with foregut fermenters. The high proportion of cellulose-degrading Ruminococcus-affiliated bacteria agrees with the ingestion of a highly fibrous diet. Further experiments are required to elucidate the role played by these novel bacteria in the digestion of this fibrous Artic diet eaten by muskoxen. PMID:28348861

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons

PubMed Central

Fischer, Sandra; Kumar, Neeraj

2017-01-01

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea. PMID:28097056

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons.

PubMed

Lagkouvardos, Ilias; Fischer, Sandra; Kumar, Neeraj; Clavel, Thomas

2017-01-01

The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well-documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha - and beta -diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.

Root-Associated Fungi Shared Between Arbuscular Mycorrhizal and Ectomycorrhizal Conifers in a Temperate Forest

PubMed Central

Toju, Hirokazu; Sato, Hirotoshi

2018-01-01

Arbuscular mycorrhizal and ectomycorrhizal symbioses are among the most important drivers of terrestrial ecosystem dynamics. Historically, the two types of symbioses have been investigated separately because arbuscular mycorrhizal and ectomycorrhizal plant species are considered to host discrete sets of fungal symbionts (i.e., arbuscular mycorrhizal and ectomycorrhizal fungi, respectively). Nonetheless, recent studies based on high-throughput DNA sequencing technologies have suggested that diverse non-mycorrhizal fungi (e.g., endophytic fungi) with broad host ranges play roles in relationships between arbuscular mycorrhizal and ectomycorrhizal plant species in forest ecosystems. By analyzing an Illumina sequencing dataset of root-associated fungi in a temperate forest in Japan, we statistically examined whether co-occurring arbuscular mycorrhizal (Chamaecyparis obtusa) and ectomycorrhizal (Pinus densiflora) plant species could share non-mycorrhizal fungal communities. Among the 919 fungal operational taxonomic units (OTUs) detected, OTUs in various taxonomic lineages were statistically designated as “generalists,” which associated commonly with both coniferous species. The list of the generalists included fungi in the genera Meliniomyces, Oidiodendron, Cladophialophora, Rhizodermea, Penicillium, and Mortierella. Meanwhile, our statistical analysis also detected fungi preferentially associated with Chamaecyparis (e.g., Pezicula) or Pinus (e.g., Neolecta). Overall, this study provides a basis for future studies on how arbuscular mycorrhizal and ectomycorrhizal plant species interactively drive community- or ecosystem-scale processes. The physiological functions of the fungi highlighted in our host-preference analysis deserve intensive investigations for understanding their roles in plant endosphere and rhizosphere. PMID:29593682

Delineating Species with DNA Barcodes: A Case of Taxon Dependent Method Performance in Moths

PubMed Central

Kekkonen, Mari; Mutanen, Marko; Kaila, Lauri; Nieminen, Marko; Hebert, Paul D. N.

2015-01-01

The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work. PMID:25849083

Altered Gut Microbiota Composition Associated with Eczema in Infants.

PubMed

Zheng, Huajun; Liang, Hong; Wang, Yuezhu; Miao, Maohua; Shi, Tao; Yang, Fen; Liu, Enuo; Yuan, Wei; Ji, Zai-Si; Li, De-Kun

2016-01-01

Eczema is frequently the first manifestation of an atopic diathesis and alteration in the diversity of gut microbiota has been reported in infants with eczema. To identify specific bacterial communities associated with eczema, we conducted a case-control study of 50 infants with eczema (cases) and 51 healthy infants (controls). We performed high-throughput sequencing for V3-V4 hypervariable regions of the 16S rRNA genes from the gut fecal material. A total of 12,386 OTUs (operational taxonomic units) at a 97% similarity level were obtained from the two groups, and we observed a difference in taxa abundance, but not the taxonomic composition, of gut microbiota between the two groups. We identified four genera enriched in healthy infants: Bifidobacterium, Megasphaera, Haemophilus and Streptococcus; and five genera enriched in infants with eczema: Escherichia/Shigella, Veillonella, Faecalibacterium, Lachnospiraceae incertae sedis and Clostridium XlVa. Several species, such as Faecalibacterium prausnitzii and Ruminococcus gnavus, that are known to be associated with atopy or inflammation, were found to be significantly enriched in infants with eczema. Higher abundance of Akkermansia muciniphila in eczematous infants might reduce the integrity of intestinal barrier function and therefore increase the risk of developing eczema. On the other hand, Bacteroides fragilis and Streptococcus salivarius, which are known for their anti-inflammatory properties, were less abundant in infants with eczema. The observed differences in genera and species between cases and controls in this study may provide insight into the link between the microbiome and eczema risk.

Altered Gut Microbiota Composition Associated with Eczema in Infants

PubMed Central

Miao, Maohua; Shi, Tao; Yang, Fen; Liu, Enuo; Yuan, Wei; Ji, Zai-Si; Li, De-Kun

2016-01-01

Eczema is frequently the first manifestation of an atopic diathesis and alteration in the diversity of gut microbiota has been reported in infants with eczema. To identify specific bacterial communities associated with eczema, we conducted a case-control study of 50 infants with eczema (cases) and 51 healthy infants (controls). We performed high-throughput sequencing for V3–V4 hypervariable regions of the 16S rRNA genes from the gut fecal material. A total of 12,386 OTUs (operational taxonomic units) at a 97% similarity level were obtained from the two groups, and we observed a difference in taxa abundance, but not the taxonomic composition, of gut microbiota between the two groups. We identified four genera enriched in healthy infants: Bifidobacterium, Megasphaera, Haemophilus and Streptococcus; and five genera enriched in infants with eczema: Escherichia/Shigella, Veillonella, Faecalibacterium, Lachnospiraceae incertae sedis and Clostridium XlVa. Several species, such as Faecalibacterium prausnitzii and Ruminococcus gnavus, that are known to be associated with atopy or inflammation, were found to be significantly enriched in infants with eczema. Higher abundance of Akkermansia muciniphila in eczematous infants might reduce the integrity of intestinal barrier function and therefore increase the risk of developing eczema. On the other hand, Bacteroides fragilis and Streptococcus salivarius, which are known for their anti-inflammatory properties, were less abundant in infants with eczema. The observed differences in genera and species between cases and controls in this study may provide insight into the link between the microbiome and eczema risk. PMID:27812181

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

DOE PAGES

Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira; ...

2016-03-21

Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using materialmore » from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within general containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. Lastly, a representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation.« less

Cellulose-Enriched Microbial Communities from Leaf-Cutter Ant (Atta colombica) Refuse Dumps Vary in Taxonomic Composition and Degradation Ability

PubMed Central

Lewin, Gina R.; Johnson, Amanda L.; Soto, Rolando D. Moreira; Perry, Kailene; Book, Adam J.; Horn, Heidi A.; Pinto-Tomás, Adrián A.; Currie, Cameron R.

2016-01-01

Deconstruction of the cellulose in plant cell walls is critical for carbon flow through ecosystems and for the production of sustainable cellulosic biofuels. Our understanding of cellulose deconstruction is largely limited to the study of microbes in isolation, but in nature, this process is driven by microbes within complex communities. In Neotropical forests, microbes in leaf-cutter ant refuse dumps are important for carbon turnover. These dumps consist of decaying plant material and a diverse bacterial community, as shown here by electron microscopy. To study the portion of the community capable of cellulose degradation, we performed enrichments on cellulose using material from five Atta colombica refuse dumps. The ability of enriched communities to degrade cellulose varied significantly across refuse dumps. 16S rRNA gene amplicon sequencing of enriched samples identified that the community structure correlated with refuse dump and with degradation ability. Overall, samples were dominated by Bacteroidetes, Gammaproteobacteria, and Betaproteobacteria. Half of abundant operational taxonomic units (OTUs) across samples were classified within genera containing known cellulose degraders, including Acidovorax, the most abundant OTU detected across samples, which was positively correlated with cellulolytic ability. A representative Acidovorax strain was isolated, but did not grow on cellulose alone. Phenotypic and compositional analyses of enrichment cultures, such as those presented here, help link community composition with cellulolytic ability and provide insight into the complexity of community-based cellulose degradation. PMID:26999749

Changes in fibre-adherent and fluid-associated microbial communities and fermentation profiles in the rumen of cattle fed diets differing in hay quality and concentrate amount.

PubMed

Klevenhusen, Fenja; Petri, Renee M; Kleefisch, Maria-Theresia; Khiaosa-Ard, Ratchaneewan; Metzler-Zebeli, Barbara U; Zebeli, Qendrim

2017-09-01

The rumen microbiota enable important metabolic functions to the host cattle. Feeding of starch-rich concentrate feedstuffs to cattle has been demonstrated to increase the risk of metabolic disorders and to significantly alter the rumen microbiome. Thus, alternative feeding strategies like the use of high-quality hay, rich in sugars, as an alternative energy source need to be explored. The aim of this study was to investigate changes in rumen microbial abundances in the liquid and solid-associated fraction of cattle fed two hay qualities differing in sugar content with graded amounts of starchy concentrate feeds using Illumina MiSeq sequencing and quantitative polymerase chain reaction. Operational taxonomic units clustered separately between the liquid and the solid-associated fraction. Phyla in the liquid fraction were identified as mainly Firmicutes, Proteobacteria and Bacteroidetes, whereas main phyla of the fibre-associated fraction were Bacteroidetes, Fibrobacteres and Firmicutes. Significant alterations in the rumen bacterial communities at all taxonomic levels as a result of changing the hay quality and concentrate proportions were observed. Several intermicrobial correlations were found. Genera Ruminobacter and Fibrobacter were significantly suppressed by feeding sugar-rich hay, whereas others such as Selenomonas and Prevotella proliferated. This study extends the knowledge about diet-induced changes in ruminal microbiome of cattle. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.