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Sample records for alkaliphilic taxa nitrogen

  1. Alkaliphiles: Some Applications of Their Products for Biotechnology

    PubMed Central

    Horikoshi, Koki

    1999-01-01

    The term “alkaliphile” is used for microorganisms that grow optimally or very well at pH values above 9 but cannot grow or grow only slowly at the near-neutral pH value of 6.5. Alkaliphiles include prokaryotes, eukaryotes, and archaea. Many different taxa are represented among the alkaliphiles, and some of these have been proposed as new taxa. Alkaliphiles can be isolated from normal environments such as garden soil, although viable counts of alkaliphiles are higher in samples from alkaline environments. The cell surface may play a key role in keeping the intracellular pH value in the range between 7 and 8.5, allowing alkaliphiles to thrive in alkaline environments, although adaptation mechanisms have not yet been clarified. Alkaliphiles have made a great impact in industrial applications. Biological detergents contain alkaline enzymes, such as alkaline cellulases and/or alkaline proteases, that have been produced from alkaliphiles. The current proportion of total world enzyme production destined for the laundry detergent market exceeds 60%. Another important application is the industrial production of cyclodextrin by alkaline cyclomaltodextrin glucanotransferase. This enzyme has reduced the production cost and paved the way for cyclodextrin use in large quantities in foodstuffs, chemicals, and pharmaceuticals. It has also been reported that alkali-treated wood pulp could be biologically bleached by xylanases produced by alkaliphiles. Other applications of various aspects of alkaliphiles are also discussed. PMID:10585964

  2. Acquisition of Iron by Alkaliphilic Bacillus Species▿

    PubMed Central

    McMillan, Duncan G. G.; Velasquez, Imelda; Nunn, Brook L.; Goodlett, David R.; Hunter, Keith A.; Lamont, Iain; Sander, Sylvia G.; Cook, Gregory M.

    2010-01-01

    The biochemical and molecular mechanisms used by alkaliphilic bacteria to acquire iron are unknown. We demonstrate that alkaliphilic (pH > 9) Bacillus species are sensitive to artificial iron (Fe3+) chelators and produce iron-chelating molecules. These alkaliphilic siderophores contain catechol and hydroxamate moieties, and their synthesis is stimulated by manganese(II) salts and suppressed by FeCl3 addition. Purification and mass spectrometric characterization of the siderophore produced by Caldalkalibacillus thermarum failed to identify any matches to previously observed fragmentation spectra of known siderophores, suggesting a novel structure. PMID:20802068

  3. Biosystematics of alkaliphilic streptomycetes isolated from seven locations across a beach and dune sand system.

    PubMed

    Antony-Babu, Sanjay; Goodfellow, Michael

    2008-11-01

    Alkaliphilic streptomycetes were isolated from composite sand samples collected from six out of seven locations across a beach and dune sand system using starch-casein-nitrate agar supplemented with cycloheximide and buffered to pH 10.5. The isolates had colonial and chemotaxonomic properties consistent with their classification in the genus Streptomyces. They were assigned to 49 multimembered and 114 single-membered colour-groups given their ability to produce pigments on oatmeal and peptone-yeast-extract-iron agars and to corresponding taxa based on whole-genome rep-PCR banding patterns. Twenty-four isolates representing the colour and rep-PCR groups grew well from pH 5 to 11, and optimally at pH 9, as did phylogenetically close members of the Streptomyces griseus 16S rRNA gene clade. One hundred and twelve representative alkaliphilic streptomycetes formed a heterogeneous but distinct clade in the Streptomyces 16S rRNA gene tree. A 3-dimensional representation of 16S rRNA sequence data showed that the alkaliphilic streptomycetes formed a distinct group in multidimensional taxospace. It is evident that alkaliphilic streptomycetes are common in the beach and dune sand system and that representatives of this community form new centers of taxonomic variation within the genus Streptomyces that can be equated with species. PMID:18777141

  4. The Respiratory Chain of Alkaliphilic Bacteria

    SciTech Connect

    Terry Ann Krulwich

    2008-01-29

    Alkaliphilic bacteria that grow at extremely high pH are confronted by particular bioenergetic problems in carrying out oxidative phosphorylation. This project focused on the properties and adaptations of the respiratory chain. The respiratory chain as a whole, the redox poises of its components and several individual complexes of the respiratory chain of alkaliphilic Bacillus pseudofirmus OF4 have been characterized as part of this project and, importantly, this project has helped support the development of genetic tools that make B. pseudofirmus OF4 the most genetically tractable and, hence, most bioenergetically characterized extreme alkaliphile. Evidence has been obtained for a pivotal role of the cca3-type terminal oxidase in oxidative phosphorylation, especially at high pH and motifs that may be relevant to that special role have been identified.

  5. Natural abundance (δ¹⁵N) indicates shifts in nitrogen relations of woody taxa along a savanna-woodland continental rainfall gradient.

    PubMed

    Soper, Fiona M; Richards, Anna E; Siddique, Ilyas; Aidar, Marcos P M; Cook, Garry D; Hutley, Lindsay B; Robinson, Nicole; Schmidt, Susanne

    2015-05-01

    Water and nitrogen (N) interact to influence soil N cycling and plant N acquisition. We studied indices of soil N availability and acquisition by woody plant taxa with distinct nutritional specialisations along a north Australian rainfall gradient from monsoonal savanna (1,600-1,300 mm annual rainfall) to semi-arid woodland (600-250 mm). Aridity resulted in increased 'openness' of N cycling, indicated by increasing δ(15)N(soil) and nitrate:ammonium ratios, as plant communities transitioned from N to water limitation. In this context, we tested the hypothesis that δ(15)N(root) xylem sap provides a more direct measure of plant N acquisition than δ(15)N(foliage). We found highly variable offsets between δ(15)N(foliage) and δ(15)N(root) xylem sap, both between taxa at a single site (1.3-3.4 ‰) and within taxa across sites (0.8-3.4 ‰). As a result, δ(15)N(foliage) overlapped between N-fixing Acacia and non-fixing Eucalyptus/Corymbia and could not be used to reliably identify biological N fixation (BNF). However, Acacia δ(15)N(root) xylem sap indicated a decline in BNF with aridity corroborated by absence of root nodules and increasing xylem sap nitrate concentrations and consistent with shifting resource limitation. Acacia dominance at arid sites may be attributed to flexibility in N acquisition rather than BNF capacity. δ(15)N(root) xylem sap showed no evidence of shifting N acquisition in non-mycorrhizal Hakea/Grevillea and indicated only minor shifts in Eucalyptus/Corymbia consistent with enrichment of δ(15)N(soil) and/or decreasing mycorrhizal colonisation with aridity. We propose that δ(15)N(root) xylem sap is a more direct indicator of N source than δ(15)N(foliage), with calibration required before it could be applied to quantify BNF. PMID:25502440

  6. Controlling Cyanobacterial Blooms in Hypertrophic Lake Taihu, China: Will Nitrogen Reductions Cause Replacement of Non-N2 Fixing by N2 Fixing Taxa?

    PubMed Central

    Paerl, Hans W.; Xu, Hai; Hall, Nathan S.; Zhu, Guangwei; Qin, Boqiang; Wu, Yali; Rossignol, Karen L.; Dong, Linghan; McCarthy, Mark J.; Joyner, Alan R.

    2014-01-01

    Excessive anthropogenic nitrogen (N) and phosphorus (P) inputs have caused an alarming increase in harmful cyanobacterial blooms, threatening sustainability of lakes and reservoirs worldwide. Hypertrophic Lake Taihu, China’s third largest freshwater lake, typifies this predicament, with toxic blooms of the non-N2 fixing cyanobacteria Microcystis spp. dominating from spring through fall. Previous studies indicate N and P reductions are needed to reduce bloom magnitude and duration. However, N reductions may encourage replacement of non-N2 fixing with N2 fixing cyanobacteria. This potentially counterproductive scenario was evaluated using replicate, large (1000 L), in-lake mesocosms during summer bloom periods. N+P additions led to maximum phytoplankton production. Phosphorus enrichment, which promoted N limitation, resulted in increases in N2 fixing taxa (Anabaena spp.), but it did not lead to significant replacement of non-N2 fixing with N2 fixing cyanobacteria, and N2 fixation rates remained ecologically insignificant. Furthermore, P enrichment failed to increase phytoplankton production relative to controls, indicating that N was the most limiting nutrient throughout this period. We propose that Microcystis spp. and other non-N2 fixing genera can maintain dominance in this shallow, highly turbid, nutrient-enriched lake by outcompeting N2 fixing taxa for existing sources of N and P stored and cycled in the lake. To bring Taihu and other hypertrophic systems below the bloom threshold, both N and P reductions will be needed until the legacy of high N and P loading and sediment nutrient storage in these systems is depleted. At that point, a more exclusive focus on P reductions may be feasible. PMID:25405474

  7. Decolorization of azo dyes (Direct Blue 151 and Direct Red 31) by moderately alkaliphilic bacterial consortium

    PubMed Central

    Lalnunhlimi, Sylvine; Krishnaswamy, Veenagayathri

    2016-01-01

    Removal of synthetic dyes is one of the main challenges before releasing the wastes discharged by textile industries. Biodegradation of azo dyes by alkaliphilic bacterial consortium is one of the environmental-friendly methods used for the removal of dyes from textile effluents. Hence, this study presents isolation of a bacterial consortium from soil samples of saline environment and its use for the decolorization of azo dyes, Direct Blue 151 (DB 151) and Direct Red 31 (DR 31). The decolorization of azo dyes was studied at various concentrations (100–300 mg/L). The bacterial consortium, when subjected to an application of 200 mg/L of the dyes, decolorized DB 151 and DR 31 by 97.57% and 95.25% respectively, within 5 days. The growth of the bacterial consortium was optimized with pH, temperature, and carbon and nitrogen sources; and decolorization of azo dyes was analyzed. In this study, the decolorization efficiency of mixed dyes was improved with yeast extract and sucrose, which were used as nitrogen and carbon sources, respectively. Such an alkaliphilic bacterial consortium can be used in the removal of azo dyes from contaminated saline environment. PMID:26887225

  8. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications

    PubMed Central

    Shivlata, L.; Satyanarayana, Tulasi

    2015-01-01

    Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications. PMID:26441937

  9. Sustainable biorefining in wastewater by engineered extreme alkaliphile Bacillus marmarensis.

    PubMed

    Wernick, David G; Pontrelli, Sammy P; Pollock, Alexander W; Liao, James C

    2016-01-01

    Contamination susceptibility, water usage, and inability to utilize 5-carbon sugars and disaccharides are among the major obstacles in industrialization of sustainable biorefining. Extremophilic thermophiles and acidophiles are being researched to combat these problems, but organisms which answer all the above problems have yet to emerge. Here, we present engineering of the unexplored, extreme alkaliphile Bacillus marmarensis as a platform for new bioprocesses which meet all these challenges. With a newly developed transformation protocol and genetic tools, along with optimized RBSs and antisense RNA, we engineered B. marmarensis to produce ethanol at titers of 38 g/l and 65% yields from glucose in unsterilized media. Furthermore, ethanol titers and yields of 12 g/l and 50%, respectively, were produced from cellobiose and xylose in unsterilized seawater and algal-contaminated wastewater. As such, B. marmarensis presents a promising approach for the contamination-resistant biorefining of a wide range of carbohydrates in unsterilized, non-potable seawater. PMID:26831574

  10. Methanohalophilus zhilinae sp. nov., an alkaliphilic, halophilic, methylotrophic methanogen

    NASA Technical Reports Server (NTRS)

    Mathrani, I. M.; Boone, D. R.; Mah, R. A.; Fox, G. E.; Lau, P. P.

    1988-01-01

    Methanohalophilus zhilinae, a new alkaliphilic, halophilic, methylotrophic species of methanogenic bacteria, is described. Strain WeN5T (T = type strain) from Bosa Lake of the Wadi el Natrun in Egypt was designated the type strain and was further characterized. This strain was nonmotile, able to catabolize dimethylsulfide, and able to grow in medium with a methyl group-containing substrate (such as methanol or trimethylamine) as the sole organic compound added. Sulfide (21 mM) inhibited cultures growing on trimethylamine. The antibiotic susceptibility pattern of strain WeN5T was typical of the pattern for archaeobacteria, and the guanine-plus-cytosine content of the deoxyribonucleic acid was 38 mol%. Characterization of the 16S ribosomal ribonucleic acid sequence indicated that strain WeN5T is phylogenetically distinct from members of previously described genera other than Methanohalophilus and supported the partition of halophilic methanogens into their own genus.

  11. A Streamlined Strategy for Biohydrogen Production with an Alkaliphilic Bacterium

    SciTech Connect

    Elias, Dwayne A; Wall, Judy D.; Mormile, Dr. Melanie R.; Begemann, Matthew B

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, biohydrogen production remains inefficient and heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium strain sapolanicus, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. sapolanicus ferments a variety of 5- and 6- carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen and acetate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources.

  12. Sustainable biorefining in wastewater by engineered extreme alkaliphile Bacillus marmarensis

    PubMed Central

    Wernick, David G.; Pontrelli, Sammy P.; Pollock, Alexander W.; Liao, James C.

    2016-01-01

    Contamination susceptibility, water usage, and inability to utilize 5-carbon sugars and disaccharides are among the major obstacles in industrialization of sustainable biorefining. Extremophilic thermophiles and acidophiles are being researched to combat these problems, but organisms which answer all the above problems have yet to emerge. Here, we present engineering of the unexplored, extreme alkaliphile Bacillus marmarensis as a platform for new bioprocesses which meet all these challenges. With a newly developed transformation protocol and genetic tools, along with optimized RBSs and antisense RNA, we engineered B. marmarensis to produce ethanol at titers of 38 g/l and 65% yields from glucose in unsterilized media. Furthermore, ethanol titers and yields of 12 g/l and 50%, respectively, were produced from cellobiose and xylose in unsterilized seawater and algal-contaminated wastewater. As such, B. marmarensis presents a promising approach for the contamination-resistant biorefining of a wide range of carbohydrates in unsterilized, non-potable seawater. PMID:26831574

  13. Alkaliphilic Bacteria with Impact on Industrial Applications, Concepts of Early Life Forms, and Bioenergetics of ATP Synthesis

    PubMed Central

    Preiss, Laura; Hicks, David B.; Suzuki, Shino; Meier, Thomas; Krulwich, Terry Ann

    2015-01-01

    Alkaliphilic bacteria typically grow well at pH 9, with the most extremophilic strains growing up to pH values as high as pH 12–13. Interest in extreme alkaliphiles arises because they are sources of useful, stable enzymes, and the cells themselves can be used for biotechnological and other applications at high pH. In addition, alkaline hydrothermal vents represent an early evolutionary niche for alkaliphiles and novel extreme alkaliphiles have also recently been found in alkaline serpentinizing sites. A third focus of interest in alkaliphiles is the challenge raised by the use of proton-coupled ATP synthases for oxidative phosphorylation by non-fermentative alkaliphiles. This creates a problem with respect to tenets of the chemiosmotic model that remains the core model for the bioenergetics of oxidative phosphorylation. Each of these facets of alkaliphilic bacteria will be discussed with a focus on extremely alkaliphilic Bacillus strains. These alkaliphilic bacteria have provided a cogent experimental system to probe adaptations that enable their growth and oxidative phosphorylation at high pH. Adaptations are clearly needed to enable secreted or partially exposed enzymes or protein complexes to function at the high external pH. Also, alkaliphiles must maintain a cytoplasmic pH that is significantly lower than the pH of the outside medium. This protects cytoplasmic components from an external pH that is alkaline enough to impair their stability or function. However, the pH gradient across the cytoplasmic membrane, with its orientation of more acidic inside than outside, is in the reverse of the productive orientation for bioenergetic work. The reversed gradient reduces the trans-membrane proton-motive force available to energize ATP synthesis. Multiple strategies are hypothesized to be involved in enabling alkaliphiles to circumvent the challenge of a low bulk proton-motive force energizing proton-coupled ATP synthesis at high pH. PMID:26090360

  14. Alkaliphilic Bacteria with Impact on Industrial Applications, Concepts of Early Life Forms, and Bioenergetics of ATP Synthesis.

    PubMed

    Preiss, Laura; Hicks, David B; Suzuki, Shino; Meier, Thomas; Krulwich, Terry Ann

    2015-01-01

    Alkaliphilic bacteria typically grow well at pH 9, with the most extremophilic strains growing up to pH values as high as pH 12-13. Interest in extreme alkaliphiles arises because they are sources of useful, stable enzymes, and the cells themselves can be used for biotechnological and other applications at high pH. In addition, alkaline hydrothermal vents represent an early evolutionary niche for alkaliphiles and novel extreme alkaliphiles have also recently been found in alkaline serpentinizing sites. A third focus of interest in alkaliphiles is the challenge raised by the use of proton-coupled ATP synthases for oxidative phosphorylation by non-fermentative alkaliphiles. This creates a problem with respect to tenets of the chemiosmotic model that remains the core model for the bioenergetics of oxidative phosphorylation. Each of these facets of alkaliphilic bacteria will be discussed with a focus on extremely alkaliphilic Bacillus strains. These alkaliphilic bacteria have provided a cogent experimental system to probe adaptations that enable their growth and oxidative phosphorylation at high pH. Adaptations are clearly needed to enable secreted or partially exposed enzymes or protein complexes to function at the high external pH. Also, alkaliphiles must maintain a cytoplasmic pH that is significantly lower than the pH of the outside medium. This protects cytoplasmic components from an external pH that is alkaline enough to impair their stability or function. However, the pH gradient across the cytoplasmic membrane, with its orientation of more acidic inside than outside, is in the reverse of the productive orientation for bioenergetic work. The reversed gradient reduces the trans-membrane proton-motive force available to energize ATP synthesis. Multiple strategies are hypothesized to be involved in enabling alkaliphiles to circumvent the challenge of a low bulk proton-motive force energizing proton-coupled ATP synthesis at high pH. PMID:26090360

  15. Nitrogen

    USGS Publications Warehouse

    Kramer, D.A.

    2006-01-01

    In 2005, ammonia was produced by 15 companies at 26 plants in 16 states in the United States. Of the total ammonia production capacity, 55% was centered in Louisiana, Oklahoma and Texas because of their large reserves of natural gas. US producers operated at 66% of their rated capacity. In descending order, Koch Nitrogen, Terra Industries, CF Industries, Agrium and PCS Nitrogen accounted for 81% of the US ammonia production capacity.

  16. Draft Genome Sequence of Bacillus pseudalcaliphilus PN-137T (DSM 8725), an Alkaliphilic Halotolerant Bacterium Isolated from Garden Soils.

    PubMed

    Wang, Jie-Ping; Liu, Bo; Liu, Guo-Hong; Xiao, Rong-Feng; Zheng, Xue-Fang; Shi, Huai; Ge, Ci-Bin

    2015-01-01

    Bacillus pseudalcaliphilus PN-137(T) (DSM 8725) is a Gram-positive, spore-forming, alkaliphilic, and halotolerant bacterium. Here, we report the 4.49-Mb genome sequence of B. pseudalcaliphilus PN-137(T), which will accelerate the application of this alkaliphile and provide useful information for genomic taxonomy and phylogenomics of Bacillus-like bacteria. PMID:26272579

  17. Nitrogen

    USGS Publications Warehouse

    Kramer, D.A.

    2004-01-01

    Ammonia is the principal source of fixed nitrogen. It was produced by 17 companies at 34 plants in the United States during 2003. Fifty-three percent of U.S. ammonia production capacity was centered in Louisiana, Oklahoma and Texas because of their large reserves of natural gas, the dominant domestic feedstock.

  18. Nitrogen

    USGS Publications Warehouse

    Kramer, D.A.

    2007-01-01

    Ammonia was produced by 15 companies at 25 plants in 16 states in the United States during 2006. Fifty-seven percent of U.S. ammonia production capacity was centered in Louisiana, Oklahoma and Texas because of their large reserves of natural gas, the dominant domestic feedstock. In 2006, U.S. producers operated at about 72 percent of their rated capacity (excluding plants that were idle for the entire year). Five companies, Koch Nitrogen, Terra Industries, CF Industries, PCS Nitro-gen, and Agrium, in descending order, accounted for 79 percent U.S. ammonia production capacity. The United States was the world's fourth-ranked ammonia producer and consumer following China, India and Russia. Urea, ammonium nitrate, ammonium phosphates, nitric acid and ammonium sulfate were the major derivatives of ammonia in the United States, in descending order of importance.

  19. Draft Genome Sequence of the Obligately Alkaliphilic Sulfate-Reducing Bacterium Desulfonatronum thiodismutans Strain MLF1

    PubMed Central

    Trubitsyn, Denis; Geurink, Corey; Pikuta, Elena; Lefèvre, Christopher T.; McShan, W. Michael; Gillaspy, Allison F.

    2014-01-01

    Desulfonatronum thiodismutans strain MLF1, an alkaliphilic bacterium capable of sulfate reduction, was isolated from Mono Lake, California. Here we report the 3.92-Mb draft genome sequence comprising 34 contigs and some results of its automated annotation. These data will improve our knowledge of mechanisms by which bacteria withstand extreme environments. PMID:25081260

  20. The ontology of biological taxa

    PubMed Central

    Schulz, Stefan; Stenzhorn, Holger; Boeker, Martin

    2008-01-01

    Motivation: The classification of biological entities in terms of species and taxa is an important endeavor in biology. Although a large amount of statements encoded in current biomedical ontologies is taxon-dependent there is no obvious or standard way for introducing taxon information into an integrative ontology architecture, supposedly because of ongoing controversies about the ontological nature of species and taxa. Results: In this article, we discuss different approaches on how to represent biological taxa using existing standards for biomedical ontologies such as the description logic OWL DL and the Open Biomedical Ontologies Relation Ontology. We demonstrate how hidden ambiguities of the species concept can be dealt with and existing controversies can be overcome. A novel approach is to envisage taxon information as qualities that inhere in biological organisms, organism parts and populations. Availability: The presented methodology has been implemented in the domain top-level ontology BioTop, openly accessible at http://purl.org/biotop. BioTop may help to improve the logical and ontological rigor of biomedical ontologies and further provides a clear architectural principle to deal with biological taxa information. Contact: stschulz@uni-freiburg.de PMID:18586729

  1. Alkaliphilic Clostridia and the Serpentinite-Hosted Deep Biosphere

    NASA Astrophysics Data System (ADS)

    Schrenk, M. O.; George, C.; Twing, K. I.; Brazelton, W. J.

    2012-12-01

    Serpentinization is a process whereby ultramafic rocks characteristic of Earth's upper mantle are exposed to fluid flow and undergo aqueous alteration. Serpentinizing ultramafic rocks can serve as important conduits for the flux of carbon and energy from Earth's deep interior into the biosphere. Highly reducing, high pH conditions associated with serpentinization produce copious hydrogen and can lead to the production of methane and abiogenic hydrocarbons. Recent studies have found low diversity microbial communities consisting primarily of Betaproteobacteria and Firmicutes in samples of high pH wells, springs, and drill cores from serpentinite terrains. Cloning and sequencing of bacterial 16S rRNA genes and pyrotag sequencing have indicated that several taxa within the Clostridia, including sequences related to the genera Dethiobacter and Desulfitibacter and the families Thermoanaerobacterales and Clostridiaceae are abundant in the sampled environments. In parallel, iron- and sulfur-containing, pH 11 microcosm experiments from these environments have resulted in the enrichment of populations of spore-forming bacteria related to the Clostridiales. Previously characterized relatives of these taxa can carry out metabolisms ranging from the fermentation of complex organic molecules, to autotrophy using hydrogen as an electron donor and sulfur compounds as electron acceptors. Metabolic and physiological studies of the microcosms combined with data on the distribution of these taxa in natural environments are being used to better understand their role in the in the functioning of serpentinite-hosted subsurface ecosystems. Areas of investigation include the supply of organic acids and fermentation products to other species in the ecosystems, the fixation of inorganic carbon into biomass, or the possibility that the Clostridia exists as spores simply surviving the harsh conditions. Spore-forming Clostridia species may play important roles in the extraction of energy and

  2. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation

    PubMed Central

    Yin, Liang; Xue, Yanfen; Ma, Yanhe

    2015-01-01

    The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress. PMID:26030352

  3. Global Microarray Analysis of Alkaliphilic Halotolerant Bacterium Bacillus sp. N16-5 Salt Stress Adaptation.

    PubMed

    Yin, Liang; Xue, Yanfen; Ma, Yanhe

    2015-01-01

    The alkaliphilic halotolerant bacterium Bacillus sp. N16-5 is often exposed to salt stress in its natural habitats. In this study, we used one-colour microarrays to investigate adaptive responses of Bacillus sp. N16-5 transcriptome to long-term growth at different salinity levels (0%, 2%, 8%, and 15% NaCl) and to a sudden salt increase from 0% to 8% NaCl. The common strategies used by bacteria to survive and grow at high salt conditions, such as K+ uptake, Na+ efflux, and the accumulation of organic compatible solutes (glycine betaine and ectoine), were observed in Bacillus sp. N16-5. The genes of SigB regulon involved in general stress responses and chaperone-encoding genes were also induced by high salt concentration. Moreover, the genes regulating swarming ability and the composition of the cytoplasmic membrane and cell wall were also differentially expressed. The genes involved in iron uptake were down-regulated, whereas the iron homeostasis regulator Fur was up-regulated, suggesting that Fur may play a role in the salt adaption of Bacillus sp. N16-5. In summary, we present a comprehensive gene expression profiling of alkaliphilic Bacillus sp. N16-5 cells exposed to high salt stress, which would help elucidate the mechanisms underlying alkaliphilic Bacillus spp. survival in and adaptation to salt stress. PMID:26030352

  4. Corridor use by diverse taxa.

    SciTech Connect

    Haddad, Nick, M.; Browne, David, R.; Cunningham, Alan; Danielson, Brent, J.; Levey, Douglas, J.; Sargent, Sarah; Spira, Tim

    2003-01-01

    Haddad, N.M., D.R. Browne, A. Cunningham, B.J. Danielson, D.J. Levey, S. Sargent, and T. Spira. 2003. Corridor use by diverse taxa. Ecology, 84(3):609-615. One of the most popular approaches for maintaining populations and conserving biodiversity in fragmented landscapes is to retain or create corridors that connect otherwise isolated habitat patches. Working in large-scale, experimental landscapes in which open-habitat patches and corridors were created by harvesting pine forest, we showed that corridors direct movements of different types of species, including butterflies, small mammals, and bird dispersed plants, causing higher movement between connected than between unconnected patches. Corridors directed the movement of all 10 species studied, with all corridor effect sizes >68%. However, this corridor effect was significant for five species, not significant for one species, and inconclusive for four species because of small sample sizes. Although we found no evidence that corridors increase emigration from a patch, our results show that movements of disparate taxa with broadly different life histories and functional roles are directed by corridors.

  5. Mechanisms of cytoplasmic pH regulation in alkaliphilic strains of Bacillus.

    PubMed

    Krulwich, T A; Ito, M; Gilmour, R; Guffanti, A A

    1997-11-01

    The central challenge for extremely alkaliphilic Bacillus species is the need to establish and sustain a cytoplasmic pH that is over two units lower than the highly alkaline medium. Its centrality is suggested by the strong correlation between the growth rate in the upper range of pH for growth, i.e., at values above pH 10.5, and the cytoplasmic pH. The diminishing growth rate at extremely high pH values correlates better with the rise in cytoplasmic pH than with other energetic parameters. There are also general adaptations of alkaliphiles that are crucial prerequisites for pH homeostasis as well as other cell functions, i.e., the reduced basic amino acid content of proteins or segments thereof that are exposed to the medium, and there are other challenges of alkaliphily that emerge from solution of the cytoplasmic pH problem, i.e., reduction of the chemiosmotic driving force. For cells growing on glucose, strong evidence exists for the importance of acidic cell wall components, teichuronic acid and teichuronopeptides, in alkaliphily. These wall macromolecules may provide a passive barrier to ion flux. For cells growing on fermentable carbon sources, this and other passive mechanisms may have a particularly substantial role, but for cells growing on both fermentable and nonfermentable substrates, an active Na+-dependent cycle is apparently required for alkaliphily and the alkaliphile's remarkable capacity for pH homeostasis. The active cycle involves primary establishment of an electrochemical gradient via proton extrusion, a secondary electrogenic Na+/H+ antiport to achieve net acidification of the cytoplasm relative to the outside pH, and mechanisms for Na+ re-entry. Recent work in several laboratories on the critical antiporters involved in this cycle has begun to clarify the number and characteristics of the porters that support active mechanisms of pH homeostasis. PMID:9680297

  6. Investigations of Iron Minerals Formed by Dissimilatory Alkaliphilic Bacterium with {sup 57}Fe Moessbauer Spectroscopy

    SciTech Connect

    Chistyakova, N. I.; Rusakov, V. S.; Shapkin, A. A.; Zhilina, T. N.; Zavarzina, D. G.; Kohout, J.

    2010-07-13

    Anaerobic alkaliphilic bacterium of Geoalkalibacter ferrihydriticus type (strain Z-0531), isolated from a bottom sediment sample from the weakly mineralized soda Lake Khadyn, have been analyzed. The strain uses the amorphous Fe(III)-hydroxide (AFH) as an electron acceptor and acetate CH{sub 3}COO{sup -} as an electron donor. Moessbauer investigations of solid phase samples obtained during the process of the bacterium growth were carried out at room temperature, 77.8 K, 4.2 K without and with the presence of an external magnetic field (6 T) applied perpendicular to the {gamma}-bebam.

  7. Bacillus oshimensis sp. nov., a moderately halophilic, non-motile alkaliphile.

    PubMed

    Yumoto, Isao; Hirota, Kikue; Goto, Toshitaka; Nodasaka, Yoshinobu; Nakajima, Kenji

    2005-03-01

    A halophilic and halotolerant, facultatively alkaliphilic strain, K11(T), was isolated from soil obtained from Oshyamanbe, Oshima, Hokkaido, Japan. The isolate grew at pH 7-10. It was non-motile, Gram-positive and aerobic. Cells comprised straight rods and produced ellipsoidal spores. The isolate grew in 0-20 % NaCl, with optimum growth at 7 % NaCl, and hydrolysed casein, gelatin, starch, DNA and Tweens 20, 40, 60 and 80. The major isoprenoid quinone was menaquinone-7, and the cellular fatty acid profile consisted of significant amounts of C(15) branched-chain acids, iso C(15 : 0) and anteiso C(15 : 0). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain K11(T) was a member of group 6 [Nielsen et al., FEMS Microbiol Lett 117 (1994), 61-66] (alkaliphiles) of the genus Bacillus. DNA-DNA hybridization revealed a low relatedness (14 %) of the isolate to its closest phylogenetic neighbour, Bacillus clausii. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA-DNA relatedness data, it was concluded that K11(T) (=JCM 12663(T)=NCIMB 14023(T)) merits classification as the type strain of a novel species, for which the name Bacillus oshimensis sp. nov. is proposed. PMID:15774684

  8. Screening and Selection of Medium Components for Cyclodextrin Glucanotransferase Production by New Alkaliphile Microbacterium terrae KNR 9 Using Plackett-Burman Design.

    PubMed

    Rajput, Kiransinh N; Patel, Kamlesh C; Trivedi, Ujjval B

    2016-01-01

    Cyclodextrin glucanotransferase (CGTase, EC 2.4.1.19) production using new alkaliphile Microbacterium terrae KNR 9 was investigated by submerged fermentation. Statistical screening for components belonging to different categories, namely, soluble and raw starches as carbon sources, complex organic and inorganic nitrogen sources, minerals, a buffering agent, and a surfactant, has been carried out for CGTase production using Plackett-Burman factorial design. To screen out k (19), number of variables, k + 1 (20), number of experiments, were performed. Among the fourteen components screened, four components, namely, soluble starch, corn flour, yeast extract, and K2HPO4, were identified as significant with reference to their concentration effect and corresponding p value. Although soluble starch showed highest significance, comparable significance was also observed with corn flour and hence it was selected as a sole carbon source along with yeast extract and K2HPO4 for further media optimization studies. Using screened components, CGTase production was increased to 45% and 87% at shake flask level and laboratory scale fermenter, respectively, as compared to basal media. PMID:26955489

  9. Screening and Selection of Medium Components for Cyclodextrin Glucanotransferase Production by New Alkaliphile Microbacterium terrae KNR 9 Using Plackett-Burman Design

    PubMed Central

    Rajput, Kiransinh N.; Patel, Kamlesh C.; Trivedi, Ujjval B.

    2016-01-01

    Cyclodextrin glucanotransferase (CGTase, EC 2.4.1.19) production using new alkaliphile Microbacterium terrae KNR 9 was investigated by submerged fermentation. Statistical screening for components belonging to different categories, namely, soluble and raw starches as carbon sources, complex organic and inorganic nitrogen sources, minerals, a buffering agent, and a surfactant, has been carried out for CGTase production using Plackett-Burman factorial design. To screen out k (19), number of variables, k + 1 (20), number of experiments, were performed. Among the fourteen components screened, four components, namely, soluble starch, corn flour, yeast extract, and K2HPO4, were identified as significant with reference to their concentration effect and corresponding p value. Although soluble starch showed highest significance, comparable significance was also observed with corn flour and hence it was selected as a sole carbon source along with yeast extract and K2HPO4 for further media optimization studies. Using screened components, CGTase production was increased to 45% and 87% at shake flask level and laboratory scale fermenter, respectively, as compared to basal media. PMID:26955489

  10. The Influence of Siderophores Produced by Alkaliphilic Microorganisms on Iron and Metal Contaminant Speciation and Solubility

    NASA Astrophysics Data System (ADS)

    Aiken, A. M.; Peyton, B. M.; Petersen, J. N.; Apel, W. A.; Camper, A. K.

    2003-12-01

    Halomonas campisalis strain 4A has been identified as capable of producing siderophores under halo-alkaliphilic growth conditions. Because of the scarcity of iron under the alkaline conditions in which Halomonas campisalis thrives, we hypothesize that the siderophores secreted by Halomonas campisalis and other alkaliphilic bacteria will have a stronger affinity for binding and solubilizing ferrous iron than siderophores produced by mesophilic bacteria. Siderophore production by Halomonas campisalis was confirmed through the use of the chrome azural S (CAS) agar plate method which showed a red orange halo around the bacterial colonies indicative of siderophore production. The siderophores were found to be produced under conditions of both high salinity and pH with a salt concentrations ranging from 0.4 - 1.8 M NaCl and pH ranging from 8 - 11. The siderophores produced have been determined to be of the hydroxamate class via the Csaky method. A negative response to the Arnow assay indicated that the siderophore produced does not contain any catechol moieties in its chemical structure. It was found that maximum siderophore production was equivalent to approximately 400 mM desferrioxamine and occurred during mid stationary phase. Similar results were found at pH 8, 10 and 11. A purification scheme was developed that involved an initial extraction of the siderophore from the growth medium into benzyl alcohol followed by precipitation with diethyl ether. Additional purification was achieved via ion exchange chromatography and size exclusion chromatography. Final purification was achieved via HPLC. The structure of the purified siderophore was analyzed via LC/MS/MS equipped with an ESI source. To date, few studies have included the siderophores produced by microorganisms capable of tolerating highly saline and alkaline environments. In addition to unique structure and high affinity for iron, it is further hypothesized that siderophores from alkaliphilic bacteria will also

  11. Anaerobic Halo-Alkaliphilic Baterial Community of Athalassic, Hypersaline Mono Lake in California

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.; Marsic, Damien; Ng, Joseph D.; Six, N. Frank (Technical Monitor)

    2002-01-01

    The microorganisms of soda Mono Lake and other similar athalassic hypersaline alkaline soda lakes are of significance to Astrobiology. The microorganisms of these regimes represent the best known terrestrial analogs for microbial life that might have inhabited the hypersaline alkaline lakes and evaporites confined within closed volcanic basins and impact craters during the late Noachian and early Hesperian epochs (3.6 - 4.2 Gya) of ancient Mars. We have investigated the anaerobic microbiota of soda Mono Lake in northern California. In this paper we discuss the astrobiological significance of these ecosystems and describe several interesting features of two novel new species of anaerobic halo-alkaliphilic bacteria (Spirochaeta americana, sp. nov. and Desulfonatronum paiuteum, sp. nov) that we have isolated from Mono Lake.

  12. A Streamlined Strategy for Biohydrogen Production with Halanaerobium hydrogeniformans, an Alkaliphilic Bacterium

    PubMed Central

    Begemann, Matthew B.; Mormile, Melanie R.; Sitton, Oliver C.; Wall, Judy D.; Elias, Dwayne A.

    2012-01-01

    Biofuels are anticipated to enable a shift from fossil fuels for renewable transportation and manufacturing fuels, with biohydrogen considered attractive since it could offer the largest reduction of global carbon budgets. Currently, lignocellulosic biohydrogen production remains inefficient with pretreatments that are heavily fossil fuel-dependent. However, bacteria using alkali-treated biomass could streamline biofuel production while reducing costs and fossil fuel needs. An alkaliphilic bacterium, Halanaerobium hydrogeniformans, is described that is capable of biohydrogen production at levels rivaling neutrophilic strains, but at pH 11 and hypersaline conditions. H. hydrogeniformans ferments a variety of 5- and 6-carbon sugars derived from hemicellulose and cellulose including cellobiose, and forms the end products hydrogen, acetate, and formate. Further, it can also produce biohydrogen from switchgrass and straw pretreated at temperatures far lower than any previously reported and in solutions compatible with growth. Hence, this bacterium can potentially increase the efficiency and efficacy of biohydrogen production from renewable biomass resources. PMID:22509174

  13. Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site

    PubMed Central

    Suzuki, Shino; Kuenen, J. Gijs; Schipper, Kira; van der Velde, Suzanne; Ishii, Shun’ichi; Wu, Angela; Sorokin, Dimitry Y.; Tenney, Aaron; Meng, XianYing; Morrill, Penny L.; Kamagata, Yoichi; Muyzer, Gerard; Nealson, Kenneth H.

    2014-01-01

    Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here we describe physiological and genomic features of three related Betaproteobacterial strains isolated from highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California. All three strains are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic growth with hydrogen, calcium carbonate and oxygen. The three strains exhibit differences, however, regarding the utilization of organic carbon and electron acceptors. Their global distribution and physiological, genomic and transcriptomic characteristics indicate that the strains are adapted to the alkaline and calcium-rich environments represented by the terrestrial serpentinizing ecosystems. We propose placing these strains in a new genus ‘Serpentinomonas’. PMID:24845058

  14. The respiratory chains of four strains of the alkaliphilic Bacillus clausii.

    PubMed

    Abbrescia, A; Martino, P L; Panelli, D; Sardanelli, A M; Papa, S; Alifano, P; Palese, L L; Gaballo, A

    2014-01-01

    A comparative analysis of terminal respiratory enzymes has been performed on four strains of Bacillus clausii used for preparation of a European probiotic. These four strains originated most probably from a common ancestor through early selection of stable clones for industrial propagation. They exhibit a low level of intra-specific diversity and a high degree of genomic conservation, making them an attractive model to study the different bioenergetics behaviors of alkaliphilic bacilli. The analysis of the different bioenergetics responses has been carried out revealing striking differences among the strains. Two out of the four strains have shown a functional redundancy of the terminal part of the respiratory chain. The biochemical data correlate with the expression level of the mRNA of cytochrome c oxidase and quinol oxidase genes (heme-copper type). The consequences of these different bioenergetics behaviors are also discussed. PMID:25161879

  15. The respiratory chains of four strains of the alkaliphilic Bacillus clausii

    PubMed Central

    Abbrescia, A.; Martino, P.L.; Panelli, D.; Sardanelli, A.M.; Papa, S.; Alifano, P.; Palese, L.L.; Gaballo, A.

    2014-01-01

    A comparative analysis of terminal respiratory enzymes has been performed on four strains of Bacillus clausii used for preparation of a European probiotic. These four strains originated most probably from a common ancestor through early selection of stable clones for industrial propagation. They exhibit a low level of intra-specific diversity and a high degree of genomic conservation, making them an attractive model to study the different bioenergetics behaviors of alkaliphilic bacilli. The analysis of the different bioenergetics responses has been carried out revealing striking differences among the strains. Two out of the four strains have shown a functional redundancy of the terminal part of the respiratory chain. The biochemical data correlate with the expression level of the mRNA of cytochrome c oxidase and quinol oxidase genes (heme-copper type). The consequences of these different bioenergetics behaviors are also discussed. PMID:25161879

  16. Desulfonatronum Thiodismutans sp. nov., a Novel Alkaliphilic, Sulfate-reducing Bacterium Capable of Lithoautotrophic Growth

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Hoover, Richard B.; Bej, Asim K.; Marsic, Damien; Whitman, William B.; Cleland, David; Krader, Paul

    2003-01-01

    A novel alkaliphilic, sulfate-reducing bacterium, strain MLF1(sup T), was isolated from sediments of soda Mono Lake, California. Gram-negative vibrio-shaped cells were observed, which were 0.6-0.7 x 1.2-2.7 microns in size, motile by a single polar flagellum and occurred singly, in pairs or as short spirilla. Growth was observed at 15-48 C (optimum, 37 C), > 1-7 % NaCI, w/v (optimum, 3%) and pH 8.0-10.0 (optimum, 9.5). The novel isolate is strictly alkaliphilic, requires a high concentration of carbonate in the growth medium and is obligately anaerobic and catalase-negative. As electron donors, strain MLF1(sup T) uses hydrogen, formate and ethanol. Sulfate, sulfite and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The novel isolate is a lithoheterotroph and a facultative lithoautotroph that is able to grow on hydrogen without an organic source of carbon. Strain MLF1(sup T) is resistant to kanamycin and gentamicin, but sensitive to chloramphenicol and tetracycline. The DNA G+C content is 63.0 mol% (HPLC). DNA-DNA hybridization with the most closely related species, Desulfonatronum lacustre Z-7951(sup T), exhibited 51 % homology. Also, the genome size (1.6 x 10(exp 9) Da) and T(sub m) value of the genomic DNA (71 +/- 2 C) for strain MLF1(sup T) were significantly different from the genome size (2.1 x 10(exp 9) Da) and T(sub m) value (63 +/- 2 C) for Desulfonatronum lacustre Z-7951(sup T). On the basis of physiological and molecular properties, the isolate was considered to be a novel species of the genus Desulfonatronum, for which the name Desulfonatronum thiodismutans sp. nov. is proposed (the type strain is MLF1(sup T) = ATCC BAA-395(sup T) = DSM 14708(sup T)).

  17. A lipid-accumulating alga maintains growth in outdoor, alkaliphilic raceway pond with mixed microbial communities

    DOE PAGESBeta

    Bell, Tisza A.S.; Prithiviraj, Bharath; Wahlen, Brad D.; Fields, Matthew W.; Peyton, Brent M.

    2016-01-07

    Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal “crop.” In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (~9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgarismore » and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteria, and Archaea were used for barcoded pyrosequence determination. The environmental parameters that most closely correlated with C. vulgaris abundance were pH and phosphate. Community analyses indicated that the pond system remained dominated by the Chlorella population (93% of eukaryotic sequences), but was also colonized by other microorganisms. Bacterial sequence diversity increased over time while archaeal sequence diversity declined over the same time period. Using SparCC co-occurrence network analysis, a positive correlation was observed between C. vulgaris and Pseudomonas sp. throughout the experiment, which may suggest a symbiotic relationship between the two organisms. The putative relationship coupled with high pH may have contributed to the success of C. vulgaris. As a result, the characterization of the microbial community dynamics of an alkaliphilic open pond system provides significant insight into open pond systems that could be used to control photoautotrophic biomass

  18. Decomposition of Alternative Chirality Amino Acids by Alkaliphilic Anaerobe from Owens Lake, California

    NASA Technical Reports Server (NTRS)

    Townsend, Alisa; Pikuta, Elena V.; Guisler, Melissa; Hoover, Richard B.

    2009-01-01

    The study of alkaliphilic microbial communities from anaerobic sediments of Owens and Mono Lakes in California led to the isolation of a bacterial strain capable of metabolizing amino acids with alternative chirality. According to the phylogenetic analysis, the anaerobic strain BK1 belongs to the genus Tindallia; however, despite the characteristics of other described species of this genus, the strain BK1 was able to grow on D-arginine and Dlysine. Cell morphology of this strain showed straight, motile, non-spore-forming rods with sizes 0.45 x 1.2-3 microns. Physiological characteristics of the strain showed that it is catalase negative, obligately anaerobic, mesophilic, and obligately alkaliphilic. This isolate is unable to grow at pH 7 and requires CO3 (2-) ions for growth. The strain has chemo-heterotrophic metabolism and is able to ferment various proteolysis products and some sugars. It plays the role of a primary anaerobe within the trophic chain of an anaerobic microbial community by the degradation of complex protein molecules to smaller and less energetic molecules. The new isolate requires NaCl for growth, and can grow within the range of 0.5-13 %, with the optimum at 1 % NaCl (w/v). The temperature range for the growth of the new isolate is 12-40 C with optimum at 35 C. The pH range for the growth of strain BK1 occurs between 7.8 and 11.0 with optimum at 9.5. This paper presents detailed physiological characteristics of the novel isolate from Owens Lake, a unique relic ecosystem of Astrobiological significance, and makes an accent on the ability of this strain to utilize L-amino acids.

  19. A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities

    PubMed Central

    Bell, Tisza A. S.; Prithiviraj, Bharath; Wahlen, Brad D.; Fields, Matthew W.; Peyton, Brent M.

    2016-01-01

    Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal “crop.” In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (∼9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgaris and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteria, and Archaea were used for barcoded pyrosequence determination. The environmental parameters that most closely correlated with C. vulgaris abundance were pH and phosphate. Community analyses indicated that the pond system remained dominated by the Chlorella population (93% of eukaryotic sequences), but was also colonized by other microorganisms. Bacterial sequence diversity increased over time while archaeal sequence diversity declined over the same time period. Using SparCC co-occurrence network analysis, a positive correlation was observed between C. vulgaris and Pseudomonas sp. throughout the experiment, which may suggest a symbiotic relationship between the two organisms. The putative relationship coupled with high pH may have contributed to the success of C. vulgaris. The characterization of the microbial community dynamics of an alkaliphilic open pond system provides significant insight into open pond systems that could be used to control photoautotrophic biomass productivity in an

  20. A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities.

    PubMed

    Bell, Tisza A S; Prithiviraj, Bharath; Wahlen, Brad D; Fields, Matthew W; Peyton, Brent M

    2015-01-01

    Algal biofuels and valuable co-products are being produced in both open and closed cultivation systems. Growing algae in open pond systems may be a more economical alternative, but this approach allows environmental microorganisms to colonize the pond and potentially infect or outcompete the algal "crop." In this study, we monitored the microbial community of an outdoor, open raceway pond inoculated with a high lipid-producing alkaliphilic alga, Chlorella vulgaris BA050. The strain C. vulgaris BA050 was previously isolated from Soap Lake, Washington, a system characterized by a high pH (∼9.8). An outdoor raceway pond (200 L) was inoculated with C. vulgaris and monitored for 10 days and then the culture was transferred to a 2,000 L raceway pond and cultivated for an additional 6 days. Community DNA samples were collected over the 16-day period in conjunction with water chemistry analyses and cell counts. Universal primers for the SSU rRNA gene sequences for Eukarya, Bacteria, and Archaea were used for barcoded pyrosequence determination. The environmental parameters that most closely correlated with C. vulgaris abundance were pH and phosphate. Community analyses indicated that the pond system remained dominated by the Chlorella population (93% of eukaryotic sequences), but was also colonized by other microorganisms. Bacterial sequence diversity increased over time while archaeal sequence diversity declined over the same time period. Using SparCC co-occurrence network analysis, a positive correlation was observed between C. vulgaris and Pseudomonas sp. throughout the experiment, which may suggest a symbiotic relationship between the two organisms. The putative relationship coupled with high pH may have contributed to the success of C. vulgaris. The characterization of the microbial community dynamics of an alkaliphilic open pond system provides significant insight into open pond systems that could be used to control photoautotrophic biomass productivity in an open

  1. Alkaline Anaerobic Respiration: Isolation and Characterization of a Novel Alkaliphilic and Metal-Reducing Bacterium

    PubMed Central

    Ye, Qi; Roh, Yul; Carroll, Susan L.; Blair, Benjamin; Zhou, Jizhong; Zhang, Chuanlun L.; Fields, Matthew W.

    2004-01-01

    Iron-reducing enrichments were obtained from leachate ponds at the U.S. Borax Company in Boron, Calif. Based on partial small-subunit (SSU) rRNA gene sequences (approximately 500 nucleotides), six isolates shared 98.9% nucleotide identity. As a representative, the isolate QYMF was selected for further analysis. QYMF could be grown with Fe(III)-citrate, Fe(III)-EDTA, Co(III)-EDTA, or Cr(VI) as electron acceptors, and yeast extract and lactate could serve as electron donors. Growth during iron reduction occurred over the pH range of 7.5 to 11.0 (optimum, pH 9.5), a sodium chloride range of 0 to 80 g/liter (optimum, 20 g/liter), and a temperature range of 4 to 45°C (optimum, approximately 35°C), and iron precipitates were formed. QYMF was a strict anaerobe that could be grown in the presence of borax, and the cells were straight rods that produced endospores. Sodium chloride and yeast extract stimulated growth. Phylogenetic analysis of the SSU rRNA gene indicated that the bacterium was a low-G+C gram-positive microorganism and had 96 and 92% nucleotide identity with Alkaliphilus transvaalensis and Alkaliphilus crotonatoxidans, respectively. The major phospholipid fatty acids were 14:1, 16:1ω7c, and 16:0, which were different from those of other alkaliphiles but similar to those of reported iron-reducing bacteria. The results demonstrated that the isolate might represent a novel metal-reducing alkaliphilic species. The name Alkaliphilus metalliredigens sp. nov. is proposed. The isolation and activity of metal-reducing bacteria from borax-contaminated leachate ponds suggest that bioremediation of metal-contaminated alkaline environments may be feasible and have implications for alkaline anaerobic respiration. PMID:15345448

  2. Diversity and enumeration of halophilic and alkaliphilic bacteria in Spanish-style green table-olive fermentations.

    PubMed

    Lucena-Padrós, Helena; Ruiz-Barba, José Luis

    2016-02-01

    The presence and enumeration of halophilic and alkaliphilic bacteria in Spanish-style table-olive fermentations was studied. Twenty 10-tonne fermenters at two large manufacturing companies in Spain, previously studied through both culture dependent and independent (PCR-DGGE) methodologies, were selected. Virtually all this microbiota was isolated during the initial fermentation stage. A total of 203 isolates were obtained and identified based on 16S rRNA gene sequences. They belonged to 13 bacterial species, included in 11 genera. It was noticeable the abundance of halophilic and alkaliphilic lactic acid bacteria (HALAB). These HALAB belonged to the three genera of this group: Alkalibacterium, Marinilactibacillus and Halolactibacillus. Ten bacterial species were isolated for the first time from table olive fermentations, including the genera Amphibacillus, Natronobacillus, Catenococcus and Streptohalobacillus. The isolates were genotyped through RAPD and clustered in a dendrogram where 65 distinct strains were identified. Biodiversity indexes found statistically significant differences between both patios regarding genotype richness, diversity and dominance. However, Jaccard similarity index suggested that the halophilic/alkaliphilic microbiota in both patios was more similar than the overall microbiota at the initial fermentation stage. Thus, up to 7 genotypes of 6 different species were shared, suggesting adaptation of some strains to this fermentation stage. Morisita-Horn similarity index indicated a high level of codominance of the same species in both patios. Halophilic and alkaliphilic bacteria, especially HALAB, appeared to be part of the characteristic microbiota at the initial stage of this table-olive fermentation, and they could contribute to the conditioning of the fermenting brines in readiness for growth of common lactic acid bacteria. PMID:26678130

  3. Halotolerant, alkaliphilic urease-producing bacteria from different climate zones and their application for biocementation of sand.

    PubMed

    Stabnikov, Viktor; Chu, Jian; Jian, Chu; Ivanov, Volodymyr; Li, Yishan

    2013-08-01

    Microbially induced calcium carbonate precipitation (MICP) is a phenomenon based on urease activity of halotolerant and alkaliphilic microorganisms that can be used for the soil bioclogging and biocementation in geotechnical engineering. However, enrichment cultures produced from indigenous soil bacteria cannot be used for large-scale MICP because their urease activity decreased with the rate about 5 % per one generation. To ensure stability of urease activity in biocement, halotolerant and alkaliphilic strains of urease-producing bacteria for soil biocementation were isolated from either sandy soil or high salinity water in different climate zones. The strain Bacillus sp. VUK5, isolated from soil in Ukraine (continental climate), was phylogenetically close in identity (99 % of 16S rRNA gene sequence) to the strain of Bacillus sp. VS1 isolated from beach sand in Singapore (tropical rainforest climate), as well as to the strains of Bacillus sp. isolated by other researchers in Ghent, Belgium (maritime temperate climate) and Yogyakarta, Indonesia (tropical rainforest climate). Both strains Bacillus sp. VS1 and VUK5 had maximum specific growth rate of 0.09/h and maximum urease activities of 6.2 and 8.8 mM of hydrolysed urea/min, respectively. The halotolerant and alkaliphilic strain of urease-producing bacteria isolated from water of the saline lake Dead Sea in Jordan was presented by Gram-positive cocci close to the species Staphylococcus succinus. However, the strains of this species could be hemolytic and toxigenic, therefore only representatives of alkaliphilic Bacillus sp. were used for the biocementation studies. Unconfined compressive strengths for dry biocemented sand samples after six batch treatments with strains VS1and VUK5 were 765 and 845 kPa, respectively. The content of precipitated calcium and the strength of dry biocemented sand at permeability equals to 1 % of initial value were 12.4 g Ca/kg of dry sand and 454 kPa, respectively, in case of

  4. [Rhodobaculum claviforme gen. nov., sp. nov., a New Alkaliphilic Nonsulfur Purple Bacterium].

    PubMed

    Bryantseva, I A; Gaisin, V A; Gorlenko, V M

    2015-01-01

    Two alkaliphilic strains of nonsulfur purple bacteria (NPB), B7-4 and B8-2, were isolated from southeast Siberia moderately saline alkaline steppe lakes with pH values above 9.0. The isolates were motile, polymorphous cells (from short rods to long spindly cells) 2.0-3.2 x 9.6-20.0 μm. Intracellular membranes of vesicular type were mostly located at the cell periphery. The microorganisms contained bacteriochlorophyll a and carotenoids of the spheroidene and spirilloxanthin series. The photosynthetic apparatus was represented by LH2 and LH1 light-harvesting complexes. In the presence of organic compounds, the strains grew aerobically in the dark or anaerobically in the light. Capacity for photo- and chemoautotrophic growth was not detected. The cbbl gene encoding RuBisCO was not revealed. Optimal growth of both strains occurred at 2% NaCl (range from 0.5 to 4%), pH 8.0-8.8 (range from 7.5 to 9.7), and 25-35 degrees C. The DNA G+C content was 67.6-69.8 mol %. Pairwise comparison of the nucleotides of the 16S rRNA genes revealed that strains B7-4 and B8-2 belonged to the same species (99.9% homology) and were most closely related to the aerobic alkaliphilic bacteriochlorophyll a-containing anoxygenic phototrophic bacterium (APB) Roseibacula alcaliphilum De (95.2%) and to NPB strains Rhodobaca barguzinensis VKM B-2406(T) (94.2%) and Rbc. bogoriensis LBB1(T) (93.9%). The isolates were closely related to the NPB Rhodobacter veldkampii DSM 11550(T) (94.8%) and to aerobic bacteriochlorophyll a-containing bacteria Roseinatronobacter monicus ROS 35(T) and Roseicitreum antarcticul ZS2-28(T) (93.5 and 93.9%, respectively). New strains were described as a new NPB genus and species of the family Rhodobacteriaceae, Rhodobaculum claviforme gen. nov., sp. nov., with B7-4(T) (VKM B-2708, LMG 28126) as the type strain. PMID:26263629

  5. New taxa of Euglenophyta from China

    NASA Astrophysics Data System (ADS)

    Shi, Zhi-Xin

    1995-12-01

    Eight new taxa of Euglenophyta are described in this paper. They were collected from several provinces in China and respectively named Euglena allorgei var. exsulcata, E. pisciformis var. globosa, E. tortilis. Lepocinclis glabra var. papillata, Phacus pisiformis, Ph. strombuliformis, Ph. trimarginatus var. truncatus and Astasia angusta.

  6. Ionic selectivity and thermal adaptations within the voltage-gated sodium channel family of alkaliphilic Bacillus.

    PubMed

    DeCaen, Paul G; Takahashi, Yuka; Krulwich, Terry A; Ito, Masahiro; Clapham, David E

    2014-01-01

    Entry and extrusion of cations are essential processes in living cells. In alkaliphilic prokaryotes, high external pH activates voltage-gated sodium channels (Nav), which allows Na(+) to enter and be used as substrate for cation/proton antiporters responsible for cytoplasmic pH homeostasis. Here, we describe a new member of the prokaryotic voltage-gated Na(+) channel family (NsvBa; Non-selective voltage-gated, Bacillus alcalophilus) that is nonselective among Na(+), Ca(2+) and K(+) ions. Mutations in NsvBa can convert the nonselective filter into one that discriminates for Na(+) or divalent cations. Gain-of-function experiments demonstrate the portability of ion selectivity with filter mutations to other Bacillus Nav channels. Increasing pH and temperature shifts their activation threshold towards their native resting membrane potential. Furthermore, we find drugs that target Bacillus Nav channels also block the growth of the bacteria. This work identifies some of the adaptations to achieve ion discrimination and gating in Bacillus Nav channels. PMID:25385530

  7. Production and Purification of Extracellular D-Xylose Isomerase from an Alkaliphilic, Thermophilic Bacillus sp. †

    PubMed Central

    Chauthaiwale, Jyoti; Rao, Mala

    1994-01-01

    An alkaliphilic, thermophilic Bacillus sp. (NCIM 59) produced extracellular xylose isomerase at pH 10 and 50°C by using xylose or wheat bran as the carbon source. The distribution of xylose isomerase as a function of growth in comparison with distributions of extra- and intracellular marker enzymes such as xylanase and β-galactosidase revealed that xylose isomerase was truly secreted as an extracellular enzyme and was not released because of sporulation or lysis. The enzyme was purified to homogeneity by ammonium sulfate precipitation followed by gel filtration, preparative polyacrylamide gel electrophoresis, and ion-exchange chromatography. The molecular weight of xylose isomerase was estimated to be 160,000 by gel filtration and 50,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating the presence of three subunits. The enzyme is most active at pH 8.0 and with incubation at 85°C for 20 min. Divalent metal ions Mg2+, Co2+, and Mn2+ were required for maximum activity of the enzyme. The Km values for D-xylose and D-glucose at 80°C and pH 7.5 were 6.66 and 142 mM, respectively, while Kcat values were 2.3 × 102 s-1 and 0.5 × 102 s-1, respectively. Images PMID:16349464

  8. Highly thermostable and alkaline α-amylase from a halotolerant-alkaliphilic Bacillus sp. AB68

    PubMed Central

    Aygan, Ashabil; Arikan, Burhan; Korkmaz, Hatice; Dinçer, Sadik; Çolak, Ömer

    2008-01-01

    An alkaliphilic and highly thermostable α-amylase producing Bacillus sp. was isolated from Van soda lake. Enzyme synthesis occurred at temperatures between 25°C and 40°C. Analysis of the enzyme by SDS-PAGE revealed a single band which was estimated to be 66 kDa. The enzyme was active in a broad temperature range, between 20°C and 90°C, with an optimum at 50°C; and maximum activity was at pH 10.5. The enzyme was almost completely stable up to 80°C with a remaining activity over 90% after 30 min pre-incubation. Thermostability was not increased in the presence of Ca2+. An average of 75% and 60°C of remaining activity was observed when the enzyme was incubated between pH 5 and 9 for 1 h and for 2 h, respectively. The activity of the enzyme was inhibited by SDS and EDTA by 38% and 34%, respectively. PMID:24031264

  9. Purification and characterization of an alkaliphilic choline oxidase of Fusarium oxysporum.

    PubMed

    Enokibara, Shogo

    2012-01-01

    A novel choline oxidase found in a fungus, Fusarium oxysporum strain V2, was purified to homogeneity as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme has a molecular mass of 128 kDa and consists of two identical subunits. The purified enzyme showed adsorption peaks at 340 nm and 450 nm. It showed alkaliphilic pH characteristics: its optimum pH was 9.0-10.0, and it was stable at pH 8.0-10.2. The Michaelis constant (Km) values for choline and betaine aldehyde were 0.28 mM and 0.39 mM respectively. Trimethylamino-alcohols, dimethylamino-alcohols, and diethylaminoethanol were substrates for the enzyme, but the Km values for them increased with decreasing numbers of methyl groups on the ammonium headgroup. A marked decrease in the maximum velocity (Vmax) and Vmax/Km values was observed when N-replaced choline analogs were used as substrate instead of choline. The enzyme had a remarkably higher affinity for choline and betaine aldehyde than do previously reported enzymes. The enzyme oxidized these two substrates more quickly than a choline oxidase from Arthrobacter globiformis, and oxidation by the V2 enzyme was accompanied by an increase in the stoichometric amount of hydrogen peroxide. PMID:23221722

  10. Extracellular Electron Transport-Mediated Fe(III) Reduction by a Community of Alkaliphilic Bacteria That Use Flavins as Electron Shuttles

    PubMed Central

    Fuller, Samuel J.; McMillan, Duncan G. G.; Renz, Marc B.; Schmidt, Martin

    2014-01-01

    The biochemical and molecular mechanisms used by alkaliphilic bacterial communities to reduce metals in the environment are currently unknown. We demonstrate that an alkaliphilic (pH > 9) consortium dominated by Tissierella, Clostridium, and Alkaliphilus spp. is capable of using iron (Fe3+) as a final electron acceptor under anaerobic conditions. Iron reduction is associated with the production of a freely diffusible species that, upon rudimentary purification and subsequent spectroscopic, high-performance liquid chromatography, and electrochemical analysis, has been identified as a flavin species displaying properties indistinguishable from those of riboflavin. Due to the link between iron reduction and the onset of flavin production, it is likely that riboflavin has an import role in extracellular metal reduction by this alkaliphilic community. PMID:24141133

  11. Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium

    PubMed Central

    Watts, Mathew P.; Khijniak, Tatiana V.; Boothman, Christopher

    2015-01-01

    Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments. PMID:26048926

  12. Treatment of Alkaline Cr(VI)-Contaminated Leachate with an Alkaliphilic Metal-Reducing Bacterium.

    PubMed

    Watts, Mathew P; Khijniak, Tatiana V; Boothman, Christopher; Lloyd, Jonathan R

    2015-08-15

    Chromium in its toxic Cr(VI) valence state is a common contaminant particularly associated with alkaline environments. A well-publicized case of this occurred in Glasgow, United Kingdom, where poorly controlled disposal of a cementitious industrial by-product, chromite ore processing residue (COPR), has resulted in extensive contamination by Cr(VI)-contaminated alkaline leachates. In the search for viable bioremediation treatments for Cr(VI), a variety of bacteria that are capable of reduction of the toxic and highly soluble Cr(VI) to the relatively nontoxic and less mobile Cr(III) oxidation state, predominantly under circumneutral pH conditions, have been isolated. Recently, however, alkaliphilic bacteria that have the potential to reduce Cr(VI) under alkaline conditions have been identified. This study focuses on the application of a metal-reducing bacterium to the remediation of alkaline Cr(VI)-contaminated leachates from COPR. This bacterium, belonging to the Halomonas genus, was found to exhibit growth concomitant to Cr(VI) reduction under alkaline conditions (pH 10). Bacterial cells were able to rapidly remove high concentrations of aqueous Cr(VI) (2.5 mM) under anaerobic conditions, up to a starting pH of 11. Cr(VI) reduction rates were controlled by pH, with slower removal observed at pH 11, compared to pH 10, while no removal was observed at pH 12. The reduction of aqueous Cr(VI) resulted in the precipitation of Cr(III) biominerals, which were characterized using transmission electron microscopy and energy-dispersive X-ray analysis (TEM-EDX) and X-ray photoelectron spectroscopy (XPS). The effectiveness of this haloalkaliphilic bacterium for Cr(VI) reduction at high pH suggests potential for its use as an in situ treatment of COPR and other alkaline Cr(VI)-contaminated environments. PMID:26048926

  13. Fermentibacillus polygoni gen. nov., sp. nov., an alkaliphile that reduces indigo dye.

    PubMed

    Hirota, Kikue; Aino, Kenichi; Yumoto, Isao

    2016-06-01

    Facultatively alkaliphilic strains, designated as strains IEB3T and IEB14, were isolated as indigo-reducing strains from a fermented Polygonum indigo (Polygonum tinctorium Lour) liquor sample prepared in our laboratory using a medium containing an indigo fermentation liquor as a sole substrate. The 16S rRNA gene sequence phylogeny and similarity suggested that strains IEB3T and IEB14 exhibit distinctive positions among the members of the genus Bacillus, and their closest neighbour was Bacillus nanhaiisediminis NH3T (similarity: 97.4 %) among the species with validly published names. The 16S rRNA sequence of strain IEB3Twas identical to that of strain IEB14. The cells of the isolates stained Gram-positive and were facultatively anaerobic, straight rods that were motile by a pair of subpolar flagella. Strains IEB3T and IEB14 grew at temperatures between 12 and 40 °C with optimum growth at 30‒33 °C and in the range of pH 7.5-12. Menaquinone-7 (MK-7) was detected as the major isoprenoid quinone. The DNA G+C contents of strains IEB3T and IEB14 were 49.1 and 49.9 mol%, respectively. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C14:0, iso-C15:0 and anteiso-C15:0. DNA-DNA hybridization revealed a low relatedness value between strain IEB3T and the phylogenetically most closely related species, Bacillus nanhaiisediminis JCM 16507T (<7 % ). On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, the isolates represent a novel species within a novel genus, for which the name Fermentibacillus polygoni gen. nov., sp. nov. is proposed. The type strain is IEB3T (=JCM 30817T=NCIMB 14984T). PMID:26971318

  14. Pseudomonas toyotomiensis sp. nov., a psychrotolerant facultative alkaliphile that utilizes hydrocarbons.

    PubMed

    Hirota, Kikue; Yamahira, Keiko; Nakajima, Kenji; Nodasaka, Yoshinobu; Okuyama, Hidetoshi; Yumoto, Isao

    2011-08-01

    A psychrotolerant, facultatively alkaliphilic strain, HT-3(T), was isolated from a sample of soil immersed in hot-spring water containing hydrocarbons in Toyotomi, Hokkaido, Japan. 16S rRNA gene sequence-based phylogeny suggested that strain HT-3(T) is a member of the genus Pseudomonas and belongs to the Pseudomonas oleovorans group. Cells of the isolate were Gram-negative, aerobic, straight rods, motile by a single polar flagellum. The strain grew at 4-42 °C, with optimum growth at 35 °C at pH 7, and at pH 6-10. It hydrolysed Tweens 20, 40, 60 and 80, but not casein, gelatin, starch or DNA. Its major isoprenoid quinone was ubiquinone-9 (Q-9) and the DNA G+C content was 65.1 mol%. The whole-cell fatty acid profile consisted mainly of C(16 : 0), C(16 : 1)ω9c and C(18 : 1)ω9c. Phylogenetic analyses based on gyrB, rpoB and rpoD sequences revealed that the isolate could be discriminated from Pseudomonas species that exhibited more than 97 % 16S rRNA gene sequence similarity and phylogenetic neighbours belonging to the P. oleovorans group including the closest relative of the isolate, Pseudomonas alcaliphila. DNA-DNA hybridization with P. alcaliphila AL15-21(T) revealed 51 ± 5 % relatedness. Owing to differences in phenotypic properties and phylogenetic analyses based on multilocus gene sequence analysis and DNA-DNA relatedness data, the isolate merits classification in a novel species, for which the name Pseudomonas toyotomiensis sp. nov. is proposed. The type strain is HT-3(T) ( = JCM 15604(T)  = NCIMB 14511(T)). PMID:20817837

  15. Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake.

    PubMed

    Dimitriu, Pedro A; Shukla, Sanjay K; Conradt, Jennifer; Márquez, M Carmen; Ventosa, Antonio; Maglia, Anne; Peyton, Brent M; Pinkart, Holly C; Mormile, Melanie R

    2005-11-01

    A novel alkaliphilic bacterium, strain 4CAT, was isolated from decomposing wood taken from the shore of Soap Lake, a saline, alkaline lake in Grant County, WA, USA. Cells of the isolate were Gram-negative, asporogenous, short, motile rods that utilized only a limited range of organic acids as sole carbon and energy sources. In addition to oxygen, the strain possessed the ability to reduce in the presence of acetate. Strain 4CAT was oxidase- and catalase-positive; it degraded Tween 60, but not DNA, urea, gelatin or starch. It grew at pH values from 7.5 to 11.0, with optimum growth occurring at pH 9.0, and growth was observed in NaCl concentrations of 0.2-1.3 M, with optimum growth at 0.8 M NaCl. The optimum temperature for growth was 37 degrees C. Strain 4CAT was resistant to erythromycin, bacitracin, novobiocin, polymyxin B, neomycin, gentamicin, streptomycin, carbenicillin, rifampicin and tetracycline, and was susceptible to nalidixic acid, chloramphenicol, ampicillin and penicillin. The isolate's 16S rRNA gene sequence indicated that it belonged to the gamma-Proteobacteria, showing 90-94 % similarity to its closest relatives. Maximum-likelihood phylogenetic inferences placed strain 4CAT within a novel lineage related to the marine bacterial genera Neptunomonas and Marinobacterium. The DNA G+C content of the isolate was 47.4 mol%. On the basis of genotypic and phenotypic characterization, it was concluded that strain 4CAT should be placed in a separate taxon as a novel genus and species, with the proposed name Nitrincola lacisaponensis gen. nov., sp. nov. The type strain is 4CAT (=ATCC BAA-920T=DSM 16316T). PMID:16280482

  16. Global Microarray Analysis of Carbohydrate Use in Alkaliphilic Hemicellulolytic Bacterium Bacillus sp. N16-5

    PubMed Central

    Song, Yajian; Xue, Yanfen; Ma, Yanhe

    2013-01-01

    The alkaliphilic hemicellulolytic bacterium Bacillus sp. N16-5 has a broad substrate spectrum and exhibits the capacity to utilize complex carbohydrates such as galactomannan, xylan, and pectin. In the monosaccharide mixture, sequential utilization by Bacillus sp. N16-5 was observed. Glucose appeared to be its preferential monosaccharide, followed by fructose, mannose, arabinose, xylose, and galactose. Global transcription profiles of the strain were determined separately for growth on six monosaccharides (glucose, fructose, mannose, galactose, arabinose, and xylose) and four polysaccharides (galactomannan, xylan, pectin, and sodium carboxymethylcellulose) using one-color microarrays. Numerous genes potentially related to polysaccharide degradation, sugar transport, and monosaccharide metabolism were found to respond to a specific substrate. Putative gene clusters for different carbohydrates were identified according to transcriptional patterns and genome annotation. Identification and analysis of these gene clusters contributed to pathway reconstruction for carbohydrate utilization in Bacillus sp. N16-5. Several genes encoding putative sugar transporters were highly expressed during growth on specific sugars, suggesting their functional roles. Two phosphoenolpyruvate-dependent phosphotransferase systems were identified as candidate transporters for mannose and fructose, and a major facilitator superfamily transporter was identified as a candidate transporter for arabinose and xylose. Five carbohydrate uptake transporter 1 family ATP-binding cassette transporters were predicted to participate in the uptake of hemicellulose and pectin degradation products. Collectively, microarray data improved the pathway reconstruction involved in carbohydrate utilization of Bacillus sp. N16-5 and revealed that the organism precisely regulates gene transcription in response to fluctuations in energy resources. PMID:23326578

  17. Ectothiorhodospira variabilis sp. nov., an alkaliphilic and halophilic purple sulfur bacterium from soda lakes.

    PubMed

    Gorlenko, Vladimir M; Bryantseva, Irina A; Rabold, Sandra; Tourova, Tatjana P; Rubtsova, Dariya; Smirnova, Ekaterina; Thiel, Vera; Imhoff, Johannes F

    2009-04-01

    During studies of moderately halophilic strains of Ectothiorhodospira from steppe soda lakes, we found a novel group of bacteria related to Ectothiorhodospira haloalkaliphila with salt optima at 50-80 g NaCl l(-1). Phylogenetic analysis using 16S rRNA gene sequences of strains from soda lakes in Mongolia, Egypt and Siberia revealed separation of the group of new isolates from other Ectothiorhodospira species, including the closely related Ect. haloalkaliphila. DNA-DNA hybridization studies demonstrated that the new isolates form a homogeneous group at the species level, but at the same time are distinct from related species such as Ect. haloalkaliphila, Ect. vacuolata, Ect. shaposhnikovii and Ect. marina. The new isolates are considered to be strains of a novel species, for which the name Ectothiorhodospira variabilis sp. nov. is proposed, with the type strain WN22(T) (=VKM B-2479(T) =DSM 21381(T)). Photosynthetic pigments of the novel species are bacteriochlorophyll a and carotenoids of the spirilloxanthin series with spirilloxanthin and derivatives thereof, together with small amounts of lycopene and rhodopin. Gas vesicles are formed by most of the strains, particularly in media containing yeast extract (0.5 g l(-1)) and acetate (0.5-2.0 g l(-1)). Sequence analysis of nifH (nitrogenase) and cbbL (RuBisCO) confirmed the assignment of the strains to the genus Ectothiorhodospira and in particular the close relationship to Ect. haloalkaliphila. The novel species Ect. variabilis is found in soda lakes separated by great geographical distances and is an alkaliphilic and halophilic bacterium that tolerates salt concentrations up to 150-200 g NaCl l(-1). PMID:19329583

  18. Phytoactinopolyspora alkaliphila sp. nov., an alkaliphilic actinomycete isolated from a saline-alkaline soil.

    PubMed

    Zhang, Yong-Guang; Lu, Xin-Hua; Ding, Yan-Bo; Zhou, Xing-Kui; Li, Li; Guo, Jian-Wei; Wang, Hong-Fei; Duan, Yan-Qing; Li, Wen-Jun

    2016-05-01

    An alkaliphilic, filamentous actinomycete, designated EGI 80629T, was isolated from a soil sample of Xinjiang, north-west China. Strain EGI 80629T grew at pH 6.0-11.0 (optimum pH 9.0-10.0) and in the presence of 0-13.0 % NaCl (optimum 3.0-5.0 %). The isolate formed fragmented substrate mycelia, and aerial hyphae with short spore chains with rod-like spores. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and mannose and rhamnose as diagnostic sugars. The major fatty acids identified were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 0. The predominant menaquinone was MK-9(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two phosphatidylinositol mannosides, five unknown phospholipids, three unknown phosphoglycolipids, one unknown glycolipid, four unknown polar lipids and one unknown aminophospholipid. The G+C content of the genomic DNA was 67.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80629T clustered with the genus Phytoactinopolyspora. The 16S rRNA gene sequence similarity between strain EGI 80629T and Phytoactinopolyspora endophytica EGI 60009T was 96.8 %. Based on morphological, chemotaxonomic and phylogenetic characteristics, strain EGI 80629T represents a novel species of the genus Phytoactinopolyspora, for which the name Phytoactinopolyspora alkaliphila sp. nov. is proposed. The type strain is EGI 80629T ( = CGMCC 4.7225T = KCTC 39701T). PMID:26920762

  19. Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake.

    PubMed

    Wu, Xiao-Yue; Zheng, Gang; Zhang, Wen-Wu; Xu, Xue-Wei; Wu, Min; Zhu, Xu-Fen

    2010-11-01

    A facultatively anaerobic, alkaliphilic, spore-forming, Gram-positive-staining rod, designated Y1(T), was isolated under strictly anaerobic conditions from sediment of a soda lake in Jilin province, China. The strain was not dependent on Na(+) but was highly halotolerant and grew optimally in medium JY with 0.5 M Na(+) (0.06 M NaHCO(3) and 0.44 M NaCl). The optimum pH for growth was 9.0, with a range of pH 7.5-10.5. No growth occurred at pH 7.0 or 11.0. The strain was mesophilic, with a temperature range of 15-45 °C and optimum growth at 32 °C. Strain Y1(T) was able to use certain mono- and oligosaccharides. Soluble starch and casein were hydrolysed. The methyl red test, Voges-Proskauer test and tests for catalase and oxidase activities were negative. The predominant fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). Comparative 16S rRNA gene sequence analysis revealed 93.4-96.8 % sequence similarity to members of the genus Amphibacillus. The DNA G+C content was 37.7 mol% (T(m) method). The DNA-DNA relatedness of strain Y1(T) with respect to Amphibacillus tropicus DSM 13870(T) and Amphibacillus sediminis DSM 21624(T) was 48 and 37 %, respectively. On the basis of its phylogenetic position and the DNA-DNA relatedness data as well as its physiological and biochemical properties, strain Y1(T) represents a novel species of the genus Amphibacillus, for which the name Amphibacillus jilinensis sp. nov. is proposed. The type strain is Y1(T) (=CGMCC 1.5123(T) =JCM 16149(T)). PMID:19965990

  20. Higher thermal acclimation potential of respiration but not photosynthesis in two alpine Picea taxa in contrast to two lowland congeners.

    PubMed

    Zhang, Xiao Wei; Wang, Jing Ru; Ji, Ming Fei; Milne, Richard Ian; Wang, Ming Hao; Liu, Jian-Quan; Shi, Sheng; Yang, Shu-Li; Zhao, Chang-Ming

    2015-01-01

    The members of the genus Picea form a dominant component in many alpine and boreal forests which are the major sink for atmospheric CO2. However, little is known about the growth response and acclimation of CO2 exchange characteristics to high temperature stress in Picea taxa from different altitudes. Gas exchange parameters and growth characteristics were recorded from four year old seedlings of two alpine (Picea likiangensis vars. rubescens and linzhiensis) and two lowland (P. koraiensis and P. meyeri) taxa. Seedlings were grown at moderate (25°C/15°C) and high (35°C/25°C) day/night temperatures, for four months. The approximated biomass increment (ΔD2H) for all taxa decreased under high temperature stress, associated with decreased photosynthesis and increased respiration. However, the two alpine taxa exhibited lower photosynthetic acclimation and higher respiratory acclimation than either lowland taxon. Moreover, higher leaf dry mass per unit area (LMA) and leaf nitrogen content per unit area (Narea), and a smaller change in the nitrogen use efficiency of photosynthesis (PNUE) for lowland taxa indicated that these maintained higher homeostasis of photosynthesis than alpine taxa. The higher respiration rates produced more energy for repair and maintenance biomass, especially for higher photosynthetic activity for lowland taxa, which causes lower respiratory acclimation. Thus, the changes of ΔD2H for alpine spruces were larger than that for lowland spruces. These results indicate that long term heat stress negatively impact on the growth of Picea seedlings, and alpine taxa are more affected than low altitude ones by high temperature stress. Hence the altitude ranges of Picea taxa should be taken into account when predicting changes to carbon fluxes in warmer conditions. PMID:25874631

  1. Desulfonatronum paiuteum sp. nov.: A New Alkaliphilic, Sulfate-Reducing Bacterium, Isolated from Soda Mono Lake, California

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena; Hoover, Richard B.; Marsic, Damien; Whitman, William; Cleland, David; Krader, Paul; Six, N. Frank (Technical Monitor)

    2002-01-01

    A novel alkaliphilic, sulfate reducing bacterium strain MLF1(sup T) was isolated from sediments of soda Mono Lake, California. Gram-negative vibrion cells, motile by singular polar flagellum, with sizes 0.5 - 0.6x 1.2 - 2.0 micron occurred singly, in pairs or short spirilla. Growth was observed over the temperature range of +15 C to +48 C (optimum +37 C), NaCl concentration range is greater than 1 - 7 %, wt/vol (optimum 3 %, wt/vol) and pH range 7.8 - 10.5 (optimum pH 9.0 - 9.4). The novel isolate is strictly alkaliphilic, requires high carbonate concentration in medium, obligately anaerobic and catalase negative. As electron donors strain MLF1(sup T) uses hydrogen, formate, ethanol. Sulfate, sulfite, and thiosulfate (but not sulfur or nitrate) can be used as electron acceptors. The sole end product of growth on formate was H2S. Strain MLF1(sup T) is resistant to kanamycin and gentamycin, but sensitive to chloramphenicol and tetracycline. Na2MoO4 inhibits growth of strain MLF1(sup T). The sum of G+C in DNA is 63.1 mol% (by HPLC method). On the basis of physiological and molecular properties, the isolate was considered as novel species of genus Desulfonatronum; and the name Desulfonatronum paiuteum sp. nov., is proposed (type strain MLF1(sup T) = ATCC BAA-395(sup T) = DSMZ 14708(sup T).

  2. ["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum].

    PubMed

    Zhilina, T N; Zavarzina, D G; Kolganova, T V; Turova, T P; Zavarzin, G A

    2005-01-01

    From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum." PMID:16400991

  3. Bioenergetics and the Role of Soluble Cytochromes c for Alkaline Adaptation in Gram-Negative Alkaliphilic Pseudomonas

    PubMed Central

    Matsuno, T.; Yumoto, I.

    2015-01-01

    Very few studies have been conducted on alkaline adaptation of Gram-negative alkaliphiles. The reversed difference of H+ concentration across the membrane will make energy production considerably difficult for Gram-negative as well as Gram-positive bacteria. Cells of the alkaliphilic Gram-negative bacterium Pseudomonas alcaliphila AL15-21T grown at pH 10 under low-aeration intensity have a soluble cytochrome c content that is 3.6-fold higher than that of the cells grown at pH 7 under high-aeration intensity. Cytochrome c-552 content was higher (64% in all soluble cytochromes c) than those of cytochrome c-554 and cytochrome c-551. In the cytochrome c-552-dificient mutant grown at pH 10 under low-aeration intensity showed a marked decrease in μmax⁡ [h−1] (40%) and maximum cell turbidity (25%) relative to those of the wild type. Considering the high electron-retaining abilities of the three soluble cytochromes c, the deteriorations in the growth of the cytochrome c-552-deficient mutant could be caused by the soluble cytochromes c acting as electron storages in the periplasmic space of the bacterium. These electron-retaining cytochromes c may play a role as electron and H+ condenser, which facilitate terminal oxidation at high pH under air-limited conditions, which is difficult to respire owing to less oxygen and less H+. PMID:25705691

  4. Alkaline iron(III) reduction by a novel alkaliphilic, halotolerant, Bacillus sp. isolated from salt flat sediments of Soap Lake.

    PubMed

    Pollock, Jarrod; Weber, Karrie A; Lack, Joe; Achenbach, Laurie A; Mormile, Melanie R; Coates, John D

    2007-12-01

    A halotolerant, alkaliphilic dissimilatory Fe(III)-reducing bacterium, strain SFB, was isolated from salt flat sediments collected from Soap Lake, WA. 16S ribosomal ribonucleic acid gene sequence analysis identified strain SFB as a novel Bacillus sp. most similar to Bacillus agaradhaerens (96.7% similarity). Strain SFB, a fermentative, facultative anaerobe, fermented various hexoses including glucose and fructose. The fructose fermentation products were lactate, acetate, and formate. Under fructose-fermenting conditions in a medium amended with Fe(III), Fe(II) accumulated concomitant with a stoichiometric decrease in lactate and an increase in acetate and CO(2). Strain SFB was also capable of respiratory Fe(III) reduction with some unidentified component(s) of Luria broth as an electron donor. In addition to Fe(III), strain SFB could also utilize nitrate, fumarate, or O(2) as alternative electron acceptors. Optimum growth was observed at 30 degrees C and pH 9. Although the optimal salinity for growth was 0%, strain SFB could grow in a medium with up to 15% NaCl by mass. These studies describe a novel alkaliphilic, halotolerant organism capable of dissimilatory Fe(III) reduction under extreme conditions and demonstrate that Bacillus species can contribute to the microbial reduction of Fe(III) in environments at elevated pH and salinity, such as soda lakes. PMID:17943280

  5. Data on optimized production and characterization of alkaline proteases from newly isolated alkaliphiles from Lonar soda lake, India.

    PubMed

    Rathod, Mukundraj Govindrao; Pathak, Anupama Prabhakarrao

    2016-09-01

    Alkaline proteases are one of the industrially important enzymes and generally preferred from alkaliphilic sources. Here we have provided the data on optimized production and characterization of alkaline proteases from five newly isolated and identified alkaliphiles from Lonar soda lake, India. The data provided for optimization of physicochemical parameters for maximum alkaline proteases production is based on OVAT (one variable at a time) approach. Alkaline protease production (U/mL) recorded by using different agro industrial residues is included in the given data. Further readers can find more information in our previously published research article where we have already described about the methods used and comparative analysis of the data recorded regarding optimized production, characterization and application of alkaline proteases isolated from Lonar soda lake isolates (http://dx.doi.org/10.1016/j.bcab.2016.06.002) [1]. The data provided here by us is useful to other researchers for setting up various suitable statistical models to perform optimization studies other than OVAT approach. PMID:27508233

  6. Numerical Survey of Some Bacterial Taxa

    PubMed Central

    Focht, D. D.; Lockhart, W. R.

    1965-01-01

    Focht, D. D. (Iowa State University, Ames), and W. R. Lockhart. Numerical survey of some bacterial taxa. J. Bacteriol. 90:1314–1319. 1965.—A numerical analysis was made of 77 properties of each of 43 bacterial strains, representing 25 genera from 8 families in the orders Eubacteriales and Pseudomonadales. Four major groups were found, related to one another at approximately the same level of similarity: (1) a large cluster containing the subgroups (1a) Athiorhodaceae-Spirillaceae, (1b) Xanthomonas, and (1c) “inactive” Micrococcaceae-Achromobacteraceae; (2) a cluster containing the “active” Micrococcaceae and Lactobacillaceae; (3) the enterobacteria; and (4) Aeromonas. There was a sharp distinction between the branches of groups 1a, 1c, and 2. The composition of groups was essentially the same whether or not fermentation of carbohydrates (28 characters) was included in the analysis. Several individual strains, notably, Bacillus subtilis, Leuconostoc mesenteroides, Pseudomonas aeruginosa, and Erwinia amylovora, were related to none of the groups, and others (two species of Proteus, Flavobacterium devorans, and Lactobacillus casei) showed only minimal quantitative relationships with their groups. These results suggest that there may be significant variation in levels of similarity within microbial groups presently accorded equivalent taxonomic rank, and that some present distinctions among taxa, particularly at the generic level, cannot be confirmed on the basis of overall similarity. PMID:5848329

  7. Lysinibacillus alkaliphilus sp. nov., an extremely alkaliphilic bacterium, and emended description of genus Lysinibacillus.

    PubMed

    Zhao, Fei; Feng, Youzhi; Chen, Ruirui; Zhang, Jianwei; Lin, Xiangui

    2015-08-01

    A novel aerobic, alkaliphilic, Gram-staining-positive, endospore-forming bacterium, strain OMN17T, was isolated from a typical sandy loam soil under long-term OMN fertilization (half organic manure N plus half mineral N fertilizer) in northern China and was subjected to a polyphasic taxonomic study. The best growth was achieved at 30 °C and pH 8-10 in medium containing 0.5% (w/v) NaCl. The cell-wall peptidoglycan of strain OMN17T was type A4α; (l-Lys-Gly-d-Asp) and the cell-wall sugars were ribose, traces of galactose and arabinose. The only respiratory quinone found in strain OMN17T was menaquinone 7 (MK-7). The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis of strain OMN17T based on the 16S rRNA gene sequence showed that the strain was most closely related to Lysinibacillus halotolerans (97.8%), Lysinibacillus sinduriensis (97.5%), Lysinibacillus chungkukjangi (97.4%) and Lysinibacillus xylanilyticus (97.0%). The DNA-DNA hybridization results indicated that this strain was distinct from other species of the genus Lysinibacillus, the degree of relatedness being 21.8 ± 0.2% with L. halotolerans, 45.6 ± 1.8% with L. sinduriensis, 33.7 ± 1.2% with L. chungkukjangi and 23.7 ± 0.7% with L. xylanilyticus. The DNA G+C content of strain OMN17T was 38.1 mol%. The phenotypic, chemotaxonomic and genetic analyses identified strain OMN17T as a novel species of the genus Lysinibacillus, for which the name Lysinibacillus alkaliphilus sp. nov. is proposed. The type strain is OMN17T ( = DSM 28019T = CCTCC AB 2014073T). An emended description of the genus Lysinibacillus is also provided. PMID:25908711

  8. Nitrincola alkalisediminis sp. nov., an alkaliphilic bacterium isolated from an alkaline lake.

    PubMed

    Joshi, Amaraja; Thite, Sonia; Kulkarni, Girish; Dhotre, Dhiraj; Joseph, Neetha; Venkata Ramana, V; Polkade, Ashish; Shouche, Yogesh

    2016-03-01

    Two Gram-stain-negative, aerobic, alkaliphilic bacteria (strains MEB087T and MEB142) were isolated from sediment and water samples, respectively, collected from the alkaline Lonar Lake in Maharashtra, India. Strains MEB087T and MEB142 shared 99.8 % 16S rRNA gene sequence similarity and were 85 % related on the basis of DNA-DNA hybridization. The 16S rRNA gene sequences of both strains showed close relationship with the genus Nitrincola, and their closest neighbour was Nitrincola lacisaponensis 4CAT with 97.7 % sequence similarity. MEB087T and MEB142 exhibited only 45 % and 54 % DNA-DNA relatedness, respectively, with Nitrincola lacisaponensis DSM 16316T. Both strains were asporogenous, short, non-motile rods capable of utilizing a limited range of organic acids as sole carbon and energy sources. They were oxidase- and catalase-positive, able to reduce nitrate and nitrite; but unable to degrade DNA, urea, gelatin, casein or starch. They grew optimally at pH 9.5 (tolerating up to pH 11) and could withstand up to 0.6 M NaCl. The predominant cellular fatty acids were summed feature 8 comprising C18 : 1ω7c/C18 : 1ω6c (47-49 %) followed by summed feature 3 comprising C16 : 1ω7c/C16 : 1ω6c (28-32 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content was 49.3-49.7 mol%. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strains MEB087T and MEB142 represent a novel species in the genus Nitrincola, for which the name Nitrincola alkalisediminis sp. nov. is proposed. The type strain is MEB087T ( = KCTC 42948T = JCM 19317T) with MEB142 ( = KCTC 42949 = JCM 19318) as an additional strain. PMID:26705145

  9. Foundational issues concerning taxa and taxon names.

    PubMed

    Ereshefsky, Marc

    2007-04-01

    In a series of articles, Rieppel (2005, Biol. Philos. 20:465-487; 2006a, Cladistics 22:186-197; 2006b, Systematist 26:5-9), Keller et al. (2003, Bot. Rev. 69:93-110), and Nixon and Carpenter (2000, Cladistics 16:298-318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render taxonomy untestable. These charges are unsound. Such charges turn on confusions over rigid designator theory and the distinction between kinds and individuals. In addition, Rieppel's, Keller et al.'s, and Nixon and Carpenter's proposed alternatives are no better and have their own problems. The individuality thesis and rigid designator theory should not be quickly abandoned. PMID:17464884

  10. Microbial ecosystems are dominated by specialist taxa.

    PubMed

    Mariadassou, Mahendra; Pichon, Samuel; Ebert, Dieter

    2015-09-01

    Abundance and specificity are two key characteristics of species distribution and biodiversity. Theories of species assembly aim to reproduce the empirical joint patterns of specificity and abundance, with the goal to explain patterns of biodiversity across habitats. The specialist-generalist paradigm predicts that specialists should have a local advantage over generalists and thus be more abundant. We developed a specificity index to analyse abundance-specificity relationships in microbial ecosystems. By analysing microbiota spanning 23 habitats from three very different data sets covering a wide range of sequencing depths and environmental conditions, we find that habitats are consistently dominated by specialist taxa, resulting in a strong, positive correlation between abundance and specificity. This finding is consistent over several levels of taxonomic aggregation and robust to errors in abundance measures. The relationship explains why shallow sequencing captures similar β-diversity as deep sequencing, and can be sufficient to capture the habitat-specific functions of microbial communities. PMID:26251267

  11. Alkalibacterium olivoapovliticus gen. nov., sp. nov., a new obligately alkaliphilic bacterium isolated from edible-olive wash-waters.

    PubMed

    Ntougias, S; Russell, N J

    2001-05-01

    A novel Gram-positive, obligately alkaliphilic, non-sporulating, rod-shaped, flagellated bacterium is described. Three different strains of the bacterium were isolated from the wash-waters of edible-olive production. The strains are motile, psychrotolerant, halotolerant, facultatively anaerobic bacteria with a pH optimum of 9.0-9.4 for two strains and 9.8-10.2 for the third. They are catalase- and oxidase-negative. A range of hexoses and some disaccharides composed of hexoses, but not pentoses are metabolized by the bacterial strains: D(+)-glucose, D(+)-glucose 6-phosphate, D(+)-cellobiose, starch or sucrose are the carbohydrates best utilized. No common amino acids are utilized by the three alkaliphilic strains, but yeast extract can serve as sole carbon and energy source. The major membrane phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid, all containing saturated and unsaturated, even-carbon-numbered fatty acyl chains with hexadecanoic and hexadecen(7)oic as the predominant components. The G+C content of the DNA in all three strains is 39.7+/-1.0 mol% and the DNA relatedness by hybridization is >88% for all pairings of the three strains. The results of 16S rRNA sequence comparisons revealed that the strains represent a new alkaliphilic linkage in the order Bacillales, belonging to the Carnobacterium/Aerococcus-like spectrum. It is proposed that the strains should be assigned to a new genus and species, Alkalibacterium olivoapovliticus. The three strains, designated WW2-SN4aT, WW2-SN4c and WW2-SN5, have been deposited with Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as DSM 13175T, DSM 12937 and DSM 12938 respectively, and in the National Collection of Industrial and Marine Bacteria as NCIMB 13710T, NCIMB 13711 and NCIMB 13712, respectively. The type species of this genus is Alkalibacterium olivoapovliticus and the type strain is WW2-SN4aT. PMID:11414268

  12. 76 FR 20558 - Endangered and Threatened Wildlife and Plants; 44 Marine and Anadromous Taxa: Adding 10 Taxa...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-13

    ...We, the U.S. Fish and Wildlife Service (Service), are amending the List of Endangered and Threatened Wildlife (List) by adding 10 marine taxa, delisting 1 marine taxon, reclassifying 1 marine taxon, and revising 32 marine taxa in accordance with the Endangered Species Act of 1973, as amended (Act). These amendments are based on previously published determinations by the National Marine......

  13. Numerical experiments with model monophyletic and paraphyletic taxa

    NASA Technical Reports Server (NTRS)

    Sepkoski, J. J. Jr; Kendrick, D. C.; Sepkoski JJ, J. r. (Principal Investigator)

    1993-01-01

    The problem of how accurately paraphyletic taxa versus monophyletic (i.e., holophyletic) groups (clades) capture underlying species patterns of diversity and extinction is explored with Monte Carlo simulations. Phylogenies are modeled as stochastic trees. Paraphyletic taxa are defined in an arbitrary manner by randomly choosing progenitors and clustering all descendants not belonging to other taxa. These taxa are then examined to determine which are clades, and the remaining paraphyletic groups are dissected to discover monophyletic subgroups. Comparisons of diversity patterns and extinction rates between modeled taxa and lineages indicate that paraphyletic groups can adequately capture lineage information under a variety of conditions of diversification and mass extinction. This suggests that these groups constitute more than mere "taxonomic noise" in this context. But, strictly monophyletic groups perform somewhat better, especially with regard to mass extinctions. However, when low levels of paleontologic sampling are simulated, the veracity of clades deteriorates, especially with respect to diversity, and modeled paraphyletic taxa often capture more information about underlying lineages. Thus, for studies of diversity and taxic evolution in the fossil record, traditional paleontologic genera and families need not be rejected in favor of cladistically-defined taxa.

  14. Identification of polyamine-responsive bacterioplankton taxa in South Atlantic Bight.

    PubMed

    Lu, Xinxin; Sun, Shulei; Hollibaugh, James T; Mou, Xiaozhen

    2015-12-01

    Putrescine and spermidine are short-chained aliphatic polyamines (PAs) that are ubiquitously distributed in seawater. These compounds may be important sources of dissolved organic carbon and nitrogen for marine bacterioplankton. Here, we used pyrotag sequencing to quantify the response of bacterioplankton to putrescine and spermidine amendments in microcosms established using surface waters collected at various stations in the South Atlantic Bight in October 2011. Our analysis showed that PA-responsive bacterioplankton consisted of bacterial taxa that are typically dominant in marine systems. Rhodobacteraceae (Alphaproteobacteria) was the taxon most responsive to PA additions at the nearshore site. Gammaproteobacteria of the families Piscirickettsiaceae; Vibrionaceae; and Vibrionaceae and Pseudoalteromonadaceae, were the dominant PA-responsive taxa in samples from the river-influenced coastal station, offshore station and open ocean station, respectively. The spatial variability of PA-responsive taxa may be attributed to differences in composition of the initial bacterial community and variations of in situ physiochemical conditions among sites. Our results also provided the first empirical evidence that Gammaproteobacteria might play an important role in PA transformation in marine systems. PMID:26109269

  15. Enzymatic Properties of an Alkaline and Chelator Resistant alpha-amylase from the Alkaliphilic Bacillus sp. Isolate L1711

    NASA Technical Reports Server (NTRS)

    Bernhardsdotter, Eva C. M. J.; Pusey, Marc L.; Ng, Joseph D.; Garriott, Owen K.

    2004-01-01

    An alkaliphilic amylase producing bacterium, Bacillus sp. strain L 711, was selected among 13 soda lakes isolates. When grown at pH 10.5 and 37 C, strain L711 produced multiple forms of amylases in the culture broth. One of these, BAA, was purified from the culture supernatant by QAE column chromatography and preparative native gel electrophoresis. The molecular weight of BAA was determined to be 51 kDa by denaturing gel electrophoresis. The pH optima for activity below and above 40 C were 9.5 - 10.0 and 7.0 - 7.5 respectively. BAA was stable in the pH range 6-11 and was completely inactivated at 55 C. The thermostability was not increased in the presence of Ca(2+). The enzyme was strongly inhibited by Ca(2+), Zn(2+), Mg(2+), Mn(2+), Ba(2+) and Cu(2+), whereas the presence of Na(+), Co(2+) and EDTA (10 mM) enhanced enzymatic activity. The K(sub m), and specific activity of BAA on soluble starch were 1.9 mg/ml and 18.5 U/mg respectively. The main end products of hydrolysis were maltotetraose, maltose and glucose.

  16. The c-ring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4

    PubMed Central

    Preiss, Laura; Klyszejko, Adriana L.; Hicks, David B.; Liu, Jun; Fackelmayer, Oliver J.; Yildiz, Özkan; Krulwich, Terry A.; Meier, Thomas

    2013-01-01

    The c-rings of ATP synthases consist of individual c-subunits, all of which harbor a conserved motif of repetitive glycine residues (GxGxGxG) important for tight transmembrane α-helix packing. The c-ring stoichiometry determines the number of ions transferred during enzyme operation and has a direct impact on the ion-to-ATP ratio, a cornerstone parameter of cell bioenergetics. In the extreme alkaliphile Bacillus pseudofirmus OF4, the glycine motif is replaced by AxAxAxA. We performed a structural study on two mutants with alanine-to-glycine changes using atomic force microscopy and X-ray crystallography, and found that mutants form smaller c12 rings compared with the WT c13. The molar growth yields of B. pseudofirmus OF4 cells on malate further revealed that the c12 mutants have a considerably reduced capacity to grow on limiting malate at high pH. Our results demonstrate that the mutant ATP synthases with either c12 or c13 can support ATP synthesis, and also underscore the critical importance of an alanine motif with c13 ring stoichiometry for optimal growth at pH >10. The data indicate a direct connection between the precisely adapted ATP synthase c-ring stoichiometry and its ion-to-ATP ratio on cell physiology, and also demonstrate the bioenergetic challenges and evolutionary adaptation strategies of extremophiles. PMID:23613590

  17. Thiocapsa imhoffii, sp. nov., an alkaliphilic purple sulfur bacterium of the family Chromatiaceae from Soap Lake, Washington (USA).

    PubMed

    Asao, Marie; Takaichi, Shinichi; Madigan, Michael T

    2007-12-01

    An alkaliphilic purple sulfur bacterium, strain SC5, was isolated from Soap Lake, a soda lake located in east central Washington state (USA). Cells of strain SC5 were gram-negative, non-motile, and non-gas vesiculate cocci, often observed in pairs or tetrads. In the presence of sulfide, elemental sulfur was deposited internally. Liquid cultures were pink to rose red in color. Cells contained bacteriochlorophyll a and spirilloxanthin as major photosynthetic pigments. Internal photosynthetic membranes were of the vesicular type. Optimal growth of strain SC5 occurred in the absence of NaCl (range 0-4%), pH 8.5 (range pH 7.5-9.5), and 32 degrees C. Photoheterotrophic growth occurred in the presence of sulfide or thiosulfate with only a limited number of organic carbon sources. Growth factors were not required, and cells could fix N2. Dark, microaerobic growth occurred in the presence of both an organic carbon source and thiosulfate. Sulfide and thiosulfate served as electron donors for photoautotrophy, which required elevated levels of CO2. Phylogenetic analysis placed strain SC5 basal to the clade of the genus Thiocapsa in the family Chromatiaceae with a 96.7% sequence similarity to its closest relative, Thiocapsa roseopersicina strain 1711T (DSM217T). The unique assemblage of physiological and phylogenetic properties of strain SC5 defines it as a new species of the genus Thiocapsa, and we describe strain SC5 herein as Tca. imhoffii, sp. nov. PMID:17661016

  18. Anditalea andensis ANESC-ST - An Alkaliphilic Halotolerant Bacterium Capable of Electricity Generation under Alkaline-Saline Conditions

    PubMed Central

    Shi, Wei; Wang, Victor Bochuan; Zhao, Cui-E; Zhang, Qichun; Loo, Say Chye Joachim; Yang, Liang; Xu, Chenjie

    2015-01-01

    A great challenge in wastewater bioremediation is the sustained activity of viable microorganisms, which can contribute to the breakdown of waste contaminants, especially in alkaline pH conditions. Identification of extremophiles with bioremediation capability can improve the efficiency of wastewater treatment. Here, we report the discovery of an electrochemically active alkaliphilic halotolerant bacterium, Anditalea andensis ANESC-ST (=CICC10485T=NCCB 100412T), which is capable of generating bioelectricity in alkaline–saline conditions. A. andensis ANESC-ST was shown to grow in alkaline conditions between pH 7.0–11.0 and also under high salt condition (up to 4 wt% NaCl). Electrical output was further demonstrated in microbial fuel cells (MFCs) with an average current density of ~0.5 µA/cm2, even under the harsh condition of 4 wt% NaCl and pH 9.0. Subsequent introduction of secreted extracellular metabolites into MFCs inoculated with Escherichia coli or Pseudomonas aeruginosa yielded enhanced electrical output. The ability of A. andensis ANESC-ST to generate energy under alkaline–saline conditions points towards a solution for bioelectricity recovery from alkaline–saline wastewater. This is the first report of A.andensis ANESC-ST producing bioelectricity at high salt concentration and pH. PMID:26171779

  19. Anditalea andensis ANESC-ST--An Alkaliphilic Halotolerant Bacterium Capable of Electricity Generation under Alkaline-Saline Conditions.

    PubMed

    Shi, Wei; Wang, Victor Bochuan; Zhao, Cui-E; Zhang, Qichun; Loo, Say Chye Joachim; Yang, Liang; Xu, Chenjie

    2015-01-01

    A great challenge in wastewater bioremediation is the sustained activity of viable microorganisms, which can contribute to the breakdown of waste contaminants, especially in alkaline pH conditions. Identification of extremophiles with bioremediation capability can improve the efficiency of wastewater treatment. Here, we report the discovery of an electrochemically active alkaliphilic halotolerant bacterium, Anditalea andensis ANESC-ST (=CICC10485T=NCCB 100412T), which is capable of generating bioelectricity in alkaline-saline conditions. A. andensis ANESC-ST was shown to grow in alkaline conditions between pH 7.0-11.0 and also under high salt condition (up to 4 wt% NaCl). Electrical output was further demonstrated in microbial fuel cells (MFCs) with an average current density of ~0.5 µA/cm2, even under the harsh condition of 4 wt% NaCl and pH 9.0. Subsequent introduction of secreted extracellular metabolites into MFCs inoculated with Escherichia coli or Pseudomonas aeruginosa yielded enhanced electrical output. The ability of A. andensis ANESC-ST to generate energy under alkaline-saline conditions points towards a solution for bioelectricity recovery from alkaline-saline wastewater. This is the first report of A.andensis ANESC-ST producing bioelectricity at high salt concentration and pH. PMID:26171779

  20. Effects of genetic modifications and fermentation conditions on 2,3-butanediol production by alkaliphilic Bacillus subtilis.

    PubMed

    Białkowska, Aneta M; Jędrzejczak-Krzepkowska, Marzena; Gromek, Ewa; Krysiak, Joanna; Sikora, Barbara; Kalinowska, Halina; Kubik, Celina; Schütt, Fokko; Turkiewicz, Marianna

    2016-03-01

    Two recombinants of alkaliphilic Bacillus subtilis LOCK 1086, constructed via different strategies such as cloning the gene encoding bacterial hemoglobin from Vitreoscilla stercoraria (vhb) and overexpression of the gene encoding acetoin reductase/2,3-butanediol dehydrogenase (bdhA) from B. subtilis LOCK 1086, did not produce more 2,3-butanediol (2,3-BD) than the parental strain. In batch fermentations, this strain synthesized 9.46 g/L in 24 h and 12.80 g/L 2,3-BD in 46 h from sugar beet molasses and an apple pomace hydrolysate, respectively. 2,3-BD production by B. subtilis LOCK 1086 was significantly enhanced in fed-batch fermentations. The highest 2,3-BD concentration (75.73 g/L in 114 h, productivity of 0.66 g/L × h) was obtained in the sugar beet molasses-based medium with four feedings with glucose. In a medium based on the apple pomace hydrolysate with three feedings with sucrose, B. subtilis LOCK 1086 produced up to 51.53 g/L 2,3-BD (in 120 h, productivity of 0.43 g/L × h). PMID:26590588

  1. Symbiont acquisition as neoseme: origin of species and higher taxa

    NASA Technical Reports Server (NTRS)

    Bermudes, D.; Margulis, L.

    1987-01-01

    We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.

  2. Instantaneous threat escape and differentiated refuge demand among zooplankton taxa.

    PubMed

    Hansson, Lars-Anders; Bianco, Giuseppe; Ekvall, Mikael; Heuschele, Jan; Hylander, Samuel; Yang, Xi

    2016-02-01

    Most animals, including aquatic crustacean zooplankton, perform strong avoidance movements when exposed to a threat, such as ultraviolet radiation (UVR). We here show that the genera Daphnia and Bosmina instantly adjust their vertical position in the water in accordance with the present UVR threat, i.e., seek refuge in deeper waters, whereas other taxa show less response to the threat. Moreover, Daphnia repeatedly respond to UVR pulses, suggesting that they spend more energy on movement than more stationary taxa, for example, during days with fluctuating cloud cover, illustrating nonlethal effects in avoiding UVR threat. Accordingly, we also show that the taxa with the most contrasting behavioral responses differ considerably in photoprotection, suggesting different morphological and behavioral strategies in handling the UVR threat. In a broader context, our studies on individual and taxa specific responses to UVR provide insights into observed spatial and temporal distribution in natural ecosystems. PMID:27145603

  3. Insects as a Nitrogen Source for Plants

    PubMed Central

    Behie, Scott W.; Bidochka, Michael J.

    2013-01-01

    Many plants have evolved adaptations in order to survive in low nitrogen environments. One of the best-known adaptations is that of plant symbiosis with nitrogen-fixing bacteria; this is the major route by which nitrogen is incorporated into plant biomass. A portion of this plant-associated nitrogen is then lost to insects through herbivory, and insects represent a nitrogen reservoir that is generally overlooked in nitrogen cycles. In this review we show three specialized plant adaptations that allow for the recovery of insect nitrogen; that is, plants gaining nitrogen from insects. First, we show specialized adaptations by carnivorous plants in low nitrogen habitats. Insect carnivorous plants such as pitcher plants and sundews (Nepenthaceae/Sarraceniaceae and Drosera respectively) are able to obtain substantial amounts of nitrogen from the insects that they capture. Secondly, numerous plants form associations with mycorrhizal fungi that can provide soluble nitrogen from the soil, some of which may be insect-derived nitrogen, obtained from decaying insects or insect frass. Finally, a specialized group of endophytic, insect-pathogenic fungi (EIPF) provide host plants with insect-derived nitrogen. These soil-inhabiting fungi form a remarkable symbiosis with certain plant species. They can infect a wide range of insect hosts and also form endophytic associations in which they transfer insect-derived nitrogen to the plant. Root colonizing fungi are found in disparate fungal phylogenetic lineages, indicating possible convergent evolutionary strategies between taxa, evolution potentially driven by access to carbon-containing root exudates. PMID:26462427

  4. Insects as a Nitrogen Source for Plants.

    PubMed

    Behie, Scott W; Bidochka, Michael J

    2013-01-01

    Many plants have evolved adaptations in order to survive in low nitrogen environments. One of the best-known adaptations is that of plant symbiosis with nitrogen-fixing bacteria; this is the major route by which nitrogen is incorporated into plant biomass. A portion of this plant-associated nitrogen is then lost to insects through herbivory, and insects represent a nitrogen reservoir that is generally overlooked in nitrogen cycles. In this review we show three specialized plant adaptations that allow for the recovery of insect nitrogen; that is, plants gaining nitrogen from insects. First, we show specialized adaptations by carnivorous plants in low nitrogen habitats. Insect carnivorous plants such as pitcher plants and sundews (Nepenthaceae/Sarraceniaceae and Drosera respectively) are able to obtain substantial amounts of nitrogen from the insects that they capture. Secondly, numerous plants form associations with mycorrhizal fungi that can provide soluble nitrogen from the soil, some of which may be insect-derived nitrogen, obtained from decaying insects or insect frass. Finally, a specialized group of endophytic, insect-pathogenic fungi (EIPF) provide host plants with insect-derived nitrogen. These soil-inhabiting fungi form a remarkable symbiosis with certain plant species. They can infect a wide range of insect hosts and also form endophytic associations in which they transfer insect-derived nitrogen to the plant. Root colonizing fungi are found in disparate fungal phylogenetic lineages, indicating possible convergent evolutionary strategies between taxa, evolution potentially driven by access to carbon-containing root exudates. PMID:26462427

  5. The role of monovalent cation/proton antiporters in Na(+)-resistance and pH homeostasis in Bacillus: an alkaliphile versus a neutralophile.

    PubMed

    Krulwich, T A; Cheng, J; Guffanti, A A

    1994-11-01

    Both neutralophilic Bacillus subtilis and alkaliphilic Bacillus firmus OF4 depend upon electrogenic Na+/H+ antiporters, which are energized by the gradients established by respiration-coupled proton extrusion, to achieve Na(+)-resistance and pH homeostasis when the external pH is very alkaline. The interplay of proton and sodium cycles is discussed. In B. subtilis, pH homeostasis, up to pH9, can be achieved using K+ when Na+ is unavailable or when the gene encoding the Na+/H+ antiporter that is involved in Na(+)-dependent pH homeostasis is disrupted. That gene is a member of the tetracycline efflux family of genes. A second gene, encoding a Na+/H+ antiporter that functions in Na(+)-resistance, has been identified, and candidates for the K+/H+ antiporter genes are under investigation. Aggregate Na+/H+ antiport activity in B. subtilis is as much as 10 times lower than in the alkaliphile, and the neutralophile cannot regulate its internal pH upon a shift to pH 10.5. Upon such a shift, there is a pronounced reduction in the generation of a primary electrochemical proton gradient. The alkaliphile, by contrast, maintains substantial driving forces and regulates its internal pH in an exclusively Na(+)-coupled manner upon shifts to either pH 8.7 or 10.5. One gene locus has been identified and a second locus has been inferred as encoding relevant antiporter activities. PMID:7823040

  6. Expression and functional analysis of two NhaD type antiporters from the halotolerant and alkaliphilic Halomonas sp. Y2.

    PubMed

    Cui, Yanbing; Cheng, Bin; Meng, Yiwei; Li, Chunfang; Yin, Huijia; Xu, Ping; Yang, Chunyu

    2016-09-01

    Na(+)/H(+) antiporters play important roles in ion and pH homeostasis. In this study, two NhaD homologues that effectively catalyze Na(+)/H(+) antiporter were identified from Halomonas sp. Y2, a halotolerant and alkaliphilic strain isolated from sodium enriched black liquor. They exhibited high sequence identity of 72 % and similar binding affinities for Na(+) and Li(+) translocation, while having different pH profiles. Ha-NhaD1 was active at pH 6.0 and most active at pH 8.0-8.5, whereas Ha-NhaD2 lacked activity at pH 6.0 but exhibited maximum activity at pH 9.5 or higher. Based on multiple alignments, 11 partially conserved residues were selected and corresponding mutants were generated for Ha-NhaD1. As expected, replacement of most of the hydrophobic residues abolished the cation exchange activities. Three serine residues at positions 200, 282 and 353 in Ha-NhaD1 were replaceable by alanines with partial retention of activity. The S353A mutant exhibited significantly reduced binding affinity for Na(+) and Li(+), while S282 mutant exhibited an alkaline shift of about 1.5 pH units, as compared to the wild type Ha-NhaD1. Serine at position 282 was predicted to be located in transmembrane segment VIII and was found to be important in regulating pH sensitivity in concert with flanking residues. PMID:27315164

  7. Bacillus daqingensis sp. nov., a halophilic, alkaliphilic bacterium isolated from saline-sodic soil in Daqing, China.

    PubMed

    Wang, Shuang; Sun, Lei; Wei, Dan; Zhou, Baoku; Zhang, Junzheng; Gu, Xuejia; Zhang, Lei; Liu, Ying; Li, Yidan; Guo, Wei; Jiang, Shuang; Pan, Yaqing; Wang, Yufeng

    2014-07-01

    An alkaliphilic, moderately halophilic, bacterium, designated strain X10-1(T), was isolated from saline-alkaline soil in Daqing, Heilongjiang Province, China. Strain X10-1(T) was determined to be a Gram-positive aerobe with rod-shaped cells. The isolate was catalase-positive, oxidase-negative, non-motile, and capable of growth at salinities of 0-16% (w/v) NaCl (optimum, 3%). The pH range for growth was 7.5-11.0 (optimum, pH 10.0). The genomic DNA G+C content was 47.7 mol%. Its major isoprenoid quinone was MK-7 and its cellular fatty acid profile mainly consisted of anteiso-C15:0, anteiso-C17:0, iso-C15:0, C16:0, and iso-C16:0. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that X10-1(T) is a member of the genus Bacillus, being most closely related to B. saliphilus DSM15402(T) (97.8% similarity) and B. agaradhaerens DSM 8721(T) (96.2%). DNA-DNA relatedness to the type strains of these species was less than 40%. On the basis of the phylogenetic, physiological, and biochemical data, strain X10-1(T) represents a novel species of the genus Bacillus, for which the name Bacillus daqingensis sp. nov. is proposed. The type strain is X10-1(T) (=NBRC 109404(T) = CGMCC 1.12295(T)). PMID:24879344

  8. Acetoanaerobium pronyense sp. nov., an anaerobic alkaliphilic bacterium isolated from a carbonate chimney of the Prony Hydrothermal Field (New Caledonia).

    PubMed

    Bes, Méline; Merrouch, Mériem; Joseph, Manon; Quéméneur, Marianne; Payri, Claude; Pelletier, Bernard; Ollivier, Bernard; Fardeau, Marie-Laure; Erauso, Gaël; Postec, Anne

    2015-08-01

    A novel anaerobic bacterial strain, ST07-YET, was isolated from a carbonate chimney of the Prony Hydrothermal Field (PHF) in New Caledonia. Cells were Gram-stain-positive, straight rods (0.7-0.8 × 3.0-5.0 μm) and motile by means of lateral flagella. Strain ST07-YET was mesophilic (optimum 35 °C), moderately alkaliphilic and halotolerant (optimum pH 8.7 and 5 g l- 1 NaCl). Elemental sulfur, sulfate, thiosulfate, sulfite, nitrate and nitrite were not used as terminal electron acceptors. Yeast extract, peptone, tryptone, Casamino acids, crotonate, pyruvate, galactose, maltose, sucrose, ribose, trehalose and glucose were used as carbon sources. Glucose fermentation led to acetate, H2 and CO2 formation. Arginine, serine, histidine, lysine, methionine and cysteine improved growth, but the Stickland reaction was negative for the combinations of amino acids tested. The major metabolic products from yeast extract fermentation were H2, CO2, acetate, butyrate, isobutyrate, isovalerate and propionate. The predominant cellular fatty acids were C16  :  0, C16  :  1cis9, C14  :  0 and C16  :  1cis7 (>5 % of total fatty acids). The G+C content of the genomic DNA was 32.9 mol%. Phylogenetic analysis revealed that strain ST07-YET was most closely related to Clostridium sticklandii DSM 519T and Acetoanaerobium noterae NOT-3T (96.7 % and 96.8 % 16S rRNA gene sequence similarity, respectively). On the basis of phylogenetic, chemotaxonomic and physiological properties, strain ST07-YET is proposed to represent a novel species of the genus Acetoanaerobium (order Clostridiales, phylum Firmicutes) with the name Acetoanaerobium pronyense sp. nov. The type strain is ST07-YET ( = DSM 27512T = JCM 19400T). PMID:25948619

  9. Halomonas alkaliphila sp. nov., a novel halotolerant alkaliphilic bacterium isolated from a salt pool in Campania (Italy).

    PubMed

    Romano, Ida; Lama, Licia; Nicolaus, Barbara; Poli, Annarita; Gambacorta, Agata; Giordano, Assunta

    2006-12-01

    A halotolerant and alkaliphilic Gram-negative bacterium, strain 18bAG(T), that grows aerobically at the optimum temperature of 37 degrees C, and at pH 7.5-10 (optimum 9.0), was isolated from a salt pool located in Montefredane in Campania Region (South of Italy). The isolate tolerated high concentration of NaCl up to 20%. Strain 18bAG(T) accumulated osmolytes and polyhydroxybutyrate, produced exopolysaccharide and possessed alpha-glucosidase activity. The predominant respiratory quinones were ubiquinones, Q8 and Q6(6H); phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol were the predominant polar lipids. Major fatty acids were C16 : 1, C16 : 0, and C18 : 0. On the basis of 16S rRNA gene sequence similarity, 18bAG(T) was shown to belong to Halomonas genus. Analysis of 16S rRNA gene revealed a high similarity of strain 18bAG(T) to Halomonas venusta (DSM 4743(T)) and Halomonas hydrothermalis (DSM 15725(T)). Level of DNA-DNA relatedness between strain 18bAG(T) and the most related species Halomonas venusta and Halomonas hydrothermalis was 56.0% and 41.2%, respectively. The G+C content (mol%) of DNA was 53.0. The RiboPrinting patterns of Halomonas venusta and 18AG(T) showed a pattern similarity of 0.50. On the basis of genomic information and phenotypic characteristics strain 18bAG(T) represents a new species, for which the name Halomonas alkaliphila sp. nov. is proposed. The type strain is 18bAG(T) (=DSM 16354T =ATCC BAA-953T). PMID:17325447

  10. Bacillus ligniniphilus sp. nov., an alkaliphilic and halotolerant bacterium isolated from sediments of the South China Sea.

    PubMed

    Zhu, Daochen; Tanabe, Shoko-Hosoi; Xie, Changxiao; Honda, Daiske; Sun, Jianzhong; Ai, Lianzhong

    2014-05-01

    An alkaliphilic and halotolerant Gram-stain-positive bacterium, which was isolated from sediment samples from the South China Sea, was subjected to a taxonomic study. The isolate, strain L1T, grew well at a wide range of temperatures and pH values, 10.0-45.0 °C and pH 6-11, with optima at 30 °C and pH 9.0, respectively. The growth of strain L1T occurred at total salt concentrations of 0-10% (w/v) with an optimum at 2% (w/v). Phylogenetic analysis based on 16S rRNA sequence comparison indicated that the isolate represented a member of the genus Bacillus. The strains most closely related to strain L1T were Bacillus nanhaiisediminis JCM 16507T, Bacillus halodurans DSM 497T and Bacillus pseudofirmus DSM 8715T, with 16S rRNA similarities of 96.5%, 95.9% and 95.7%, respectively. DNA-DNA hybridization of strain L1T with the type strains of the most closely related species, B. nanhaiisediminis JCM 16507T, B. halodurans DSM 497T and B. pseudofirmus DSM 8715T, showed reassociation values of about 21.7%, 14.3% and 13.9%, respectively. The DNA G+C content of strain L1T was 40.76 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant cellular fatty acids of strain L1T were iso-C14 : 0 and anteiso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the phenotypic and phylogenetic characteristics, it is proposed that strain L1T (=JCM 18543T=DSM 26145T) should be classified as the type strain of Bacillus ligniniphilus sp. nov. PMID:24554634

  11. New taxa, notes and new synonymy in Neoibidionini (Cerambycidae, Coleoptera).

    PubMed

    Martins, Ubirajara R; Galileo, Maria Helena M

    2014-01-01

    New taxa, notes, and new synonymy in Neoibidionini (Cerambycidae, Coleoptera) are given. New taxa are described from Ecuador: Compsibidion inflatum sp. nov., Bezarkia gen. nov. and B. suturalis sp. nov., Corimbion antennatum sp. nov. and Neocompsa muira sp. nov.; from México: Neocompsa chiapensis sp. nov., and from French Guyana: Kunaibidion giesberti sp. nov. Pygmodeon maculatum Martins & Galileo, 2012 is considered a new synonym of Heterachthes xyleus Martins, 1974 which is transferred to the genus Pygmodeon as a new combination. Notes on variability and new records of Asynapteron equatorianum (Martins, 1960) are presented. PMID:24869549

  12. The enrichment of an alkaliphilic biofilm consortia capable of the anaerobic degradation of isosaccharinic acid from cellulosic materials incubated within an anthropogenic, hyperalkaline environment

    PubMed Central

    Charles, C. J.; Rout, S. P.; Garratt, E. J.; Patel, K.; Laws, A. P.; Humphreys, P. N.

    2015-01-01

    Anthropogenic hyperalkaline sites provide an environment that is analogous to proposed cementitious geological disposal facilities (GDF) for radioactive waste. Under anoxic, alkaline conditions cellulosic wastes will hydrolyze to a range of cellulose degradation products (CDP) dominated by isosaccharinic acids (ISA). In order to investigate the potential for microbial activity in a cementitious GDF, cellulose samples were incubated in the alkaline (∼pH 12), anaerobic zone of a lime kiln waste site. Following retrieval, these samples had undergone partial alkaline hydrolysis and were colonized by a Clostridia-dominated biofilm community, where hydrogenotrophic, alkaliphilic methanogens were also present. When these samples were used to establish an alkaline CDP fed microcosm, the community shifted away from Clostridia, methanogens became undetectable and a flocculate community dominated by Alishewanella sp. established. These flocs were composed of bacteria embedded in polysaccharides and proteins stabilized by extracellular DNA. This community was able to degrade all forms of ISA with >60% of the carbon flow being channelled into extracellular polymeric substance (EPS) production. This study demonstrated that alkaliphilic microbial communities can degrade the CDP associated with some radioactive waste disposal concepts at pH 11. These communities divert significant amounts of degradable carbon to EPS formation, suggesting that EPS has a central role in the protection of these communities from hyperalkaline conditions. PMID:26195600

  13. The enrichment of an alkaliphilic biofilm consortia capable of the anaerobic degradation of isosaccharinic acid from cellulosic materials incubated within an anthropogenic, hyperalkaline environment.

    PubMed

    Charles, C J; Rout, S P; Garratt, E J; Patel, K; Laws, A P; Humphreys, P N

    2015-08-01

    Anthropogenic hyperalkaline sites provide an environment that is analogous to proposed cementitious geological disposal facilities (GDF) for radioactive waste. Under anoxic, alkaline conditions cellulosic wastes will hydrolyze to a range of cellulose degradation products (CDP) dominated by isosaccharinic acids (ISA). In order to investigate the potential for microbial activity in a cementitious GDF, cellulose samples were incubated in the alkaline (∼pH 12), anaerobic zone of a lime kiln waste site. Following retrieval, these samples had undergone partial alkaline hydrolysis and were colonized by a Clostridia-dominated biofilm community, where hydrogenotrophic, alkaliphilic methanogens were also present. When these samples were used to establish an alkaline CDP fed microcosm, the community shifted away from Clostridia, methanogens became undetectable and a flocculate community dominated by Alishewanella sp. established. These flocs were composed of bacteria embedded in polysaccharides and proteins stabilized by extracellular DNA. This community was able to degrade all forms of ISA with >60% of the carbon flow being channelled into extracellular polymeric substance (EPS) production. This study demonstrated that alkaliphilic microbial communities can degrade the CDP associated with some radioactive waste disposal concepts at pH 11. These communities divert significant amounts of degradable carbon to EPS formation, suggesting that EPS has a central role in the protection of these communities from hyperalkaline conditions. PMID:26195600

  14. Contribution of the Cell Wall Component Teichuronopeptide to pH Homeostasis and Alkaliphily in the Alkaliphile Bacillus lentus C-125

    PubMed Central

    Aono, Rikizo; Ito, Masahiro; Machida, Takayoshi

    1999-01-01

    A teichuronopeptide (TUP) is one of major structural components of the cell wall of the facultative alkaliphilic strain Bacillus lentus C-125. A mutant defective in TUP synthesis grows slowly at alkaline pH. An upper limit of pH for growth of the mutant was 10.4, while that of the parental strain C-125 was 10.8. Gene tupA, directing synthesis of TUP, was cloned from C-125 chromosomal DNA. The primary translation product of this gene is likely a cytoplasmic protein (57.3 kDa) consisting of 489 amino acid residues. Introduction of the tupA gene into the TUP-defective mutant complemented the mutation responsible for the pleiotropic phenotypes of the mutant, leading to simultaneous disappearance of the defect in TUP synthesis, the diminished ability for cytoplasmic pH homeostasis, and the low tolerance for alkaline conditions. These results demonstrate that the acidic polymer TUP in the cell wall plays a role in pH homeostasis in this alkaliphile. PMID:10542159

  15. Production of extremely alkaliphilic, halotolerent, detergent, and thermostable mannanase by the free and immobilized cells of Bacillus halodurans PPKS-2. Purification and characterization.

    PubMed

    Vijayalaxmi, S; Prakash, P; Jayalakshmi, S K; Mulimani, V H; Sreeramulu, K

    2013-09-01

    The alkaliphilic Bacillus halodurans strain PPKS-2 was shown to produce extracellular extreme alkaliphilic, halotolerent, detergent, and thermostable mannanase activity. The cultural conditions for the maximum enzyme production were optimized with respect to pH, temperature, NaCl, and inexpensive agro wastes as substrates. Mannanase production was enhanced more than 4-fold in the presence of 1 % defatted copra meal and 0.5 % peptone or feather hydrolysate at pH 11 and 40 °C. Mannanase was purified to 10.3-fold with 34.6 % yield by ion exchange and gel filtration chromatography methods. Its molecular mass was estimated to be 22 kDa by SDS-PAGE. The mannanase had maximal activity at pH 11 and 70 °C. This enzyme was active over a broad range of NaCl (0-16 %) and thermostable retaining 100 % of the original activity at 70 °C for 3 h. Immobilization of whole cells proved to be effective for continuous production of mannanase. Since the strain PPKS-2 grows on cheaper agro wastes such as defatted copra meal, corn husk, jowar bagasse, and wheat bran, these can be exploited for mannanase production on an industrial scale. PMID:23839508

  16. Determining phylogenetic networks from inter-taxa distances.

    PubMed

    Bordewich, Magnus; Semple, Charles

    2016-08-01

    We consider the problem of determining the topological structure of a phylogenetic network given only information about the path-length distances between taxa. In particular, one of the main results of the paper shows that binary tree-child networks are essentially determined by such information. PMID:26666756

  17. IDENTIFICATION OF ERYTHROXYLUM TAXA BY AFLP DNA ANALYSIS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Erythroxylum coca, indigenous to the Andean region of South America, is grown historically as a source of homeopathic medicine. However, in the last century, cultivation of E. coca var. coca and three closely-related taxa for the production of illicit cocaine has become a major global problem. Two s...

  18. Eliciting the Functional Taxonomy from protein annotations and taxa

    PubMed Central

    Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

    2016-01-01

    The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

  19. STORAGE BEHAVIOR OF SEEDS FROM NATIVE HAWAIIAN TAXA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ex situ conservation is required to preserve genetic diversity of the 956 species native to Hawai’i (89% endemism, 30% federally-listed as endangered or threatened). Optimizing storage procedures to maximize seed longevity is critical to the effort. Storage behavior of seeds from about 280 taxa was ...

  20. Eliciting the Functional Taxonomy from protein annotations and taxa.

    PubMed

    Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

    2016-01-01

    The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

  1. The hominin fossil record: taxa, grades and clades

    PubMed Central

    Wood, Bernard; Lonergan, Nicholas

    2008-01-01

    This paper begins by reviewing the fossil evidence for human evolution. It presents summaries of each of the taxa recognized in a relatively speciose hominin taxonomy. These taxa are grouped in grades, namely possible and probable hominins, archaic hominins, megadont archaic hominins, transitional hominins, pre-modern Homo and anatomically modern Homo. The second part of this contribution considers some of the controversies that surround hominin taxonomy and systematics. The first is the vexed question of how you tell an early hominin from an early panin, or from taxa belonging to an extinct clade closely related to the Pan-Homo clade. Secondly, we consider how many species should be recognized within the hominin fossil record, and review the philosophies and methods used to identify taxa within the hominin fossil record. Thirdly, we examine how relationships within the hominin clade are investigated, including descriptions of the methods used to break down an integrated structure into tractable analytical units, and then how cladograms are generated and compared. We then review the internal structure of the hominin clade, including the problem of how many subclades should be recognized within the hominin clade, and we examine the reliability of hominin cladistic hypotheses. The last part of the paper reviews the concepts of a genus, including the criteria that should be used for recognizing genera within the hominin clade. PMID:18380861

  2. Na+-stimulated ATPase of alkaliphilic halotolerant cyanobacterium Aphanothece halophytica translocates Na+ into proteoliposomes via Na+ uniport mechanism

    PubMed Central

    2010-01-01

    Background When cells are exposed to high salinity conditions, they develop a mechanism to extrude excess Na+ from cells to maintain the cytoplasmic Na+ concentration. Until now, the ATPase involved in Na+ transport in cyanobacteria has not been characterized. Here, the characterization of ATPase and its role in Na+ transport of alkaliphilic halotolerant Aphanothece halophytica were investigated to understand the survival mechanism of A. halophytica under high salinity conditions. Results The purified enzyme catalyzed the hydrolysis of ATP in the presence of Na+ but not K+, Li+ and Ca2+. The apparent Km values for Na+ and ATP were 2.0 and 1.2 mM, respectively. The enzyme is likely the F1F0-ATPase based on the usual subunit pattern and the protection against N,N'-dicyclohexylcarbodiimide inhibition of ATPase activity by Na+ in a pH-dependent manner. Proteoliposomes reconstituted with the purified enzyme could take up Na+ upon the addition of ATP. The apparent Km values for this uptake were 3.3 and 0.5 mM for Na+ and ATP, respectively. The mechanism of Na+ transport mediated by Na+-stimulated ATPase in A. halophytica was revealed. Using acridine orange as a probe, alkalization of the lumen of proteoliposomes reconstituted with Na+-stimulated ATPase was observed upon the addition of ATP with Na+ but not with K+, Li+ and Ca2+. The Na+- and ATP-dependent alkalization of the proteoliposome lumen was stimulated by carbonyl cyanide m - chlorophenylhydrazone (CCCP) but was inhibited by a permeant anion nitrate. The proteoliposomes showed both ATPase activity and ATP-dependent Na+ uptake activity. The uptake of Na+ was enhanced by CCCP and nitrate. On the other hand, both CCCP and nitrate were shown to dissipate the preformed electric potential generated by Na+-stimulated ATPase of the proteoliposomes. Conclusion The data demonstrate that Na+-stimulated ATPase from A. halophytica, a likely member of F-type ATPase, functions as an electrogenic Na+ pump which transports only

  3. Bacillus lindianensis sp. nov., a novel alkaliphilic and moderately halotolerant bacterium isolated from saline and alkaline soils.

    PubMed

    Dou, Guiming; Liu, Hongcan; He, Wei; Ma, Yuchao

    2016-01-01

    Two alkaliphilic and halotolerant Gram-stain positive, rod-shaped and endospore-forming bacteria, designated strains 12-3(T) and 12-4, were isolated from saline and alkaline soils collected in Lindian county, Heilongjiang province, China. Both strains were observed to grow well at a wide range of temperature and pH values, 10-45 °C and pH 8-12, with optimal growth at 37 °C and pH 9.0, respectively. Growth of the two strains was found to occur at total salt concentrations of 0-12 % (w/v), with an optimum at 4 % (w/v). The G+C contents of the genomic DNA of strains 12-3(T) and 12-4 were determined to be 42.7 and 42.4 mol%, respectively, and the major cellular fatty acids were identified as anteiso-C15:0 and anteiso-C17:0. In isolate 12-3(T), meso-diaminopimelic acid was found to be the diagnostic diamino acid of the cell wall peptidoglycan; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol were identified as the major cellular polar lipids; and menaquinone-7 was identified as the predominant isoprenoid quinone. Strains 12-3(T) and 12-4 share very close 16S rRNA gene sequence similarity (99.74 %) and their DNA-DNA relatedness was 95.3 ± 0.63 %, meaning that the two strains can be considered to belong to the same species. 16S rRNA gene sequence-based phylogenetic analysis revealed strains 12-3(T) and 12-4 exhibit high similarities to Bacillus pseudofirmus DSM 8715(T) (98.7 %), Bacillus marmarensis DSM 21297(T) (97.2 %) and Bacillus nanhaiisediminis CGMCC 1.10116(T) (97.1 and 97.0 %, respectively). DNA-DNA hybridization values between isolate 12-3(T) and the type strains of closely related Bacillus species were below 30 %. On the basis of the polyphasic evidence presented, strains 12-3(T) and 12-4 are considered to represent a novel species of the genus Bacillus, for which the name Bacillus lindianensis sp. nov. is proposed. The type strain is 12-3(T) (DSM 26864(T) = CGMCC 1.12717(T)). PMID:26604103

  4. Alkalitalea saponilacus gen. nov., sp. nov., an obligately anaerobic, alkaliphilic, xylanolytic bacterium from a meromictic soda lake.

    PubMed

    Zhao, Baisuo; Chen, Shulin

    2012-11-01

    A Gram-positive, obligately anaerobic, motile, slender, flexible rod, designated SC/BZ-SP2(T), was isolated from mixed alkaline water and sediment of Soap Lake, Washington State, USA. Strain SC/BZ-SP2(T) formed salmon to pink colonies and was alkaliphilic. The isolate grew at pH(35 °C) 7.5-10.5 (optimum pH(35 °C) 9.7), at 8-40 °C (optimum 35-37 °C) and with 0.35-1.38 M Na(+) (optimum 0.44-0.69 M Na(+)). The isolate utilized L-arabinose, D-ribose, D-xylose, D-fructose, D-mannose, D-galactose, cellobiose, maltose, sucrose, trehalose, sorbitol, xylan, malate and yeast extract as carbon and energy sources; best growth was observed with L-arabinose, cellobiose, maltose and trehalose. The major fermentation products from beechwood xylan were propionate and acetate. The dominant fatty acids were iso-C(15:0), anteiso-C(15:0), iso-C(17:0) 3-OH, C(17:0) 3-OH and C(15:0) 3-OH. The cell-wall sugars were ribose, xylose, galactose and glucose. Thiosulfate and sulfite could be reduced to sulfide. The genomic DNA G+C content was 39.5 ± 0.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SC/BZ-SP2(T) belonged to the family Marinilabiliaceae of the order Bacteroidales, class Bacteroidia. The most closely related strains were Alkaliflexus imshenetskii Z-7010(T) (91.8% 16S rRNA gene sequence similarity), Marinilabilia salmonicolor Cy s1(T) (91.0%) and Anaerophaga thermohalophila Fru22(T) (90.4%). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain SC/BZ-SP2(T) represents a novel species in a new genus of the family Marinilabiliaceae, for which the name Alkalitalea saponilacus gen. nov., sp. nov. is proposed. The type strain of Alkalitalea saponilacus is SC/BZ-SP2(T) (=ATCC BAA-2172(T) =DSM 24412(T)). PMID:22199219

  5. Anaerovirgula multivorans gen. nov., sp. nov., a Novel Spore-Forming, Alkaliphilic Anaerobe Isolated from Owens Lake, California, USA

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena V.; Itoh, Takashi; Krader, Paul; Whitman, William B.; Hoover, Richard B.

    2006-01-01

    A novel, alkaliphilic, obligately anaerobic bacterium, strain SCAT, was isolated from mud sediments of a soda lake in California, USA. The rod-shaped cells were motile, Gram-positive, formed spores and were 0.4-0.5x2.5-5.0 micrometers in size. Growth occurred within the pH range 6.7-10.0 and was optimal at pH 8.5. The temperature range for growth was 10-45 degrees C, with optimal growth at 35 degrees C. NaCl was required for growth. Growth occurred at 0.5-9.0% (w/v) NaCl and was optimal at 1-2% (w/v). The novel isolate was a catalase-negative chemo-organoheterotroph that fermented sugars, proteolysis products, some organic and amino acids, glycerol, d-cellobiose and cellulose. It was also capable of growth by the Stickland reaction. Strain SCAT was sensitive to tetracycline, chloramphenicol, rifampicin and gentamicin, but it was resistant to ampicillin and kanamycin. The G+C content of the genomic DNA was 34.2 mol%. Major fatty acid components were C14:0, iso-C15:0, C16:1omega9c and C16:0. 16S rRNA gene sequence analysis of strain SCAT showed a similarity of approximately 97% with the type strains of Clostridium formicaceticum and Clostridium aceticum in clostridial cluster XI and a similarity of less than 94.2% to any other recognized Clostridium species and those of related genera in this cluster. Strain SCAT was clearly differentiated from C. formicaceticum and C. aceticum based on comparison of their phenotypic properties and fatty acid profiles, as well as low levels of DNA-DNA relatedness between strain SCAT and the type strains of these two species. Therefore, strain SCAT is considered to represent a novel species of a new genus, Anaerovirgula multivorans gen. nov., sp. nov., in clostridial cluster XI. The type strain is SCAT (=ATCC BAA-1084T=JCM 12857T=DSM 17722T=CIP 107910T).

  6. Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches.

    PubMed

    Schirrmeister, Bettina E; Anisimova, Maria; Antonelli, Alexandre; Bagheri, Homayoun C

    2011-07-01

    Within prokaryotes cyanobacteria represent one of the oldest and morphologically most diverse phyla on Earth. The rise of oxygen levels in the atmosphere 2.32-2.45 billion years ago is assigned to the photosynthetic activity of ancestors from this phylum. Subsequently cyanobacteria were able to adapt to various habitats evolving a comprehensive set of different morphotypes. In a recent study we showed that this evolution is not a gradual transition from simple unicellular to more complex multicellular forms as often assumed. Instead complexity was lost several times and regained at least once. An understanding of the genetic basis of these transitions would be further strengthened by phylogenomic approaches. However, considering that new methods for phylogenomic analyses are emerging, it is unfortunate that genomes available today are comprised of an unbalanced sampling of taxa. We propose avenues to remedy this by identifying taxa that would improve the representation of phylogenetic diversity in this phylum. PMID:21966561

  7. Deciphering The Role of Plankton Taxa in Particle Flux

    NASA Astrophysics Data System (ADS)

    Neuer, Susanne; Amacher, Jessica; DeMartini, Francesca; Wilson, Stephanie

    2015-04-01

    The sinking of phytoplankton derived particulate organic matter to the deep ocean constitutes an important removal process of atmospheric CO2 and is termed the biological carbon pump. Understanding the taxon specific connection between phytoplankton communities in the euphotic zone and their contribution to particle flux is a high priority in current oceanographic research and provides a basis to evaluate how carbon export might change in a future ocean. Here we present results from DNA-based molecular studies that investigate the taxonomic composition of cyanobacterial and protist communities retrieved from shallow particle traps in comparison to those living in the euphotic zone. This research has been mainly carried out in the Sargasso Sea at the Bermuda Atlantic Time-series Study site (BATS). Trap material collected at this oligotrophic ocean site reveals a surprisingly high diversity of small, non-mineral ballasted taxa, some of which are over-represented compared to the euphotic zone communities. But the majority of clones in the traps belong to mostly heterotrophic protist taxa. By analyzing the fingerprints of prey DNA in guts and fecal pellets of dominant zooplankton grazers we find that there is a close link between prey utilization and the recovery of those taxa in the traps, showing the importance of fecal pellets in packaging and mediating their flux out of the euphotic zone.

  8. Multi-taxa trait and functional responses to physical disturbance.

    PubMed

    Pedley, Scott M; Dolman, Paul M

    2014-11-01

    Examining assemblage trait responses to environmental stressors extends our understanding beyond patterns of taxonomic diversity and composition, with results potentially transferable among bioregions. But the degree to which trait responses may be generalized across taxonomic groups remains incompletely understood. We compared trait responses among carabids, spiders and plants to an experimentally manipulated gradient of physical disturbance, replicated in open habitats within a forested landscape. Recolonization of recently disturbed habitats is expected to favour species with traits that promote greater dispersal ability, independent of taxa. We specifically predicted that physical disturbance would increase the representation of carabids with smaller body size, wings or wing dimorphism, spiders able to disperse aerially, and plants with therophyte life-history and wind-dispersed seed. We sampled 197 arthropod species (14,738 individuals) and 164 species of plant. The strength of association between each trait and the disturbance intensity was quantified by correlating matrices of species by traits, species abundance by sites and sites by environment, with significance assessed by comparison with a null model. Responses of biological traits varied among taxa but could be consistently interpreted in terms of dispersal ability. Trait shifts for carabid and plant assemblages were as predicted and correspond to those observed in other disturbance regimes. Assemblages after disturbance comprised smaller and winged carabids, and smaller plants with wind-dispersed seed, consistent with selection for species with better dispersal ability. In contrast, aerial dispersal did not appear important in spider recolonization, instead terrestrial dispersal ability was suggested by the increased abundance of larger-bodied and cursorial species. However, larger spider body size was also associated with an active-hunting strategy, also favoured in the post-disturbance environment

  9. Tindallia Californiensis sp. nov.: A New Halo-Alkaliphilic Primary Anaerobe, Isolated from Meromictic soda Mono Lake in California and the Correction of Diagnosis for Genus Tindallia

    NASA Technical Reports Server (NTRS)

    Pikuta, Elena; Marsic, Damien; Hoover, Richard B.; Kevbrin, Vadim; Whitman, William B.; Krader, Paul; Cleland, Dave; Six, N. Frank (Technical Monitor)

    2002-01-01

    A novel extremely halo-alkaliphilic, bacterium strain APO (sup T) was isolated from sediments of the athalassic, meromictic, soda Mono Lake in California. Gram positive, spore-forming, slightly curved rods with sizes 0.6-0.7x 2.5-4.0 micrometers which occur singly, in pairs or short curved chains. Cells, are motile by singular subcentral flagellum. Strain APO (sup T) is mesophilic: growth was observed over the temperature range of +10 C to +48 C (optimum +37 C), NaCl concentration range 1-20 %, wt/vol (optimum 3-5%, wt/vol) and pH range 8.0-11.0 (optimum pH 9.5). The novel isolate is strictly halo-alkaliphilic, requires sodium chloride in medium, obligately anaerobic and catalase-negative. Strain APO (sup T) is organo-heterotroph with fermentative type of metabolism, and uses as substrates: peptone, badotryptone, casamino acids, yeast extract, L-serine, L-lysine, L-histidine, L-arginine, and pyruvate. The main end products of growth on peptone medium were: lactate, acetate, propionate, and ethanol. Strain APO (sup T) is resistant to kanamycin, but sensitive to chloramphenicol, tetracycline, and gentamycin. The sum of G+C in DNA is 44.4 mol% (by HPLC method). On the bait of physiological and molecular properties, the isolate was considered as novel species of genus Tindallia; and the name Tindallia californiensis sp. nov., is proposed for new isolate (type strain APO (sup T) - ATCC BAA_393(sup T) = DSMZ 14871 (sup T)).

  10. Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov.

    PubMed

    Zhang, Yong-Guang; Wang, Hong-Fei; Yang, Ling-Ling; Zhou, Xing-Kui; Zhi, Xiao-Yang; Duan, Yan-Qing; Xiao, Min; Zhang, Yuan-Ming; Li, Wen-Jun

    2016-01-01

    A novel obligately halophilic, facultatively alkaliphilic actinobacterium, designated EGI 80759T, was isolated from the rhizosphere of Tamarix hispida Willd, Karamay, Xinjiang province, north-west China. Cells of strain EGI 80759T were Gram-stain-positive, non-motile and non-endospore-forming rods. Strain EGI 80759T showed obligately halophilic growth with a tolerance to 8-25 % (w/v) NaCl (optimum growth at 10-12 %, w/v) and facultatively alkaliphilic growth within the pH range 7.0-11.0 (optimum growth at pH 9.0-10.0). Cell-wall hydrolysates of the isolate contained meso-diaminopimelic acid (peptidoglycan type A1γ), with glucose, glucosamine, ribose and mannose as the major sugars. The major fatty acids identified were 10-methyl-C17 : 0, C17 : 1ω8c and C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA was 72.1 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain EGI 80759T clustered with members of the class Nitriliruptoria and showed highest 16S rRNA gene sequence similarities with Euzebya tangerina F10T (90.3 %) and Nitriliruptor alkaliphilus ANL-iso2T (88.1 %). On the basis of the data obtained from phenotypic and chemotaxonomic studies and the phylogenetic analysis, the isolate is proposed to be a representative of a novel genus and a novel species, Egibacter rhizosphaerae gen. nov., sp. nov., of a proposed novel family, Egibacteraceae fam. nov., and order, Egibacterales ord. nov., within the class Nitriliruptoria. The type strain of the type species, Egibacter rhizosphaerae, is EGI 80759T ( = CGMCC 1.14997T = KCTC 39588T). PMID:26510781

  11. Three-dimensional Magnetic Resonance Imaging of fossils across taxa

    NASA Astrophysics Data System (ADS)

    Mietchen, D.; Aberhan, M.; Manz, B.; Hampe, O.; Mohr, B.; Neumann, C.; Volke, F.

    2007-08-01

    The visibility of life forms in the fossil record is largely determined by the extent to which they were mineralised at the time of their death. In addition to mineral structures, many fossils nonetheless contain detectable amounts of residual water or organic molecules, the analysis of which has become an integral part of current palaeontological research. The methods available for this sort of investigations, though, typically require dissolution or ionisation of the fossil sample or parts thereof, which is an issue with rare taxa and outstanding materials like pathological or type specimens. In such cases, non-destructive techniques could provide an interesting methodological alternative. While Computed Tomography has long been used to study palaeontological specimens, a number of complementary approaches have recently gained ground. These include Magnetic Resonance Imaging (MRI) which had previously been employed to obtain three-dimensional images of pathological belemnites non-invasively on the basis of intrinsic contrast. The present study was undertaken to investigate whether 1H MRI can likewise provide anatomical information about non-pathological belemnites and specimens of other fossil taxa. To this end, three-dimensional MR image series were acquired from intact non-pathological invertebrate, vertebrate and plant fossils. At routine voxel resolutions in the range of several dozens to some hundreds of micrometers, these images reveal a host of anatomical details and thus highlight the potential of MR techniques to effectively complement existing methodological approaches for palaeontological investigations in a wide range of taxa. As for the origin of the MR signal, relaxation and diffusion measurements as well as 1H and 13C MR spectra acquired from a belemnite suggest intracrystalline water or hydroxyl groups, rather than organic residues.

  12. Three-dimensional Magnetic Resonance Imaging of fossils across taxa

    NASA Astrophysics Data System (ADS)

    Mietchen, D.; Aberhan, M.; Manz, B.; Hampe, O.; Mohr, B.; Neumann, C.; Volke, F.

    2008-01-01

    The frequency of life forms in the fossil record is largely determined by the extent to which they were mineralised at the time of their death. In addition to mineral structures, many fossils nonetheless contain detectable amounts of residual water or organic molecules, the analysis of which has become an integral part of current palaeontological research. The methods available for this sort of investigations, though, typically require dissolution or ionisation of the fossil sample or parts thereof, which is an issue with rare taxa and outstanding materials like pathological or type specimens. In such cases, non-destructive techniques could provide a valuable methodological alternative. While Computed Tomography has long been used to study palaeontological specimens, a number of complementary approaches have recently gained ground. These include Magnetic Resonance Imaging (MRI) which had previously been employed to obtain three-dimensional images of pathological belemnites non-invasively on the basis of intrinsic contrast. The present study was undertaken to investigate whether 1H MRI can likewise provide anatomical information about non-pathological belemnites and specimens of other fossil taxa. To this end, three-dimensional MR image series were acquired from intact non-pathological invertebrate, vertebrate and plant fossils. At routine voxel resolutions in the range of several dozens to some hundreds of micrometers, these images reveal a host of anatomical details and thus highlight the potential of MR techniques to effectively complement existing methodological approaches for palaeontological investigations in a wide range of taxa. As for the origin of the MR signal, relaxation and diffusion measurements as well as 1H and 13C MR spectra acquired from a belemnite suggest intracrystalline water or hydroxyl groups, rather than organic residues.

  13. Nuclear DNA Content Variation among Central European Koeleria Taxa

    PubMed Central

    PECINKA, ALES; SUCHÁNKOVÁ, PAVLA; LYSAK, MARTIN A.; TRÁVNÍČEK, BOHUMIL; DOLEŽEL, JAROSLAV

    2006-01-01

    • Background and Aims Polyploidization plays an important role in the evolution of many plant genera, including Koeleria. The knowledge of ploidy, chromosome number and genome size may enable correct taxonomic treatment when other features are insufficient as in Koeleria. Therefore, these characteristics and their variability were determined for populations of six central European Koeleria taxa. • Methods Chromosome number analysis was performed by squashing root meristems, and ploidy and 2C nuclear DNA content were estimated by flow cytometry. • Key Results Three diploids (K. glauca, K. macrantha var. macrantha and var. pseudoglauca), one tetraploid (K. macrantha var. majoriflora), one decaploid (K. pyramidata) and one dodecaploid (K. tristis) were found. The 2C nuclear DNA content of the diploids ranged from 4·85 to 5·20 pg. The 2C DNA contents of tetraploid, decaploid and dodecaploid taxa were 9·31 pg, 22·89 pg and 29·23 pg, respectively. The DNA content of polyploids within the K. macrantha aggregate (i.e. within K. macrantha and K. pyramidata) was smaller than the expected multiple of the diploid genome (K. macrantha var. macrantha). Geography-correlated variation of DNA content was found for some taxa. Czech populations of K. macrantha var. majoriflora had a 5·06 % smaller genome than the Slovak ones. An isolated eastern Slovakian population of K. tristis revealed 8·04 % less DNA than populations from central Slovakia. In central and north-west Bohemia, diploid and tetraploid cytotypes of K. macrantha were sympatric; east from this region diploid populations, and towards the west tetraploid populations were dominant. • Conclusions Remarkable intra-specific inter-population differences in nuclear DNA content were found between Bohemian and Pannonian populations of Koeleria macrantha var. majoriflora and between geographically isolated central and eastern Slovakian populations of K. tristis. These differences occur over a relatively small

  14. Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time

    PubMed Central

    O'Connor, Anne; Wills, Matthew A.

    2016-01-01

    The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence—however measured—also varied throughout the Phanerozoic

  15. Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.

    PubMed

    O'Connor, Anne; Wills, Matthew A

    2016-09-01

    The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpinned claims about temporal and taxonomic patterns of completeness in the fossil record. The most widely used stratigraphic congruence indices are the stratigraphic consistency index (SCI), the modified Manhattan stratigraphic measure (MSM*), and the gap excess ratio (GER) (plus its derivatives; the topological GER and the modified GER). Many factors are believed to variously bias these indices, with several empirical and simulation studies addressing some subset of the putative interactions. This study combines both approaches to quantify the effects (on all five indices) of eight variables reasoned to constrain the distribution of possible values (the number of taxa, tree balance, tree resolution, range of first occurrence (FO) dates, center of gravity of FO dates, the variability of FO dates, percentage of extant taxa, and percentage of taxa with no fossil record). Our empirical data set comprised 647 published animal and plant cladograms spanning the entire Phanerozoic, and for these data we also modeled the effects of mean age of FOs (as a proxy for clade age), the taxonomic rank of the clade, and the higher taxonomic group to which it belonged. The center of gravity of FO dates had not been investigated hitherto, and this was found to correlate most strongly with some measures of stratigraphic congruence in our empirical study (top-heavy clades had better congruence). The modified GER was the index least susceptible to bias. We found significant differences across higher taxa for all indices; arthropods had lower congruence and tetrapods higher congruence. Stratigraphic congruence-however measured-also varied throughout the Phanerozoic, reflecting

  16. Biological communities at the Florida Escarpment resemble hydrothermal vent taxa

    USGS Publications Warehouse

    Paull, C.K.; Hecker, Barbara; Commeau, R.; Freeman-Lynde, R. P.; Neumann, C.; Corso, W.P.; Golubic, S.; Hook, J.E.; Sikes, E.; Curray, J.

    1984-01-01

    Dense biological communities of large epifaunal taxa similar to those found along ridge crest vents at the East Pacific Rise were discovered in the abyssal Gulf of Mexico. These assemblages occur on a passive continental margin at the base of the Florida Escarpment, the interface between the relatively impermeable hemipelagic clays of the distal Mississippi Fan and the jointed Cretaceous limestone of the Florida Platform. The fauna apparently is nourished by sulfide rich hypersaline waters seeping out at near ambient temperatures onto the sea floor.

  17. Nitrogen Index

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is a need to improve the management of nitrogen inputs to agricultural systems because they increase the potential for losses of reactive nitrogen to the environment, resulting in negative impacts to water and air resources. There is a need to reduce nitrate leaching, emissions of N2O from agr...

  18. Alkalispirochaeta cellulosivorans gen. nov., sp. nov., a cellulose-hydrolysing, alkaliphilic, halotolerant bacterium isolated from the gut of a wood-eating cockroach (Cryptocercus punctulatus), and reclassification of four species of Spirochaeta as new combinations within Alkalispirochaeta gen. nov.

    PubMed

    Sravanthi, T; Tushar, L; Sasikala, Ch; Ramana, Ch V

    2016-04-01

    An obligately anaerobic spirochaete designated strain JC227T was isolated from the gut of a wood-eating cockroach, Cryptocercus punctulatus (Scudder), from the Rann of Kutch, Gujarat, India. Strain JC227T was Gram-stain-negative, mesophilic, halotolerant and alkaliphilic. Based on 16S rRNA gene sequence analysis, strain JC227T belongs to the genus Spirochaeta, with Spirochaeta sphaeroplastigenens JC133T (99.51 %), S. odontotermitis JC202T (99.30 %), S. alkalica Z-7491T (99.10 %), S. americana (98.54 %) and other members of the genus Spirochaeta ( < 92.7 %) as its closest phylogenetic neighbours. However, DNA-DNA hybridization between strain JC227T and S. sphaeroplastigenens JC133T, S. odontotermitis JC202T, S. alkalica DSM 8900T and S. americana DSM 14872T was 62 ± 2, 63, 58 ± 2 and 48 ± 4 %, respectively. Strain JC227T contained phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and six unidentified lipids. Summed feature C18 : 1ω7c/C18 : 1ω6c was the predominant cellular fatty acid, with significant proportions of C16 : 0, C14 : 0, C12 : 0, C15 : 1ω6c, C16 : 1ω5c, C16 : 1ω6c/C16 : 1ω7c and C17 : 0 2-OH. The DNA G+C content of strain JC227T was 55.5 mol%. On the basis of physiological, biochemical, chemotaxonomic (including metabolomic) and genomic differences from previously described taxa, strain JC227T can be differentiated from members of the genus Spirochaeta and represents a novel species of a new genus, for which the name Alkalispirochaeta cellulosivorans gen. nov., sp. nov. is proposed. The type strain of Alkalispirochaeta cellulosivorans is JC227T ( = KCTC 15343T = NBRC 110105T). We also propose the reclassification of Spirochaeta sphaeroplastigenens, Spirochaeta odontotermitis, Spirochaeta alkalica and Spirochaeta americana as Alkalispirochaeta sphaeroplastigenens comb. nov. (type strain JC133T = KCTC 15220T = NBRC 109056T

  19. Sensitivities of extant animal taxa to ocean acidification

    NASA Astrophysics Data System (ADS)

    Wittmann, Astrid C.; Pörtner, Hans-O.

    2013-11-01

    Anthropogenic CO2 emitted to the atmosphere is absorbed by the oceans, causing a progressive increase in ocean inorganic carbon concentrations and resulting in decreased water pH and calcium carbonate saturation. This phenomenon, called ocean acidification, is in addition to the warming effects of CO2 emissions. Ocean acidification has been reported to affect ocean biota, but the severity of this threat to ocean ecosystems (and humans depending on these ecosystems) is poorly understood. Here we evaluate the scale of this threat in the context of widely used representative concentration pathways (RCPs) by analysing the sensitivities of five animal taxa (corals, echinoderms, molluscs, crustaceans and fishes) to a wide range of CO2 concentrations. Corals, echinoderms and molluscs are more sensitive to RCP8.5 (936 ppm in 2100) than are crustaceans. Larval fishes may be even more sensitive than the lower invertebrates, but taxon sensitivity on evolutionary timescales remains obscure. The variety of responses within and between taxa, together with observations in mesocosms and palaeo-analogues, suggest that ocean acidification is a driver for substantial change in ocean ecosystems this century, potentially leading to long-term shifts in species composition.

  20. A microarray for assessing transcription from pelagic marine microbial taxa

    PubMed Central

    Shilova, Irina N; Robidart, Julie C; James Tripp, H; Turk-Kubo, Kendra; Wawrik, Boris; Post, Anton F; Thompson, Anne W; Ward, Bess; Hollibaugh, James T; Millard, Andy; Ostrowski, Martin; J Scanlan, David; Paerl, Ryan W; Stuart, Rhona; Zehr, Jonathan P

    2014-01-01

    Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions. PMID:24477198

  1. The evolutionary reality of higher taxa in mammals

    PubMed Central

    Humphreys, Aelys M.; Barraclough, Timothy G.

    2014-01-01

    Species are generally regarded as a fundamental unit of biodiversity. By contrast, higher taxa such as genera and families, while widely used as biodiversity metrics and for classification and communication, are generally not believed to be shaped by shared evolutionary processes in the same way as species. We use simulations to show that processes which are important for emergence of evolutionarily significant units (ESUs) at the species level, namely geographical isolation and ecological divergence, can generate evolutionary independence above the species level and thereby lead to emergence of discrete phylogenetic clusters (higher ESUs). Extending phylogenetic approaches for delimiting evolutionarily significant species to broader phylogenetic scales, we find evidence for the existence of higher ESUs in mammals. In carnivores, euungulates and lagomorphs the hierarchical level of units detected correspond, on average, to the level of family or genus in traditional taxonomy. The units in euungulates are associated with divergent patterns of body mass, consistent with occupation of distinct ecological zones. Our findings demonstrate a new framework for studying biodiversity that unifies approaches at species and higher levels, thus potentially restoring higher taxa to their historical status as natural entities. PMID:24695424

  2. The genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4

    PubMed Central

    Janto, Benjamin; Ahmed, Azad; Ito, Masahiro; Liu, Jun; Hicks, David B.; Pagni, Sarah; Fackelmayer, Oliver J.; Smith, Terry-Ann; Earl, Joshua; Elbourne, Liam D.H.; Hassan, Karl; Paulsen, Ian T.; Kolstø, Anne-Brit; Tourasse, Nicolas J.; Ehrlich, Garth D.; Boissy, Robert; Ivey, D. Mack; Li, Gang; Xue, Yanfen; Ma, Yanhe; Hu, Fen Z.; Krulwich, Terry A.

    2011-01-01

    Summary Bacillus pseudofirmus OF4 is an extreme but facultative alkaliphile that grows non-fermentatively in a pH range from 7.5 to above 11.4 and can withstand large sudden increases in external pH. It is a model organism for studies of bioenergetics at high pH, at which energy demands are higher than at neutral pH because both cytoplasmic pH homeostasis and ATP synthesis require more energy. The alkaliphile also tolerates a cytoplasmic pH > 9.0 at external pH values at which the pH homeostasis capacity is exceeded, and manages other stresses that are exacerbated at alkaline pH, e.g. sodium, oxidative and cell wall stresses. The genome of B. pseudofirmus OF4 includes two plasmids that are lost from some mutants without viability loss. The plasmids may provide a reservoir of mobile elements that promote adaptive chromosomal rearrangements under particular environmental conditions. The genome also reveals a more acidic pI profile for proteins exposed on the outer surface than found in neutralophiles. A large array of transporters and regulatory genes are predicted to protect the alkaliphile from its overlapping stresses. In addition, unanticipated metabolic versatility was observed, which could ensure requisite energy for alkaliphily under diverse conditions. PMID:21951522

  3. The impact of rare taxa on a fish index of biotic integrity

    USGS Publications Warehouse

    Wan, H.; Chizinski, C.J.; Dolph, C.L.; Vondracek, B.; Wilson, B.N.

    2010-01-01

    The index of biotic integrity (IBI) is a commonly used bioassessment tool that integrates abundance and richness measures to assess water quality. In developing IBIs that are both responsive to human disturbance and resistant to natural variability and sampling error, water managers must decide how to weigh information about rare and abundant taxa, which in turn requires an understanding of the sensitivity of indices to rare taxa. Herein, we investigated the influence of rare fish taxa (within the lower 5% of rank abundance curves) on IBI metric and total scores for stream sites in two of Minnesota's major river basins, the St. Croix (n = 293 site visits) and Upper Mississippi (n = 210 site visits). We artificially removed rare taxa from biological samples by (1) separately excluding each individual taxon that fell within the lower 5% of rank abundance curves; (2) simultaneously excluding all taxa that had an abundance of one (singletons) or two (doubletons); and (3) simultaneously excluding all taxa that fell within the lower 5% of rank abundance curves. We then compared IBI metric and total scores before and after removal of rare taxa using the normalized root mean square error (nRMSE) and regression analysis. The difference in IBI metric and total scores increased as more taxa were removed. Moreover, when multiple rare taxa were removed, the nRMSE was related to sample abundance and to total taxa richness, with greater nRMSE observed in samples with a larger number of taxa or sample abundance. Metrics based on relative abundance of fish taxa were less sensitive to the loss of rare taxa, whereas those based on taxa richness were more sensitive, because taxa richness metrics give more weight to rare taxa compared to the relative abundance metrics. ?? 2010 Elsevier Ltd.

  4. Fungal Taxa Target Different Carbon Substrates in Harvard Forest Soils

    NASA Astrophysics Data System (ADS)

    Hanson, C. A.; Allison, S. D.; Wallenstein, M. D.; Mellilo, J. M.; Treseder, K. K.

    2006-12-01

    The mineralization of soil organic carbon is a major component of the global carbon cycle and is largely controlled by soil microbial communities. However, little is known about the functional roles of soil microbes or whether different microbial taxa target different carbon substrates under natural conditions. To examine this possibility, we assessed the community composition of active fungi by using a novel nucleotide analog technique in soils from the Harvard Forest. We hypothesized that fungal community composition would shift in response to the addition of different substrates and that specific fungal taxa would respond differentially to particular carbon sources. To test this hypothesis, we added a nucleotide analog probe directly to soils in conjunction with one of five carbon compounds of increasing recalcitrance: glycine, sucrose, cellulose, tannin-protein complex, and lignin. During 48 hour incubations, the nucleotide analog was incorporated into newly replicated DNA of soil organisms that proliferated following the addition of the substrates. In this way, we labeled the DNA of microbes that respond to a particular carbon source. Labeled DNA was isolated and fungal Internal Transcribed Spacer (ITS) regions of ribosomal DNA (rDNA) were sequenced and analyzed to identify active fungi to near-species resolution. Diversity analyses at the ≥97% sequence similarity level indicated that taxonomic richness was greater under cellulose (Shannon Index: 3.23 ± 0.11 with ± 95% CI) and lignin (2.87 ± 0.15) additions than the other treatments (2.34 ± 0.16 to 2.64 ± 0.13). In addition, community composition of active fungi shifted under glycine, sucrose, and cellulose additions. Specifically, the community under glycine was significantly different from communities under control, cellulose, and tannin-protein (P<0.05). Additionally, the sucrose and cellulose communities were marginally different from the control community (P = 0.059 and 0.054, respectively) and

  5. Extinction, diversity and survivorship of taxa in the fossil record

    PubMed Central

    Newman, M. E. J.; Sibani, P.

    1999-01-01

    Using data drawn from large-scale databases, a number of interesting trends in the fossil record have been observed in recent years. These include the average decline in extinction rates throughout the Phanerozoic, the average increase in standing diversity, correlations between rates of origination and extinction, and simple laws governing the form of survivorship curves and the distribution of the lifetimes of taxa. In this paper we derive a number of mathematical relationships between these quantities and show how these different trends are interrelated. We also derive a variety of constraints on the possible forms of these trends, such as limits on the rate at which extinction may decline and limits on the allowed difference between extinction and origination rates at any given time.

  6. Transposable elements in sexual and ancient asexual taxa

    PubMed Central

    Arkhipova, Irina; Meselson, Matthew

    2000-01-01

    Sexual reproduction allows deleterious transposable elements to proliferate in populations, whereas the loss of sex, by preventing their spread, has been predicted eventually to result in a population free of such elements [Hickey, D. A. (1982) Genetics 101, 519–531]. We tested this expectation by screening representatives of a majority of animal phyla for LINE-like and gypsy-like reverse transcriptases and mariner/Tc1-like transposases. All species tested positive for reverse transcriptases except rotifers of the class Bdelloidea, the largest eukaryotic taxon in which males, hermaphrodites, and meiosis are unknown and for which ancient asexuality is supported by molecular genetic evidence. Mariner-like transposases are distributed sporadically among species and are present in bdelloid rotifers. The remarkable lack of LINE-like and gypsy-like retrotransposons in bdelloids and their ubiquitous presence in other taxa support the view that eukaryotic retrotransposons are sexually transmitted nuclear parasites and that bdelloid rotifers evolved asexually. PMID:11121049

  7. More taxa, more characters: the hoatzin problem is still unresolved.

    PubMed

    Sorenson, Michael D; Oneal, Elen; Garcia-Moreno, Jaime; Mindell, David P

    2003-09-01

    The apparently rapid and ancient diversification of many avian orders complicates the resolution of their relationships using molecular data. Recent studies based on complete mitochondrial DNA (mtDNA) sequences or shorter lengths of nuclear sequence have helped corroborate the basic structure of the avian tree (e.g., a basal split between Paleognathae and Neognathae) but have made relatively little progress in resolving relationships among the many orders within Neoaves. We explored the potential of a moderately sized mtDNA data set ( approximately 5000 bp for each of 41 taxa), supplemented with data from a nuclear intron ( approximately 700 bp per taxon), to resolve relationships among avian orders. Our sampling of taxa addresses two issues: (1). the sister relationship and monophyly, respectively, of Anseriformes and Galliformes and (2). relationships of the enigmatic hoatzin Opisthocomus hoazin. Our analyses support a basal split between Galloanserae and Neoaves within Neognathae and monophyly of both Galliformes and Anseriformes. Within Galliformes, megapodes and then cracids branch basally. Within Anseriformes, mitochondrial data support a screamer (Anhimidae) plus magpie goose (Anseranatidae) clade. This result, however, may be an artifact of divergent base composition in one of the two anatids we sampled. With deletion of the latter taxon, Anseranas is sister to anatids as in traditional arrangements and recent morphological studies. Although our data provide limited resolution of relationships within Neoaves, we find no support for a sister relationship between either cuckoos (Cuculiformes) or turacos (Musophagiformes) and hoatzin. Both mitochondrial and nuclear data are consistent with a relationship between hoatzin and doves (Columbiformes), although this result is weakly supported. We also show that mtDNA sequences reported in another recent study included pervasive errors that biased the analysis towards finding a sister relationship between hoatzin and

  8. Identifying sighting clusters of endangered taxa with historical records.

    PubMed

    Duffy, Karl J

    2011-04-01

    The probability and time of extinction of taxa is often inferred from statistical analyses of historical records. Many of these analyses require the exclusion of multiple records within a unit of time (i.e., a month or a year). Nevertheless, spatially explicit, temporally aggregated data may be useful for identifying clusters of sightings (i.e., sighting clusters) in space and time. Identification of sighting clusters highlights changes in the historical recording of endangered taxa. I used two methods to identify sighting clusters in historical records: the Ederer-Myers-Mantel (EMM) test and the space-time permutation scan (STPS). I applied these methods to the spatially explicit sighting records of three species of orchids that are listed as endangered in the Republic of Ireland under the Wildlife Act (1976): Cephalanthera longifolia, Hammarbya paludosa, and Pseudorchis albida. Results with the EMM test were strongly affected by the choice of the time interval, and thus the number of temporal samples, used to examine the records. For example, sightings of P. albida clustered when the records were partitioned into 20-year temporal samples, but not when they were partitioned into 22-year temporal samples. Because the statistical power of EMM was low, it will not be useful when data are sparse. Nevertheless, the STPS identified regions that contained sighting clusters because it uses a flexible scanning window (defined by cylinders of varying size that move over the study area and evaluate the likelihood of clustering) to detect them, and it identified regions with high and regions with low rates of orchid sightings. The STPS analyses can be used to detect sighting clusters of endangered species that may be related to regions of extirpation and may assist in the categorization of threat status. PMID:21129031

  9. Fossil preservation and the stratigraphic ranges of taxa

    NASA Technical Reports Server (NTRS)

    Foote, M.; Raup, D. M.

    1996-01-01

    The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy. Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased.(3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of

  10. Pollinator sharing and gene flow among closely related sympatric dioecious fig taxa.

    PubMed

    Wang, Gang; Cannon, Charles H; Chen, Jin

    2016-04-13

    Hybridization and insect pollination are widely believed to increase rates of plant diversification. The extreme diversity of figs (Ficus) and their obligate pollinators, fig wasps (Agaonidae), provides an opportunity to examine the possible role of pollinator-mediated hybridization in plant diversification. Increasing evidence suggests that pollinator sharing and hybridization occurs among fig taxa, despite relatively strict coevolution with the pollinating wasp. Using five sympatric dioecious fig taxa and their pollinators, we examine the degree of pollinator sharing and inter-taxa gene flow. We experimentally test pollinator preference for floral volatiles, the main host recognition signal, from different figs. All five fig taxa shared pollinators with other taxa, and gene flow occurred between fig taxa within and between sections. Floral volatiles of each taxon attracted more than one pollinator species. Floral volatiles were more similar between closely related figs, which experienced higher levels of pollinator sharing and inter-taxa gene flow. This study demonstrates that pollinator sharing and inter-taxa gene flow occurs among closely related sympatric dioecious fig taxa and that pollinators choose the floral volatiles of multiple fig taxa. The implications of pollinator sharing and inter-taxa gene flow on diversification, occurring even in this highly specialized obligate pollination system, require further study. PMID:27075252

  11. Taxa-area Relationship (TAR) of Microbial Functional Genes with Long-TGerm Fertilization

    SciTech Connect

    Liang, Yuting; Wu, Liyou; Clark, Ian; Xue, Kai; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Hirsch, Penny; Mcgrath, Steve; Zhou, Jizhong

    2010-05-17

    Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that the turnover in space of microorganisms may be higher with long-term fertilization.

  12. Enzymatic Properties of an Alkaline and Chelator Resistant Proportional to alpha-Amylase from the Alkaliphilic Bacillus sp. Isolate L1711

    NASA Technical Reports Server (NTRS)

    Bernhardsdotter, Eva C. M. J.; Pusey, Marc L.; Ng, Joseph D.; Garriott, Owen K.

    2004-01-01

    An alkaliphilic amylase producing bacterium, Bacillus sp. strain L1711, was selected among 13 soda lakes isolates. When grown at pH 10.5 and 370 C, strain L1711 produced multiple forms of amylases in the culture broth. One of these, BAA, was purified from the culture supernatant by QAE column chromatography and preparative native gel electrophoresis. The molecular weight of BAA was determined to be 51 kDa by denaturing gel electrophoresis. The pH optima for activity below and above 40 C were 9.5-10.0 and 7.0-7.5 respectively. BAA was stable in the pH range 6-11 and was completely inactivated at 55?C. The thermostability was not increased in the presence of Ca(2+). The enzyme was strongly inhibited by Ca(2+), Zn(2+), Mg(2+), Mn(2+), Ba(2+) and Cu(2+), whereas the presence of Na(+), Co2+ and EDTA (10 mM) enhanced enzymatic activity. The K(sub m) and specific activity of BAA on soluble starch were 1.9 mg/ml and 18.5 U/mg respectively. The main end products of hydrolysis were maltotetraose, maltose and glucose .

  13. Stepwise error-prone PCR and DNA shuffling changed the pH activity range and product specificity of the cyclodextrin glucanotransferase from an alkaliphilic Bacillus sp.

    PubMed Central

    Melzer, Susanne; Sonnendecker, Christian; Föllner, Christina; Zimmermann, Wolfgang

    2015-01-01

    Cyclodextrin glucanotransferase (EC 2.4.1.19) from the alkaliphilic Bacillus sp. G-825-6 converts starch mainly to γ-cyclodextrin (CD8). A combination of error-prone PCR and DNA shuffling was used to obtain variants of this enzyme with higher product specificity for CD8 and a broad pH activity range. The variant S54 with seven amino acid substitutions showed a 1.2-fold increase in CD8-synthesizing activity and the product ratio of CD7:CD8 was shifted to 1:7 compared to 1:3 of the wild-type enzyme. Nine amino acid substitutions of the cyclodextrin glucanotransferase were performed to generate the variant S35 active in a pH range 4.0–10.0. Compared to the wild-type enzyme which is inactive below pH 6.0, S35 retained 70% of its CD8-synthesizing activity at pH 4.0. PMID:26155461

  14. Production of Alkaline Protease by Solvent-Tolerant Alkaliphilic Bacillus circulans MTCC 7942 Isolated from Hydrocarbon Contaminated Habitat: Process Parameters Optimization.

    PubMed

    Patil, Ulhas; Chaudhari, Ambalal

    2013-01-01

    In the present investigation, a newly isolated organic solvent-tolerant and alkaliphilic bacterial strain was reported from a hydrocarbon (gasoline and diesel) contaminated soil collected from the petrol station, Shirpur (India). The strain was identified as Bacillus circulans MTCC 7942, based on phenotype, biochemical, and phylogenetic analysis of 16S rRNA gene sequence. The capability of Bacillus circulans to secrete an extracellular, thermostable, alkaline protease and grow in the presence of organic solvents was explored. Bacillus circulans produced maximum alkaline protease (412 U/mL) in optimized medium (g/L): soybean meal, 15; starch, 10; KH2PO4, 1; MgSO4·7H2O, 0.05; CaCl2, 1; Na2CO3, 8; pH 10.0 at 37°C and 100 rpm. The competence of strain to grow in various organic solvents-n-octane, dodecane, n-decane, N,N-dimethylformamide, n-hexane, and dimethyl sulfoxide, establishes its potential as solvent-stable protease source for the possible applications in nonaqueous reactions and fine chemical synthesis. PMID:25937965

  15. Characterization of Alkaliphilus hydrothermalis sp. nov., a novel alkaliphilic anaerobic bacterium, isolated from a carbonaceous chimney of the Prony hydrothermal field, New Caledonia.

    PubMed

    Ben Aissa, Fatma; Postec, Anne; Erauso, Gaël; Payri, Claude; Pelletier, Bernard; Hamdi, Moktar; Fardeau, Marie-Laure; Ollivier, Bernard

    2015-01-01

    A novel anaerobic, alkaliphilic, Gram-positive staining bacterium was isolated from a hydrothermal chimney in the Prony Bay, New Caledonia. This strain designated FatMR1(T) grew at temperatures from 20 to 55 °C (optimum 37 °C) and at pH between 7.5 and 10.5 (optimum 8.8-9). NaCl is not required for growth (optimum 0.2-0.5%), but is tolerated up to 3%. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite are not used as terminal electron acceptors. Strain FatMR1(T) fermented pyruvate, yeast extract, peptone and biotrypcase and used fructose as the only sugar. The main fermentation products from fructose and proteinaceous compounds (e.g. peptone and biotrypcase) were acetate, H2 and CO2. Crotonate was disproportionated to acetate and butyrate. The predominant cellular fatty acids were C14:0 and C16:0. The G + C content of the genomic DNA was 37.1 mol%. On the basis of phylogenetic, genetic, and physiological properties, strain FatMR1(T) (=DSM 25890(T), =JCM 18390(T)) belonging to the phylum Firmicutes, class Clostridia, order Clostridiales, is proposed as a novel species of the genus Alkaliphilus, A. hydrothermalis sp. nov. PMID:25319677

  16. Production of Alkaline Protease by Solvent-Tolerant Alkaliphilic Bacillus circulans MTCC 7942 Isolated from Hydrocarbon Contaminated Habitat: Process Parameters Optimization

    PubMed Central

    Patil, Ulhas; Chaudhari, Ambalal

    2013-01-01

    In the present investigation, a newly isolated organic solvent-tolerant and alkaliphilic bacterial strain was reported from a hydrocarbon (gasoline and diesel) contaminated soil collected from the petrol station, Shirpur (India). The strain was identified as Bacillus circulans MTCC 7942, based on phenotype, biochemical, and phylogenetic analysis of 16S rRNA gene sequence. The capability of Bacillus circulans to secrete an extracellular, thermostable, alkaline protease and grow in the presence of organic solvents was explored. Bacillus circulans produced maximum alkaline protease (412 U/mL) in optimized medium (g/L): soybean meal, 15; starch, 10; KH2PO4, 1; MgSO4·7H2O, 0.05; CaCl2, 1; Na2CO3, 8; pH 10.0 at 37°C and 100 rpm. The competence of strain to grow in various organic solvents—n-octane, dodecane, n-decane, N,N-dimethylformamide, n-hexane, and dimethyl sulfoxide, establishes its potential as solvent-stable protease source for the possible applications in nonaqueous reactions and fine chemical synthesis. PMID:25937965

  17. Nitrogen species

    NASA Astrophysics Data System (ADS)

    Harries, J. E.; Brasseur, G.; Coffey, M. T.; Fischer, H.; Gille, J.; Jones, R.; Louisnard, N.; McCormick, M. P.; Noxon, J.; Owens, A. J.

    Total odd nitrogen, NO(y), may be defined as the sum of all active nitrogen species that interchange photochemically with one another on a time scale of the order of weeks or less. As noted, NO + NO2 reactions dominate the processes controlling the ozone balance in the contemporary stratosphere. The observational data from non-satellite platforms are reviewed. The growth in available satellite data in the past four years is considered. Some of the most important scientific issues are discussed, taking into account new results from atmospheric models (mainly 2-D). The model results are compared with the observational data.

  18. Nitrogen species

    NASA Technical Reports Server (NTRS)

    Harries, J. E.; Brasseur, G.; Coffey, M. T.; Fischer, H.; Gille, J.; Jones, R.; Louisnard, N.; Mccormick, M. P.; Noxon, J.; Owens, A. J.

    1985-01-01

    Total odd nitrogen, NO(y), may be defined as the sum of all active nitrogen species that interchange photochemically with one another on a time scale of the order of weeks or less. As noted, NO + NO2 reactions dominate the processes controlling the ozone balance in the contemporary stratosphere. The observational data from non-satellite platforms are reviewed. The growth in available satellite data in the past four years is considered. Some of the most important scientific issues are discussed, taking into account new results from atmospheric models (mainly 2-D). The model results are compared with the observational data.

  19. DNA barcoding and taxonomy: dark taxa and dark texts.

    PubMed

    Page, Roderic D M

    2016-09-01

    Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline ('dark texts'). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These 'dark taxa' hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global 'digital dashboard' to assess the extent to which biodiversity data are available online.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481786

  20. Nested taxa-area curves for eastern United States floras

    USGS Publications Warehouse

    Bennett, J.P.

    1997-01-01

    The slopes of log-log species-area curves have been studied extensively and found to be influenced by the range of areas under study. Two such studies of eastern United States floras have yielded species-area curve slopes which differ by more than 100%: 0.251 and 0.113. The first slope may be too steep because the flora of the world was included, and both may be too steep because noncontiguous areas were used. These two hypotheses were tested using a set of nested floras centered in Ohio and continuing up to the flora of the world. The results suggest that this set of eastern United States floras produces a log-log species-area curve with a slope of approximately 0.20 with the flora of the world excluded, and regardless of whether or not the floras are from nested areas. Genera- and family-area curves are less steep than species-area curves and show similar patterns. Taxa ratio curves also increase with area, with the species/family ratio showing the steepest slope.

  1. Comparing mechanisms of host manipulation across host and parasite taxa

    USGS Publications Warehouse

    Lafferty, Kevin D.; Shaw, Jenny C.

    2013-01-01

    Parasites affect host behavior in several ways. They can alter activity, microhabitats or both. For trophically transmitted parasites (the focus of our study), decreased activity might impair the ability of hosts to respond to final-host predators, and increased activity and altered microhabitat choice might increase contact rates between hosts and final-host predators. In an analysis of trophically transmitted parasites, more parasite groups altered activity than altered microhabitat choice. Parasites that infected vertebrates were more likely to impair the host’s reaction to predators, whereas parasites that infected invertebrates were more likely to increase the host’s contact with predators. The site of infection might affect how parasites manipulate their hosts. For instance, parasites in the central nervous system seem particularly suited to manipulating host behavior. Manipulative parasites commonly occupy the body cavity, muscles and central nervous systems of their hosts. Acanthocephalans in the data set differed from other taxa in that they occurred exclusively in the body cavity of invertebrates. In addition, they were more likely to alter microhabitat choice than activity. Parasites in the body cavity (across parasite types) were more likely to be associated with increased host contact with predators. Parasites can manipulate the host through energetic drain, but most parasites use more sophisticated means. For instance, parasites target four physiological systems that shape behavior in both invertebrates and vertebrates: neural, endocrine, neuromodulatory and immunomodulatory. The interconnections between these systems make it difficult to isolate specific mechanisms of host behavioral manipulation.

  2. Phylogenetic perspectives of nitrogen-fixing actinobacteria.

    PubMed

    Gtari, Maher; Ghodhbane-Gtari, Faten; Nouioui, Imen; Beauchemin, Nicholas; Tisa, Louis S

    2012-01-01

    It was assumed for a long time that the ability to catalyze atmospheric nitrogen (diazotrophy) has a narrow distribution among actinobacteria being limited to the genus Frankia. Recently, the number of nitrogen fixation (nifH) genes identified in other non-Frankia actinobacteria has dramatically increased and has opened investigation on the origin and emergence of diazotrophy among actinobacteria. During the last decade, Mycobacterium flavum, Corynebacterium autotrophicum and a fluorescent Arthrobacter sp. have been reported to have nitrogenase activity, but these studies have not been further verified. Additional reports of nitrogen fixation by Agromyces, Microbacterium, Corynebacterium and Micromonospora isolated from root nodules of leguminous and actinorhizal plants have increased. For several actinobacteria, nitrogen fixation was demonstrated by the ability to grow on nitrogen-free medium, acetylene reduction activity, 15N isotope dilution analysis and identification of a nifH gene via PCR amplification. Moreover, the analyses of draft genome sequences of actinobacteria including Slackia exigua, Rothia mucilaginosa and Gordonibacter pamelaeae have also revealed the presence of nifH-like sequences. Whether these nifH sequences are associated with effective nitrogen fixation in these actinobacteria taxa has not yet been demonstrated. These genes may be vertically or horizontally transferred and be silent sequences. These ideas merit further investigation. This minireview presents a phylogenetic comparison of nitrogen fixation gene (nifH) with the aim of elucidating the processes underlying the evolutionary history of this catalytic ability among actinobacteria. PMID:21779790

  3. Nitrogen dioxide

    Integrated Risk Information System (IRIS)

    Nitrogen dioxide ; CASRN 10102 - 44 - 0 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogeni

  4. Sustaining salmonid populations: A caring understanding of naturalness of taxa

    USGS Publications Warehouse

    Nielsen, J.L.; Regier, H.A.

    2004-01-01

    Species of the family of Salmonidae occur naturally in Northern Hemisphere waters that remain clear and cool to cold in summer. For purposes of reproduction, salmonids generally behaviorally respond to the currents of streams and lakes in recently glaciated areas. For feeding and maturation, many larger species migrate into existing systems of large lakes, seas, and oceans. The subfamilies include Salmoninae, Coregoninae, and Thymallinae. In many locales and regions of the hemisphere, numerous species of these subfamilies evolved and self-organized into species flocks or taxocenes of bewildering complexity. For example, any individual species may play different or unique ecological roles in different taxocenes. The northern Pacific and Atlantic Ocean ecosystems, with their seas and tributaries, each contained a metacomplex of such taxocenes that, in their natural state some centuries ago, resembled each other but differed in many ways. Humans have valued all species of this family for subsistence, ceremonial, naturalist, gustatory, angling, and commercial reasons for centuries. Modern progressive humans (MPHs), whose industrial and commercial enterprises have gradually spread over this hemisphere in recent time, now affect aquatic ecosystems at all scales from local to global. These human effects mingle in complex ways that together induce uniquely natural salmonid taxocenes to disintegrate with the loss of species, including those groups least tolerant to human manipulations, but extending more recently to those taxa more adapted to anthropogenic change. As we leave the modern era, dominated by MPHs, will we find ways to live sustainably with salmonid taxocenes that still exhibit self-organizational integrity, or will only individual, isolated populations of salmonid species, derived from those most tolerant of MPHs, survive? To achieve future sustainability of salmonids, we suggest implementation of a search for intuitive knowledge based on faith in the wisdom of

  5. Phytoplankton taxa in relation to primary production in the equatorial Pacific

    NASA Astrophysics Data System (ADS)

    Chavez, Francisco P.; Buck, Kurt R.; Barber, Richard T.

    1990-11-01

    Equatorial regions, especially the equatorial Pacific, are important to the global carbon and nitrogen cycle, yet little is known about the processes regulating phytoplankton dynamics in these areas. Here we report on the abundance of planktonic groups, in the picoplankton to netplankton range, estimated using epifluorescence microscopy, in samples collected in the equatorial Pacific from 110 to 140°W, and discuss their relation to primary production, chlorophyll, chemical and physical properties. Microscopic examination supports previous reports ( CHAVEZ, 1989, Global Biogeochemical Cycles, 3, 27-35), based on size separations of biomass and production, that the equatorial Pacific is dominated by small phytoplankton, most of them smaller then 5 μm. The phytoplankton in this region is dominated by relatively few taxa: Synechococcus spp., red fluorescing picoplankton, a small naked dinoflaellate (4 × 7 μm), small prymnesiophytes (on the order of 3-5 μm), and small single-celled pennate diatoms (2 × 15 μm). The spatial variability in phytoplankton biomass, composition and production could be clearly related to distinct physical features of the equatorial circulation, such as equatorial upwelling, Long or Legeckis waves and the Equatorial Front. During November 1988, a period of abnormally cool sea surface temperatures, changes in the abundance of pennate diatoms accounted for the largest proportion of the variability in chlorophyll and primary production even though this group was a relatively minor contributor to the total biomass of the phytoplankton community. Since primary production and particulate organic flux are well correlated in the equatorial Pacific ( BETZERet al., 1984, Deep-Sea Research, 31, 1-11), variations in the abundance of pennate diatoms also must have important consequences to variations in particulate organic flux. Before a predictive model for particulate organic flux in the equatorial Pacific can be established further understanding of

  6. DNA barcode data accurately assign higher spider taxa.

    PubMed

    Coddington, Jonathan A; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina; Kuntner, Matjaž

    2016-01-01

    The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios "barcodes" (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families-taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the

  7. DNA barcode data accurately assign higher spider taxa

    PubMed Central

    Coddington, Jonathan A.; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina

    2016-01-01

    The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of

  8. Spirochaeta odontotermitis sp. nov., an obligately anaerobic, cellulolytic, halotolerant, alkaliphilic spirochaete isolated from the termite Odontotermes obesus (Rambur) gut.

    PubMed

    Sravanthi, T; Tushar, L; Sasikala, Ch; Ramana, Ch V

    2015-12-01

    A Gram-stain-negative spirochaete (strain JC202T) was isolated from the gut of the termite Odontotermes obesus (Rambur) from Rann of Kutch, Gujarat, India. This strain was obligately anaerobic, mesophilic, halotolerant and required alkaline conditions for growth. Strain JC202T was resistant to rifampicin and kanamycin, but sensitive to gentamicin, tetracycline, ampicillin and chloramphenicol. Strain JC202T possessed phosphatidylglycerol, diphosphatidylglycerol, glycolipid and six unidentified lipids. C18 : 1ω7c was the predominant cellular fatty acid with significant proportions of C16 : 0, C18 : 1ω9c, C14 : 0, C18 : 0, C16 : 1ω5c, C18 : 1ω5c and C20 : 1ω9c. The DNA G+C content of strain JC202T was 59 mol%. Based on 16S rRNA gene sequence analysis, strain JC202T is considered to belong to the genus Spirochaeta with Spirochaeta sphaeroplastigenens JC133T (100 % similarity), Spirochaeta alkalica Z-7491T (99.92 %), Spirochaeta americana ATCC BAA-392T (99.47 %) and other members of the genus Spirochaeta ( < 93.83 %) as the closest phylogenetic neighbours. However, mean DNA-DNA hydridization values between strain JC202T and S. sphaeroplastigenens JC133T, S. alkalica DSM 8900T ( = Z-7491T) and S. americana DSM 14872T ( = ASpG1T) were 55 ± 2, 22 ± 3 and 32 ± 1 %, respectively. On the basis of physiological, biochemical, chemotaxonomic (including metabolome) and genomic differences from the previously described taxa, strain JC202T is differentiated from other members of the genus Spirochaeta and is considered to represent a novel species, for which the name Spirochaeta odontotermitis sp. nov. is proposed. The type strain is JC202T ( = KCTC 15324T = NBRC 110104T). PMID:26377069

  9. Humic substance-mediated reduction of iron(III) oxides and degradation of 2,4-D by an alkaliphilic bacterium, Corynebacterium humireducens MFC-5.

    PubMed

    Wu, Chun-yuan; Zhuang, Li; Zhou, Shun-gui; Yuan, Yong; Yuan, Tian; Li, Fang-bai

    2013-03-01

    With the use of an alkaliphilic bacterium, Corynebacterium humireducens MFC-5, this study investigated the reduction of goethite (α-FeOOH) and degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) mediated by different humic substances (humics) and quinones in alkaline conditions (pH of 9.0). The results indicated that (i) using sucrose as the electron donor, the strain MFC-5 was capable of reducing anthraquinone-2,6-disulfonic acid (AQDS), anthraquinone-2-disulfonic acid (AQS), anthraquinone-2-carboxylic acid (AQC), humic acid (HA) and fulvic acid (FA), and its reducing capability ranked as AQC > AQS > AQDS > FA > HA; (ii) the anaerobic reduction of α-FeOOH and 2,4-D by the strain was insignificant, while the reductions were greatly enhanced by the addition of quinones/humics serving as redox mediators; (iii) the Fe(III) reduction rate was positively related to the content of quinone functional groups and the electron-accepting capacities (EAC) of quinones/humics based on fourier-transform infrared spectroscopy (FT-IR) and electrochemical analyses; however, such a relationship was not found in 2,4-D degradation probably because quinone reduction was not the rate-limiting step of quinone-mediated reduction of 2,4-D. Using the example of α-FeOOH and 2,4-D, this study well demonstrated the important role of humics reduction on the Fe(III)/Fe(II) biogeochemical cycle and chlorinated organic compounds degradation in alkaline reducing environments. PMID:23217085

  10. Detergent-, solvent- and salt-compatible thermoactive alkaline serine protease from halotolerant alkaliphilic Bacillus sp. NPST-AK15: purification and characterization.

    PubMed

    Ibrahim, Abdelnasser S S; Al-Salamah, Ali A; El-Badawi, Yahya B; El-Tayeb, Mohamed A; Antranikian, Garabed

    2015-09-01

    Alkaline protease produced by the halotolerant alkaliphilic Bacillus sp. strain NPST-AK15 was purified to homogeneity by the combination of ammonium sulfate precipitation, anion-exchange and gel permeation chromatography. The purified enzyme was a monomeric protein with an estimated molecular weight of 32 kDa. NPST-AK15 protease was highly active and stable over a wide pH range, with a maximal activity at pH 10.5. The enzyme showed optimum activity at 60 °C and was stable at 30-50 °C for at least 1 h. Thermal stability of the purified protease was substantially improved by CaCl2 (1.1- to 6.6-fold). The K m, V max and k cat values for the enzyme were 2.5 mg ml(-1), 42.5 µM min(-1) mg(-1), and 392.46 × 10(3) min(-1), respectively. NPST-AK15 protease activity was strongly inhibited by PMSF, suggesting that the enzyme is a serine protease. The enzyme was highly stable in NaCl up to 20 % (w/v). Moreover, the purified enzyme was stable in several organic solvents such as diethyl ether, benzene, toluene, and chloroform. In addition, it showed high stability and compatibility with a wide range of surfactants and commercial detergents and was slightly activated by hydrogen peroxide. These features of NPST-AK15 protease make this enzyme a promising candidate for application in the laundry and pharmaceutical industries. PMID:26159877

  11. Cloning of the aapT gene and characterization of its product, alpha-amylase-pullulanase (AapT), from thermophilic and alkaliphilic Bacillus sp. strain XAL601.

    PubMed Central

    Lee, S P; Morikawa, M; Takagi, M; Imanaka, T

    1994-01-01

    A thermophilic and alkaliphilic Bacillus sp. strain, XAL601, was isolated from soil. It produces a thermostable and alkaline-stable enzyme with both alpha-amylase and pullulanase activities. The alpha-amylase-pullulanase gene (aapT) from this Bacillus strain was cloned, and its nucleotide sequence was determined (GenBank accession number D28467). A very large open reading frame composed of 6,096 bases, which encodes 2,032 amino acid residues with an M(r) of 224,992, was found. The deduced amino acid sequence revealed that the four highly conserved regions that are common among amylolytic enzymes were well conserved. These include an active center and common substrate-binding sites of various amylases. In the C-terminal region, a six-amino-acid sequence (Gly-Ser-Gly-Thr-Thr-Pro) is repeated 12 times. The aapT gene was then subcloned in Escherichia coli and overexpressed under the control of the lac promoter. Purification of AapT from this recombinant E. coli was performed, and it was shown that the aapT gene product exhibits both alpha-amylase and pullulanase activities with one active site. The optimum temperature and pH for enzyme activity were found to be 70 degrees C and pH 9, respectively. Furthermore, AapT was found to strongly adsorb to crystalline cellulose (Avicel) and raw corn starch. Final hydrolyzed products from soluble starch range from maltose (G2) to maltotetraose (G4). Only maltotriose (G3) was produced from pullulan. The enzyme also hydrolyzes raw starch under a broad range of conditions (60 to 70 degrees C and pH 8 to 9). Images PMID:7986049

  12. Humic substance-mediated reduction of iron(III) oxides and degradation of 2,4-D by an alkaliphilic bacterium, Corynebacterium humireducens MFC-5

    PubMed Central

    Wu, Chun-yuan; Zhuang, Li; Zhou, Shun-gui; Yuan, Yong; Yuan, Tian; Li, Fang-bai

    2013-01-01

    With the use of an alkaliphilic bacterium, Corynebacterium humireducens MFC-5, this study investigated the reduction of goethite (α-FeOOH) and degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) mediated by different humic substances (humics) and quinones in alkaline conditions (pH of 9.0). The results indicated that (i) using sucrose as the electron donor, the strain MFC-5 was capable of reducing anthraquinone-2,6-disulfonic acid (AQDS), anthraquinone-2-disulfonic acid (AQS), anthraquinone-2-carboxylic acid (AQC), humic acid (HA) and fulvic acid (FA), and its reducing capability ranked as AQC > AQS > AQDS > FA > HA; (ii) the anaerobic reduction of α-FeOOH and 2,4-D by the strain was insignificant, while the reductions were greatly enhanced by the addition of quinones/humics serving as redox mediators; (iii) the Fe(III) reduction rate was positively related to the content of quinone functional groups and the electron-accepting capacities (EAC) of quinones/humics based on fourier-transform infrared spectroscopy (FT-IR) and electrochemical analyses; however, such a relationship was not found in 2,4-D degradation probably because quinone reduction was not the rate-limiting step of quinone-mediated reduction of 2,4-D. Using the example of α-FeOOH and 2,4-D, this study well demonstrated the important role of humics reduction on the Fe(III)/Fe(II) biogeochemical cycle and chlorinated organic compounds degradation in alkaline reducing environments. Funding Information This study was supported by the National Natural Science Foundation of China (Nos 41101211, 31070460, 41101477), and The Project Sponsored by the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry. PMID:23217085

  13. Registers of family-group and genus-group taxa of Aphidoidea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This “Register of the genus-group taxa of Aphidoidea” corresponds to the proposal approved by the delegates attending the Eighth International Symposium on Aphids with the addition of taxa described since 31 December 2005, the cutoff date for the proposal. The genus-group names included here belong...

  14. Isolation and characterization of novel bacterial taxa from extreme alkali-saline soil.

    PubMed

    Shi, Wei; Takano, Tetsuo; Liu, Shenkui

    2012-05-01

    In northeast China there are large areas of nearly bare soda saline-alkali soil, in which plant survival is exteremely difficult because the land has a pH greater than 10.5. In order to obtain resistant microbial resources able to grow in such conditions, we analyzed environmental microbial samples from this extreme saline-alkali soil region. Through selective culture conditions, 8 bacterial strains were isolated from medium with no less than 1.5 M NaCl, 12 were isolated in the medium with a pH value of no less than 11.0, and 8 were isolated in the medium with of no less than 200 mM Na(2)CO(3). Based on 16S rRNA gene sequence analysis 20 novel strains of bacteria were identified and classified into four groups: 8 group I strains belong to the genus Bacillus; three group II belong to genus Nesterenkonia (2 strains) and genus Zhihengliuella (1 strain); eight group III strains belong to the genera Halomonas (6), Stenotrophomonas (1) and Alkalimonas (1); one group IV strain belongs to genus Litoribacter. These four groups belong to the phylum Firmicutes, phylum Actinobacteria, phylum Gamma-Proteobacteria and phylum Bacteroidetes, respectively. The sequence homology of 16S rRNA in strains ANESC-S, H.sp.C4 and H.sp.C6 with that of known strains was 93.2, 96.5 and 96.5%, respectively. Based on the 97.0% identity cutoff commonly used to discriminate bacterial species, our data suggest that H. sp.C4 and H.sp.C6 may be new species, and ANESC-S may be belong to a new genus of classified into order Cytophagales. The morphological characteristics by scanning electron microscopy (SEM) showed that, in addition to the coccal N.sp.N3, the majority (19) of the isolates are bacilli of various lengths. In culture the colonies appeared red, orange, yellow, light yellow, and milk-white, with milk-white being predominant. Based on the resistance to NaCl and pH, the 20 novel strains were classified into obligate alkaliphilic and halophilic bacteria, obligate alkaliphilic halotolerant

  15. Screening Prosopis (mesquite) germplasm for biomass production and nitrogen fixation

    SciTech Connect

    Felker, P.; Cannell, G.H.; Clark, P.R.; Osborn, J.F.

    1980-01-01

    The nitrogen-fixing trees of the genus Prosopis (mesquite or algaroba) are well adapted to the semi-arid and often saline regions of the world. These trees may produce firewood or pods for livestock food, they may stabilize sand dunes and they may enrich the soil by production of leaf litter supported by nitrogen fixation. A collection of nearly 500 Prosopis accessions representing North and South American and African germplasm has been established. Seventy of these accessions representing 14 taxa are being grown under field conditions where a 30-fold range in biomass productivity among accessions has been estimated. In a greehouse experiment, 13 Prosopis taxa grew on nitrogen-free medium nodulated, and had a 10-fold difference in nitrogen fixation (acetylene reduction). When Prosopis is propagated by seed the resulting trees are extremely variable in growth rate and presence or absence of thorns. Propagation of 6 Prosopis taxa by stem cuttings has been achieved with low success (1 to 10%) in field-grown plants and with higher success (50 to 100%) with young actively growing greenhouse plants.

  16. Keratinolytic activities of alkaliphilic Bacillus sp. MBRL 575 from a novel habitat, limestone deposit site in Manipur, India.

    PubMed

    Kshetri, Pintubala; Ningthoujam, Debananda S

    2016-01-01

    Microbial degradation of keratinous wastes is preferred over physicochemical methods as the latter is costlier and not eco-friendly. Novel habitats are promising for discovery of new microbial strains. Towards discovery of novel keratinolytic bacteria, screening of bacterial strains from a novel limestone habitat in Hundung, Manipur, India was done and a promising isolate, MBRL 575, was found to degrade native chicken feather efficiently. It could grow over a broad pH range (Langeveld et al. in J Infect Dis 188:1782-1789, 2003; Park and Son in Microbiol Res 164:478-485, 2009; Zaghloul et al. in Biodegradation 22:111-128, 2011; Takami et al. in Biosci Biotechnol Biochem 56:1667-1669, 1992; Riffel et al. in J Biotechnol 128:693-703, 2007; Wang et al. in Bioresour Technol 99:5679-5686, 2008) and in presence of 0-15 % NaCl. Based on phenotypic characterization and 16S rRNA gene sequence analysis, the new keratinolytic limestone isolate was identified as Bacillus sp. MBRL 575. It produced 305 ± 12 U/ml keratinase and liberated 120 ± 5.5 mg of soluble peptides and 158 ± 4 mg of amino acids per gram of feather after 48 h of incubation at 30 °C in chicken feather medium. The strain could also degrade feathers of other species besides chicken. The cell-free enzyme was also able to degrade feather. Citrate and soybean meal were found to be the best carbon and nitrogen supplements for enhanced enzyme, soluble peptide and amino acid production. In addition to keratinolytic activity, MBRL 575 also exhibited antagonistic activity against two major rice fungal pathogens, Rhizoctonia oryzae-sativae (65 %) and Rhizoctonia solani (58 %). PMID:27247891

  17. Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

    PubMed Central

    2016-01-01

    Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies. PMID:27146442

  18. Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses.

    PubMed

    Guillerme, Thomas; Cooper, Natalie

    2016-05-01

    Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies. PMID:27146442

  19. Cyanobacteria and Cyanotoxins: The Influence of Nitrogen versus Phosphorus

    PubMed Central

    Dolman, Andrew M.; Rücker, Jacqueline; Pick, Frances R.; Fastner, Jutta; Rohrlack, Thomas; Mischke, Ute; Wiedner, Claudia

    2012-01-01

    The importance of nitrogen (N) versus phosphorus (P) in explaining total cyanobacterial biovolume, the biovolume of specific cyanobacterial taxa, and the incidence of cyanotoxins was determined for 102 north German lakes, using methods to separate the effects of joint variation in N and P concentration from those of differential variation in N versus P. While the positive relationship between total cyanobacteria biovolume and P concentration disappeared at high P concentrations, cyanobacteria biovolume increased continually with N concentration, indicating potential N limitation in highly P enriched lakes. The biovolumes of all cyanobacterial taxa were higher in lakes with above average joint NP concentrations, although the relative biovolumes of some Nostocales were higher in less enriched lakes. Taxa were found to have diverse responses to differential N versus P concentration, and the differences between taxa were not consistent with the hypothesis that potentially N2-fixing Nostocales taxa would be favoured in low N relative to P conditions. In particular Aphanizomenon gracile and the subtropical invasive species Cylindrospermopsis raciborskii often reached their highest biovolumes in lakes with high nitrogen relative to phosphorus concentration. Concentrations of all cyanotoxin groups increased with increasing TP and TN, congruent with the biovolumes of their likely producers. Microcystin concentration was strongly correlated with the biovolume of Planktothrix agardhii but concentrations of anatoxin, cylindrospermopsin and paralytic shellfish poison were not strongly related to any individual taxa. Cyanobacteria should not be treated as a single group when considering the potential effects of changes in nutrient loading on phytoplankton community structure and neither should the N2-fixing Nostocales. This is of particular importance when considering the occurrence of cyanotoxins, as the two most abundant potentially toxin producing Nostocales in our study were

  20. Microbial Community Diversities and Taxa Abundances in Soils along a Seven-Year Gradient of Potato Monoculture Using High Throughput Pyrosequencing Approach

    PubMed Central

    Liu, Xing; Zhang, Junlian; Gu, Tianyu; Zhang, Wenming; Shen, Qirong; Yin, Shixue; Qiu, Huizhen

    2014-01-01

    Background Previous studies have focused on linking soil community structure, diversity, or specific taxa to disturbances. Relatively little attention has been directed to crop monoculture soils, particularly potato monoculture. Information about microbial community changes over time between monoculture and non-monoculture treatments is lacking. Furthermore, few studies have examined microbial communities in potato monoculture soils using a high throughput pyrosequencing approach. Methodology/Principal Findings Soils along a seven-year gradient of potato monoculture were collected and microbial communities were characterized using high throughput pyrosequencing approach. Principal findings are as follows. First, diversity (HShannon) and richness (SChao1) indices of bacterial community, but not of fungal community, were linearly decreased over time and corresponded to a decline of soil sustainability represented by yield decline and disease incidence increase. Second, Fusarium, the only soilborne pathogen-associated fungal genus substantially detected, was linearly increased over time in abundance and was closely associated with yield decline. Third, Fusarium abundance was negatively correlated with soil organic matter (OM) and total nitrogen (TN) but positively with electrical conductivity (EC). Fourth, Fusarium was correlated in abundances with 6 bacterial taxa over time. Conclusions Soil bacterial and fungal communities exhibited differential responses to the potato monoculture. The overall soil bacterial communities were shaped by potato monoculture. Fusarium was the only soilborne pathogen-associated genus associated with disease incidence increase and yield decline. The changes of soil OM, TN and EC were responsible for Fusarium enrichment, in addition to selections by the monoculture crop. Acidobacteria and Nitrospirae were linearly decreased over time in abundance, corresponding to the decrease of OM, suggesting their similar ecophysiologial trait

  1. Nitrogen Supply Uses Hydrazine

    NASA Technical Reports Server (NTRS)

    Heppner, D. B.

    1984-01-01

    Liquid hydrazine dissociated and residual gas removed to produce almost pure nitrogen. Nitrogen-generation module catalytically dissociates liquid hydrazine then dissociates and separates product gases to yield almost pure nitrogen.

  2. A nomenclator of extant and fossil taxa of the Valvatidae (Gastropoda, Ectobranchia)

    PubMed Central

    Haszprunar, Gerhard

    2014-01-01

    Abstract A compilation of all supra- and (infra-) specific taxa of extant and fossil Valvatidae, a group of freshwater operculate snails, is provided, including taxa initially described in this family and subsequently classified in other families, as well as names containing errors or misspellings. The extensive reference list is directly linked to the available electronic source (digital view or pdf-download) of the respective papers. PMID:24578604

  3. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.

    PubMed

    Fortunato, Caroline S; Eiler, Alexander; Herfort, Lydie; Needoba, Joseph A; Peterson, Tawnya D; Crump, Byron C

    2013-10-01

    Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=-0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments. PMID:23719153

  4. Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

    PubMed Central

    Fortunato, Caroline S; Eiler, Alexander; Herfort, Lydie; Needoba, Joseph A; Peterson, Tawnya D; Crump, Byron C

    2013-01-01

    Bacterioplankton communities are deeply diverse and highly variable across space and time, but several recent studies demonstrate repeatable and predictable patterns in this diversity. We expanded on previous studies by determining patterns of variability in both individual taxa and bacterial communities across coastal environmental gradients. We surveyed bacterioplankton diversity across the Columbia River coastal margin, USA, using amplicon pyrosequencing of 16S rRNA genes from 596 water samples collected from 2007 to 2010. Our results showed seasonal shifts and annual reassembly of bacterioplankton communities in the freshwater-influenced Columbia River, estuary, and plume, and identified indicator taxa, including species from freshwater SAR11, Oceanospirillales, and Flavobacteria groups, that characterize the changing seasonal conditions in these environments. In the river and estuary, Actinobacteria and Betaproteobacteria indicator taxa correlated strongly with seasonal fluctuations in particulate organic carbon (ρ=−0.664) and residence time (ρ=0.512), respectively. In contrast, seasonal change in communities was not detected in the coastal ocean and varied more with the spatial variability of environmental factors including temperature and dissolved oxygen. Indicator taxa of coastal ocean environments included SAR406 and SUP05 taxa from the deep ocean, and Prochlorococcus and SAR11 taxa from the upper water column. We found that in the Columbia River coastal margin, freshwater-influenced environments were consistent and predictable, whereas coastal ocean community variability was difficult to interpret due to complex physical conditions. This study moves beyond beta-diversity patterns to focus on the occurrence of specific taxa and lends insight into the potential ecological roles these taxa have in coastal ocean environments. PMID:23719153

  5. Global diversity patterns and cross-taxa convergence in freshwater systems.

    PubMed

    Tisseuil, Clement; Cornu, Jean-François; Beauchard, Olivier; Brosse, Sebastien; Darwall, William; Holland, Robert; Hugueny, Bernard; Tedesco, Pablo A; Oberdorff, Thierry

    2013-03-01

    Whereas global patterns and predictors of species diversity are well known for numerous terrestrial taxa, our understanding of freshwater diversity patterns and their predictors is much more limited. Here, we examine spatial concordance in global diversity patterns for five freshwater taxa (i.e. aquatic mammals, aquatic birds, fishes, crayfish and aquatic amphibians) and investigate the environmental factors driving these patterns at the river drainage basin grain. We find that species richness and endemism patterns are significantly correlated among taxa. We also show that cross-taxon congruence patterns are often induced by common responses of taxa to their contemporary and historical environments (i.e. convergent patterns). Apart from some taxa distinctiveness (i.e. fishes), the 'climate/productivity' hypothesis is found to explain the greatest variance in species richness and endemism patterns, followed by factors related to the 'history/dispersion' and 'area/environmental heterogeneity' hypotheses. As aquatic amphibians display the highest levels of congruency with other taxa, this taxon appears to be a good 'surrogate' candidate for developing global freshwater conservation planning at the river drainage basin grain. PMID:23173605

  6. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

    PubMed Central

    Luo, Chengwei; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

    2014-01-01

    Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies. PMID:24589583

  7. A swainsonine survey of North American Astragalus and Oxytropis taxa implicated as locoweeds.

    PubMed

    Cook, Daniel; Gardner, Dale R; Lee, Stephen T; Pfister, James A; Stonecipher, Clinton A; Welsh, Stanley L

    2016-08-01

    Swainsonine, an indolizidine alkaloid with significant physiological activity, is an α-mannosidase and mannosidase II inhibitor that causes lysosomal storage disease and alters glycoprotein processing. Swainsonine is found in a number of plant species worldwide, and causes severe toxicosis in livestock grazing these plants, leading to a chronic wasting disease characterized by weight loss, depression, altered behavior, decreased libido, infertility, and death. Swainsonine has been detected in 19 Astragalus and 2 Oxytropis species in North America by thin layer chromatography, gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry and a jack bean α-mannosidase inhibition assay. In addition, 5 species in North America are presumed to contain swainsonine based upon reports from field cases. Many of these plant species have not been analyzed for swainsonine using modern instrumentation such as gas or liquid chromatography coupled with mass spectrometry. To provide clarification, 22 Astragalus species representing 93 taxa and 4 Oxytropis species representing 18 taxa were screened for swainsonine using both liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. Swainsonine was detected in 48 Astragalus taxa representing 13 species and 5 Oxytropis taxa representing 4 species. Forty of the fifty-three swainsonine-positive taxa had not been determined to contain swainsonine previously using liquid or gas chromatography coupled with mass spectrometry. The list of swainsonine-containing taxa reported here will serve as a reference for risk assessment and diagnostic purposes. PMID:27085305

  8. Do foliar endophytic bacteria fix nitrogen?

    NASA Astrophysics Data System (ADS)

    Kueppers, L. M.; Moyes, A. B.; Frank, C.; Pett-Ridge, J.; Carper, D.; Vandehey, N.; O'Neil, J.; Dekas, A.

    2015-12-01

    Endophytic microorganisms - bacteria and fungi that live inside healthy plant tissue - are a relatively unexplored source of functional diversity in natural ecosystems. Prior to modern sequencing technology, detecting uncultured endophytic bacteria and assessing their putative functions was challenging. However, recent work has revealed a remarkable diversity of as yet non-culturable endophytic taxa and is beginning to identify functional roles within plant microbiomes. We recently examined bacterial communities in the foliage of a long-lived, high-elevation conifer species, limber pine (Pinus flexilis), and discovered a community strongly dominated by acetic acid bacteria (Acetobacteraceae), with several taxa closely related to known nitrogen fixers. Given limber pine's status as a pioneer species that is able to grow in low fertility soils, we hypothesized that this bacterial community has a potential functional role in fixing atmospheric nitrogen, providing a source of this limiting nutrient to the host tree. We used the radioisotope 13N2 to confirm that N2 rapidly diffuses into pine needles, where it could potentially be fixed. With an acetylene reduction assay we confirmed nitrogenase enzyme activity inside excised twigs 4 times over a growing season, and estimate potential rates of N2 fixation at 0.1 nmol N2 g needle-1 hr-1. Scaled to the stand level, this N input could be on the order of ~20 mg N m-2 d-1 over a growing season. While these rates are low, the long lifespan of individual trees (~1000 years) makes them biologically meaningful. Still, measured rates of acetylene reduction and bulk 15N2 incorporation are quite variable in space and time. Much work remains to better characterize the plant-microbial interactions in this system, including the rates of nitrogen fixation and their variability over the growing season, across edaphic conditions, among host species, and through plant development; and to determine which community members are responsible

  9. Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

    PubMed Central

    Carr, Rogan; Shen-Orr, Shai S.; Borenstein, Elhanan

    2013-01-01

    Metagenomics has transformed our understanding of the microbial world, allowing researchers to bypass the need to isolate and culture individual taxa and to directly characterize both the taxonomic and gene compositions of environmental samples. However, associating the genes found in a metagenomic sample with the specific taxa of origin remains a critical challenge. Existing binning methods, based on nucleotide composition or alignment to reference genomes allow only a coarse-grained classification and rely heavily on the availability of sequenced genomes from closely related taxa. Here, we introduce a novel computational framework, integrating variation in gene abundances across multiple samples with taxonomic abundance data to deconvolve metagenomic samples into taxa-specific gene profiles and to reconstruct the genomic content of community members. This assembly-free method is not bounded by various factors limiting previously described methods of metagenomic binning or metagenomic assembly and represents a fundamentally different approach to metagenomic-based genome reconstruction. An implementation of this framework is available at http://elbo.gs.washington.edu/software.html. We first describe the mathematical foundations of our framework and discuss considerations for implementing its various components. We demonstrate the ability of this framework to accurately deconvolve a set of metagenomic samples and to recover the gene content of individual taxa using synthetic metagenomic samples. We specifically characterize determinants of prediction accuracy and examine the impact of annotation errors on the reconstructed genomes. We finally apply metagenomic deconvolution to samples from the Human Microbiome Project, successfully reconstructing genus-level genomic content of various microbial genera, based solely on variation in gene count. These reconstructed genera are shown to correctly capture genus-specific properties. With the accumulation of metagenomic

  10. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity.

    PubMed

    Shade, Ashley; Jones, Stuart E; Caporaso, J Gregory; Handelsman, Jo; Knight, Rob; Fierer, Noah; Gilbert, Jack A

    2014-01-01

    Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial "rare biosphere" to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified "one-hit wonder" CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time. Importance: Microbial communities and their processes are the foundations of ecosystems. The ecological roles of rare microorganisms are largely unknown, but it is thought that they contribute to community stability by acting as a reservoir that can rapidly respond to environmental changes. We investigated the occurrence of typically rare taxa that very occasionally become more prominent in their communities ("conditionally rare"). We quantified conditionally rare

  11. Comparative and evolutionary insights into CD4 gene across mammalian and avian taxa

    PubMed Central

    Khan, Naazneen

    2015-01-01

    The present day genetic architecture of a species bears much significance to its closely related species which is due to species-specific differences, shaped by different evolutionary forces across time scale. With the availability of whole genome sequence of several closely related species, it is now possible to infer evolutionary patterns of genes and genomes in specific lineages. To this respect, CD4 gene, primarily responsible for defensive mechanism in human, is conserved across a few taxa, and thus, comparative genomic studies could be useful for better understanding of host–pathogen biology. Comparative and evolutionary analyses were performed in eleven taxa (10 mammalian and avian) with different statistical algorithms. Phylogenetic inferences revealed recent divergence of human and chimpanzee, and pig was found to be diverged from rest of the taxa significantly. Additionally, gene length, microsatellites, and secondary structures were observed across taxa. The genetic architecture of CD4 gene and its evolutionary history in different mammalian taxa provide crucial evidence in support of the fact that this gene might have been evolving at a similar rate to other human immune system genes. Future population-based study and structural modeling would unravel the differential ability to interact with HIV virus and influence immune system in humans. PMID:26767121

  12. Differences among Major Taxa in the Extent of Ecological Knowledge across Four Major Ecosystems

    PubMed Central

    Fisher, Rebecca; Knowlton, Nancy; Brainard, Russell E.; Caley, M. Julian

    2011-01-01

    Existing knowledge shapes our understanding of ecosystems and is critical for ecosystem-based management of the world's natural resources. Typically this knowledge is biased among taxa, with some taxa far better studied than others, but the extent of this bias is poorly known. In conjunction with the publically available World Registry of Marine Species database (WoRMS) and one of the world's premier electronic scientific literature databases (Web of Science®), a text mining approach is used to examine the distribution of existing ecological knowledge among taxa in coral reef, mangrove, seagrass and kelp bed ecosystems. We found that for each of these ecosystems, most research has been limited to a few groups of organisms. While this bias clearly reflects the perceived importance of some taxa as commercially or ecologically valuable, the relative lack of research of other taxonomic groups highlights the problem that some key taxa and associated ecosystem processes they affect may be poorly understood or completely ignored. The approach outlined here could be applied to any type of ecosystem for analyzing previous research effort and identifying knowledge gaps in order to improve ecosystem-based conservation and management. PMID:22073172

  13. Signals of speciation: volatile organic compounds resolve closely related sagebrush taxa, suggesting their importance in evolution.

    PubMed

    Jaeger, Deidre M; Runyon, Justin B; Richardson, Bryce A

    2016-09-01

    Volatile organic compounds (VOCs) play important roles in the environmental adaptation and fitness of plants. Comparison of the qualitative and quantitative differences in VOCs among closely related taxa and assessing the effects of environment on their emissions are important steps to deducing VOC function and evolutionary importance. Headspace VOCs from five taxa of sagebrush (Artemisia, subgenus Tridentatae) growing in two common gardens were collected and analyzed using GC-MS. Of the 74 total VOCs emitted, only 15 were needed to segregate sagebrush taxa using Random Forest analysis with a low error of 4%. All but one of these 15 VOCs showed qualitative differences among taxa. Ordination of results showed strong clustering that reflects taxonomic classification. Random Forest identified five VOCs that classify based on environment (2% error), which do not overlap with the 15 VOCs that segregated taxa. We show that VOCs can discriminate closely related species and subspecies of Artemisia, which are difficult to define using molecular markers or morphology. Thus, it appears that changes in VOCs either lead the way or follow closely behind speciation in this group. Future research should explore the functions of VOCs, which could provide further insights into the evolution of sagebrushes. PMID:27112551

  14. An analysis of tooth and body size relationship in five primate taxa.

    PubMed

    Wood, B A

    1979-01-01

    The strength and the nature of the covariance between tooth and body size was investigated in Homo, Gorilla, Pan, Papio and Colobus. When sexes are combined in each taxon, the correlations are strong enough to compare the allometry coefficients of taxa, and the non-human taxa show a sufficiently strong linear relationship to compute 'interspecific' allometry coefficients. Allometry coefficients for each variable were not uniform among the taxa, and coefficients also differed from one variable to another. Computed 'intra' and 'inter' specific allometry coefficients from these data suggest that canine size will usually scale at a higher level than molar crown area, which is at most isometric, and not positively allometric with respect to body size. The consequence is that larger representatives of a taxon would be expected to combine relatively larger canines with a proportional, or relatively smaller, molar crown area. It is pointed out that these differences do not correspond to those found between 'gracile' and 'robust' australopithecines. PMID:116945

  15. New records for Albania based on taxa from the Prespa National Park

    PubMed Central

    2013-01-01

    Abstract Twelve taxa are enumerated as new and three taxa confirmed for the flora of Albania. They were collected between 2007 and 2012 in the Prespa National Park of Albania which is part of the Prespa International Park, a biological protected area at the borders with F.Y.R. Macedonia and Greece. Four taxa, viz., Centaurea galicicae, Festuca galicicae, Laserpitium ochridanum and Micromeria cristata subsp. kosaninii are restricted to Dry and Galičica Mountains. Centaurea decora, a recently described species, is treated as a synonym of Centaurea soskae thus extending the known localities of the latter to the southeast. Detailed information on distribution, occurrence and habitats in Albania are provided for each taxon. PMID:24723753

  16. Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape

    PubMed Central

    Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

    2015-01-01

    Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km2, by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships

  17. Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape.

    PubMed

    Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

    2015-06-01

    Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km(2) , by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships

  18. Benefits to poorly studied taxa of conservation of bird and mammal diversity on islands.

    PubMed

    Aslan, Clare; Holmes, Nick; Tershy, Bernie; Spatz, Dena; Croll, Donald A

    2015-02-01

    Protected area delineation and conservation action are urgently needed on marine islands, but the potential biodiversity benefits of these activities can be difficult to assess due to lack of species diversity information for lesser known taxa. We used linear mixed effects modeling and simple spatial analyses to investigate whether conservation activities based on the diversity of well-known insular taxa (birds and mammals) are likely to also capture the diversity of lesser known taxa (reptiles, amphibians, vascular land plants, ants, land snails, butterflies, and tenebrionid beetles). We assembled total, threatened, and endemic diversity data for both well-known and lesser known taxa and combined these with physical island biogeography characteristics for 1190 islands from 109 archipelagos. Among physical island biogeography factors, island area was the best indicator of diversity of both well-known and little-known taxa. Among taxonomic factors, total mammal species richness was the best indicator of total diversity of lesser known taxa, and the combination of threatened mammal and threatened bird diversity was the best indicator of lesser known endemic richness. The results of other intertaxon diversity comparisons were highly variable, however. Based on our results, we suggest that protecting islands above a certain minimum threshold area may be the most efficient use of conservation resources. For example, using our island database, if the threshold were set at 10 km(2) and the smallest 10% of islands greater than this threshold were protected, 119 islands would be protected. The islands would range in size from 10 to 29 km(2) and would include 268 lesser known species endemic to a single island, along with 11 bird and mammal species endemic to a single island. Our results suggest that for islands of equivalent size, prioritization based on total or threatened bird and mammal diversity may also capture opportunities to protect lesser known species endemic to

  19. Crickets (Insecta, Orthoptera, Grylloidea) from Southern New Caledonia,
    with descriptions of new taxa.

    PubMed

    Anso, Jérémy; Jourdan, Hervé; Desutter-Grandcolas, Laure

    2016-01-01

    Intensive sampling of cricket communities has been undertaken in southern New Caledonia in selected plots of vegetation, i.e. rain forest, preforest and maquis shrubland. This leads to the discovery of many new taxa, which are described in the present paper, together with closely related species from nearby areas. Descriptions are based on general morphology and characters of genitalia. Calling songs are described for all acoustic taxa but two, and observations about species habitats are given. In total, 35 species belonging to 13 genera are studied, including 21 new species and two new genera. The pattern of assemblages of cricket species in New Caledonia is discussed. PMID:27395569

  20. Short-Term Protein Stable Isotope Probing of Microbial Communities to Associate Functions with Taxa (Invited)

    NASA Astrophysics Data System (ADS)

    Lipton, M. S.; Slysz, G. W.; Steinke, L. A.; Ward, D. M.; Klatt, C. G.; Clauss, T. R.; Purvine, S. O.; Anderson, G. A.; Payne, S. H.; Bryant, D. A.

    2013-12-01

    Determining which taxa in a community perform which functions is essential for understanding metabolite fluxes and metabolic interactions among community members. Specific taxa will alter their metabolism in order to acclimate to changing environmental factors such as light through the diel cycle, changing temperature and other factors. Monitoring which proteins are being expressed, and the quantitative protein expression patterns in the individual taxa as a response to external stimuli is key to understanding these mechanisms. Protein stable isotope probing (Pro-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. In Pro-SIP studies, label incorporation is determined by the extent of the change in the isotopic profile of peptides when measured by mass spectrometry. While most Pro-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism(s), these techniques have not been applied to short term in situ studies due to the small degree of partial labeling of the proteins. We have applied Pro-SIP to study the assimilation of a labeled substrate into proteins to determine which taxa are responsible for sequestration of dissolved inorganic carbon in microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park. This community is fueled by sunlight as it transitions from dark to light; the aim was to understand the light-dependent pathway of inorganic carbon incorporation into different taxa during the early morning hours when the mat was in low light and anoxic. Each mat sample was incubated with 13C-bicarbonate for 3 h. Substrate assimilation was determined through standard proteomic techniques along with the use of SIPPER, a collection of algorithms that sensitively measure small changes in peptide isotopic patterns, allowing the determination of which taxa assimilated the substrate during this period. For the

  1. The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application.

    PubMed

    Yeoh, Yun Kit; Paungfoo-Lonhienne, Chanyarat; Dennis, Paul G; Robinson, Nicole; Ragan, Mark A; Schmidt, Susanne; Hugenholtz, Philip

    2016-05-01

    Diazotrophic bacteria potentially supply substantial amounts of biologically fixed nitrogen to crops, but their occurrence may be suppressed by high nitrogen fertilizer application. Here, we explored the impact of high nitrogen fertilizer rates on the presence of diazotrophs in field-grown sugarcane with industry-standard or reduced nitrogen fertilizer application. Despite large differences in soil microbial communities between test sites, a core sugarcane root microbiome was identified. The sugarcane root-enriched core taxa overlap with those of Arabidopsis thaliana raising the possibility that certain bacterial families have had long association with plants. Reduced nitrogen fertilizer application had remarkably little effect on the core root microbiome and did not increase the relative abundance of root-associated diazotrophs or nif gene counts. Correspondingly, low nitrogen fertilizer crops had lower biomass and nitrogen content, reflecting a lack of major input of biologically fixed nitrogen, indicating that manipulating nitrogen fertilizer rates does not improve sugarcane yields by enriching diazotrophic populations under the test conditions. Standard nitrogen fertilizer crops had improved biomass and nitrogen content, and corresponding soils had higher abundances of nitrification and denitrification genes. These findings highlight that achieving a balance in maximizing crop yields and minimizing nutrient pollution associated with nitrogen fertilizer application requires understanding of how microbial communities respond to fertilizer use. PMID:26032777

  2. [Conditionally neutral phylogenetic markers of major taxa: a new aspect of the evolution of macromolecules].

    PubMed

    Petrov, N B; Aleshin, V V

    2002-08-01

    The current phase of molecular phylogenetics can be named the 18S rRNA gene era, which is now approaching the end. To date, almost all phyla of metazoans and many taxa of protists are represented in databases of 18S rRNA gene sequences. The elements of the phylogenetic tree of Metazoa inferred from 18S rRNA genes are characterized by unequal validity: some of them seem to be well grounded; others are not adequately supported, and probably will be revised later. The validity of phylogenetic reconstruction is influenced by two main factors: (1) erroneous grouping of long branches that occur because of abnormally high evolution rate; (2) deficit of phylogenetically informative characters. A method for overcoming these difficulties is suggested in addition to known tools: using phylogenetic markers that are stable within individual taxa and evolve by punctuated equilibrium. These markers are least influenced by the convergence caused by a high evolution rate of the entire gene. The nature of these markers of ancient taxa, paradoxical from the perspective of neutral evolution, is discussed, as well as their importance for establishing monophyly of both new large-scale taxonomic groups of invertebrates (Bilateria + Rhombozoa + Orthonectida + Myxozoa + Cnidaria + Placozoa and Echinodermata + Hemichordata) and some major taxa of Nematoda. PMID:12244690

  3. Twelve invasive plant taxa in U.S. western riparian ecosystems

    EPA Science Inventory

    Assessments of stream ecosystems often include an evaluation of riparian condition; a key stressor in riparian ecosystems is the presence of invasive plants. We analyzed the distribution of 12 invasive taxa (common burdock [Arctium minus], giant reed [Arundo donax], cheatgrass [B...

  4. Can the freshwater bacterial communities shift to the "marine-like" taxa?

    PubMed

    Zhang, Lei; Gao, Guang; Tang, Xiangming; Shao, Keqiang

    2014-11-01

    A mesocosm experiment was used to study the response of a freshwater bacterial community to increasing salinity. Bacterial community composition in the control and saline groups was analyzed using polymerase chain reaction (PCR)-terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA genes, followed by clonal sequencing of eight selected samples. Cluster analysis and phylogenetic analysis revealed that the bacterial communities in pre- and post-salt addition samples were significantly different. Detailed analysis showed: (i) the existing bacterial taxa markedly declined from freshwater to hypersaline habitats, although some taxa maintain balanced growth over a small salinity range through inter-genus changes in community structures; (ii) the addition of salt induced a clear shift in the community structure toward a striking increase in the relative abundance of the latent "marine-like" genera (e.g., Alcanivorax and Roseovarius). The reasons may be that freshwater bacteria adapt to live in low salt concentrations and low osmotic pressure. They were not adapted to high concentrations of salt, and their acute response to increasing salinity resulted in significantly decreased numbers. However, as the salinity increases, rare members of the ever-present community (rare or dormant bacterial taxa in the "microbial seed bank") rise to the fore, while previous dominant members drop away. This study provides direct evidence for bacterial succession from halosensitive taxa in freshwater to halotolerant ones in response to water salinization. PMID:24687773

  5. Pyrosequencing detects human and animal pathogenic taxa in the grapevine endosphere

    PubMed Central

    Yousaf, Sohail; Bulgari, Daniela; Bergna, Alessandro; Pancher, Michael; Quaglino, Fabio; Casati, Paola; Campisano, Andrea

    2014-01-01

    Generally, plants are not considered as hosts for human and animal pathogens (HAP). The recent produce-associated outbreaks of food-borne diseases have drawn attention toward significant deficiencies in our understanding of the ecology of HAP, and their potential for interkingdom transfer. To examine the association of microorganisms classified as HAP with plants, we surveyed the presence and distribution of HAP bacterial taxa (henceforth HAPT, for brevity's sake) in the endosphere of grapevine (Vitis vinifera L.) both in the plant stems and leaves. An enrichment protocol was used on leaves to detect taxa with very low abundance in undisturbed tissues. We used pyrosequencing and phylogenetic analyses of the 16S rDNA gene. We identified several HAPT, and focused on four genera (Propionibacterium, Staphylococcus, Clostridium, and Burkholderia). The majority of the bacterial sequences in the genus Propionibacterium, from grapevine leaf and stem, were identified as P. acnes. Clostridia were detected in leaves and stems, but their number was much higher in leaves after enrichment. HAPT were indentified both in leaves and wood of grapevines. This depicts the ability of these taxa to be internalized within plant tissues and maintain their population levels in a variety of environments. Our analysis highlighted the presence of HAPT in the grapevine endosphere and unexpected occurrence of these bacterial taxa in this atypical environment. PMID:25071740

  6. Gene Flow Among Different Teosinte Taxa and Into the Domesticated Maize Gene Pool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maize (Zea mays ssp. mays) was domesticated from one wild species ancestor, the Balsas teosinte (Zea mays ssp. parviglumis) about 9000 years ago. Higher levels of gene diversity are found in teosinte taxa compared to maize following domestication and selection bottlenecks. Diversity in maize can b...

  7. Trait-based diversification shifts reflect differential extinction among fossil taxa

    PubMed Central

    Wagner, Peter J.; Estabrook, George F.

    2014-01-01

    Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898

  8. Floral traits driving reproductive isolation of two co-flowering taxa that share vertebrate pollinators.

    PubMed

    Queiroz, Joel A; Quirino, Zelma G M; Machado, Isabel C

    2015-01-01

    Floral attributes evolve in response to frequent and efficient pollinators, which are potentially important drivers of floral diversification and reproductive isolation. In this context, we asked, how do flowers evolve in a bat-hummingbird pollination system? Hence, we investigated the pollination ecology of two co-flowering Ipomoea taxa (I. marcellia and I. aff. marcellia) pollinated by bats and hummingbirds, and factors favouring reproductive isolation and pollinator sharing in these plants. To identify the most important drivers of reproductive isolation, we compared the flowers of the two Ipomoea taxa in terms of morphometry, anthesis and nectar production. Pollinator services were assessed using frequency of visits, fruit set and the number of seeds per fruit after visits. The studied Ipomoea taxa differed in corolla size and width, beginning and duration of anthesis, and nectar attributes. However, they shared the same diurnal and nocturnal visitors. The hummingbird Heliomaster squamosus was more frequent in I. marcellia (1.90 visits h(-1)) than in I. aff. marcellia (0.57 visits h(-1)), whereas glossophagine bats showed similar visit rates in both taxa (I. marcellia: 0.57 visits h(-1) and I. aff. marcellia: 0.64 visits h(-1)). Bat pollination was more efficient in I. aff. marcellia, whereas pollination by hummingbirds was more efficient in I. marcellia. Differences in floral attributes between Ipomoea taxa, especially related to the anthesis period, length of floral parts and floral arrangement in the inflorescence, favour reproductive isolation from congeners through differential pollen placement on pollinators. This bat-hummingbird pollination system seems to be advantageous in the study area, where the availability of pollinators and floral resources changes considerably throughout the year, mainly as a result of rainfall seasonality. This interaction is beneficial for both sides, as it maximizes the number of potential pollen vectors for plants and

  9. Representative taxa in field trials for environmental risk assessment of genetically modified maize.

    PubMed

    Albajes, R; Lumbierres, B; Pons, X; Comas, J

    2013-12-01

    When assessing the benefits and risks of transgenic crops, one consideration is their relative effects on non-target arthropod (NTA) abundance and functions within agroecosystems. Several laboratory and field trials have been conducted in Spain since the late 1990s to assess this issue. A consideration in the design of field trials is whether it is necessary to sample most NTAs living in the crop or only representative taxa that perform main ecological functions and have a good capacity to detect small changes in their abundance. Small changes in the field abundance of an effective representative taxon should be detectable using standard experimental protocols. The ability of a species to reveal differences across treatments may be analysed by examining the detectable treatment effects for surveyed non-target organisms. Analysis of data from several NTAs recorded in 14 field trials conducted over 10 years using complete block designs allowed us to select a number of representative taxa capable of detecting changes in the density or activity of arthropod herbivores, predators, parasitoids and decomposers in transgenic and non-transgenic maize varieties. The most suitable NTA as representative taxa (with detectable treatment effects below 50%) included leafhoppers among arthropod herbivores, Orius spp., Araneae, and Carabidae among predators, chalcidids, particularly the family Mymaridae, among parasitoids and Chloropidae as decomposer. Details of sampling techniques for each sampled taxa and their advantages and disadvantages are discussed. It is concluded that abundance of taxa is the most influential factor determining their capacity to detect changes caused by genetically modified varieties. PMID:23987801

  10. Climate sensitivity of allergenic taxa in Central Europe associated with new climate change related forces.

    PubMed

    Deák, Aron József; Makra, László; Matyasovszky, István; Csépe, Zoltán; Muladi, Beáta

    2013-01-01

    The aim of the study was to analyse trends of the pollen season with its duration, start and end dates, as well as trends of the annual total pollen count and annual peak pollen concentration for the Szeged agglomeration in Southern Hungary. The data set covered an 11-year period (1997-2007) that included eight taxa and seven daily climate variables. Trend analysis was performed on both annual and daily bases. Trend analysis on a daily basis is a new approach that provides information on the annual cycles of the trends. To quantify the strength of the relationship between the annual cycle of the slope of a pollen concentration trend and the annual cycles of the slopes of the climate variable trends, an association measure and a multiple association measure are introduced. Individual taxa were sorted into three categories according to their climate sensitivities. These were compared with two novel climate change-related forces, namely risk potential and expansion potential due to the climate change. The total annual pollen counts indicated significant trends for 4 taxa and 3 of these 4 trends increased on a daily basis. At the same time, significant changes were detected for the pollen season characteristics of three taxa. The association measures performed well when compared to the climate change-related forces. Significant changes in pollen season characteristics were also in accordance with the risk potential and expansion potential due to the climate change. A novel procedure was applied to separate the effects of the past and current weather conditions that influence the current Ambrosia pollen concentrations. The potential effect of land use changes on pollen release of the given taxa was also discussed using the CORINE Land Cover Database. PMID:23178762

  11. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

    SciTech Connect

    Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.; Santee, C.A.; Bradford, M.A.; Treseder, K.K.; Wallenstein, M.D.; Brodie, E.L.

    2011-04-18

    Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.

  12. Floral traits driving reproductive isolation of two co-flowering taxa that share vertebrate pollinators

    PubMed Central

    Queiroz, Joel A.; Quirino, Zelma G. M.; Machado, Isabel C.

    2015-01-01

    Floral attributes evolve in response to frequent and efficient pollinators, which are potentially important drivers of floral diversification and reproductive isolation. In this context, we asked, how do flowers evolve in a bat–hummingbird pollination system? Hence, we investigated the pollination ecology of two co-flowering Ipomoea taxa (I. marcellia and I. aff. marcellia) pollinated by bats and hummingbirds, and factors favouring reproductive isolation and pollinator sharing in these plants. To identify the most important drivers of reproductive isolation, we compared the flowers of the two Ipomoea taxa in terms of morphometry, anthesis and nectar production. Pollinator services were assessed using frequency of visits, fruit set and the number of seeds per fruit after visits. The studied Ipomoea taxa differed in corolla size and width, beginning and duration of anthesis, and nectar attributes. However, they shared the same diurnal and nocturnal visitors. The hummingbird Heliomaster squamosus was more frequent in I. marcellia (1.90 visits h−1) than in I. aff. marcellia (0.57 visits h−1), whereas glossophagine bats showed similar visit rates in both taxa (I. marcellia: 0.57 visits h−1 and I. aff. marcellia: 0.64 visits h−1). Bat pollination was more efficient in I. aff. marcellia, whereas pollination by hummingbirds was more efficient in I. marcellia. Differences in floral attributes between Ipomoea taxa, especially related to the anthesis period, length of floral parts and floral arrangement in the inflorescence, favour reproductive isolation from congeners through differential pollen placement on pollinators. This bat–hummingbird pollination system seems to be advantageous in the study area, where the availability of pollinators and floral resources changes considerably throughout the year, mainly as a result of rainfall seasonality. This interaction is beneficial for both sides, as it maximizes the number of potential pollen vectors for plants and

  13. Nitrogen segregation in nanocarbons.

    PubMed

    Ewels, C P; Erbahar, D; Wagner, Ph; Rocquefelte, X; Arenal, R; Pochet, P; Rayson, M; Scardamaglia, M; Bittencourt, C; Briddon, P

    2014-01-01

    We explore the behaviour of nitrogen doping in carbon nanomaterials, notably graphene, nanotubes, and carbon thin films. This is initially via a brief review of the literature, followed by a series of atomistic density functional calculations. We show that at low concentrations, substitutional nitrogen doping in the sp(2)-C graphenic basal plane is favoured, however once the nitrogen concentration reaches a critical threshold there is a transition towards the formation of the more thermodynamically-favoured nitrogen terminated 'zigzag' type edges. These can occur either via formation of finite patches (polycyclic aromatic azacarbons), strips of sp(2) carbon with zigzag nitrogen edges, or internal nitrogen-terminated hole edges within graphenic planes. This transition to edge formation is especially favoured when the nitrogen can be partially functionalised with, e.g. hydrogen. By comparison with available literature results, notably from electron energy loss spectroscopy and X-ray spectroscopy, the current results suggest that much of the nitrogen believed to be incorporated into carbon nanoobjects is instead likely to be present terminating the edges of carbonaceous impurities attached to nanoobject's surface. By comparison to nitrogen-doped tetrahedrally amorphous carbon, we suggest that this transition at around 10-20% nitrogen concentration and above towards sp(2) coordination via internal nitrogen-terminated edge formation may be a general property of nitrogen-doped carbon materials. PMID:25468305

  14. Nitrogen dioxide detection

    DOEpatents

    Sinha, Dipen N.; Agnew, Stephen F.; Christensen, William H.

    1993-01-01

    Method and apparatus for detecting the presence of gaseous nitrogen dioxide and determining the amount of gas which is present. Though polystyrene is normally an insulator, it becomes electrically conductive in the presence of nitrogen dioxide. Conductance or resistance of a polystyrene sensing element is related to the concentration of nitrogen dioxide at the sensing element.

  15. Ambiguous taxa: Effects on the characterization and interpretation of invertebrate assemblages

    USGS Publications Warehouse

    Cuffney, T.F.; Bilger, M.D.; Haigler, A.M.

    2007-01-01

    Damaged and immature specimens often result in macroinvertebrate data that contain ambiguous parent-child pairs (i.e., abundances associated with multiple related levels of the taxonomic hierarchy such as Baetis pluto and the associated ambiguous parent Baetis sp.). The choice of method used to resolve ambiguous parent-child pairs may have a very large effect on the characterization of invertebrate assemblages and the interpretation of responses to environmental change because very large proportions of taxa richness (73-78%) and abundance (79-91%) can be associated with ambiguous parents. To address this issue, we examined 16 variations of 4 basic methods for resolving ambiguous taxa: RPKC (remove parent, keep child), MCWP (merge child with parent), RPMC (remove parent or merge child with parent depending on their abundances), and DPAC (distribute parents among children). The choice of method strongly affected assemblage structure, assemblage characteristics (e.g., metrics), and the ability to detect responses along environmental (urbanization) gradients. All methods except MCWP produced acceptable results when used consistently within a study. However, the assemblage characteristics (e.g., values of assemblage metrics) differed widely depending on the method used, and data should not be combined unless the methods used to resolve ambiguous taxa are well documented and are known to be comparable. The suitability of the methods was evaluated and compared on the basis of 13 criteria that considered conservation of taxa richness and abundance, consistency among samples, methods, and studies, and effects on the interpretation of the data. Methods RPMC and DPAC had the highest suitability scores regardless of whether ambiguous taxa were resolved for each sample separately or for a group of samples. Method MCWP gave consistently poor results. Methods MCWP and DPAC approximate the use of family-level identifications and operational taxonomic units (OTU), respectively. Our

  16. Estimating vertebrate, benthic macroinvertebrate, and diatom taxa richness in raftable Pacific Northwest rivers for bioassessment purposes.

    PubMed

    Hughes, Robert M; Herlihy, Alan T; Gerth, William J; Pan, Yangdong

    2012-05-01

    The number of sites sampled must be considered when determining the effort necessary for adequately assessing taxa richness in an ecosystem for bioassessment purposes; however, there have been few studies concerning the number of sites necessary for bioassessment of large rivers. We evaluated the effect of sample size (i.e., number of sites) necessary to collect vertebrate (fish and aquatic amphibians), macroinvertebrate, and diatom taxa from seven large rivers in Oregon and Washington, USA during the summers of 2006-2008. We used Monte Carlo simulation to determine the number of sites needed to collect 90-95% of the taxa 75-95% of the time from 20 randomly located sites on each river. The river wetted widths varied from 27.8 to 126.0 m, mean substrate size varied from 1 to 10 cm, and mainstem distances sampled varied from 87 to 254 km. We sampled vertebrates at each site (i.e., 50 times the mean wetted channel width) by nearshore-raft electrofishing. We sampled benthic macroinvertebrates nearshore through the use of a 500-μm mesh kick net at 11 systematic stations. From each site composite sample, we identified a target of 500 macroinvertebrate individuals to the lowest possible taxon, usually genus. We sampled benthic diatoms nearshore at the same 11 stations from a 12-cm(2) area. At each station, we sucked diatoms from soft substrate into a 60-ml syringe or brushed them off a rock and rinsed them with river water into the same jar. We counted a minimum of 600 valves at 1,000× magnification for each site. We collected 120-211 diatom taxa, 98-128 macroinvertebrate taxa, and 14-33 vertebrate species per river. To collect 90-95% of the taxa 75-95% of the time that were collected at 20 sites, it was necessary to sample 11-16 randomly distributed sites for vertebrates, 13-17 sites for macroinvertebrates, and 16-18 sites for diatoms. We conclude that 12-16 randomly distributed sites are needed for cost-efficient sampling of vertebrate richness in the main stems of

  17. A method for subsampling terrestrial invertebrate samples in the laboratory: estimating abundance and taxa richness.

    PubMed

    Doğramaci, Mahmut; DeBano, Sandra J; Wooster, David E; Kimoto, Chiho

    2010-01-01

    Significant progress has been made in developing subsampling techniques to process large samples of aquatic invertebrates. However, limited information is available regarding subsampling techniques for terrestrial invertebrate samples. Therefore a novel subsampling procedure was evaluated for processing samples of terrestrial invertebrates collected using two common field techniques: pitfall and pan traps. A three-phase sorting protocol was developed for estimating abundance and taxa richness of invertebrates. First, large invertebrates and plant material were removed from the sample using a sieve with a 4 mm mesh size. Second, the sample was poured into a specially designed, gridded sampling tray, and 16 cells, comprising 25% of the sampling tray, were randomly subsampled and processed. Third, the remainder of the sample was scanned for 4-7 min to record rare taxa missed in the second phase. To compare estimated abundance and taxa richness with the true values of these variables for the samples, the remainder of each sample was processed completely. The results were analyzed relative to three sample size categories: samples with less than 250 invertebrates (low abundance samples), samples with 250-500 invertebrates (moderate abundance samples), and samples with more than 500 invertebrates (high abundance samples). The number of invertebrates estimated after subsampling eight or more cells was highly precise for all sizes and types of samples. High accuracy for moderate and high abundance samples was achieved after even as few as six subsamples. However, estimates of the number of invertebrates for low abundance samples were less reliable. The subsampling technique also adequately estimated taxa richness; on average, subsampling detected 89% of taxa found in samples. Thus, the subsampling technique provided accurate data on both the abundance and taxa richness of terrestrial invertebrate samples. Importantly, subsampling greatly decreased the time required to

  18. Two-Dimensional Gel Electrophoresis Analyses of pH-Dependent Protein Expression in Facultatively Alkaliphilic Bacillus pseudofirmus OF4 Lead to Characterization of an S-Layer Protein with a Role in Alkaliphily

    PubMed Central

    Gilmour, Raymond; Messner, Paul; Guffanti, Arthur A.; Kent, Rebecca; Scheberl, Andrea; Kendrick, Nancy; Krulwich, Terry Ann

    2000-01-01

    The large majority of proteins of alkaliphilic Bacillus pseudofirmus OF4 grown at pH 7.5 and 10.5, as studied by two-dimensional gel electrophoresis analyses, did not exhibit significant pH-dependent variation. A new surface layer protein (SlpA) was identified in these studies. Although the prominence of some apparent breakdown products of SlpA in gels from pH 10.5-grown cells led to discovery of the alkaliphile S-layer, the largest and major SlpA forms were present in large amounts in gels from pH 7.5-grown cells as well. slpA RNA abundance was, moreover, unchanged by growth pH. SlpA was similar in size to homologues from nonalkaliphiles but contained fewer Arg and Lys residues. An slpA mutant strain (RG21) lacked an exterior S-layer that was identified in the wild type by electron microscopy. Electrophoretic analysis of whole-cell extracts further indicated the absence of a 90-kDa band in the mutant. This band was prominent in wild-type extracts from both pH 7.5- and 10.5-grown cells. The wild type grew with a shorter lag phase than RG21 at either pH 10.5 or 11 and under either Na+-replete or suboptimal Na+ concentrations. The extent of the adaptation deficit increased with pH elevation and suboptimal Na+. By contrast, the mutant grew with a shorter lag and faster growth rate than the wild type at pH 7.5 under Na+-replete and suboptimal Na+ conditions, respectively. Logarithmically growing cells of the two strains exhibited no significant differences in growth rate, cytoplasmic pH regulation, starch utilization, motility, Na+-dependent transport of α-aminoisobutyric acid, or H+-dependent synthesis of ATP. However, the capacity for Na+-dependent pH homeostasis was diminished in RG21 upon a sudden upward shift of external pH from 8.5 to 10.5. The energy cost of retaining the SlpA layer at near-neutral pH is apparently adverse, but the constitutive presence of SlpA enhances the capacity of the extremophile to adjust to high pH. PMID:11029415

  19. 7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... of proven hosts and associated plant taxa. 301.92-2 Section 301.92-2 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...; lists of proven hosts and associated plant taxa. (a) Restricted articles. The following are...

  20. 7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... of proven hosts and associated plant taxa. 301.92-2 Section 301.92-2 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...; lists of proven hosts and associated plant taxa. (a) Restricted articles. The following are...

  1. 7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... of proven hosts and associated plant taxa. 301.92-2 Section 301.92-2 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...; lists of proven hosts and associated plant taxa. (a) Restricted articles. The following are...

  2. 7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... of proven hosts and associated plant taxa. 301.92-2 Section 301.92-2 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...; lists of proven hosts and associated plant taxa. (a) Restricted articles. The following are...

  3. 7 CFR 301.92-2 - Restricted, regulated, and associated articles; lists of proven hosts and associated plant taxa.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... of proven hosts and associated plant taxa. 301.92-2 Section 301.92-2 Agriculture Regulations of the Department of Agriculture (Continued) ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE...; lists of proven hosts and associated plant taxa. (a) Restricted articles. The following are...

  4. Overcoming the effects of rogue taxa: Evolutionary relationships of the bee flies

    PubMed Central

    Trautwein, Michelle D.; Wiegmann, Brian M.; Yeates, David K

    2011-01-01

    Bombyliidae (5000 sp.), or bee flies, are a lower brachyceran family of flower-visiting flies that, as larvae, act as parasitoids of other insects. The evolutionary relationships are known from a morphological analysis that yielded minimal support for higher-level groupings. We use the protein-coding gene CAD and 28S rDNA to determine phylogeny and to test the monophyly of existing subfamilies, the divisions Tomophtalmae, and ‘the sand chamber subfamilies’. Additionally, we demonstrate that consensus networks can be used to identify rogue taxa in a Bayesian framework. Pruning rogue taxa post-analysis from the final tree distribution results in increased posterior probabilities. We find 8 subfamilies to be monophyletic and the subfamilies Heterotropinae and Mythicomyiinae to be the earliest diverging lineages. The large subfamily Bombyliinae is found to be polyphyletic and our data does not provide evidence for the monophyly of Tomophthalmae or the ‘sand chamber subfamilies’. PMID:21686308

  5. Overcoming the effects of rogue taxa: Evolutionary relationships of the bee flies.

    PubMed

    Trautwein, Michelle D; Wiegmann, Brian M; Yeates, David K

    2011-01-01

    Bombyliidae (5000 sp.), or bee flies, are a lower brachyceran family of flower-visiting flies that, as larvae, act as parasitoids of other insects. The evolutionary relationships are known from a morphological analysis that yielded minimal support for higher-level groupings. We use the protein-coding gene CAD and 28S rDNA to determine phylogeny and to test the monophyly of existing subfamilies, the divisions Tomophtalmae, and 'the sand chamber subfamilies'. Additionally, we demonstrate that consensus networks can be used to identify rogue taxa in a Bayesian framework. Pruning rogue taxa post-analysis from the final tree distribution results in increased posterior probabilities. We find 8 subfamilies to be monophyletic and the subfamilies Heterotropinae and Mythicomyiinae to be the earliest diverging lineages. The large subfamily Bombyliinae is found to be polyphyletic and our data does not provide evidence for the monophyly of Tomophthalmae or the 'sand chamber subfamilies'. PMID:21686308

  6. Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity.

    PubMed

    Nolte, Viola; Pandey, Ram Vinay; Jost, Steffen; Medinger, Ralph; Ottenwälder, Birgit; Boenigk, Jens; Schlötterer, Christian

    2010-07-01

    With the advent of molecular methods, it became clear that microbial biodiversity had been vastly underestimated. Since then, species abundance patterns were determined for several environments, but temporal changes in species composition were not studied to the same level of resolution. Using massively parallel sequencing on the 454 GS FLX platform we identified a highly dynamic turnover of the seasonal abundance of protists in the Austrian lake Fuschlsee. We show that seasonal abundance patterns of protists closely match their biogeographic distribution. The stable predominance of few highly abundant taxa, which previously led to the suggestion of a low global protist species richness, is contrasted by a highly dynamic turnover of rare species. We suggest that differential seasonality of rare and abundant protist taxa explains the--so far--conflicting evidence in the 'everything is everywhere' dispute. Consequently temporal sampling is basic for adequate diversity and species richness estimates. PMID:20609083

  7. A nomenclator of extant and fossil taxa of the Melanopsidae (Gastropoda, Cerithioidea)

    PubMed Central

    Neubauer, Thomas A.

    2016-01-01

    Abstract This nomenclator provides details on all published names in the family-, genus-, and species-group, as well as for a few infrasubspecific names introduced for, or attributed to, the family Melanopsidae. It includes nomenclaturally valid names, as well as junior homonyms, junior objective synonyms, nomina nuda, common incorrect subsequent spellings, and as far as possible discussion on the current status in taxonomy. The catalogue encompasses three family-group names, 79 genus-group names, and 1381 species-group names. All of them are given in their original combination and spelling (except mandatory corrections requested by the Code), along with their original source. For each family- and genus-group name, the original classification and the type genus and type species, respectively, are given. Data provided for species-group taxa are type locality, type horizon (for fossil taxa), and type specimens, as far as available. PMID:27551193

  8. Chemical composition and antioxidant activity of essential oil of six pinus taxa native to China.

    PubMed

    Xie, Qing; Liu, Zhihong; Li, Zhouqi

    2015-01-01

    The essential oils obtained by steam distillation from needles of six China endemic Pinus taxa (P. tabulaeformis, P. tabulaeformis f. shekanensis, P. tabulaeformis var. mukdensis, P. tabulaeformis var. umbraculifera, P. henryi and P. massoniana) were analysed by GC/MS. A total of 72 components were separated and identified by GC/MS from the six taxa. The major constituents of the essential oils were: α-pinene (6.78%-20.55%), bornyl acetale (3.32%-12.71%), β-caryophellene (18.26%-26.31%), α-guaiene (1.23%-8.19%), and germacrene D (1.26%-9.93%). Moreover, the essential oils were evaluated for antioxidant potential by three assays (DPPH, FRAP and ABTS) and tested for their total phenolic content. The results showed that all essential oils exhibited acceptable antioxidant activities and these strongly suggest that these pine needles may serve as a potential source of natural antioxidants for food and medical purposes. PMID:26007189

  9. Synopsis of valid species-group taxa for freshwater Gastropoda recorded from the European Neogene

    PubMed Central

    Neubauer, Thomas A.; Kroh, Andreas; Harzhauser, Mathias; Georgopoulou, Elisavet; Mandic, Oleg

    2014-01-01

    Abstract Here we present a complete list of all valid species-group taxa of freshwater gastropods reported from Miocene and Pliocene deposits in Europe. The last comparable work dates back to the 1920s and covered about 1,600 names. The extensive literature research underlying the present work revealed considerable changes in the taxonomic and systematic frameworks of Neogene freshwater gastropods and yielded a total number of 2,156 accepted taxa. Each taxon is accompanied by a full citation of its first description; where the information is available, page number and illustration reference are provided. First descriptions available as open-access full-text sources on the web were linked via hyperlink to the first page of the publication. PMID:25152683

  10. Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes.

    PubMed

    Saleem, Muhammad; Law, Audrey D; Moe, Luke A

    2016-02-01

    Root-associated microbes have a profound impact on plant health, yet little is known about the distribution of root-associated microbes among different root morphologies or between rhizosphere and root environments. We explore these issues here with two commercial varieties of burley tobacco (Nicotiana tabacum) using 16S rRNA gene amplicon sequencing from rhizosphere soil, as well as from primary, secondary, and fine roots. While rhizosphere soils exhibited a fairly rich and even distribution, root samples were dominated by Proteobacteria. A comparison of abundant operational taxonomic units (OTUs) between rhizosphere and root samples indicated that Nicotiana roots select for rare taxa (predominantly Proteobacteria, Verrucomicrobia, Actinobacteria, Bacteroidetes, and Acidobacteria) from their corresponding rhizosphere environments. The majority of root-inhabiting OTUs (~80 %) exhibited habitat generalism across the different root morphological habitats, although habitat specialists were noted. These results suggest a specific process whereby roots select rare taxa from a larger community. PMID:26391804

  11. Flameless nitrogen skid unit

    SciTech Connect

    Loesch, S.B.; John, J.C.; Mints, D.K.

    1984-03-27

    A flameless nitrogen vaporizing unit includes a first internal combustion engine driving a nitrogen pump through a transmission. A second internal combustion engine drives three hydraulic oil pumps against a variable back pressure so that a variable load may be imposed upon the second engine. Liquid nitrogen is pumped from the nitrogen pump driven by the first engine into a first heat exchanger where heat is transferred from exhaust gases from the first and second internal combustion engines to the liquid nitrogen to cause the nitrogen to be transformed into a gaseous state. The gaseous nitrogen then flows into a second heat exchanger where it is superheated by an engine coolant fluid to heat the gaseous nitrogen to essentially an ambient temperature. The superheated nitrogen is then injected into the well. The engine coolant fluid flows in a coolant circulation system. Heat is transferred to the coolant fluid directly from the internal combustion engine. Heat is also provided to the coolant fluid from lubrication oil pumped by the three pumps attached to the second internal combustion engine. The coolant fluid circulating system includes a comingling chamber for comingling warmer coolant fluid flowing from the internal combustion engines to the second heat exchanger with cooler coolant fluids flowing from the second heat exchanger to the internal combustion engines. Methods of vaporizing nitrogen are also disclosed.

  12. Nitrogen spark denoxer

    DOEpatents

    Ng, Henry K.; Novick, Vincent J.; Sekar, Ramanujam R.

    1997-01-01

    A NO.sub.X control system for an internal combustion engine includes an oxygen enrichment device that produces oxygen and nitrogen enriched air. The nitrogen enriched air contains molecular nitrogen that is provided to a spark plug that is mounted in an exhaust outlet of an internal combustion engine. As the nitrogen enriched air is expelled at the spark gap of the spark plug, the nitrogen enriched air is exposed to a pulsating spark that is generated across the spark gap of the spark plug. The spark gap is elongated so that a sufficient amount of atomic nitrogen is produced and is injected into the exhaust of the internal combustion engine. The injection of the atomic nitrogen into the exhaust of the internal combustion engine causes the oxides of nitrogen to be reduced into nitrogen and oxygen such that the emissions from the engine will have acceptable levels of NO.sub.X. The oxygen enrichment device that produces both the oxygen and nitrogen enriched air can include a selectively permeable membrane.

  13. Nine endangered taxa, one recovering ecosystem: Identifying common ground for recovery on Santa Cruz Island, California

    USGS Publications Warehouse

    McEachern, A. Kathryn; Wilken, Dieter H.

    2011-01-01

    It is not uncommon to have several rare and listed taxa occupying habitats in one landscape or management area where conservation amounts to defense against the possibility of further loss. It is uncommon and extremely exciting, however, to have several listed taxa occupying one island that is managed cooperatively for conservation and recovery. On Santa Cruz Island, the largest of the northern California island group in the Santa Barbara Channel, we have a golden opportunity to marry ecological knowledge and institutional "good will" in a field test of holistic rare plant conservation. Here, the last feral livestock have been removed, active weed control is underway, and management is focused on understanding and demonstrating system response to conservation management. Yet funding limitations still exist and we need to plan the most fiscally conservative and marketable approach to rare plant restoration. We still experience the tension between desirable quick results and the ecological pace of system recovery. Therefore, our research has focused on identifying fundamental constraints on species recovery at individual, demographic, habitat, and ecosystem levels, and then developing suites of actions that might be taken across taxa and landscapes. At the same time, we seek a performance middle ground that balances an institutional need for quick demonstration of hands-on positive results with a contrasting approach that allows ecosystem recovery to facilitate species recovery in the long term. We find that constraints vary across breeding systems, life-histories, and island locations. We take a hybrid approach in which we identify several actions that we can take now to enhance population size or habitat occupancy for some taxa by active restoration, while allowing others to recover at the pace of ecosystem change. We make our recommendations on the basis of data we have collected over the last decade, so that management is firmly grounded in ecological observation.

  14. Bias and Sensitivity in the Placement of Fossil Taxa Resulting from Interpretations of Missing Data

    PubMed Central

    Sansom, Robert S.

    2015-01-01

    The utility of fossils in evolutionary contexts is dependent on their accurate placement in phylogenetic frameworks, yet intrinsic and widespread missing data make this problematic. The complex taphonomic processes occurring during fossilization can make it difficult to distinguish absence from non-preservation, especially in the case of exceptionally preserved soft-tissue fossils: is a particular morphological character (e.g., appendage, tentacle, or nerve) missing from a fossil because it was never there (phylogenetic absence), or just happened to not be preserved (taphonomic loss)? Missing data have not been tested in the context of interpretation of non-present anatomy nor in the context of directional shifts and biases in affinity. Here, complete taxa, both simulated and empirical, are subjected to data loss through the replacement of present entries (1s) with either missing (?s) or absent (0s) entries. Both cause taxa to drift down trees, from their original position, toward the root. Absolute thresholds at which downshift is significant are extremely low for introduced absences (two entries replaced, 6% of present characters). The opposite threshold in empirical fossil taxa is also found to be low; two absent entries replaced with presences causes fossil taxa to drift up trees. As such, only a few instances of non-preserved characters interpreted as absences will cause fossil organisms to be erroneously interpreted as more primitive than they were in life. This observed sensitivity to coding non-present morphology presents a problem for all evolutionary studies that attempt to use fossils to reconstruct rates of evolution or unlock sequences of morphological change. Stem-ward slippage, whereby fossilization processes cause organisms to appear artificially primitive, appears to be a ubiquitous and problematic phenomenon inherent to missing data, even when no decay biases exist. Absent characters therefore require explicit justification and taphonomic

  15. Applying a biomedical top-level ontology to encode biological taxa.

    PubMed

    Boeker, Martin; Stenzhorn, Holger; Schulz, Stefan

    2008-01-01

    Classifying biological entities in terms of species and taxa is an important endeavor in biology. But even though many statements within current biomedical ontologies are indeed taxon-dependent, no standard way exists to properly introduce taxon or species information into current ontological architectures. Therefore we discuss various practices to represent such information by applying a biomedical top-level ontology combined with other standard approaches like description logics or the OBO Foundry. PMID:18999119

  16. Lectotypification of names of Himalayan Brassicaceae taxa currently placed in the genus Cardamine.

    PubMed

    Marhold, Karol; Kempa, Matúš; Al-Shehbaz, Ihsan A

    2015-01-01

    Lectotypes of twenty-eight names of taxa currently recognized or synonymized in Cardamine are designated as part of the work on the account of the genus for the Pan-Himalayan Flora. Among them, the previous first-step lectotypification of the name Cardaminecalthifolia is finalized. In cases when specimen images are available online, stable identifiers for specimens, other permanent links, or links via JSTOR Global Plants are provided. PMID:26140016

  17. Immunological Change in a Parasite-Impoverished Environment: Divergent Signals from Four Island Taxa

    PubMed Central

    Beadell, Jon S.; Atkins, Colm; Cashion, Erin; Jonker, Michelle; Fleischer, Robert C.

    2007-01-01

    Dramatic declines of native Hawaiian avifauna due to the human-mediated emergence of avian malaria and pox prompted an examination of whether island taxa share a common altered immunological signature, potentially driven by reduced genetic diversity and reduced exposure to parasites. We tested this hypothesis by characterizing parasite prevalence, genetic diversity and three measures of immune response in two recently-introduced species (Neochmia temporalis and Zosterops lateralis) and two island endemics (Acrocephalus aequinoctialis and A. rimitarae) and then comparing the results to those observed in closely-related mainland counterparts. The prevalence of blood parasites was significantly lower in 3 of 4 island taxa, due in part to the absence of certain parasite lineages represented in mainland populations. Indices of genetic diversity were unchanged in the island population of N. temporalis; however, allelic richness was significantly lower in the island population of Z. lateralis while both allelic richness and heterozygosity were significantly reduced in the two island-endemic species examined. Although parasite prevalence and genetic diversity generally conformed to expectations for an island system, we did not find evidence for a pattern of uniformly altered immune responses in island taxa, even amongst endemic taxa with the longest residence times. The island population of Z. lateralis exhibited a significantly reduced inflammatory cell-mediated response while levels of natural antibodies remained unchanged for this and the other recently introduced island taxon. In contrast, the island endemic A. rimitarae exhibited a significantly increased inflammatory response as well as higher levels of natural antibodies and complement. These measures were unchanged or lower in A. aequinoctialis. We suggest that small differences in the pathogenic landscape and the stochastic history of mutation and genetic drift are likely to be important in shaping the unique

  18. Crisis of Japanese vascular flora shown by quantifying extinction risks for 1618 taxa.

    PubMed

    Kadoya, Taku; Takenaka, Akio; Ishihama, Fumiko; Fujita, Taku; Ogawa, Makoto; Katsuyama, Teruo; Kadono, Yasuro; Kawakubo, Nobumitsu; Serizawa, Shunsuke; Takahashi, Hideki; Takamiya, Masayuki; Fujii, Shinji; Matsuda, Hiroyuki; Muneda, Kazuo; Yokota, Masatsugu; Yonekura, Koji; Yahara, Tetsukazu

    2014-01-01

    Although many people have expressed alarm that we are witnessing a mass extinction, few projections have been quantified, owing to limited availability of time-series data on threatened organisms, especially plants. To quantify the risk of extinction, we need to monitor changes in population size over time for as many species as possible. Here, we present the world's first quantitative projection of plant species loss at a national level, with stochastic simulations based on the results of population censuses of 1618 threatened plant taxa in 3574 map cells of ca. 100 km2. More than 500 lay botanists helped monitor those taxa in 1994-1995 and in 2003-2004. We projected that between 370 and 561 vascular plant taxa will go extinct in Japan during the next century if past trends of population decline continue. This extinction rate is approximately two to three times the global rate. Using time-series data, we show that existing national protected areas (PAs) covering ca. 7% of Japan will not adequately prevent population declines: even core PAs can protect at best <60% of local populations from decline. Thus, the Aichi Biodiversity Target to expand PAs to 17% of land (and inland water) areas, as committed to by many national governments, is not enough: only 29.2% of currently threatened species will become non-threatened under the assumption that probability of protection success by PAs is 0.5, which our assessment shows is realistic. In countries where volunteers can be organized to monitor threatened taxa, censuses using our method should be able to quantify how fast we are losing species and to assess how effective current conservation measures such as PAs are in preventing species extinction. PMID:24922311

  19. Lectotypification of names of Himalayan Brassicaceae taxa currently placed in the genus Cardamine

    PubMed Central

    Marhold, Karol; Kempa, Matúš; Al-Shehbaz, Ihsan A.

    2015-01-01

    Abstract Lectotypes of twenty-eight names of taxa currently recognized or synonymized in Cardamine are designated as part of the work on the account of the genus for the Pan-Himalayan Flora. Among them, the previous first-step lectotypification of the name Cardamine calthifolia is finalized. In cases when specimen images are available online, stable identifiers for specimens, other permanent links, or links via JSTOR Global Plants are provided. PMID:26140016

  20. Dominant plant taxa predict plant productivity responses to CO2 enrichment across precipitation and soil gradients.

    PubMed

    Fay, Philip A; Newingham, Beth A; Polley, H Wayne; Morgan, Jack A; LeCain, Daniel R; Nowak, Robert S; Smith, Stanley D

    2015-01-01

    The Earth's atmosphere will continue to be enriched with carbon dioxide (CO2) over the coming century. Carbon dioxide enrichment often reduces leaf transpiration, which in water-limited ecosystems may increase soil water content, change species abundances and increase the productivity of plant communities. The effect of increased soil water on community productivity and community change may be greater in ecosystems with lower precipitation, or on coarser-textured soils, but responses are likely absent in deserts. We tested correlations among yearly increases in soil water content, community change and community plant productivity responses to CO2 enrichment in experiments in a mesic grassland with fine- to coarse-textured soils, a semi-arid grassland and a xeric shrubland. We found no correlation between CO2-caused changes in soil water content and changes in biomass of dominant plant taxa or total community aboveground biomass in either grassland type or on any soil in the mesic grassland (P > 0.60). Instead, increases in dominant taxa biomass explained up to 85 % of the increases in total community biomass under CO2 enrichment. The effect of community change on community productivity was stronger in the semi-arid grassland than in the mesic grassland, where community biomass change on one soil was not correlated with the change in either the soil water content or the dominant taxa. No sustained increases in soil water content or community productivity and no change in dominant plant taxa occurred in the xeric shrubland. Thus, community change was a crucial driver of community productivity responses to CO2 enrichment in the grasslands, but effects of soil water change on productivity were not evident in yearly responses to CO2 enrichment. Future research is necessary to isolate and clarify the mechanisms controlling the temporal and spatial variations in the linkages among soil water, community change and plant productivity responses to CO2 enrichment. PMID

  1. Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time.

    PubMed

    Bagchi, Samik; Tellez, Berenice G; Rao, Hari Ananda; Lamendella, Regina; Saikaly, Pascal E

    2015-03-01

    In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the diversity and dynamics of total, dominant, and rare bacterial taxa in replicate lab-scale sequencing batch reactors (SBRs) operated at different solids retention time (SRT). Rank-abundance curves showed few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2 vs. 10 days) on Shannon diversity index and OTU richness of both dominant and rare taxa. Nonmetric multidimensional scaling analysis showed that the total, dominant, and rare bacterial taxa were highly dynamic during the entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media. PMID:25326778

  2. Spatial Scaling of Microbial Diversity across Various Functional and Phylogenetic Taxa

    SciTech Connect

    Schadt, Christopher Warren; Garten Jr, Charles T; Kang, S.; Zhou, Jizhong

    2008-01-01

    Understanding the spatial patterns of organisms and the underlying mechanisms shaping biotic communities is a central goal in community ecology. One of the most well documented spatial patterns in plant and animal communities is the positive-power law relationship between species (or taxa) richness and area. Such a taxa-area relationships (TARs) are one of the principal generalizations in ecology, and are fundamental to our understanding of the distribution of global biodiversity. However, TARs remain elusive and controversial in microbial communities, especially in soil habitats, due to inadequate sampling methodologies. Here, we describe TARs, at a whole-community level, across various microbial functional and phylogenetic groups in a forest soil using a comprehensive functional gene array (FGA) with > 24,000 probes. Our analysis indicated that the forest soil microbial community exhibited a relatively flat taxa-area relationship (slope z = 0.0624), but the z values varied considerably across different functional and phylogenetic groups (z = 0.0475-0.0959), which are several times lower than those commonly observed in higher plants and animals. These results suggest that the turnover in space of microorganisms may be, in general, lower than that of plants and animals.

  3. Clade age and not diversification rate explains species richness among animal taxa.

    PubMed

    McPeek, Mark A; Brown, Jonathan M

    2007-04-01

    Animal taxa show remarkable variability in species richness across phylogenetic groups. Most explanations for this disparity postulate that taxa with more species have phenotypes or ecologies that cause higher diversification rates (i.e., higher speciation rates or lower extinction rates). Here we show that clade longevity, and not diversification rate, has primarily shaped patterns of species richness across major animal clades: more diverse taxa are older and thus have had more time to accumulate species. Diversification rates calculated from 163 species-level molecular phylogenies were highly consistent within and among three major animal phyla (Arthropoda, Chordata, Mollusca) and did not correlate with species richness. Clades with higher estimated diversification rates were younger, but species numbers increased with increasing clade age. A fossil-based data set also revealed a strong, positive relationship between total extant species richness and crown group age across the orders of insects and vertebrates. These findings do not negate the importance of ecology or phenotype in influencing diversification rates, but they do show that clade longevity is the dominant signal in major animal biodiversity patterns. Thus, some key innovations may have acted through fostering clade longevity and not by heightening diversification rate. PMID:17427118

  4. Functional gains of including non-commercial epibenthic taxa in coastal beam trawl surveys: A note

    NASA Astrophysics Data System (ADS)

    Brind'Amour, Anik; Rouyer, Armelle; Martin, Jocelyne

    2009-05-01

    The development of ecosystem-based indicators requires the broadening of a view of the community, from fish species to all the species (macrobenthic and fish) correctly captured by a given sampling gear. Many scientific surveys already have such integrated databases. The present note aims to demonstrate that existing databases, herein from dedicated coastal nursery surveys, are actually underexploited. Such databases contain information on non-commercial taxa, which could greatly improve our knowledge on the organisation and functioning of coastal ecosystems. Using two datasets, a "complete" dataset composed of commercial and not-commercial epibenthic trawled species (fish and invertebrate) and a "subset" dataset characterized by commercial and routinely surveyed species (mainly fish and cephalopods), different measures of functional diversity are compared to identify the functional gains of including epibenthic species. The results show that, when included in the analyses, epibenthic taxa provide gains of functional information, associated mainly with the community feeding traits, i.e. organisms composing the primary and secondary consumer levels of the coastal nursery food web. Failure to include some of the primary (zooplanktivores and suspension feeders) and secondary consumers (detritivores-scavengers) in coastal survey analyses may, for instance, hamper our understanding of energy flux between the benthic and water column compartments of these ecosystems. The results also suggest that the exclusion of some taxa associated with these two food web compartments, may lead to the underestimation of the functional redundancy in coastal ecosystems.

  5. Biomechanical modeling and sensitivity analysis of bipedal running ability. II. Extinct taxa.

    PubMed

    Hutchinson, John R

    2004-10-01

    Using an inverse dynamics biomechanical analysis that was previously validated for extant bipeds, I calculated the minimum amount of actively contracting hindlimb extensor muscle that would have been needed for rapid bipedal running in several extinct dinosaur taxa. I analyzed models of nine theropod dinosaurs (including birds) covering over five orders of magnitude in size. My results uphold previous findings that large theropods such as Tyrannosaurus could not run very quickly, whereas smaller theropods (including some extinct birds) were adept runners. Furthermore, my results strengthen the contention that many nonavian theropods, especially larger individuals, used fairly upright limb orientations, which would have reduced required muscular force, and hence muscle mass. Additional sensitivity analysis of muscle fascicle lengths, moment arms, and limb orientation supports these conclusions and points out directions for future research on the musculoskeletal limits on running ability. Although ankle extensor muscle support is shown to have been important for all taxa, the ability of hip extensor muscles to support the body appears to be a crucial limit for running capacity in larger taxa. I discuss what speeds were possible for different theropod dinosaurs, and how running ability evolved in an inverse relationship to body size in archosaurs. PMID:15352202

  6. Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.)

    PubMed Central

    Dierking, Jan; Phelps, Luke; Præbel, Kim; Ramm, Gesine; Prigge, Enno; Borcherding, Jost; Brunke, Matthias; Eizaguirre, Christophe

    2014-01-01

    Natural hybridization plays a key role in the process of speciation. However, anthropogenic (human induced) hybridization of historically isolated taxa raises conservation issues. Due to weak barriers to gene flow and the presence of endangered taxa, the whitefish species complex is an excellent study system to investigate the consequences of hybridization in conservation. We focused on three naturally reproductively isolated whitefish taxa in Germany: the endangered, anadromous North Sea houting (NSH) and Baltic houting (BH), which were reintroduced after local extinction, and the commercially stocked European whitefish (EW). To evaluate the genetic integrity of each taxon, source and reintroduced populations of NSH and BH, and EW populations were characterized based on two mitochondrial and 17 microsatellite loci. Additionally, we investigated gill raker counts as an adaptive phenotypic trait. Even though clear genetic and phenotypic differentiation confirmed the houtings as separate evolutionarily significant units, admixture analyses revealed an extensive hybrid zone. Hybridizations were introgressive, positively correlated with genetic diversity, and were reflected in the gill raker counts. The BH distribution range showed higher heterogeneity and stronger admixture than the NSH range. Erroneous stocking with non-native genotypes best explained these patterns, which pose challenges for the conservation of the endangered NSH and BH. PMID:25553068

  7. Darwin's diagram of divergence of taxa as a causal model for the origin of species.

    PubMed

    Bouzat, Juan L

    2014-03-01

    On the basis that Darwin's theory of evolution encompasses two logically independent processes (common descent and natural selection), the only figure in On the Origin of Species (the Diagram of Divergence of Taxa) is often interpreted as illustrative of only one of these processes: the branching patterns representing common ancestry. Here, I argue that Darwin's Diagram of Divergence of Taxa represents a broad conceptual model of Darwin's theory, illustrating the causal efficacy of natural selection in producing well-defined varieties and ultimately species. The Tree Diagram encompasses the idea that natural selection explains common descent and the origin of organic diversity, thus representing a comprehensive model of Darwin's theory on the origin of species. I describe Darwin's Tree Diagram in relation to his argumentative strategy under the vera causa principle, and suggest that the testing of his theory based on the evidence from the geological record, the geographical distribution of organisms, and the mutual affinities of organic beings can be framed under the hypothetico-deductive method. Darwin's Diagram of Divergence of Taxa therefore represents a broad conceptual model that helps understanding the causal construction of Darwin's theory of evolution, the structure of his argumentative strategy, and the nature of his scientific methodology. PMID:24672902

  8. Using computational fluid dynamics to test functional and ecological hypotheses in fossil taxa

    NASA Astrophysics Data System (ADS)

    Rahman, Imran

    2016-04-01

    Reconstructing how ancient organisms moved and fed is a major focus of study in palaeontology. Traditionally, this has been hampered by a lack of objective data on the functional morphology of extinct species, especially those without a clear modern analogue. However, cutting-edge techniques for characterizing specimens digitally and in three dimensions, coupled with state-of-the-art computer models, now provide a robust framework for testing functional and ecological hypotheses even in problematic fossil taxa. One such approach is computational fluid dynamics (CFD), a method for simulating fluid flows around objects that has primarily been applied to complex engineering-design problems. Here, I will present three case studies of CFD applied to fossil taxa, spanning a range of specimen sizes, taxonomic groups and geological ages. First, I will show how CFD enabled a rigorous test of hypothesized feeding modes in an enigmatic Ediacaran organism with three-fold symmetry, revealing previously unappreciated complexity of pre-Cambrian ecosystems. Second, I will show how CFD was used to evaluate hydrodynamic performance and feeding in Cambrian stem-group echinoderms, shedding light on the probable feeding strategy of the latest common ancestor of all deuterostomes. Third, I will show how CFD allowed us to explore the link between form and function in Mesozoic ichthyosaurs. These case studies serve to demonstrate the enormous potential of CFD for addressing long-standing hypotheses for a variety of fossil taxa, opening up an exciting new avenue in palaeontological studies of functional morphology.

  9. Diatoms from Brazil: the taxa recorded by Christian Gottfried Ehrenberg

    PubMed Central

    da Silva, Weliton José; Jahn, Regine; Menezes, Mariângela

    2012-01-01

    Abstract The flora of diatoms from Brazil has been studied by several authors from the beginning of the 19th up to now. Some of the old lists and descriptions are unknown or have been ignored by Brazilian researchers and the situation of the names cited was not assessed. Here we compiled a list of 101 taxa of diatoms from Brazil registered by Christian Gottfried Ehrenberg during the 19th century. We checked the current nomenclatural status of those taxa and lectotypified species from Brazil described by this author. For this, we accessed the Ehrenberg collection in the Museum für Naturkunde, Berlin, Germany, where 11 samples from Brazil studied by Ehrenberg are housed and published in different papers. Using these samples, we found 101 taxa (specific and infraspecific) published by Ehrenberg from Brazil. Five species (Eunotia bidens Ehrenb., Eunotia depressa Ehrenb., Eunotia elephas Ehrenb., Pinnularia microstauron Ehrenb., and Terpsinoe brasiliensis Ehrenb.) were new descriptions and were lectotypified here. The other species cited for Brazil were described initially from other places. However, 23 names were invalid and one illegitimate. PMID:23730191

  10. Evidence of Taxa-, Clone-, and Kin-discrimination in Protists: Ecological and Evolutionary Implications

    PubMed Central

    Espinosa, Avelina; Paz-y-Miño-C, Guillermo

    2014-01-01

    Unicellular eukaryotes, or protists, are among the most ancient organisms on Earth. Protists belong to multiple taxonomic groups; they are widely distributed geographically and in all environments. Their ability to discriminate among con- and heterospecifics has been documented during the past decade. Here we discuss exemplar cases of taxa-, clone-, and possible kin-discrimination in five major lineages: Mycetozoa (Dictyostelium, Polysphondylium), Dikarya (Saccharomyces), Ciliophora (Tetrahymena), Apicomplexa (Plasmodium) and Archamoebae (Entamoeba). We summarize the proposed genetic mechanisms involved in discrimination-mediated aggregation (self versus different), including the csA, FLO and trg (formerly lag) genes, and the Proliferation Activation Factors (PAFs), which facilitate clustering in some protistan taxa. We caution about the experimental challenges intrinsic to studying recognition in protists, and highlight the opportunities for exploring the ecology and evolution of complex forms of cell-cell communication, including social behavior, in a polyphyletic, still superficially understood group of organisms. Because unicellular eukaryotes are the evolutionary precursors of multicellular life, we infer that their mechanisms of taxa-, clone-, and possible kin-discrimination gave origin to the complex diversification and sophistication of traits associated with species and kin recognition in plants, fungi, invertebrates and vertebrates. PMID:25400313

  11. Spatial genetic structure of Aquilegia taxa endemic to the island of Sardinia

    PubMed Central

    Garrido, J. L.; Fenu, G.; Mattana, E.; Bacchetta, G.

    2012-01-01

    Background and Aims The Mediterranean Basin is one of the most important regions for the Earth's plant biodiversity; however, the scarcity of studies on fine scale patterns of genetic variation in this region is striking. Here, an assessment is made of the spatial genetic structure of all known locations of the three Sardinian endemic species of Aquilegia in order to determine the relative roles of gene flow and genetic drift as underlying evolutionary forces canalizing the divergence of Sardinian Aquilegia taxa, and to see if the spatial genetic structure found fits the current taxonomic differentiation of these taxa. Methods DNA from 89 individuals from all known locations of Aquilegia across Sardinia was analysed by means of amplified fragment length polymorphism (AFLP) markers. Both principal co-ordinates analysis (PCoA) and Bayesian clustering analyses were used to determine the spatial genetic structure irrespective of any taxonomic affiliation. Historical effects of gene flow and genetic drift were assessed by checking for the existence of isolation-by-distance patterns. Key Results STRUCTURE and PCoA analyses revealed a pattern of genetic variation geographically structured into four spatial genetic groups. No migration–drift equilibrium was detected for Aquilegia in Sardinia, when analysed either as a whole or in individual groups. The scenario approached a Case III pattern sensu Hutchinson and Templeton, which is associated with extreme isolation conditions where genetic drift has historically played a dominant role over gene flow. Conclusions The pattern of genetic variation of Sardinian taxa of Aquilegia indicates that genetic drift has been historically more influential than gene flow on population structure of Sardinian species of Aquilegia. Limited seed dispersal and divergent selection imposed by habitat conditions have been probably the main causes reinforcing post-Pleistocene geographical isolation of Aquilegia populations. The spatial genetic

  12. Nitrogen In Saturn's Magnetosphere

    NASA Astrophysics Data System (ADS)

    Smith, H. T.; Sittler, E. C.; Johnson, R. E.; McComas, D. J.; Reisenfeld, D.; Shappirio, M. D.; Baragiola, R.; Michael, M.; Shematovich, V. I.; Crary, F.; Young, D. T.

    2004-12-01

    We are analyzing CAPS instrument data on Cassini to look for nitrogen ions in Saturn's magnetosphere. Because Voyager could not separate oxygen and nitrogen, there has been considerable controversy on nitrogen's presence and relative importance. Two principal sources have been suggested: Titan's atmosphere and nitrogen species trapped in Saturn's icy satellite surfaces (Sittler et al 2004). The latter may be primordial nitrogen, likely as NH3 in ice (Stevenson 1982; Squyers et al. 1983) or nitrogen ions that have been implanted in the surface (Delitsky and Lane 2002). We will present the results of Saturnian nitrogen cloud modeling and relevant CAPS observations. We recently described the Titan source (Michael, et al. 2004; Shematovich et al. 2003; Smith et al. 2004; Sittler et al. 2004) in preparation for Cassini's Saturnian plasma measurements. Two components were identified: energetic nitrogen ions formed near Titan and energized as they diffused inward (Sittler et al. 2004) and neutrals in orbits with small perigee that became ionized in the inner magnetosphere (Smith et al 2004). The latter component would be a source of lower energy, co-rotating nitrogen ions in the inner magnetosphere. Such a component would have an energy spectrum similar to nitrogen species sputtered from the icy satellite surfaces (Johnson and Sittler 1990). However, the mass spectrum would differ, likely containing NHx and NOx species also, and, hence, may be separated from the Titan source. Our preliminary analysis for nitrogen species in the CAPS data will be compared to our models. Of interest will be the energy spectra, which can indicate whether any nitrogen present is formed locally or near Titan's orbit and diffused inward. This work is supported by the NASA Planetary Atmospheres, NASA Graduate Student Research, Virginia Space Grant Consortium Graduate Research Fellowship and CAPS Cassini instrument team programs.

  13. Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia

    PubMed Central

    Mei, Nan; Postec, Anne; Monnin, Christophe; Pelletier, Bernard; Payri, Claude E.; Ménez, Bénédicte; Frouin, Eléonore; Ollivier, Bernard; Erauso, Gaël; Quéméneur, Marianne

    2016-01-01

    High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ. PMID:27625634

  14. Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia.

    PubMed

    Mei, Nan; Postec, Anne; Monnin, Christophe; Pelletier, Bernard; Payri, Claude E; Ménez, Bénédicte; Frouin, Eléonore; Ollivier, Bernard; Erauso, Gaël; Quéméneur, Marianne

    2016-01-01

    High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ. PMID:27625634

  15. Nitrogen trading tool

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The nitrogen cycle is impacted by human activities, including those that increase the use of nitrogen in agricultural systems, and this impact can be seen in effects such as increased nitrate (NO3) levels in groundwater or surface water resources, increased concentration of nitrous oxide (N2O) in th...

  16. Update: Biological Nitrogen Fixation.

    ERIC Educational Resources Information Center

    Wiseman, Alan; And Others

    1985-01-01

    Updates knowledge on nitrogen fixation, indicating that investigation of free-living nitrogen-fixing organisms is proving useful in understanding bacterial partners and is expected to lead to development of more effective symbioses. Specific areas considered include biochemistry/genetics, synthesis control, proteins and enzymes, symbiotic systems,…

  17. The Fixation of Nitrogen.

    ERIC Educational Resources Information Center

    Andrew, S. P. S.

    1978-01-01

    Discusses the fixation of atmospheric nitrogen in the form of ammonia as one of the foundations of modern chemical industry. The article describes ammonia production and synthesis, purifying the hydrogen-nitrogen mix, nitric acid production, and its commericial plant. (HM)

  18. Modeling Atmospheric Reactive Nitrogen

    EPA Science Inventory

    Nitrogen is an essential building block of all proteins and thus an essential nutrient for all life. Reactive nitrogen, which is naturally produced via enzymatic reactions, forest fires and lightning, is continually recycled and cascades through air, water, and soil media. Human ...

  19. Soil Nitrogen Budgets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nitrogen (N) recoveries are commonly 45% to 70% for modern field-crop systems. Nitrogen budgets are a valuable tool for improving N efficiency because they assess the size of various N pools, N gains from the atmosphere, N losses to the environment, and the interactions among soil-N-cycle processes...

  20. The structure of cystoliths in selected taxa of the genus Ficus L. (Moraceae) in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Ummu-Hani, B.; Noraini, T.

    2013-11-01

    A study was undertaken on mature leaves of 15 taxa of the genus Ficus in Peninsular Malaysia. The main objectives of this study are to determine the morphology and distribution of cystoliths in the epidermal layers of the leaf lamina in selected taxa of Ficus. The morphology of cystoliths is classified based on its size, shape, colour, and the presence of stalk cystolith. There are seven types of cystolith morphology observed in this study. Most of the cystoliths are either solitary, elongated, narrow or broad, and pointed or blunt at one or both ends. However, double- and rarely triple-cystoliths are also present in some species. The size of the cystoliths varies even within the same species. Based on the position of cystoliths, all the 15 taxa studied can be generally classified into three groups: Group 1 - with cystoliths adjacent to the adaxial epidermis layer (F. annulata, F. benghalensis and F. superba), Group 2 - with cystoliths adjacent to the abaxial epidermis layer (F. aurantiacea, F. lepicarpa, F. hispida, F. obscura var. borneensis, F. religiosa, F. schwarzii, F. ucinata and F. vasculosa), and Group 3 - with cystoliths present in both adaxial and abaxial epidermis layers (F. benjamina, F. depressa, F. microcarpa and F. tinctoria). Based on the occurrence of cystoliths, the types of lithocysts were related to the number of epidermal layers, i.e. hair-like lithocysts in uniseriate epidermis is present in all species studied. However, the characteristics of the cystoliths may not suitably be used as a taxonomic marker but it can be useful as additional character for group identification in Ficusper.

  1. Bathymetric distribution patterns of Southern Ocean macrofaunal taxa: Bivalvia, Gastropoda, Isopoda and Polychaeta

    NASA Astrophysics Data System (ADS)

    Brandt, Angelika; Linse, Katrin; Schüller, Myriam

    2009-11-01

    The aim of this study is to compare the depth distributions of four major Southern Ocean macrobenthic epi- and infaunal taxa, the Bivalvia, Gastropoda, Isopoda, and Polychaeta, from subtidal to abyssal depth. All literature data up to summer 2008, as well as the unpublished data from the most recent ANDEEP I-III (Antarctic benthic deep-sea biodiversity: colonisation history and recent community patterns) expeditions to the Southern Ocean deep sea are included in the analysis. Benthic invertebrates in the Southern Ocean are known for their wide bathymetric ranges. We analysed the distributions of four of the most abundant and species-rich taxa from intertidal to abyssal (5200 m) depths in depth zones of 100 m. The depth distributions of three macrofaunal classes (Bivalvia, Gastropoda, Polychaeta) and one order (Isopoda) showed distinct differences. In the case of bivalves, gastropods and polychaetes, the number of species per depth zone decreased from the shelf to the slope at around 1000 m depth and then showed stable low numbers. The isopods showed the opposite trend; they were less species rich in the upper 1000 m but increased in species numbers from the slope to bathyal and abyssal depths. Depth ranges of families of the studied taxa (Bivalvia: 31 families, Gastropoda: 60, Isopoda: 32, and Polychaeta: 46 families) were compiled and illustrated. At present vast areas of the deep sea in the Southern Ocean remain unexplored and species accumulation curves showed that only a fraction of the species have been discovered to date. We anticipate that further investigations will greatly increase the number of species known in the Southern Ocean deep sea.

  2. Post-zygotic Reproductive Isolation Between Sympatric Taxa in the Chamaecrista desvauxii Complex (Leguminosae–Caesalpinioideae)

    PubMed Central

    Costa, Cristiana Barros Nascimento; Lambert, Sabrina Mota; Borba, Eduardo Leite; de Queiroz, Luciano Paganucci

    2007-01-01

    Background and Aims Differences in the mating systems and the mechanisms of reproductive isolation between Chamaecrista desvauxii var. graminea and C. desvauxii var. latistipula were examined in the Chapada Diamantina, Brazil. These taxa occur sympatrically, and their populations demonstrate marked morphological differences. The objective of the present work was to determine if reproductive isolation mechanisms exist between these two populations of C. desvauxii, and to determine the influence of these putative mechanisms on their genetic differentiation. Methods Field observations were made of floral biology, phenology and floral visitation, and experiments on intra- and interpopulation pollination and germination rates of the resultant seeds were performed. A genetic examination of the populations was undertaken using four allozyme loci. Key Results The varieties examined demonstrated overlapping of flowering periods during the months of June to September. The main pollinator for both varieties was the bee Bombus brevivillus. Both varieties are self-compatible, and a large number of fruits are formed in cross-pollinations with high seed germination rates. Inter-taxa pollinations result in high levels of fruit production, but no seeds are formed. Two of the four loci examined were diagnostic for the varieties, and exclusive high-frequency alleles were encountered at the other loci, leading to a high genetic distance between the two populations (0·495). Conclusions Pre-zygotic barriers were not found between the two varieties, and these remain isolated due to post-zygotic events. The two varieties demonstrate marked differences in their morphology, floral biology, phenology and genetic make-up, all of which indicate that they should be treated as two distinct species. A complete revision involving the other varieties of the C. desvauxii complex will be necessary in order to define these two taxa formally. PMID:17331960

  3. Larger ejaculate volumes are associated with a lower degree of polyandry across bushcricket taxa

    PubMed Central

    Vahed, Karim

    2006-01-01

    In numerous insects, including bushcrickets (Tettigoniidae), males are known to transfer substances in the ejaculate that inhibit the receptivity of females to further matings, but it has not yet been established whether these substances reduce the lifetime degree of polyandry of the female. The aim of this study was to test the hypothesis that larger ejaculate volumes should be associated with a lower degree of polyandry across tettigoniid taxa, controlling for male body mass and phylogeny. Data on ejaculate mass, sperm number, nuptial gift mass and male mass were taken primarily from the literature. The degree of polyandry for 14 species of European bushcrickets was estimated by counting the number of spermatodoses within the spermathecae of field-caught females towards the end of their adult lifespans. Data for four further species were obtained from the literature. Data were analysed by using both species regression and independent contrasts to control for phylogeny. Multiple regression analysis revealed that, as predicted, there was a significant negative association between the degree of polyandry and ejaculate mass, relative to male body mass, across bushcricket taxa. Nuptial gift size and sperm number, however, did not contribute further to interspecific variation in the degree of polyandry. A positive relationship was found, across bushcricket taxa, between relative nuptial gift size and relative ejaculate mass, indicating that larger nuptial gifts allow the male to overcome female resistance to accepting large ejaculates. This appears to be the first comparative evidence that males can manipulate the lifetime degree of polyandry of their mates through the transfer of large ejaculates. PMID:16928643

  4. Brachyceran Diptera (Insecta) in Cretaceous ambers, Part IV, Significant New Orthorrhaphous Taxa

    PubMed Central

    Grimaldi, David A.; Arillo, Antonio; Cumming, Jeffrey M.; Hauser, Martin

    2011-01-01

    Abstract Thirteen species of basal Brachycera (11 described as new) are reported, belonging to nine families and three infraorders. They are preserved in amber from the Early Cretaceous (Neocomian) of Lebanon, Albian of northern Spain, upper Albian to lower Cenomanian of northern Myanmar, and Late Cretaceous of New Jersey USA (Turonian) and Alberta, Canada (Campanian). Taxa are as follows, with significance as noted: In Stratiomyomorpha: Stratiomyidae (Cretaceogaster pygmaeus Teskey [2 new specimens in Canadian amber], Lysistrata emerita Grimaldi & Arillo, gen. et sp. n. [stem-group species of the family in Spanish amber]), and Xylomyidae (Cretoxyla azari Grimaldi & Cumming, gen. et sp. n. [in Lebanese amber], and an undescribed species from Spain). In Tabanomorpha: Tabanidae (Cratotabanus newjerseyensis Grimaldi, sp. n., in New Jersey amber). In Muscomorpha: Acroceridae (Schlingeromyia minuta Grimaldi & Hauser, gen. et sp. n. and Burmacyrtus rusmithi Grimaldi & Hauser gen. et sp. n., in Burmese amber, the only definitive species of the family from the Cretaceous); Mythicomyiidae (Microburmyia analvena Grimaldi & Cumming gen. et sp. n. and Microburmyia veanalvena Grimaldi & Cumming, sp. n., stem-group species of the family, both in Burmese amber); Apsilocephalidae or near (therevoid family-group) (Kumaromyia burmitica Grimaldi & Hauser, gen. et sp. n. [in Burmese amber]); Apystomyiidae (Hilarimorphites burmanica Grimaldi & Cumming, sp. n. [in Burmese amber], whose closest relatives are from the Late Jurassic of Kazachstan, the Late Cretaceous of New Jersey, and Recent of California). Lastly, two species belonging to families incertae sedis, both in Burmese amber: Tethepomyiidae (Tethepomyia zigrasi Grimaldi & Arillo sp. n., the aculeate oviscapt of which indicates this family was probably parasitoidal and related to Eremochaetidae); and unplaced to family is Myanmyia asteiformia Grimaldi, gen. et sp. n., a minute fly with highly reduced venation. These new taxa

  5. Diversity among Cynodon accessions and taxa based on DNA amplification fingerprinting.

    PubMed

    Assefa, S; Taliaferro, C M; Anderson, M P; de los Reyes, B G; Edwards, R M

    1999-06-01

    The genus Cynodon (Gramineae), comprised of 9 species, is geographically widely distributed and genetically diverse. Information on the amounts of molecular genetic variation among and within Cynodon taxa is needed to enhance understanding of phylogenetic relations and facilitate germplasm management and breeding improvement efforts. Genetic relatedness among 62 Cynodon accessions, representing eight species, was assessed using DNA amplification fingerprinting (DAF). Ten 8-mer oligonucleotides were used to amplify specific Cynodon genomic sequences. The DNA amplification products of individual accessions were scored for presence (1) or absence (0) of bands. Similarity matrices were developed and the accessions were grouped by cluster (UPGMA) and principal coordinate analysis. Analyses were conducted within ploidy level (2x = 18 and 4x = 36) and over ploidy levels. Each primer revealed polymorphic loci among accessions within species. Of 539 loci (bands) scored, 496 (92%) were polymorphic. Cynodon arcuatus was clearly separated from other species by numerous monomorphic bands. The strongest species similarities were between C. aethiopicus and C. arcuatus, C. transvaalensis and C. plectostachyus, and C. incompletus and C. nlemfuensis. Intraspecific variation was least for C. aethiopicus, C. arcuatus, and C. transvaalensis, and greatest for C. dactylon. Accessions of like taxonomic classification were generally clustered, except the cosmopolitan C. dactylon var. dactylon and C. dactylon var. afganicus. Within taxa, accessions differing in chromosome number clustered in all instances indicating the 2x and 4x forms to be closely related. Little, if any, relationship was found between relatedness as indicated by the DAF profiles and previous estimates of hybridization potential between the different taxa. PMID:10382294

  6. Nitrogen in Chinese coals

    USGS Publications Warehouse

    Wu, D.; Lei, J.; Zheng, B.; Tang, X.; Wang, M.; Hu, Jiawen; Li, S.; Wang, B.; Finkelman, R.B.

    2011-01-01

    Three hundred and six coal samples were taken from main coal mines of twenty-six provinces, autonomous regions, and municipalities in China, according to the resource distribution and coal-forming periods as well as the coal ranks and coal yields. Nitrogen was determined by using the Kjeldahl method at U. S. Geological Survey (USGS), which exhibit a normal frequency distribution. The nitrogen contents of over 90% Chinese coal vary from 0.52% to 1.41% and the average nitrogen content is recommended to be 0.98%. Nitrogen in coal exists primarily in organic form. There is a slight positive relationship between nitrogen content and coal ranking. ?? 2011 Science Press, Institute of Geochemistry, CAS and Springer Berlin Heidelberg.

  7. Typification of names of South American taxa related to Woodsia montevidensis (Woodsiaceae)

    PubMed Central

    Arana, Marcelo D.; Mynssen, Claudine M.; Zimmer, Brigitte; Ponce, M. Monica

    2016-01-01

    Abstract A revision of the nomenclature of six South American taxa related to Woodsia is presented, as a part of a taxonomic revision of the genus in South America. Lectotypes are selected for Cheilanthes crenata, Woodsia crenata var. pallidipes, Woodsia incisa, Woodsia montevidensis var. fuscipes and the second step lectotypification for Dicksonia montevidensis and Woodsia peruviana, based on the analysis of their protologues and original herbarium material. All names are currently synonyms of Woodsia montevidensis. Physematium incisum (Gillies ex Hook. & Grev.) Kunze constitutes an illegitimate name and Physematium cumingianum is considered as nomen inquirendum. PMID:27489474

  8. Typification of names of South American taxa related to Woodsia montevidensis (Woodsiaceae).

    PubMed

    Arana, Marcelo D; Mynssen, Claudine M; Zimmer, Brigitte; Ponce, M Monica

    2016-01-01

    A revision of the nomenclature of six South American taxa related to Woodsia is presented, as a part of a taxonomic revision of the genus in South America. Lectotypes are selected for Cheilanthes crenata, Woodsia crenata var. pallidipes, Woodsia incisa, Woodsia montevidensis var. fuscipes and the second step lectotypification for Dicksonia montevidensis and Woodsia peruviana, based on the analysis of their protologues and original herbarium material. All names are currently synonyms of Woodsia montevidensis. Physematium incisum (Gillies ex Hook. & Grev.) Kunze constitutes an illegitimate name and Physematium cumingianum is considered as nomen inquirendum. PMID:27489474

  9. A proposal for a multivariate quantitative approach to infer karyological relationships among taxa.

    PubMed

    Peruzzi, Lorenzo; Altınordu, Fahim

    2014-01-01

    Until now, basic karyological parameters have been used in different ways by researchers to infer karyological relationships among organisms. In the present study, we propose a standardized approach to this aim, integrating six different, not redundant, parameters in a multivariate PCoA analysis. These parameters are chromosome number, basic chromosome number, total haploid chromosome length, MCA (Mean Centromeric Asymmetry), CVCL (Coefficient of Variation of Chromosome Length) and CVCI (Coefficient of Variation of Centromeric Index). The method is exemplified with the application to several plant taxa, and its significance and limits are discussed in the light of current phylogenetic knowledge of these groups. PMID:25610547

  10. A proposal for a multivariate quantitative approach to infer karyological relationships among taxa

    PubMed Central

    Peruzzi, Lorenzo; Altınordu, Fahim

    2014-01-01

    Abstract Until now, basic karyological parameters have been used in different ways by researchers to infer karyological relationships among organisms. In the present study, we propose a standardized approach to this aim, integrating six different, not redundant, parameters in a multivariate PCoA analysis. These parameters are chromosome number, basic chromosome number, total haploid chromosome length, MCA (Mean Centromeric Asymmetry), CVCL (Coefficient of Variation of Chromosome Length) and CVCI (Coefficient of Variation of Centromeric Index). The method is exemplified with the application to several plant taxa, and its significance and limits are discussed in the light of current phylogenetic knowledge of these groups. PMID:25610547

  11. Phylogenetic relationships among higher Nemertean (Nemertea) Taxa inferred from 18S rDNA sequences.

    PubMed

    Sundberg, P; Turbeville, J M; Lindh, S

    2001-09-01

    We estimated the phylogenetic relationships of 15 nemertean (phylum Nemertea) species from the four subclasses Hoplo-, Hetero-, Palaeo-, and Bdellonemertea with 18S rDNA sequence data. Three outgroup taxa were used for rooting: Annelida, Platyhelminthes, and Mollusca. Parsimony and maximum-likelihood analyses supported the monophyletic status of the Heteronemertea and a taxon consisting of hoplonemerteans and Bdellonemertea, while indicating that Palaeonemertea is paraphyletic. The monophyletic status of the two nemertean classes Anopla and Enopla is not supported by the data. The unambiguous clades are well supported, as assessed by a randomization test (bootstrapping) and branch support values. PMID:11527461

  12. Demonstrating Paramagnetism Using Liquid Nitrogen.

    ERIC Educational Resources Information Center

    Simmonds, Ray; And Others

    1994-01-01

    Describes how liquid nitrogen is attracted to the poles of neodymium magnets. Nitrogen is not paramagnetic, so the attraction suggests that the liquid nitrogen contains a small amount of oxygen, which causes the paramagnetism. (MVL)

  13. Molecular Biology of Nitrogen Fixation

    ERIC Educational Resources Information Center

    Shanmugam, K. T.; Valentine, Raymond C.

    1975-01-01

    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  14. The nitrogen cycle.

    PubMed

    Stein, Lisa Y; Klotz, Martin G

    2016-02-01

    Nitrogen is the fourth most abundant element in cellular biomass, and it comprises the majority of Earth's atmosphere. The interchange between inert dinitrogen gas (N2) in the extant atmosphere and 'reactive nitrogen' (those nitrogen compounds that support, or are products of, cellular metabolism and growth) is entirely controlled by microbial activities. This was not the case, however, in the primordial atmosphere, when abiotic reactions likely played a significant role in the inter-transformation of nitrogen oxides. Although such abiotic reactions are still important, the extant nitrogen cycle is driven by reductive fixation of dinitrogen and an enzyme inventory that facilitates dinitrogen-producing reactions. Prior to the advent of the Haber-Bosch process (the industrial fixation of N2 into ammonia, NH3) in 1909, nearly all of the reactive nitrogen in the biosphere was generated and recycled by microorganisms. Although the Haber-Bosch process more than quadrupled the productivity of agricultural crops, chemical fertilizers and other anthropogenic sources of fixed nitrogen now far exceed natural contributions, leading to unprecedented environmental degradation. PMID:26859274

  15. Nitrogen control in bacteria.

    PubMed Central

    Merrick, M J; Edwards, R A

    1995-01-01

    Nitrogen metabolism in prokaryotes involves the coordinated expression of a large number of enzymes concerned with both utilization of extracellular nitrogen sources and intracellular biosynthesis of nitrogen-containing compounds. The control of this expression is determined by the availability of fixed nitrogen to the cell and is effected by complex regulatory networks involving regulation at both the transcriptional and posttranslational levels. While the most detailed studies to date have been carried out with enteric bacteria, there is a considerable body of evidence to show that the nitrogen regulation (ntr) systems described in the enterics extend to many other genera. Furthermore, as the range of bacteria in which the phenomenon of nitrogen control is examined is being extended, new regulatory mechanisms are also being discovered. In this review, we have attempted to summarize recent research in prokaryotic nitrogen control; to show the ubiquity of the ntr system, at least in gram-negative organisms; and to identify those areas and groups of organisms about which there is much still to learn. PMID:8531888

  16. Possible effects of global environmental changes on Antarctic benthos: a synthesis across five major taxa.

    PubMed

    Ingels, Jeroen; Vanreusel, Ann; Brandt, Angelika; Catarino, Ana I; David, Bruno; De Ridder, Chantal; Dubois, Philippe; Gooday, Andrew J; Martin, Patrick; Pasotti, Francesca; Robert, Henri

    2012-02-01

    Because of the unique conditions that exist around the Antarctic continent, Southern Ocean (SO) ecosystems are very susceptible to the growing impact of global climate change and other anthropogenic influences. Consequently, there is an urgent need to understand how SO marine life will cope with expected future changes in the environment. Studies of Antarctic organisms have shown that individual species and higher taxa display different degrees of sensitivity to environmental shifts, making it difficult to predict overall community or ecosystem responses. This emphasizes the need for an improved understanding of the Antarctic benthic ecosystem response to global climate change using a multitaxon approach with consideration of different levels of biological organization. Here, we provide a synthesis of the ability of five important Antarctic benthic taxa (Foraminifera, Nematoda, Amphipoda, Isopoda, and Echinoidea) to cope with changes in the environment (temperature, pH, ice cover, ice scouring, food quantity, and quality) that are linked to climatic changes. Responses from individual to the taxon-specific community level to these drivers will vary with taxon but will include local species extinctions, invasions of warmer-water species, shifts in diversity, dominance, and trophic group composition, all with likely consequences for ecosystem functioning. Limitations in our current knowledge and understanding of climate change effects on the different levels are discussed. PMID:22423336

  17. Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response

    PubMed Central

    Oshkin, Igor Y; Beck, David AC; Lamb, Andrew E; Tchesnokova, Veronika; Benuska, Gabrielle; McTaggart, Tami L; Kalyuzhnaya, Marina G; Dedysh, Svetlana N; Lidstrom, Mary E; Chistoserdova, Ludmila

    2015-01-01

    We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples. We first measured taxonomic compositions of long-term enrichment cultures and determined that, although dominated by Methylococcaceae types, these cultures also contained accompanying types belonging to a limited number of bacterial taxa, methylotrophs and non-methylotrophs. We then followed the short-term community dynamics, in two oxygen tension regimens (150 μM and 15 μM), observing rapid loss of species diversity. In all microcosms, a single type of Methylobacter represented the major methane-oxidizing partner. The accompanying members of the communities revealed different trajectories in response to different oxygen tensions, with Methylotenera species being the early responders to methane stimulus under both conditions. The communities in both conditions were convergent in terms of their assemblage, suggesting selection for specific taxa. Our results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are likely responsible for methane cycling, rather than a single type of microbe. PMID:25333464

  18. Temporal scaling of bacterial taxa is influenced by both stochastic and deterministic ecological factors.

    PubMed

    van der Gast, Christopher J; Ager, Duane; Lilley, Andrew K

    2008-06-01

    Microorganisms operate at a range of spatial and temporal scales acting as key drivers of ecosystem properties. Therefore, many key questions in microbial ecology require the consideration of both spatial and temporal scales. Spatial scaling, in particular the species-area relationship (SAR), has a long history in ecology and has recently been addressed in microbial ecology. However, the temporal analogue of the SAR, the species-time relationship, has received far less attention even in the science of general ecology. Here we focus upon the role of temporal scaling in microbial ecological patterns by coupling molecular characterization of bacterial communities in discrete island (bioreactor) systems with a macroecological approach. Our findings showed that the temporal scaling exponent (slope), and therefore taxa turnover of the bacterial taxa-time relationship decreased as selective pressure (industrial wastewater concentration) increased. Also, as the concentration of industrial wastewater increased across the bioreactors, we observed a gradual switch from stochastic community assembly to more deterministic (niche)-based considerations. The identification of broad-scale statistical patterns is particularly relevant to microbial ecology, as it is frequently difficult to identify individual species or their functions. In this study, we identify wide-reaching statistical patterns of diversity and show that they are shaped by the prevalent underlying ecological factors. PMID:18205822

  19. Climate-driven C4 plant distributions in China: divergence in C4 taxa

    PubMed Central

    Wang, Renzhong; Ma, Linna

    2016-01-01

    There have been debates on the driving factors of C4 plant expansion, such as PCO2 decline in the late Micocene and warmer climate and precipitation at large-scale modern ecosystems. These disputes are mainly due to the lack of direct evidence and extensive data analysis. Here we use mass flora data to explore the driving factors of C4 distribution and divergent patterns for different C4 taxa at continental scale in China. The results display that it is mean annual climate variables driving C4 distribution at present-day vegetation. Mean annual temperature is the critical restriction of total C4 plants and the precipitation gradients seem to have much less impact. Grass and sedge C4 plants are largely restricted to mean annual temperature and precipitation respectively, while Chenopod C4 plants are strongly restricted by aridity in China. Separate regression analysis can succeed to detect divergences of climate distribution patterns of C4 taxa at global scale. PMID:27302686

  20. Unraveling Trichoderma species in the attine ant environment: description of three new taxa.

    PubMed

    Montoya, Quimi Vidaurre; Meirelles, Lucas Andrade; Chaverri, Priscila; Rodrigues, Andre

    2016-05-01

    Fungus-growing "attine" ants forage diverse substrates to grow fungi for food. In addition to the mutualistic fungal partner, the colonies of these insects harbor a rich microbiome composed of bacteria, filamentous fungi and yeasts. Previous work reported some Trichoderma species in the fungus gardens of leafcutter ants. However, no studies systematically addressed the putative association of Trichoderma with attine ants, especially in non-leafcutter ants. Here, a total of 62 strains of Trichoderma were analyzed using three molecular markers (ITS, tef1 and rpb2). In addition, 30 out of 62 strains were also morphologically examined. The strains studied correspond to the largest sampling carried out so far for Trichoderma in the attine ant environment. Our results revealed the richness of Trichoderma in this environment, since we found 20 Trichoderma species, including three new taxa described in the present work (Trichoderma attinorum, Trichoderma texanum and Trichoderma longifialidicum spp. nov.) as well as a new phylogenetic taxon (LESF 545). Moreover, we show that all 62 strains grouped within different clades across the Trichoderma phylogeny, which are identical or closely related to strains derived from several other environments. This evidence supports the transient nature of the genus Trichoderma in the attine ant colonies. The discovery of three new species suggests that the dynamic foraging behavior of these insects might be responsible for accumulation of transient fungi into their colonies, which might hold additional fungal taxa still unknown to science. PMID:26885975

  1. Taxonomic and nomenclatural aspects of Hypoxylon taxa from southern South America proposed by Spegazzini.

    PubMed

    Hladki, Adriana I; Romero, Andrea I

    2009-01-01

    The holotypes and isotypes of 20 Hypoxylon taxa described by Spegazzini have been examined and their taxonomic positions and nomenclatural problems are discussed. Two new combinations, Annulohypoxylon apiahynum comb. nov. and A. subeffusum comb. nov., are proposed. H. goliath is considered a synonym of Rosellinia bunodes. H. albostigmatosum and H. guarapiense are synonyms of H. anthochroum, H. anthracoderma of H. monticulosum, H. mbaiense of H. notatum, H. paulistanum of H. diatrypeoides, H. plumbeum and H. rubiginosum var. microcarpum of H. perforatum. H. porteri and H. intermedium belong in Biscogniauxia capnodes, H. puiggarii in Annulophypoxylon subeffusum, H. subvinosum. in H. lenormandii, H. turbinatum var. guaraniticum in Phylacia turbinata and H. valsarioides in Creosphaeria sassafras. H. leptascum is transferred to A. leptascum, H. circostomum to Nemania circostoma and H. latissimum to N. latissima. The holotype of H. albostigmatosum has been recovered, thus the lectotypification by Shear no longer is needed. H. subnigricans and H. umbilicatum are confirmed as good taxa. H. anthochroum and H. lenormandii are reported as first records from Argentina (Tucumán). PMID:19750953

  2. Fission and fusion in island taxa--serendipity, or something to be expected?

    PubMed

    Emerson, Brent C; Faria, Christiana M A

    2014-11-01

    A well-used metaphor for oceanic islands is that they act as 'natural laboratories' for the study of evolution. But how can islands or archipelagos be considered analogues of laboratories for understanding the evolutionary process itself? It is not necessarily the case that just because two or more related species occur on an island or archipelago, somehow, this can help us understand more about their evolutionary history. But in some cases, it can. In this issue of Molecular Ecology, Garrick et al. () use population-level sampling within closely related taxa of Galapagos giant tortoises to reveal a complex demographic history of the species Chelonoidis becki - a species endemic to Isabela Island, and geographically restricted to Wolf Volcano. Using microsatellite genotyping and mitochondrial DNA sequencing, they provide a strong case for C. becki being derived from C. darwini from the neighbouring island of Santiago. But the interest here is that colonization did not happen only once. Garrick et al. () reveal C. becki to be the product of a double colonization event, and their data reveal these two founding lineages to be now fusing back into one. Their results are compelling and add to a limited literature describing the evolutionary consequences of double colonization events. Here, we look at the broader implications of the findings of Garrick et al. () and suggest genomic admixture among multiple founding populations may be a characteristic feature within insular taxa. PMID:25330853

  3. Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

    PubMed Central

    Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J.

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement. PMID:25803280

  4. Essential oils of three taxa of the Nepeta argolica aggregate from Greece.

    PubMed

    Hanlidou, Effie; Karousou, Regina; Lazari, Diamanto

    2012-08-01

    The essential-oil composition of three not previously studied taxa belonging to the Nepeta argolica aggregate was examined. The oils of N. argolica ssp. malacotrichos and N. argolica ssp. vourinensis (both Greek endemics) are rich in 1,8-cineole (30.9-55.6% of the total oil composition), while those of the Balkan endemic N. spruneri are rich in either sesquiterpenes (mainly caryophyllene oxide, 14.6-19.8%) or in 4aα,7α,7aβ- and 4aα,7α,7aα-nepetalactones (total content 17.5-40.5%), accompanied by caryophyllene oxide (11.5-11.7%) and 1,8-cineole (up to 16.5%). The comparison of our results with published information concerning the related taxa of the N. argolica aggregate showed that while oils with as main components nepetalactones or 1,8-cineole are common, sesquiterpene-rich oils are reported for the first time within the aggregate. PMID:22899616

  5. Methane-fed microbial microcosms show differential community dynamics and pinpoint taxa involved in communal response.

    PubMed

    Oshkin, Igor Y; Beck, David A C; Lamb, Andrew E; Tchesnokova, Veronika; Benuska, Gabrielle; McTaggart, Tami L; Kalyuzhnaya, Marina G; Dedysh, Svetlana N; Lidstrom, Mary E; Chistoserdova, Ludmila

    2015-05-01

    We report observations on the dynamics of bacterial communities in response to methane stimulus in laboratory microcosm incubations prepared with lake sediment samples. We first measured taxonomic compositions of long-term enrichment cultures and determined that, although dominated by Methylococcaceae types, these cultures also contained accompanying types belonging to a limited number of bacterial taxa, methylotrophs and non-methylotrophs. We then followed the short-term community dynamics, in two oxygen tension regimens (150 μM and 15 μM), observing rapid loss of species diversity. In all microcosms, a single type of Methylobacter represented the major methane-oxidizing partner. The accompanying members of the communities revealed different trajectories in response to different oxygen tensions, with Methylotenera species being the early responders to methane stimulus under both conditions. The communities in both conditions were convergent in terms of their assemblage, suggesting selection for specific taxa. Our results support prior observations from metagenomics on distribution of carbon from methane among diverse bacterial populations and further suggest that communities are likely responsible for methane cycling, rather than a single type of microbe. PMID:25333464

  6. Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial.

    PubMed

    Freedberg, Daniel E; Toussaint, Nora C; Chen, Sway P; Ratner, Adam J; Whittier, Susan; Wang, Timothy C; Wang, Harris H; Abrams, Julian A

    2015-10-01

    We conducted an open-label crossover trial to test whether proton pump inhibitors (PPIs) affect the gastrointestinal microbiome to facilitate Clostridium difficile infection (CDI). Twelve healthy volunteers each donated 2 baseline fecal samples, 4 weeks apart (at weeks 0 and 4). They then took PPIs for 4 weeks (40 mg omeprazole, twice daily) and fecal samples were collected at week 8. Six individuals took the PPIs for an additional 4 weeks (from week 8 to 12) and fecal samples were collected from all subjects at week 12. Samples were analyzed by 16S ribosomal RNA gene sequencing. We found no significant within-individual difference in microbiome diversity when we compared changes during baseline vs changes on PPIs. There were, however, significant changes during PPI use in taxa associated with CDI (increased Enterococcaceae and Streptococcaceae, decreased Clostridiales) and taxa associated with gastrointestinal bacterial overgrowth (increased Micrococcaceae and Staphylococcaceae). In a functional analysis, there were no changes in bile acids on PPIs, but there was an increase in genes involved in bacterial invasion. These alterations could provide a mechanism by which PPIs predispose to CDI. ClinicalTrials.gov ID NCT01901276. PMID:26164495

  7. Climate-driven C4 plant distributions in China: divergence in C4 taxa.

    PubMed

    Wang, Renzhong; Ma, Linna

    2016-01-01

    There have been debates on the driving factors of C4 plant expansion, such as PCO2 decline in the late Micocene and warmer climate and precipitation at large-scale modern ecosystems. These disputes are mainly due to the lack of direct evidence and extensive data analysis. Here we use mass flora data to explore the driving factors of C4 distribution and divergent patterns for different C4 taxa at continental scale in China. The results display that it is mean annual climate variables driving C4 distribution at present-day vegetation. Mean annual temperature is the critical restriction of total C4 plants and the precipitation gradients seem to have much less impact. Grass and sedge C4 plants are largely restricted to mean annual temperature and precipitation respectively, while Chenopod C4 plants are strongly restricted by aridity in China. Separate regression analysis can succeed to detect divergences of climate distribution patterns of C4 taxa at global scale. PMID:27302686

  8. Taxonomic significance of leaf micromorphology in some selected taxa of Acanthaceae (Peninsular Malaysia)

    NASA Astrophysics Data System (ADS)

    Nurul-Aini, C. A. C.; Noraini, T.; Latiff, A.; Amirul-Aiman, A. J.; Ruzi, A. R.; Idris, S.

    2014-09-01

    Comparative leaf micromorphology study was conducted in eight taxa of Acanthaceae from Peninsular Malaysia. Eight chosen taxa were Acanthus ebracteatus Vahl, A. ilicifolius L., A. volubilis Wall, A. montanus T. Anderson, Andrographis paniculata (Burm.f.) Wall. ex Nees, Asystasia gangetica subsp. micrantha (Nees) Ensermu, Chroesthes longifolia (Wight) B. Hansen and Peristrophe roxburghiana (Schult.) Bremek. The objective of this study was to identify the leaf micromorphological characteristics that can be used in species identification and also as supportive data in classification. The procedures involved such as dehydration, critical point drying, gold coated and examination under scanning electron microscope. Findings in this study have demonstrated the similarities and variations in leaf micromorphological characteristics such as in type of epicuticular waxes, cuticular ornamentations, stomata characteristics and in the presence of trichomes. Six types of epicuticular waxes and five types of trichomes were observed. Variations in cuticular ornamentations and stomata structure can be used to differentiate species. One diagnostic character was found and proven to be very useful to identify Acanthus via the presence of simple trichomes (short-conicle like). In conclusion, the results of this study have shown that leaf micromorphological characteristics have taxonomic significance that can be useful in classifications and identification especially at species level.

  9. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    PubMed

    Reeder, Tod W; Townsend, Ted M; Mulcahy, Daniel G; Noonan, Brice P; Wood, Perry L; Sites, Jack W; Wiens, John J

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement. PMID:25803280

  10. Possible effects of global environmental changes on Antarctic benthos: a synthesis across five major taxa

    PubMed Central

    Ingels, Jeroen; Vanreusel, Ann; Brandt, Angelika; Catarino, Ana I; David, Bruno; De Ridder, Chantal; Dubois, Philippe; Gooday, Andrew J; Martin, Patrick; Pasotti, Francesca; Robert, Henri

    2012-01-01

    Because of the unique conditions that exist around the Antarctic continent, Southern Ocean (SO) ecosystems are very susceptible to the growing impact of global climate change and other anthropogenic influences. Consequently, there is an urgent need to understand how SO marine life will cope with expected future changes in the environment. Studies of Antarctic organisms have shown that individual species and higher taxa display different degrees of sensitivity to environmental shifts, making it difficult to predict overall community or ecosystem responses. This emphasizes the need for an improved understanding of the Antarctic benthic ecosystem response to global climate change using a multitaxon approach with consideration of different levels of biological organization. Here, we provide a synthesis of the ability of five important Antarctic benthic taxa (Foraminifera, Nematoda, Amphipoda, Isopoda, and Echinoidea) to cope with changes in the environment (temperature, pH, ice cover, ice scouring, food quantity, and quality) that are linked to climatic changes. Responses from individual to the taxon-specific community level to these drivers will vary with taxon but will include local species extinctions, invasions of warmer-water species, shifts in diversity, dominance, and trophic group composition, all with likely consequences for ecosystem functioning. Limitations in our current knowledge and understanding of climate change effects on the different levels are discussed. PMID:22423336

  11. Multiple origins of circumboreal taxa in Pyrola (Ericaceae), a group with a Tertiary relict distribution

    PubMed Central

    Liu, Zhen-Wen; Jolles, Diana D.; Zhou, Jing; Peng, Hua; Milne, Richard I.

    2014-01-01

    Background and Aims In the Northern Hemisphere, Tertiary relict disjunctions involve older groups of warm affinity and wide disjunctions, whereas circumboreal distributions in Arctic-Alpine taxa tend to be younger. Arctic-Alpine species are occasionally derived from Tertiary relict groups, but Pyrola species, in particular, are exceptional and they might have occurred multiple times. The aim of this study was to reconstruct the biogeographic history of Pyrola based on a clear phylogenetic analysis and to explore how the genus attained its circumboreal distribution. Methods Estimates of divergence times and ancestral geographical distributions based on neutrally evolving DNA sequence variation were used to develop a spatio-temporal model of colonization patterns for Pyrola. Key Results Pyrola originated and most diversification occurred in Asia; North America was reached first by series Scotophyllae in the late Miocene, then by sub-clades of series Pyrola and Ellipticae around the Pliocene. The three circumboreal taxa, P. minor, P. chlorantha and the P. rotundifolia complex, originated independently of one another, with the last two originating in Asia. Conclusions Three circumboreal Pyrola lineages have arisen independently and at least two of these appear to have originated in Asia. The cool, high-altitude habitats of many Pyrola species and the fact that diversification in the genus coincided with global cooling from the late Miocene onwards fits a hypothesis of pre-adaptation to become circumboreal within this group. PMID:25326138

  12. Nitrogen Backbone Oligomers

    PubMed Central

    Wang, Hongbo; Eremets, Mikhail I.; Troyan, Ivan; Liu, Hanyu; Ma, Yanming; Vereecken, Luc

    2015-01-01

    We found that nitrogen and hydrogen directly react at room temperature and pressures of ~35 GPa forming chains of single-bonded nitrogen atom with the rest of the bonds terminated with hydrogen atoms - as identified by IR absorption, Raman, X-ray diffraction experiments and theoretical calculations. At releasing pressures below ~10 GPa, the product transforms into hydrazine. Our findings might open a way for the practical synthesis of these extremely high energetic materials as the formation of nitrogen-hydrogen compounds is favorable already at pressures above 2 GPa according to the calculations. PMID:26286836

  13. Nitrogen Backbone Oligomers

    NASA Astrophysics Data System (ADS)

    Wang, Hongbo; Eremets, Mikhail I.; Troyan, Ivan; Liu, Hanyu; Ma, Yanming; Vereecken, Luc

    2015-08-01

    We found that nitrogen and hydrogen directly react at room temperature and pressures of ~35 GPa forming chains of single-bonded nitrogen atom with the rest of the bonds terminated with hydrogen atoms - as identified by IR absorption, Raman, X-ray diffraction experiments and theoretical calculations. At releasing pressures below ~10 GPa, the product transforms into hydrazine. Our findings might open a way for the practical synthesis of these extremely high energetic materials as the formation of nitrogen-hydrogen compounds is favorable already at pressures above 2 GPa according to the calculations.

  14. Effects of Nitrogen Availability and Form on Phytoplankton Growth in a Eutrophied Estuary (Neuse River Estuary, NC, USA)

    PubMed Central

    Paerl, Hans W.; Wetz, Michael S.

    2016-01-01

    Nitrogen availability and form are important controls on estuarine phytoplankton growth. This study experimentally determined the influence of urea and nitrate additions on phytoplankton growth throughout the growing season (March 2012, June 2011, August 2011) in a temperate, eutrophied estuary (Neuse River Estuary, North Carolina, USA). Photopigments (chlorophyll a and diagnostic photopigments: peridinin, fucoxanthin, alloxanthin, zeaxanthin, chlorophyll b) and microscopy-based cell counts were used as indicators of phytoplankton growth. In March, the phytoplankton community was dominated by Gyrodinium instriatum and only fucoxanthin-based growth rates were stimulated by nitrogen addition. The limited response to nitrogen suggests other factors may control phytoplankton growth and community composition in early spring. In June, inorganic nitrogen concentrations were low and stimulatory effects of both nitrogen forms were observed for chlorophyll a- and diagnostic photopigment-based growth rates. In contrast, cell counts showed that only cryptophyte and dinoflagellate (Heterocapsa rotundata) growth were stimulated. Responses of other photopigments may have been due to an increase in pigment per cell or growth of plankton too small to be counted with the microscopic methods used. Despite high nitrate concentrations in August, growth rates were elevated in response to urea and/or nitrate addition for all photopigments except peridinin. However, this response was not observed in cell counts, again suggesting that pigment-based growth responses may not always be indicative of a true community and/or taxa-specific growth response. This highlights the need to employ targeted microscopy-based cell enumeration concurrent with pigment-based technology to facilitate a more complete understanding of phytoplankton dynamics in estuarine systems. These results are consistent with previous studies showing the seasonal importance of nitrogen availability in estuaries, and also

  15. Effects of Nitrogen Availability and Form on Phytoplankton Growth in a Eutrophied Estuary (Neuse River Estuary, NC, USA).

    PubMed

    Cira, Emily K; Paerl, Hans W; Wetz, Michael S

    2016-01-01

    Nitrogen availability and form are important controls on estuarine phytoplankton growth. This study experimentally determined the influence of urea and nitrate additions on phytoplankton growth throughout the growing season (March 2012, June 2011, August 2011) in a temperate, eutrophied estuary (Neuse River Estuary, North Carolina, USA). Photopigments (chlorophyll a and diagnostic photopigments: peridinin, fucoxanthin, alloxanthin, zeaxanthin, chlorophyll b) and microscopy-based cell counts were used as indicators of phytoplankton growth. In March, the phytoplankton community was dominated by Gyrodinium instriatum and only fucoxanthin-based growth rates were stimulated by nitrogen addition. The limited response to nitrogen suggests other factors may control phytoplankton growth and community composition in early spring. In June, inorganic nitrogen concentrations were low and stimulatory effects of both nitrogen forms were observed for chlorophyll a- and diagnostic photopigment-based growth rates. In contrast, cell counts showed that only cryptophyte and dinoflagellate (Heterocapsa rotundata) growth were stimulated. Responses of other photopigments may have been due to an increase in pigment per cell or growth of plankton too small to be counted with the microscopic methods used. Despite high nitrate concentrations in August, growth rates were elevated in response to urea and/or nitrate addition for all photopigments except peridinin. However, this response was not observed in cell counts, again suggesting that pigment-based growth responses may not always be indicative of a true community and/or taxa-specific growth response. This highlights the need to employ targeted microscopy-based cell enumeration concurrent with pigment-based technology to facilitate a more complete understanding of phytoplankton dynamics in estuarine systems. These results are consistent with previous studies showing the seasonal importance of nitrogen availability in estuaries, and also

  16. Mineral commodity profiles: nitrogen

    USGS Publications Warehouse

    Kramer, Deborah A.

    2004-01-01

    Overview -- Nitrogen (N) is an essential element of life and a part of all animal and plant proteins. As a part of the DNA and RNA molecules, nitrogen is an essential constituent of each individual's genetic blueprint. As an essential element in the chlorophyll molecule, nitrogen is vital to a plant's ability to photosynthesize. Some crop plants, such as alfalfa, peas, peanuts, and soybeans, can convert atmospheric nitrogen into a usable form by a process referred to as 'fixation.' Most of the nitrogen that is available for crop production, however, comes from decomposing animal and plant waste or from commercially produced fertilizers. Commercial fertilizers contain nitrogen in the form of ammonium and/or nitrate or in a form that is quickly converted to the ammonium or nitrate form once the fertilizer is applied to the soil. Ammonia is generally the source of nitrogen in fertilizers. Anhydrous ammonia is commercially produced by reacting nitrogen with hydrogen under high temperatures and pressures. The source of nitrogen is the atmosphere, which is almost 80 percent nitrogen. Hydrogen is derived from a variety of raw materials, which include water, and crude oil, coal, and natural gas hydrocarbons. Nitrogen-based fertilizers are produced from ammonia feedstocks through a variety of chemical processes. Small quantities of nitrates are produced from mineral resources principally in Chile. In 2002, anhydrous ammonia and other nitrogen materials were produced in more than 70 countries. Global ammonia production was 108 million metric tons (Mt) of contained nitrogen. With 28 percent of this total, China was the largest producer of ammonia. Asia contributed 46 percent of total world ammonia production, and countries of the former U.S.S.R. represented 13 percent. North America also produced 13 percent of the total; Western Europe, 9 percent; the Middle East, 7 percent; Central America and South America, 5 percent; Eastern Europe, 3 percent; and Africa and Oceania

  17. High level extracellular production of a truncated alkaline β-mannanase from alkaliphilic Bacillus sp. N16-5 in Escherichia coli by the optimization of induction condition and fed-batch fermentation.

    PubMed

    Zheng, Hongchen; Yu, Zhenxiao; Fu, Xiaoping; Li, Shufang; Xu, Jianyong; Song, Hui; Ma, Yanhe

    2016-07-01

    To improve the extracellular production of alkaline β-mannanase from alkaliphilic Bacillus sp. N16-5 in Escherichia coli, two truncated recombinant mannanases (32a-ManAR2 and 22b-ManAR2) were obtained. Compared with the full-length mannanases (32a-ManAR1 and 22b-ManAR1), the truncated mannanases not only showed higher secretion rate, but also exhibited higher thermostability and alkalistability. The K m value (11 mg/mL) of 32a-ManAR2 was higher than that (1.46 mg/mL) of 32a-ManAR1. The specific activity of 22b-ManAR2 was 2.7 times higher than that of 22b-ManAR1. 22b-ManAR2 showed the highest k cat/K m value of 602.7 ml/mg s. The parameters of induction for recombinant mannanase production of E. coli BL21 (pET32a-manAR2) and E. coli BL21 (pET22b-manAR2) were subsequently optimized. The yield of soluble mannanase was found to be enhanced with lower induction temperature (25 °C), lower IPTG concentration (0.01-0.05 mM), and Triton X-100 supplement (0.1 %) in a shake flask. Moreover, a one-time feeding strategy and Triton X-100 supplement were applied in production of 22b-ManAR2 in a 10 L fermentor. The productivity of the total soluble mannanase reached 9284.64 U/mL with the extracellular rate of 74 % at 46 h of fermentation, which was the highest productive level of alkaline β-mannanase in recombinant E. coli to date. PMID:27130461

  18. Protein Nitrogen Determination

    NASA Astrophysics Data System (ADS)

    Nielsen, S. Suzanne

    The protein content of foods can be determined by numerous methods. The Kjeldahl method and the nitrogen combustion (Dumas) method for protein analysis are based on nitrogen determination. Both methods are official for the purposes of nutrition labeling of foods. While the Kjeldahl method has been used widely for over a hundred years, the recent availability of automated instrumentation for the Dumas method in many cases is replacing use of the Kjeldahl method.

  19. Atmospheric Nitrogen Fluorescence Yield

    NASA Technical Reports Server (NTRS)

    Adams, J. H., Jr.; Christl, M. J.; Fountain, W. F.; Gregory, J. C.; Martens, K. U.; Sokolsky, Pierre; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Several existing and planned experiments estimate the energies of ultra-high energy cosmic rays from air showers using the atmospheric nitrogen fluorescence. The nitrogen fluorescence yield from air shower electrons depends on the atmospheric composition. We will discuss the uncertainties in the fluorescence yield form electrons in the real atmosphere and describe a concept for a small balloon payload to measure the atmospheric fluorescence yield as a function of attitude.

  20. Brucella, nitrogen and virulence.

    PubMed

    Ronneau, Severin; Moussa, Simon; Barbier, Thibault; Conde-Álvarez, Raquel; Zuniga-Ripa, Amaia; Moriyon, Ignacio; Letesson, Jean-Jacques

    2016-08-01

    The brucellae are α-Proteobacteria causing brucellosis, an important zoonosis. Although multiplying in endoplasmic reticulum-derived vacuoles, they cause no cell death, suggesting subtle but efficient use of host resources. Brucellae are amino-acid prototrophs able to grow with ammonium or use glutamate as the sole carbon-nitrogen source in vitro. They contain more than twice amino acid/peptide/polyamine uptake genes than the amino-acid auxotroph Legionella pneumophila, which multiplies in a similar vacuole, suggesting a different nutritional strategy. During these two last decades, many mutants of key actors in nitrogen metabolism (transporters, enzymes, regulators, etc.) have been described to be essential for full virulence of brucellae. Here, we review the genomic and experimental data on Brucella nitrogen metabolism and its connection with virulence. An analysis of various aspects of this metabolism (transport, assimilation, biosynthesis, catabolism, respiration and regulation) has highlighted differences and similarities in nitrogen metabolism with other α-Proteobacteria. Together, these data suggest that, during their intracellular life cycle, the brucellae use various nitrogen sources for biosynthesis, catabolism and respiration following a strategy that requires prototrophy and a tight regulation of nitrogen use. PMID:25471320

  1. Nitrogen Uptake in Spinach

    NASA Astrophysics Data System (ADS)

    Ramirez, J.; VanBenthem, P.

    2013-12-01

    A plant's absorption of nitrogen can be encouraged by a variety of environmental factors, especially the application of fertilizers. As a common limiting factor in plant growth, not up taking enough nitrogen can be a result of an unhealthy plant. Moreover, as farmers seek out methods to increase growth of plants, fertilizers are used as a solution to the issue of nitrogen deficiency to incorporate additional nitrogen from chemical or organic sources, by not using the right fertilizer can greatly affect the plats. The point of this research project is to determine the effect of various fertilizers on the plant growth, and to correlate the measured nitrogen, water and chlorophyll content in spinach leaves. Spinach leaves were used because they are known to quickly uptake chemicals in the environment. The spinach plants were exposed to four different growing parameters, which are referred to as control, ammonium nitrate, MiracleGro , and organic. The spinach was originally placed in nitrogen deficient soil with only 2.2x10 4 weight percent (wt. %) nitrogen. The leaves in the control group were grown in this nitrogen deficient soil without any fertilizer added. Ammomium nitrate and MiracleGro were added to the spinach in the A and MG groups, respectively, and organic chicken stool was used for the O group. By using a spectral imaging system and flame combustion techniques, the chlorophyll content can be related to the nitrogen content in the spinach leaves. In these spinach leaves, nitrogen and chlorophyll content were measured, chlorophyll is a green pigment that plays a crucial role in producing nutrients for green plants. The lack of chlorophyll will allow the plant to become susceptible to diseases, so it is extremely important that the plants have a high content of chlorophyll. The role of nitrogen in chlorophyll is very important and helps in the creation of chlorophyll; therefore it is necessary that an appropriate amount of nitrogen is added for optimal growth

  2. PRECISION FARMING FOR NITROGEN MANAGEMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Approaches to precision nitrogen management vary from region to region depending on crop, soils, landscape, and climate yet all strategies essentially attempt to estimate crop nitrogen demand or plant available nitrogen. In this chapter, we provide case studies that illustrate precision nitrogen ma...

  3. Characterization of Two New Records of Zygomycete Species Belonging to Undiscovered Taxa in Korea

    PubMed Central

    Nguyen, Thi Thuong Thuong; Lee, Seo Hee; Bae, Sarah; Jeon, Sun Jeong; Mun, Hye Yeon

    2016-01-01

    During a biodiversity survey of undiscovered taxa in Korea, two zygomycetous fungal strains were isolated. The first strain, EML-FSDY6-1 was isolated from a soil sample collected at Dokdo Island in the East Sea of Korea in 2013, and the second strain, EML-DG-NH3-1 was isolated from a rat dung sample collected at Chonnam National University garden, Gwangju, Korea in 2014. Based on the morphological characteristics and phylogenetic analysis of the internal transcribed spacer, 18S and 28S rDNA, actin and translation elongation factor-1α genes. EML-FSDY6-1 and EML-DG-NH3-1 isolates were confirmed as zygomycete species, Absidia pseudocylindrospora and Absidia glauca, respectively. Neither species has previously been described in Korea. PMID:27103852

  4. Firmicutes dominate the bacterial taxa within sugar-cane processing plants.

    PubMed

    Sharmin, Farhana; Wakelin, Steve; Huygens, Flavia; Hargreaves, Megan

    2013-01-01

    Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p < 0.05) in community structure occurred between samples collected from 'floor dump sediment', 'cooling tower water', and 'bagasse leachate'. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as 'lactic acid bacteria', capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria. PMID:24177592

  5. Biodiversity conservation across taxa and landscapes requires many small as well as single large habitat fragments.

    PubMed

    Rösch, Verena; Tscharntke, Teja; Scherber, Christoph; Batáry, Péter

    2015-09-01

    Agricultural intensification has been shown to reduce biodiversity through processes such as habitat degradation and fragmentation. We tested whether several small or single large habitat fragments (re-visiting the 'single large or several small' debate) support more species across a wide range of taxonomic groups (plants, leafhoppers, true bugs, snails). Our study comprised 14 small (<1 ha) and 14 large (1.5-8 ha) fragments of calcareous grassland in Central Germany along orthogonal gradients of landscape complexity and habitat connectivity. Each taxon was sampled on six plots per fragment. Across taxa, species richness did not differ between large and small fragments, whereas species-area accumulation curves showed that both overall and specialist species richness was much higher on several small fragments of calcareous grassland than on few large fragments. On average, 85% of the overall species richness was recorded on all small fragments taken together (4.6 ha), whereas the two largest ones (15.1 ha) only accounted for 37% of the species. This could be due to the greater geographic extent covered by many small fragments. However, community composition differed strongly between large and small fragments, and some of the rarest specialist species appeared to be confined to large fragments. The surrounding landscape did not show any consistent effects on species richness and community composition. Our results show that both single large and many small fragments are needed to promote landscape-wide biodiversity across taxa. We therefore question the focus on large fragments only and call for a new diversified habitat fragmentation strategy for biodiversity conservation. PMID:25911274

  6. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters.

    PubMed

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-09-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29-30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75-87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy-diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome. PMID:26953601

  7. Explaining Spatial Variation in the Recording Effort of Citizen Science Data across Multiple Taxa.

    PubMed

    Mair, Louise; Ruete, Alejandro

    2016-01-01

    The collation of citizen science data in open-access biodiversity databases makes temporally and spatially extensive species' observation data available to a wide range of users. Such data are an invaluable resource but contain inherent limitations, such as sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. Any technical assessment, monitoring program or scientific research applying citizen science data should therefore include an evaluation of the uncertainty of its results. We use 'ignorance' scores, i.e. spatially explicit indices of sampling bias across a study region, to further understand spatial patterns of observation behaviour for 13 reference taxonomic groups. The data is based on voluntary observations made in Sweden between 2000 and 2014. We compared the effect of six geographical variables (elevation, steepness, population density, log population density, road density and footpath density) on the ignorance scores of each group. We found substantial variation among taxonomic groups in the relative importance of different geographic variables for explaining ignorance scores. In general, road access and logged population density were consistently important variables explaining bias in sampling effort, indicating that access at a landscape-scale facilitates voluntary reporting by citizen scientists. Also, small increases in population density can produce a substantial reduction in ignorance score. However the between-taxa variation in the importance of geographic variables for explaining ignorance scores demonstrated that different taxa suffer from different spatial biases. We suggest that conservationists and researchers should use ignorance scores to acknowledge uncertainty in their analyses and conclusions, because they may simultaneously include many correlated variables that are difficult to disentangle. PMID:26820846

  8. Regional differences in seasonal timing of rainfall discriminate between genetically distinct East African giraffe taxa.

    PubMed

    Thomassen, Henri A; Freedman, Adam H; Brown, David M; Buermann, Wolfgang; Jacobs, David K

    2013-01-01

    Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated

  9. Diurnal variation in airborne pollen concentrations of the selected taxa in Zagreb, Croatia.

    PubMed

    Toth, Ivan; Peternel, Renata; Srnec, Lidija; Vojniković, Bozo

    2011-09-01

    The number of individuals allergic to plant pollen has recently been on a constant increase. The knowledge of diurnal distribution and abundance of allergenic pollen types, their patterns and response to source position and weather is useful to correlate hay fever symptoms with the presence of allergenic pollen in the atmosphere. The aim of this study was to determine diurnal distribution of total airborne pollen, pollen of particular allergenic taxa, possible variation in diurnal pollen distribution at measuring sites placed at different heights, and effect of some meteorological parameters on airborne pollen concentrations. A 7-day Hirst-type volumetric pollen trap was used for pollen sampling. Qualitative and quantitative pollen analysis was performed under a light microscope (magnification x400). Total pollen of all plant taxa (Ambrosia sp., Betula sp., Cupressaceae, Urticaceae, Poaceae, Quercus sp., Fraxinus sp., Alnus sp., Corylus sp., Populus sp., Pinus sp., Picea sp.) observed showed a regular diurnal distribution at both sampling sites in both study years, with a rise in the pollen concentration recorded after 4.00 a.m. and 6.00 a.m., respectively. The peak pollen concentration occurred between 12.00 a.m. and 4.00 p.m., and the lowest diurnal pollen concentrations were recorded overnight. About 50% of the 24-h pollen concentration were released to the atmosphere between 10.00 a.m. and 4.00 p.m. The timing and size of diurnal peaks were closely related to high temperature, low humidity and south-west maximum wind direction. PMID:22220402

  10. Taxas de eventos para as fontes astrofísicas do detector Mario Schenberg

    NASA Astrophysics Data System (ADS)

    Castro, C. S.; Araujo, J. C. N.; Miranda, O. D.; Aguiar, O. D.

    2003-08-01

    O detector de ondas gravitacionais Mario Schenberg será sensível a sinais que cheguem à Terra com amplitude h~10-21 e dentro da faixa em frequências que varia de 3,0 a 3,4 kHz. As principais fontes astrofísicas em condições de gerar um sinal detectável pela antena Schenberg são: colapsos estelares que produzam eventos do tipo supernova; instabilidades hidrodinâmicas em estrelas de nêutrons; excitação dos modos fluído (modos f) de estrelas de nêutrons; excitação dos primeiros modos quadrupolares de buracos negros com massa ~ 3,8 M¤; coalescências de estrelas de nêutrons e buracos negros em sistemas binários e, ainda, espiralações de mini-buracos negros. Neste trabalho nós determinamos as taxas de eventos para o Schenberg associadas a dois tipos de fontes: através da de-excitação dos modos f de estrelas de nêutrons e através da coalescência de mini-buracos negros de 0,5 M¤ (que atualmente têm sido colocados como possíveis candidatos a objetos massivos do halo Galáctico). Nós mostramos que esses tipos de fontes poderão produzir sinais em ondas gravitacionais com uma taxa em torno de um evento por ano dentro da banda do Schenberg.

  11. Spatial Patterns of Parrotfish Corallivory in the Caribbean: The Importance of Coral Taxa, Density and Size

    PubMed Central

    Roff, George; Ledlie, Mary H.; Ortiz, Juan C.; Mumby, Peter J.

    2011-01-01

    The past few decades have seen an increase in the frequency and intensity of disturbance on coral reefs, resulting in shifts in size and composition of coral populations. These changes have lead to a renewed focus on processes that influence demographic rates in corals, such as corallivory. While previous research indicates selective corallivory among coral taxa, the importance of coral size and the density of coral colonies in influencing corallivory are unknown. We surveyed the size, taxonomy and number of bites by parrotfish per colony of corals and the abundance of three main corallivorous parrotfish (Sparisoma viride, Sparisoma aurofrenatum, Scarus vetula) at multiple spatial scales (reefs within islands: 1–100 km, and between islands: >100 km) within the Bahamas Archipelago. We used a linear mixed model to determine the influence of coral taxa, colony size, colony density, and parrotfish abundance on the intensity of corallivory (bites per m2 of coral tissue). While the effect of colony density was significant in determining the intensity of corallivory, we found no significant influence of colony size or parrotfish abundance (density, biomass or community structure). Parrotfish bites were most frequently observed on the dominant species of reef building corals (Montastraea annularis, Montastraea faveolata and Porites astreoides), yet our results indicate that when the confounding effects of colony density and size were removed, selective corallivory existed only for the less dominant Porites porites. As changes in disturbance regimes result in the decline of dominant frame-work building corals such as Montastraea spp., the projected success of P. porites on Caribbean reefs through high reproductive output, resistance to disease and rapid growth rates may be attenuated through selective corallivory by parrotfish. PMID:22216184

  12. Systematics of the family Plectopylidae in Vietnam with additional information on Chinese taxa (Gastropoda, Pulmonata, Stylommatophora)

    PubMed Central

    Páll-Gergely, Barna; Hunyadi, András; Ablett, Jonathan; Lương, Hào Văn; Fred Naggs; Asami, Takahiro

    2015-01-01

    Abstract Vietnamese species from the family Plectopylidae are revised based on the type specimens of all known taxa, more than 600 historical non-type museum lots, and almost 200 newly-collected samples. Altogether more than 7000 specimens were investigated. The revision has revealed that species diversity of the Vietnamese Plectopylidae was previously overestimated. Overall, thirteen species names (anterides Gude, 1909, bavayi Gude, 1901, congesta Gude, 1898, fallax Gude, 1909, gouldingi Gude, 1909, hirsuta Möllendorff, 1901, jovia Mabille, 1887, moellendorffi Gude, 1901, persimilis Gude, 1901, pilsbryana Gude, 1901, soror Gude, 1908, tenuis Gude, 1901, verecunda Gude, 1909) were synonymised with other species. In addition to these, Gudeodiscus hemmeni sp. n. and Gudeodiscus messageri raheemi ssp. n. are described from north-western Vietnam. Sixteen species and two subspecies are recognized from Vietnam. The reproductive anatomy of eight taxa is described. Based on anatomical information, Halongella gen. n. is erected to include Plectopylis schlumbergeri and Plectopylis fruhstorferi. Additionally, the genus Gudeodiscus is subdivided into two subgenera (Gudeodiscus and Veludiscus subgen. n.) on the basis of the morphology of the reproductive anatomy and the radula. The Chinese Gudeodiscus phlyarius werneri Páll-Gergely, 2013 is moved to synonymy of Gudeodiscus phlyarius. A spermatophore was found in the organ situated next to the gametolytic sac in one specimen. This suggests that this organ in the Plectopylidae is a diverticulum. Statistically significant evidence is presented for the presence of calcareous hook-like granules inside the penis being associated with the absence of embryos in the uterus in four genera. This suggests that these probably play a role in mating periods before disappearing when embryos develop. Sicradiscus mansuyi is reported from China for the first time. PMID:25632253

  13. Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume.

    PubMed

    Kleindienst, Sara; Grim, Sharon; Sogin, Mitchell; Bracco, Annalisa; Crespo-Medina, Melitza; Joye, Samantha B

    2016-02-01

    The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico's deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas, oil and dispersant biodegradation in the wake of oil spills. Here, we document a previously unrecognized diversity of closely related taxa affiliating with Cycloclasticus, Colwellia and Oceanospirillaceae and describe their spatio-temporal distribution in the Gulf's deepwater, in close proximity to the discharge site and at increasing distance from it, before, during and after the discharge. A highly sensitive, computational method (oligotyping) applied to a data set generated from 454-tag pyrosequencing of bacterial 16S ribosomal RNA gene V4-V6 regions, enabled the detection of population dynamics at the sub-operational taxonomic unit level (0.2% sequence similarity). The biogeochemical signature of the deep-sea samples was assessed via total cell counts, concentrations of short-chain alkanes (C1-C5), nutrients, (colored) dissolved organic and inorganic carbon, as well as methane oxidation rates. Statistical analysis elucidated environmental factors that shaped ecologically relevant dynamics of oligotypes, which likely represent distinct ecotypes. Major hydrocarbon degraders, adapted to the slow-diffusive natural hydrocarbon seepage in the Gulf of Mexico, appeared unable to cope with the conditions encountered during the DWH spill or were outcompeted. In contrast, diverse, rare taxa increased rapidly in abundance, underscoring the importance of specialized sub-populations and potential ecotypes during massive deep-sea oil discharges and perhaps other large-scale perturbations. PMID:26230048

  14. Physiological and ecological performance differs in four coral taxa at a volcanic carbon dioxide seep.

    PubMed

    Strahl, J; Stolz, I; Uthicke, S; Vogel, N; Noonan, S H C; Fabricius, K E

    2015-06-01

    Around volcanic carbon dioxide (CO2) seeps in Papua New Guinea, partial pressures of CO2 (pCO2) approximate those as predicted for the end of this century, and coral communities have low diversity and low structural complexity. To assess the mechanisms for such community shifts in response to ocean acidification, we examined the physiological performance of two hard corals that occur with increased or unaltered abundance at a seep site (mean pHTotal=7.8, pCO2=862 μatm) compared to a control site (mean pHTotal=8.1, pCO2=323 μatm), namely massive Porites spp. and Pocillopora damicornis, and two species with reduced abundance, Acropora millepora and Seriatopora hystrix. Oxygen fluxes, calcification, and skeletal densities were analyzed in corals originating from the seep and control site. Net photosynthesis rates increased considerably in Porites spp. and A. millepora and slightly in P. damicornis at increased pCO2, but remained unaltered in S. hystrix. Dark respiration rates remained constant in all corals investigated from both sites. Rates of light calcification declined in S. hystrix at high pCO2, but were unaffected by pCO2 in the other three coral taxa. Dark and net calcification rates remained unchanged in massive Porites and P. damicornis, but were drastically reduced at high pCO2 in A. millepora and S. hystrix. However, skeletal densities were similar at both seep and control sites in all coral taxa investigated. Our data suggest that the pCO2-tolerant corals were characterized by an increased ability to acclimatize to ocean acidification, e.g. by maintaining net calcification. Thus, robust corals, such as Porites spp. and P. damicornis, are more likely to persist for longer in a future high pCO2 world than those unable to acclimatize. PMID:25727938

  15. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

    PubMed Central

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-01-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29–30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75–87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome. PMID:26953601

  16. Regional Differences in Seasonal Timing of Rainfall Discriminate between Genetically Distinct East African Giraffe Taxa

    PubMed Central

    Thomassen, Henri A.; Freedman, Adam H.; Brown, David M.; Buermann, Wolfgang; Jacobs, David K.

    2013-01-01

    Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated

  17. Explaining Spatial Variation in the Recording Effort of Citizen Science Data across Multiple Taxa

    PubMed Central

    Mair, Louise; Ruete, Alejandro

    2016-01-01

    The collation of citizen science data in open-access biodiversity databases makes temporally and spatially extensive species’ observation data available to a wide range of users. Such data are an invaluable resource but contain inherent limitations, such as sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. Any technical assessment, monitoring program or scientific research applying citizen science data should therefore include an evaluation of the uncertainty of its results. We use ‘ignorance’ scores, i.e. spatially explicit indices of sampling bias across a study region, to further understand spatial patterns of observation behaviour for 13 reference taxonomic groups. The data is based on voluntary observations made in Sweden between 2000 and 2014. We compared the effect of six geographical variables (elevation, steepness, population density, log population density, road density and footpath density) on the ignorance scores of each group. We found substantial variation among taxonomic groups in the relative importance of different geographic variables for explaining ignorance scores. In general, road access and logged population density were consistently important variables explaining bias in sampling effort, indicating that access at a landscape-scale facilitates voluntary reporting by citizen scientists. Also, small increases in population density can produce a substantial reduction in ignorance score. However the between-taxa variation in the importance of geographic variables for explaining ignorance scores demonstrated that different taxa suffer from different spatial biases. We suggest that conservationists and researchers should use ignorance scores to acknowledge uncertainty in their analyses and conclusions, because they may simultaneously include many correlated variables that are difficult to disentangle. PMID:26820846

  18. Cellular differentiation and individuality in the “minor” multicellular taxa

    PubMed Central

    Herron, Matthew D.; Rashidi, Armin; Shelton, Deborah E.; Driscoll, William W.

    2014-01-01

    Biology needs a concept of individuality in order to distinguish organisms from parts of organisms and from groups of organisms, to count individuals and compare traits across taxa, and to distinguish growth from reproduction. Most of the proposed criteria for individuality were designed for ‘unitary’ or ‘paradigm’ organisms: contiguous, functionally and physiologically integrated, obligately sexually reproducing multicellular organisms with a germ line sequestered early in development. However, the vast majority of the diversity of life on Earth does not conform to all of these criteria. We consider the issue of individuality in the ‘minor’ multicellular taxa, which collectively span a large portion of the eukaryotic tree of life, reviewing their general features and focusing on a model species for each group. When the criteria designed for unitary organisms are applied to other groups, they often give conflicting answers or no answer at all to the question of whether or not a given unit is an individual. Complex life cycles, intimate bacterial symbioses, aggregative development, and strange genetic features complicate the picture. The great age of some of the groups considered shows that ‘intermediate’ forms, those with some but not all of the traits traditionally associated with individuality, cannot reasonably be considered ephemeral or assumed transitional. We discuss a handful of recent attempts to reconcile the many proposed criteria for individuality and to provide criteria that can be applied across all the domains of life. Finally, we argue that individuality should be defined without reference to any particular taxon and that understanding the emergence of new kinds of individuals requires recognizing individuality as a matter of degree. PMID:23448295

  19. Nitrogen Inputs via Nitrogen Fixation in Northern Plants and Soils

    NASA Astrophysics Data System (ADS)

    Thorp, N. R.; Wieder, R. K.; Vile, M. A.

    2015-12-01

    Dominated by cold and often acidic water logged environments, mineralization of organic matter is slow in the majority of northern ecosystems. Measures of extractable ammonium and nitrate are generally low and can be undetectable in peat pore waters. Despite this apparent nitrogen limitation, many of these environments produce deep deposits of soil organic matter. Biological nitrogen fixation carried out by autotrophic and heterotrophic diazotrophs associated with cryptograms provides the majority of known nitrogen inputs in these northern ecosystems. Nitrogen fixation was assessed in a variety of northern soils within rhizospheres of dominant plant communities. We investigated the availability of this newly fixed nitrogen to the vascular plant community in nitrogen limited northern plant communities. We tracked nitrogen flow from 15N2 gas fixed in Sphagnum mosses into tissues of two native vascular plant species, boreal cranberry (Vaccinium oxycoccus) and black spruce (Picea mariana). 15N-labeled Sphagnum microcosms were grown within variable mesh size exclusion/inclusion fabrics in a nitrogen addition experiment in situ in order to investigate the role of mycorrhizal fungi in the uptake of newly fixed nitrogen. Up to 24% of daily fixed 15N label was transferred to vascular plant tissues during 2 months. Nitrogen addition resulted in decreased N2 fixation rates; however, with higher nitrogen availability there was a higher rate of 15N label uptake into the vascular plants, likely the result of increased production of dissolved organic nitrogen. Reliance on mycorrhizal networks for nitrogen acquisition was indicated by nitrogen isotope fractionation patterns. Moreover, N2 fixation activities in mosses were stimulated when vascular plants were grown in moss microcosms versus "moss only" treatments. Results indicate that bog vascular plants may derive considerable nitrogen from atmospheric N2 biologically fixed within Sphagnum mosses. This work demonstrates that

  20. The nitrogen cycle: Atmosphere interactions

    NASA Technical Reports Server (NTRS)

    Levine, J. S.

    1984-01-01

    Atmospheric interactions involving the nitrogen species are varied and complex. These interactions include photochemical reactions, initiated by the absorption of solar photons and chemical kinetic reactions, which involve both homogeneous (gas-to-gas reactions) and heterogeneous (gas-to-particle) reactions. Another important atmospheric interaction is the production of nitrogen oxides by atmospheric lightning. The nitrogen cycle strongly couples the biosphere and atmosphere. Many nitrogen species are produced by biogenic processes. Once in the atmosphere nitrogen oxides are photochemically and chemically transformed to nitrates, which are returned to the biosphere via precipitation, dry deposition and aerosols to close the biosphere-atmosphere nitrogen cycle. The sources, sinks and photochemistry/chemistry of the nitrogen species; atmospheric nitrogen species; souces and sinks of nitrous oxide; sources; sinks and photochemistry/chemistry of ammonia; seasonal variation of the vertical distribution of ammonia in the troposphere; surface and atmospheric sources of the nitrogen species, and seasonal variation of ground level ammonia are summarized.

  1. Arginine and nitrogen storage.

    PubMed

    Llácer, José L; Fita, Ignacio; Rubio, Vicente

    2008-12-01

    When nitrogen is abundant, prokaryotic and eukaryotic oxygen-producing photosynthetic organisms store nitrogen as arginine, by relieving feedback inhibition of the arginine biosynthesis controlling enzyme, N-acetylglutamate kinase (NAGK). The signalling protein PII, an ancient and widely distributed nitrogen/carbon/ADP/ATP sensor, mediates feedback inhibition relief of NAGK by binding to this enzyme. PII phosphorylation or PII binding of ADP or 2-oxoglutarate prevents PII-NAGK complex formation. Crystal structures of NAGK, cyanobacterial and plant PII and corresponding PII-NAGK complexes have been recently determined. In these complexes, two polar PII trimers sandwich one ring-like NAGK hexamer. Each PII subunit contacts one NAGK subunit, triggering a symmetry-restricted narrowing of the NAGK ring, with concomitant adoption by the arginine sites of a low-affinity conformation. PMID:19013524

  2. The Global Nitrogen Story

    NASA Astrophysics Data System (ADS)

    Galloway, J. N.

    2001-05-01

    In the absence of human activities, biotic nitrogen fixation is the primary source of reactive N to the environment. Over the last few decades, human activity has surpassed natural terrestrial nitrogen fixation rates by energy production (fossil fuel combustion) and food production (Haber-Bosch based fertilizer production and crop cultivation). An amount equivalent to over half of the anthropogenic N fixed each year is emitted to the atmosphere or discharged to rivers, for dispersion to environmental systems. An unknown amount of this anthropogenic N is accumulating in the environment resulting in a enhanced greenhouse effect, acid deposition, photochemical smog, stratospheric ozone depletion and eutrophication of fresh and marine waters. This paper will assess the state of knowledge on the global N cycle and present a context in which to place the impacts of humans on nitrogen cycling at regional scales.

  3. A taxa summary for the Simulium damnosum complex, with special reference to distribution outside the control areas of West Africa.

    PubMed

    Crosskey, R W

    1987-04-01

    A synoptic list is provided of currently recognized taxa in the Simulium damnosum complex, with an indication of their geographical distributions. Outline maps are given for the distribution of S. damnosum sensu lato, and for the West African cytospecies of the complex. Short reports on the identities and distributions of member taxa are given for countries other than those of the Onchocerciasis Control Programme in the Volta River Basin (OCP) and its Senegambia Extension; these are mainly based on collation of published and unpublished data for the post-1976 period (since the last WHO Expert Committee Report on Onchocerciasis). PMID:3689026

  4. Reliability and refinement of the higher taxa approach for bee richness and composition assessments.

    PubMed

    Rijn, Itai Van; Neeson, Thomas M; Mandelik, Yael

    2015-01-01

    Limited resources and taxonomic expertise in biodiversity surveys often lead to the application of the higher taxa approach (HTA),i.e., the identification of specimens to genus or higher taxonomic levels rather than to species. The reliability of the HTA varies significantly among studies, yet the factors underlying this variability have rarely been investigated. Bees are an ideal model taxon for testing the HTA because they are highly diverse, challenging to identify, and there is widespread interest in their role as native pollinators, driving demand for efficient diversity assessment tools. Using extensive bee data sets collected across three biomes and various habitats, we assessed the performance of the HTA in reflecting bee species richness and composition patterns at local scales, factors affecting this performance, and ways to improve it. The performance of the HTA varied considerably among biomes, taxonomic levels (genera and subfamilies), and diversity measures (species richness and composition); genus and subfamily richness accounted for 55-77% and 32-61% of the variation in species richness, respectively; genus and subfamily composition accounted for 28-87% and 26-80% of the variation in species composition, respectively. The number of species per higher taxon was a main factor influencing this performance (accounting for 63% of the variation), while the co-occurrence of taxonomically related species had no significant influence on the performance of the HTA. Further subdividing genera by body size contributed to the performance of the HTA and increased its accuracy in representation of compositional patterns by ~16%. Our results have several practical implications. The considerable variability found in the performance of the HTA in representing local-scale richness and composition patterns of bee species dictates caution in implementing this tool in bee surveys. When possible, an a priori evaluation of the expected performance of the HTA should be done

  5. A cross-taxa phenological dataset from Mohonk Lake, NY and its relationship to climate

    NASA Astrophysics Data System (ADS)

    Cook, B. I.; Cook, E. R.; Huth, P. C.; Thompson, J. E.; Forster, A.; Smiley, D.

    2007-12-01

    We present a detailed analysis of a rare cross-taxa native species phenology dataset (plant flowering, insect first sighting, and amphibian first sighting) from Mohonk Lake, NY. This dataset is highly unusual in North America for its longevity of record, consistency of methodology and location, diversity of species available, and availability of local daily meteorological data. For each phenology series, we examined the flowering and first sighting Julian calendar dates for the existence of temporal trends. Only one of the five animal species (katydid) showed any evidence for a significant trend in first sighting. In contrast, the plant species showed a rich mixture of temporal trends in flowering that could be divided into four classes: woody plant (no trend), woody plant (negative trend), herbaceous plant (negative trend), and herbaceous plant (positive trend). Many of the trends were found to be statistically significant and robust to the method of trend estimation. The data within each of the four plant classes were also pooled as anomalies to provide more complete temporal coverage for tests of trend robustness. The results were strongly consistent with the individual species trends within each class and highly significant statistically. We next correlated the flowering and first sighting dates against growing degree-day (GDD) summations for each day of the year to measure the sensitivity of each species to this common form of climatic forcing on phenology. All species showed a significant sensitivity to GDD summations, with peak correlations falling on or near the varying median flowering or first sighting dates. These results were robust whether the GDD analyses were conducted over the complete set of observations for each species (beginning on or after 1928) or over a latter period with a more serially complete set of cross-taxa observations (1970-2002). The GDD correlations indicate significant climate sensitivity in all species, but the different

  6. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility

    PubMed Central

    Raji, Adebola AJ; Anderson, James V; Kolade, Olufisayo A; Ugwu, Chike D; Dixon, Alfred GO; Ingelbrecht, Ivan L

    2009-01-01

    Background Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. Results A total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. Conclusion A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification

  7. Biodiversity Risks from Atmospheric Nitrogen Deposition in California

    NASA Astrophysics Data System (ADS)

    Weiss, S. B.

    2004-12-01

    Atmospheric nitrogen deposition alters structure and function of terrestrial ecosystems, because nitrogen availability is often limits overall productivity. These alterations can drive losses of biodiversity, as nitrophilous species increase in abundance and outcompete species adapted to more oligotrophic conditions. California is recognized as a "biodiversity hotspot," with a high fraction of endemic taxa with narrow ranges. A state-wide risk screening includes: 1) a 36 x 36 km map of total N-deposition for 2002, developed from the Community Multiscale Air Quality Model (CMAQ); 2) identification of sensitive habitat types from literature and local expertise; 3) overlay of a statewide vegetation map (FRAP); 4) overlay of species occurrence data from the California Natural Diversity Data Base (CNDDB); and 5)species life-history and habitat requirements. The CMAQ model indicates that 55,000 km2 (total area 405,205 km2) are exposed to >5 kg-N ha -1 year -1, and 10,000 km2 are exposed to >10 kg-N ha -1 year -1. Deposition hotspots include coastal urban areas (Los Angeles-San Diego, and the San Francisco Bay Area), the agricultural Central Valley, and parts of the Sierra Nevada foothills. The major known impact of N-deposition in California is increased growth and dominance of invasive annual grasses in low biomass ecosystems, such as coastal sage scrub, serpentine grassland, desert scrub, and vernal pools. For example, 800 km2 out of a total 6300 km2 of coastal sage scrub are exposed to more than 10 kg-N ha -1 year -1, primarily in Southern California. Of 225 federal and state "Threatened" and "Endangered" plant taxa, 101 are exposed on average to >5 kg-N ha -1 year -1. Of an additional 1022 plant taxa listed as "rare," 288 are exposed to >5 kg-N ha -1 year -1. Many of these highly exposed taxa are associated with sensitive habitat types and are vulnerable to annual grass invasions. This broad-scale screening outlines potential impacts on California's biodiversity, and

  8. Nitrogen Trading Tool (NTT)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Natural Resources Conservation Service (NRCS) recently developed a prototype web-based nitrogen trading tool to facilitate water quality credit trading. The development team has worked closely with the Agriculture Research Service Soil Plant Nutrient Research Unit (ARS-SPNR) and the Environmenta...

  9. The Global Nitrogen Cycle

    NASA Astrophysics Data System (ADS)

    Galloway, J. N.

    2003-12-01

    Once upon a time nitrogen did not exist. Today it does. In the intervening time the universe was formed, nitrogen was created, the Earth came into existence, and its atmosphere and oceans were formed! In this analysis of the Earth's nitrogen cycle, I start with an overview of these important events relative to nitrogen and then move on to the more traditional analysis of the nitrogen cycle itself and the role of humans in its alteration.The universe is ˜15 Gyr old. Even after its formation, there was still a period when nitrogen did not exist. It took ˜300 thousand years after the big bang for the Universe to cool enough to create atoms; hydrogen and helium formed first. Nitrogen was formed in the stars through the process of nucleosynthesis. When a star's helium mass becomes great enough to reach the necessary pressure and temperature, helium begins to fuse into still heavier elements, including nitrogen.Approximately 10 Gyr elapsed before Earth was formed (˜4.5 Ga (billion years ago)) by the accumulation of pre-assembled materials in a multistage process. Assuming that N2 was the predominate nitrogen species in these materials and given that the temperature of space is -270 °C, N2 was probably a solid when the Earth was formed since its boiling point (b.p.) and melting point (m.p.) are -196 °C and -210 °C, respectively. Towards the end of the accumulation period, temperatures were probably high enough for significant melting of some of the accumulated material. The volcanic gases emitted by the resulting volcanism strongly influenced the surface environment. Nitrogen was converted from a solid to a gas and emitted as N2. Carbon and sulfur were probably emitted as CO and H2S (Holland, 1984). N2 is still the most common nitrogen volcanic gas emitted today at a rate of ˜2 TgN yr-1 (Jaffee, 1992).Once emitted, the gases either remained in the atmosphere or were deposited to the Earth's surface, thus continuing the process of biogeochemical cycling. The rate of

  10. The nitrogen cascade

    SciTech Connect

    Galloway J.N.; Aber J.D.; Erisman J.W.; Seitzinger S.P.; Howarth R.W.; Cowling E.B.; Cosby B.J.

    2003-04-01

    Human production of food and energy is the dominant continental process that breaks the triple bond in molecular nitrogen (N{sub 2}) and creates reactive nitrogen (Nr) species. Circulation of anthropogenic Nr in Earth's atmosphere, hydrosphere, and biosphere has a wide variety of consequences, which are magnified with time as Nr moves along its biogeochemical pathway. The same atom of Nr can cause multiple effects in the atmosphere, in terrestrial ecosystems, in freshwater and marine systems, and on human health. We call this sequence of effects the nitrogen cascade. As the cascade progresses, the origin of Nr becomes unimportant. Reactive nitrogen does not cascade at the same rate through all environmental systems; some systems have the ability to accumulate Nr, which leads to lag times in the continuation of the cascade. These lags slow the cascade and result in Nr accumulation in certain reservoirs, which in turn can enhance the effects of Nr on that environment. The only way to eliminate Nr accumulation and stop the cascade is to convert Nr back to nonreactive N{sub 2}.

  11. Soil and fertilizer nitrogen

    SciTech Connect

    Winteringham, F.P.W.

    1985-01-01

    This book describes a study of plant nutrition and environmental protection, and also discusses soil nitrogen in relation to agriculture, forestry, the environment and conservation. It also includes the Summary Report on the Final Meeting of the FAO/IAEA/GSF.

  12. California Nitrogen Index

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The California N Index User Manual is designed to help you become accustomed to the software environment in which the N Index runs. This manual will use an example scenario to demonstrate how to use the N Index to assess nitrogen losses. The objective of this theoretical example is to guide you towa...

  13. Nitrogen catch crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High costs of nitrogen (N) fertilizer and the potential for N losses to ground and surface water have resulted in increased interest in using catch crops to recover this N. Research on potatoes has shown that the amount of N lost to leaching can be as much as the amount of N removed from the field ...

  14. Nitrogen in chondritic metal

    NASA Astrophysics Data System (ADS)

    Mathew, K. J.; Marti, K.; Kim, Y.

    2005-02-01

    We report new nitrogen isotopic data in metals of H-, L- and one LL -chondrites, with N abundances in the range of ˜0.3 to 3.3 ppm and half of these <1 ppm. Nitrogen isotopic signatures in metals with low indigenous N concentrations are modified by cosmic ray spallation components; corrections are required to determine the indigenous N signatures. The metals of type 4 and 5 show uniform indigenous nitrogen (δ 15N = -6.8 ± 0.5 ‰) and confirm a reported possible genetic association of chondritic metal with metal in IIE and IVA iron meteorites. Distinct isotopic signatures are observed in two metal samples of the Portales Valley (H6) meteorite which both are inconsistent with signatures in H4 and H5 chondrites, but possibly reveal a record of impact-induced melting and metamorphism on the parent asteroid. Anomalous nitrogen signatures in metals of type 3 chondrites, on the other hand, may reflect residues of surviving presolar isotopic signatures.

  15. Ruminant nitrogen usage

    SciTech Connect

    Not Available

    1985-01-01

    This book brings together the latest research on protein absorption by ruminants and takes a look at the calculation of optimum nutrient requirements, including bacterial digestion, in the calculations. It also describes the parameters of nitrogen conversion in the ruminant and examines the different kinds of protein found in animal feedstuffs.

  16. ODD NITROGEN PROCESSES

    SciTech Connect

    Johnston, Harold S.

    1980-01-01

    This chapter is in three parts. The first concerns interpretations that can be made from atmospheric observations regarding nitrogen compounds and ozone, the second reviews some predictions made by atmospheric models, and the third compares between certain model results and atmospheric measurements with an emphasis on detecting evidence of significant disagreements.

  17. Simple life-history traits explain key effective population size ratios across diverse taxa

    PubMed Central

    Waples, Robin S.; Luikart, Gordon; Faulkner, James R.; Tallmon, David A.

    2013-01-01

    Effective population size (Ne) controls both the rate of random genetic drift and the effectiveness of selection and migration, but it is difficult to estimate in nature. In particular, for species with overlapping generations, it is easier to estimate the effective number of breeders in one reproductive cycle (Nb) than Ne per generation. We empirically evaluated the relationship between life history and ratios of Ne, Nb and adult census size (N) using a recently developed model (agene) and published vital rates for 63 iteroparous animals and plants. Nb/Ne varied a surprising sixfold across species and, contrary to expectations, Nb was larger than Ne in over half the species. Up to two-thirds of the variance in Nb/Ne and up to half the variance in Ne/N was explained by just two life-history traits (age at maturity and adult lifespan) that have long interested both ecologists and evolutionary biologists. These results provide novel insights into, and demonstrate a close general linkage between, demographic and evolutionary processes across diverse taxa. For the first time, our results also make it possible to interpret rapidly accumulating estimates of Nb in the context of the rich body of evolutionary theory based on Ne per generation. PMID:23926150

  18. Convergent evolution of cucurbitacin feeding in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini).

    PubMed

    Gillespie, Joseph J; Kjer, Karl M; Duckett, Catherine N; Tallamy, Douglas W

    2003-10-01

    Historically, chemical ecologists assumed that cucurbitacin feeding and sequestration in rootworm leaf beetles is a remnant of an ancient association between the Luperini (Coleoptera: Chrysomelidae; Galerucinae) and Cucurbitaceae (ancestral host hypothesis). Under this premise, rootworms that do not develop on cucurbits but undergo pharmacophagous forays for cucurbitacins are thought to do so to supplement novel host diets that lack these bitter compounds. The ancestral host hypothesis is supported from studies of pyrrolizidine alkaloid pharmacophagy in Lepidoptera but has not been subjected to phylogenetic analysis within the Luperini. New evidence that this feeding behavior is better correlated with an adult affinity for pollen than with larval host offers the possibility that Old and New World rootworm species with an affinity for cucurbitacins converged on this behavior through apomorphic taste receptor modifications (loose receptor hypothesis). Here we test the monophyly of cucurbitacin feeding within the Luperini by using nuclear and mitochondrial sequence data to infer phylogenetic relationships among 49 taxa representing tribes of the Galerucinae and subtribes of the Luperini. The resulting phylogenetic hypothesis is mostly concordant with existing tribal and subtribal delineations within the Subfamily Galerucinae sensu stricto (Galerucinae not including the flea beetles). The establishment of ancestry among the subtribes of the Luperini refutes the monophyly of cucurbitacin feeding and cucurbit specialization, with the New World Diabroticina being paraphyletic to the Old World Aulacophorina and cosmopolitan Luperina. These data unambiguously support the convergent evolution of cucurbitacin feeding in rootworms and are inconsistent with the ancestral host hypothesis. PMID:12967617

  19. Assessment of the antioxidant potential and fatty acid composition of four Centaurea L. taxa from Turkey.

    PubMed

    Aktumsek, Abdurrahman; Zengin, Gokhan; Guler, Gokalp Ozmen; Cakmak, Yavuz Selim; Duran, Ahmet

    2013-11-01

    This paper focused on the assessment of antioxidant property and fatty acid composition of four Centaurea species. The antioxidant activity of its methanol extract was evaluated by several in vitro experiments including phosphomolybedum assay, DPPH assay, β-carotene/linoleic acid, ferric and cupric reducing power. Total phenolic and flavonoid contents were also evaluated. The methanol extract of Centaurea pulcherrima var. pulcherrima showed the superior free radical scavenging activity, linoleic acid inhibition capacity, reducing power and also had the highest total phenolic content. A significant relationship between antioxidant capacity and total phenolic components was found. The oils of Centaurea taxa were also analysed for fatty acid concentration by gas chromatography. The principal fatty acids in the species were palmitic acid (23.38-30.49%) and linoleic acid (20.19-29.93%). These findings suggest that the Centaurea species could be used as a potential source of new natural antioxidants and unsaturated fatty acids in food industry, cosmetics and pharmaceutical preparations. PMID:23768332

  20. Multi-taxa integrated landscape genetics for zoonotic infectious diseases: deciphering variables influencing disease emergence.

    PubMed

    Leo, Sarah S T; Gonzalez, Andrew; Millien, Virginie

    2016-05-01

    Zoonotic disease transmission systems involve sets of species interacting with each other and their environment. This complexity impedes development of disease monitoring and control programs that require reliable identification of spatial and biotic variables and mechanisms facilitating disease emergence. To overcome this difficulty, we propose a framework that simultaneously examines all species involved in disease emergence by integrating concepts and methods from population genetics, landscape ecology, and spatial statistics. Multi-taxa integrated landscape genetics (MTILG) can reveal how interspecific interactions and landscape variables influence disease emergence patterns. We test the potential of our MTILG-based framework by modelling the emergence of a disease system across multiple species dispersal, interspecific interaction, and landscape scenarios. Our simulations showed that both interspecific-dependent dispersal patterns and landscape characteristics significantly influenced disease spread. Using our framework, we were able to detect statistically similar inter-population genetic differences and highly correlated spatial genetic patterns that imply species-dependent dispersal. Additionally, species that were assigned coupled-dispersal patterns were affected to the same degree by similar landscape variables. This study underlines the importance of an integrated approach to investigating emergence of disease systems. MTILG is a robust approach for such studies and can identify potential avenues for targeted disease management strategies. PMID:27074898

  1. [Regularities of the ubiquitous polyhostal microorganisms selection by the example of three taxa].

    PubMed

    Voronina, O L; Kunda, M S; Ryzhova, N N; Aksenova, E I; Semenov, A N; Kurnaeva, M A; Ananyina, Yu V; Lunin, V G; Gintsburg, A L

    2015-01-01

    The investigation of the bacterial populations' heterogeneity contributes to the control of natural foci, causative agents of nosocomial infections, to the analysis of the microbial evolution. Multilocus sequence typing (MLST) was employed for the analysis of the diversity and features of the distribution of polyhostal ubiquitous microorganisms of the genera Burkholderia, Leptospira, and Listeria, which belong to three bacterial phyla: Proteobacteria, Spirochaetes, and Firmicutes. According to the bacterial samples analysis microbial genotypes prevalent and unique to Russia were identified; their occurrence in different Federal Regions was investigated; their similarity with global spread genotypes was appreciated. Obtained results allowed identifying common regularities of the selection of the microorganisms capable to cause the diseases of human and animals. The formation of genotypes that are most pathogenic for the host was demonstrated for all groups of bacteria. Leptospira spp. and Listeria monocytogenes strains with these genotypes have been circulating for a long time, being supported by natural foci. The formation of a wide variety of genotypes with different pathogenicity was demonstrated in the local geographic areas. In Russia, the zonal difference in all three groups of bacteria is most clearly traced to the Far Eastern Federal Region. The results are thought to contribute to analyzing the factors of selection and the phylogeny of the taxa under study. PMID:26107896

  2. Distribution of Mytilus taxa in European coastal areas as inferred from molecular markers

    NASA Astrophysics Data System (ADS)

    Kijewski, T.; Śmietanka, B.; Zbawicka, M.; Gosling, E.; Hummel, H.; Wenne, R.

    2011-02-01

    The genetic constitution of mussels ( Mytilus spp.) was studied by means of three nuclear (Me 15/16, EF-bis, ITS) and one mtDNA (ND2-COIII) marker on a large European scale. In addition to a sharp cline between Atlantic and Mediterranean M. galloprovincialis, we observed a clear genetic distinction between the Black Sea and Mediterranean populations and a higher incidence of M. trossulus than reported so far in northern European populations. The frequency of M. galloprovincialis nuclear alleles was high along the Iberian Peninsula and decreased abruptly along the French coasts with a high frequency of M. edulis alleles in the Bay of Biscay, The Netherlands, Germany, Iceland, Barents and White Seas, and with little evidence of introgression between the two taxa. M. trossulus alleles were observed in the Baltic Sea and Danish Straits as expected. In addition, occurrence of M. trossulus alleles in cold waters of Iceland, Barents Sea and White Sea is reported for the first time.

  3. I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation

    PubMed Central

    Mooers, Arne Ø.; Caccone, Adalgisa; Russello, Michael A.

    2016-01-01

    In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization.

  4. Ecological structuring of bacterial and archaeal taxa in surface ocean waters.

    PubMed

    Yilmaz, Pelin; Iversen, Morten H; Hankeln, Wolfgang; Kottmann, Renzo; Quast, Christian; Glöckner, Frank O

    2012-08-01

    The Global Ocean Sampling (GOS) expedition is currently the largest and geographically most comprehensive metagenomic dataset, including samples from the Atlantic, Pacific, and Indian Oceans. This study makes use of the wide range of environmental conditions and habitats encompassed within the GOS sites in order to investigate the ecological structuring of bacterial and archaeal taxon ranks. Community structures based on taxonomically classified 16S ribosomal RNA (rRNA) gene fragments at phylum, class, order, family, and genus rank levels were examined using multivariate statistical analysis, and the results were inspected in the context of oceanographic environmental variables and structured habitat classifications. At all taxon rank levels, community structures of neritic, oceanic, estuarine biomes, as well as other exotic biomes (salt marsh, lake, mangrove), were readily distinguishable from each other. A strong structuring of the communities with chlorophyll a concentration and a weaker yet significant structuring with temperature and salinity were observed. Furthermore, there were significant correlations between community structures and habitat classification. These results were used for further investigation of one-to-one relationships between taxa and environment and provided indications for ecological preferences shaped by primary production for both cultured and uncultured bacterial and archaeal clades. PMID:22416918

  5. Brachiopod taxa and shell portions reliably recording past ocean environments: Toward establishing a robust paleoceanographic proxy

    NASA Astrophysics Data System (ADS)

    Yamamoto, Kazuyuki; Asami, Ryuji; Iryu, Yasufumi

    2011-07-01

    Fossils of rhynchonelliform brachiopods (marine invertebrates) constitute ˜70% of the samples used for delineating a well-known Phanerozoic trend in oxygen isotope composition (δ18O) of low-Mg calcite shells. The trend represents secular variations in temperature and/or δ18O of ancient seawater. However, the use of brachiopods as a paleoceanographic proxy is based on the presupposition that the shell calcite is precipitated in isotopic equilibrium with ambient seawater. Here, we show that high-resolution time series of the shell δ18O values along the maximum growth axes of two long-lived cool-water brachiopods are identical to, greater than, or less than those of calcite precipitated in isotopic equilibrium with ambient seawater, depending on the difference in shell growth rates. Coupled with δ18O data from subtropical and warm-temperate brachiopod species examined in our previous studies, we provide a sound framework illustrating which taxa and shell portions reliably recorded past ocean environments.

  6. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    PubMed

    Mou, Xiaozhen; Lu, Xinxin; Jacob, Jisha; Sun, Shulei; Heath, Robert

    2013-01-01

    Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems. PMID:23637924

  7. Modelling the presence and identifying the determinant factors of dominant macroinvertebrate taxa in a karst river.

    PubMed

    Lin, Yuqing; Chen, Qiuwen; Chen, Kai; Yang, Qingrui

    2016-06-01

    Modelling the macroinvertebrate community is important for evaluating the status of aquatic ecosystem health. Alternative to physical-based approaches, this study proposed two data-driven methods, support vector machine (SVM) and artificial neural network (ANN), to model the presence of macroinvertebrate species in rivers based on abiotic features. A famous karst river, Lijiang River, in Southwest China was selected as the study case. A total of 300 records containing data on 11 physicochemical parameters were collected from the upstream, midstream and downstream reaches of the river over a 2-year period (2009-2010) and were used for model construction and verification. Ten dominant macroinvertebrate taxa in the study area were modelled. In addition, the performance of the two methods was compared, and the relative importance of the independent variables was identified. The obtained results mapped abiotic factors to the species presence and could be used in combination with a two-dimensional hydro-environmental model to assess the impacts of flow regulation on macroinvertebrate dynamics. Furthermore, the SVM model performed slightly better than the ANN model in the studied case. PMID:27138003

  8. Campylobacter concisus utilizes blood but not short chain fatty acids despite showing associations with Firmicutes taxa.

    PubMed

    Kaakoush, Nadeem O; Thomas, Donald S; Ruzayqat, Mahmoud M; Lynch, David; Leach, Steven T; Lemberg, Daniel A; Day, Andrew S; Mitchell, Hazel M

    2016-08-01

    Campylobacter concisus is a member of the oral microbiota that has been associated with the development of inflammatory bowel diseases. However, the role of the bacterium in disease aetiology remains poorly understood. Here, we examine optimal conditions for the growth of C. concisus, and the pathogenic potential of this bacterium in human gastrointestinal cells from the upper tract. Further, the presence of C. concisus in the lower tract of Crohn's disease (CD) patients undergoing therapy is observed, and the associations of C. concisus with the abundance of other microbial taxa and compounds they produce are evaluated. C. concisus strains had the ability to tolerate moderate levels of acidity, adhere to and invade esophageal and gastric cells; however, these properties did not correlate with their pathogenic potential in intestinal cells. The presence of the bacterium in the lower gut of CD patients was associated with an increased relative abundance of Faecalibacterium and Lachnospiraceae incertae sedis. Short chain fatty acids that can be produced by these microbial species did not appear to be responsible for this association. However, we identified genetic similarity between C. concisus and Firmicutes, specifically within aspartate and glutamate racemases. The potential pathogenesis of C. concisus in the upper gastrointestinal tract, and the responsiveness of the bacterium to therapy in a subset of CD patients warrant further investigation into whether this bacterium has a causal role in disease or its presence is incidental. PMID:27339421

  9. Aerobiological study in east-central Iberian Peninsula: pollen diversity and dynamics for major taxa.

    PubMed

    Pérez-Badia, Rosa; Rapp, Ana; Vaquero, Consolación; Fernández-González, Federico

    2011-01-01

    A study was made of airborne pollen counts in Cuenca (east-central Iberian Peninsula, Spain), using data obtained over a 3-year period (2008-2010). This is the first such study carried out in the World Heritage city of Cuenca, situated in the large region of Castilla-La Mancha. Air monitoring was performed using the sampling and analysis procedures recommended by the Spanish Aerobiology Network. Sampling commenced in mid- 2007, and provided the first recorded pollen-spectrum for the area. The greatest pollen-type diversity was recorded in spring, whilst the highest pollen counts (over 80 percent of the annual total) were observed between February and June. The lowest counts were found in September, November and December. The 10 leading taxa, in order of abundance, were: Cupressaceae, Quercus, Urticaceae, Pinus, Olea, Poaceae, Populus, Platanus, Chenopodiaceae-Amaranthaceae and Plantago. The pollen calendar was thus typically Mediterrean, and comprised the 27 pollen types reaching 10-day mean counts of over 1 grain/m(3) of air. Maximum concentration values during the day were recorded between 12:00-20:00, coinciding with the highest temperatures and lowest humidity levels. The pollen types responsible for most allergies in the city of Cuenca, ordered by the number of days on which risk levels were reached, were: Poaceae, Urticaceae, Cupressaceae, Olea, Platanus and Chenopodiaceae-Amaranthaceae. PMID:21736275

  10. Wolbachia distribution in selected beetle taxa characterized by PCR screens and MLST data.

    PubMed

    Sontowski, Rebekka; Bernhard, Detlef; Bleidorn, Christoph; Schlegel, Martin; Gerth, Michael

    2015-10-01

    Wolbachia (Alphaproteobacteria) is an inherited endosymbiont of arthropods and filarial nematodes and was reported to be widespread across insect taxa. While Wolbachia's effects on host biology are not understood from most of these hosts, known Wolbachia-induced phenotypes cover a spectrum from obligate beneficial mutualism to reproductive manipulations and pathogenicity. Interestingly, data on Wolbachia within the most species-rich order of arthropods, the Coleoptera (beetles), are scarce. Therefore, we screened 128 species from seven beetle families (Buprestidae, Hydraenidae, Dytiscidae, Hydrophilidae, Gyrinidae, Haliplidae, and Noteridae) for the presence of Wolbachia. Our data show that, contrary to previous estimations, Wolbachia frequencies in beetles (31% overall) are comparable to the ones in other insects. In addition, we used Wolbachia MLST data and host phylogeny to explore the evolutionary history of Wolbachia strains from Hydraenidae, an aquatic lineage of beetles. Our data suggest that Wolbachia from Hydraenidae might be largely host genus specific and that Wolbachia strain phylogeny is not independent to that of its hosts. As this contrasts with most terrestrial Wolbachia-arthropod systems, one potential conclusion is that aquatic lifestyle of hosts may result in Wolbachia distribution patterns distinct from those of terrestrial hosts. Our data thus provide both insights into Wolbachia distribution among beetles in general and a first glimpse of Wolbachia distribution patterns among aquatic host lineages. PMID:26664683

  11. Impacts of invasive plants on resident animals across ecosystems, taxa, and feeding types: a global assessment.

    PubMed

    Schirmel, Jens; Bundschuh, Mirco; Entling, Martin H; Kowarik, Ingo; Buchholz, Sascha

    2016-02-01

    As drivers of global change, biological invasions have fundamental ecological consequences. However, it remains unclear how invasive plant effects on resident animals vary across ecosystems, animal classes, and functional groups. We performed a comprehensive meta-analysis covering 198 field and laboratory studies reporting a total of 3624 observations of invasive plant effects on animals. Invasive plants had reducing (56%) or neutral (44%) effects on animal abundance, diversity, fitness, and ecosystem function across different ecosystems, animal classes, and feeding types while we could not find any increasing effect. Most importantly, we found that invasive plants reduced overall animal abundance, diversity and fitness. However, this significant overall effect was contingent on ecosystems, taxa, and feeding types of animals. Decreasing effects of invasive plants were most evident in riparian ecosystems, possibly because frequent disturbance facilitates more intense plant invasions compared to other ecosystem types. In accordance with their immediate reliance on plants for food, invasive plant effects were strongest on herbivores. Regarding taxonomic groups, birds and insects were most strongly affected. In insects, this may be explained by their high frequency of herbivory, while birds demonstrate that invasive plant effects can also cascade up to secondary consumers. Since data on impacts of invasive plants are rather limited for many animal groups in most ecosystems, we argue for overcoming gaps in knowledge and for a more differentiated discussion on effects of invasive plant on native fauna. PMID:26390918

  12. Firmicutes dominate the bacterial taxa within sugar-cane processing plants

    PubMed Central

    Sharmin, Farhana; Wakelin, Steve; Huygens, Flavia; Hargreaves, Megan

    2013-01-01

    Sugar cane processing sites are characterised by high sugar/hemicellulose levels, available moisture and warm conditions, and are relatively unexplored unique microbial environments. The PhyloChip microarray was used to investigate bacterial diversity and community composition in three Australian sugar cane processing plants. These ecosystems were highly complex and dominated by four main Phyla, Firmicutes (the most dominant), followed by Proteobacteria, Bacteroidetes, and Chloroflexi. Significant variation (p < 0.05) in community structure occurred between samples collected from ‘floor dump sediment’, ‘cooling tower water’, and ‘bagasse leachate’. Many bacterial Classes contributed to these differences, however most were of low numerical abundance. Separation in community composition was also linked to Classes of Firmicutes, particularly Bacillales, Lactobacillales and Clostridiales, whose dominance is likely to be linked to their physiology as ‘lactic acid bacteria’, capable of fermenting the sugars present. This process may help displace other bacterial taxa, providing a competitive advantage for Firmicutes bacteria. PMID:24177592

  13. Metagenomic Identification of Bacterioplankton Taxa and Pathways Involved in Microcystin Degradation in Lake Erie

    PubMed Central

    Mou, Xiaozhen; Lu, Xinxin; Jacob, Jisha; Sun, Shulei; Heath, Robert

    2013-01-01

    Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems. PMID:23637924

  14. Multiple taxa in the Phoma-complex associate with black elder (Sambucus nigra L.).

    PubMed

    Walter, Hildrun; Muggia, Lucia; Fritscher, Michael; Holler, Alessandro; Horvat, Deborah; Guttenberger, Helmut; Simon, Uwe K

    2016-01-01

    The fungus Boeremia sambuci-nigrae (formerly Phoma sambuci-nigrae) causes the corymb wilt disease in elder (Sambucus nigra L.). Here, we assessed the genetic diversity of fungi within the Phoma-complex which associate with commercially cultivated elder in Styria (Austria). We sampled leaves, corymb stalks and berries of elder trees in one organically and in four conventionally managed orchards. In each orchard an area was left untreated allowing a sampling of fungicide treated and untreated trees. Nineteen taxa in the Phoma-complex were isolated and identified based on ITS and LSU nucDNA sequences. One isolate is closely related to Chaetosphaeronema, whereas the majority of the strains belong to the genera Epicoccum and Boeremia in Didymellaceae. Six isolates are monophyletic with Boeremia sambuci-nigrae. The results indicate a varying effectiveness of fungicide treatment for the different fungal groups investigated. The diverse distribution of isolates among the sampling sites suggests the influence of treatment effects and possibly also of climatic conditions. PMID:26693683

  15. Understanding lichenicolous heterobasidiomycetes: new taxa and reproductive innovations in Tremella s.l.

    PubMed

    Zamora, Juan Carlos; Millanes, Ana María; Wedin, Mats; Rico, Víctor J; Pérez-Ortega, Sergio

    2016-01-01

    Four new lichenicolous Tremella species are described and characterized morphologically and molecularly. Tremella celata grows on Ramalina fraxinea, inducing the formation of inconspicuous galls, and having hyphae with incomplete clamps. Tremella endosporogena develops intrahymenially in the apothecia of Lecanora carpinea, having single-celled basidia and clampless hyphae. Tremella diederichiana is the name proposed for a species micromorphologically close to T. christiansenii but inducing the formation of small, pale galls on the thallus and apothecia of Lecidea aff. erythrophaea Tremella variae grows on Lecanora varia thallus, instead of on the apothecia, as do the other known Tremella species parasitizing Lecanora s.l. Phylogenetic relationships and host specificity of these species are investigated and compared with other taxa that show morphological resemblances, phylogenetic affinities or similar hosts. The formation of mitotic conidia inside old basidia (endospores), which is a poorly known reproductive strategy in the Basidiomycota, is also a distinctive character of Tremella endosporogena A discussion on the reproductive role and systematic implications of endospores is included. PMID:27127212

  16. Phylogenetic overview of the genus Genea (Pezizales, Ascomycota) with an emphasis on European taxa.

    PubMed

    Alvarado, Pablo; Cabero, Julio; Moreno, Gabriel; Bratek, Zoltán; van Vooren, Nicolas; Kaounas, Vasileios; Konstantinidis, Giorgos; Agnello, Carlo; Merényi, Zsolt; Smith, Matthew E; Vizzini, Alfredo; Trappe, James M

    2016-01-01

    We constructed a comprehensive phylogeny of the genus Genea, with new molecular data from samples collected in several countries in temperate and Mediterranean Europe, as well as North America. Type specimens and authentic material of most species were examined to support identifications. The molecular identity of the most common species in Genea was compared with nuc rDNA internal transcribed spacer (ITS), D1-D2 domains of 28S nuc rDNA (28S rDNA) and translation elongation factor 1-α ene (TEF1) profiles of 10 recently proposed taxa, G. brunneocarpa, G. compressa, G. dentata, G. fageticola, G. lobulata, G. oxygala, G. pinicola, G. pseudobalsleyi, G. pseudoverrucosa and G. tuberculata, supporting their status as distinct species. Genea mexicana and G. thaxteri on the one hand and G. sphaerica and G. lespiaultii on the other are closely related. Multiple lineages were recorded for G. verrucosa and G. fragrans, but we found no morphological traits to discriminate among them, so we tentatively interpreted them as cryptic species. A key to species of the genus Genea is provided to facilitate identification. We provide macroscopic images of fresh specimens and of representative spores of most species. Finally, we conducted a molecular analysis of the divergence time for Genea and discuss the implications of our results. PMID:26740538

  17. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach.

    PubMed

    Sun, Keping; Meiklejohn, Kelly A; Faircloth, Brant C; Glenn, Travis C; Braun, Edward L; Kimball, Rebecca T

    2014-09-01

    The most striking feature of peafowl (Pavo) is the males' elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera within the Phasianidae (Polyplectron and Argusianus) exhibit ocelli, but the appearance and location of these ornamental eyespots exhibit substantial variation among these genera, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence among genera. However, it remains unclear whether Pavo, Polyplectron and Argusianus form a monophyletic clade in which ocelli evolved once. We estimated the phylogeny of the ocellated species using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The three ocellated genera did form a strongly supported clade, but each ocellated genus was sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were sister genera. The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation. PMID:25030982

  18. The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach

    PubMed Central

    Sun, Keping; Meiklejohn, Kelly A.; Faircloth, Brant C.; Glenn, Travis C.; Braun, Edward L.; Kimball, Rebecca T.

    2014-01-01

    The most striking feature of peafowl (Pavo) is the males' elaborate train, which exhibits ocelli (ornamental eyespots) that are under sexual selection. Two additional genera within the Phasianidae (Polyplectron and Argusianus) exhibit ocelli, but the appearance and location of these ornamental eyespots exhibit substantial variation among these genera, raising the question of whether ocelli are homologous. Within Polyplectron, ocelli are ancestral, suggesting ocelli may have evolved even earlier, prior to the divergence among genera. However, it remains unclear whether Pavo, Polyplectron and Argusianus form a monophyletic clade in which ocelli evolved once. We estimated the phylogeny of the ocellated species using sequences from 1966 ultraconserved elements (UCEs) and three mitochondrial regions. The three ocellated genera did form a strongly supported clade, but each ocellated genus was sister to at least one genus without ocelli. Indeed, Polyplectron and Galloperdix, a genus not previously suggested to be related to any ocellated taxon, were sister genera. The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation. PMID:25030982

  19. The Global Nitrogen Cycle

    NASA Astrophysics Data System (ADS)

    Galloway, J. N.

    2003-12-01

    Once upon a time nitrogen did not exist. Today it does. In the intervening time the universe was formed, nitrogen was created, the Earth came into existence, and its atmosphere and oceans were formed! In this analysis of the Earth's nitrogen cycle, I start with an overview of these important events relative to nitrogen and then move on to the more traditional analysis of the nitrogen cycle itself and the role of humans in its alteration.The universe is ˜15 Gyr old. Even after its formation, there was still a period when nitrogen did not exist. It took ˜300 thousand years after the big bang for the Universe to cool enough to create atoms; hydrogen and helium formed first. Nitrogen was formed in the stars through the process of nucleosynthesis. When a star's helium mass becomes great enough to reach the necessary pressure and temperature, helium begins to fuse into still heavier elements, including nitrogen.Approximately 10 Gyr elapsed before Earth was formed (˜4.5 Ga (billion years ago)) by the accumulation of pre-assembled materials in a multistage process. Assuming that N2 was the predominate nitrogen species in these materials and given that the temperature of space is -270 °C, N2 was probably a solid when the Earth was formed since its boiling point (b.p.) and melting point (m.p.) are -196 °C and -210 °C, respectively. Towards the end of the accumulation period, temperatures were probably high enough for significant melting of some of the accumulated material. The volcanic gases emitted by the resulting volcanism strongly influenced the surface environment. Nitrogen was converted from a solid to a gas and emitted as N2. Carbon and sulfur were probably emitted as CO and H2S (Holland, 1984). N2 is still the most common nitrogen volcanic gas emitted today at a rate of ˜2 TgN yr-1 (Jaffee, 1992).Once emitted, the gases either remained in the atmosphere or were deposited to the Earth's surface, thus continuing the process of biogeochemical cycling. The rate of

  20. Do the rich get richer? Varying effects of tree species identity and diversity on the richness of understory taxa

    USGS Publications Warehouse

    Champagne, Juilette; Paine, C. E. Timothy; Schoolmaster, Donald; Stejskal, Robert; Volařík, Daniel; Šebesta, Jan; Trnka, Filip; Koutecký, Tomáš; Švarc, Petr; Svátek, Martin; Hector, Andy; Matula, Radim

    2016-01-01

    Understory herbs and soil invertebrates play key roles in soil formation and nutrient cycling in forests. Studies suggest that diversity in the canopy and in the understory are positively associated, but these studies often confound the effects of tree species diversity with those of tree species identity and abiotic conditions. We combined extensive field sampling with structural equation modeling to evaluate the simultaneous effects of tree diversity on the species diversity of understory herbs, beetles, and earthworms. The diversity of earthworms and saproxylic beetles was directly and positively associated with tree diversity, presumably because species of both these taxa specialize on certain species of trees. Tree identity also strongly affected diversity in the understory, especially for herbs, likely as a result of interspecific differences in canopy light transmittance or litter decomposition rates. Our results suggest that changes in forest management will disproportionately affect certain understory taxa. For instance, changes in canopy diversity will affect the diversity of earthworms and saproxylic beetles more than changes in tree species composition, whereas the converse would be expected for understory herbs and detritivorous beetles. We conclude that the effects of tree diversity on understory taxa can vary from positive to negative and may affect biogeochemical cycling in temperate forests. Thus, maintaining high diversity in temperate forests can promote the diversity of multiple taxa in the understory.

  1. The roles of Lazarus taxa and refugia through the Ordovician-Silurian transition: data from the Brachiopoda

    NASA Astrophysics Data System (ADS)

    Rong, J.-Y.; Boucot, A. J.; Harper, D. A.; Zhan, R.-B.; Neuman, R. B.

    2003-04-01

    Global analyses of nearly 90 families and 275 genera of brachiopods from the middle Ashgill through the Hirnantian (Ordovician) to the lower-middle Rhuddanian (Silurian) suggest that about 60% and 40% of the total number of genera were eliminated at the first and second phases of the end Ordovician extinction event, respectively. Among the 85 surviving genera, about 50 with declining and 10 with proliferating abundances are known from the Hirnantian together with about 20 provisional Lazarus taxa. The Lazarus taxa are essentially survivors and form the extremity of the declining genera. The distributions of declining genera and relicts during the crisis interval shows a random and sporadic pattern, suggesting there was no single, common refugium for end Ordovician brachiopods. In addition to their biological attributes, a markedly decreased population size together with taphonomic failure and poor preservation, and collecting bias have contributed towards the distributional trends apparent during the event. The development of declining genera during the extinction may be linked to their palaeogeographical setting, the phylogenetic history of the taxa, and the ambient environmental conditions. This new global database has significantly reduced the number of Lazarus taxa and minimizes the number of possible locations for collective refugia during the end Ordovician crisis. Nevertheless, the atrypids, athyridids, pentamerids, and spiriferids had more limited distributions during the crisis interval but formed the locus for a Silurian diversification of the phylum into carbonate environments possibly around the Rhuddanian-Aeronian boundary.

  2. Taxa-area relationship and neutral dynamics influence the diversity of fungal communities on senesced tree leaves.

    PubMed

    Feinstein, Larry M; Blackwood, Christopher B

    2012-06-01

    This study utilized individual senesced sugar maple and beech leaves as natural sampling units within which to quantify saprotrophic fungal diversity. Quantifying communities in individual leaves allowed us to determine if fungi display a classic taxa-area relationship (species richness increasing with area). We found a significant taxa-area relationship for sugar maple leaves, but not beech leaves, consistent with Wright's species-energy theory. This suggests that energy availability as affected plant biochemistry is a key factor regulating the scaling relationships of fungal diversity. We also compared taxa rank abundance distributions to models associated with niche or neutral theories of community assembly, and tested the influence of leaf type as an environmental niche factor controlling fungal community composition. Among rank abundance distribution models, the zero-sum model derived from neutral theory showed the best fit to our data. Leaf type explained only 5% of the variability in community composition. Habitat (vernal pool, upland or riparian forest floor) and site of collection explained > 40%, but could be attributed to either niche or neutral processes. Hence, although niche dynamics may regulate fungal communities at the habitat scale, our evidence points towards neutral assembly of saprotrophic fungi on individual leaves, with energy availability constraining the taxa-area relationship. PMID:22489632

  3. Chemical and principal-component analyses of the essential oils of Apioideae taxa (Apiaceae) from central Balkan.

    PubMed

    Kapetanos, Chrysostomos; Karioti, Anastasia; Bojović, Srdjan; Marin, Petar; Veljić, Milan; Skaltsa, Helen

    2008-01-01

    The volatile constituents of the essential oils of 23 taxa belonging to the Apioideae subfamily were studied in detail. The investigated taxa were Pimpinella serbica (Vis.) Bentham & Hooker, Libanotis montana Cr., Cnidium silaifolium (Jacq.) Simk. ssp. orientale (Boiss.) Tutin, Bupleurum praealtum L., B. sibthorpianum S. S. var. diversifolium (Roch.) Hay, Aegopodium podagraria L., Torilis anthriscus (L.) Gmel., Orlaya grandiflora (L.) Hoffm., Laserpitium siler L., Laser trilobum (L.) Brokh., Chaerophyllum aureum L., C. hirsutum L., C. temulum L., Pastinaca sativa L., P. hirsuta Pancic., Tordylium maximum L., Physospermum cornubiense (L.) DC., Peucedanum alsaticum L., P. oreoselinum (L.) Moench, P. cervaria (L.) Cuss., P. austriacum (Jacq.) Koch, P. longifolium W. et K., and P. officinale L. All of these species grow wild in the central part of the Balkan Peninsula. The essential oils were found to be complex mixtures of various compounds, more than 100 constituents being in each taxon, with contributions of main products never exceeding 25% of the total content. Sesquiterpene hydrocarbons were found to be the main group of constituents of all taxa, except for Peucedanum species, where monoterpene hydrocarbons were identified as the main components. The chemotaxonomic value of the essential-oil composition is discussed according to results of principal-component analysis (PCA). The essential-oil composition mainly reflects current taxonomic relationships between the investigated taxa. PMID:18205131

  4. Soil sand content can alter effects of different taxa of mycorrhizal fungi on plant biomass production of grassland species

    PubMed Central

    Zaller, Johann G.; Frank, Thomas; Drapela, Thomas

    2011-01-01

    In this greenhouse experiment we tested whether (i) ubiquitous arbuscular mycorrhizal fungi (AMF) taxa (Glomus claroideum, Glomus geosporum, Glomus intraradices, Glomus mosseae) singly and in a mixture differently affect growth and biomass production of four co-occurring grassland species (grass: Arrhenatherum elatius, non-leguminous forbs: Plantago lanceolata, Salvia pratensis and leguminous forb Trifolium pratense), and (ii) different soil sand contents alter AMF influence. We hypothesized that AMF effects on plants will increase with an increased AMF diversity and with increasing sand content. Percent AMF colonization of roots differed between plant species and AMF taxa and was higher with higher sand content. Plant growth responses to AMF were species-specific both regarding plants and AMF. Generally, biomass production of the non-leguminous forbs was the most responsive, the grass species the least and the legume intermediate both for AMF treatments and sand content. Across species, AMF influence on plant biomass increased with increasing soil sand content. Plant species growing in soil containing a mix of four AMF taxa showed similar growth responses than species in soil containing only one AMF taxon. These results suggest that both interference among AMF taxa and soil sand content can trigger the influence of AMF on plant production in grassland species. PMID:26109837

  5. Selection of Nontarget Arthropod Taxa for Field Research on Transgenic Insecticidal Crops: Using Empirical Data and Statistical Power

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One of the possible adverse effects of transgenic insecticidal crops is the unintended decline in the abundance of nontarget arthropods. Field trials designed to evaluate potential nontarget effects can be more complex than expected because decisions to conduct field trials and the selection of taxa...

  6. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

    PubMed Central

    Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C.; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A.G.; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J.M.; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H. Thorsten; Schmull, Michaela; Schoch, Conrad; Sérusiaux, Emmanuël; Maddison, David R.; Arnold, A. Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-01-01

    The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed

  7. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

    PubMed

    Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A G; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J M; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H Thorsten; Schmull, Michaela; Schoch, Conrad L; Sérusiaux, Emmanuël; Maddison, David R; Arnold, A Elizabeth; Lutzoni, François; Stenroos, Soili

    2014-10-01

    The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed

  8. Aqueous phase removal of nitrogen from nitrogen compounds

    DOEpatents

    Fassbender, Alex G.

    1993-01-01

    A method is disclosed for denitrification of compounds containing nitrogen present in aqueous waste streams. The method comprises the steps of (1) identifying the types of nitrogen compounds present in a waste stream, (2) determining the concentrations of nitrogen compounds, (3) balancing oxidized and reduced form of nitrogen by adding a reactant, and (4) heating the mixture to a predetermined reaction temperature from about 300.degree. C. to about 600.degree. C., thereby resulting in less harmful nitrogen and oxygen gas, hydroxides, alcohols, and hydrocarbons.

  9. The nitrogen and sulphur cycles

    SciTech Connect

    Cole, J.A.; Ferguson, S.J.

    1988-01-01

    This book contains 17 selections. Some of the titles are: Genetic regulation of nitrogen fixation; On the analysis of symbiotic genes of Rhizobium; Regulation of nitrogen assimilation by bacteria; Alternative and conventional nitrogenases; and The role of oxygen and hydrogen in nitrogen fixation.

  10. PERSONAL MONITOR FOR NITROGEN DIOXIDE

    EPA Science Inventory

    An attempt was made to develop a personal monitor to measure nitrogen dioxide. Sampling of nitrogen dioxide is accomplished by permeation through a silicone membrane into a alkaline thymol blue solution. The nitrogen dioxide is converted to nitrite and is then quantitated by colo...

  11. Bacteria and the Nitrogen Economy.

    ERIC Educational Resources Information Center

    Ayanaba, A.

    1982-01-01

    Biological nitrogen fixation accounts for almost 70 percent of nitrogen for plant growth. If food is to keep abreast of population growth, even more nitrogen must be fixed. For this international research institutes continue the search for natural variants in the bacterial population while also pursuing novel genetic engineering methods. (Author)

  12. The Ophiostoma clavatum species complex: a newly defined group in the Ophiostomatales including three novel taxa.

    PubMed

    Linnakoski, Riikka; Jankowiak, Robert; Villari, Caterina; Kirisits, Thomas; Solheim, Halvor; de Beer, Z Wilhelm; Wingfield, Michael J

    2016-07-01

    Two species of blue-stain fungi with similar morphologies, Ophiostoma brunneo-ciliatum and Ophiostoma clavatum, are associates of bark beetles infesting Pinus spp. in Europe. This has raised questions whether they represent distinct taxa. Absence of herbarium specimens and contaminated or mistakenly identified cultures of O. brunneo-ciliatum and O. clavatum have accentuated the uncertainty regarding their correct identification. The aim of this study was to reconsider the identity of European isolates reported as O. brunneo-ciliatum and O. clavatum by applying DNA-based identification methods, and to provide appropriate type specimens for them. Phylogenetic analyses of the ITS, βT, TEF-1α and CAL gene sequences revealed that the investigated isolates represent a complex of seven cryptic species. The study confirmed that ITS data is insufficient to delineate species in some Ophiostoma species clusters. Lectotypes and epitypes were designated for O. clavatum and O. brunneo-ciliatum, and three new species, Ophiostoma brunneolum, Ophiostoma macroclavatum and Ophiostoma pseudocatenulatum, are described in the newly defined O. clavatum-complex. The other two species included in the complex are Ophiostoma ainoae and Ophiostoma tapionis. The results suggest co-evolution of these fungi in association with specific bark beetles. The results also confirm the identity of the fungus associated with the pine bark beetle Ips acuminatus as O. clavatum, while O. brunneo-ciliatum appears to be mainly associated with another pine bark beetle, Ips sexdentatus. PMID:27142088

  13. How territoriality and host-tree taxa determine the structure of ant mosaics

    NASA Astrophysics Data System (ADS)

    Dejean, Alain; Ryder, Suzanne; Bolton, Barry; Compin, Arthur; Leponce, Maurice; Azémar, Frédéric; Céréghino, Régis; Orivel, Jérôme; Corbara, Bruno

    2015-06-01

    Very large colonies of territorially dominant arboreal ants (TDAAs), whose territories are distributed in a mosaic pattern in the canopies of many tropical rainforests and tree crop plantations, have a generally positive impact on their host trees. We studied the canopy of an old Gabonese rainforest (ca 4.25 ha sampled, corresponding to 206 "large" trees) at a stage just preceding forest maturity (the Caesalpinioideae dominated; the Burseraceae were abundant). The tree crowns sheltered colonies from 13 TDAAs plus a co-dominant species out of the 25 ant species recorded. By mapping the TDAAs' territories and using a null model co-occurrence analysis, we confirmed the existence of an ant mosaic. Thanks to a large sampling set and the use of the self-organizing map algorithm (SOM), we show that the distribution of the trees influences the structure of the ant mosaic, suggesting that each tree taxon attracts certain TDAA species rather than others. The SOM also improved our knowledge of the TDAAs' ecological niches, showing that these ant species are ecologically distinct from each other based on their relationships with their supporting trees. Therefore, TDAAs should not systematically be placed in the same functional group even when they belong to the same genus. We conclude by reiterating that, in addition to the role played by TDAAs' territorial competition, host trees contribute to structuring ant mosaics through multiple factors, including host-plant selection by TDAAs, the age of the trees, the presence of extrafloral nectaries, and the taxa of the associated hemipterans.

  14. How territoriality and host-tree taxa determine the structure of ant mosaics.

    PubMed

    Dejean, Alain; Ryder, Suzanne; Bolton, Barry; Compin, Arthur; Leponce, Maurice; Azémar, Frédéric; Céréghino, Régis; Orivel, Jérôme; Corbara, Bruno

    2015-06-01

    Very large colonies of territorially dominant arboreal ants (TDAAs), whose territories are distributed in a mosaic pattern in the canopies of many tropical rainforests and tree crop plantations, have a generally positive impact on their host trees. We studied the canopy of an old Gabonese rainforest (ca 4.25 ha sampled, corresponding to 206 "large" trees) at a stage just preceding forest maturity (the Caesalpinioideae dominated; the Burseraceae were abundant). The tree crowns sheltered colonies from 13 TDAAs plus a co-dominant species out of the 25 ant species recorded. By mapping the TDAAs' territories and using a null model co-occurrence analysis, we confirmed the existence of an ant mosaic. Thanks to a large sampling set and the use of the self-organizing map algorithm (SOM), we show that the distribution of the trees influences the structure of the ant mosaic, suggesting that each tree taxon attracts certain TDAA species rather than others. The SOM also improved our knowledge of the TDAAs' ecological niches, showing that these ant species are ecologically distinct from each other based on their relationships with their supporting trees. Therefore, TDAAs should not systematically be placed in the same functional group even when they belong to the same genus. We conclude by reiterating that, in addition to the role played by TDAAs' territorial competition, host trees contribute to structuring ant mosaics through multiple factors, including host-plant selection by TDAAs, the age of the trees, the presence of extrafloral nectaries, and the taxa of the associated hemipterans. PMID:26004265

  15. DNA taxonomy in morphologically plastic taxa: algorithmic species delimitation in the Boodlea complex (Chlorophyta: Cladophorales).

    PubMed

    Leliaert, Frederik; Verbruggen, Heroen; Wysor, Brian; De Clerck, Olivier

    2009-10-01

    DNA-based taxonomy provides a convenient and reliable tool for species delimitation, especially in organisms in which morphological discrimination is difficult or impossible, such as many algal taxa. A group with a long history of confusing species circumscriptions is the morphologically plastic Boodlea complex, comprising the marine green algal genera Boodlea, Cladophoropsis, Phyllodictyon and Struveopsis. In this study, we elucidate species boundaries in the Boodlea complex by analysing nrDNA internal transcribed spacer sequences from 175 specimens collected from a wide geographical range. Algorithmic methods of sequence-based species delineation were applied, including statistical parsimony network analysis, and a maximum likelihood approach that uses a mixed Yule-coalescent model and detects species boundaries based on differences in branching rates at the level of species and populations. Sequence analyses resulted in the recognition of 13 phylogenetic species, although we failed to detect sharp species boundaries, possibly as a result of incomplete reproductive isolation. We found considerable conflict between traditional and phylogenetic species definitions. Identical morphological forms were distributed in different clades (cryptic diversity), and at the same time most of the phylogenetic species contained a mixture of different morphologies (indicating intraspecific morphological variation). Sampling outside the morphological range of the Boodlea complex revealed that the enigmatic, sponge-associated Cladophoropsis (Spongocladia) vaucheriiformis, also falls within the Boodlea complex. Given the observed evolutionary complexity and nomenclatural problems associated with establishing a Linnaean taxonomy for this group, we propose to discard provisionally the misleading morphospecies and genus names, and refer to clade numbers within a single genus, Boodlea. PMID:19524052

  16. Evaluating green infrastructure in urban environments using a multi-taxa and functional diversity approach.

    PubMed

    Pinho, Pedro; Correia, Otília; Lecoq, Miguel; Munzi, Silvana; Vasconcelos, Sasha; Gonçalves, Paula; Rebelo, Rui; Antunes, Cristina; Silva, Patrícia; Freitas, Catarina; Lopes, Nuno; Santos-Reis, Margarida; Branquinho, Cristina

    2016-05-01

    Forested areas within cities host a large number of species, responsible for many ecosystem services in urban areas. The biodiversity in these areas is influenced by human disturbances such as atmospheric pollution and urban heat island effect. To ameliorate the effects of these factors, an increase in urban green areas is often considered sufficient. However, this approach assumes that all types of green cover have the same importance for species. Our aim was to show that not all forested green areas are equal in importance for species, but that based on a multi-taxa and functional diversity approach it is possible to value green infrastructure in urban environments. After evaluating the diversity of lichens, butterflies and other-arthropods, birds and mammals in 31 Mediterranean urban forests in south-west Europe (Almada, Portugal), bird and lichen functional groups responsive to urbanization were found. A community shift (tolerant species replacing sensitive ones) along the urbanization gradient was found, and this must be considered when using these groups as indicators of the effect of urbanization. Bird and lichen functional groups were then analyzed together with the characteristics of the forests and their surroundings. Our results showed that, contrary to previous assumptions, vegetation density and more importantly the amount of urban areas around the forest (matrix), are more important for biodiversity than forest quantity alone. This indicated that not all types of forested green areas have the same importance for biodiversity. An index of forest functional diversity was then calculated for all sampled forests of the area. This could help decision-makers to improve the management of urban green infrastructures with the goal of increasing functionality and ultimately ecosystem services in urban areas. PMID:26777032

  17. Two Distinct Triatoma dimidiata (Latreille, 1811) Taxa Are Found in Sympatry in Guatemala and Mexico

    PubMed Central

    Moguel, Barbara; Solorzano, Elizabeth; Dumonteil, Eric; Rodas, Antonieta; de la Rua, Nick; Garnica, Roberto; Monroy, Carlota

    2009-01-01

    Approximately 10 million people are infected with Trypanosoma cruzi, the causative agent of Chagas disease, which remains the most serious parasitic disease in the Americas. Most people are infected via triatomine vectors. Transmission has been largely halted in South America in areas with predominantly domestic vectors. However, one of the main Chagas vectors in Mesoamerica, Triatoma dimidiata, poses special challenges to control due to its diversity across its large geographic range (from Mexico into northern South America), and peridomestic and sylvatic populations that repopulate houses following pesticide treatment. Recent evidence suggests T. dimidiata may be a complex of species, perhaps including cryptic species; taxonomic ambiguity which confounds control. The nuclear sequence of the internal transcribed spacer 2 (ITS2) of the ribosomal DNA and the mitochondrial cytochrome b (mt cyt b) gene were used to analyze the taxonomy of T. dimidiata from southern Mexico throughout Central America. ITS2 sequence divides T. dimidiata into four taxa. The first three are found mostly localized to specific geographic regions with some overlap: (1) southern Mexico and Guatemala (Group 2); (2) Guatemala, Honduras, El Salvador, Nicaragua, and Costa Rica (Group 1A); (3) and Panama (Group 1B). We extend ITS2 Group 1A south into Costa Rica, Group 2 into southern Guatemala and show the first information on isolates in Belize, identifying Groups 2 and 3 in that country. The fourth group (Group 3), a potential cryptic species, is dispersed across parts of Mexico, Guatemala, and Belize. We show it exists in sympatry with other groups in Peten, Guatemala, and Yucatan, Mexico. Mitochondrial cyt b data supports this putative cryptic species in sympatry with others. However, unlike the clear distinction of the remaining groups by ITS2, the remaining groups are not separated by mt cyt b. This work contributes to an understanding of the taxonomy and population subdivision of T

  18. Aciduric microbial taxa including Scardovia wiggsiae and Bifidobacterium spp. in caries and caries free subjects.

    PubMed

    Henne, Karsten; Rheinberg, Anke; Melzer-Krick, Beate; Conrads, Georg

    2015-10-01

    Actinobacteria came into focus of being potential caries-associated pathogens and could, together with the established Streptococcus mutans and lactobacilli thus function as caries indicator species. Here we analyzed the role and diagnostic predictive value of the acidogenic-aciduric species Scardovia wiggsiae and Bifidobacterium dentium together with S. mutans, lactobacilli and bifidobacteria in biofilm of non-cavitated (n = 20) and cavitated (n = 6) caries lesions versus controls (n = 30). For the genus Bifidobacterium and for B. dentium new sets of primers were designed. Based on real-time quantitative PCR and confirmed by DNA sequencing we found a higher prevalence (61.5%) of S. wiggsiae in caries lesions than in controls (40%). However, among the controls we found three individuals with both the highest absolute and relative S. wiggsiae numbers. Testing for S. mutans revealed the same prevalence as S. wiggsiae in caries lesions (61.5%) but in controls its prevalence was only 10%. B. dentium was never found in healthy plaque but in 30.8% of clinical cases, with the highest numbers in cavitated lesions. The Bifidobacterium-genus specific PCR had less discriminative power as more control samples were positive. We calculated the relative abundances and applied receiver operating characteristic analyses. The top results of specificity (93% and 87%) and sensitivity (100% and 88%) were found when the constraint set was "Lactobacillus relative abundance ≥0.02%" and "two aciduric species with a relative abundance of each ≥0.007%". Combinatory measurement of several aciduric taxa may be useful to reveal caries activity or even to predict caries progression. PMID:25933689

  19. Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa.

    PubMed

    Webster, N S; Negri, A P; Flores, F; Humphrey, C; Soo, R; Botté, E S; Vogel, N; Uthicke, S

    2013-04-01

    Microorganisms form symbiotic partnerships with a diverse range of marine organisms and can be critical to the health and survival of their hosts. Despite the importance of these relationships, the sensitivity of symbiotic microbes to ocean acidification (OA) is largely unknown and this needs to be redressed to adequately predict marine ecosystem resilience in a changing climate. We adopted a profiling approach to explore the sensitivity of microbes associated with coral reef biofilms and representatives of three ecologically important calcifying invertebrate phyla [corals, foraminifera and crustose coralline algae (CCA)] to OA. The experimental design for this study comprised four pHs consistent with current IPCC predictions for the next few centuries (pHNIST 8.1, 7.9, 7.7, 7.5); these pH/pCO₂ conditions were produced in flow-through aquaria using CO₂ bubbling. All reduced pH/increased pCO₂ treatments caused clear differences in the microbial communities associated with coral, foraminifera, CCA and reef biofilms over 6 weeks, while no visible signs of host stress were detected over this period. The microbial communities of coral, foraminifera, CCA and biofilms were significantly different between pH 8.1 (pCO₂ = 464 μatm) and pH 7.9 (pCO₂ = 822 μatm), a concentration likely to be exceeded by the end of the present century. This trend continued at lower pHs/higher pCO₂. 16S rRNA gene sequencing revealed variable and species-specific changes in the microbial communities with no microbial taxa consistently present or absent from specific pH treatments. The high sensitivity of coral, foraminifera, CCA and biofilm microbes to OA conditions projected to occur by 2100 is a concern for reef ecosystems and highlights the need for urgent research to assess the implications of microbial shifts for host health and coral reef processes. PMID:23584968

  20. Reproductive biology and species geographical distribution in the Melastomataceae: a survey based on New World taxa

    PubMed Central

    dos Santos, Ana Paula Milla; Fracasso, Carla Magioni; Luciene dos Santos, Mirley; Romero, Rosana; Sazima, Marlies; Oliveira, Paulo Eugênio

    2012-01-01

    Background and Aims Apomictic plants are less dependent on pollinator services and able to occupy more diverse habitats than sexual species. However, such assumptions are based on temperate species, and comparable evaluation for species-rich Neotropical taxa is lacking. In this context, the Melastomataceae is a predominantly Neotropical angiosperm family with many apomictic species, which is common in the Campos Rupestres, endemism-rich vegetation on rocky outcrops in central Brazil. In this study, the breeding system of some Campo Rupestre Melastomataceae was evaluated, and breeding system studies for New World species were surveyed to test the hypothesis that apomixis is associated with wide distributions, whilst sexual species have more restricted areas. Methods The breeding systems of 20 Campo Rupestre Melastomataceae were studied using hand pollinations and pollen-tube growth analysis. In addition, breeding system information was compiled for 124 New World species of Melastomataceae with either wide (>1000 km) or restricted distributions. Key Results Most (80 %) of the Campo Rupestre species studied were self-compatible. Self-incompatibility in Microlicia viminalis was associated with pollen-tube arrest in the style, as described for other Melastomataceae, but most self-incompatible species analysed showed pollen-tube growth to the ovary irrespective of pollination treatment. Apomictic species showed lower pollen viability and were less frequent among the Campo Rupestre plants. Among the New World species compiled, 43 were apomictic and 77 sexual (24 self-incompatible and 53 self-compatible). Most apomictic (86 %) and self-incompatible species (71 %) presented wide distributions, whilst restricted distributions predominate only among the self-compatible ones (53 %). Conclusions Self-compatibility and dependence on biotic pollination were characteristic of Campo Rupestre and narrowly distributed New World Melastomataceae species, whilst apomictics are widely

  1. Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata.

    PubMed

    Kartzinel, Rebecca Y; Spalink, Daniel; Waller, Donald M; Givnish, Thomas J

    2016-05-01

    The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self-fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterized SNP variation in 128 individuals in southern Wisconsin to assess within- and among-population variation at 3928 SNPs. We also assessed genotype and leaf morphology in an additional 76 individuals to connect phenotypic variation with genetic variation. Genetic variation maps onto three strongly divergent and highly inbred genetic groups showing little relation to site location. Each group has a distinct phenotype, but the divergence of these groups differs from the varietal divisions previously identified based on morphological characters. Like previous authors, we argue that the taxonomy of this species should be revised. Despite extensive sympatry, estimates of among-group migration rates are low, and hybrid individuals were at low frequency (<2%) in our dataset. Restricted gene flow likely results from high selfing rates and partial reproductive incompatibility as evidenced by the U-shaped distribution of pairwise F ST values reflecting "islands" of genomic divergence. These islands may be associated with hybrid incompatibility loci that arose in allopatry. The coexistence of lineages within sites may reflect density-dependent attack by species-specific strains of pathogenic fungi and/or root-nodulating bacteria specializing on distinct genotypes. PMID:27103991

  2. Solar nitrogen: evidence for a secular increase in the ratio of nitrogen-15 to nitrogen-14.

    PubMed

    Kerridge, J F

    1975-04-11

    Solar wind nitrogen, implanted in lunar soil samples, exhibits isotopic variations that are related to the time, although not to the duration, of implantation, with earlier samples characterized by lower ratios of nitrogen-15 to nitrogen-14. An increase in the solar nitrogen-15 content during the lifetime of the lunar regolith is probably caused by spallation of oxygen-16 in the surface regions of the sun. PMID:17813736

  3. Methane/nitrogen separation process

    DOEpatents

    Baker, Richard W.; Lokhandwala, Kaaeid A.; Pinnau, Ingo; Segelke, Scott

    1997-01-01

    A membrane separation process for treating a gas stream containing methane and nitrogen, for example, natural gas. The separation process works by preferentially permeating methane and rejecting nitrogen. We have found that the process is able to meet natural gas pipeline specifications for nitrogen, with acceptably small methane loss, so long as the membrane can exhibit a methane/nitrogen selectivity of about 4, 5 or more. This selectivity can be achieved with some rubbery and super-glassy membranes at low temperatures. The process can also be used for separating ethylene from nitrogen.

  4. Methane/nitrogen separation process

    DOEpatents

    Baker, R.W.; Lokhandwala, K.A.; Pinnau, I.; Segelke, S.

    1997-09-23

    A membrane separation process is described for treating a gas stream containing methane and nitrogen, for example, natural gas. The separation process works by preferentially permeating methane and rejecting nitrogen. The authors have found that the process is able to meet natural gas pipeline specifications for nitrogen, with acceptably small methane loss, so long as the membrane can exhibit a methane/nitrogen selectivity of about 4, 5 or more. This selectivity can be achieved with some rubbery and super-glassy membranes at low temperatures. The process can also be used for separating ethylene from nitrogen. 11 figs.

  5. Nitrogen in germanium

    NASA Astrophysics Data System (ADS)

    Chambouleyron, I.; Zanatta, A. R.

    1998-07-01

    The known properties of nitrogen as an impurity in, and as an alloy element of, the germanium network are reviewed in this article. Amorphous and crystalline germanium-nitrogen alloys are interesting materials with potential applications for protective coatings and window layers for solar conversion devices. They may also act as effective diffusion masks for III-V electronic devices. The existing data are compared with similar properties of other group IV nitrides, in particular with silicon nitride. To a certain extent, the general picture mirrors the one found in Si-N systems, as expected from the similar valence structure of both elemental semiconductors. However, important differences appear in the deposition methods and alloy composition, the optical properties of as grown films, and the electrical behavior of nitrogen-doped amorphous layers. Structural studies are reviewed, including band structure calculations and the energies of nitrogen-related defects, which are compared with experimental data. Many important aspects of the electronic structure of Ge-N alloys are not yet completely understood and deserve a more careful investigation, in particular the structure of defects associated with N inclusion. The N doping of the a-Ge:H network appears to be very effective, the activation energy of the most effectively doped samples becoming around 120 meV. This is not the case with N-doped a-Si:H, the reasons for the difference remaining an open question. The lack of data on stoichiometric β-Ge3N4 prevents any reasonable assessment on the possible uses of the alloy in electronic and ceramic applications.

  6. Sealing Nitrogen Tetroxide Leaks

    NASA Technical Reports Server (NTRS)

    Garrard, George G.; Houston, Donald W.; Scott, Frank D.

    1990-01-01

    Use of Furmanite FSC-N-6B sealant in clam-shell sealing device makes it possible to stop leaks of nitrogen tetroxide through defective or improperly-seated plumbing fittings. Devised to stop leaks in vent line of small rocket motor on Space Shuttle. Also used on plumbing containing hydrazine and other hazardous fluids, and repair withstands severe temperature, vibration, and shock. Leaks stopped in place, without draining or replacement of leaking parts.

  7. Nitrogen metabolism in haloarchaea

    PubMed Central

    Bonete, María José; Martínez-Espinosa, Rosa María; Pire, Carmen; Zafrilla, Basilio; Richardson, David J

    2008-01-01

    The nitrogen cycle (N-cycle), principally supported by prokaryotes, involves different redox reactions mainly focused on assimilatory purposes or respiratory processes for energy conservation. As the N-cycle has important environmental implications, this biogeochemical cycle has become a major research topic during the last few years. However, although N-cycle metabolic pathways have been studied extensively in Bacteria or Eukarya, relatively little is known in the Archaea. Halophilic Archaea are the predominant microorganisms in hot and hypersaline environments such as salted lakes, hot springs or salted ponds. Consequently, the denitrifying haloarchaea that sustain the nitrogen cycle under these conditions have emerged as an important target for research aimed at understanding microbial life in these extreme environments. The haloarchaeon Haloferax mediterranei was isolated 20 years ago from Santa Pola salted ponds (Alicante, Spain). It was described as a denitrifier and it is also able to grow using NO3-, NO2- or NH4+ as inorganic nitrogen sources. This review summarizes the advances that have been made in understanding the N-cycle in halophilic archaea using Hfx mediterranei as a haloarchaeal model. The results obtained show that this microorganism could be very attractive for bioremediation applications in those areas where high salt, nitrate and nitrite concentrations are found in ground waters and soils. PMID:18593475

  8. Ice sheets and nitrogen

    PubMed Central

    Wolff, Eric W.

    2013-01-01

    Snow and ice play their most important role in the nitrogen cycle as a barrier to land–atmosphere and ocean–atmosphere exchanges that would otherwise occur. The inventory of nitrogen compounds in the polar ice sheets is approximately 260 Tg N, dominated by nitrate in the much larger Antarctic ice sheet. Ice cores help to inform us about the natural variability of the nitrogen cycle at global and regional scale, and about the extent of disturbance in recent decades. Nitrous oxide concentrations have risen about 20 per cent in the last 200 years and are now almost certainly higher than at any time in the last 800 000 years. Nitrate concentrations recorded in Greenland ice rose by a factor of 2–3, particularly between the 1950s and 1980s, reflecting a major change in NOx emissions reaching the background atmosphere. Increases in ice cores drilled at lower latitudes can be used to validate or constrain regional emission inventories. Background ammonium concentrations in Greenland ice show no significant recent trend, although the record is very noisy, being dominated by spikes of input from biomass burning events. Neither nitrate nor ammonium shows significant recent trends in Antarctica, although their natural variations are of biogeochemical and atmospheric chemical interest. Finally, it has been found that photolysis of nitrate in the snowpack leads to significant re-emissions of NOx that can strongly impact the regional atmosphere in snow-covered areas. PMID:23713125

  9. The evolution of nitrogen cycling

    NASA Technical Reports Server (NTRS)

    Mancinelli, Rocco L.; Mckay, Christopher P.

    1988-01-01

    The energetics of nitrogen transformation reactions and the evolution of nitrogen cycling are examined. It is suggested that meteor impact-produced fixed nitrogen could have caused the entire reservoir of the earth's N2 to convert into fixed nitrogen at the end of accretion. The abiotic fixation rate on the early earth by lightning is estimated at about 1-3 X 10 to the 16th molecules of NO/J. It is found that biological nitrogen fixation may have evolved after the development of an aerobic atmosphere. It is shown that HNO could eventually become NO2(-) and NO3(-) after reaching the earth's surface. It is concluded that the evolutionary sequence for the biological transformation of nitrogen compounds is ammonification - denitrification - nitrification - nitrogen fixation.

  10. Nitrogen chemistry and lung physiology.

    PubMed

    Marozkina, Nadzeya V; Gaston, Benjamin

    2015-01-01

    The versatile chemistry of nitrogen is important to pulmonary physiology. Indeed, almost all redox forms of nitrogen are relevant to pulmonary physiology and to pathophysiology. Here we review the relevance to pulmonary biology of (a) elemental nitrogen; (b) reduced forms of nitrogen such as amines, ammonia, and hydroxylamine; and (c) oxidized forms of nitrogen such as the nitroxyl anion, the nitric oxide free radical, and S-nitrosothiols. Our focus is on oxidized nitrogen in the form of S-nitrosothiol bond-containing species, which are now appreciated to be important to every type of cell-signaling process in the lung. We also review potential clinical applications of nitrogen oxide biochemistry. These principles are being translated into clinical practice as diagnostic techniques and therapies for a range of pulmonary diseases including asthma, cystic fibrosis, adult respiratory distress syndrome, primary ciliary dyskinesia, and pulmonary hypertension. PMID:25668023

  11. How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards.

    PubMed

    Streicher, Jeffrey W; Schulte, James A; Wiens, John J

    2016-01-01

    Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or to minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g., anoles, basilisks, iguanas, and spiny lizards) but relationships among families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1179 to approximately 2.4 million characters per matrix and approximately 30% to 60% total missing data. We then compared mean branch support for interfamilial relationships under these 15 different sampling strategies for both concatenated (maximum likelihood) and species tree (NJst) approaches (after showing that mean branch support appears to be related to accuracy). We found that both approaches had the highest support when including loci with up to 50% missing taxa (matrices with ~40-55% missing data overall). Thus, our results show that simply excluding all missing data may be highly problematic as the primary guiding principle for the inclusion or exclusion of taxa and genes. The optimal strategy was somewhat different for each approach, a pattern that has not been shown previously. For concatenated analyses, branch support was maximized when including many taxa (44) but fewer characters (1.1 million). For species-tree analyses, branch support was maximized with minimal taxon sampling (16) but many loci (4789 of 4921). We also show that the choice of these sampling

  12. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation.

    PubMed

    Agler, Matthew T; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M

    2016-01-01

    Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe-microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe-microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial "hubs," are strongly interconnected and have a severe effect on communities. By documenting these microbe-microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on "hub" microbes, which, via microbe-microbe interactions, transmit the effects to the microbial community. We analyzed two "hub" microbes (the obligate biotrophic

  13. Diversity of Polychaeta (Annelida) and other worm taxa in mangrove habitats of Darwin Harbour, northern Australia

    NASA Astrophysics Data System (ADS)

    Metcalfe, K. N.; Glasby, C. J.

    2008-02-01

    In this paper data on the diversity, distribution and abundance of polychaetes and other worm taxa in the mangroves of Darwin Harbour, northern Australia, are presented and compared with those of other tropical mangrove areas. Aspects of the feeding guild ecology and the effects of disturbance on mangrove worms are also examined. Data were collected over a period of four years, across four mangrove assemblages. Samples were obtained using three sampling techniques: 1 m × 1 m quadrat searches, epifauna searches and a new infaunal sampling technique, the anoxic mat. A total of 76 species (68 polychaetes, 1 oligochaete, 1 echiuran, 3 sipunculans, 2 nemerteans, 1 turbellarian) were recorded from the four main mangrove assemblages. Of these, 30 species are widespread, occurring in mangrove and non-mangrove habitats throughout the Indo-west Pacific. Only seven species (all polychaetes) appear to be restricted to the mangroves of Darwin Harbour and northern Australia. Polychaetes are predominant, comprising 80-96% of all worms sampled, with three families—Nereididae, Capitellidae and Spionidae—accounting for 46% of all species. The highest diversity and abundance was recorded in the soft, unconsolidated substrates of the seaward assemblage, with diversity and abundance decreasing progressively in the landward assemblages. Most of the worm fauna was infaunal (70%), but the intensive sampling regime revealed a hitherto unknown significant percentage of epifaunal species (18%) and species occurring as both infauna and epifauna (12%). Univariate analyses showed annual and seasonal differences in worm species richness and abundance—presumably associated with the intensity of the monsoon and recruitment success. The worm fauna differed between mangrove assemblages but the proportion of species in each feeding guild was relatively consistent across the four assemblages studied. Herbivores were the most species-rich and abundant, followed by carnivores and sub

  14. Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

    PubMed Central

    Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M.

    2016-01-01

    Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the

  15. The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa.

    PubMed

    Moore, Jason R; Varricchio, David J

    2016-01-01

    Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care

  16. The Evolution of Diapsid Reproductive Strategy with Inferences about Extinct Taxa

    PubMed Central

    Varricchio, David J.

    2016-01-01

    Diapsids show an extremely wide range of reproductive strategies. Offspring may receive no parental care, care from only one sex, care from both parents, or care under more complex regimes. Young may vary from independent, super-precocial hatchlings to altricial neonates needing much care before leaving the nest. Parents can invest heavily in a few young, or less so in a larger number. Here we examine the evolution of these traits across a composite phylogeny spanning the extant diapsids and including the limited number of extinct taxa for which reproductive strategies can be well constrained. Generalized estimating equation(GEE)-based phylogenetic comparative methods demonstrate the influences of body mass, parental care strategy and hatchling maturity on clutch volume across the diapsids. The influence of polygamous reproduction is not important despite a large sample size. Applying the results of these models to the dinosaurs supports the hypothesis of paternal care (male only) in derived non-avian theropods, previously suggested based on simpler analyses. These data also suggest that sauropodomorphs did not care for their young. The evolution of parental-care occurs in an almost linear series of transitions. Paternal care rarely gives rise to other care strategies. Where hatchling condition changes, diapsids show an almost unidirectional tendency of evolution towards increased altriciality. Transitions to social monogamy from the ancestral state in diapsids, where both sexes are polygamous, are common. In contrast, once evolved, polygyny and polyandry are very evolutionarily stable. Polygyny and maternal care correlate, as do polyandry and paternal care. Ancestral-character estimation (ACE) of these care strategies with the character transition likelihoods estimated from the original data gives good confidence at most important nodes. These analyses suggest that the basalmost diapsids had no parental care. Crocodilians independently evolved maternal care

  17. Nitrogen and Oxygen Isotopic Studies of the Marine Nitrogen Cycle

    NASA Astrophysics Data System (ADS)

    Casciotti, Karen L.

    2016-01-01

    The marine nitrogen cycle is a complex web of microbially mediated reactions that control the inventory, distribution, and speciation of nitrogen in the marine environment. Because nitrogen is a major nutrient that is required by all life, its availability can control biological productivity and ecosystem structure in both surface and deep-ocean communities. Stable isotopes of nitrogen and oxygen in nitrate and nitrite have provided new insights into the rates and distributions of marine nitrogen cycle processes, especially when analyzed in combination with numerical simulations of ocean circulation and biogeochemistry. This review highlights the insights gained from dual-isotope studies applied at regional to global scales and their incorporation into oceanic biogeochemical models. These studies represent significant new advances in the use of isotopic measurements to understand the modern nitrogen cycle, with implications for the study of past ocean productivity, oxygenation, and nutrient status.

  18. Nitrogen and Oxygen Isotopic Studies of the Marine Nitrogen Cycle.

    PubMed

    Casciotti, Karen L

    2016-01-01

    The marine nitrogen cycle is a complex web of microbially mediated reactions that control the inventory, distribution, and speciation of nitrogen in the marine environment. Because nitrogen is a major nutrient that is required by all life, its availability can control biological productivity and ecosystem structure in both surface and deep-ocean communities. Stable isotopes of nitrogen and oxygen in nitrate and nitrite have provided new insights into the rates and distributions of marine nitrogen cycle processes, especially when analyzed in combination with numerical simulations of ocean circulation and biogeochemistry. This review highlights the insights gained from dual-isotope studies applied at regional to global scales and their incorporation into oceanic biogeochemical models. These studies represent significant new advances in the use of isotopic measurements to understand the modern nitrogen cycle, with implications for the study of past ocean productivity, oxygenation, and nutrient status. PMID:26747521

  19. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and urine... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Nitrogen (amino-nitrogen) test system....

  20. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and urine... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Nitrogen (amino-nitrogen) test system....

  1. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and urine... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Nitrogen (amino-nitrogen) test system....

  2. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and urine... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Nitrogen (amino-nitrogen) test system....

  3. 21 CFR § 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2013 CFR

    2008-04-01

    ... 21 Food and Drugs 8 2008-04-01 2008-04-01 false Nitrogen (amino-nitrogen) test system. § 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  4. 21 CFR § 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2012 CFR

    2016-04-01

    ... 21 Food and Drugs 8 2016-04-01 2016-04-01 false Nitrogen (amino-nitrogen) test system. § 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  5. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2014 CFR

    2004-04-01

    ... 21 Food and Drugs 8 2004-04-01 2004-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  6. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2012 CFR

    2007-04-01

    ... 21 Food and Drugs 8 2007-04-01 2007-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  7. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2013 CFR

    2009-04-01

    ... 21 Food and Drugs 8 2009-04-01 2009-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  8. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2013 CFR

    2003-04-01

    ... 21 Food and Drugs 8 2003-04-01 2003-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  9. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2013 CFR

    2006-04-01

    ... 21 Food and Drugs 8 2006-04-01 2006-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  10. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2012 CFR

    2002-04-01

    ... 21 Food and Drugs 8 2002-04-01 2002-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  11. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2010 CFR

    1998-04-01

    ... 21 Food and Drugs 8 1998-04-01 1998-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Test Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma,...

  12. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2012 CFR

    2000-04-01

    ... 21 Food and Drugs 8 2000-04-01 2000-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Clinical Chemistry Test Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in...

  13. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2011 CFR

    2001-04-01

    ... 21 Food and Drugs 8 2001-04-01 2001-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  14. 21 CFR § 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2011 CFR

    2015-04-01

    ... 21 Food and Drugs 8 2015-04-01 2015-04-01 false Nitrogen (amino-nitrogen) test system. § 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  15. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2013 CFR

    2005-04-01

    ... 21 Food and Drugs 8 2005-04-01 2005-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... Systems § 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure amino acid nitrogen levels in serum, plasma, and...

  16. Comparative sequence analyses of the genes coding for 16S rRNA of Lactobacillus casei-related taxa.

    PubMed

    Mori, K; Yamazaki, K; Ishiyama, T; Katsumata, M; Kobayashi, K; Kawai, Y; Inoue, N; Shinano, H

    1997-01-01

    The primary structures of the 16S rRNA genes of the type strains of Lactobacillus casei and related taxa were determined by PCR DNA-sequencing methods. The sequences of Lactobacillus casei, Lactobacillus zeae, Lactobacillus paracasei, and Lactobacillus rhamnosus were different. The Knuc values ranged from 0.0040 to 0.0126. On the basis of the Knuc values and the levels of DNA-DNA relatedness among the strains of these species, the L. casei-related taxa should be classified in the following three species: L. zeae, which includes the type strains of L. zeae and L. casei; a species that includes the strains of L. paracasei and L. casei ATCC 334; and L. rhamnosus. PMID:8995801

  17. Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata.

    PubMed

    Graur, D; Gouy, M; Duret, L

    1997-04-01

    Contrary to morphological claims, molecular data indicate that the order Perissodactyla (e.g., horses, rhinoceroses, and tapirs) is neither part of the superordinal taxon Paenungulata (Sirenia, Proboscidea, and Hyracoidea) nor an immediate outgroup of the paenungulates. Rather, Perissodactyla is closer to Carnivora and Cetartiodactyla (Cetacea+Artiodactyla) than it is to the paenungulates. Therefore, two morphologically defined superordinal taxa, Altungulata (Proboscidea, Sirenia, Hyracoidea, and Perissodactyla) and Ungulata (Altungulata and Cetartiodactyla), are invalidated. Perissodactyla, Carnivora, and Cetartiodactyla are shown to constitute a rather tight trichotomy. However, a molecular analysis of 36 protein sequences with a total concatenated length of 7885 aligned amino acids indicates that Perissodactyla is closer to Cetartiodactyla than either taxa is to Carnivora. The relationships among Paenungulata, Primates, and the clade consisting of Perissodactyla, Carnivora, and Cetartiodactylaa could not be resolved on the basis of the available data. PMID:9126561

  18. Nitrogen fixation and nitrogen transformations in marine symbioses.

    PubMed

    Fiore, Cara L; Jarett, Jessica K; Olson, Nathan D; Lesser, Michael P

    2010-10-01

    Many marine organisms have coevolved symbiotic relationships with nitrogen-fixing bacteria in nitrogen limited environments such as coral reefs. In addition, some of these organisms also harbor microbes that carry out nitrification and denitrification. Prokaryotes involved in nitrogen fixation and other nitrogen transformations are symbionts in a range of eukaryotic hosts in the marine environment including shipworms, diatoms, corals and sponges. Molecular genetic approaches, and other analytical techniques, have provided exciting new insights into symbiont diversity and the relationship between host and symbiont. We review the current state of knowledge of these symbioses and highlight important avenues for future studies. PMID:20674366

  19. Multi-taxa approach shows consistent shifts in arthropod functional traits along grassland land-use intensity gradient.

    PubMed

    Simons, Nadja K; Weisser, Wolfgang W; Gossner, Martin M

    2016-03-01

    Intensification of land use reduces biodiversity but may also shift the trait composition of communities. Understanding how land use affects single traits and community trait composition, helps to understand why some species are more affected by land use than others. Trait-based analyses are common for plants, but rare for arthropods. We collected literature-based traits for nearly 1000 insect and spider species to test how land- use intensity (including mowing, fertilization, and grazing) across 124 grasslands in three regions of Germany affects community-weighted mean traits across taxa and in single taxa. We additionally measured morphometric traits for more than 150 Heteroptera species and tested whether the weighted mean morphometric traits change with increasing land-use intensity. Community average body size decreased and community average dispersal ability increased from low to high land-use intensity. Furthermore, the relative abundance of herbivores and of specialists among herbivores decreased and the relative abundance of species using the herb layer increased with increasing land-use intensity. Community-weighted means of the morphometric traits in Heteroptera also changed from low to high land-use intensity toward longer and thinner shapes as well as longer appendices (legs, wings, and antenna). While changes in traits with increasing mowing and fertilization intensity were consistent with the combined land-use intensity, community average traits did often not change or with opposite direction under increasing grazing intensity. We conclude that high land-use intensity acts as an environmental filter selecting for on average smaller, more mobile, and less specialized species across taxa. Although trait collection across multiple arthropod taxa is laborious and needs clear trait definitions, it is essential for understanding the functional consequences of biodiversity loss due to land-use intensification. PMID:27197401

  20. Positive correlation of trophic level and proportion of sexual taxa of oribatid mites (Acari: Oribatida) in alpine soil systems.

    PubMed

    Fischer, Barbara M; Meyer, Erwin; Maraun, Mark

    2014-08-01

    We investigated community structure, trophic ecology (using stable isotope ratios; (15)N/(14)N, (13)C/(12)C) and reproductive mode of oribatid mites (Acari, Oribatida) along an altitudinal gradient (2,050-2,900 m) in the Central Alps (Obergurgl, Austria). We hypothesized that (1) the community structure changes with altitude, (2) oribatid mites span over four trophic levels, (3) the proportion of sexual taxa increases with altitude, and (4) the proportion of sexual taxa increases with trophic level, i.e. is positively correlated with the δ(15)N signatures. Oribatid mite community structure changed with altitude indicating that oribatid mites occupy different niches at different altitudes. Oribatid mites spanned over 12 δ(15)N units, i.e. about four trophic levels, which is similar to lowland forest ecosystems. The proportion of sexually reproducing taxa increased from 2,050 to 2,900 m suggesting that limited resource availability at high altitudes favors sexual reproduction. Sexual taxa more frequently occurred higher in the food web indicating that the reproductive mode is related to nutrition of oribatid mites. Generally, oribatid mite community structure changed from being decomposer dominated at lower altitude to being dominated by fungal and lichen feeders, and predators at higher altitude. This supports the view that resources from dead organic material become less available with increasing altitude forcing species to feed on living resources such as fungi, lichens and nematodes. Our findings support the hypothesis that limited resource accessibility (at high altitudes) favors sexually reproducing species whereas ample resource supply (at lower altitudes) favors parthenogenetic species. PMID:24687174

  1. Understanding Nitrogen Fixation

    SciTech Connect

    Paul J. Chirik

    2012-05-25

    The purpose of our program is to explore fundamental chemistry relevant to the discovery of energy efficient methods for the conversion of atmospheric nitrogen (N{sub 2}) into more value-added nitrogen-containing organic molecules. Such transformations are key for domestic energy security and the reduction of fossil fuel dependencies. With DOE support, we have synthesized families of zirconium and hafnium dinitrogen complexes with elongated and activated N-N bonds that exhibit rich N{sub 2} functionalization chemistry. Having elucidated new methods for N-H bond formation from dihydrogen, C-H bonds and Broensted acids, we have since turned our attention to N-C bond construction. These reactions are particularly important for the synthesis of amines, heterocycles and hydrazines with a range of applications in the fine and commodity chemicals industries and as fuels. One recent highlight was the discovery of a new N{sub 2} cleavage reaction upon addition of carbon monoxide which resulted in the synthesis of an important fertilizer, oxamide, from the diatomics with the two strongest bonds in chemistry. Nitrogen-carbon bonds form the backbone of many important organic molecules, especially those used in the fertilizer and pharamaceutical industries. During the past year, we have continued our work in the synthesis of hydrazines of various substitution patterns, many of which are important precursors for heterocycles. In most instances, the direct functionalization of N{sub 2} offers a more efficient synthetic route than traditional organic methods. In addition, we have also discovered a unique CO-induced N{sub 2} bond cleavage reaction that simultaneously cleaves the N-N bond of the metal dinitrogen compound and assembles new C-C bond and two new N-C bonds. Treatment of the CO-functionalized core with weak Broensted acids liberated oxamide, H{sub 2}NC(O)C(O)NH{sub 2}, an important slow release fertilizer that is of interest to replace urea in many applications. The

  2. Nitrogen fixation apparatus

    DOEpatents

    Chen, Hao-Lin

    1984-01-01

    A method and apparatus for achieving nitrogen fixation includes a volumetric electric discharge chamber. The volumetric discharge chamber provides an even distribution of an electron beam, and enables the chamber to be maintained at a controlled energy to pressure (E/p) ratio. An E/p ratio of from 5 to 15 kV/atm of O.sub.2 /cm promotes the formation of vibrationally excited N.sub.2. Atomic oxygen interacts with vibrationally excited N.sub.2 at a much quicker rate than unexcited N.sub.2, greatly improving the rate at which NO is formed.

  3. Desiccation as a mitigation tool to manage biofouling risks: trials on temperate taxa to elucidate factors influencing mortality rates.

    PubMed

    Hopkins, Grant A; Prince, Madeleine; Cahill, Patrick L; Fletcher, Lauren M; Atalah, Javier

    2016-01-01

    The desiccation tolerance of biofouling taxa (adults and early life-stages) was determined under both controlled and 'realistic' field conditions. Adults of the ascidian Ciona spp. died within 24 h. Mortality in the adult blue mussel Mytilus galloprovincialis occurred within 11 d under controlled conditions, compared with 7 d when held outside. The Pacific oyster Crassostrea gigas was the most desiccation-tolerant taxon tested (up to 34 d under controlled conditions). Biofouling orientated to direct sunlight showed faster mortality rates for all the taxa tested. Mortality in Mytilus juveniles took up to 24 h, compared with 8 h for Ciona, with greater survival at the higher temperature (18.5°C) and humidity (~95% RH) treatment combination. This study demonstrated that desiccation can be an effective mitigation method for a broad range of fouling taxa, especially their early life-stages. Further work is necessary to assess risks from other high-risk species such as algae and cyst forming species. PMID:26691450

  4. Abundance of broad bacterial taxa in the sargasso sea explained by environmental conditions but not water mass.

    PubMed

    Sjöstedt, Johanna; Martiny, Jennifer B H; Munk, Peter; Riemann, Lasse

    2014-05-01

    To explore the potential linkage between distribution of marine bacterioplankton groups, environmental conditions, and water mass, we investigated the factors determining the abundance of bacterial taxa across the hydrographically complex Subtropical Convergence Zone in the Sargasso Sea. Based on information from 16S rRNA gene clone libraries from various locations and two depths, abundances of the predominant taxa (eubacteria, Archaea, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and the Roseobacter, SAR11, and SAR86 clades) were quantified by real-time PCR. In addition, the abundances of Synechococcus, Prochlorococcus, and picoalgae were determined by flow cytometry. Linear multiple-regression models determining the relative effects of eight environmental variables and of water mass explained 35 to 86% of the variation in abundance of the quantified taxa, even though only one to three variables were significantly related to any particular taxon's abundance. Most of the variation in abundance was explained by depth and chlorophyll a. The predominant phototrophs, Prochlorococcus and picoalgae, were negatively correlated with phosphate, whereas eubacteria, heterotrophic bacteria, and SAR86 were negatively correlated with nitrite. Water mass showed limited importance for explaining the abundance of the taxonomical groups (significant only for Roseobacter, explaining 14% of the variation). The results suggest the potential for predicting the abundance of broad bacterioplankton groups throughout the Sargasso Sea using only a few environmental parameters. PMID:24561593

  5. Cambro-ordovician sea-level fluctuations and sequence boundaries: The missing record and the evolution of new taxa

    USGS Publications Warehouse

    Lehnert, O.; Miller, J.F.; Leslie, Stephen A.; Repetski, J.E.; Ethington, Raymond L.

    2005-01-01

    The evolution of early Palaeozoic conodont faunas shows a clear connection to sea-level changes. One way that this connection manifests itself is that thick successions of carbonates are missing beneath major sequence boundaries due to karstification and erosion. From this observation arises the question of how many taxa have been lost from different conodont lineages in these incomplete successions. Although many taxa suffered extinction due to the environmental stresses associated with falling sea-levels, some must have survived in these extreme conditions. The number of taxa missing in the early Palaeozoic tropics always will be unclear, but it will be even more difficult to evaluate the missing record in detrital successions of higher latitudes. A common pattern in the evolution of Cambrian-Ordovician conodont lineages is appearances of new species at sea-level rises and disappearances at sea-level drops. This simple picture can be complicated by intervals that consistently have no representatives of a particular lineage, even after extensive sampling of the most complete sections. Presumably the lineages survived in undocumented refugia. In this paper, we give examples of evolution in Cambrian-Ordovician shallowmarine conodont faunas and highlight problems of undiscovered or truly missing segments of lineages. ?? The Palaeontological Association.

  6. DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

    PubMed Central

    Rawlence, Nicolas J.; Wood, Jamie R.; Armstrong, Kyle N.; Cooper, Alan

    2009-01-01

    Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains. PMID:19570784

  7. Biogeography of Heterotrophic Flagellate Populations Indicates the Presence of Generalist and Specialist Taxa in the Arctic Ocean

    PubMed Central

    Thaler, Mary

    2015-01-01

    Heterotrophic marine flagellates (HF) are ubiquitous in the world's oceans and represented in nearly all branches of the domain Eukaryota. However, the factors determining distributions of major taxonomic groups are poorly known. The Arctic Ocean is a good model environment for examining the distribution of functionally similar but phylogenetically diverse HF because the physical oceanography and annual ice cycles result in distinct environments that could select for microbial communities or favor specific taxa. We reanalyzed new and previously published high-throughput sequencing data from multiple studies in the Arctic Ocean to identify broad patterns in the distribution of individual taxa. HF accounted for fewer than 2% to over one-half of the reads from the water column and for up to 60% of reads from ice, which was dominated by Cryothecomonas. In the water column, many HF phylotypes belonging to Telonemia and Picozoa, uncultured marine stramenopiles (MAST), and choanoflagellates were geographically widely distributed. However, for two groups in particular, Telonemia and Cryothecomonas, some species level taxa showed more restricted distributions. For example, several phylotypes of Telonemia favored open waters with lower nutrients such as the Canada Basin and offshore of the Mackenzie Shelf. In summary, we found that while some Arctic HF were successful over a range of conditions, others could be specialists that occur under particular conditions. We conclude that tracking species level diversity in HF not only is feasible but also provides a potential tool for understanding the responses of marine microbial ecosystems to rapidly changing ice regimes. PMID:25595764

  8. Pollen Performance in Clarkia Taxa with Contrasting Mating Systems: Implications for Male Gametophytic Evolution in Selfers and Outcrossers

    PubMed Central

    Hove, Alisa A.; Mazer, Susan J.

    2013-01-01

    We tested three predictions regarding the joint evolution of pollen performance and mating system. First, due to the potential for intense intrasexual competition in outcrossing populations, we predicted that outcrossers would produce faster-growing pollen than their selfing relatives. Second, if elevated competition promotes stronger selection on traits that improve pollen performance, then, among-plant variation in pollen performance would be lower in outcrossers than in selfers. Third, given successive generations of adaptation to the same maternal genotype in selfers, we predicted that, in selfing populations (but not in outcrossing ones), pollen would perform better following self- than cross-pollinations. We tested these predictions in field populations of two pairs of Clarkia (Onagraceae) sister taxa. Consistent with our predictions, one outcrosser (C. unguiculata) exhibited faster pollen germination and less variation in pollen tube growth rate (PTGR) among pollen donors than its selfing sister species, C. exilis. Contrary to our predictions, the selfing C. xantiana ssp. parviflora exhibited faster PTGR than the outcrossing ssp. xantiana, and these taxa showed similar levels of variation in this trait. Pollen performance following self- vs. cross-pollinations did not differ within either selfing or outcrossing taxa. While these findings suggest that mating system and pollen performance may jointly evolve in Clarkia, other factors clearly contribute to pollen performance in natural populations. PMID:27137375

  9. KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa.

    PubMed

    Lobo, Francisco P; Rodrigues, Maíra R; Rodrigues, Gisele O L; Hilário, Heron O; Souza, Raoni A; Tauch, Andreas; Miyoshi, Anderson; Franco, Glaura C; Azevedo, Vasco; Franco, Glória R

    2012-07-01

    The enrichment analysis is a standard procedure to interpret 'omics' experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org. PMID:22675073

  10. KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa

    PubMed Central

    Lobo, Francisco P.; Rodrigues, Maíra R.; Rodrigues, Gisele O. L.; Hilário, Heron O.; Souza, Raoni A.; Tauch, Andreas; Miyoshi, Anderson; Franco, Glaura C.; Azevedo, Vasco; Franco, Glória R.

    2012-01-01

    The enrichment analysis is a standard procedure to interpret ‘omics’ experiments that generate large gene lists as outputs, such as transcriptomics and protemics. However, despite the huge success of enrichment analysis in these classes of experiments, there is a surprising lack of application of this methodology to survey other categories of large-scale biological data available. Here, we report Kegg Orthology enrichMent-Online DetectiOn (KOMODO), a web tool to systematically investigate groups of monophyletic genomes in order to detect significantly enriched groups of homologous genes in one taxon when compared with another. The results are displayed in their proper biochemical roles in a visual, explorative way, allowing users to easily formulate and investigate biological hypotheses regarding the taxonomical distribution of genomic elements. We validated KOMODO by analyzing portions of central carbon metabolism in two taxa extensively studied regarding their carbon metabolism profile (Enterobacteriaceae family and Lactobacillales order). Most enzymatic activities significantly biased were related to known key metabolic traits in these taxa, such as the distinct fates of pyruvate (the known tendency of lactate production in Lactobacillales and its complete oxidation in Enterobacteriaceae), demonstrating that KOMODO could detect biologically meaningful differences in the frequencies of shared genomic elements among taxa. KOMODO is freely available at http://komodotool.org. PMID:22675073

  11. Nitrogen In Saturn's Inner Magnetosphere

    NASA Astrophysics Data System (ADS)

    Smith, H. T.; Sittler, E. C.; Johnson, R. E.; McComas, D.; Reisenfeld, D.; Shappirio, M.; Michael, M.; Shematovich, V. I.; Baragiola, R. A.; Crary, F.; Young, D.

    2004-11-01

    We are analyzing CAPS instrument data on Cassini to look for nitrogen ions in Saturn's magnetosphere. Because Voyager could not separate oxygen and nitrogen, there has been considerable controversy on nitrogen's presence and relative importance. Two principal sources have been suggested: Titan's atmosphere and nitrogen species trapped in Saturn's icy satellite surfaces (Sittler et al 2004). The latter may be primordial nitrogen, likely as NH3 in ice (Stevenson 1982; Squyers et al. 1983) or nitrogen ions that have been implanted in the surface (Delitsky and Lane 2002). We will present the results of Saturnian nitrogen cloud modeling and relevant CAPS observations. We recently described the Titan source (Michael, et al. 2004; Shematovich et al. 2003; Smith et al. 2004; Sittler et al. 2004) in preparation for Cassini's Saturnian plasma measurements. Two components were identified: energetic nitrogen ions formed near Titan and energized as they diffused inward (Sittler et al. 2004) and neutrals in orbits with small perigee that became ionized in the inner magnetosphere (Smith et al 2004). The latter component would be a source of lower energy, co-rotating nitrogen ions to the inner magnetosphere. Such a component would have an energy spectrum similar to nitrogen species sputtered from the icy satellite surfaces (Johnson and Sittler 1990). However, the mass spectrum would differ, likely containing NHx and NOx species also, and, hence, may be separated from the Titan source. Our preliminary analysis for nitrogen species in the CAPS data will be compared to the models. Of interest will be the energy spectra, which can indicate whether any nitrogen present is formed locally or near Titan's orbit and diffused inward. This work is supported by the NASA Planetary Atmospheres, NASA Graduate Student Research, Virginia Space Grant Consortium Graduate Research Fellowship and the CAPS Cassini instrument team programs.

  12. Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium

    PubMed Central

    Samson, R.A.; Yilmaz, N.; Houbraken, J.; Spierenburg, H.; Seifert, K.A.; Peterson, S.W.; Varga, J.; Frisvad, J.C.

    2011-01-01

    The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocomaceae was further studied by sequencing a part of the RPB1 (RNA polymerase II largest subunit) gene. Talaromyces species and most species of Penicillium subgenus Biverticillium sensu Pitt reside in a monophyletic clade distant from species of other subgenera of Penicillium. For detailed phylogenetic analysis of species relationships, the ITS region (incl. 5.8S nrDNA) was sequenced for the available type strains and/or representative isolates of Talaromyces and related biverticillate anamorphic species. Extrolite profiles were compiled for all type strains and many supplementary cultures. All evidence supports our conclusions that Penicillium subgenus Biverticillium is distinct from other subgenera in Penicillium and should be taxonomically unified with the Talaromyces species that reside in the same clade. Following the concepts of nomenclatural priority and single name nomenclature, we transfer all accepted species of Penicillium subgenus Biverticillium to Talaromyces. A holomorphic generic diagnosis for the expanded concept of Talaromyces, including teleomorph and anamorph characters, is provided. A list of accepted Talaromyces names and newly combined Penicillium names is given. Species of biotechnological and medical importance, such as P. funiculosum and P. marneffei, are now combined in Talaromyces. Excluded species and taxa that need further taxonomic study are discussed. An appendix lists other generic names, usually considered synonyms of Penicillium sensu lato that

  13. Nitrogen quantification with SNMS

    NASA Astrophysics Data System (ADS)

    Goschnick, J.; Natzeck, C.; Sommer, M.

    1999-04-01

    Plasma-based secondary neutral mass spectrometry (plasma SNMS) is a powerful analytical method for determining the elemental concentrations of almost any kind of material at low cost by using a cheap quadrupole mass filter. However, a quadrupole-based mass spectrometer is limited to nominal mass resolution. Atomic signals are sometimes superimposed by molecular signals (2 or 3 atomic clusters such as CH +, CH 2+ or metal oxide clusters) and/or intensities of double-charged species. Especially in the case of nitrogen several interferences can impede the quantification. This article reports on methods to recognize and deconvolute superpositions of N + with CH 2+, Li 2+, and Si 2+ at mass 14 D (Debye) occurring during analysis of organic and inorganic substances. The recognition is based on the signal pattern of N +, Li +, CH +, and Si +. The latter serve as indicators for a probable interference of molecular or double-charged species with N on mass 14 D. The subsequent deconvolution use different shapes of atomic and cluster kinetic energy distributions (kEDs) to determine the quantities of the intensity components by a linear fit of N + and non-atomic kEDs obtained from several organic and inorganic standards into the measured kED. The atomic intensity fraction yields a much better nitrogen concentration than the total intensity of mass 14 D after correction.

  14. Orchard nitrogen management: Which nitrogen source is best?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Suboptimal management of nitrogen fertility in pecan orchards leads to a loss of nutmeat yield and quality, but also a waste of natural resources and money. This article reviews several basic guiding principles useful to orchard managers when developing nitrogen management strategies, and determini...

  15. Nitrogen release during coal combustion

    SciTech Connect

    Baxter, L.L.; Mitchell, R.E.; Fletcher, T.H.; Hurt, R.H.

    1995-02-01

    Experiments in entrained flow reactors at combustion temperatures are performed to resolve the rank dependence of nitrogen release on an elemental basis for a suite of 15 U.S. coals ranging from lignite to low-volatile bituminous. Data were obtained as a function of particle conversion, with overall mass loss up to 99% on a dry, ash-free basis. Nitrogen release rates are presented relative to both carbon loss and overall mass loss. During devolatilization, fractional nitrogen release from low-rank coals is much slower than fractional mass release and noticeably slower than fractional carbon release. As coal rank increases, fractional nitrogen release rate relative to that of carbon and mass increases, with fractional nitrogen release rates exceeding fractional mass and fractional carbon release rates during devolatilization for high-rank (low-volatile bituminous) coals. At the onset of combustion, nitrogen release rates increase significantly. For all coals investigated, cumulative fractional nitrogen loss rates relative to those of mass and carbon passes through a maximum during the earliest stages of oxidation. The mechanism for generating this maximum is postulated to involve nascent thermal rupture of nitrogen-containing compounds and possible preferential oxidation of nitrogen sites. During later stages of oxidation, the cumulative fractional loss of nitrogen approaches that of carbon for all coals. Changes in the relative release rates of nitrogen compared to those of both overall mass and carbon during all stages of combustion are attributed to a combination of the chemical structure of coals, temperature histories during combustion, and char chemistry.

  16. Investigating Nitrogen Pollution: Activities and Models.

    ERIC Educational Resources Information Center

    Green Teacher, 2000

    2000-01-01

    Introduces activities on nitrogen, nitrogen pollution from school commuters, nitrogen response in native and introduced species, and nutrient loading models. These activities help students determine the nitrogen contribution from their parents' cars, test native plant responses to nitrogen, and experiment with the results of removing water from…

  17. Seasonal Nitrogen Cycles on Pluto

    NASA Technical Reports Server (NTRS)

    Hansen, C. J.; Paige, D. A.

    1994-01-01

    A thermal model, developed to predict seasonal nitrogen cycles on Triton, has been modified and applied to Pluto. The model is used to calculate the partitioning of nitrogen between surface frost deposits and the atmosphere, as a function of time for various sets of input parameters.

  18. Nitrogen chiller acceptance test procedure

    SciTech Connect

    Kostelnik, A.J.

    1995-03-07

    This document includes the inspection and testing requirements for the Nitrogen Chiller unit. The Chiller will support the Rotary Mode core Sampling System during the summer. The Chiller cools the Nitrogen Purge Gas that is used when drilling in tank wastes to cool the drill bit.

  19. Swivel Joint For Liquid Nitrogen

    NASA Technical Reports Server (NTRS)

    Milner, James F.

    1988-01-01

    Swivel joint allows liquid-nitrogen pipe to rotate through angle of 100 degree with respect to mating pipe. Functions without cracking hard foam insulation on lines. Pipe joint rotates on disks so mechanical stress not transmitted to thick insulation on pipes. Inner disks ride on fixed outer disks. Disks help to seal pressurized liquid nitrogen flowing through joint.

  20. Alternative nitrogen sources for cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several alternative nitrogen (N) sources, rates of N, and amendments were evaluated at Prattville, Alabama, on cotton in 2008. Nitrogen rates reported are for sidedress application only. Dry urea produced the highest yield, averaging 1100 pounds lint per acre. Ammonia volatilization was measured fr...

  1. 21 CFR 862.1515 - Nitrogen (amino-nitrogen) test system.

    Code of Federal Regulations, 2010 CFR

    1999-04-01

    ... 21 FOOD AND DRUGS 8 1999-04-01 1999-04-01 false Nitrogen (amino-nitrogen) test system. 862.1515... CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems Sec. 862.1515 Nitrogen (amino-nitrogen) test system. (a) Identification. A nitrogen (amino-nitrogen) test system is a device intended to measure...

  2. The ontogeny of talo-crural appositional articular morphology among catarrhine taxa: adult shape reflects substrate use.

    PubMed

    Turley, Kevin; Frost, Stephen R

    2014-07-01

    The upper ankle joint forms a single articular plane between organism and the foot and substrate. Singular warp analysis shows that its shape reflects substrate use. This study explores whether the differences in shape are genetic with a developmental trajectory evident during ontogeny or epigenetic and the result of substrate use by the individual. A total of 418 matched distal tibial and proximal talar landmarked surfaces from adult and subadult specimens from 12 diverse catarrhine taxa were studied. Specimens were grouped by molar eruption (M1, M2, and M3) for comparative analysis. Generalized Procrustes analysis, multivariate regression, relative warp analysis, singular warp analysis, and permutation tests were used. Singular warp analysis for the entire cohort was highly significant in the first singular warp, with the adult taxa sorting by substrate use. All 173 subadults clustered with an adult "arboreal" shape profile. Among Hominoidea, adults (M3) sorted by substrate use with Pan paniscus and Hylobatidae assuming an "arboreal" shape separate from Pan troglodytes and the remaining taxa with "terrestrial" shape. Cercopithecoid adults sorted by substrate use as well, with the M3 specimens of Papio hamadryas and Macaca thibetana demonstrating a "terrestrial" shape. Differences in mode of locomotion did not affect the findings in the first singular warp. Results confirmed the convergence of talo-crural shape among superfamilies based on substrate use and divergence in shape within Pan and Macaca, based on substrate use. The shape differences among adults (M3) are consistent with a plastic response to the behavioral stimulus of substrate use. PMID:24842582

  3. Leaf-Associated Bacterial and Fungal Taxa Shifts in Response to Larvae of the Tree Hole Mosquito, Ochlerotatus triseriatus

    PubMed Central

    Kaufman, Michael G.; Chen, Shicheng; Walker, Edward D.

    2014-01-01

    Larvae of the eastern tree hole mosquito, Ochlerotatus triseriatus (Say), and related container-breeding species are known to feed upon substrate-associated microorganisms. Although the importance of these microbial resources to larval growth has been established, almost nothing is known about the taxonomic composition and dynamics of these critical microbial food sources. We examined bacterial and fungal community compositional changes on oak leaves tethered in natural tree hole habitats of O. triseriatus. We eliminated larvae experimentally in a subset of the tree holes and examined 16S rDNA gene sequences for bacteria and ergosterol concentrations and 18S rRNA gene sequences for fungi collected from leaf material subsamples. Leaf ergosterol content varied significantly with time, but not treatment. Principal component analysis (PCA) was used to compare microbial taxonomic patterns found in leaves incubated with or without larvae present, and we found that larval presence affected both bacterial and fungal groups, either from loosely attached or strongly adherent categories. Bacterial communities generally grouped more tightly when larvae were present, and class level taxa proportions changed when larvae were present, suggesting selection by larval feeding or activities for particular taxa such as members of the Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria classes. Fungal taxa composite scores also separated along PC axes related to the presence of larvae and indicated larval feeding effects on several higher taxonomic groups, including Saccharomycetes, Dothideomycetes, and Chytridiomycota. These results support the hypothesis that larval mosquito feeding and activities altered microbial communities associated with substrate surfaces, potentially leading to decreased food value of the resource and affecting decomposition of particulate matter in the system. PMID:17899246

  4. Three-dimensional geometric morphometric analysis of talar morphology in extant gorilla taxa from highland and lowland habitats.

    PubMed

    Knigge, Ryan P; Tocheri, Matthew W; Orr, Caley M; Mcnulty, Kieran P

    2015-01-01

    Western gorillas (Gorilla gorilla) are known to climb significantly more often than eastern gorillas (Gorilla beringei), a behavioral distinction attributable to major differences in their respective habitats (i.e., highland vs. lowland). Genetic evidence suggests that the lineages leading to these taxa began diverging from one another between approximately 1 and 3 million years ago. Thus, gorillas offer a special opportunity to examine the degree to which morphology of recently diverged taxa may be "fine-tuned" to differing ecological requirements. Using three-dimensional (3D) geometric morphometrics, we compared talar morphology in a sample of 87 specimens including western (lowland), mountain (highland), and grauer gorillas (lowland and highland populations). Talar shape was captured with a series of landmarks and semilandmarks superimposed by generalized Procrustes analysis. A between-group principal components analysis of overall talar shape separates gorillas by ecological habitat and by taxon. An analysis of only the trochlea and lateral malleolar facet identifies subtle variations in trochlear shape between western lowland and lowland grauer gorillas, potentially indicative of convergent evolution of arboreal adaptations in the talus. Lastly, talar shape scales differently with centroid size for highland and lowland gorillas, suggesting that ankle morphology may track body-size mediated variation in arboreal behaviors differently depending on ecological setting. Several of the observed shape differences are linked biomechanically to the facilitation of climbing in lowland gorillas and to stability and load-bearing on terrestrial substrates in the highland taxa, providing an important comparative model for studying morphological variation in groups known only from fossils (e.g., early hominins). PMID:25338937

  5. Controlling Harmful Cyanobacteria: Taxa-Specific Responses of Cyanobacteria to Grazing by Large-Bodied Daphnia in a Biomanipulation Scenario

    PubMed Central

    Urrutia-Cordero, Pablo; Ekvall, Mattias K.; Hansson, Lars-Anders

    2016-01-01

    Lake restoration practices based on reducing fish predation and promoting the dominance of large-bodied Daphnia grazers (i.e., biomanipulation) have been the focus of much debate due to inconsistent success in suppressing harmful cyanobacterial blooms. While most studies have explored effects of large-bodied Daphnia on cyanobacterial growth at the community level and/or on few dominant species, predictions of such restoration practices demand further understanding on taxa-specific responses in diverse cyanobacterial communities. In order to address these questions, we conducted three grazing experiments during summer in a eutrophic lake where the natural phytoplankton community was exposed to an increasing gradient in biomass of the large-bodied Daphnia magna. This allowed evaluating taxa-specific responses of cyanobacteria to Daphnia grazing throughout the growing season in a desired biomanipulation scenario with limited fish predation. Total cyanobacterial and phytoplankton biomasses responded negatively to Daphnia grazing both in early and late summer, regardless of different cyanobacterial densities. Large-bodied Daphnia were capable of suppressing the abundance of Aphanizomenon, Dolichospermum, Microcystis and Planktothrix bloom-forming cyanobacteria. However, the growth of the filamentous Dolichospermum crassum was positively affected by grazing during a period when this cyanobacterium dominated the community. The eutrophic lake was subjected to biomanipulation since 2005 and nineteen years of lake monitoring data (1996–2014) revealed that reducing fish predation increased the mean abundance (50%) and body-size (20%) of Daphnia, as well as suppressed the total amount of nutrients and the growth of the dominant cyanobacterial taxa, Microcystis and Planktothrix. Altogether our results suggest that lake restoration practices solely based on grazer control by large-bodied Daphnia can be effective, but may not be sufficient to control the overgrowth of all

  6. Controlling Harmful Cyanobacteria: Taxa-Specific Responses of Cyanobacteria to Grazing by Large-Bodied Daphnia in a Biomanipulation Scenario.

    PubMed

    Urrutia-Cordero, Pablo; Ekvall, Mattias K; Hansson, Lars-Anders

    2016-01-01

    Lake restoration practices based on reducing fish predation and promoting the dominance of large-bodied Daphnia grazers (i.e., biomanipulation) have been the focus of much debate due to inconsistent success in suppressing harmful cyanobacterial blooms. While most studies have explored effects of large-bodied Daphnia on cyanobacterial growth at the community level and/or on few dominant species, predictions of such restoration practices demand further understanding on taxa-specific responses in diverse cyanobacterial communities. In order to address these questions, we conducted three grazing experiments during summer in a eutrophic lake where the natural phytoplankton community was exposed to an increasing gradient in biomass of the large-bodied Daphnia magna. This allowed evaluating taxa-specific responses of cyanobacteria to Daphnia grazing throughout the growing season in a desired biomanipulation scenario with limited fish predation. Total cyanobacterial and phytoplankton biomasses responded negatively to Daphnia grazing both in early and late summer, regardless of different cyanobacterial densities. Large-bodied Daphnia were capable of suppressing the abundance of Aphanizomenon, Dolichospermum, Microcystis and Planktothrix bloom-forming cyanobacteria. However, the growth of the filamentous Dolichospermum crassum was positively affected by grazing during a period when this cyanobacterium dominated the community. The eutrophic lake was subjected to biomanipulation since 2005 and nineteen years of lake monitoring data (1996-2014) revealed that reducing fish predation increased the mean abundance (50%) and body-size (20%) of Daphnia, as well as suppressed the total amount of nutrients and the growth of the dominant cyanobacterial taxa, Microcystis and Planktothrix. Altogether our results suggest that lake restoration practices solely based on grazer control by large-bodied Daphnia can be effective, but may not be sufficient to control the overgrowth of all

  7. Character phylogenies in Candacia and Paracandacia (Copepoda, Calanoida) and the inevitably paraphyletic nature of many nominal taxa above subspecies level

    NASA Astrophysics Data System (ADS)

    von Vaupel Klein, J. C.; Gassmann, D.

    1998-06-01

    Examination of the phylogenetic structure of the family Candaciidae shows the genus Paracandacia to comprise a strongly modified branch emerging from the clade commonly denoted as Candacia. This has been confirmed by studying selected character phylogenies. It is argued that the resulting paraphyletic nature of Candacia auct., though in a cladistic context undesirable on theoretical grounds, has to be accepted as inevitable. Recent studies on molluscs and arthropods, viz., have demonstrated that the continuous origin of paraphyletic taxa from previously monophyletic ones is nothing but a naturally occurring process, intrinsically embodied in the course of evolution.

  8. Eighth international congress on nitrogen fixation

    SciTech Connect

    Not Available

    1990-01-01

    This volume contains the proceedings of the Eighth International Congress on Nitrogen Fixation held May 20--26, 1990 in Knoxville, Tennessee. The volume contains abstracts of individual presentations. Sessions were entitled Recent Advances in the Chemistry of Nitrogen Fixation, Plant-microbe Interactions, Limiting Factors of Nitrogen Fixation, Nitrogen Fixation and the Environment, Bacterial Systems, Nitrogen Fixation in Agriculture and Industry, Plant Function, and Nitrogen Fixation and Evolution.

  9. A strategy for designing multi-taxa specific reference gene systems. example of application--ppi phosphofructokinase (ppi-PPF) used for the detection and quantification of three taxa: maize (Zea mays), cotton (Gossypium hirsutum) and rice (Oryza sativa).

    PubMed

    Chaouachi, Maher; Giancola, Sandra; Romaniuk, Marcel; Laval, Valérie; Bertheau, Yves; Brunel, Dominique

    2007-10-01

    In the first part of the paper, we report the description of a new strategy for the development of a plant reference gene system that can be used for genetically modified organism (GMO) analysis. On the basis of in silico research for candidate genes, the design of degenerate primers allowed the obtention of genomic sequences of the selected gene ppi-phosphofructokinase ( ppi-PPF) for nine taxa in which GMOs have been developed. The comparison and the analysis of inter- and intraspecies sequence variability were performed using a large number of species and cultivars. As an example of application following the detection of single nucleotide polymorphism, we designed specific conventional and real-time polymerase chain reaction tests for the detection and quantification of three taxa, namely, maize, cotton, and rice. This system was highly specific and sensitive. The gene copy number conservation among different cultivars was analyzed and confirmed with a sequencing step. This reference gene system is adequate for use in routine assays for the quantification of GMOs. We then explain briefly the constraints faced and propose recommendations when designing a reference gene system depending on the species to be targeted. PMID:17824661

  10. Nitrogen in rock: Occurrences and biogeochemical implications

    USGS Publications Warehouse

    Holloway, J.M.; Dahlgren, R.A.

    2002-01-01

    There is a growing interest in the role of bedrock in global nitrogen cycling and potential for increased ecosystem sensitivity to human impacts in terrains with elevated background nitrogen concentrations. Nitrogen-bearing rocks are globally distributed and comprise a potentially large pool of nitrogen in nutrient cycling that is frequently neglected because of a lack of routine analytical methods for quantification. Nitrogen in rock originates as organically bound nitrogen associated with sediment, or in thermal waters representing a mixture of sedimentary, mantle, and meteoric sources of nitrogen. Rock nitrogen concentrations range from trace levels (>200 mg N kg -1) in granites to ecologically significant concentrations exceeding 1000 mg N kg -1 in some sedimentary and metasedimentary rocks. Nitrate deposits accumulated in arid and semi-arid regions are also a large potential pool. Nitrogen in rock has a potentially significant impact on localized nitrogen cycles. Elevated nitrogen concentrations in water and soil have been attributed to weathering of bedrock nitrogen. In some environments, nitrogen released from bedrock may contribute to nitrogen saturation of terrestrial ecosystems (more nitrogen available than required by biota). Nitrogen saturation results in leaching of nitrate to surface and groundwaters, and, where soils are formed from ammonium-rich bedrock, the oxidation of ammonium to nitrate may result in soil acidification, inhibiting revegetation in certain ecosystems. Collectively, studies presented in this article reveal that geologic nitrogen may be a large and reactive pool with potential for amplification of human impacts on nitrogen cycling in terrestrial and aquatic ecosystems.

  11. High-nitrogen explosives

    SciTech Connect

    Naud, D.; Hiskey, M. A.; Kramer, J. F.; Bishop, R. L.; Harry, H. H.; Son, S. F.; Sullivan, G. K.

    2002-01-01

    The syntheses and characterization of various tetrazine and furazan compounds offer a different approach to explosives development. Traditional explosives - such as TNT or RDX - rely on the oxidation of the carbon and hydrogen atoms by the oxygen carrying nitro group to produce the explosive energy. High-nitrogen compounds rely instead on large positive heats of formation for that energy. Some of these high-nitrogen compounds have been shown to be less sensitive to initiation (e.g. by impact) when compared to traditional nitro-containing explosives of similar performances. Using the precursor, 3,6-bis-(3,5-dimethylpyrazol-1-yl)-s-tetrazine (BDT), several useful energetic compounds based on the s-tetrazine system have been synthesized and studied. The compound, 3,3{prime}-azobis(6-amino-s-tetrazine) or DAAT, detonates as a half inch rate stick despite having no oxygen in the molecule. Using perfluoroacetic acid, DAAT can be oxidized to give mixtures of N-oxide isomers (DAAT03.5) with an average oxygen content of about 3.5. This energetic mixture burns at extremely high rates and with low dependency on pressure. Another tetrazine compound of interest is 3,6-diguanidino-s-tetrazine(DGT) and its dinitrate and diperchlorate salts. DGT is easily synthesized by reacting BDT with guanidine in methanol. Using Caro's acid, DGT can be further oxidized to give 3,6-diguanidino-s-tetrazine-1,4-di-N-oxide (DGT-DO). Like DGT, the di-N-oxide can react with nitric acid or perchloric acid to give the dinitrate and the diperchlorate salts. The compounds, 4,4{prime}-diamino-3,3{prime}-azoxyfurazan (DAAF) and 4,4{prime}-diamino-3,3{prime}-azofurazan (DAAzF), may have important future roles in insensitive explosive applications. Neither DAAF nor DAAzF can be initiated by laboratory impact drop tests, yet both have in some aspects better explosive performances than 1,3,5-triamino-2,4,6-trinitrobenzene TATB - the standard of insensitive high explosives. The thermal stability of DAAzF is

  12. Preprototype nitrogen supply subsystem development

    NASA Technical Reports Server (NTRS)

    Heppner, D. B.; Fort, J. H.; Schubert, F. H.

    1982-01-01

    The design and development of a test stand for the Nitrogen Generation Module (NGM) and a series of tests which verified its operation and performance capability are described. Over 900 hours of parametric testing were achieved. The results from this testing were then used to design an advanced NGM and a self contained, preprototype Nitrogen Supply Subsystem. The NGM consists of three major components: nitrogen generation module, pressure controller and hydrazine storage tank and ancillary components. The most important improvement is the elimination of all sealing surfaces, achieved with a total welded or brazed construction. Additionally, performance was improved by increasing hydrogen separating capability by 20% with no increase in overall packaging size.

  13. Cooling balloons with liquid nitrogen

    NASA Astrophysics Data System (ADS)

    Moreno, A. J.; Ferrari, H.; Bekeris, V.

    2010-12-01

    We present an undergraduate level experiment in which the radius of a rubber balloon is measured as it is cooled with liquid nitrogen. For balloons filled with simple gases that condense at liquid nitrogen temperatures, we found that the volume decreases linearly with time. We compared our measurements with a simplified model based on elementary kinetic theory and thermodynamics that explains this behavior. Students are encouraged to test the validity of the model by repeating the experiment using gas mixtures and gases that do not condense at liquid nitrogen temperatures.

  14. Melting line of polymeric nitrogen

    NASA Astrophysics Data System (ADS)

    Yakub, L. N.

    2013-05-01

    We made an attempt to predict location of the melting line of polymeric nitrogen using two equations for Helmholtz free energy: proposed earlier for cubic gauche-structure and developed recently for liquid polymerized nitrogen. The P-T relation, orthobaric densities and latent heat of melting were determined using a standard double tangent construction. The estimated melting temperature decreases with increasing pressure, alike the temperature of molecular-nonmolecular transition in solid. We discuss the possibility of a triple point (solid-molecular fluid-polymeric fluid) at ˜80 GPa and observed maximum of melting temperature of nitrogen.

  15. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa

    PubMed Central

    Raupach, Michael J.; Hannig, Karsten; Morinière, Jérome; Hendrich, Lars

    2016-01-01

    Abstract As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well. PMID:27408547

  16. Cantharellaceae of Guyana I: new species, combinations and distribution records of Craterellus and a synopsis of known taxa.

    PubMed

    Wilson, Andrew W; Aime, M Catherine; Dierks, Janina; Mueller, Gregory M; Henkel, Terry W

    2012-01-01

    Members of the Cantharellaceae (Cantharellales, Basidiomycota) are common ectomycorrhizal associates of the leguminous genus Dicymbe in the Pakaraima Mountains of Guyana. Eight distinct species or morphospecies currently are recognized in Craterellus Pers. or Cantharellus Adans. ex Fr. from Guyanese Dicymbe-dominated forests. We evaluated the systematics of these taxa with phylogenetic analyses of DNA sequence data from the nuclear ribosomal regions of the internal transcribed spacer (ITS) and 28S large subunit (LSU). The results of these analyses along with careful assessment of morphology let us described two new species, Craterellus atratoides sp. nov. and Craterellus strigosus sp. nov., redescribe Craterellus atratus (Corner) Yomyart et al. based on new material from Guyana, and propose a new combination in Craterellus for Cantharellus pleurotoides T.W. Henkel, Aime & S.L. Mill. Macroscopic illustrations are provided for two additional cantharelloid morphospecies confirmed in Craterellus, as well as the regionally endemic Cantharellus guyanensis Mont. Macromorphological, micromorphological and habitat data are provided for C. atratoides, C. strigosus and C. atratus, and ITS and LSU sequence data are provided for each of the eight known Guyanese taxa. PMID:22684285

  17. Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots

    PubMed Central

    Lewison, Rebecca L.; Crowder, Larry B.; Wallace, Bryan P.; Moore, Jeffrey E.; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C.; Kot, Connie Y.; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R.; Sims, Michelle; Boustany, Andre; Read, Andrew J.; Halpin, Patrick; Nichols, W. J.; Safina, Carl

    2014-01-01

    Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce—in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers—and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority. PMID:24639512

  18. Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms.

    PubMed

    Shiba, Takahiko; Watanabe, Takayasu; Kachi, Hirokazu; Koyanagi, Tatsuro; Maruyama, Noriko; Murase, Kazunori; Takeuchi, Yasuo; Maruyama, Fumito; Izumi, Yuichi; Nakagawa, Ichiro

    2016-01-01

    Polymicrobial diseases, which can be life threatening, are caused by the presence and interactions of multiple microbes. Peri-implantitis and periodontitis are representative polymicrobial diseases that show similar clinical symptoms. To establish a means of differentiating between them, we compared microbial species and functional genes in situ by performing metatranscriptomic analyses of peri-implantitis and periodontitis samples obtained from the same subjects (n = 12 each). Although the two diseases differed in terms of 16S rRNA-based taxonomic profiles, they showed similarities with respect to functional genes and taxonomic and virulence factor mRNA profiles. The latter-defined as microbial virulence types-differed from those of healthy periodontal sites. We also showed that networks based on co-occurrence relationships of taxonomic mRNA abundance (co-occurrence networks) were dissimilar between the two diseases. Remarkably, these networks consisted mainly of taxa with a high relative mRNA-to-rRNA ratio, with some showing significant co-occurrence defined as interacting core taxa, highlighting differences between the two groups. Thus, peri-implantitis and periodontitis have shared as well as distinct microbiological characteristics. Our findings provide insight into microbial interactions in polymicrobial diseases with unknown etiologies. PMID:27499042

  19. Unique method of tooth replacement in durophagous placodont marine reptiles, with new data on the dentition of Chinese taxa.

    PubMed

    Neenan, James M; Li, Chun; Rieppel, Olivier; Bernardini, Federico; Tuniz, Claudio; Muscio, Giuseppe; Scheyer, Torsten M

    2014-05-01

    The placodonts of the Triassic period (~252-201 mya) represent one of the earliest and most extreme specialisations to a durophagous diet of any known reptile group. Exceptionally enlarged crushing tooth plates on the maxilla, dentary and palatine cooperated to form functional crushing areas in the buccal cavity. However, the extreme size of these teeth, combined with the unusual way they occluded, constrained how replacement occurred. Using an extensive micro-computed tomographic dataset of 11 specimens that span all geographic regions and placodont morphotypes, tooth replacement patterns were investigated. In addition, the previously undescribed dental morphologies and formulae of Chinese taxa are described for the first time and incorporated into the analysis. Placodonts have a unique tooth replacement pattern and results follow a phylogenetic trend. The plesiomorphic Placodus species show many replacement teeth at various stages of growth, with little or no discernible pattern. On the other hand, the more derived cyamodontoids tend to have fewer replacement teeth growing at any one time, replacing teeth unilaterally and/or in functional units, thus maintaining at least one functional crushing area at all times. The highly derived placochelyids have fewer teeth and, as a result, only have one or two replacement teeth in the upper jaw. This supports previous suggestions that these taxa had an alternative diet to other placodonts. Importantly, all specimens show at least one replacement tooth growing at the most posterior palatine tooth plates, indicating increased wear at this point and thus the most efficient functional crushing area. PMID:24517163

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

    PubMed

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

    2015-01-01

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

  1. New taxa of angiosperm pollen, miospores and associated palynomorphs from the early Late Cretaceous of Egypt (Maghrabi Formation, Kharga Oasis).

    PubMed

    Schrank; Mahmoud

    2000-10-01

    A palynological investigation of samples from various boreholes in the Maghrabi Formation (Kharga Oasis, southern Egypt) resulted in the recovery of pollen and spore assemblages associated with rare marine palynofossils (dinoflagellates, foraminiferal linings) and freshwater algae (e.g. Botryococcus, Ovoidites parvus, Pediastrum, Scenedesmus). The general composition of the assemblages is largely consistent with the estuarine and tidal flat conditions characteristic of the Maghrabi Formation.The formal descriptions of the following new taxa are given: Cicatricosisporites kedvesii Schrank, sp. nov., Equisetosporites lawalii Schrank, sp. nov., Dettmannaepollenites clavatus Schrank, sp. nov., and Integritetradites porosus Schrank and Mahmoud, gen. nov. and sp. nov. Combined scanning electron microscopic and light microscopic techniques have been applied to hand-picked grains to illustrate the new taxa. The palynological ages assigned to the Maghrabi samples are mainly based on angiosperm pollen and range from undifferentiated Cenomanian for an Integritetradites porosus assemblage without triporates to Late Cenomanian-Early Turonian for another assemblage which has I. porosus associated with rare triporate pollen grains (Proteacidites/'Triorites' spp.). PMID:11042331

  2. Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots.

    PubMed

    Pei, Nancai; Erickson, David L; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G; Zhang, Jin-Long; Jones, Frank A; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A; Parker, John D; Zimmerman, Jess K; McShea, William J; Lopez, Ida C; Sun, I-Fang; Davies, Stuart J; Ma, Keping; Kress, W John

    2015-01-01

    To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities. PMID:26456472

  3. Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots

    PubMed Central

    Pei, Nancai; Erickson, David L.; Chen, Bufeng; Ge, Xuejun; Mi, Xiangcheng; Swenson, Nathan G.; Zhang, Jin-Long; Jones, Frank A.; Huang, Chun-Lin; Ye, Wanhui; Hao, Zhanqing; Hsieh, Chang-Fu; Lum, Shawn; Bourg, Norman A.; Parker, John D.; Zimmerman, Jess K.; McShea, William J.; Lopez, Ida C.; Sun, I-Fang; Davies, Stuart J.; Ma, Keping; Kress, W. John

    2015-01-01

    To determine how well DNA barcodes from the chloroplast region perform in forest dynamics plots (FDPs) from global CTFS-ForestGEO network, we analyzed DNA barcoding sequences of 1277 plant species from a wide phylogenetic range (3 FDPs in tropics, 5 in subtropics and 5 in temperate zone) and compared the rates of species discrimination (RSD). We quantified RSD by two DNA barcode combinations (rbcL + matK and rbcL + matK + trnH-psbA) using a monophyly-based method (GARLI). We defined two indexes of closely-related taxa (Gm/Gt and S/G ratios) and correlated these ratios with RSD. The combination of rbcL + matK averagely discriminated 88.65%, 83.84% and 72.51% at the local, regional and global scales, respectively. An additional locus trnH-psbA increased RSD by 2.87%, 1.49% and 3.58% correspondingly. RSD varied along a latitudinal gradient and were negatively correlated with ratios of closely-related taxa. Successes of species discrimination generally depend on scales in global FDPs. We suggested that the combination of rbcL + matK + trnH-psbA is currently applicable for DNA barcoding-based phylogenetic studies on forest communities. PMID:26456472

  4. Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots.

    PubMed

    Lewison, Rebecca L; Crowder, Larry B; Wallace, Bryan P; Moore, Jeffrey E; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C; Kot, Connie Y; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R; Sims, Michelle; Boustany, Andre; Read, Andrew J; Halpin, Patrick; Nichols, W J; Safina, Carl

    2014-04-01

    Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce--in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers--and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority. PMID:24639512

  5. Adaptations and Predispositions of Different Middle European Arthropod Taxa (Collembola, Araneae, Chilopoda, Diplopoda) to Flooding and Drought Conditions

    PubMed Central

    Marx, Michael Thomas; Guhmann, Patrick; Decker, Peter

    2012-01-01

    Simple Summary This review summarizes adaptations and predispositions of different arthropod taxa (springtails, web spiders, millipedes and centipedes) to flood and drought conditions. The main focus sis directed to arthropod species, which are living in Middle European floodplain forests and wetlands, because of the fast change of flood and drought conditions in these habitats. Furthermore the effects of the predicted regional climate change like increasing aperiodic summer flooding and decreasing winter and spring floods are also discussed. Abstract Floodplain forests and wetlands are amongst the most diverse and species rich habitats on earth. Arthropods are a key group for the high diversity pattern of these landscapes, due to the fact that the change between flooding and drought causes in different life cycles and in a variety of adaptations in the different taxa. The floodplain forests and wetlands of Central Amazonia are well investigated and over the last 50 years many adaptations of several hexapod, myriapod and arachnid orders were described. In contrast to Amazonia the Middle European floodplains were less investigated concerning the adaptations of arthropods to flood and drought conditions. This review summarizes the adaptations and predispositions of springtails, web spiders, millipedes and centipedes to the changeable flood and drought conditions of Middle European floodplain forests and wetlands. Furthermore the impact of regional climate change predictions like increasing aperiodic summer floods and the decrease of typical winter and spring floods are discussed in this article. PMID:26487164

  6. From Problem Taxa to Problem Solver: A New Miocene Family, Tranatocetidae, Brings Perspective on Baleen Whale Evolution

    PubMed Central

    Gol’din, Pavel; Steeman, Mette Elstrup

    2015-01-01

    Miocene baleen whales were highly diverse and included tens of genera. However, their taxonomy and phylogeny, as well as relationships with living whales, are still a subject of controversy. Here, “Mesocetus” argillarius, a poorly known specimen from Denmark, is redescribed with a focus on the cranial anatomy. It was found to represent not only a new genus, Tranatocetus gen. nov., but also a new family; Tranatocetidae. The whales of this family have the rostral bones either overriding or dividing the frontals; the rostral bones are contacting the parietals and nasals dividing the maxillae on the vertex; the occipital shield is dorsoventrally bent. The tympanic bulla is particularly characteristic of this family featuring a short, narrow anterior portion with a rounded or squared anterior end and a wider and higher posterior portion that is swollen in the posteroventral area. A phylogenetic analysis including 51 taxa supports a monophyletic group comprising most Neogene and modern whales, with Tranatocetidae being possibly closer related to Balaenopteridae (rorquals) than to Cetotheriidae. Tranatocetidae exhibit a charahteristic bulla shape. In fact, all Neogene and modern mysticete families examined have a unique shape of the tympanic bulla that is diagnostic at family-level. Inclusion of problematic taxa like Tranatocetus argillarius in phylogenies brings new understanding of the distribution and diagnostic value of character traits. This underlines the need for re-examination of earlier described specimens in the light of the wealth of new information published in later years. PMID:26331471

  7. Life history profiles for 27 strepsirrhine primate taxa generated using captive data from the Duke Lemur Center

    PubMed Central

    Zehr, Sarah M; Roach, Richard G; Haring, David; Taylor, Julie; Cameron, Freda H; Yoder, Anne D

    2014-01-01

    Since its establishment in 1966, the Duke Lemur Center (DLC) has accumulated detailed records for nearly 4,200 individuals from over 40 strepsirrhine primate taxa—the lemurs, lorises, and galagos. Here we present verified data for 3,627 individuals of 27 taxa in the form of a life history table containing summarized species values for variables relating to ancestry, reproduction, longevity, and body mass, as well as the two raw data files containing direct and calculated variables from which this summary table is built. Large sample sizes, longitudinal data that in many cases span an animal’s entire life, exact dates of events, and large numbers of individuals from closely related yet biologically diverse primate taxa make these datasets unique. This single source for verified raw data and systematically compiled species values, particularly in combination with the availability of associated biological samples and the current live colony for research, will support future studies from an enormous spectrum of disciplines. PMID:25977776

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

    PubMed Central

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

    2015-01-01

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

  9. Quantitation of Crocins and picrocrocin in saffron by HPLC: application to quality control and phytochemical differentiation from other crocus taxa.

    PubMed

    Koulakiotis, Nikolaos Stavros; Gikas, Evangelos; Iatrou, Gregoris; Lamari, Fotini N; Tsarbopoulos, Anthony

    2015-05-01

    A chromatographic method was developed and fully validated for the determination of the major saffron constituents, i.e., picrocrocin and five major crocins. Dried samples (styles of Crocus sativus and other Crocus taxa) were extracted with MeOH : water (1 : 1, v/v), and chromatographic separation of the analytes was achieved by reversed-phase chromatography using a gradient elution. Full validation was performed using spiked samples with analytes, which were isolated, purified, and characterized by MS due to a lack of commercial standards. The method showed a good fit (r2 > 0.999) for all analytes with limit of quantitation values in the range of 1-15 µg/mL, and demonstrated adequate intra- and inter-precision (< 15 % RSD) and accuracy (< 7 % RE). The method was applied to the analysis of various commercial saffron samples and of indigenous Crocus taxa and allowed for the first time the absolute quantitation of several Crocus components. PMID:26018797

  10. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa.

    PubMed

    Raupach, Michael J; Hannig, Karsten; Morinière, Jérome; Hendrich, Lars

    2016-01-01

    As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well. PMID:27408547

  11. Distance-Decay and Taxa-Area Relationships for Bacteria, Archaea and Methanogenic Archaea in a Tropical Lake Sediment

    PubMed Central

    Barreto, Davi Pedroni; Conrad, Ralf; Klose, Melanie; Claus, Peter; Enrich-Prast, Alex

    2014-01-01

    The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship. PMID:25330320

  12. Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms

    PubMed Central

    Shiba, Takahiko; Watanabe, Takayasu; Kachi, Hirokazu; Koyanagi, Tatsuro; Maruyama, Noriko; Murase, Kazunori; Takeuchi, Yasuo; Maruyama, Fumito; Izumi, Yuichi; Nakagawa, Ichiro

    2016-01-01

    Polymicrobial diseases, which can be life threatening, are caused by the presence and interactions of multiple microbes. Peri-implantitis and periodontitis are representative polymicrobial diseases that show similar clinical symptoms. To establish a means of differentiating between them, we compared microbial species and functional genes in situ by performing metatranscriptomic analyses of peri-implantitis and periodontitis samples obtained from the same subjects (n = 12 each). Although the two diseases differed in terms of 16S rRNA-based taxonomic profiles, they showed similarities with respect to functional genes and taxonomic and virulence factor mRNA profiles. The latter—defined as microbial virulence types—differed from those of healthy periodontal sites. We also showed that networks based on co-occurrence relationships of taxonomic mRNA abundance (co-occurrence networks) were dissimilar between the two diseases. Remarkably, these networks consisted mainly of taxa with a high relative mRNA-to-rRNA ratio, with some showing significant co-occurrence defined as interacting core taxa, highlighting differences between the two groups. Thus, peri-implantitis and periodontitis have shared as well as distinct microbiological characteristics. Our findings provide insight into microbial interactions in polymicrobial diseases with unknown etiologies. PMID:27499042

  13. Energy, industry and nitrogen: strategies for decreasing reactive nitrogen emissions.

    PubMed

    Moomaw, William R

    2002-03-01

    Nitrogen oxides are released during atmospheric combustion of fossil fuels and biomass, and during the production of certain chemicals and products. They can react with natural or man-made volatile organic compounds to produce smog, or else can be further oxidized to produce particulate haze, or acid rain that can eutrophy land and water. The reactive nitrogen that begins in the energy sector thus cascades through the atmosphere, the hydrosphere and soils before being eventually partially denitrifed to the global warming and stratospheric ozone-depleting gas nitrous oxide or molecular nitrogen. This paper will suggest how an economic analysis of the nitrogen cycle can identify the most cost-effective places to intervene. Nitrogen oxides released during fossil-fuel combustion in vehicles, power plants and heating boilers can either be controlled by add-on emission control technology, or can be eliminated by many of the same technical options that lead to carbon dioxide reduction. These integrated strategies also address sustainability, economic development and national security issues. Similarly in industrial production, it is more effective to focus on redesigning industrial processes rather than on nitrogen oxide pollution elimination from the current system. This paper will suggest which strategies might be utilized to address multiple benefits rather than focusing on single pollutants. PMID:12078008

  14. Metazoan meiofauna in deep-sea canyons and adjacent open slopes: A large-scale comparison with focus on the rare taxa

    NASA Astrophysics Data System (ADS)

    Bianchelli, S.; Gambi, C.; Zeppilli, D.; Danovaro, R.

    2010-03-01

    Metazoan meiofaunal abundance, total biomass, nematode size and the richness of taxa were investigated along bathymetric gradients (from the shelf break down to ca. 5000-m depth) in six submarine canyons and on five adjacent open slopes of three deep-sea regions. The investigated areas were distributed along >2500 km, on the Portuguese to the Catalan and South Adriatic margins. The Portuguese and Catalan margins displayed the highest abundances, biomass and richness of taxa, while the lowest values were observed in the Central Mediterranean Sea. The comparison between canyons and the nearby open slopes showed the lack of significant differences in terms of meiofaunal abundance and biomass at any sampling depth. In most canyons and on most slopes, meiofaunal variables did not display consistent bathymetric patterns. Conversely, we found that the different topographic features were apparently responsible for significant differences in the abundance and distribution of the rare meiofaunal taxa (i.e. taxa accounting for <1% of total meiofaunal abundance). Several taxa belonging to the temporary meiofauna, such as larvae/juveniles of Priapulida, Holothuroidea, Ascidiacea and Cnidaria, were encountered exclusively on open slopes, while others (including the Tanaidacea and Echinodea larvae) were found exclusively in canyons sediments. Results reported here indicate that, at large spatial scales, differences in deep-sea meiofaunal abundance and biomass are not only controlled by the available food sources, but also by the region or habitat specific topographic features, which apparently play a key role in the distribution of rare benthic taxa.

  15. The nitrogen cycle on Mars

    NASA Technical Reports Server (NTRS)

    Mancinelli, Rocco L.

    1989-01-01

    Nirtogen is an essential element for the evolution of life, because it is found in a variety of biologically important molecules. Therefore, N is an important element to study from a exobiological perspective. In particular, fixed nitrogen is the biologically useful form of nitrogen. Fixed nitrogen is generally defines as NH3, NH4(+), NO(x), or N that is chemically bound to either inorganic or organic molecules, and releasable by hydrolysis to NH3 or NH4(+). On Earth, the vast majority of nitrogen exists as N2 in the atmosphere, and not in the fixes form. On early Mars the same situations probably existed. The partial pressure of N2 on early Mars was thought to be 18 mb, significantly less than that of Earth. Dinitrogen can be fixed abiotically by several mechanisms. These mechanisms include thernal shock from meteoritic infall and lightning, as well as the interaction of light and sand containing TiO2 which produces NH3 that would be rapidly destroyed by photolysis and reaction with OH radicals. These mechanisms could have been operative on primitive Mars.The chemical processes effecting these compounds and possible ways of fixing or burying N in the Martian environment are described. Data gathered in this laboratory suggest that the low abundance of nitrogen along (compared to primitive Earth) may not significantly deter the origin and early evolution of a nitrogen utilizing organisms. However, the conditions on current Mars with respect to nitrogen are quite different, and organisms may not be able to utilize all of the available nitrogen.

  16. Enhanced nitrogen deposition over China.

    PubMed

    Liu, Xuejun; Zhang, Ying; Han, Wenxuan; Tang, Aohan; Shen, Jianlin; Cui, Zhenling; Vitousek, Peter; Erisman, Jan Willem; Goulding, Keith; Christie, Peter; Fangmeier, Andreas; Zhang, Fusuo

    2013-02-28

    China is experiencing intense air pollution caused in large part by anthropogenic emissions of reactive nitrogen. These emissions result in the deposition of atmospheric nitrogen (N) in terrestrial and aquatic ecosystems, with implications for human and ecosystem health, greenhouse gas balances and biological diversity. However, information on the magnitude and environmental impact of N deposition in China is limited. Here we use nationwide data sets on bulk N deposition, plant foliar N and crop N uptake (from long-term unfertilized soils) to evaluate N deposition dynamics and their effect on ecosystems across China between 1980 and 2010. We find that the average annual bulk deposition of N increased by approximately 8 kilograms of nitrogen per hectare (P < 0.001) between the 1980s (13.2 kilograms of nitrogen per hectare) and the 2000s (21.1 kilograms of nitrogen per hectare). Nitrogen deposition rates in the industrialized and agriculturally intensified regions of China are as high as the peak levels of deposition in northwestern Europe in the 1980s, before the introduction of mitigation measures. Nitrogen from ammonium (NH4(+)) is the dominant form of N in bulk deposition, but the rate of increase is largest for deposition of N from nitrate (NO3(-)), in agreement with decreased ratios of NH3 to NOx emissions since 1980. We also find that the impact of N deposition on Chinese ecosystems includes significantly increased plant foliar N concentrations in natural and semi-natural (that is, non-agricultural) ecosystems and increased crop N uptake from long-term-unfertilized croplands. China and other economies are facing a continuing challenge to reduce emissions of reactive nitrogen, N deposition and their negative effects on human health and the environment. PMID:23426264

  17. Nitrogen removal from natural gas

    SciTech Connect

    1997-04-01

    According to a 1991 Energy Information Administration estimate, U.S. reserves of natural gas are about 165 trillion cubic feet (TCF). To meet the long-term demand for natural gas, new gas fields from these reserves will have to be developed. Gas Research Institute studies reveal that 14% (or about 19 TCF) of known reserves in the United States are subquality due to high nitrogen content. Nitrogen-contaminated natural gas has a low Btu value and must be upgraded by removing the nitrogen. In response to the problem, the Department of Energy is seeking innovative, efficient nitrogen-removal methods. Membrane processes have been considered for natural gas denitrogenation. The challenge, not yet overcome, is to develop membranes with the required nitrogen/methane separation characteristics. Our calculations show that a methane-permeable membrane with a methane/nitrogen selectivity of 4 to 6 would make denitrogenation by a membrane process viable. The objective of Phase I of this project was to show that membranes with this target selectivity can be developed, and that the economics of the process based on these membranes would be competitive. Gas permeation measurements with membranes prepared from two rubbery polymers and a superglassy polymer showed that two of these materials had the target selectivity of 4 to 6 when operated at temperatures below - 20{degrees}C. An economic analysis showed that a process based on these membranes is competitive with other technologies for small streams containing less than 10% nitrogen. Hybrid designs combining membranes with other technologies are suitable for high-flow, higher-nitrogen-content streams.

  18. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    PubMed

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats. PMID:26790863

  19. Anaerobic Nitrogen Fixers on Mars

    NASA Astrophysics Data System (ADS)

    Lewis, B. G.

    2000-07-01

    The conversion of atmospheric nitrogen gas to the protein of living systems is an amazing process of nature. The first step in the process is biological nitrogen fixation, the transformation of N2 to NH3. The phenomenon is crucial for feeding the billions of our species on Earth. On Mars, the same process may allow us to discover how life can adapt to a hostile environment, and render it habitable. Hostile environments also exist on Earth. For example, nothing grows in coal refuse piles due to the oxidation of pyrite and marcasite to sulfuric acid. Yet, when the acidity is neutralized, alfalfa and soybean plants develop root nodules typical of symbiotic nitrogen fixation with Rhizobium species possibly living in the pyritic material. When split open, these nodules exhibited the pinkish color of leghemoglobin, a protein in the nodule protecting the active nitrogen-fixing enzyme nitrogenase against the toxic effects of oxygen. Although we have not yet obtained direct evidence of nitrogenase activity in these nodules (reduction of acetylene to ethylene, for example), these findings suggested the possibility that nitrogen fixation was taking place in this hostile, non-soil material. This immediately raises the possibility that freeliving anaerobic bacteria which fix atmospheric nitrogen on Earth, could do the same on Mars.

  20. Atlas of relations between climatic parameters and distributions of important trees and shrubs in North America: Revisions for all taxa from the United States and Canada and new taxa from the western United States

    USGS Publications Warehouse

    Thompson, Robert S.; Anderson, Katherine H.; Pelltier, Richard T.; Strickland, Laura E.; Shafer, Sarah L.; Bartlein, Patrick J.; McFadden, Andrew K.

    2015-01-01

    This volume of the atlas provides numerous changes, updates, and enhancements from previous volumes. Its geographic coverage is now restricted to Canada and the continental United States, and the source and time period of the climatic data have changed. New variables were added, including monthly values for temperature and precipitation, and measures of interannual variability. The distribution maps for all previously published species were redigitized, some distribution maps were revised, and 148 new species were added from the arid and semiarid western United States. The graphical displays were expanded to illustrate the new climatic variables, and the data tables were modified to provide more detail on the population distributions of plant taxa relative to climatic variables.

  1. Belowground processes regulate ecosystem nitrogen retention during a multi-year forest dieback event

    NASA Astrophysics Data System (ADS)

    Nave, L. E.; Le Moine, J.; Gough, C. M.; Vogel, C.; Nadelhoffer, K. J.; Curtis, P.

    2013-12-01

    In the absence of disturbances, forests typically have strong retention capacity for nitrogen (N), which is internally recycled between soil, microbial and plant pools. However, disturbances that trigger senescence or mortality of forest vegetation may alter internal N cycling processes and lead to the loss of ecosystem N retention capacity. Here, we present an assessment of the role played by belowground processes in governing ecosystem N cycling and retention during an experimental disturbance that killed the dominant canopy taxa in a Great Lakes forest over a 4-year period. After applying stem girdling to hasten the age-related senescence of the dominant taxa (Populus and Betula spp.; ~35% of the basal area), we observed a 38% decrease in stand-level allocation of nonstructural carbohydrates to fine roots, which triggered a tenfold increase in the rate of fine root turnover and increased soil NH4+ and NO3- availability. Elevated soil N availability decreased mycorrhizal hyphal foraging and N uptake, effectively down-regulating the role of symbiotic fungi in the N nutrition of the residual (longer-lived) tree taxa. However, even as residual trees took up less N from mycorrhizal sources, their overall N uptake increased and served to offset the loss of the dominant taxa. The net result of this offset was that canopy N stocks remained constant through the disturbance period and there was no appreciable loss of ecosystem N stocks due to leaching or gaseous export. In sum, the cascade of changes in root, microbial, and soil processes during this experiment indicates that these interdependent components of the belowground system comprised a mechanism responsible for retention and redistribution of ecosystem N stocks during the disturbance period.

  2. Sources and fate of bioavailable dissolved organic nitrogen in the Neuse River Estuary, North Carolina

    NASA Astrophysics Data System (ADS)

    Paerl, H. W.; Peierls, B. L.; Hounshell, A.; Osburn, C. L.

    2015-12-01

    Eutrophication is a widespread problem affecting the structure and function of estuaries and is often linked to anthropogenic nitrogen (N) enrichment, since N is the primary nutrient limiting algal production. Watershed management actions typically have ignored dissolved organic nitrogen (DON) loading because of its perceived refractory nature and instead focused on inorganic N as targets for loading reductions. A fluorescence-based model indicated that anthropogenic sources of DON near the head of the microtidal Neuse River Estuary (NRE), NC were dominated by septic systems and poultry waste. A series of bioassays were used to determine the bioavailability of river DON and DON-rich sources to primary producers and whether those additions promoted the growth of certain phytoplankton taxa, particularly harmful species. Overall, at time scales up to two to three weeks, estuarine phytoplankton and bacteria only showed limited responses to additions of high molecular weight (HMW, >1 kDa) river DON. When increases in productivity and biomass did occur, they were quite small compared with the response to inorganic N. Low molecular weight (LMW) river DON, waste water treatment plant effluent, and poultry litter extract did have a positive effect on phytoplankton and bacterial production, indicating a bioavailable fraction. High variability of bulk DON concentration suggested that bioavailable compounds added in the experimental treatments were low in concentration and turned over quite rapidly. Some phytoplankton taxa, as measured by diagnostic photopigments, appeared to be selectively enhanced by the HMW and specific source DON additions, although the taxa could not be positively identified as harmful species. Preliminary tests show that labile autochthonous organic matter may act as a primer for the mineralization of the HMW DON. These and other, longer-term bioavailability studies will be needed to adequately address the fate of watershed DON in estuarine ecosystems.

  3. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2013 CFR

    2007-04-01

    ... 21 Food and Drugs 3 2007-04-01 2007-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... Substances Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9... air. (b) The Food and Drug Administration is developing food-grade specifications for nitrogen...

  4. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2012 CFR

    2003-04-01

    ... 21 Food and Drugs 3 2003-04-01 2003-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... Substances Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9... air. (b) The Food and Drug Administration is developing food-grade specifications for nitrogen...

  5. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2011 CFR

    2005-04-01

    ... 21 Food and Drugs 3 2005-04-01 2005-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... Substances Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9... air. (b) The Food and Drug Administration is developing food-grade specifications for nitrogen...

  6. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2013 CFR

    2002-04-01

    ... 21 Food and Drugs 3 2002-04-01 2002-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9) is a...) The Food and Drug Administration is developing food-grade specifications for nitrogen in...

  7. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2013 CFR

    2000-04-01

    ... 21 Food and Drugs 3 2000-04-01 2000-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9) is a...) The Food and Drug Administration is developing food-grade specifications for nitrogen in...

  8. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2013 CFR

    1999-04-01

    ... 21 Food and Drugs 3 1999-04-01 1999-04-01 false Nitrogen. 184.1540 Section 184.1540 FOOD FOR HUMAN... Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9) is a...) The Food and Drug Administration is developing food-grade specifications for nitrogen in...

  9. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2013 CFR

    1998-04-01

    ... 21 Food and Drugs 3 1998-04-01 1998-04-01 false Nitrogen. 184.1540 Section 184.1540 FOOD FOR HUMAN... Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9) is a...) The Food and Drug Administration is developing food-grade specifications for nitrogen in...

  10. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2011 CFR

    1996-04-01

    ... 21 FOOD AND DRUGS 3 1996-04-01 1996-04-01 false Nitrogen. 184.1540 Sec. 184.1540 FOOD AND DRUGS... Affirmed as GRAS Sec. 184.1540 Nitrogen. (a) Nitrogen (empirical formula N 2, CAS Reg. No. 7727-37-9) is a...) The Food and Drug Administration is developing food-grade specifications for nitrogen in...

  11. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2011 CFR

    2001-04-01

    ... 21 Food and Drugs 3 2001-04-01 2001-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9) is a...) The Food and Drug Administration is developing food-grade specifications for nitrogen in...

  12. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2012 CFR

    1997-04-01

    ... 21 Food and Drugs 3 1997-04-01 1997-04-01 false Nitrogen. 184.1540 Section 184.1540 FOOD FOR HUMAN... Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9) is a...) The Food and Drug Administration is developing food-grade specifications for nitrogen in...

  13. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2010 CFR

    2004-04-01

    ... 21 Food and Drugs 3 2004-04-01 2004-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... Substances Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9... air. (b) The Food and Drug Administration is developing food-grade specifications for nitrogen...

  14. 21 CFR 184.1540 - Nitrogen.

    Code of Federal Regulations, 2011 CFR

    2006-04-01

    ... 21 Food and Drugs 3 2006-04-01 2006-04-01 false Nitrogen. 184.1540 Section 184.1540 Food and Drugs... Substances Affirmed as GRAS § 184.1540 Nitrogen. (a) Nitrogen (empirical formula N2, CAS Reg. No. 7727-37-9... air. (b) The Food and Drug Administration is developing food-grade specifications for nitrogen...

  15. Seasonality and paleoecology of the late Cretaceous multi-taxa vertebrate assemblage of "Lo Hueco" (central eastern Spain).

    PubMed

    Domingo, Laura; Barroso-Barcenilla, Fernando; Cambra-Moo, Oscar

    2015-01-01

    Isotopic studies of multi-taxa terrestrial vertebrate assemblages allow determination of paleoclimatic and paleoecological aspects on account of the different information supplied by each taxon. The late Campanian-early Maastrichtian "Lo Hueco" Fossil-Lagerstätte (central eastern Spain), located at a subtropical paleolatitude of ~31°N, constitutes an ideal setting to carry out this task due to its abundant and diverse vertebrate assemblage. Local δ18OPO4 values estimated from δ18OPO4 values of theropods, sauropods, crocodyliforms, and turtles are close to δ18OH2O values observed at modern subtropical latitudes. Theropod δ18OH2O values are lower than those shown by crocodyliforms and turtles, indicating that terrestrial endothermic taxa record δ18OH2O values throughout the year, whereas semiaquatic ectothermic taxa δ18OH2O values represent local meteoric waters over a shorter time period when conditions are favorable for bioapatite synthesis (warm season). Temperatures calculated by combining theropod, crocodyliform, and turtle δ18OH2O values and gar δ18OPO4 have enabled us to estimate seasonal variability as the difference between mean annual temperature (MAT, yielded by theropods) and temperature of the warmest months (TWMs, provided by crocodyliforms and turtles). ΔTWMs-MAT value does not point to a significantly different seasonal thermal variability when compared to modern coastal subtropical meteorological stations and Late Cretaceous rudists from eastern Tethys. Bioapatite and bulk organic matter δ13C values point to a C3 environment in the "Lo Hueco" area. The estimated fractionation between sauropod enamel and diet is ~15‰. While waiting for paleoecological information yielded by the ongoing morphological study of the "Lo Hueco" crocodyliforms, δ13C and δ18OCO3 results point to incorporation of food items with brackish influence, but preferential ingestion of freshwater. "Lo Hueco" turtles showed the lowest δ13C and δ18OCO3 values of the

  16. Seasonality and Paleoecology of the Late Cretaceous Multi-Taxa Vertebrate Assemblage of “Lo Hueco” (Central Eastern Spain)

    PubMed Central

    Domingo, Laura; Barroso-Barcenilla, Fernando; Cambra-Moo, Oscar

    2015-01-01

    Isotopic studies of multi-taxa terrestrial vertebrate assemblages allow determination of paleoclimatic and paleoecological aspects on account of the different information supplied by each taxon. The late Campanian-early Maastrichtian “Lo Hueco” Fossil-Lagerstätte (central eastern Spain), located at a subtropical paleolatitude of ~31°N, constitutes an ideal setting to carry out this task due to its abundant and diverse vertebrate assemblage. Local δ18OPO4 values estimated from δ18OPO4 values of theropods, sauropods, crocodyliforms, and turtles are close to δ18OH2O values observed at modern subtropical latitudes. Theropod δ18OH2O values are lower than those shown by crocodyliforms and turtles, indicating that terrestrial endothermic taxa record δ18OH2O values throughout the year, whereas semiaquatic ectothermic taxa δ18OH2O values represent local meteoric waters over a shorter time period when conditions are favorable for bioapatite synthesis (warm season). Temperatures calculated by combining theropod, crocodyliform, and turtle δ18OH2O values and gar δ18OPO4 have enabled us to estimate seasonal variability as the difference between mean annual temperature (MAT, yielded by theropods) and temperature of the warmest months (TWMs, provided by crocodyliforms and turtles). ΔTWMs-MAT value does not point to a significantly different seasonal thermal variability when compared to modern coastal subtropical meteorological stations and Late Cretaceous rudists from eastern Tethys. Bioapatite and bulk organic matter δ13C values point to a C3 environment in the “Lo Hueco” area. The estimated fractionation between sauropod enamel and diet is ~15‰. While waiting for paleoecological information yielded by the ongoing morphological study of the “Lo Hueco” crocodyliforms, δ13C and δ18OCO3 results point to incorporation of food items with brackish influence, but preferential ingestion of freshwater. “Lo Hueco” turtles showed the lowest δ13C and δ18OCO3

  17. New proposals for naming lower-ranked taxa within the frame of the International Code of Zoological Nomenclature.

    PubMed

    Dubois, Alain

    2006-10-01

    The recent multiplication of cladistic hypotheses for many zoological groups poses a challenge to zoological nomenclature following the International Code of Zoological Nomenclature: in order to account for these hypotheses, we will need many more ranks than currently allowed in this system, especially in lower taxonomy (around the ranks genus and species). The current Code allows the use of as many ranks as necessary in the family-series of nomina (except above superfamily), but forbids the use of more than a few ranks in the genus and species-series. It is here argued that this limitation has no theoretical background, does not respect the freedom of taxonomic thoughts or actions, and is harmful to zoological taxonomy in two respects at least: (1) it does not allow to express in detail hypothesized cladistic relationships among taxa at lower taxonomic levels (genus and species); (2) it does not allow to point taxonomically to low-level differentiation between populations of the same species, although this would be useful in some cases for conservation biology purposes. It is here proposed to modify the rules of the Code in order to allow use by taxonomists of an indeterminate number of ranks in all nominal-series. Such an 'expanded nomenclatural system' would be highly flexible and likely to be easily adapted to any new finding or hypothesis regarding cladistic relationships between taxa, at genus and species level and below. This system could be useful for phylogeographic analysis and in conservation biology. In zoological nomenclature, whereas robustness of nomina is necessary, the same does not hold for nomenclatural ranks, as the latter are arbitrary and carry no special biological, evolutionary or other information, except concerning the mutual relationships between taxa in the taxonomic hierarchy. Compared to the Phylocode project, the new system is equally unambiguous within the frame of a given taxonomic frame, but it provides more explicit and

  18. Towards a phylogenetic generic classification of Thelypteridaceae: Additional sampling suggests alterations of neotropical taxa and further study of paleotropical genera.

    PubMed

    Almeida, Thaís Elias; Hennequin, Sabine; Schneider, Harald; Smith, Alan R; Batista, João Aguiar Nogueira; Ramalho, Aline Joseph; Proite, Karina; Salino, Alexandre

    2016-01-01

    Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 68 taxa and 134 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 73 rps4 and 72 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 149 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta

  19. Evaluation of a spacecraft nitrogen generator

    NASA Technical Reports Server (NTRS)

    Marshall, R. D.; Powell, J. D.

    1976-01-01

    A method is discussed of generating nitrogen for cabin leakage makeup aboard space vehicles having longer duration missions. The nitrogen generation concept is based on using liquid hydrazine as the stored form of nitrogen to reduce the higher tankage and expendables weight associated with high pressure gaseous or cryogenic liquid nitrogen storage. The hydrazine is catalytically dissociated to yield a mixture of nitrogen and hydrogen. The nitrogen/hydrogen mixture is then separated to yield the makeup nitrogen. The excess supply of hydrogen would be available for use in the reduction of metabolic carbon dioxide. A detailed comparison was completed of Palladium/Silver and Polymer Electrochemical-based Nitrogen Generation Systems. The palladium/silver-based system was judged better than the Polymer Electrochemical Nitrogen Generation System because of lower expendable weight and palladium/silver nitrogen/hydrogen separation represents 'off-the-shelf' technology.

  20. [Diversity of nitrogen-fixing microorganisms in biological soil crusts of copper mine wastelands].

    PubMed

    Zhan, Jing; Yang, Gui-De; Sun, Qing-Ye

    2014-06-01

    Biological soil crusts play an important role in increasing the accumulation of organic matter and nitrogen in re-vegetated mining wastelands. The diversity of nitrogen-fixing microorganisms in three types of biological soil crusts (algal crust, moss crust and algal-moss crust) from two wastelands of copper mine tailings were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis, based on the nifH gene of diazotrophs, to investigate: The diversity of nifH gene in the crusts of mine wastelands, and whether and how the nifH gene diversity in the crusts could be affected by the development of plant communities. The algal crust on the barren area displayed the highest nifH gene diversity, followed by the algal-moss crusts within vascular plant communities, and the moss crust displayed the lowest nifH gene diversity. The diversity of diazotrophs in algal-moss crust within vascular plant communities decreased with the increase of height and cover of vascular plant communities. No significant relationship was found between wasteland properties (pH, water content, contents of organic matter, nitrogen and phosphorus and heavy metal concentration) and nifH gene diversity in the crusts. Sequencing and phylogenetic analysis indicated that most nitrogen-fixing taxa in the crusts of mine wastelands belonged to Cyanobacteria, especially nonheterocystous filamentous Cyanobacteria. PMID:25223036

  1. On cockroaches of the subfamily Epilamprinae (Dictyoptera: Blaberidae) from South India and Sri Lanka, with descriptions of new taxa.

    PubMed

    Anisyutkin, Leonid N

    2014-01-01

    The new genus Indoapterolampra, gen. nov. and two new species (I. rugosiuscula sp. nov. and Morphna lucida sp. nov.) are described. Rhabdoblatta praecipua (Walker, 1868) is removed from the synonymy with 'Polyzosteria' terranea Walker, 1868. The latter species is considered Epilamprinae gen. sp. The lectotype of Phoraspis (Thorax) porcellana Saussure, 1862 is designated. A key for the genera of Epilamprinae from South India and Sri Lanka is provided. Detailed morphological descriptions of the studied taxa are given. The structure of the male genitalia of I. rugosiuscula sp. nov., M. lucida sp. nov., M. plana (Brunner von Wattenwyl, 1865), M. decolyi (Bolivar, 1897) and R. praecipua and that of the female genital complex of M. decolyi, P. (T.) porcellana and Phlebonotus anomalus (Saussure, 1863) are described for the first time. Some aspects of the cockroach evolution are briefly discussed.  PMID:25112343

  2. Adaptations and Predispositions of Different Middle European Arthropod Taxa (Collembola, Araneae, Chilopoda, Diplopoda) to Flooding and Drought Conditions.

    PubMed

    Marx, Michael Thomas; Guhmann, Patrick; Decker, Peter

    2012-01-01

    Floodplain forests and wetlands are amongst the most diverse and species rich habitats on earth. Arthropods are a key group for the high diversity pattern of these landscapes, due to the fact that the change between flooding and drought causes in different life cycles and in a variety of adaptations in the different taxa. The floodplain forests and wetlands of Central Amazonia are well investigated and over the last 50 years many adaptations of several hexapod, myriapod and arachnid orders were described. In contrast to Amazonia the Middle European floodplains were less investigated concerning the adaptations of arthropods to flood and drought conditions. This review summarizes the adaptations and predispositions of springtails, web spiders, millipedes and centipedes to the changeable flood and drought conditions of Middle European floodplain forests and wetlands. Furthermore the impact of regional climate change predictions like increasing aperiodic summer floods and the decrease of typical winter and spring floods are discussed in this article. PMID:26487164

  3. Development of 14 microsatellite markers in Odontites vernus s.l. (Orobanchaceae) and cross-amplification in related taxa1

    PubMed Central

    Pinto-Carrasco, Daniel; Košnar, Jiří; López-González, Noemí; Koutecký, Petr; Těšitel, Jakub; Rico, Enrique; Martínez-Ortega, M. Montserrat

    2016-01-01

    Premise of the study: Microsatellite primers were developed for the first time in the root hemiparasite herb Odontites vernus (Orobanchaceae). These markers will be useful to investigate the role of polyploidization in the evolution of this diploid-tetraploid complex, as well as the extent of gene flow between different ploidy levels. Methods and Results: Fourteen polymorphic and reproducible loci were identified and optimized from O. vernus using a microsatellite-enriched library and 454 Junior sequencing. The set of primers amplified di- to pentanucleotide repeats and showed two to 13 alleles per locus. Transferability was tested in 30 taxa (19 belonging to Odontites and 11 from eight other genera of Orobanchaceae tribe Rhinantheae). Conclusions: The results indicate the utility of the newly developed microsatellites in O. vernus and several other species, which will be useful for taxon delimitation and conservation genetics studies. PMID:27011897

  4. Eucalyptus microfungi known from culture. 1. Cladoriella and Fulvoflamma genera nova, with notes on some other poorly known taxa

    PubMed Central

    Crous, Pedro W.; Verkley, Gerard J.M.; Groenewald, Johannes Z.

    2006-01-01

    A study of microfungi associated with living Eucalyptus leaves and leaf litter revealed several novel and interesting taxa. Cladoriella eucalypti gen. et sp. nov. is described as a Cladosporium-like genus associated with litter collected in South Africa, while Fulvoflamma eucalypti gen. et. sp. nov. is newly described from leaf litter collected in Spain. Beta-conidia are newly reported for species of Pestalotiopsis, namely Pestalotiopsis disseminata in New Zealand, and a Pestalotiopsis sp. from Colombia. Satchmopsis brasiliensis is reported from litter in Colombia and Indonesia, while Torrendiella eucalypti is reported from leaf litter in Indonesia, and shown to have a Sporothrix-like anamorph. Leptospora rubella is reported from living Eucalyptus leaves in Colombia, where it is associated with leaf spots of Mycosphaerella longibasalis, while Macrohilum eucalypti is reported from leaf spots of Eucalyptus in New Zealand. PMID:18490971

  5. The identity of the treehopper genus Dysyncritus Fowler, with descriptions of new related taxa (Hemiptera: Membracidae: Heteronotinae).

    PubMed

    Evangelista, Olivia; Flórez-V, Camilo; Sakakibara, Albino M

    2014-01-01

    Dysyncritus Fowler is revised based on the examination of primary types, and restructured to exclusively accomodate Dysyncritus intectus Fowler, 1895. Allodrilus Evangelista gen. nov. (type species: Cymbomorpha nitidipennis Funkhouser, 1922 = Allodrilus nitidipennis (Funkhouser, 1922) comb. nov.) is erected with seven newly discovered taxa: A. alboferrugineus Evangelista sp. nov. (Brazil, Colombia, Guyana), A. colombiensis Flórez-V sp. nov. (Colombia), A. deitzi Evangelista sp. nov. (Ecuador), A. granulatus Evangelista sp. nov. (Ecuador), A. horizontalis Evangelista sp. nov. (Bolivia), A. intermedius Evangelista sp. nov. (Ecuador), and A. similis Evangelista sp. nov. (Peru). A key to males is provided, in addition to annotated descriptions and illustrations. Nomenclatural changes are proposed to species formerly included in Dysyncritus: Smiliorachis nubilis (Goding, 1930) comb. nov., Smiliorachis discrepans (Goding, 1930) comb. nov., and Dysyncritus lineatus Goding, 1930 (= Smiliorachis octilinea Stål, 1869 syn. nov.).  PMID:25112355

  6. Habitat structure and body size distributions: cross-ecosystem comparison for taxa with determinate and indeterminate growth

    USGS Publications Warehouse

    Nash, Kirsty L.; Allen, Craig R.; Barichievy, Chris; Nystrom, Magnus; Sundstrom, Shana M.; Graham, Nicholas A.J.

    2014-01-01

    Habitat structure across multiple spatial and temporal scales has been proposed as a key driver of body size distributions for associated communities. Thus, understanding the relationship between habitat and body size is fundamental to developing predictions regarding the influence of habitat change on animal communities. Much of the work assessing the relationship between habitat structure and body size distributions has focused on terrestrial taxa with determinate growth, and has primarily analysed discontinuities (gaps) in the distribution of species mean sizes (species size relationships or SSRs). The suitability of this approach for taxa with indeterminate growth has yet to be determined. We provide a cross-ecosystem comparison of bird (determinate growth) and fish (indeterminate growth) body mass distributions using four independent data sets. We evaluate three size distribution indices: SSRs, species size–density relationships (SSDRs) and individual size–density relationships (ISDRs), and two types of analysis: looking for either discontinuities or abundance patterns and multi-modality in the distributions. To assess the respective suitability of these three indices and two analytical approaches for understanding habitat–size relationships in different ecosystems, we compare their ability to differentiate bird or fish communities found within contrasting habitat conditions. All three indices of body size distribution are useful for examining the relationship between cross-scale patterns of habitat structure and size for species with determinate growth, such as birds. In contrast, for species with indeterminate growth such as fish, the relationship between habitat structure and body size may be masked when using mean summary metrics, and thus individual-level data (ISDRs) are more useful. Furthermore, ISDRs, which have traditionally been used to study aquatic systems, present a potentially useful common currency for comparing body size distributions

  7. Taxonomic complexity in the halophyte Limonium vulgare and related taxa (Plumbaginaceae): insights from analysis of morphological, reproductive and karyological data

    PubMed Central

    Cortinhas, Ana; Erben, Matthias; Paula Paes, Ana; Espírito Santo, Dalila; Guara-Requena, Miguel; Caperta, Ana D.

    2015-01-01

    Background and Aims Limonium is a well-known example of a group of plants that is taxonomically complex due to certain biological characteristics that hamper species' delineation. The closely related polyploid species Limonium vulgare Mill., L. humile Mill. and L. narbonense Mill. are defined species and can be used for studying patterns of morphological and reproductive variation. The first two taxa are usually found in Atlantic Europe and the third in the Mediterranean region, but a number of intermediate morphological forms may be present alongside typical examples of these species. This study attempts to elucidate morphological, floral and karyological diversity representative of these taxa in the Iberian Peninsula. Methods The extent of morphological differentiation was tested through comparison of 197 specimens from both Portugal and Spain using 17 descriptive morphological characters and 19 diagnostic morphometric characters. Analyses of floral morphisms (heterostyly and pollen–stigma dimorphism) and karyological determinations were also conducted. Key Results and Conclusions Discriminant analysis using morphometric variables reliably assigned individuals in natural populations to their respective groups. In addition, the results provide the first direct evidence that L. narbonense and a new species, Limonium maritimum Caperta, Cortinhas, Paes, Guara, Espírito-Santo and Erben, sp. nov., related to L. vulgare are present on Portuguese coasts. Most of these species are found together in mixed populations, especially L. vulgare and L. narbonense. It is hypothesized that taxonomic biodiversity found in sites where distinct species co-occur facilitates the evolutionary processes of hybridization, introgression and apomixis. This study therefore contributes to the elucidation of the taxonomic diversity in L. vulgare-related species and may also help in implementing future conservation programmes to maintain the evolutionary processes generating biodiversity

  8. Unique method of tooth replacement in durophagous placodont marine reptiles, with new data on the dentition of Chinese taxa

    PubMed Central

    Neenan, James M; Li, Chun; Rieppel, Olivier; Bernardini, Federico; Tuniz, Claudio; Muscio, Giuseppe; Scheyer, Torsten M

    2014-01-01

    The placodonts of the Triassic period (˜252–201 mya) represent one of the earliest and most extreme specialisations to a durophagous diet of any known reptile group. Exceptionally enlarged crushing tooth plates on the maxilla, dentary and palatine cooperated to form functional crushing areas in the buccal cavity. However, the extreme size of these teeth, combined with the unusual way they occluded, constrained how replacement occurred. Using an extensive micro-computed tomographic dataset of 11 specimens that span all geographic regions and placodont morphotypes, tooth replacement patterns were investigated. In addition, the previously undescribed dental morphologies and formulae of Chinese taxa are described for the first time and incorporated into the analysis. Placodonts have a unique tooth replacement pattern and results follow a phylogenetic trend. The plesiomorphic Placodus species show many replacement teeth at various stages of growth, with little or no discernible pattern. On the other hand, the more derived cyamodontoids tend to have fewer replacement teeth growing at any one time, replacing teeth unilaterally and/or in functional units, thus maintaining at least one functional crushing area at all times. The highly derived placochelyids have fewer teeth and, as a result, only have one or two replacement teeth in the upper jaw. This supports previous suggestions that these taxa had an alternative diet to other placodonts. Importantly, all specimens show at least one replacement tooth growing at the most posterior palatine tooth plates, indicating increased wear at this point and thus the most efficient functional crushing area. PMID:24517163

  9. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae).

    PubMed

    Daïnou, K; Mahy, G; Duminil, J; Dick, C W; Doucet, J-L; Donkpégan, A S L; Pluijgers, M; Sinsin, B; Lejeune, P; Hardy, O J

    2014-07-01

    The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically. PMID:24549110

  10. Water deficit induces swainsonine of some locoweed taxa, but with no swainsonine-growth trade-off

    NASA Astrophysics Data System (ADS)

    Vallotton, Amber D.; Murray, Leigh W.; Delaney, Kevin J.; Sterling, Tracy M.

    2012-08-01

    Environmental factors like nutrient availability (e.g., C:N) and water deficit can influence secondary metabolites levels in plants and fungal endophytes. Locoweeds (Astragalus and Oxytropis spp.) contain swainsonine (SWA), an alkaloid that causes chronic vertebrate toxicity. In two greenhouse experiments, we studied field transplants of three Astragalus mollissimus varieties that vary in SWA levels (barely detectable SWA in var. 'thompsonae', intermediate SWA in var. 'bigelovii', and high SWA in var. 'mollissimus'), and intermediate SWA in Oxytropis sericea; our results confirmed these rankings. We tested whether SWA induction after water deficit (three 14d water-deficit periods separated by two 7d water recovery periods) was taxon-specific and whether degree of induction was influenced by taxon average SWA. We also looked for signs of a trade-off between primary physiology (photosynthesis) or growth (biomass, relative growth rate) with fungal endophyte SWA production; and if so, whether water stress magnified such a trade-off. Leaf photosynthetic activity decreased during the experiments and often more in water-deficit than control plants; leaf gs and Ci results suggest that stomatal closure reduced photosynthetic activity from mild water deficit. Yet, water-deficit affected plants in other ways: there were more dropped senesced leaves for all tested taxa; higher water-use efficiency for var. mollissimus, var. thompsonae, and O. sericea; higher root mass ratios for var. bigelovii, var. thompsonae, and O. sericea; and lower relative water content for var. thompsonae. Positive SWA increases of 1.6-fold for var. mollissimus and 4-fold for var. bigelovii occurred, so positive SWA induction was taxon-specific and limited to medium/high SWA A. mollissimus varieties. There was little evidence for a clear SWA trade-off with total (shoot + root) biomass, relative growth rate, or photosynthetic rate. Additional studies will need to test whether water deficit positively

  11. Late Neogene and Early Quaternary Paleoenvironmental and Paleoclimatic Conditions in Southwestern Europe: Isotopic Analyses on Mammalian Taxa

    PubMed Central

    Domingo, Laura; Koch, Paul L.; Hernández Fernández, Manuel; Fox, David L.; Domingo, M. Soledad; Alberdi, María Teresa

    2013-01-01

    Climatic and environmental shifts have had profound impacts on faunal and floral assemblages globally since the end of the Miocene. We explore the regional expression of these fluctuations in southwestern Europe by constructing long-term records (from ∼11.1 to 0.8 Ma, late Miocene–middle Pleistocene) of carbon and oxygen isotope variations in tooth enamel of different large herbivorous mammals from Spain. Isotopic differences among taxa illuminate differences in ecological niches. The δ13C values (relative to VPDB, mean −10.3±1.1‰; range −13.0 to −7.4‰) are consistent with consumption of C3 vegetation; C4 plants did not contribute significantly to the diets of the selected taxa. When averaged by time interval to examine secular trends, δ13C values increase at ∼9.5 Ma (MN9–MN10), probably related to the Middle Vallesian Crisis when there was a replacement of vegetation adapted to more humid conditions by vegetation adapted to drier and more seasonal conditions, and resulting in the disappearance of forested mammalian fauna. The mean δ13C value drops significantly at ∼4.2−3.7 Ma (MN14–MN15) during the Pliocene Warm Period, which brought more humid conditions to Europe, and returns to higher δ13C values from ∼2.6 Ma onwards (MN16), most likely reflecting more arid conditions as a consequence of the onset of the Northern Hemisphere glaciation. The most notable feature in oxygen isotope records (and mean annual temperature reconstructed from these records) is a gradual drop between MN13 and the middle Pleistocene (∼6.3−0.8 Ma) most likely due to cooling associated with Northern Hemisphere glaciation. PMID:23717470

  12. Late neogene and early quaternary paleoenvironmental and paleoclimatic conditions in southwestern Europe: isotopic analyses on mammalian taxa.

    PubMed

    Domingo, Laura; Koch, Paul L; Hernández Fernández, Manuel; Fox, David L; Domingo, M Soledad; Alberdi, María Teresa

    2013-01-01

    Climatic and environmental shifts have had profound impacts on faunal and floral assemblages globally since the end of the Miocene. We explore the regional expression of these fluctuations in southwestern Europe by constructing long-term records (from ~11.1 to 0.8 Ma, late Miocene-middle Pleistocene) of carbon and oxygen isotope variations in tooth enamel of different large herbivorous mammals from Spain. Isotopic differences among taxa illuminate differences in ecological niches. The δ(13)C values (relative to VPDB, mean -10.3 ± 1.1‰; range -13.0 to -7.4‰) are consistent with consumption of C3 vegetation; C4 plants did not contribute significantly to the diets of the selected taxa. When averaged by time interval to examine secular trends, δ(13)C values increase at ~9.5 Ma (MN9-MN10), probably related to the Middle Vallesian Crisis when there was a replacement of vegetation adapted to more humid conditions by vegetation adapted to drier and more seasonal conditions, and resulting in the disappearance of forested mammalian fauna. The mean δ(13)C value drops significantly at ~4.2-3.7 Ma (MN14-MN15) during the Pliocene Warm Period, which brought more humid conditions to Europe, and returns to higher δ(13)C values from ~2.6 Ma onwards (MN16), most likely reflecting more arid conditions as a consequence of the onset of the Northern Hemisphere glaciation. The most notable feature in oxygen isotope records (and mean annual temperature reconstructed from these records) is a gradual drop between MN13 and the middle Pleistocene (~6.3-0.8 Ma) most likely due to cooling associated with Northern Hemisphere glaciation. PMID:23717470

  13. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae)

    PubMed Central

    Daïnou, K; Mahy, G; Duminil, J; Dick, C W; Doucet, J-L; Donkpégan, A S L; Pluijgers, M; Sinsin, B; Lejeune, P; Hardy, O J

    2014-01-01

    The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically. PMID:24549110

  14. Membrane rejection of nitrogen compounds

    NASA Technical Reports Server (NTRS)

    Lee, S.; Lueptow, R. M.

    2001-01-01

    Rejection characteristics of nitrogen compounds were examined for reverse osmosis, nanofiltration, and low-pressure reverse osmosis membranes. The rejection of nitrogen compounds is explained by integrating experimental results with calculations using the extended Nernst-Planck model coupled with a steric hindrance model. The molecular weight and chemical structure of nitrogen compounds appear to be less important in determining rejection than electrostatic properties. The rejection is greatest when the Donnan potential exceeds 0.05 V or when the ratio of the solute radius to the pore radius is greater than 0.8. The transport of solute in the pore is dominated by diffusion, although convective transport is significant for organic nitrogen compounds. Electromigration contributes negligibly to the overall solute transport in the membrane. Urea, a small organic compound, has lower rejection than ionic compounds such as ammonium, nitrate, and nitrite, indicating the critical role of electrostatic interaction in rejection. This suggests that better treatment efficiency for organic nitrogen compounds can be obtained after ammonification of urea.

  15. Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie.

    PubMed

    Coolon, Joseph D; Jones, Kenneth L; Todd, Timothy C; Blair, John M; Herman, Michael A

    2013-01-01

    Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important

  16. Long-Term Nitrogen Amendment Alters the Diversity and Assemblage of Soil Bacterial Communities in Tallgrass Prairie

    PubMed Central

    Todd, Timothy C.; Blair, John M.; Herman, Michael A.

    2013-01-01

    Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs) experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion). The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have important

  17. NITROGEN OUTPUTS OF SMALL MAMMALS FROM FECAL AND URINE DEPOSITION: IMPLICATIONS FOR NITROGEN CYCLING

    EPA Science Inventory

    The contribution of small mammals in nitrogen cycling is poorly understood and could have reverberations back to the producer community by maintaining or even magnifying increased nitrogen availability. Our objective was to model nitrogen outputs (deposition of feces and urine) ...