New finding and optimal production of a novel extracellular alkaline lipase from Yarrowia lipolytica NRRL Y-2178.

PubMed

Lee, Geon-Ho; Bae, Jae-Han; Suh, Min-Jung; Kim, In-Hwan; Hou, Ching T; Kim, Hak-Ryul

2007-06-01

Lipases are industrially useful versatile enzymes that catalyze numerous different reactions including hydrolysis of triglycerides, transesterification, and chiral synthesis of esters under natural conditions. Although lipases from various sources have been widely used in industrial applications, such as in food, chemical, pharmaceutical, and detergent industries, there are still substantial current interests in developing new microbial lipases, specifically those functioning in abnormal conditions. We screened 17 lipase-producing yeast strains, which were prescreened for substrate specificity of lipase from more than 500 yeast strains from the Agricultural Research Service Culture Collection (Peoria, IL, U.S.A.), and selected Yarrowia lipolytica NRRL Y-2178 as a best lipase producer. This report presents new finding and optimal production of a novel extracellular alkaline lipase from Y. lipolytica NRRL Y-2178. Optimal c ulture conditions f orlipase production by Y. lipolytica NRRL Y-2178 were 72 h incubation time, 27.5 degrees C, pH 9.0. Glycerol and glucose were efficiently used as the most efficient carbon sources, and a combination of yeast extract and peptone was a good nitrogen source for lipase production by Y. lipolytica NRRL Y-2178. These results suggested that Y. lipolytica NRRL Y-2178 showsgood industrial potential as a new alkaline lipase producer.

Enzymatic Synthesis of Structured Lipids using a Novel Cold-Active Lipase from Pichia lynferdii NRRL Y-7723

USDA-ARS?s Scientific Manuscript database

Structured lipids (SL) were synthesized by the acidolysis of borage oil with caprylic acid using lipases. Six commercial lipases from different sources and a novel lipase from Pichia lynferdii NRRL Y-7723 were screened for their acidolysis activities and Lipozyme RM IM and NRRL Y-7723 lipase were s...

Evaluation of Enterococcus faecium NRRL B-2354 as a Surrogate for Salmonella During Extrusion of Low-Moisture Food.

PubMed

Verma, Tushar; Wei, Xinyao; Lau, Soon Kiat; Bianchini, Andreia; Eskridge, Kent M; Subbiah, Jeyamkondan

2018-04-01

Salmonella in low-moisture foods is an emerging challenge due to numerous food product recalls and foodborne illness outbreaks. Identification of suitable surrogate is critical for process validation at industry level due to implementation of new Food Safety Modernization Act of 2011. The objective of this study was to evaluate Enterococcus faecium NRRL B-2354 as a surrogate for Salmonella during the extrusion of low-moisture food. Oat flour, a low-moisture food, was adjusted to different moisture (14% to 26% wet basis) and fat (5% to 15% w/w) contents and was inoculated with E. faecium NRRL B-2354. Inoculated material was then extruded in a lab-scale single-screw extruder running at different screw speeds (75 to 225 rpm) and different temperatures (75, 85, and 95 °C). A split-plot central composite 2nd order response surface design was used, with the central point replicated six times. The data from the selective media (m-Enterococcus agar) was used to build the response surface model for inactivation of E. faecium NRRL B-2354. Results indicated that E. faecium NRRL B-2354 always had higher heat resistance compared to Salmonella at all conditions evaluated in this study. However, the patterns of contour plots showing the effect of various product and process parameters on inactivation of E. faecium NRRL B-2354 was different from that of Salmonella. Although E. faecium NRRL B-2354 may be an acceptable surrogate for extrusion of low-moisture products due to higher resistance than Salmonella, another surrogate with similar inactivation behavior may be preferred and needs to be identified. Food Safety Modernization Act requires the food industry to validate processing interventions. This study validated extrusion processing and demonstrated that E. faecium NRRL B-2354 is an acceptable surrogate for extrusion of low-moisture products. The developed response surface model allows the industry to identify process conditions to achieve a desired lethality for their

Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov.

PubMed Central

Doroghazi, J. R.; Ju, K.-S.; Metcalf, W. W.

2014-01-01

In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp. albus NRRL B-1811T forms a cluster with five other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these other species, including Streptomyces almquistii NRRL B-1685T, Streptomyces flocculus NRRL B-2465T, Streptomyces gibsonii NRRL B-1335T and Streptomyces rangoonensis NRRL B-12378T are quite similar. This cluster is of particular taxonomic interest because Streptomyces albus is the type species of the genus Streptomyces. The related strains were subjected to multilocus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB and confirmation of previously reported phenotypic characteristics. The five strains formed a coherent cluster supported by a 100 % bootstrap value in phylogenetic trees generated from sequence alignments prepared by concatenating the sequences of the housekeeping genes, and identical tree topology was observed using various different tree-making algorithms. Moreover, all but one strain, S. flocculus NRRL B-2465T, exhibited identical sequences for all of the five housekeeping gene loci sequenced, but NRRL B-2465T still exhibited an MLSA evolutionary distance of 0.005 from the other strains, a value that is lower than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. These data support a proposal to reclassify S. almquistii, S. flocculus, S. gibsonii and S. rangoonensis as later heterotypic synonyms of S. albus with NRRL B-1811T as the type strain. The MLSA sequence database also demonstrated utility for quickly and conclusively confirming that numerous strains within the ARS Culture Collection had been previously misidentified as subspecies of S. albus and that Streptomyces albus subsp. pathocidicus should be redescribed as a novel species, Streptomyces

Novel antibacterial polypeptide produced by Lactobacillus paracasei strain NRRL B-50314

USDA-ARS?s Scientific Manuscript database

This study reports the production and characterization of a novel antibacterial polypeptide, designated as laparaxin, which is secreted by Lactobacillus paracasei NRRL B-50314. The crude laparaxin has antibacterial activity against a range of Gram-positive bacteria including the following: lactic a...

Proteomic Analyses of Ethanol Tolerance in Lactobacillus buchneri NRRL B-30929

USDA-ARS?s Scientific Manuscript database

The Lactobacillus buchneri NRRL B-30929 strain, isolated from a fuel ethanol production facility, exhibits high tolerance to environmental ethanol concentrations. In this study, the ethanol tolerance trait was elucidated at the molecular level by using proteomics comparison and analyses. Cellular p...

Proteomic analyses of ethanol tolerance in Lactobacillus buchneri NRRL B-30929

USDA-ARS?s Scientific Manuscript database

The Lactobacillus buchneri NRRL B-30929 strain, isolated from a fuel ethanol production facility, exhibits high tolerance to environmental ethanol concentrations. This study aimed to identify proteins produced by B-30929 in response to environmental ethanol. Cellular proteins expressed by B-30929 gr...

Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species.

PubMed

Sylvester, Kayla; Wang, Qi-Ming; James, Brielle; Mendez, Russell; Hulfachor, Amanda Beth; Hittinger, Chris Todd

2015-05-01

Compared to its status as an experimental model system and importance to industry, the ecology and genetic diversity of the genus Saccharomyces has received less attention. To investigate systematically the biogeography, community members and habitat of these important yeasts, we isolated and identified nearly 600 yeast strains using sugar-rich enrichment protocols. Isolates were highly diverse and contained representatives of more than 80 species from over 30 genera, including eight novel species that we describe here: Kwoniella betulae f.a. (yHKS285(T) = NRRL Y-63732(T) = CBS 13896(T)), Kwoniella newhampshirensis f.a. (yHKS256(T) = NRRL Y-63731(T) = CBS 13917(T)), Cryptococcus wisconsinensis (yHKS301(T) = NRRL Y-63733(T) = CBS 13895(T)), Cryptococcus tahquamenonensis (yHAB242(T) = NRRL Y-63730(T) = CBS 13897(T)), Kodamaea meredithiae f.a. (yHAB239(T) = NRRL Y-63729(T) = CBS 13899(T)), Blastobotrys buckinghamii (yHAB196(T) = NRRL Y-63727(T) = CBS 13900(T)), Candida sungouii (yHBJ21(T) = NRRL Y-63726(T) = CBS 13907(T)) and Cyberlindnera culbertsonii f.a. (yHAB218(T) = NRRL Y-63728(T) = CBS 13898(T)), spp. nov. Saccharomyces paradoxus was one of the most frequently isolated species and was represented by three genetically distinct lineages in Wisconsin alone. We found a statistically significant association between Quercus (oak) samples and the isolation of S. paradoxus, as well as several novel associations. Variation in temperature preference was widespread across taxonomic ranks and evolutionary timescales. This survey highlights the genetic and taxonomic diversity of yeasts and suggests that host and temperature preferences are major ecological factors. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparative Chemistry of Aspergillus oryzae (RIB40) and A. flavus (NRRL 3357)

PubMed Central

Rank, Christian; Klejnstrup, Marie Louise; Petersen, Lene Maj; Kildgaard, Sara; Frisvad, Jens Christian; Gotfredsen, Charlotte Held; Larsen, Thomas Ostenfeld

2012-01-01

Aspergillus oryzae and A. flavus are important species in industrial biotechnology and food safety and have been some of the first aspergilli to be fully genome sequenced. Bioinformatic analysis has revealed 99.5% gene homology between the two species pointing towards a large coherence in the secondary metabolite production. In this study we report on the first comparison of secondary metabolite production between the full genome sequenced strains of A. oryzae (RIB40) and A. flavus (NRRL 3357). Surprisingly, the overall chemical profiles of the two strains were mostly very different across 15 growth conditions. Contrary to previous studies we found the aflatrem precursor 13-desoxypaxilline to be a major metabolite from A. oryzae under certain growth conditions. For the first time, we additionally report A. oryzae to produce parasiticolide A and two new analogues hereof, along with four new alkaloids related to the A. flavus metabolites ditryptophenalines and miyakamides. Generally the secondary metabolite capability of A. oryzae presents several novel end products likely to result from the domestication process from A. flavus. PMID:24957367

New anamorphic yeast species: Candida infanticola sp. nov., Candida polysorbophila sp. nov., Candida transvaalensis sp. nov. and Trigonopsis californica sp. nov.

PubMed

Kurtzman, Cletus P

2007-08-01

Three new species of Candida and a new species of Trigonopsis are described based on their recognition from phylogenetic analysis of gene sequences from large subunit ribosomal RNA, ITS1/ITS2 rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II. Candida infanticola sp. nov. (type strain NRRL Y-17858, CBS 7922) was isolated from the ear of an infant in Germany and is closely related to Candida sorbophila. Candida polysorbophila sp. nov. (type strain NRRL Y-27161, CBS 7317) is a member of the Zygoascus clade and was isolated in South Africa as a contaminant from an emulsion of white oil and polysorbate. Candida transvaalensis sp. nov. (type strain NRRL Y-27140, CBS 6663) was obtained from forest litter, the Transvaal, South Africa, and forms an isolated clade with Candida santjacobensis. Trigonopsis californica sp. nov. (type strain NRRL Y-27307, CBS 10351) represents a contaminant from wine in California, and forms a well-supported clade with Trigonopsis cantarellii, Trigonopsis variabilis and Trigonopsis vinaria.

Purification and Characterization of Phosphonoglycans from Glycomyces sp. Strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338

PubMed Central

Yu, Xiaomin; Price, Neil P. J.; Evans, Bradley S.

2014-01-01

Two related actinomycetes, Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338, were identified as potential phosphonic acid producers by screening for the gene encoding phosphoenolpyruvate (PEP) mutase, which is required for the biosynthesis of most phosphonates. Using a variety of analytical techniques, both strains were subsequently shown to produce phosphonate-containing exopolysaccharides (EPS), also known as phosphonoglycans. The phosphonoglycans were purified by sequential organic solvent extractions, methanol precipitation, and ultrafiltration. The EPS from the Glycomyces strain has a mass of 40 to 50 kDa and is composed of galactose, xylose, and five distinct partially O-methylated galactose residues. Per-deutero-methylation analysis indicated that galactosyl residues in the polysaccharide backbone are 3,4-linked Gal, 2,4-linked 3-MeGal, 2,3-linked Gal, 3,6-linked 2-MeGal, and 4,6-linked 2,3-diMeGal. The EPS from the Stackebrandtia strain is comprised of glucose, galactose, xylose, and four partially O-methylated galactose residues. Isotopic labeling indicated that the O-methyl groups in the Stackebrandtia phosphonoglycan arise from S-adenosylmethionine. The phosphonate moiety in both phosphonoglycans was shown to be 2-hydroxyethylphosphonate (2-HEP) by 31P nuclear magnetic resonance (NMR) and mass spectrometry following strong acid hydrolysis of the purified molecules. Partial acid hydrolysis of the purified EPS from Glycomyces yielded 2-HEP in ester linkage to the O-5 or O-6 position of a hexose and a 2-HEP mono(2,3-dihydroxypropyl)ester. Partial acid hydrolysis of Stackebrandtia EPS also revealed the presence of 2-HEP mono(2,3-dihydroxypropyl)ester. Examination of the genome sequences of the two strains revealed similar pepM-containing gene clusters that are likely to be required for phosphonoglycan synthesis. PMID:24584498

Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS Culture Collection (NRRL) using multi-locus sequence analysis.

PubMed

Labeda, David P

2016-03-01

Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 strains identified as Streptomyces scabiei deposited at various times since the 1950s and these were subjected to multi-locus sequence analysis utilising partial sequences of the house-keeping genes atpD, gyrB, recA, rpoB and trpB. Phylogenetic analyses confirmed the identity of 17 of these strains as Streptomyces scabiei, 9 of the strains as the potato-pathogenic species Streptomyces europaeiscabiei and 6 strains as potentially new phytopathogenic species. Of the 16 other strains, 12 were identified as members of previously described non-pathogenic Streptomyces species while the remaining 4 strains may represent heretofore unrecognised non-pathogenic species. This study demonstrated the value of this technique for the relatively rapid, simple and sensitive molecular identification of Streptomyces strains held in culture collections.

Draft Genome Sequence of Clostridium pasteurianum NRRL B-598, a Potential Butanol or Hydrogen Producer.

PubMed

Kolek, Jan; Sedlár, Karel; Provazník, Ivo; Patáková, Petra

2014-03-20

We present a draft genome sequence of Clostridium pasteurianum NRRL B-598. This strain ferments saccharides by two-stage acetone-butanol (AB) fermentation, is oxygen tolerant, and has high hydrogen yields.

Novel antibacterial polypeptide laparaxin produced by Lactobacillus paracasei strain NRRL B-50314 via fermentation

USDA-ARS?s Scientific Manuscript database

This study reports the production and characterization of a novel antibacterial polypeptide, designated laparaxin, which is secreted by Lactobacillus paracasei NRRL B-50314. Crude laparaxin has antibacterial activity against a wide variety of Gram-positive bacteria, including: lactic acid bacteria ...

Genome Sequences of Ilzat and Eleri, Two Phages Isolated Using Microbacterium foliorum NRRL B-24224

PubMed Central

Ali, Ilzat; Jones, Acacia Eleri; Mohamed, Aleem

2018-01-01

ABSTRACT Bacteriophages Ilzat and Eleri are newly isolated Siphoviridae infecting Microbacterium foliorum NRRL B-24224. The phage genomes are similar in length, G+C content, and architecture and share 62.9% nucleotide sequence identity. PMID:29650566

1-Ene-steroid reductase of Mycobacterium sp. NRRL B-3805.

PubMed

Goren, T; Harnik, M; Rimon, S; Aharonowitz, Y

1983-12-01

The microbial enzymatic reduction of 1,4-androstadiene-3,17-dione (ADD) to 4-androstene-3,17-dione (AD), testosterone and 1-dehydrotestosterone (DHT) is described. Two reducing activities observed in washed cell suspensions and cell free extracts of Mycobacterium sp. NRRL B-3805 were found to account for these bioconversions. One was a 1-ene-steroid reductase and the other a 17-keto steroid reductase. The first reducing activity was found to appear in the soluble cell fraction whereas the latter could be precipitated by centrifugation. Maximum 1-ene-steroid reductase specific activity was achieved during the exponential growth phase of the organism and significantly increased upon induction with ADD. The 1-ene-steroid reductase was partially purified (30-fold) by ammonium sulfate fractionation, gel-filtration and ion-exchange chromatography, and was eluted from a Sephacryl S-300 column with an Mr = 115,000. The 1-ene-steroid reductase activity was NADPH-dependent and had specificity towards steroid compounds containing C-1,2 double bond with an apparent Km for ADD of 2.2 X 10(-5) M. The reverse reaction catalyzing C-1,2 dehydrogenation could not be detected in our preparations. The results suggest that in Mycobacterium sp NRRL B-3805 and B-3683 the steroid C-1,2 dehydrogenation and 1-ene reduction are two separable activities.

Complete genome sequence of 'Mycobacterium neoaurum' NRRL B-3805, an androstenedione (AD) producer for industrial biotransformation of sterols.

PubMed

Rodríguez-García, Antonio; Fernández-Alegre, Estela; Morales, Alejandro; Sola-Landa, Alberto; Lorraine, Jess; Macdonald, Sandy; Dovbnya, Dmitry; Smith, Margaret C M; Donova, Marina; Barreiro, Carlos

2016-04-20

Microbial bioconversion of sterols into high value steroid precursors, such as 4-androstene-3,17-dione (AD), is an industrial challenge. Genes and enzymes involved in sterol degradation have been proposed, although the complete pathway is not yet known. The genome sequencing of the AD producer strain 'Mycobacterium neoaurum' NRRL B-3805 (formerly Mycobacterium sp. NRRL B-3805) will serve to elucidate the critical steps for industrial processes and will provide the basis for further genetic engineering. The genome comprises a circular chromosome (5 421 338bp), is devoid of plasmids and contains 4844 protein-coding genes. Copyright © 2016 Elsevier B.V. All rights reserved.

Insoluble Glucans from Planktonic and Biofilm Cultures of Mutants of Leuconostoc mesenteroides NRRL B-1355

USDA-ARS?s Scientific Manuscript database

Leuconostoc mesenteroides strain NRRL B-1355 produces the soluble exopolysaccharides alternan and dextran in planktonic cultures. Mutants of this strain are available that are deficient in the production of alternan, dextran, or both. Our recent work demonstrated that biofilms from all strains con...

Description of Ambrosiozyma oregonensis sp. nov., and reassignment of Candida species of the Ambrosiozyma clade to Ambrosiozyma kashinagacola f.a., comb. nov., Ambrosiozyma llanquihuensis f.a., comb. nov., etc.

USDA-ARS?s Scientific Manuscript database

Ambrosiozyma oregonensis sp. nov. (NRRL Y-6106T = CBS 5560, type strain) is described from two strains, one isolated from a mountain stream in Oregon, USA, and a second (NRRL YB-4169) from an unknown substrate from Marion, Illinois, USA. The species forms four hat-shaped ascospores in each deliquesc...

40 CFR 180.1254 - Aspergillus flavus NRRL 21882; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2011 CFR

2011-07-01

... NRRL 21882 on corn, field, forage; corn, field, grain; corn, field, stover; corn, field, aspirated grain fractions; corn, sweet, kernel plus cob with husk removed; corn, sweet, forage; corn, sweet, stover; corn, pop, grain; and corn, pop, stover. [75 FR 6576, Feb. 10, 2010] ...

40 CFR 180.1254 - Aspergillus flavus NRRL 21882; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2012 CFR

2012-07-01

... NRRL 21882 on corn, field, forage; corn, field, grain; corn, field, stover; corn, field, aspirated grain fractions; corn, sweet, kernel plus cob with husk removed; corn, sweet, forage; corn, sweet, stover; corn, pop, grain; and corn, pop, stover. [75 FR 6576, Feb. 10, 2010] ...

40 CFR 180.1254 - Aspergillus flavus NRRL 21882; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2013 CFR

2013-07-01

... NRRL 21882 on corn, field, forage; corn, field, grain; corn, field, stover; corn, field, aspirated grain fractions; corn, sweet, kernel plus cob with husk removed; corn, sweet, forage; corn, sweet, stover; corn, pop, grain; and corn, pop, stover. [75 FR 6576, Feb. 10, 2010] ...

40 CFR 180.1254 - Aspergillus flavus NRRL 21882; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2010 CFR

2010-07-01

... NRRL 21882 on corn, field, forage; corn, field, grain; corn, field, stover; corn, field, aspirated grain fractions; corn, sweet, kernel plus cob with husk removed; corn, sweet, forage; corn, sweet, stover; corn, pop, grain; and corn, pop, stover. [75 FR 6576, Feb. 10, 2010] ...

40 CFR 180.1254 - Aspergillus flavus NRRL 21882; exemption from the requirement of a tolerance.

Code of Federal Regulations, 2014 CFR

2014-07-01

... NRRL 21882 on corn, field, forage; corn, field, grain; corn, field, stover; corn, field, aspirated grain fractions; corn, sweet, kernel plus cob with husk removed; corn, sweet, forage; corn, sweet, stover; corn, pop, grain; and corn, pop, stover. [75 FR 6576, Feb. 10, 2010] ...

Effects of mutations on the insoluble glucan synthesized by Leuconostoc mesenteroides NRRL B-1118 glucansucrase

USDA-ARS?s Scientific Manuscript database

Twelve different amino acids were each substituted for Threonine-654 in a cloned glucansucrase from Leuconostoc mesenteroides NRRL B-1118 (DSR-I). The native enzyme produces a water-insoluble glucan containing approximately 44 mol% 1,3-disubstituted a-D-glucopyranosyl units and 29 mol% 1,6-disubstit...

Phylogeny of marine Bacillus isolates from the Gulf of Mexico

NASA Technical Reports Server (NTRS)

Siefert, J. L.; Larios-Sanz, M.; Nakamura, L. K.; Slepecky, R. A.; Paul, J. H.; Moore, E. R.; Fox, G. E.; Jurtshuk, P. Jr

2000-01-01

The phylogeny of 11 pigmented, aerobic, spore-forming isolates from marine sources was studied. Forty-two biochemical characteristics were examined, and a 16S rDNA sequence was obtained for each isolate. In a phylogenetic tree based on 16S sequencing, four isolates (NRRL B-14850, NRRL B-14904, NRRL B-14907, and NRRL B-14908) clustered with B. subtilis and related organisms; NRRL B-14907 was closely related to B. amyloliquefaciens. NRRL B-14907 and NRRL B-14908 were phenotypically similar to B. amyloliquefaciens and B. pumilus, respectively. Three strains (NRRL B-14906, NRRL B-14910, and NRRL B-14911) clustered in a clade that included B. firmus, B. lentus, and B. megaterium. NRRL B-14910 was closely related phenotypically and phylogenetically to B. megaterium. NRRL B-14905 clustered with the mesophilic round spore-producing species, B. fusiformis and B. sphaericus; the isolate was more closely related to B. fusiformis. NRRL B-14905 displayed characteristics typical of the B. sphaericus-like organisms. NRRL B-14909 and NRRL B-14912 clustered with the Paenibacillus species and displayed characteristics typical of the genus. Only NRRL B-14851, an unusually thin rod that forms very small spores, may represent a new Bacillus species.

Inactivation of Salmonella, Listeria monocytogenes and Enterococcus faecium NRRL B-2354 in a selection of low moisture foods.

PubMed

Rachon, Grzegorz; Peñaloza, Walter; Gibbs, Paul A

2016-08-16

The aims of this study were to obtain data on survival and heat resistance of cocktails of Salmonella, Listeria monocytogenes and the surrogate Enterococcus faecium (NRRL B-2354) in four low moisture foods (confectionery formulation, chicken meat powder, pet food and savoury seasoning) during storage before processing. Inoculated samples were stored at 16°C and cell viability examined at day 0, 3, 7 and 21. At each time point, the heat resistance at 80°C was determined. The purpose was to determine a suitable storage time of inoculated foods that can be applied in heat resistance studies or process validations with similar cell viability and heat resistance characteristics. The main inactivation study was carried out within 7days after inoculation, the heat resistance of each bacterial cocktail was evaluated in each low moisture food heated in thermal cells exposed to temperatures between 70 and 140°C. The Weibull model and the first order kinetics (D-value) were used to express inactivation data and calculate the heating time to achieve 5 log reduction at each temperature. Results showed that the pathogens Salmonella and L. monocytogenes and the surrogate E. faecium NRRL B-2354, can survive well (maximum reduction <0.8 log) in low moisture foods maintained at 16°C, as simulation of warehouse raw material storage in winter and before processing. The D80 value of the pathogens and surrogate did not significantly change during the 21day storage (p>0.05). The inactivation kinetics of the pathogens and surrogate at temperatures between 70 and 140°C, were different between each organism and product. E. faecium NRRL B-2354 was a suitable Salmonella surrogate for three of the low moisture foods studied, but not for the sugar-containing confectionery formulation. Heating low moisture food in moisture-tight environments (thermal cells) to 111.2, 105.3 or 111.8°C can inactivate 5 log of Salmonella, L. monocytogenes or E. faecium NRRL B-2354 respectively. Copyright �

Lactobacillus amylovorus, a new starch-hydrolyzing species from cattle waste-corn fermentations

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

Nakamura, L.K.

1981-01-01

The morphology, physiology and fermentation characteristics of this hitherto unrecognized species are described. The new Lactobacillus species can be differentiated from L. acidophilus, L. jensenii, and L. leichmannii on the basis of starch fermentation, G + C content, vitamin requirements and stereoisomerism of lactic acid produced. The type strain of L. amylovorus is NRRL B-4540. (Refs. 39).

Functional analyses of the cell wall hydrolase from Lactobacillus paracasei NRRL B-50314 expressed in Bacillus megaterium

USDA-ARS?s Scientific Manuscript database

This study reports the production and characterization of a novel antibacterial polypeptide, designated laparaxin, which is secreted by Lactobacillus paracasei NRRL B-50314. Crude laparaxin has antibacterial activity against a range of Gram-positive bacteria including the following: lactic acid bact...

Cloning, expression, and characterization of an insoluble glucan-producing glucansucrase from Leuconostoc mesenteroides NRRL B-1118

USDA-ARS?s Scientific Manuscript database

We have cloned a glucansucrase from the type strain of Leuconostoc mesenteroides (NRRL B-1118; ATCC 8293) and successfully expressed the enzyme in Escherichia coli. The recombinant processed enzyme has a putative sequence identical to the predicted secreted native enzyme (1,473 amino acids; 161,468...

Protection of Lactobacillus acidophilus NRRL-B 4495 under in vitro gastrointestinal conditions with whey protein/pullulan microcapsules.

PubMed

Çabuk, Burcu; Tellioğlu Harsa, Şebnem

2015-12-01

In this research, whey protein/pullulan (WP/pullulan) microcapsules were developed in order to assess its protective effect on the viability of Lactobacillus acidophilus NRRL-B 4495 under in vitro gastrointestinal conditions. Results demonstrated that WP/pullulan microencapsulated cells exhibited significantly (p ≤ 0.05) higher resistance to simulated gastric acid and bile salt. Pullulan incorporation into protein wall matrix resulted in improved survival as compared to free cells after 3 h incubation in simulated gastric solution. Moreover WP/pullulan microcapsules were found to release over 70% of encapsulated L. acidophilus NRRL-B 4495 cells within 1 h. The effect of encapsulation during refrigerated storage was also studied. Free bacteria exhibited 3.96 log reduction while, WP/pullulan encapsulated bacteria showed 1.64 log reduction after 4 weeks of storage. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Revised structure for the phenazine antibiotic from Pseudomonas fluorescens 2-79 (NRRL B-15132).

PubMed Central

Brisbane, P G; Janik, L J; Tate, M E; Warren, R F

1987-01-01

A phenazine antibiotic (mp, 243 to 244 degrees C), isolated in a yield of 134 micrograms/ml from cultures of Pseudomonas fluorescens 2-79 (NRRL B-15132), was indistinguishable in all of its measured physicochemical (melting point, UV and infrared spectra, and gas chromatography-mass spectrometry data) and biological properties from synthetic phenazine-1-carboxylic acid. Gurusiddaiah et al. (S. Gurusiddaiah, D. M. Weller, A. Sarkar, and R. J. Cook, Antimicrob. Agents Chemother. 29:488-495, 1986) attributed a dimeric phenazine structure to an antibiotic with demonstrably similar properties obtained from the same bacterial strain. Direct comparison of the physicochemical properties of the authentic antibiotic obtained from D. M. Weller with synthetic phenazine-1-carboxylic acid and with the natural product from the present study established that all three samples were indistinguishable within the experimental error of each method. No evidence to support the existence of a biologically active dimeric species was obtained. Phenazine-1-carboxylic acid has a pKa of 4.24 +/- 0.01 (25 degrees C; I = 0.09), and its carboxylate anion shows no detectable antimicrobial activity compared with the active uncharged carboxylic acid species. These data suggest that phenazine-1-carboxylic acid is probably not an effective biological control agent for phytopathogens in environments with a pH greater than 7. Images PMID:3125789

Identification of molecular species of acylglycerols of Philippine wild edible mushroom, Ganoderma lucidum

USDA-ARS?s Scientific Manuscript database

Wild edible mushrooms are widely consumed in many countries. We successfully cultivated four edible, medicinal Philippine mushrooms in liquid culture. Recently, we identified the molecular species of acylglycerols in the lipid extract of mushroom G. lucidum NRRL66208. One hundred and three molecular...

Isolation of Lactobacillus salivarius 1077 (NRRL B-50053) and characterization of its bacteriocin and spectra of antimicrobial activity

USDA-ARS?s Scientific Manuscript database

Lactobacillus salivarius 1077 (NRRL B-50053) was isolated from poultry intestinal materials after demonstrating in-vitro anti-Campylobacter jejuni activity. The isolate was then used for in-vitro fermentation. The protein content of the cell-free supernatant from the spent medium was precipitated ...

Enhanced cellulosic ethanol production from mild-alkali pretreated rice straw in SSF using Clavispora NRRL Y-50464

USDA-ARS?s Scientific Manuscript database

This study reports the first lower-cost cellulosic ethanol production from mild alkali retreated rice straw using a native ß-glucosidase producing yeast strain, Clavispora NRRL Y-50464 by SSF. Ethanol production and efficiency of ethanol conversion from 10, 15, and 20% of solids loading of rice stra...

Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis

USDA-ARS?s Scientific Manuscript database

In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp. albus NRRL B-1811T formed a cluster with 5 other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these ot...

Two new native ß-glucosidases from Clavispora NRRL Y-50464 confer its dual function as cellobiose fermenting ethanologenic yeast

USDA-ARS?s Scientific Manuscript database

Clavispora NRRL Y-50464, a dual functional cellobiose fermenting and ethanologenic yeast strain, is a candidate biocatalyst for lower cost lignocellulose-to-ethanol production using simultaneous saccharification and fermentation. A ß-glucosidase BGL1 protein from this strain was recently reported an...

Genome Sequence of Aspergillus flavus NRRL 3357, a Strain That Causes Aflatoxin Contamination of Food and Feed.

PubMed

Nierman, William C; Yu, Jiujiang; Fedorova-Abrams, Natalie D; Losada, Liliana; Cleveland, Thomas E; Bhatnagar, Deepak; Bennett, Joan W; Dean, Ralph; Payne, Gary A

2015-04-16

Aflatoxin contamination of food and livestock feed results in significant annual crop losses internationally. Aspergillus flavus is the major fungus responsible for this loss. Additionally, A. flavus is the second leading cause of aspergillosis in immunocompromised human patients. Here, we report the genome sequence of strain NRRL 3357. Copyright © 2015 Nierman et al.

Draft Genome Sequence of Streptomyces clavuligerus NRRL 3585, a Producer of Diverse Secondary Metabolites▿

PubMed Central

Song, Ju Yeon; Jeong, Haeyoung; Yu, Dong Su; Fischbach, Michael A.; Park, Hong-Seog; Kim, Jae Jong; Seo, Jeong-Sun; Jensen, Susan E.; Oh, Tae Kwang; Lee, Kye Joon; Kim, Jihyun F.

2010-01-01

Streptomyces clavuligerus is an important industrial strain that produces a number of antibiotics, including clavulanic acid and cephamycin C. A high-quality draft genome sequence of the S. clavuligerus NRRL 3585 strain was produced by employing a hybrid approach that involved Sanger sequencing, Roche/454 pyrosequencing, optical mapping, and partial finishing. Its genome, comprising four linear replicons, one chromosome, and four plasmids, carries numerous sets of genes involved in the biosynthesis of secondary metabolites, including a variety of antibiotics. PMID:20889745

Draft genome sequence of Coniochaeta ligniaria NRRL 30616, a lignocellulolytic fungus for bioabatement of inhibitors in plant biomass hydrolysates

USDA-ARS?s Scientific Manuscript database

Here, we report the first draft genome sequence (42.38 Mb that contains 13,657 genes) of Coniochaeta ligniaria NRRL30616, an ascomycete with high biotechnological relevance in the bioenergy field given its high potential for bioabatement of toxic furanic compounds in plant biomass hydrolysates and i...

Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains

PubMed Central

2013-01-01

Background S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338. Based on the genomic data and transcriptpmic data of these two strains, we carried out comparative analysis of high-producing strain and wild-type strain at both the genomic level and the transcriptomic level. Results We observed a large number of genetic variants including 60 insertions, 46 deletions and 584 single nucleotide variations (SNV) in E3 in comparison with NRRL23338, and the analysis of time series transcriptomic data indicated that the genes involved in erythromycin biosynthesis and feeder pathways were significantly up-regulated during the 60 hours time-course. According to our data, BldD, a previously identified ery cluster regulator, did not show any positive correlations with the expression of ery cluster, suggesting the existence of alternative regulation mechanisms of erythromycin synthesis in S. erythraea. Several potential regulators were then proposed by integration analysis of genomic and transcriptomic data. Conclusion This is a demonstration of the functional comparative genomics between an industrial S. erythraea strain and the wild-type strain. These findings help to understand the global regulation mechanisms of erythromycin biosynthesis in S. erythraea, providing useful clues for genetic and metabolic engineering in the future. PMID:23902230

Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe

USDA-ARS?s Scientific Manuscript database

Background: We recently reported the identification of Bacillus sp. NRRL B-14911 that induces heart autoimmunity by generating cardiac-reactive T cells through molecular mimicry. This marine bacterium was originally isolated from the Gulf of Mexico, but no associations with human diseases were rep...

Bandoniozyma gen. nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species

PubMed Central

Landell, Melissa Fontes; Crestani, Juliana; Pagnocca, Fernando Carlos; Sette, Lara Durães; Passarini, Michel Rodrigo Zambrano; Rosa, Carlos Augusto; Brandão, Luciana R.; Pimenta, Raphael S.; Ribeiro, José Roberto; Garcia, Karina Marques; Lee, Ching-Fu; Suh, Sung-Oui; Péter, Gábor; Dlauchy, Dénes; Fell, Jack W.; Scorzetti, Gloria; Theelen, Bart; Vainstein, Marilene H.

2012-01-01

Background Independent surveys across the globe led to the proposal of a new basidiomycetous yeast genus within the Bulleromyces clade of the Tremellales, Bandoniozyma gen. nov., with seven new species. Methodology/Principal Findings The species were characterized by multiple methods, including the analysis of D1/D2 and ITS nucleotide sequences, and morphological and physiological/biochemical traits. Most species can ferment glucose, which is an unusual trait among basidiomycetous yeasts. Conclusions/Significance In this study we propose the new yeast genus Bandoniozyma, with seven species Bandoniozyma noutii sp. nov. (type species of genus; CBS 8364T  =  DBVPG 4489T), Bandoniozyma aquatica sp. nov. (UFMG-DH4.20T  =  CBS 12527T  =  ATCC MYA-4876T), Bandoniozyma complexa sp. nov. (CBS 11570T  =  ATCC MYA-4603T  =  MA28aT), Bandoniozyma fermentans sp. nov. (CBS 12399T  =  NU7M71T  =  BCRC 23267T), Bandoniozyma glucofermentans sp. nov. (CBS 10381T  =  NRRL Y-48076T  =  ATCC MYA-4760T  =  BG 02-7-15-015A-1-1T), Bandoniozyma tunnelae sp. nov. (CBS 8024T  =  DBVPG 7000T), and Bandoniozyma visegradensis sp. nov. (CBS 12505T  =  NRRL Y-48783T  =  NCAIM Y.01952T). PMID:23056233

Complete genome sequence of Clostridium pasteurianum NRRL B-598, a non-type strain producing butanol.

PubMed

Sedlar, Karel; Kolek, Jan; Skutkova, Helena; Branska, Barbora; Provaznik, Ivo; Patakova, Petra

2015-11-20

The strain Clostridium pasteurianum NRRL B-598 is non-type, oxygen tolerant, spore-forming, mesophilic and heterofermentative strain with high hydrogen production and ability of acetone-butanol fermentation (ethanol production being negligible). Here, we present the annotated complete genome sequence of this bacterium, replacing the previous draft genome assembly. The genome consisting of a single circular 6,186,879 bp chromosome with no plasmid was determined using PacBio RSII and Roche 454 sequencing. Copyright © 2015 Elsevier B.V. All rights reserved.

Flow cytometry analysis of Clostridium beijerinckii NRRL B-598 populations exhibiting different phenotypes induced by changes in cultivation conditions.

PubMed

Branska, Barbora; Pechacova, Zora; Kolek, Jan; Vasylkivska, Maryna; Patakova, Petra

2018-01-01

Biobutanol production by clostridia via the acetone-butanol-ethanol (ABE) pathway is a promising future technology in bioenergetics , but identifying key regulatory mechanisms for this pathway is essential in order to construct industrially relevant strains with high tolerance and productivity. We have applied flow cytometric analysis to C. beijerinckii NRRL B-598 and carried out comparative screening of physiological changes in terms of viability under different cultivation conditions to determine its dependence on particular stages of the life cycle and the concentration of butanol. Dual staining by propidium iodide (PI) and carboxyfluorescein diacetate (CFDA) provided separation of cells into four subpopulations with different abilities to take up PI and cleave CFDA, reflecting different physiological states. The development of a staining pattern during ABE fermentation showed an apparent decline in viability, starting at the pH shift and onset of solventogenesis, although an appreciable proportion of cells continued to proliferate. This was observed for sporulating as well as non-sporulating phenotypes at low solvent concentrations, suggesting that the increase in percentage of inactive cells was not a result of solvent toxicity or a transition from vegetative to sporulating stages. Additionally, the sporulating phenotype was challenged with butanol and cultivation with a lower starting pH was performed; in both these experiments similar trends were obtained-viability declined after the pH breakpoint, independent of the actual butanol concentration in the medium. Production characteristics of both sporulating and non-sporulating phenotypes were comparable, showing that in C. beijerinckii NRRL B-598, solventogenesis was not conditional on sporulation. We have shown that the decline in C. beijerinckii NRRL B-598 culture viability during ABE fermentation was not only the result of accumulated toxic metabolites, but might also be associated with a special survival

UV-C mutagenesis of Kluyveromyces marxianus NRRL Y-1109 strain for improved anaerobic growth at elevated temperature on pentose and hexose sugars

USDA-ARS?s Scientific Manuscript database

More robust industrial yeast strains from Kluyveromyces marxianus NRRL Y-1109 and have been produced using UV-C irradiation specifically for anaerobic conversion of lignocellulosic sugar streams to fuel ethanol at elevated temperature (45°C). This type of random mutagenesis offers the possibility o...

Candida aechmeae sp. nov. and Candida vrieseae sp. nov., novel yeast species isolated from the phylloplane of bromeliads in Southern Brazil.

PubMed

Landell, Melissa Fontes; Billodre, Raisa; Ramos, Jesus P; Leoncini, Orílio; Vainstein, Marilene H; Valente, Patrícia

2010-01-01

Two novel yeast species, Candida aechmeae sp. nov. and Candida vrieseae sp. nov., were isolated from bromeliads in Itapuã Park, Rio Grande do Sul, Brazil. These species are genetically isolated from all other currently recognized ascomycetous yeasts based on their sequence divergence in the D1/D2 domain of the LSU rRNA gene. C. aechmeae sp. nov. is phylogenetically close to Candida ubatubensis, a species also isolated from bromeliads in Brazil, but the novel species can be differentiated on the basis of differences in the D1/D2 domain and positive results for the assimilation of l-arabinose, raffinose, inulin and citrate. Candida vrieseae sp. nov. is phylogenetically placed in a clade near Candida membranifaciens that is composed of several species associated with insects, but the novel species can be differentiated from them by the D1/D2 and ITS gene sequences, positive results for the assimilation of nitrite and a negative result for the assimilation of ethylamine. The type strain for Candida aechmeae sp. nov. is BI153(T) (=CBS 10831(T)=NRRL Y-48456(T)) and the type strain for C. vrieseae sp. nov. is BI146(T) (=CBS 10829(T)=NRRL Y-48461(T)).

Effect of salt nutrients on mannitol production by Lactobacillus intermedius NRRL B-3693.

PubMed

Saha, Badal C

2006-10-01

The effects of four salt nutrients (ammonium citrate, sodium phosphate, magnesium sulfate, and manganese sulfate) on the production of mannitol by Lactobacillus intermedius NRRL B-3693 in a simplified medium containing 300 g fructose, 5 g soy peptone, and 50 g corn steep liquor per liter in pH-controlled fermentation at 5.0 at 37 degrees C were evaluated using a fractional factorial design. Only manganese sulfate was found to be essential for mannitol production. Added manganese sulfate concentration of 0.033 g/l was found to support maximum production. The bacterium produced 200.6 +/- 0.2 g mannitol, 61.9 +/- 0.1 g lactic acid, and 40.4 +/- 0.3 g acetic acid from 300 g fructose per liter in 67 h.

Automated UV-C mutagenesis of Kluyveromyces marxianus NRRL Y-1109 and selection for microaerophilic growth and ethanol production at elevated temperature on biomass sugars

USDA-ARS?s Scientific Manuscript database

The yeast Kluyveromyces marxianus is a potential microbial catalyst for producing ethanol from lignocellulosic substrates at elevated temperatures. To improve its growth and ethanol yield under anaerobic conditions, K. marxianus NRRL Y-1109 was irradiated with UV-C, and surviving cells were grown a...

Wickerhamomyces queroliae sp. nov. and Candida jalapaonensis sp. nov., two yeast species isolated from Cerrado ecosystem in North Brazil.

PubMed

Rosa, Carlos A; Morais, Paula B; Lachance, Marc-André; Santos, Renata O; Melo, Weilan G P; Viana, Rodney H O; Bragança, Marcos A L; Pimenta, Raphael S

2009-05-01

Two novel yeast species, Wickerhamomyces queroliae sp. nov. and Candida jalapaonensis sp. nov., were isolated, respectively, from larvae of Anastrepha mucronata (Diptera: Tephritidae) collected from ripe fruit of Peritassa campestris ('Bacupari', Hippocrateaceae) and from flowers of Centropogon cornutus (Campanulaceae) in the Cerrado ecosystem of the state of Tocantins, Brazil. Analysis of the D1/D2 large-subunit rRNA gene sequences placed W. queroliae in the Wickerhamomyces clade near Wickerhamomyces ciferri and Candida silvicultrix. Candida jalapaonensis belongs to the Wickerhamiella clade and is related to Candida drosophilae. The type strain of Wickerhamomyces queroliae is UFMG-05-T200.1(T) (=CBS 10936(T)=NRRL Y-48478(T)) and the type strain of Candida jalapaonensis is UFMG-03-T210(T) (=CBS 10935(T)=NRRL Y-48477(T)).

Carbon Concentration and Carbon-to-Nitrogen Ratio Influence Submerged-Culture Conidiation by the Potential Bioherbicide Colletotrichum truncatum NRRL 13737

PubMed Central

Jackson, Mark A.; Bothast, Rodney J.

1990-01-01

We assessed the influence of various carbon concentrations and carbon-to-nitrogen (C:N) ratios on Colletotrichum truncatum NRRL 13737 conidium formation in submerged cultures grown in a basal salts medium containing various amounts of glucose and Casamino Acids. Under the nutritional conditions tested, the highest conidium concentrations were produced in media with carbon concentrations of 4.0 to 15.3 g/liter. High carbon concentrations (20.4 to 40.8 g/liter) inhibited sporulation and enhanced the formation of microsclerotiumlike hyphal masses. At all the carbon concentrations tested, a culture grown in a medium with a C:N ratio of 15:1 produced more conidia than cultures grown in media with C:N ratios of 40:1 or 5:1. While glucose exhaustion was often coincident with conidium formation, cultures containing residual glucose sporulated and those with high carbon concentrations (>25 g/liter) exhausted glucose without sporulation. Nitrogen source studies showed that the levels of C. truncatum NRRL 13737 conidiation were similar for all protein hydrolysates tested. Reduced conidiation occurred when amino acid and inorganic nitrogen sources were used. Of the nine carbon sources evaluated, acetate as the sole carbon source resulted in the lowest level of sporulation. Images PMID:16348348

High performance microbiological transformation of L-tyrosine to L-dopa by Yarrowia lipolytica NRRL-143

PubMed Central

Ali, Sikander; Shultz, Jeffry L; Ikram-ul-Haq

2007-01-01

Background The 3,4-dihydroxy phenyl L-alanine (L-dopa) is a drug of choice for Parkinson's disease, controlling changes in energy metabolism enzymes of the myocardium following neurogenic injury. Aspergillus oryzae is commonly used for L-dopa production; however, potential improvements in ease of handling, growth rate and environmental impact have led to an interest in exploiting alternative yeasts. The two important elements required for L-dopa production are intracellular tyrosinases (thus pre-grown yeast cells are required for the transformation of L-tyrosine to L-dopa) and L-ascorbate, which acts as a reducing agent. Results Pre-grown cells of Yarrowia lipolytica NRRL-143 were used for the microbiological transformation of L-tyrosine to L-dopa. Different diatomite concentrations (0.5–3.0 mg/ml) were added to the acidic (pH 3.5) reaction mixture. Maximum L-dopa biosynthesis (2.96 mg/ml L-dopa from 2.68 mg/ml L-tyrosine) was obtained when 2.0 mg/ml diatomite was added 15 min after the start of the reaction. After optimizing reaction time (30 min), and yeast cell concentration (2.5 mg/ml), an overall 12.5 fold higher L-dopa production rate was observed when compared to the control. Significant enhancements in Yp/s, Qs and qs over the control were observed. Conclusion Diatomite (2.0 mg/ml) addition 15 min after reaction commencement improved microbiological transformation of L-tyrosine to L-dopa (3.48 mg/ml; p ≤ 0.05) by Y. lipolytica NRRL-143. A 35% higher substrate conversion rate was achieved when compared to the control. PMID:17705832

Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa).

PubMed

Rooney, Alejandro P; Dunlap, Christopher A; Flor-Weiler, Lina B

2016-09-01

Strain NRRL B-41902T and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, Gram-stain-negative rods that formed cocci in late stationary phase. 16S rRNA gene sequence analysis showed that strain NRRL B-41902T was most closely related to species within the genera Acinetobacter, and that a grouping of it and the three other closely related strains was most closely related to the type strain of Acinetobacter pittii, which was also confirmed through a phylogenomic analysis. Moreover, in silico DNA-DNA hybridization analysis revealed a substantial amount of genomic divergence (39.1 %) between strain NRRL B-41902T and the type strain of A. pittii, which is expected if the strains represent distinct species. Further phenotypic analysis revealed that strain NRRL B-41902T was able to utilize a combination of l-serine, citraconic acid and citramalic acid, which differentiated it from other, closely related Acinetobacter species. Therefore, strain NRRL B-41902T (=CCUG 68785T) is proposed as the type strain of a novel species, Acinetobacter lactucae sp. nov.

Expanding the Species and Chemical Diversity of Penicillium Section Cinnamopurpurea

PubMed Central

Peterson, Stephen W.; Jurjević, Željko; Frisvad, Jens C.

2015-01-01

A set of isolates very similar to or potentially conspecific with an unidentified Penicillium isolate NRRL 735, was assembled using a BLAST search of ITS similarity among described (GenBank) and undescribed Penicillium isolates in our laboratories. DNA was amplified from six loci of the assembled isolates and sequenced. Two species in section Cinnamopurpurea are self-compatible sexual species, but the asexual species had polymorphic loci suggestive of sexual reproduction and variation in conidium size suggestive of ploidy level differences typical of heterothallism. Accordingly we use genealogical concordance analysis, a technique valid only in heterothallic organisms, for putatively asexual species. Seven new species were revealed in the analysis and are described here. Extrolite analysis showed that two of the new species, P. colei and P. monsserratidens produce the mycotoxin citreoviridin that has demonstrated pharmacological activity against human lung tumors. These isolates could provide leads in pharmaceutical research. PMID:25853891

Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov

USDA-ARS?s Scientific Manuscript database

In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp. albus NRRL B-1811T forms a cluster with 5 other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these oth...

Dam and Dcm methylations prevent gene transfer into Clostridium pasteurianum NRRL B-598: development of methods for electrotransformation, conjugation, and sonoporation.

PubMed

Kolek, Jan; Sedlar, Karel; Provaznik, Ivo; Patakova, Petra

2016-01-01

Butanol is currently one of the most discussed biofuels. Its use provides many benefits in comparison to bio-ethanol, but the price of its fermentative production is still high. Genetic improvements could help solve many problems associated with butanol production during ABE fermentation, such as its toxicity, low concentration achievable in the cultivation medium, the need for a relatively expensive substrate, and many more. Clostridium pasteurianum NRRL B-598 is non-type strain producing butanol, acetone, and a negligible amount of ethanol. Its main benefits are high oxygen tolerance, utilization of a wide range of carbon and nitrogen sources, and the availability of its whole genome sequence. However, there is no established method for the transfer of foreign DNA into this strain; this is the next step necessary for progress in its use for butanol production. We have described functional protocols for conjugation and transformation of the bio-butanol producer C. pasteurianum NRRL B-598 by foreign plasmid DNA. We show that the use of unmethylated plasmid DNA is necessary for efficient transformation or successful conjugation. Genes encoding DNA methylation and those for restriction-modification systems and antibiotic resistance were searched for in the whole genome sequence and their homologies with other clostridial bacteria were determined. Furthermore, activity of described novel type I restriction system was proved experimentally. The described electrotransformation protocol achieved an efficiency 1.2 × 10(2) cfu/μg DNA after step-by-step optimization and an efficiency of 1.6 × 10(2) cfu/μg DNA was achieved by the sonoporation technique using a standard laboratory ultrasound bath. The highest transformation efficiency was achieved using a combination of these approaches; sono/electroporation led to an increase in transformation efficiency, to 5.3 × 10(2) cfu/μg DNA. Both Dam and Dcm methylations are detrimental for transformation of C

Description of Kuraishia piskuri f.a., sp. nov., a new methanol assimilating yeast and transfer of phylogenetically related Candida species to the genera Kuraishia and Nakazawaea as new combinations

USDA-ARS?s Scientific Manuscript database

The new anamorphic yeast Kuraishia piskuri, f.a., sp. nov. is described for three strains that were isolated from insect frass from trees growing in Florida, USA (type strain, NRRL YB-2544, CBS 13714). Species placement was based on phylogenetic analysis of nuclear gene sequences for the D1/D2 domai...

Description of Martiniozyma gen. nov. and transfer of seven Candida species to Saturnispora as new combinations

USDA-ARS?s Scientific Manuscript database

DNA sequence analysis has shown Candida abiesophila (NRRL Y-11514T, CBS 5366T) and Candida asiatica (NRRL Y-63747T, CBS 10863T) to be members of a small clade that is phylogenetically separate from other yeasts. In view of their isolation from neighboring genera, such as Pichia and Saturnispora, the...

Mucor nidicola sp. nov., a fungal species isolated from an invasive paper wasp nest.

PubMed

Madden, A A; Stchigel, A M; Guarro, J; Sutton, D; Starks, P T

2012-07-01

A strain of a novel mucoralean fungus was isolated from a nest of the invasive paper wasp, Polistes dominulus. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and 5.8S rRNA gene sequences, along with physiological tests, revealed that this strain represents a novel species within the genus Mucor. The novel species also includes a representative that had previously been characterized as part of the Mucor hiemalis complex. Unlike the type strain of M. hiemalis, these two strains can grow at 37 °C and sporulate at 35 °C. Here, we present a partial resolution of the M. hiemalis species complex and propose the novel species Mucor nidicola sp. nov. to accommodate the isolate; the type strain of M. nidicola is F53(T) (=NRRL 54520(T)=UAMH 11442(T)=CBS 130359(T)).

Identification and Characterization of the Pyridomycin Biosynthetic Gene Cluster of Streptomyces pyridomyceticus NRRL B-2517*

PubMed Central

Huang, Tingting; Wang, Yemin; Yin, Jun; Du, Yanhua; Tao, Meifeng; Xu, Jing; Chen, Wenqing; Lin, Shuangjun; Deng, Zixin

2011-01-01

Pyridomycin is a structurally unique antimycobacterial cyclodepsipeptide containing rare 3-(3-pyridyl)-l-alanine and 2-hydroxy-3-methylpent-2-enoic acid moieties. The biosynthetic gene cluster for pyridomycin has been cloned and identified from Streptomyces pyridomyceticus NRRL B-2517. Sequence analysis of a 42.5-kb DNA region revealed 26 putative open reading frames, including two nonribosomal peptide synthetase (NRPS) genes and a polyketide synthase gene. A special feature is the presence of a polyketide synthase-type ketoreductase domain embedded in an NRPS. Furthermore, we showed that PyrA functioned as an NRPS adenylation domain that activates 3-hydroxypicolinic acid and transfers it to a discrete peptidyl carrier protein, PyrU, which functions as a loading module that initiates pyridomycin biosynthesis in vivo and in vitro. PyrA could also activate other aromatic acids, generating three pyridomycin analogues in vivo. PMID:21454714

Rhodotorula bloemfonteinensis sp. nov., Rhodotorula eucalyptica sp. nov., Rhodotorula orientis sp. nov. and Rhodotorula pini sp. nov., yeasts isolated from monoterpene-rich environments.

PubMed

Pohl, Carolina H; Smit, Martha S; Albertyn, Jacobus

2011-09-01

Recent rDNA sequencing of 25 isolates from a previous study, during which limonene-utilizing yeasts were isolated from monoterpene-rich environments by using 1,4-disubstituted cyclohexanes as sole carbon sources, led to the identification of four hitherto unknown Rhodotorula species. Analyses of the 26S rDNA D1/D2 region as well as the internal transcribed spacer (ITS) domain indicated that two isolates (CBS 8499(T) and CBS 10736) were identical and were closely related to Rhodotorula cycloclastica, a previously described limonene-utilizing yeast. These novel isolates differed from known yeast species and could be distinguished from R. cycloclastica by standard physiological tests. The other three isolates represent three novel Rhodotorula species, closely related to Sporobolomyces magnisporus. These three species could also be distinguished from other Rhodotorula species by standard physiological tests. Based on these results, we suggest that the new isolates represent novel species, for which the names Rhodotorula eucalyptica sp. nov. (type strain CBS 8499(T)  = NRRL Y-48408(T)), Rhodotorula pini sp. nov. (type strain CBS 10735(T)  = NRRL Y-48410(T)), Rhodotorula bloemfonteinensis sp. nov. (type strain CBS 8598(T)  = NRRL Y-48407(T)) and Rhodotorula orientis sp. nov. (type strain CBS 8594(T)  = NRRL Y-48719(T)) are proposed. R. eucalyptica and R. pini can also utilize limonene.

Candida spencermartinsiae sp. nov., Candida taylorii sp. nov. and Pseudozyma abaconensis sp. nov., novel yeasts from mangrove and coral reef ecosystems.

PubMed

Statzell-Tallman, Adele; Scorzetti, Gloria; Fell, Jack W

2010-08-01

Three species of yeasts are taxonomically described for strains isolated from marine environments. Candida spencermartinsiae sp. nov. (type strain CBS 10894T =NRRL Y-48663T) and Candida taylorii sp. nov. (type strain CBS 8508T =NRRL Y-27213T) are anamorphic ascomycetous yeasts in a phylogenetic cluster of marine yeasts in the Debaryomyces/Lodderomyces clade of the Saccharomycetales. The two species were isolated from multiple locations among coral reefs and mangrove habitats. Pseudozyma abaconensis sp. nov. (type strain CBS 8380T =NRRL Y-17380T) is an anamorphic basidiomycete that is related to the smut fungi of the genus Ustilago in the Ustilaginales. P. abaconensis was collected from waters adjacent to a coral reef.

Genomic Islands in Pathogenic Filamentous Fungus Aspergillus fumigatus

USDA-ARS?s Scientific Manuscript database

We present the genome sequences of a new clinical isolate, CEA10, of an important human pathogen, Aspergillus fumigatus, and two closely related, but rarely pathogenic species, Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1. Comparative genomic analysis of CEA10 with the recently sequen...

Phytotoxins Produced by Fungi Associated with Grapevine Trunk Diseases

PubMed Central

Andolfi, Anna; Mugnai, Laura; Luque, Jordi; Surico, Giuseppe; Cimmino, Alessio; Evidente, Antonio

2011-01-01

Up to 60 species of fungi in the Botryosphaeriaceae family, genera Cadophora, Cryptovalsa, Cylindrocarpon, Diatrype, Diatrypella, Eutypa, Eutypella, Fomitiporella, Fomitiporia, Inocutis, Phaeoacremonium and Phaeomoniella have been isolated from decline-affected grapevines all around the World. The main grapevine trunk diseases of mature vines are Eutypa dieback, the esca complex and cankers caused by the Botryospheriaceae, while in young vines the main diseases are Petri and black foot diseases. To understand the mechanism of these decline-associated diseases and the symptoms associated with them, the toxins produced by the pathogens involved in these diseases were isolated and characterised chemically and biologically. So far the toxins of only a small number of these decline fungi have been studied. This paper presents an overview of the toxins produced by the most serious of these vine wood pathogens: Eutypa lata, Phaeomoniella chlamydospora, Phaeoacremonium aleophilum and some taxa in the Botryosphaeriaceae family, and examines how these toxins produce decline symptoms. The chemical structure of these metabolites and in some cases their vivotoxin nature are also discussed. PMID:22295177

Description of Groenewaldozyma gen. nov. for placement of Candida auringiensis, Candida salmanticensis and Candida tartarivorans.

PubMed

Kurtzman, Cletus P

2016-07-01

DNA sequence analyses have demonstrated that species of the polyphyletic anamorphic ascomycete genus Candida may be members of described teleomorphic genera, members of the Candida tropicalis clade upon which the genus Candida is circumscribed, or members of isolated clades that represent undescribed genera. From phylogenetic analysis of gene sequences from nuclear large subunit rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II, Candida auringiensis (NRRL Y-17674(T), CBS 6913(T)), Candida salmanticensis (NRRL Y-17090(T), CBS 5121(T)), and Candida tartarivorans (NRRL Y-27291(T), CBS 7955(T)) were shown to be members of an isolated clade and are proposed for reclassification in the genus Groenewaldozyma gen. nov. (MycoBank MB 815817). Neighbouring taxa include species of the Wickerhamiella clade and Candida blankii.

Flowers as a reservoir of yeast diversity: description of Wickerhamiella nectarea f.a. sp. nov., and Wickerhamiella natalensis f.a. sp. nov. from South African flowers and pollinators, and transfer of related Candida species to the genus Wickerhamiella as new combinations.

PubMed

de Vega, Clara; Albaladejo, Rafael G; Guzmán, Beatriz; Steenhuisen, Sandy-Lynn; Johnson, Steven D; Herrera, Carlos M; Lachance, Marc-André

2017-08-01

Flowers offer favourable microenvironments for yeast growth, and are increasingly recognised as a rich source of novel yeast species. Independent surveys of yeasts associated with flowers and pollinators in South Africa led to the discovery of 38 strains of two new species. Physiological profiles and analysis of the internal transcribed spacer and the D1/D2 domains of the large subunit rRNA gene showed that they represent two novel species that belong to the Wickerhamiella clade. We describe the species as Wickerhamiella nectarea f.a. sp. nov. (type strain EBDCdVSA11-1T, CBS 14162T, NRRL Y-63791T) and W. natalensis f.a. sp. nov. (type strain EBDCdVSA7-1T, CBS 14161T, NRRL Y-63790T). We extend the known range of flower-associated Wickerhamiella species to South Africa and discuss the ecology and phylogenetic relationships of the clade in relation to its host species and biogeography. Examination of growth characteristics supports that the Wickerhamiella clade exhibits a high degree of evolutionary lability, and that specialisation to different niches may occur rapidly. We review the current status of floral yeast biodiversity and nectar as a reservoir of species diversity, and the importance of pollinators and biogeography. In addition, 18 species formerly assigned to the genus Candida are reassigned formally to the genus Wickerhamiella. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Enzyme-resistant isomalto-oligosaccharides produced from Leuconostoc mesenteroides NRRL B-1426 dextran hydrolysis for functional food application.

PubMed

Kothari, Damini; Goyal, Arun

2016-07-01

The extracellular dextransucrase from Leuconostoc mesenteroides NRRL B-1426 was produced and purified using polyethylene glycol fractionation. In our earlier study, it was reported that L. mesenteroides dextransucrase synthesizes a high-molecular mass dextran (>2 × 10(6)  Da) with ∼85.5% α-(1→6) linear and ∼14.5% α-(1→3) branched linkages. Isomalto-oligosaccharides (IMOs) were synthesized through depolymerization of dextran by the action of dextranase. The degree of polymerization of IMOs was 2-10 as confirmed by mass spectrometry. The nuclear magnetic resonance spectroscopic analysis revealed the presence of α-(1→3) linkages in the synthesized IMOs. The IMOs were resistant to dextranase, α-glucosidase, and α-amylase, and therefore can have potential application as food additives in the functional foods. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

Candida queiroziae sp. nov., a cellobiose-fermenting yeast species isolated from rotting wood in Atlantic Rain Forest.

PubMed

Santos, Renata O; Cadete, Raquel M; Badotti, Fernanda; Mouro, Adriane; Wallheim, Daniela O; Gomes, Fátima C O; Stambuk, Boris U; Lachance, Marc-André; Rosa, Carlos A

2011-03-01

Eight strains of a novel yeast species were isolated from rotting wood and wood-boring insects in Atlantic Rain Forest ecosystems in Brazil. Sequences of the D1/D2 domains of the large subunit of the rRNA gene showed that the yeast belongs to the Scheffersomyces clade and that it is related to Candida lignicola and Candida coipomoensis. The new species was isolated from rotting wood of three different localities and a wood-boring insect suggesting that these substrates are its ecological niche. This new yeast species is able to assimilate cellobiose and other compounds related to rotting wood. Strong fermentation of cellobiose in Durham tubes was observed for the strains of this new yeast. The new species produced an intracellular β-glucosidase responsible for cellobiose hydrolysis. The novel species, Candida queiroziae sp. nov., is proposed to accommodate these isolates. The type strain of C. queiroziae is UFMG-CLM 5.1(T) (=CBS 11853(T) = NRRL Y-48722(T)).

Identity of the xerophilic species Aspergillus penicillioides: Integrated analysis of the genotypic and phenotypic characters.

PubMed

Tamura, Miki; Kawasaki, Hiroko; Sugiyama, Junta

1999-02-01

We examined the identity of Aspergillus penicillioides, the typical xerophilic and strictly anamorphic species, using an integrated analysis of the genotypic and phenotypic characters. Our experimental methods on two genotypic characters, i.e., DNA base composition using the HPLC method and DNA relatedness using the nitrocellulose filter hybridization technique between A. flavus, A. oryzae, and their close relations revealed a good agreement with the values by buoyant density (for DNA base composition) and spectrophotometric determination (for DNA relatedness) reported by Kurtzman et al. in 1986. On the basis of these comparisons, we examined DNA base composition and DNA relatedness of six selected strains of A. penicillioides, including IFO 8155 (originally described as A. vitricola), one strain of A. restrictus, and the respective strains from Eurotium amstelodami, E. repens, and E. rubrum. As a result, five strains within A. penicillioides, including the neotype strain NRRL 4548, had G+C contents of 46 to 49 mol%, whereas IFO 8155 had 50 mol%. A. restrictus had 52 mol%, and three Eurotium species ranged from 46 to 49 mol%. The DNA relatedness between A. penicillioides (five strains), except for IFO 8155, exhibited values greater than 70%, but the DNA complementarity between four strains and IFO 8155 in A. penicillioides revealed values of less than 40%. DNA relatedness values between three species of Eurotium were 65 to 72%. We determined 18S, 5.8S, and ITS rDNA sequences as other genotypic characters from A. penicillioides (six strains), A. restrictus, and related teleomorphic species of Eurotium. In three phylogenetic trees inferred from these sequences, five strains of A. penicillioides, including the neotype strain, were closely related to each other, whereas IFO 8155 was distantly related and grouped with other xerophilic species. Our results have suggested that A. penicillioides typified by NRRL 4548 and A. penicillioides IFO 8155 (ex holotype of A

Proteomic analyses of ethanol tolerance in Lactobacillus buchneri NRRL B-30929.

PubMed

Liu, Siqing

2014-11-01

The Lactobacillus buchneri NRRL B-30929 strain, isolated from a fuel ethanol (EtOH) production facility, exhibits high tolerance to environmental EtOH concentrations. This study aimed to identify proteins produced by B-30929 in response to environmental EtOH. Cellular proteins expressed by B-30929 growing in media with 10 versus 0% EtOH were compared by 2DE, followed by in-gel digestion and MALDI-MS analyses. Twenty EtOH responsive proteins were identified. These include a proline-specific peptidase (Lbuc_1852); a membrane protein (Lbuc_0921), two general stress-related proteins including a 10 kDa chaperonin (GroESL Lbuc_1359) and a 29 kDa member of the HK 97 family (Lbuc_1523); metabolic enzymes involving redox potential balances (Lbuc_2051 and Lbuc_0522) and carbohydrate fermentation (Lbuc_1319 and Lbuc_2157); nitrogen, amino acid, and fatty acid metabolism proteins (Lbuc_1994, Lbuc_0446, Lbuc_0858, Lbuc_0707, and Lbuc_0787). These changes suggested B-30929 cells respond to EtOH by degradation of available proteins and fatty acids and increased production of specific enzymes and molecular chaperons. These results can be used to guide genetic modifications to increase EtOH tolerance in industrial biocatalysts. The data have been deposited to World-2DPAGE (http://world-2dpage.expasy.org/repository/0068/; username liu, password 1h8d6Mg1). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Antifungal metabolites (monorden, monocillin IV, and cerebrosides) from Humicola fuscoatra traaen NRRL 22980, a mycoparasite of Aspergillus flavus sclerotia.

PubMed

Wicklow, D T; Joshi, B K; Gamble, W R; Gloer, J B; Dowd, P F

1998-11-01

The mycoparasite Humicola fuscoatra NRRL 22980 was isolated from a sclerotium of Aspergillus flavus that had been buried in a cornfield near Tifton, Ga. When grown on autoclaved rice, this fungus produced the antifungal metabolites monorden, monocillin IV, and a new monorden analog. Each metabolite produced a clear zone of inhibition surrounding paper assay disks on agar plates seeded with conidia of A. flavus. Monorden was twice as inhibitory to A. flavus mycelium extension (MIC > 28 microg/ml) as monocillin IV (MIC > 56 microg/ml). Cerebrosides C and D, metabolites known to potentiate the activity of cell wall-active antibiotics, were separated from the ethyl acetate extract but were not inhibitory to A. flavus when tested as pure compounds. This is the first report of natural products from H. fuscoatra.

Antifungal Metabolites (Monorden, Monocillin IV, and Cerebrosides) from Humicola fuscoatra Traaen NRRL 22980, a Mycoparasite of Aspergillus flavus Sclerotia

PubMed Central

Wicklow, Donald T.; Joshi, Biren K.; Gamble, William R.; Gloer, James B.; Dowd, Patrick F.

1998-01-01

The mycoparasite Humicola fuscoatra NRRL 22980 was isolated from a sclerotium of Aspergillus flavus that had been buried in a cornfield near Tifton, Ga. When grown on autoclaved rice, this fungus produced the antifungal metabolites monorden, monocillin IV, and a new monorden analog. Each metabolite produced a clear zone of inhibition surrounding paper assay disks on agar plates seeded with conidia of A. flavus. Monorden was twice as inhibitory to A. flavus mycelium extension (MIC > 28 μg/ml) as monocillin IV (MIC > 56 μg/ml). Cerebrosides C and D, metabolites known to potentiate the activity of cell wall-active antibiotics, were separated from the ethyl acetate extract but were not inhibitory to A. flavus when tested as pure compounds. This is the first report of natural products from H. fuscoatra. PMID:9797310

Automated UV-C mutagenesis of Kluyveromyces marxianus NRRL Y-1109 and selection for microaerophilic growth and ethanol production at elevated temperature on biomass sugars.

PubMed

Hughes, Stephen R; Bang, Sookie S; Cox, Elby J; Schoepke, Andrew; Ochwat, Kate; Pinkelman, Rebecca; Nelson, Danielle; Qureshi, Nasib; Gibbons, William R; Kurtzman, Cletus P; Bischoff, Kenneth M; Liu, Siqing; Cote, Gregory L; Rich, Joseph O; Jones, Marjorie A; Cedeño, David; Doran-Peterson, Joy; Riaño-Herrera, Nestor M; Rodríguez-Valencia, Nelson; López-Núñez, Juan C

2013-08-01

The yeast Kluyveromyces marxianus is a potential microbial catalyst for fuel ethanol production from a wide range of biomass substrates. To improve its growth and ethanol yield at elevated temperature under microaerophilic conditions, K. marxianus NRRL Y-1109 was irradiated with UV-C using automated protocols on a robotic platform for picking and spreading irradiated cultures and for processing the resulting plates. The plates were incubated under anaerobic conditions on xylose or glucose for 5 mo at 46 °C. Two K. marxianus mutant strains (designated 7-1 and 8-1) survived and were isolated from the glucose plates. Both mutant strains, but not wild type, grew aerobically on glucose at 47 °C. All strains grew anaerobically at 46 °C on glucose, galactose, galacturonic acid, and pectin; however, only 7-1 grew anaerobically on xylose at 46 °C. Saccharomyces cerevisiae NRRL Y-2403 did not grow at 46 °C on any of these substrates. With glucose as a carbon source, ethanol yield after 3 d at 46 °C was higher for 8-1 than for wild type (0.51 and 0.43 g ethanol/g glucose, respectively). With galacturonic acid as a carbon source, the ethanol yield after 7 d at 46 °C was higher for 7-1 than for wild type (0.48 and 0.34 g ethanol/g galacturonic acid, respectively). These mutant strains have potential application in fuel ethanol production at elevated temperature from sugar constituents of starch, sucrose, pectin, and cellulosic biomass.

Phylogenetic Reconstruction of the Calosphaeriales and Togniniales Using Five Genes and Predicted RNA Secondary Structures of ITS, and Flabellascus tenuirostris gen. et sp. nov.

PubMed Central

Réblová, Martina; Jaklitsch, Walter M.; Réblová, Kamila; Štěpánek, Václav

2015-01-01

The Calosphaeriales is revisited with new collection data, living cultures, morphological studies of ascoma centrum, secondary structures of the internal transcribed spacer (ITS) rDNA and phylogeny based on novel DNA sequences of five nuclear ribosomal and protein-coding loci. Morphological features, molecular evidence and information from predicted RNA secondary structures of ITS converged upon robust phylogenies of the Calosphaeriales and Togniniales. The current concept of the Calosphaeriales includes the Calosphaeriaceae and Pleurostomataceae encompassing five monophyletic genera, Calosphaeria, Flabellascus gen. nov., Jattaea, Pleurostoma and Togniniella, strongly supported by Bayesian and Maximum Likelihood methods. The structural elements of ITS1 form characteristic patterns that are phylogenetically conserved, corroborate observations based on morphology and have a high predictive value at the generic level. Three major clades containing 44 species of Phaeoacremonium were recovered in the closely related Togniniales based on ITS, actin and β-tubulin sequences. They are newly characterized by sexual and RNA structural characters and ecology. This approach is a first step towards understanding of the molecular systematics of Phaeoacremonium and possibly its new classification. In the Calosphaeriales, Jattaea aphanospora sp. nov. and J. ribicola sp. nov. are introduced, Calosphaeria taediosa is combined in Jattaea and epitypified. The sexual morph of Phaeoacremonium cinereum was encountered for the first time on decaying wood and obtained in vitro. In order to achieve a single nomenclature, the genera of asexual morphs linked with the Calosphaeriales are transferred to synonymy of their sexual morphs following the principle of priority, i.e. Calosphaeriophora to Calosphaeria, Phaeocrella to Togniniella and Pleurostomophora to Pleurostoma. Three new combinations are proposed, i.e. Pleurostoma ochraceum comb. nov., P. repens comb. nov. and P. richardsiae comb

Metschnikowia drakensbergensis sp. nov. and Metschnikowia caudata sp. nov., endemic yeasts associated with Protea flowers in South Africa.

PubMed

de Vega, Clara; Guzmán, Beatriz; Steenhuisen, Sandy-Lynn; Johnson, Steven D; Herrera, Carlos M; Lachance, Marc-André

2014-11-01

In a taxonomic study of yeasts recovered from nectar of flowers and associated insects in South Africa, 11 strains were found to represent two novel species. Morphological and physiological characteristics and sequence analyses of the large-subunit rRNA gene D1/D2 region, as well as the actin, RNA polymerase II and elongation factor 2 genes, showed that the two novel species belonged to the genus Metschnikowia. Metschnikowia drakensbergensis sp. nov. (type strain EBD-CdVSA09-2(T) =CBS 13649(T) =NRRL Y-63721(T); MycoBank no. MB809688; allotype EBD-CdVSA10-2(A) =CBS13650(A) =NRRL Y-63720(A)) was recovered from nectar of Protea roupelliae and the beetle Heterochelus sp. This species belongs to the large-spored Metschnikowia clade and is closely related to Metschnikowia proteae, with which mating reactions and single-spored asci were observed. Metschnikowia caudata sp. nov. (type strain EBD-CdVSA08-1(T) =CBS 13651(T) =NRRL Y-63722(T); MycoBank no. MB809689; allotype EBD-CdVSA57-2(A) =CBS 13729(A) =NRRL Y-63723(A)) was isolated from nectar of Protea dracomontana, P. roupelliae and P. subvestita and a honeybee, and is a sister species to Candida hainanensis and Metschnikowia lopburiensis. Analyses of the four sequences demonstrated the existence of three separate phylotypes. Intraspecies matings led to the production of mature asci of unprecedented morphology, with a long, flexuous tail. A single ascospore was produced in all compatible crosses, regardless of sequence phylotype. The two species appear to be endemic to South Africa. The ecology and habitat specificity of these novel species are discussed in terms of host plant and insect host species. © 2014 IUMS.

Zygosaccharomyces favi sp. nov., an obligate osmophilic yeast species from bee bread and honey.

PubMed

Čadež, Neža; Fülöp, László; Dlauchy, Dénes; Péter, Gábor

2015-03-01

Five yeast strains representing a hitherto undescribed yeast species were isolated from bee bread and honey in Hungary. They are obligate osmophilic, i.e. they are unable to grow in/on high water activity culture media. Following isogamous conjugation, they form 1-4 spheroid or subspheroid ascospores in persistent asci. The analysis of the sequences of their large subunit rRNA gene D1/D2 domain placed the new species in the Zygosaccharomyces clade. In terms of pairwise sequence similarity, Zygosaccharomyces gambellarensis is the most closely related species. Comparisons of D1/D2, internal transcribed spacer and translation elongation factor-1α (EF-1α) gene sequences of the five strains with that of the type strain of Z. gambellarensis revealed that they represent a new yeast species. The name Zygosaccharomyces favi sp. nov. (type strain: NCAIM Y.01994(T) = CBS 13653(T) = NRRL Y-63719(T) = ZIM 2551(T)) is proposed for this new yeast species, which based on phenotype can be distinguished from related Zygosaccharomyces species by its obligate osmophilic nature. Some intragenomic sequence variability, mainly indels, was detected among the ITS copies of the strains of the new species.

Molecular and Phenotypic Characterization of Phialemonium and Lecythophora Isolates from Clinical Samples▿

PubMed Central

Perdomo, H.; Sutton, D. A.; García, D.; Fothergill, A. W.; Gené, J.; Cano, J.; Summerbell, R. C.; Rinaldi, M. G.; Guarro, J.

2011-01-01

Several members of the fungal genera Phialemonium and Lecythophora are occasional agents of severe human and animal infections. These species are difficult to identify, and relatively little is known about their frequency in the clinical setting. The objective of this study was to characterize morphologically and molecularly, on the basis of the analysis of large-subunit ribosomal DNA sequences, a set of 68 clinical isolates presumed to belong to these genera. A total of 59 isolates were determined to be Phialemonium species (n = 32) or a related Cephalotheca species (n = 6) or Lecythophora species (n = 20) or a related Coniochaeta species (n = 1). Nine isolates identified to be Acremonium spp. or Phaeoacremonium spp. were excluded from further study. The most common species were Phialemonium obovatum and Phialemonium curvatum, followed by Lecythophora hoffmannii, Cephalotheca foveolata, and Lecythophora mutabilis. PMID:21270235

Exopolysaccharide production from Sclerotium glucanicum NRRL 3006 and Botryosphaeria rhodina DABAC-P82 on raw and hydrolysed starchy materials.

PubMed

Selbmann, L; Crognale, S; Petruccioli, M

2002-01-01

Evaluation of fermentative usage of raw starchy materials for exopolysaccharide (EPS) production by Sclerotium glucanicum NRRL 3006 and Botryosphaeria rhodina DABAC-P82. Non-hydrolysed corn starch, soft wheat flour, potato flour, cassava flour, sweet and industrial potato flours, and corn starch hydrolysed to different dextrose equivalent (DE) were tested in shaken culture for EPS production. Both fungal strains produced EPS on all tested materials but the production was maximum on hydrolysed corn starch (30.5 and 19.8 g l(-1) by B. rhodina and S. glucanicum on corn starch at 100 and 62 DE, respectively). Raw starchy materials as such and, in particular, partially or totally hydrolysed corn starch could be used profitably for EPS production by S. glucanicum and B. rhodina. The excellent EPS production, productivity and yield of B. rhodina DABAC-P82 when grown on 60 g l(-1) of totally hydrolysed corn starch.

Lime application for the efficient production of nutraceutical glucooligosaccharides from Leuconostoc mesenteroides NRRL B-742 (ATCC13146).

PubMed

Moon, Young Hwan; Madsen, Lee; Chung, Chang-Ho; Kim, Doman; Day, Donal F

2015-02-01

We have previously demonstrated the production of glucooligosaccharides via a fermentation of sucrose with Leuconostoc mesenteroides NRRL B-742 using sodium hydroxide (NaOH) to control the pH. Because NaOH is expensive, we sought to minimize the cost of our process by substituting hydrated lime and saccharate of lime (lime sucrate) in its place. The yield of glucooligosaccharides using either 5 % lime (41.4 ± 0.5 g/100 g) or 5 % lime sucrate (40.0 ± 1.4 g/100 g) were both similar to the NaOH control (42.4 ± 1.5 g/100 g). Based on this, it appears that the cost associated with pH control in our process can be reduced by a factor of approximately 2.4 using lime instead of NaOH. Because our chromatographic stage is based on a Ca(2+)-form resin to separate glucooligosaccharides, the use of lime not only negates the need for costly de-salting via ion-exchange (elimination of two ion-exchange sections) prior to separation, but also greatly reduces the resin regeneration cost.

Candida olivae sp. nov., a novel yeast species from 'Greek-style' black olive fermentation.

PubMed

Nisiotou, Aspasia A; Panagou, Efstathios Z; Nychas, George-John E

2010-05-01

Two yeast strains (FMCC Y-1(T) and FMCC Y-2) were recovered during a survey of the yeast biota associated with fermenting black olives, collected from an olive tree (Olea europaea L. cv. 'Conservolea') orchard in Central Greece. Phylogenetic analysis based on rRNA gene sequences (18S, 26S, and 5.8S-ITS) indicated that the two strains represent a separate species within the Candida membranifaciens clade, in close relation to Candida blattariae NRRL Y-27703(T). Electrophoretic karyotyping and physiological analysis support the affiliation of the two strains to a novel species as Candida olivae sp. nov. The novel strains are conspecific with two Candida sp. strains previously isolated from the Mid-Atlantic Ridge hydrothermal fields [Gadanho & Sampaio (2005). Microb Ecol 50, 408-417], indicating that Candida olivae sp. nov. may occupy diverse ecological niches. FMCC Y-1(T) (=CBS 11171(T) =ATCC MYA-4568(T)) is the type strain.

Metschnikowia maroccana f.a., sp. nov., a new yeast species associated with floral nectar from Morocco.

PubMed

de Vega, Clara; Albaladejo, Rafael G; Lachance, Marc-André

2018-04-24

Wild flowers, and in particular, nectar of flowers, have been shown to be a rich reservoir of yeast biodiversity. In a taxonomic study of yeasts recovered from floral nectar in Morocco, nine strains were found to represent a novel species. Morphological and physiological characteristics and sequence analyses of the D1/D2 region of the large subunit rRNA gene as well as the internal transcribed spacer region showed that the novel species belonged to the genus Metschnikowia. The name Metschnikowia maroccana f.a., sp. nov. (EBDCdVMor24-1 T =CBS 15053 T =NRRL Y-63972 T ) is proposed to accommodate this new species. Metschnikowia maroccana was isolated from floral nectar of Teucrium pseudochamaepitys, Teucrium polium and Gladiolus italicus. The ascosporic state of the novel species was not found. Metschnikowia maroccana was phylogenetically distinct from any currently recognized species and forms a well-supported subclade (bootstrap value 81 %) containing species associated with flowers and flower-visiting insects, including Metschnikowia gruessii, Metschnikowia lachancei and Metschnikowia vanudenii. The close genealogical relationship of M. maroccana with the M. gruessii clade is also consistent with the striking similarity of their 'aeroplane' cells morphologies and the lack of utilization of the α-glucoside trehalose. The ecology of these novel species and its probable endemicity are discussed.

Expanding the species and chemical diversity of Penicillium section Cinnamopurpurea

USDA-ARS?s Scientific Manuscript database

A set of isolates genetically similar to or potentially conspecific with an unidentified Penicillium isolate NRRL 735, was assembled using a Basic Local Alignment Search Tool (BLAST) search of internal transcribed spacer (ITS) similarity among described (GenBank) and undescribed Penicillium isolates...

Purification and general properties of pectin methyl esterase from Curvularia inaequalis NRRL 13884 in solid state culture using orange peels as an inducer.

PubMed

Afifi, A F; Fawzi, E M; Foaad, M A

2002-01-01

Pectin methyl esterase (PME) [E.C.3. 1.1.11] production by Curvularia inaequalis (Shear) Boedijn NRRL 13884 was investigated using solid-state culture. The highest level of extracellular pectin methyl esterase was detected with orange peels as an inducing substrate and as a sole carbon source. The enzyme was partially purified using Sephadex G-100 and DEAE-Cellulose column chromatography. It was purified about 40 fold with optimum activity at pH 4.4 and 45 degrees C. The enzyme was activated by Co++, Mg++, Na+, whereas it was slightly activated in the presence of Cu++, K+, Mn++, Zn++. On the other hand Ag++, Ca++ and Hg++ inhibited the activity of the enzyme. The Km was calculated to be 0.52 mM.

Aspergillus asper sp. nov. and Aspergillus collinsii sp. nov., from Aspergillus section Usti.

PubMed

Jurjevic, Zeljko; Peterson, Stephen W

2016-07-01

In sampling fungi from the built environment, two isolates that could not confidently be placed in described species were encountered. Phenotypic analysis suggested that they belonged in Aspergillus sect. Usti. In order to verify the sectional placement and to assure that they were undescribed rather than phenotypically aberrant isolates, DNA was isolated and sequenced at the beta-tubulin, calmodulin, internal transcribed spacer and RNA polymerase II loci and sequences compared with those from other species in the genus Aspergillus. At each locus, each new isolate was distant from existing species. Phylogenetic trees calculated from these data and GenBank data for species of the section Usti excluded the placement of these isolates in existing species, with statistical support. Because they were excluded from existing taxa, the distinct species Aspergillus asper (type strain NRRL 35910 T ) and Aspergillus collinsii (type strain NRRL 66196 T ) in sect. Usti are proposed to accommodate these strains.

Munumbicins, wide-spectrum antibiotics produced by Streptomyces NRRL 30562, endophytic on Kennedia nigriscans.

PubMed

Castillo, Uvidelio F; Strobel, Gary A; Ford, Eugene J; Hess, Wilford M; Porter, Heidi; Jensen, James B; Albert, Heather; Robison, Richard; Condron, Margret A M; Teplow, David B; Stevens, Dennis; Yaver, Debbie

2002-09-01

Munumbicins A, B, C and D are newly described antibiotics with a wide spectrum of activity against many human as well as plant pathogenic fungi and bacteria, and a Plasmodium sp. These compounds were obtained from Streptomyces NRRL 3052, which is endophytic in the medicinal plant snakevine (Kennedia nigriscans), native to the Northern Territory of Australia. This endophyte was cultured, the broth was extracted with an organic solvent and the contents of the residue were purified by bioassay-guided HPLC. The major components were four functionalized peptides with masses of 1269.6, 1298.5, 1312.5 and 1326.5 Da. Numerous other related compounds possessing bioactivity, with differing masses, were also present in the culture broth extract in lower quantities. With few exceptions, the peptide portion of each component contained only the common amino acids threonine, aspartic acid (or asparagine), glutamic acid (or glutamine), valine and proline, in varying ratios. The munumbicins possessed widely differing biological activities depending upon the target organism. For instance, munumbicin B had an MIC of 2.5 microg x ml(-1) against a methicillin-resistant strain of Staphylococcus aureus, whereas munumbicin A was not active against this organism. In general, the munumbicins demonstrated activity against Gram-positive bacteria such as Bacillus anthracis and multidrug-resistant Mycobacterium tuberculosis. However, the most impressive biological activity of any of the munumbicins was that of munumbicin D against the malarial parasite Plasmodium falciparum, having an IC(50) of 4.5+/-0.07 ng x ml(-1). This report also describes the potential of the munumbicins in medicine and agriculture.

Saitoella coloradoensis sp. nov., a new species of the Ascomycota, subphylum Taphrinomycotina

USDA-ARS?s Scientific Manuscript database

Saitoella coloradoensis sp. nov. (NRRL YB-2330, CBS 12360, type strain) is described. This new member of the phylum Ascomycotina, subphylum Taphrinomycotina was isolated from insect frass occurring in an Engelmann spruce (Picea engelmannii) that was growing in Colorado, USA. Multigene sequence analy...

Brettanomyces acidodurans sp. nov., a new acetic acid producing yeast species from olive oil.

PubMed

Péter, Gábor; Dlauchy, Dénes; Tóbiás, Andrea; Fülöp, László; Podgoršek, Martina; Čadež, Neža

2017-05-01

Two yeast strains representing a hitherto undescribed yeast species were isolated from olive oil and spoiled olive oil originating from Spain and Israel, respectively. Both strains are strong acetic acid producers, equipped with considerable tolerance to acetic acid. The cultures are not short-lived. Cellobiose is fermented as well as several other sugars. The sequences of their large subunit (LSU) rRNA gene D1/D2 domain are very divergent from the sequences available in the GenBank. They differ from the closest hit, Brettanomyces naardenensis by about 27%, mainly substitutions. Sequence analyses of the concatenated dataset from genes of the small subunit (SSU) rRNA, LSU rRNA and translation elongation factor-1α (EF-1α) placed the two strains as an early diverging member of the Brettanomyces/Dekkera clade with high bootstrap support. Sexual reproduction was not observed. The name Brettanomyces acidodurans sp. nov. (holotype: NCAIM Y.02178 T ; isotypes: CBS 14519 T  = NRRL Y-63865 T  = ZIM 2626 T , MycoBank no.: MB 819608) is proposed for this highly divergent new yeast species.

Liamocin oil from Aureobasidium pullulans has antibacterial activity with specificity for species of Streptococcus

USDA-ARS?s Scientific Manuscript database

Liamocin oil from Aureobasidium pullulans NRRL 50380 was tested for antibacterial activity. Liamocins inhibited growth of Streptococcus agalactiae, S. uberis, S. mitis, S. infantarius, and S. mutans, with minimum inhibitory concentrations from 20 'g/ml to 78 'g/ml. Enterococcus faecalis was less sus...

Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov. and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers.

PubMed

McFrederick, Quinn S; Vuong, Hoang Q; Rothman, Jason A

2018-06-01

Gram-stain-positive, rod-shaped, non-spore forming bacteria have been isolated from flowers and the guts of adult wild bees in the families Megachilidae and Halictidae. Phylogenetic analysis of the 16S rRNA gene indicated that these bacteria belong to the genus Lactobacillus, and are most closely related to the honey-bee associated bacteria Lactobacillus kunkeei (97.0 % sequence similarity) and Lactobacillus apinorum (97.0 % sequence similarity). Phylogenetic analyses of 16S rRNA genes and six single-copy protein coding genes, in situ and in silico DNA-DNA hybridization, and fatty-acid profiling differentiates the newly isolated bacteria as three novel Lactobacillus species: Lactobacillus micheneri sp. nov. with the type strain Hlig3 T (=DSM 104126 T ,=NRRL B-65473 T ), Lactobacillus timberlakei with the type strain HV_12 T (=DSM 104128 T ,=NRRL B-65472 T ), and Lactobacillus quenuiae sp. nov. with the type strain HV_6 T (=DSM 104127 T ,=NRRL B-65474 T ).

Production of ochratoxin A by Aspergillus ochraceus NRRL-3174 before and after exposures to 60Co irradiation.

PubMed Central

Applegate, K L; Chipley, J R

1976-01-01

Spores from the toxigenic organism Aspergillus ochraceus NRRL-3174 were exposed to specific levels of gamma irradiation and then allowed to germinate on selected media. Increases in ochratoxin A production by irradiated, compared to non-irradiated, spores were observed after inoculation of spores onto a cracked red wheat or into a synthetic liquid medium. Variations in daily ochratoxin production were also observed for control and irradiated spore-derived cultures developing on both media, with maximum toxin production varying from 7 to 11 days of incubation. The most notable increases in ochratoxin A production occurred from cultures developing from spores having been irradiated with 10, 25, or 50 krad. Exposures to 400 or 600 krad resulted in complete inhibition of spore germination and, consequently, no ochratoxin production. Of the two substrates used, wheat and synthetic, the quantities of ochratoxin A produced were significantly lower in the synthetic media than on the natural substrate. Higher and more rapid toxin production occurred from spores having been irradiated with 10, 25, 50, and 100 krad than occurred from the non-irradiated control spores when grown on synthetic media. Cultures derived from spores having been exposed to 10, 25, 50, and 100 krad produced significantly higher levels of ochratoxin A after 8 days of incubation on natural substrate than did the controls. Analysis of variance revealed that substrate, length of incubation, as well as irradiation levels all affected the time required to produce maximum levels of ochratoxin A. PMID:938031

Novel ferulate esterase from Gram-positive lactic acid bacteria and analyses of the recombinant enzyme produced in E. coli

USDA-ARS?s Scientific Manuscript database

Using a plate containing ethyl ferulate as sole carbon source, various bacteria cultures were screened for ferulate esterase (FAE). Among a dozen of species showing positive FAE, one Lactobacillus fermentum strain NRRL 1932 demonstrated the strongest activity. Using a published sequence of ferulate ...

New Insight into Sugarcane Industry Waste Utilization (Press Mud) for Cleaner Biobutanol Production by Using C. acetobutylicum NRRL B-527.

PubMed

Nimbalkar, Pranhita R; Khedkar, Manisha A; Gaikwad, Shashank G; Chavan, Prakash V; Bankar, Sandip B

2017-11-01

In the present study, press mud, a sugar industry waste, was explored for biobutanol production to strengthen agricultural economy. The fermentative production of biobutanol was investigated via series of steps, viz. characterization, drying, acid hydrolysis, detoxification, and fermentation. Press mud contains an adequate amount of cellulose (22.3%) and hemicellulose (21.67%) on dry basis, and hence, it can be utilized for further acetone-butanol-ethanol (ABE) production. Drying experiments were conducted in the temperature range of 60-120 °C to circumvent microbial spoilage and enhance storability of press mud. Furthermore, acidic pretreatment variables, viz. sulfuric acid concentration, solid to liquid ratio, and time, were optimized using response surface methodology. The corresponding values were found to be 1.5% (v/v), 1:5 g/mL, and 15 min, respectively. In addition, detoxification studies were also conducted using activated charcoal, which removed almost 93-97% phenolics and around 98% furans, which are toxic to microorganisms during fermentation. Finally, the batch fermentation of detoxified press mud slurry (the sample dried at 100 °C and pretreated) using Clostridium acetobutylicum NRRL B-527 resulted in a higher butanol production of 4.43 g/L with a total ABE of 6.69 g/L.

Molecular phylogenetic, morphological, and mycotoxin data support reidentification of the Quorn mycoprotein fungus as Fusarium venenatum.

PubMed

O'Donnell, K; Cigelnik, E; Casper, H H

1998-02-01

Molecular phylogenetic, morphological, and mycotoxin data were obtained in order to investigate the relationships and identity of the Quorn mycoprotein fungus within Fusarium and to examine Quorn strains and commercial Quorn food products for trichothecene mycotoxins. Phylogenetic analyses of aligned DNA sequences obtained via the polymerase chain reaction from the nuclear 28S ribosomal DNA, nuclear ribosomal internal transcribed spacer region, and beta-tubulin gene exons and introns indicate that the Quorn fungus is Fusarium venenatum, rather than F. graminearum as previously reported. All of the Quorn strains examined were morphologically degenerate aconidial colonial mutants except for NRRL 25139, which produced chlamydospores in recurved terminal chains together with mostly 5-septate sporodochial conidia on doliform monophialides diagnostic of F. venenatum. Bootstrap and decay analyses provide strong support for a monophyletic lineage containing F. venenatum and several other type A trichothecene-producing species, while reference strains of F. graminearum were nested in a separate clade of species that produce type B trichothecenes and/or zearalenone. Analysis of mycotoxins from rice cultures inoculated with Quorn strain NRRL 25416 revealed that four type A trichothecenes are produced, but at low levels relative to strain NRRL 22198 of F. venenatum. No trichothecene mycotoxins, however, were detected from the analysis of three commercial Quorn products marketed for human consumption in England.

Purification and characterization of a thermostable α-galactosidase from Thielavia terrestris NRRL 8126 in solid state fermentation.

PubMed

Saad, Rawia R; Fawzi, Eman M

2012-03-01

Several seeds and husks of some plants belonging to leguminosae, Graminae, Compositae and Palmae were evaluated as carbon substrates to produce α-galactosidase (α-Gal) by the thermophilic fungus, Thielavia terrestris NRRL 8126 in solid substrate fermentation. The results showed that Cicer arietinum (chick pea seed) was the best substrate for α-Gal production. The crude enzyme was precipitated by ammonium sulphate (60%) and purified by gel filtration on sephadex G-100 followed by ion exchange chromatography on DEAE-Cellulose. The final purification fold of the enzyme was 30.42. The temperature and pH optima of purified α-Gal from Thielavia terrestris were 70 °C and 6.5, respectively. The enzyme showed high thermal stability at 70 °C and 75 °C and the half-life of the α-Gal at 90 °C was 45 min. Km of the purified enzyme was 1.31 mM. The purified enzyme was inhibited by Ag2+, Hg2+, Zn2+, Ba2+, Mg2+, Mn2+ and Fe2+ at 5 mM and 10 mM. Also, EDTA, sodium arsenate, L-cysteine and iodoacetate inhibited the enzyme activity. On the other hand, Ca2+, Cu2+, K+ and Na+ slightly enhanced the enzyme activity at 5 mM while at 10 mM they caused inhibition. The molecular weight of the α-Gal was estimated to be 82 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This enzyme displays a number of biochemical properties that make it a potentially strong candidate for biotechnological and medicinal applications.

Description of Kuraishia piskuri f.a., sp. nov., a new methanol assimilating yeast and transfer of phylogenetically related Candida species to the genera Kuraishia and Nakazawaea as new combinations.

PubMed

Kurtzman, Cletus P; Robnett, Christie J

2014-11-01

The new anamorphic yeast Kuraishia piskuri, f.a., sp. nov. is described for three strains that were isolated from insect frass from trees growing in Florida, USA (type strain, NRRL YB-2544, CBS 13714). Species placement was based on phylogenetic analysis of nuclear gene sequences for the D1/D2 domains of large subunit rRNA, small subunit rRNA, translation elongation factor-1α, and subunits B1 and B2 of RNA polymerase II B. From this analysis, the anamorphic species Candida borneana, Candida cidri, Candida floccosa, Candida hungarica, and Candida ogatae were transferred to the genus Kuraishia as new combinations and Candida anatomiae, Candida ernobii, Candida ishiwadae, Candida laoshanensis, Candida molendini-olei, Candida peltata, Candida pomicola, Candida populi, Candida wickerhamii, and Candida wyomingensis were transferred to the genus Nakazawaea. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Lachancea lanzarotensis sp. nov., an ascomycetous yeast isolated from grapes and wine fermentation in Lanzarote, Canary Islands.

PubMed

González, Sara S; Alcoba-Flórez, Julia; Laich, Federico

2013-01-01

During the characterization of the microbiota biodiversity associated with grapes and wineries in different bioclimatic conditions of the Canary Islands (Spain), a novel yeast species was isolated from Lanzarote, the driest wine-producing region of the archipelago. Seven strains isolated from grapes, microvinifications and wineries are described. Sequence analysis of the D1/D2 domain of the LSU rDNA gene and 5.8S-ITS regions revealed that the isolates were phylogenetically a member of the genus Lachancea and are closely related to Lachancea meyersii NRRL Y-27269(T) and Lachancea nothofagi NRRL Y-48670(T). On the basis of morphological, biochemical and physiological characterization and phylogenetic analysis, a novel ascosporogenous yeast species, Lachancea lanzarotensis sp. nov., is proposed. The type strain is L2C-15(T) ( = CBS 12615(T) = CECT 13066(T)) which was isolated from grape berries of Vitis vinifera L. cv. Listán Negro red grape variety in Tinajo, Lanzarote. The MycoBank no. is MB 801390.

Occultifur kilbournensis f.a. sp. nov., a new member of the Cystobasidiales associated with maize (Zea mays) cultivation.

PubMed

Kurtzman, Cletus P; Robnett, Christie J

2015-05-01

During a study of microorganisms associated with maize (Zea mays) cultivation, yeasts were isolated from overwintered stalks, cobs and surrounding soil, which were collected from an agricultural field in south-central Illinois, USA. Predominant among isolates were two species of Cryptococcus (Cr. flavescens, Cr. magnus) and a red yeast that D1/D2 LSU rRNA gene sequences revealed to be a new species of the basidiomycete yeast genus Occultifur. The species, which was not detected in the same field during the growing season, is described here as Occultifur kilbournensis (MycoBank number MB 811259; type strain NRRL Y-63695, CBS 13982, GenBank numbers, D1/D2 LSU rRNA gene, KP413160, ITS, KP413162; allotype strain NRRL Y-63699, CBS 13983). Mixture of the type and allotype strains resulted in formation of hyphae with clamp connections and a small number of apparent basidia following incubation on 5% malt extract agar at 15 °C for 2 months. In view of the uncertainty of the life cycle, the new species is being designated as forma asexualis. From analysis of D1/D2 and ITS nucleotide sequences, the new species is most closely related to Occultifur externus.

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

Compere, A.L.; Griffith, W.L.

The production was evaluated of ethanol, acetone, and butanol from several different carbohydrate materials by five strains of Clostridia and two mixed cultures. The substrates, which were tested at concn ranging between 2.5 and 10% w/v, included pentoses, hexoses, disaccharides, and polysaccharides. The organisms used were Clostridium acetobutylicum strains NRRL B527 and NRRL B3179; Clostridium butylicum strains NRRL B592 and NRRL B593; and Clostridium pasteurianum strain NRRL B598. The mixed cultures contained all of these organisms. Mixed culture 1 contained in addition to the Clostridia, Klebsiella pneumoniae strain NRRL B427. Mixed culture 2 contained mixed culture 1 plus a yeastmore » isolated from kefir culture. Where possible, maxima were found for the conversion of different substrates. 7 tables.« less

Enzymatic modification of schizophyllan

USDA-ARS?s Scientific Manuscript database

An enzymatic method was developed for the progressive modification of the polysaccharide schizophyllan. Fungal strains Hypocrea nigricans NRRL 62555, Penicillium crustosum NRRL 62558, and Penicillium simplicissimum NRRL 62550 were previously identified as novel sources of ß-endoglucanase with specif...

Cloning and heterologous expression of the entire gene clusters for PD 116740 from Streptomyces strain WP 4669 and tetrangulol and tetrangomycin from Streptomyces rimosus NRRL 3016.

PubMed Central

Hong, S T; Carney, J R; Gould, S J

1997-01-01

The genes for the complete pathways for two polycyclic aromatic polyketides of the angucyclinone class have been cloned and heterologously expressed. Genomic DNAs of Streptomyces rimosus NRRL 3016 and Streptomyces strain WP 4669 were partially digested with MboI, and libraries (ca. 40-kb fragments) in Escherichia coli XL1-Blue MR were prepared with the cosmid vector pOJ446. Hybridization with the actI probe from the actinorhodin polyketide synthase genes identified two clusters of polyketide genes from each organism. After transfer of the four clusters to Streptomyces lividans TK24, expression of one cluster from each organism was established through the identification of pathway-specific products by high-performance liquid chromatography with photodiode array detection. Peaks were identified from the S. rimosus cluster (pksRIM-1) for tetrangulol, tetrangomycin, and fridamycin E. Peaks were identified from the WP 4669 cluster (pksWP-2) for tetrangulol, 19-hydroxytetrangulol, 8-O-methyltetrangulol, 19-hydroxy-8-O-methyltetrangulol, and PD 116740. Structures were confirmed by 1H nuclear magnetic resonance spectroscopy and high-resolution mass spectrometry. PMID:8990300

Cloning and heterologous expression of the entire gene clusters for PD 116740 from Streptomyces strain WP 4669 and tetrangulol and tetrangomycin from Streptomyces rimosus NRRL 3016.

PubMed

Hong, S T; Carney, J R; Gould, S J

1997-01-01

The genes for the complete pathways for two polycyclic aromatic polyketides of the angucyclinone class have been cloned and heterologously expressed. Genomic DNAs of Streptomyces rimosus NRRL 3016 and Streptomyces strain WP 4669 were partially digested with MboI, and libraries (ca. 40-kb fragments) in Escherichia coli XL1-Blue MR were prepared with the cosmid vector pOJ446. Hybridization with the actI probe from the actinorhodin polyketide synthase genes identified two clusters of polyketide genes from each organism. After transfer of the four clusters to Streptomyces lividans TK24, expression of one cluster from each organism was established through the identification of pathway-specific products by high-performance liquid chromatography with photodiode array detection. Peaks were identified from the S. rimosus cluster (pksRIM-1) for tetrangulol, tetrangomycin, and fridamycin E. Peaks were identified from the WP 4669 cluster (pksWP-2) for tetrangulol, 19-hydroxytetrangulol, 8-O-methyltetrangulol, 19-hydroxy-8-O-methyltetrangulol, and PD 116740. Structures were confirmed by 1H nuclear magnetic resonance spectroscopy and high-resolution mass spectrometry.

Characterization of the Amicetin Biosynthesis Gene Cluster from Streptomyces vinaceusdrappus NRRL 2363 Implicates Two Alternative Strategies for Amide Bond Formation

PubMed Central

Zhang, Gaiyun; Zhang, Haibo; Li, Sumei; Xiao, Ji; Zhang, Guangtao; Zhu, Yiguang; Niu, Siwen; Ju, Jianhua

2012-01-01

Amicetin, an antibacterial and antiviral agent, belongs to a group of disaccharide nucleoside antibiotics featuring an α-(1→4)-glycoside bond in the disaccharide moiety. In this study, the amicetin biosynthesis gene cluster was cloned from Streptomyces vinaceusdrappus NRRL 2363 and localized on a 37-kb contiguous DNA region. Heterologous expression of the amicetin biosynthesis gene cluster in Streptomyces lividans TK64 resulted in the production of amicetin and its analogues, thereby confirming the identity of the ami gene cluster. In silico sequence analysis revealed that 21 genes were putatively involved in amicetin biosynthesis, including 3 for regulation and transportation, 10 for disaccharide biosynthesis, and 8 for the formation of the amicetin skeleton by the linkage of cytosine, p-aminobenzoic acid (PABA), and the terminal (+)-α-methylserine moieties. The inactivation of the benzoate coenzyme A (benzoate-CoA) ligase gene amiL and the N-acetyltransferase gene amiF led to two mutants that accumulated the same two compounds, cytosamine and 4-acetamido-3-hydroxybenzoic acid. These data indicated that AmiF functioned as an amide synthethase to link cytosine and PABA. The inactivation of amiR, encoding an acyl-CoA-acyl carrier protein transacylase, resulted in the production of plicacetin and norplicacetin, indicating AmiR to be responsible for attachment of the terminal methylserine moiety to form another amide bond. These findings implicated two alternative strategies for amide bond formation in amicetin biosynthesis. PMID:22267658

Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain

PubMed Central

2012-01-01

Background The molecular mechanisms altered by the traditional mutation and screening approach during the improvement of antibiotic-producing microorganisms are still poorly understood although this information is essential to design rational strategies for industrial strain improvement. In this study, we applied comparative genomics to identify all genetic changes occurring during the development of an erythromycin overproducer obtained using the traditional mutate-and- screen method. Results Compared with the parental Saccharopolyspora erythraea NRRL 2338, the genome of the overproducing strain presents 117 deletion, 78 insertion and 12 transposition sites, with 71 insertion/deletion sites mapping within coding sequences (CDSs) and generating frame-shift mutations. Single nucleotide variations are present in 144 CDSs. Overall, the genomic variations affect 227 proteins of the overproducing strain and a considerable number of mutations alter genes of key enzymes in the central carbon and nitrogen metabolism and in the biosynthesis of secondary metabolites, resulting in the redirection of common precursors toward erythromycin biosynthesis. Interestingly, several mutations inactivate genes coding for proteins that play fundamental roles in basic transcription and translation machineries including the transcription anti-termination factor NusB and the transcription elongation factor Efp. These mutations, along with those affecting genes coding for pleiotropic or pathway-specific regulators, affect global expression profile as demonstrated by a comparative analysis of the parental and overproducer expression profiles. Genomic data, finally, suggest that the mutate-and-screen process might have been accelerated by mutations in DNA repair genes. Conclusions This study helps to clarify the mechanisms underlying antibiotic overproduction providing valuable information about new possible molecular targets for rationale strain improvement. PMID:22401291

Screening of agro-industrial wastes for citric acid bioproduction by Aspergillus niger NRRL 2001 through solid state fermentation.

PubMed

Dhillon, Gurpreet S; Brar, Satinder K; Kaur, Surinder; Verma, Mausam

2013-05-01

The citric acid (CA) industry is currently struggling to develop a sustainable and economical process owing to high substrate and energy costs. Increasing interest in the replacement of costly synthetic substrates by renewable waste biomass has fostered research on agro-industrial wastes and screening of raw materials for economical CA production. The food-processing industry generates substantial quantities of waste biomass that could be used as a valuable low-cost fermentation substrate. The present study evaluated the potential of different agro-industrial wastes, namely apple pomace (AP), brewer's spent grain, citrus waste and sphagnum peat moss, as substrates for solid state CA production using Aspergillus niger NRRL 2001. Among the four substrates, AP resulted in highest CA production of 61.06 ± 1.9 g kg(-1) dry substrate (DS) after a 72 h incubation period. Based on the screening studies, AP was selected for optimisation studies through response surface methodology (RSM). Maximum CA production of 312.32 g kg(-1) DS was achieved at 75% (v/w) moisture and 3% (v/w) methanol after a 144 h incubation period. The validation of RSM-optimised parameters in plastic trays resulted in maximum CA production of 364.4 ± 4.50 g kg(-1) DS after a 120 h incubation period. The study demonstrated the potential of AP as a cheap substrate for higher CA production. This study contributes to knowledge about the future application of carbon rich agro-industrial wastes for their value addition to CA. It also offers economic and environmental benefits over traditional ways used to dispose off agro-industrial wastes. © 2012 Society of Chemical Industry.

Wickerhamiella pagnoccae sp. nov. and Candida tocantinsensis sp. nov., two ascomycetous yeasts from flower bracts of Heliconia psittacorum (Heliconiaceae).

PubMed

Barbosa, Anne C; Morais, Camila G; Morais, Paula B; Rosa, Luiz H; Pimenta, Raphael S; Lachance, Marc-André; Rosa, Carlos A

2012-02-01

Two novel yeast species were isolated from nectar of flower bracts of Heliconia psittacorum (Heliconiaceae) collected in a Cerrado ecosystem in the state of Tocantins, northern Brazil. Wickerhamiella pagnoccae sp. nov., which is closely related to Candida jalapaonensis, is heterothallic and produces one spheroid ascospore per ascus. Candida tocantinsensis sp. nov. belongs to the Metschnikowiaceae clade and its nearest relative is Candida ubatubensis, but the sequence identity (%) in the D1/D2 domains of the rRNA gene is low. The type strain of W. pagnoccae is UFMG-F18C1(T) ( = CBS 12178(T) = NRRL Y-48735(T)) and the type strain of C. tocantinsensis is UFMG-F16D1(T) ( = CBS 12177(T) = NRRL Y-48734(T)).

Conversion of Biomass Hydrolysates and Other Substrates to Ethanol and Other Chemicals by Lactobacillus buchneri

USDA-ARS?s Scientific Manuscript database

A Lactobacillus buchneri strain NRRL B-30929 can convert xylose and glucose into ethanol and chemicals. In this paper, L. buchneri NRRL B-30929 was initially compared with the type strains L. buchneri NRRL 1837 and DSM 5987 for growth and fermentation using single substrate derived from plant mater...

Identification of Mur34 as the Novel Negative Regulator Responsible for the Biosynthesis of Muraymycin in Streptomyces sp. NRRL30471

PubMed Central

Xu, Dongmei; Liu, Guang; Cheng, Lin; Lu, Xinhua; Chen, Wenqing; Deng, Zixin

2013-01-01

Background Muraymycin, a potent translocase I (MraY) inhibitor, is produced by Streptomyces sp. NRRL30471. The muraymycin gene cluster (mur) was recently cloned, and bioinformatic analysis of mur34 revealed its encoding product exhibits high homology to a large family of proteins, including KanI and RacI in individual biosynthetic pathway of kanamycin and ribostamycin. However, the precise role of these proteins remains unknown. Principal Findings Here we report the identification of Mur34 as the novel negative regulator involved in muraymycin biosynthesis. Independent disruption of mur34 on chromosome and cosmid directly resulted in significant improvement of muraymycin production by at least 10 folds, thereof confirming the negative function of Mur34 during muraymycin biosynthesis and realizing the engineered production of muraymycin in heterologous host. Gene expression analysis indicated that the transcription level of the mur genes in mur34 mutant (DM-5) was dramatically enhanced by ca. 30 folds. Electrophoretic mobility shift assay (EMSA) showed that Mur34 specifically bound to the promoter region of mur33. Further experiments showed that a 28-bp region downstream of the transcription start point (TSP) was protected by His6Mur34, and the −10 region is essential for the activity of mur33 promoter. Conclusions Mur34 plays an unambiguously negative role in muraymycin biosynthesis via binding to the upstream of mur33. More importantly, Mur34 represents a novel family of regulators acting in negative manner to regulate the secondary metabolites biosynthesis in bacteria. PMID:24143177

Determination of some significant batch culture conditions affecting acetyl-xylan esterase production by Penicillium notatum NRRL-1249

PubMed Central

2011-01-01

Background Acetyl-xylan esterase (AXE, EC 3.1.1.72) hydrolyses acetate group from the linear chain of xylopyranose residues bound by β-1,4-linkage. The enzyme finds commercial applications in bio-bleaching of wood pulp, treating animal feed to increase digestibility, processing food to increase clarification and converting lignocellulosics to feedstock and fuel. In the present study, we report on the production of an extracellular AXE from Penicillium notatum NRRL-1249 by solid state fermentation (SSF). Results Wheat bran at a level of 10 g (with 4 cm bed height) was optimized as the basal substrate for AXE production. An increase in enzyme activity was observed when 7.5 ml of mineral salt solution (MSS) containing 0.1% KH2PO4, 0.05% KCl, 0.05% MgSO4.7H2O, 0.3% NaNO3, 0.001% FeSO4.2H2O and 0.1% (v/w) Tween-80 as an initial moisture content was used. Various nitrogen sources including ammonium sulphate, urea, peptone and yeast extract were compared for enzyme production. Maximal enzyme activity of 760 U/g was accomplished which was found to be highly significant (p ≤ 0.05). A noticeable enhancement in enzyme activity was observed when the process parameters including incubation period (48 h), initial pH (5), 0.2% (w/w) urea as nitrogen source and 0.5% (v/w) Tween-80 as a stimulator were further optimized using a 2-factorial Plackett-Burman design. Conclusion From the results it is clear that an overall improvement of more than 35% in terms of net enzyme activity was achieved compared to previously reported studies. This is perhaps the first report dealing with the use of P. notatum for AXE production under batch culture SSF. The Plackett-Burman model terms were found highly significant (HS), suggesting the potential commercial utility of the culture used (df = 3, LSD = 0.126). PMID:21575210

Mannitol production by lactic acid bacteria grown in supplemented carob syrup.

PubMed

Carvalheiro, Florbela; Moniz, Patrícia; Duarte, Luís C; Esteves, M Paula; Gírio, Francisco M

2011-01-01

Detailed kinetic and physiological characterisation of eight mannitol-producing lactic acid bacteria, Leuconostoc citreum ATCC 49370, L. mesenteroides subsp. cremoris ATCC19254, L. mesenteroides subsp. dextranicum ATCC 19255, L. ficulneum NRRL B-23447, L. fructosum NRRL B-2041, L. lactis ATCC 19256, Lactobacillus intermedius NRRL 3692 and Lb. reuteri DSM 20016, was performed using a carob-based culture medium, to evaluate their different metabolic capabilities. Cultures were thoroughly followed for 30 h to evaluate consumption of sugars, as well as production of biomass and metabolites. All strains produced mannitol at high yields (>0.70 g mannitol/g fructose) and volumetric productivities (>1.31 g/l h), and consumed fructose and glucose simultaneously, but fructose assimilation rate was always higher. The results obtained enable the studied strains to be divided mainly into two groups: one for which glucose assimilation rates were below 0.78 g/l h (strains ATCC 49370, ATCC 19256 and ATCC 19254) and the other for which they ranged between 1.41 and 1.89 g/l h (strains NRRL B-3692, NRRL B-2041, NRRL B-23447 and DSM 20016). These groups also exhibited different mannitol production rates and yields, being higher for the strains with faster glucose assimilation. Besides mannitol, all strains also produced lactic acid and acetic acid. The best performance was obtained for L. fructosum NRRL B-2041, with maximum volumetric productivity of 2.36 g/l h and the highest yield, stoichiometric conversion of fructose to mannitol.

Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates.

PubMed

Lindquist, Mitch R; López-Núñez, Juan Carlos; Jones, Marjorie A; Cox, Elby J; Pinkelman, Rebecca J; Bang, Sookie S; Moser, Bryan R; Jackson, Michael A; Iten, Loren B; Kurtzman, Cletus P; Bischoff, Kenneth M; Liu, Siqing; Qureshi, Nasib; Tasaki, Kenneth; Rich, Joseph O; Cotta, Michael A; Saha, Badal C; Hughes, Stephen R

2015-11-01

Increased interest in sustainable production of renewable diesel and other valuable bioproducts is redoubling efforts to improve economic feasibility of microbial-based oil production. Yarrowia lipolytica is capable of employing a wide variety of substrates to produce oil and valuable co-products. We irradiated Y. lipolytica NRRL YB-567 with UV-C to enhance ammonia (for fertilizer) and lipid (for biodiesel) production on low-cost protein and carbohydrate substrates. The resulting strains were screened for ammonia and oil production using color intensity of indicators on plate assays. Seven mutant strains were selected (based on ammonia assay) and further evaluated for growth rate, ammonia and oil production, soluble protein content, and morphology when grown on liver infusion medium (without sugars), and for growth on various substrates. Strains were identified among these mutants that had a faster doubling time, produced higher maximum ammonia levels (enzyme assay) and more oil (Sudan Black assay), and had higher maximum soluble protein levels (Bradford assay) than wild type. When grown on plates with substrates of interest, all mutant strains showed similar results aerobically to wild-type strain. The mutant strain with the highest oil production and the fastest doubling time was evaluated on coffee waste medium. On this medium, the strain produced 0.12 g/L ammonia and 0.20 g/L 2-phenylethanol, a valuable fragrance/flavoring, in addition to acylglycerols (oil) containing predominantly C16 and C18 residues. These mutant strains will be investigated further for potential application in commercial biodiesel production.

Description of Teunomyces gen. nov. for the Candida kruisii clade, Suhomyces gen. nov. for the Candida tanzawaensis clade and Suhomyces kilbournensis sp. nov.

PubMed

Kurtzman, Cletus P; Robnett, Christie J; Blackwell, Meredith

2016-08-01

DNA sequence analysis has shown that species of the Candida kruisii clade and species of the C. tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T kruisii, and Suhomyces gen. nov., type species S tanzawaensis Many of the species are distributed worldwide and they are often isolated from fungus-feeding insects and their habitats. Included is the description of S. kilbournensis (type strain NRRL Y-17864, CBS 14276), a species found almost exclusively on maize kernels (Zea mays) in IL, USA. Published by Oxford University Press on behalf of FEMS 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Improvement of Aspergillus oryzae NRRL 3484 by mutagenesis and optimization of culture conditions in solid-state fermentation for the hyper-production of extracellular cellulase.

PubMed

El-Ghonemy, Dina Helmy; Ali, Thanaa Hamed; El-Bondkly, Ahmed Mohamed; Moharam, Maysa El-Sayed; Talkhan, Fatma Nabeeh

2014-11-01

Spore suspensions of Aspergillus oryzae NRRL 3484 were subjected to mutagenesis using ultraviolet-irradiation followed by chemical treatments to improve the biosynthesis of cellulase. Ten mutant strains namely UEAC7, UEAR5, UNAC4, UNAC16, UNAR19, UNBC7, UNBR3, UNBR10, UNBR23 and UNBR25 were selected and their extracellular cellulase activities were assayed. Mutant UNAC4 gave the highest cellulase production [2,455 ± 28 U/g-dry substrate (ds) for filter paper-ase (FP-ase)] in a yield 4-fold exceeding that of the wild type strain (578 ± 5.0 U/g-ds for FP-ase). Rice straw (RS) was used as a sole carbon source for the enzyme production at a concentration of 10 % (w/v). Maximum cellulase production was achieved at initial medium pH 5.5, initial moisture content 77 % and an incubation temperature 28 °C on the fifth day of growth. NH4Cl proved to be the suitable added nitrogen source for maximum enzyme production followed by peptone. These results clearly indicate the cost-effectiveness of solid state fermentation technology in the economic production of extracellular cellulase. The hyper-production of cellulase by mutant strain UNAC4 has potential for industrial processes that convert lignocellulosic material (e.g. RS) into products of commercial value such as glucose and biofuels.

Streptomyces roietensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of jasmine rice, Oryza sativa KDML 105.

PubMed

Kaewkla, Onuma; Franco, Christopher Milton Mathew

2017-11-01

An endophytic actinobacterium, strain WES2 T , was isolated from the stem of a jasmine rice plant collected from a paddy field in Thung Gura Rong Hai, Roi Et province, Thailand. As a result of a polyphasic study, this strain was identified as representing a novel member of the genus Streptomyces. This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelia and forming chains of looped spores. The closest phylogenetic relations, which shared the highest 16S rRNA gene sequence similarity, were Streptomyces nogalater JCM 4799 T and Streptomyces lavenduligriseus NRRL-ISP 5487 T at 99.1 and 99.0 %, respectively. Chemotaxonomic data, including major fatty acids, cell wall components and major menaquinones, confirmed the affiliation of WES2 T to the genus Streptomyces. The data from the phylogenetic analysis, including physiological and biochemical studies and DNA-DNA hybridization, revealed the genotypic and phenotypic differentiation of WES2 T from the most closely related species with validly published names. The name proposed for the novel species is Streptomycesroietensis sp. nov. The type strain is WES2 T (=DSM 101729=NRRL B-65344).

Candida amazonensis sp. nov., an ascomycetous yeast isolated from rotting wood in the Amazonian forest.

PubMed

Cadete, Raquel M; Melo, Monaliza A; Lopes, Mariana R; Pereira, Gilmara M D; Zilli, Jerri E; Vital, Marcos J S; Gomes, Fátima C O; Lachance, Marc-André; Rosa, Carlos A

2012-06-01

Five strains of a novel yeast species were isolated from rotting wood samples collected in an Amazonian forest site in the state of Roraima, northern Brazil. The sequences of the D1/D2 domains of the large subunit of the rRNA gene showed that this species belongs to the Scheffersomyces clade and is related to Candida coipomoensis, Candida lignicola and Candida queiroziae. The novel species Candida amazonensis sp. nov. is proposed to accommodate these isolates. The type strain of C. amazonensis sp. nov. is UFMG-HMD-26.3(T) ( = CBS 12363(T) = NRRL Y-48762(T)).

Single-step purification and characterization of an extreme halophilic, ethanol tolerant and acidophilic xylanase from Aureobasidium pullulans NRRL Y-2311-1 with application potential in the food industry.

PubMed

Yegin, Sirma

2017-04-15

An extracellular xylanase from Aureobasidium pullulans NRRL Y-2311-1 produced on wheat bran was purified by a single-step chromatographic procedure. The enzyme had a molecular weight of 21.6kDa. The optimum pH and temperature for xylanase activity were 4.0 and 30-50°C, respectively. The enzyme was stable in the pH range of 3.0-8.0. The inactivation energy of the enzyme was calculated as 218kJmol -1 . The xylanase was ethanol tolerant and kept complete activity in the presence of 10% ethanol. Likewise, it retained almost complete activity at a concentration range of 0-20% NaCl. In general, the enzyme was resistant to several metal ions and reagents. Mg 2+ , Zn 2+ , Cu 2+ , K 1+ , EDTA and β-mercaptoethanol resulted in enhanced xylanase activity. The K m and V max values on beechwood xylan were determined to be 19.43mgml -1 and 848.4Uml -1 , respectively. The enzyme exhibits excellent characteristics and could, therefore, be a promising candidate for application in food and bio-industries. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis.

PubMed

Haase, Max A B; Kominek, Jacek; Langdon, Quinn K; Kurtzman, Cletus P; Hittinger, Chris Todd

2017-05-01

Xylose fermentation is a rare trait that is immensely important to the cellulosic biofuel industry, and Candida tenuis is one of the few yeasts that has been reported with this trait. Here we report the isolation of two strains representing a candidate sister species to C. tenuis. Integrated analysis of genome sequence and physiology suggested the genetic basis of a number of traits, including variation between the novel species and C. tenuis in lactose metabolism due to the loss of genes encoding lactose permease and β-galactosidase in the former. Surprisingly, physiological characterization revealed that neither the type strain of C. tenuis nor this novel species fermented xylose in traditional assays. We reexamined three xylose-fermenting strains previously identified as C. tenuis and found that these strains belong to the genus Scheffersomyces and are not C. tenuis. We propose Yamadazyma laniorum f.a. sp. nov. to accommodate our new strains and designate its type strain as yHMH7 (=CBS 14780 = NRRL Y-63967T). Furthermore, we propose the transfer of Candida tenuis to the genus Yamadazyma as Yamadazyma tenuis comb. nov. This approach provides a roadmap for how integrated genome sequence and physiological analysis can yield insight into the mechanisms that generate yeast biodiversity. Published by Oxford University Press on behalf of FEMS 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

iso-Migrastatin, migrastatin, and dorrigocin production in Streptomyces platensis NRRL 18993 is governed by a single biosynthetic machinery featuring an acyltransferase-less type I polyketide synthase.

PubMed

Lim, Si-Kyu; Ju, Jianhua; Zazopoulos, Emmanuel; Jiang, Hui; Seo, Jeong-Woo; Chen, Yihua; Feng, Zhiyang; Rajski, Scott R; Farnet, Chris M; Shen, Ben

2009-10-23

iso-Migrastatin and related glutarimide-containing polyketides are potent inhibitors of tumor cell migration and their implied potential as antimetastatic agents for human cancers has garnered significant attention. Genome scanning of Streptomyces platensis NRRL 18993 unveiled two candidate gene clusters (088D and mgs); each encodes acyltransferase-less type I polyketide synthases commensurate with iso-migrastatin biosynthesis. Both clusters were inactivated by lambda-RED-mediated PCR-targeting mutagenesis in S. platensis; iso-migrastatin production was completely abolished in the DeltamgsF mutant SB11012 strain, whereas inactivation of 088D-orf7 yielded the SB11006 strain that exhibited no discernible change in iso-migrastatin biosynthesis. These data indicate that iso-migrastatin production is governed by the mgs cluster. Systematic gene inactivation allowed determination of the precise boundaries of the mgs cluster and the essentiality of the genes within the mgs cluster in iso-migrastatin production. The mgs cluster consists of 11 open reading frames that encode three acyltransferase-less type I polyketide synthases (MgsEFG), one discrete acyltransferase (MgsH), a type II thioesterase (MgsB), three post-PKS tailoring enzymes (MgsIJK), two glutarimide biosynthesis enzymes (MgsCD), and one regulatory protein (MgsA). A model for iso-migrastatin biosynthesis is proposed based on functional assignments derived from bioinformatics and is further supported by the results of in vivo gene inactivation experiments.

iso-Migrastatin, Migrastatin, and Dorrigocin Production in Streptomyces platensis NRRL 18993 Is Governed by a Single Biosynthetic Machinery Featuring an Acyltransferase-less Type I Polyketide Synthase*

PubMed Central

Lim, Si-Kyu; Ju, Jianhua; Zazopoulos, Emmanuel; Jiang, Hui; Seo, Jeong-Woo; Chen, Yihua; Feng, Zhiyang; Rajski, Scott R.; Farnet, Chris M.; Shen, Ben

2009-01-01

iso-Migrastatin and related glutarimide-containing polyketides are potent inhibitors of tumor cell migration and their implied potential as antimetastatic agents for human cancers has garnered significant attention. Genome scanning of Streptomyces platensis NRRL 18993 unveiled two candidate gene clusters (088D and mgs); each encodes acyltransferase-less type I polyketide synthases commensurate with iso-migrastatin biosynthesis. Both clusters were inactivated by λ-RED-mediated PCR-targeting mutagenesis in S. platensis; iso-migrastatin production was completely abolished in the ΔmgsF mutant SB11012 strain, whereas inactivation of 088D-orf7 yielded the SB11006 strain that exhibited no discernible change in iso-migrastatin biosynthesis. These data indicate that iso-migrastatin production is governed by the mgs cluster. Systematic gene inactivation allowed determination of the precise boundaries of the mgs cluster and the essentiality of the genes within the mgs cluster in iso-migrastatin production. The mgs cluster consists of 11 open reading frames that encode three acyltransferase-less type I polyketide synthases (MgsEFG), one discrete acyltransferase (MgsH), a type II thioesterase (MgsB), three post-PKS tailoring enzymes (MgsIJK), two glutarimide biosynthesis enzymes (MgsCD), and one regulatory protein (MgsA). A model for iso-migrastatin biosynthesis is proposed based on functional assignments derived from bioinformatics and is further supported by the results of in vivo gene inactivation experiments. PMID:19726666

Biological Assays for Two Mycotoxins Produced by Fusarium tricinctum

PubMed Central

Burmeister, H. R.; Hesseltine, C. W.

1970-01-01

A survey was made to detect microorganisms useful for assaying butenolide [4-acetamido-4-hydroxy-2-butenoic acid γ-lactone] and T-2 toxin [4β, 15-diacetoxy-8α-(3-methylbutyryloxy)-12,13-epoxytricothec -9-en-3α-ol]. These mycotoxins produced by strains of Fusarium tricinctum have been implicated in mycotoxicosis of livestock. Although butenolide proved to be a very weak antibiotic, assay discs containing 100 μg of this toxin inhibited Sprillum serpens NRRL B-2052, Vibrio tyrogenus NRRL B-1033, and Xanthomonas campestris NRRL B-1459. T-2 toxin had no effect on 54 bacterial strains but inhibited 6 of 11 fungi. Growth of Rhodotorula rubra NRRL Y-7222 and Penicillium digitatum NRRL 1202 was retarded by assay discs containing 4 μg of T-2 toxin. Solutions with less than 1 μg of T-2 per ml toxin were readily detected by a pea seed germination test. Germination was reduced more than 50% when seeds imbibed solutions of 0.5 μg of T-2 toxin per ml. Butenolide had no effect on pea seed germination at concentrations as high as 200 μg/ml. PMID:5485724

Cloning and heterologous expression of plnE, -F, -J and -K genes derived from soil metagenome and purification of active plantaricin peptides.

PubMed

Pal, Gargi; Srivastava, Sheela

2014-02-01

Plantaricin gene-specific primers were used to obtain plnE, -F, -J and -K structural gene amplicons from soil metagenome. These amplicons were cloned and expressed in pET32a (+) vector in Escherichia coli BL21 (DE3). PlnE, -F, -J and -K peptides were expressed as His-tagged-fusion proteins and were separated by Ni(2+) -chelating affinity chromatography. The peptides were released from the fusion by enterokinase cleavage and separated from the carrier thioredoxin. The cleaved peptides were further analysed for antimicrobial activity and found to be active against Listeria innocua NRRL B33314, Micrococcus luteus MTCC 106 and lactic acid bacteria, such as Enterococcus casseliflavus NRRL B3502, Lactococcus lactis lactis NRRL 1821, Lactobacillus curvatus NRRL B4562 and Lactobacillus plantarum NRRL B4496. E. coli has been successfully exploited as a host for heterologous expression with a significant yield of fused and cleaved peptides in the range of 8-12 and 1-1.5 mg/l of the culture, respectively. Heterologous expression, therefore, can be used to overcome the constraints of low yield often reported from a native strain.

Effect of inoculum concentrations of Aspergillus flavus and A. parasiticus on aflatoxin accumulation and kernel infection in resistant and susceptible maize hybrids

USDA-ARS?s Scientific Manuscript database

Over a three year period, we compared aflatoxin accumulation and kernel infection in maize hybrids inoculated with six inoculum concentrations of Aspergillus flavus isolate NRRL 3357 or A. parasiticus isolate NRRL 6111 which is a norsolorinic acid producer. Aflatoxin resistant and susceptible mai...

High sequence variations in the region containing genes encoding a cellular morphogenesis protein and the repressor of sexual development help to reveal origins of Aspergillus oryzae.

PubMed

Chang, Perng-Kuang; Scharfenstein, Leslie L; Solorzano, Cesar D; Abbas, Hamed K; Hua, Sui-Sheng T; Jones, Walker A; Zablotowicz, Robert M

2015-05-04

Aspergillus oryzae and Aspergillus flavus are closely related fungal species. The A. flavus morphotype that produces numerous small sclerotia (S strain) and aflatoxin has a unique 1.5 kb deletion in the norB-cypA region of the aflatoxin gene cluster (i.e. the S genotype). Phylogenetic studies have indicated that an isolate of the nonaflatoxigenic A. flavus with the S genotype is the ancestor of A. oryzae. Genome sequence comparison between A. flavus NRRL3357, which produces large sclerotia (L strain), and S-strain A. flavus 70S identified a region (samA-rosA) that was highly variable in the two morphotypes. A third type of samA-rosA region was found in A. oryzae RIB40. The three samA-rosA types were later revealed to be commonly present in A. flavus L-strain populations. Of the 182 L-strain A. flavus field isolates examined, 46%, 15% and 39% had the samA-rosA type of NRRL3357, 70S and RIB40, respectively. The three types also were found in 18 S-strain A. flavus isolates with different proportions. For A. oryzae, however, the majority (80%) of the 16 strains examined had the RIB40 type and none had the NRRL3357 type. The results suggested that A. oryzae strains in the current culture collections were mostly derived from the samA-rosA/RIB40 lineage of the nonaflatoxigenic A. flavus with the S genotype. Published by Elsevier B.V.

Comparison of expression of key sporulation, solventogenic and acetogenic genes in C. beijerinckii NRRL B-598 and its mutant strain overexpressing spo0A.

PubMed

Kolek, J; Diallo, M; Vasylkivska, M; Branska, B; Sedlar, K; López-Contreras, A M; Patakova, P

2017-11-01

The production of acetone, butanol and ethanol by fermentation of renewable biomass has potential to become a valuable industrial process. Mechanisms of solvent production and sporulation involve some common regulators in some ABE-producing clostridia, although details of the links between the pathways are not clear. In this study, we compare a wild-type (WT) Clostridium beijerinckii NRRL B-598 with its mutant strain OESpo0A, in which the gene encoding Spo0A, an important regulator of both sporulation and solventogenesis, is overexpressed in terms of solvent and acid production. We also compare morphologies during growth on two different media: TYA broth, where the WT culture sporulates, and RCM, where the WT culture does not. In addition, RT-qPCR-based analysis of expression profiles of spo0A, spoIIE, sigG, spoVD, ald and buk1 genes involved in sporulation or solvent production in these strains, were compared. The OESpo0A mutant did not produce spores and butanol titre was lower compared to the WT, but increased amounts of butyric acid and ethanol were produced. The gene spo0A had high levels of expression in the WT under non-sporulating culture conditions while other selected genes for sporulation factors were downregulated significantly. Similar observations were obtained for OESpo0A where spo0A overexpression and downregulation of other sporulation genes were demonstrated. Higher expression of spo0A led to higher expression of buk1 and ald, which could confirm the role of spo0A in activation of the solventogenic pathway, although solvent production was not affected significantly in the WT and was weakened in the OESpo0A mutant.

Acinetobacter lactucae sp. nov., isolated from iceberg lettuce (Asteraceae: Lactuca sativa)

USDA-ARS?s Scientific Manuscript database

Strain NRRL B-41902 and three closely related strains were isolated from iceberg lettuce. The strain was found to consist of strictly aerobic, gram-negative rods that formed cocci in late stationary phase. Subsequent to sequencing the 16S ribosomal RNA gene, it was found that strain NRRL B-41902 was...

High-Quality Draft Genome Sequence of Candida apicola NRRL Y-50540

PubMed Central

Vega-Alvarado, Leticia; Gómez-Angulo, Jorge; Escalante-García, Zazil; Grande, Ricardo; Gschaedler-Mathis, Anne; Amaya-Delgado, Lorena

2015-01-01

Candida apicola, a highly osmotolerant ascomycetes yeast, produces sophorolipids (biosurfactants), membrane fatty acids, and enzymes of biotechnological interest. The genome obtained has a high-quality draft for this species and can be used as a reference to perform further analyses, such as differential gene expression in yeast from Candida genera. PMID:26067948

Production of astaxanthin from corn fiber as a value-added co-product of fuel ethanol fermentation

USDA-ARS?s Scientific Manuscript database

Five strains of the yeast Phaffia rhodozyma, NRRL Y-17268, NRRL Y-17270, ATCC 96594 (CBS 6938), ATCC 24202 (UCD 67-210), and ATCC 74219 (UBV-AX2) were tested for astaxanthin production using the major sugars derived from corn fiber, a byproduct from the wet milling of corn kernels that contains prim...

Antihypertensive and hypolipidemic effect of milk fermented by specific Lactococcus lactis strains.

PubMed

Rodríguez-Figueroa, J C; González-Córdova, A F; Astiazaran-García, H; Hernández-Mendoza, A; Vallejo-Cordoba, B

2013-07-01

The antihypertensive and hypolipidemic effects of milk fermented by specific Lactococcus lactis strains in spontaneously hypertensive rats (SHR) were investigated. The SHR were fed ad libitum milk fermented by Lc. lactis NRRL B-50571, Lc. lactis NRRL B-50572, Captopril (40mg/kg of body weight, Sigma-Aldrich Co., St. Louis, MO) or purified water for 4 wk. Results suggested that Lc. lactis fermented milks presented a significant blood pressure-lowering effect. No significant difference was noted among milk fermented by Lc. lactis NRRL B-50571 and Captopril by the second and third week of treatment. Additionally, milk fermented by Lc. lactis strains modified SHR lipid profiles. Milk fermented by Lc. lactis NRRL B-50571 and B-50572 were able to reduce plasma low-density lipoprotein cholesterol and triglyceride contents. Thus, milk fermented by Lc. lactis strains may be a coadjuvant in the reduction of hypertension and hyperlipidemia and may be used as a functional food for better cardiovascular health. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Tempeh: a mold-modified indigenous fermented food made from soybeans and/or cereal grains.

PubMed

Hachmeister, K A; Fung, D Y

1993-01-01

A variety of indigenous fermented foods exist today; however, tempeh has been one of the most widely accepted and researched mold-modified fermented products. Tempeh is a traditional fermented food made from soaked and cooked soybeans inoculated with a mold, usually of the genus Rhizopus. After fermentation has occurred, the soybeans are bound together into a compact cake by dense cottony mycelium. An important function of the mold in the fermentation process is the synthesis of enzymes, which hydrolyze soybean constituents and contribute to the development of a desirable texture, flavor, and aroma of the product. Enzymatic hydrolysis also may decrease or eliminate antinutritional constituents; consequently, the nutritional quality of the fermented product may be improved. Current technology and new scientific advancements have enabled researchers to examine specific strains of Rhizopus and new substrates such as cereal grains. Because Kansas produces numerous cereal grains, production of a fermented tempeh-like product using wheat, sorghum (milo), oats, rye, barley, corn, and triticale is a definite possibility for generating a Kansas Value-Added Product. In this study, several different tempeh-like products were produced using various cereal grains inoculated with Rhizopus oligosporus NRRL 2549 or R. oligosporus NRRL 2710. Grains used included hard red winter wheat, triticale, yellow sorghum (milo), and red sorghum (milo). The grain source as well as the strain of R. oligosporus used influenced the product's appearance, flavor, and patty integrity. Results showed that R. oligosporus NRRL 2549 produced more mycelium at a more rapid rate than did the R. oligosporus NRRL 2710 strain. The combination of red sorghum and R. oligosporus NRRL 2549 yielded a product with good patty texture, aroma, and appearance. Furthermore, the red sorghum fermented product was well suited for slicing. On the other hand, yellow sorghum inoculated with either R. oligosporus NRRL 2549 or

Enzymatic synthesis of dithiolopyrrolone antibiotics using cell-free extract of Saccharothrix algeriensis NRRL B-24137 and biochemical characterization of two pyrrothine N-acyltransferases in this extract.

PubMed

Saker, Safwan; Almousa Almaksour, Ziade; Chorin, Anne-Claire; Lebrihi, Ahmed; Mathieu, Florence

2014-01-01

Saccharothrix algeriensis NRRL B-24137 produces naturally different dithiolopyrrolone derivatives. The enzymatic activity of pyrrothine N-acyltransferase was determined to be responsible for the transfer of an acyl group from acyl-CoA to pyrrothine core. This activity was also reported to be responsible for the diversity of the dithiolopyrrolone derivatives. Based on this fact, nine dithiolopyrrolone derivatives were produced in vitro via the crude extract of Sa. algeriensis. Three of them have never been obtained before by natural fermentation: acetoacetyl-pyrrothine, hydroxybutyryl-pyrrothine, and dimethyl thiolutin (holomycin). Two acyltransferase activities, acetyltransferase and benzoyltransferase catalyzing the incorporation of linear and cyclic acyl groups to the pyrrothine core, respectively, were biochemically characterized in this crude extract. The first one is responsible for formation of acetyl-pyrrothine and the second for benzoyl-pyrrothine. Both enzymes were sensitive to temperature changes: For example, the loss of acetyltransferase and benzoyltransferase activity was 53% and 80% respectively after pre-incubation of crude extract for 60 min at 20°C. The two enzymes were more active in neutral and basal media (pH 7-10) than in the acidic one (pH 3-6). The optimum temperature and pH of acetyltransferase were 40°C and 7, with a Km value of 7.9 μM and a Vmax of 0.63 μM/min when acetyl-CoA was used as limited substrate. Benzoyltransferase had a temperature and a pH optimum at 55°C and 9, a Km value of 14.7 μM, and a Vmax of 0.67 μM/min when benzoyl- CoA was used as limited substrate.

Cloning and Characterization of the Tetrocarcin A Gene Cluster from Micromonospora chalcea NRRL 11289 Reveals a Highly Conserved Strategy for Tetronate Biosynthesis in Spirotetronate Antibiotics▿ †

PubMed Central

Fang, Jie; Zhang, Yiping; Huang, Lijuan; Jia, Xinying; Zhang, Qi; Zhang, Xu; Tang, Gongli; Liu, Wen

2008-01-01

Tetrocarcin A (TCA), produced by Micromonospora chalcea NRRL 11289, is a spirotetronate antibiotic with potent antitumor activity and versatile modes of action. In this study, the biosynthetic gene cluster of TCA was cloned and localized to a 108-kb contiguous DNA region. In silico sequence analysis revealed 36 putative genes that constitute this cluster (including 11 for unusual sugar biosynthesis, 13 for aglycone formation, and 4 for glycosylations) and allowed us to propose the biosynthetic pathway of TCA. The formation of d-tetronitrose, l-amicetose, and l-digitoxose may begin with d-glucose-1-phosphate, share early enzymatic steps, and branch into different pathways by competitive actions of specific enzymes. Tetronolide biosynthesis involves the incorporation of a 3-C unit with a polyketide intermediate to form the characteristic spirotetronate moiety and trans-decalin system. Further substitution of tetronolide with five deoxysugars (one being a deoxynitrosugar) was likely due to the activities of four glycosyltransferases. In vitro characterization of the first enzymatic step by utilization of 1,3-biphosphoglycerate as the substrate and in vivo cross-complementation of the bifunctional fused gene tcaD3 (with the functions of chlD3 and chlD4) to ΔchlD3 and ΔchlD4 in chlorothricin biosynthesis supported the highly conserved tetronate biosynthetic strategy in the spirotetronate family. Deletion of a large DNA fragment encoding polyketide synthases resulted in a non-TCA-producing strain, providing a clear background for the identification of novel analogs. These findings provide insights into spirotetronate biosynthesis and demonstrate that combinatorial-biosynthesis methods can be applied to the TCA biosynthetic machinery to generate structural diversity. PMID:18586939

Zygosaccharomyces kombuchaensis, a new ascosporogenous yeast from 'Kombucha tea'.

PubMed

Kurtzman, C P; Robnett, C J; Basehoar-Powers, E

2001-07-01

A new ascosporogenous yeast, Zygosaccharomyces kombuchaensis sp. n. (type strain NRRL YB-4811, CBS 8849), is described; it was isolated from Kombucha tea, a popular fermented tea-based beverage. The four known strains of the new species have identical nucleotide sequences in domain D1/D2 of 26S rDNA. Phylogenetic analysis of D1/D2 and 18S rDNA sequences places Z. kombuchaensis near Zygosaccharomyces lentus. The two species are indistinguishable on standard physiological tests used for yeast identification, but can be recognized from differences in restriction fragment length polymorphism patterns obtained by digestion of 18S-ITS1 amplicons with the restriction enzymes DdeI and MboI.

Streptomyces aridus sp. nov., isolated from a high altitude Atacama Desert soil and emended description of Streptomyces noboritoensis Isono et al. 1957.

PubMed

Idris, Hamidah; Labeda, David P; Nouioui, Imen; Castro, Jean Franco; Del Carmen Montero-Calasanz, Maria; Bull, Alan T; Asenjo, Juan A; Goodfellow, Michael

2017-05-01

A polyphasic study was undertaken to determine the taxonomic status of a Streptomyces strain which had been isolated from a high altitude Atacama Desert soil and shown to have bioactive properties. The strain, isolate H9 T , was found to have chemotaxonomic, cultural and morphological properties that place it in the genus Streptomyces. 16S rRNA gene sequence analyses showed that the isolate forms a distinct branch at the periphery of a well-delineated subclade in the Streptomyces 16S rRNA gene tree together with the type strains of Streptomyces crystallinus, Streptomyces melanogenes and Streptomyces noboritoensis. Multi-locus sequence analysis (MLSA) based on five house-keeping gene alleles showed that isolate H9 T is closely related to the latter two type strains and to Streptomyces polyantibioticus NRRL B-24448 T . The isolate was distinguished readily from the type strains of S. melanogenes, S. noboritoensis and S. polyantibioticus using a combination of phenotypic properties. Consequently, the isolate is considered to represent a new species of Streptomyces for which the name Streptomyces aridus sp. nov. is proposed; the type strain is H9 T (=NCIMB 14965 T =NRRL B65268 T ). In addition, the MLSA and phenotypic data show that the S. melanogenes and S. noboritoensis type strains belong to a single species, it is proposed that S. melanogenes be recognised as a heterotypic synonym of S. noboritoensis for which an emended description is given.

Bacillus odysseyi isolate

NASA Technical Reports Server (NTRS)

La Duc, Myron Thomas (Inventor); Venkateswaran, Kasthuri (Inventor)

2007-01-01

The present invention relates to discovery and isolation of a biologically pure culture of a Bacillus odysseyi isolate with high adherence and sterilization resistant properties. B. odysseyi is a round spore forming Bacillus species that produces an exosporium. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA-DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus and the type strain is 34hs-1.sup.T (=ATCC PTA-4993.sup.T=NRRL B-30641.sup.T=NBRC 100172.sup.T). The GenBank accession number for the 16S rDNA sequence of strain 34hs-1.sup.T is AF526913.

Strain Selection and Optimization of Mixed Culture Conditions for Lactobacillus pentosus K1-23 with Antibacterial Activity and Aureobasidium pullulans NRRL 58012 Producing Immune-Enhancing β-Glucan.

PubMed

Sekar, Ashokkumar; Kim, Myoungjin; Jeong, Hyeong Chul; Kim, Keun

2018-05-28

Lactobacillus pentosus K1-23 was selected from among 25 lactic acid bacterial strains owing to its high inhibitory activity against several pathogenic bacteria, including Escherichia coli , Salmonella typhimurium , S. gallinarum , Staphylococcus aureus , Pseudomonas aeruginosa , Clostridium perfringens , and Listeria monocytogenes . Additionally, among 13 strains of Aureobasidium spp., A. pullulans NRRL 58012 was shown to produce the highest amount of β-glucan (15.45 ± 0.07%) and was selected. Next, the optimal conditions for a solid-phase mixed culture with these two different microorganisms (one bacterium and one yeast) were determined. The optimal inoculum sizes for L. pentosus and A. pullulans were 1% and 5%, respectively. The appropriate inoculation time for L. pentosus K1-23 was 3 days after the inoculation of A. pullulans to initiate fermentation. The addition of 0.5% corn steep powder and 0.1% FeSO₄ to the basal medium resulted in the increased production of lactic acid bacterial cells and β-glucan. The following optimal conditions for solid-phase mixed culture were also statistically determined by using the response surface method: 37.84°C, pH 5.25, moisture content of 60.82%, and culture time of 6.08 days for L. pentosus ; and 24.11°C, pH 5.65, moisture content of 60.08%, and culture time of 5.71 days for A. pullulans. Using the predicted optimal conditions, the experimental production values of L. pentosus cells and β-glucan were 3.15 ± 0.10 × 10⁸ CFU/g and 13.41 ± 0.04%, respectively. This mixed culture may function as a highly efficient antibiotic substitute based on the combined action of its anti-pathogenic bacterial and immune-enhancing activities.

Fusarium agapanthi sp. nov., a novel bikaverin and fusarubin-producing leaf and stem spot pathogen of Agapanthus praecox (African lily) from Australia and Italy.

PubMed

Edwards, Jacqueline; Auer, Desmond; de Alwis, Sri-Kanthi; Summerell, Brett; Aoki, Takayuki; Proctor, Robert H; Busman, Mark; O'Donnell, Kerry

2016-09-01

This study was conducted to characterize a novel Fusarium species that caused leaf and stem spot on Agapanthus praecox (Agapanthus, African lily) in northern Italy and leaf rot and spot on the same host in Melbourne, Australia. Formally described as Fusarium agapanthi, this pathogen was analyzed using phenotypic, phytopathogenic, secondary metabolite, molecular phylogenetic and genomic data. Five strains were characterized, including one isolated in 1999 from symptomatic A. praecox in Saluzzo, Italy, and four in 2010 from diseased leaf tissue from the same host exhibiting leaf rot and spot symptoms in the Melbourne Gardens, Royal Botanic Gardens Victoria, Australia. Maximum parsimony and maximum likelihood molecular phylogenetic analyses of portions of six individual genes and the combined dataset all strongly supported F. agapanthi either as the earliest diverging genealogically exclusive lineage in the American Clade of the F. fujikuroi species complex, or alternatively a novel monotypic lineage sister to the American Clade. Koch's postulates were completed on dwarf blue- and large white-flowering varieties of A. praecox, where two isolates of F. agapanthi produced slowly spreading necrotic lesions when inoculated onto leaves and flower stems. Fusarium agapanthi is distinguished from other fusaria by the production of densely branched aerial conidiophores with polyphialides throughout the aerial mycelium on synthetic nutrient-poor agar. BLASTn searches of the F. agapanthi NRRL 31653 and NRRL 54464 (= VPRI 41787) genome sequences were conducted to predict sexual reproductive mode and mycotoxin potential. Results indicated that they possessed MAT1-2 and MAT1-1 idiomorphs, respectively, indicating that this species might be heterothallic. Furthermore, based on the presence of homologs of the bikaverin and fusarubin biosynthetic gene clusters in the F. agapanthi genomes, liquid chromatography-mass spectrometry analysis was conducted and confirmed production of these

Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant.

PubMed

Vaz-Moreira, Ivone; Figueira, Vânia; Lopes, Ana R; Lobo-da-Cunha, Alexandre; Spröer, Cathrin; Schumann, Peter; Nunes, Olga C; Manaia, Célia M

2012-01-01

A Gram-positive, aerobic, non-motile, endospore-forming rod, designated DS22(T), was isolated from a drinking-water treatment plant. Cells were catalase- and oxidase-positive. Growth occurred at 15-37 °C, at pH 7-10 and with <8% (w/v) NaCl (optimum growth: 30 °C, pH 7-8 and 1-3% NaCl). The major respiratory quinone was menaquinone 7, the G+C content of the genomic DNA was 36.5 mol% and the cell wall contained meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis, strain DS22(T) was a member of the genus Bacillus. Its closest phylogenetic neighbours were Bacillus horneckiae NRRL B-59162(T) (98.5% 16S rRNA gene sequence similarity), Bacillus oceanisediminis H2(T) (97.9%), Bacillus infantis SMC 4352-1(T) (97.4%), Bacillus firmus IAM 12464(T) (96.8%) and Bacillus muralis LMG 20238(T) (96.8%). DNA-DNA hybridization, and biochemical and physiological characterization allowed the differentiation of strain DS22(T) from its closest phylogenetic neighbours. The data supports the proposal of a novel species, Bacillus purgationiresistans sp. nov.; the type strain is DS22(T) (=DSM 23494(T)=NRRL B-59432(T)=LMG 25783(T)).

Isolation of pyrrolocins A-C: cis- and trans-decalin tetramic acid antibiotics from an endophytic fungal-derived pathway.

PubMed

Jadulco, Raquel C; Koch, Michael; Kakule, Thomas B; Schmidt, Eric W; Orendt, Anita; He, Haiyin; Janso, Jeffrey E; Carter, Guy T; Larson, Erica C; Pond, Christopher; Matainaho, Teatulohi K; Barrows, Louis R

2014-11-26

Three new decalin-type tetramic acid analogues, pyrrolocins A (1), B (2), and C (3), were defined as products of a metabolic pathway from a fern endophyte, NRRL 50135, from Papua New Guinea. NRRL 50135 initially produced 1 but ceased its production before chemical or biological evaluation could be completed. Upon transfer of the biosynthetic pathway to a model host, 1-3 were produced. All three compounds are structurally related to equisetin-type compounds, with 1 and 3 having a trans-decalin ring system, while 2 has a cis-fused decalin. All were active against Mycobacterium tuberculosis, with the trans-decalin analogues 1 and 3 exhibiting lower MICs than the cis-decalin analogue 2. Here we report the isolation, structure elucidation, and antimycobacterial activities of 1-3 from the recombinant expression as well as the isolation of 1 from the wild-type fungus NRRL 50135.

Genetically modified luminescent bacteria Ralostonia solanacerum, Pseudomonas syringae, Pseudomonas savastanoi, and wild type bacterium Vibrio fischeri in biosynthesis of gold nanoparticles from gold chloride trihydrate.

PubMed

Attaran, Neda; Eshghi, Hossein; Rahimizadeh, Mohammad; Mashreghi, Mansour; Bakavoli, Mehdi

2014-08-04

The effect of different genetically engineered bacteria, Pseudomonas syringae, Pseudomonas savastanoi, and Ralostonia solanacerum and also a natural marine bacterial species, Vibrio fischeri NRRL B-11177, is studied in producing gold nanoparticles. This is the first report about the biosynthesis of gold nanoparticles by natural and genetically engineered luminescent bacteria. These microorganisms reduced gold ions and produced fairly monodisperse nanoparticles. TEM analysis indicated that spherical nano gold particles in the different diameters and shapes were obtained at pH values of 6.64. In this biosynthesis protocol, the gold nanoparticles with desired shape and size can be prepared.

Yamadazyma kitorensis f.a., sp. nov. and Zygoascus biomembranicola f.a., sp. nov., novel yeasts from the stone chamber interior of the Kitora tumulus, and five novel combinations in Yamadazyma and Zygoascus for species of Candida.

PubMed

Nagatsuka, Yuka; Ninomiya, Shinya; Kiyuna, Tomohiko; Kigawa, Rika; Sano, Chie; Sugiyama, Junta

2016-04-01

Analysis of D1/D2 large-subunit (LSU) rRNA gene sequences predicted that 17 yeast isolates, mainly from viscous gels (biofilms) taken from the stone chamber interior of the Kitora tumulus in Nara, Japan, were placed in the Yamadazyma and Zygoascus clades. Polyphasic characterization, including morphological, physiological and chemotaxonomic characteristics, multigene sequence divergence and DNA-DNA hybridization, strongly suggested the assignment of one novel species to each of the clades; these are Yamadazyma kitorensis f.a., sp. nov., with the type strain JCM 31005T (ex-type CBS 14158T=isolate K8617-6-8T), and Zygoascus biomembranicola f.a., sp. nov., with the type strain JCM 31007T (ex-type CBS 14157T=isolate K61208-2-11T). Furthermore, the transfer of five known species of the genus Candida as novel combinations to the genera Yamadazyma and Zygoascus is proposed; these are Yamadazyma olivae f.a., comb. nov. (type strain CBS 11171T=ATCC MYA-4568T), Yamadazyma tumulicola f.a., comb. nov. (type strain JCM 15403T=ex-type CBS 10917T=isolate T6517-9-5T), Yamadazyma takamatsuzukensis f.a., comb. nov. (type strain JCM 15410T=CBS 10916T = isolate T4922-1-1T), Zygoascus polysorbophila f.a., comb. nov. (type strain NRRL Y-27161T=CBS 7317T) and Zygoascus bituminiphila f.a., comb. nov. (type strain CBS 8813T=MUCL 41424T).

Comparison of major biocontrol strains of non-aflatoxigenic Aspergillus flavus for the reduction of aflatoxins and cyclopiazonic acid in maize.

PubMed

Abbas, H K; Zablotowicz, R M; Horn, B W; Phillips, N A; Johnson, B J; Jin, X; Abel, C A

2011-02-01

Biological control of toxigenic Aspergillus flavus in maize through competitive displacement by non-aflatoxigenic strains was evaluated in a series of field studies. Four sets of experiments were conducted between 2007 and 2009 to assess the competitiveness of non-aflatoxigenic strains when challenged against toxigenic strains using a pin-bar inoculation technique. In three sets of experiments the non-aflatoxigenic strain K49 effectively displaced toxigenic strains at various concentrations or combinations. The fourth study compared the relative competitiveness of three non-aflatoxigenic strains (K49, NRRL 21882 from Afla-Guard®, and AF36) when challenged on maize against two aflatoxin- and cyclopiazonic acid (CPA)-producing strains (K54 and F3W4). These studies indicate that K49 and NRRL 21882 are superior to AF36 in reducing total aflatoxin contamination. Neither K49 nor NRRL 21882 produce CPA and when challenged with K54 and F3W4, CPA and aflatoxins were reduced by 84-97% and 83-98%, respectively. In contrast, AF36 reduced aflatoxins by 20% with F3W4 and 93% with K54 and showed no reduction in CPA with F3W4 and only a 62% reduction in CPA with K54. Because AF36 produces CPA, high levels of CPA accumulate when maize is inoculated with AF36 alone or in combination with F3W4 or K54. These results indicate that K49 may be equally effective as NRRL 21882 in reducing both aflatoxins and CPA in maize.

Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales.

PubMed

Cavaletti, Linda; Monciardini, Paolo; Schumann, Peter; Rohde, Manfred; Bamonte, Ruggiero; Busti, Elena; Sosio, Margherita; Donadio, Stefano

2006-08-01

Two novel Gram-positive, acidophilic bacterial strains were isolated from forest soil. According to their 16S rRNA gene sequences, these strains are related closely to each other and form a distinct cluster within the order Actinomycetales. They show the typical features of filamentous actinomycetes, with branched vegetative hyphae and production of aerial hyphae. The distinct phylogenetic positions and the combination of chemotaxonomic characteristics of these strains justify the proposal of Actinospica gen. nov. Both strains display 3-hydroxydiaminopimelic acid plus traces of meso-diaminopimelic acid, the phospholipids diphosphatidylglycerol, phosphatidylethanolamine, methylphosphatidylethanolamine and phosphatidylinositol, the predominant cellular fatty acids i-C(15 : 0), i-C(16 : 0) and ai-C(15 : 0) and the whole-cell sugars mannose and rhamnose. They differ in the fatty acid profiles, in the quantitative ratios of the major menaquinones MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)) and in the occurrence of additional whole-cell sugars (arabinose and xylose in strain GE134766(T) and galactose in strain GE134769(T)). Differences in the phenotypic characteristics and in the 16S rRNA gene sequences suggest the description of two species, Actinospica robiniae gen. nov., sp. nov. (the type species) and Actinospica acidiphila sp. nov., with the type strains GE134769(T) (=DSM 44927(T)=NRRL B-24432(T)) and GE134766(T) (=DSM 44926(T)=NRRL B-24431(T)), respectively. The DNA G+C contents of strains GE134769(T) and GE134766(T) are 70.8 and 69.2 mol%, respectively. Due to the large phylogenetic distance from known actinomycete genera, it is proposed to accommodate Actinospica gen. nov. in Actinospicaceae fam. nov. In addition, Catenulisporineae subord. nov. is proposed to harbour Actinospicaceae fam. nov. and the newly proposed family Catenulisporaceae, described in the accompanying paper.

Streptomyces amphotericinicus sp. nov., an amphotericin-producing actinomycete isolated from the head of an ant (Camponotus japonicus Mayr).

PubMed

Cao, Tingting; Mu, Shan; Lu, Chang; Zhao, Shanshan; Li, Dongmei; Yan, Kai; Xiang, Wensheng; Liu, Chongxi

2017-12-01

A novel actinomycete, designated strain 1H-SSA8 T , was isolated from the head of an ant (Camponotus japonicus Mayr) and was found to produce amphotericin. A polyphasic approach was employed to determine the status of strain 1H-SSA8 T . Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Streptomyces. The menaquinones detected were MK-9(H6), MK-9(H8) and MK-9(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylinositol mannoside. The major fatty acids were identified as iso-C16 : 0, C16 : 0, C15 : 0 and anteiso-C15 : 0. Analysis of the 16S rRNA gene sequence showed that strain 1H-SSA8 T belongs to the genus Streptomyces with high sequence similarity to Streptomyces ramulosus NRRL B-2714 T (99.2 %). Two tree-making algorithms based on 16S rRNA gene sequences showed that the isolate formed a phyletic line with Streptomyces himastatinicus ATCC 53653 T (98.7 %). The MLSA utilizing partial sequences of the housekeeping genes (atpD, gyrB, recA, rpoB and trpB) also supported the position. However, evolutionary distances were higher than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. Moreover, the low level of DNA-DNA relatedness and phenotypic differences allowed the novel isolate to be differentiated from its most closely related strain S. ramulosus NRRL B-2714 T and strain S. himastatinicus ATCC 53653 T . It is concluded that the organism can be classified as representing a novel species of the genus Streptomyces, for which the name Streptomyces amphotericinicus sp. nov. is proposed. The type strain is 1H-SSA8 T (=CGMCC 4.7350 T =DSM 103128 T ).

Soybean hull induced production of carbohydrases and protease among Aspergillus and their effectiveness in soy flour carbohydrate and protein separation.

PubMed

Li, Qian; Loman, Abdullah Al; Coffman, Anthony M; Ju, Lu-Kwang

2017-04-20

Soybean hull consists mainly of three major plant carbohydrates, i.e., cellulose, hemicellulose and pectin. It is inexpensive and a good potential substrate for carbohydrase production because it is capable of inducing a complete spectrum of activities to hydrolyze complex biomass. Aspergillus is known for carbohydrase production but no studies have evaluated and compared, among Aspergillus species and strains, the soybean hull induced production of various carbohydrases. In this study, A. aculeatus, A. cinnamomeus, A. foetidus, A. phoenicis and 11 A. niger strains were examined together with T. reesei Rut C30, another known carbohydrase producer. The carbohydrases evaluated included pectinase, polygalacturonase, xylanase, cellulase, α-galactosidase and sucrase. Growth morphology and pH profiles were also followed. Among Aspergillus strains, morphology was found to correlate with both carbohydrase production and pH decrease profile. Filamentous strains gave higher carbohydrase production while causing slower pH decrease. The enzyme broths produced were also tested for separation of soy flour carbohydrate and protein. Defatted soy flour contains about 53% protein and 32% carbohydrate. The enzymatic treatment can increase protein content and remove indigestible oligo-/poly-saccharides, and improve use of soy flour in feed and food. Protease production by different strains was therefore also compared for minimizing protein degradation. A. niger NRRL 322 and A. foetidus NRRL 341 were found to be the most potent strains that produced maximal carbohydrases and minimal protease under soybean hull induction. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of the Composition of Culture Medium for Yeast Biomass Production Using Raw Glycerol from Biodiesel Synthesis

PubMed Central

dos Santos, Elisane Odriosolla; Michelon, Mariano; Furlong, Eliana Badiale; Burkert, Janaína Fernandes de Medeiros; Kalil, Susana Juliano; Burkert, Carlos André Veiga

2012-01-01

The work herewith investigated the production of yeast biomass as a source of protein, using Yarrowia lipolytica NRRL YB-423 and raw glycerol from biodiesel synthesis as the main carbon source. A significant influence of glycerol concentration, initial pH and yeast extract concentration on biomass and protein content was observed according to the 2v5-1 fractional design. These factors were further evaluated using a central composite design and response surface methodology, and an empirical model for protein content was established and validated. The biomass of Yarrowia lipolytica NRRL YB-423 reached 19.5 ± 1.0 g/L in shaken flasks cultivation, with a protein content of 20.1 ± 0.6% (w/w). PMID:24031849

21 CFR 186.1275 - Dextrans.

Code of Federal Regulations, 2014 CFR

2014-04-01

... by bacterial fermentation of sucrose. Commercially available dextrans are synthesized from sucrose by Leuconostoc mesenteroides strain NRRL B-512(F). Partial depolymerization and purification of the fermented...

In vitro digestibility and prebiotic potential of curdlan (1 → 3)-β-d-glucan oligosaccharides in Lactobacillus species.

PubMed

Shi, Yuqin; Liu, Jun; Yan, Qiaojuan; You, Xin; Yang, Shaoqing; Jiang, Zhengqiang

2018-05-15

Prebiotic effects of curdlan (1 → 3)-β-d-glucan oligosaccharides (GOS) were examined. GOS was tolerant against simulated gastrointestinal digestion, as well as low pH, thermal, and Maillard reaction conditions likely occurred during food processing. Growth of tested Lactobacillus (L.) strains was improved by GOS except L. brevis NRRL B-4527. E. coli did not grow on GOS as the only carbon source. In vitro batch fermentation using human faecal microbiota showed that GOS significantly increased the population of Lactobacillus sp. followed by Bifidobacterium sp. and Bacteroides sp. Growth of L. strains on GOS produced lactic acid, acetic, and propionic acid with decreased culture medium pH. Utilization pattern of GOS by representative L. strains was strain dependent. GOS with degree of polymerization (DP) of 2 and 3 were readily consumed. Findings here indicated that curdlan GOS (DP = 2 and 3) are promising physiologically active prebiotics for improvement of human intestinal health. Copyright © 2018 Elsevier Ltd. All rights reserved.

Glycopeptide Resistance vanA Operons in Paenibacillus Strains Isolated from Soil

PubMed Central

Guardabassi, Luca; Perichon, Bruno; van Heijenoort, Jean; Blanot, Didier; Courvalin, Patrice

2005-01-01

The sequence and gene organization of the van operons in vancomycin (MIC of >256 μg/ml)- and teicoplanin (MIC of ≥32 μg/ml)-resistant Paenibacillus thiaminolyticus PT-2B1 and Paenibacillus apiarius PA-B2B isolated from soil were determined. Both operons had regulatory (vanR and vanS), resistance (vanH, vanA, and vanX), and accessory (vanY, vanZ, and vanW) genes homologous to the corresponding genes in enterococcal vanA and vanB operons. The vanAPT operon in P. thiaminolyticus PT-2B1 had the same gene organization as that of vanA operons whereas vanAPA in P. apiarius PA-B2B resembled vanB operons due to the presence of vanW upstream from the vanHAX cluster but was closer to vanA operons in sequence. Reference P. apiarius strains NRRL B-4299 and NRRL B-4188 were found to harbor operons indistinguishable from vanAPA by PCR mapping, restriction fragment length polymorphism, and partial sequencing, suggesting that this operon was species specific. As in enterococci, resistance was inducible by glycopeptides and associated with the synthesis of pentadepsipeptide peptidoglycan precursors ending in d-Ala-d-Lac, as demonstrated by d,d-dipeptidase activities, high-pressure liquid chromatography, and mass spectrometry. The precursors differed from those in enterococci by the presence of diaminopimelic acid instead of lysine in the peptide chain. Altogether, the results are compatible with the notion that van operons in soil Paenibacillus strains and in enterococci have evolved from a common ancestor. PMID:16189102

Glycopeptide resistance vanA operons in Paenibacillus strains isolated from soil.

PubMed

Guardabassi, Luca; Perichon, Bruno; van Heijenoort, Jean; Blanot, Didier; Courvalin, Patrice

2005-10-01

The sequence and gene organization of the van operons in vancomycin (MIC of >256 microg/ml)- and teicoplanin (MIC of > or =32 microg/ml)-resistant Paenibacillus thiaminolyticus PT-2B1 and Paenibacillus apiarius PA-B2B isolated from soil were determined. Both operons had regulatory (vanR and vanS), resistance (vanH, vanA, and vanX), and accessory (vanY, vanZ, and vanW) genes homologous to the corresponding genes in enterococcal vanA and vanB operons. The vanA(PT) operon in P. thiaminolyticus PT-2B1 had the same gene organization as that of vanA operons whereas vanA(PA) in P. apiarius PA-B2B resembled vanB operons due to the presence of vanW upstream from the vanHAX cluster but was closer to vanA operons in sequence. Reference P. apiarius strains NRRL B-4299 and NRRL B-4188 were found to harbor operons indistinguishable from vanA(PA) by PCR mapping, restriction fragment length polymorphism, and partial sequencing, suggesting that this operon was species specific. As in enterococci, resistance was inducible by glycopeptides and associated with the synthesis of pentadepsipeptide peptidoglycan precursors ending in D-Ala-D-Lac, as demonstrated by D,D-dipeptidase activities, high-pressure liquid chromatography, and mass spectrometry. The precursors differed from those in enterococci by the presence of diaminopimelic acid instead of lysine in the peptide chain. Altogether, the results are compatible with the notion that van operons in soil Paenibacillus strains and in enterococci have evolved from a common ancestor.

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Streptomyces luozhongensis sp. nov., a novel actinomycete with antifungal activity and antibacterial activity.

PubMed

Zhang, Renwen; Han, Xiaoxue; Xia, Zhanfeng; Luo, Xiaoxia; Wan, Chuanxing; Zhang, Lili

2017-02-01

A novel actinomycete strain, designated TRM 49605 T , was isolated from a desert soil sample from Lop Nur, Xinjiang, north-west China, and characterised using a polyphasic taxonomic approach. The strain exhibited antifungal activity against the following strains: Saccharomyces cerevisiae, Curvularia lunata, Aspergillus flavus, Aspergillus niger, Fusarium oxysporum, Penicillium citrinum, Candida albicans and Candida tropicalis; Antibacterial activity against Bacillus subtilis, Staphylococcus epidermidis and Micrococcus luteus; and no antibacterial activity against Escherichia coli. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 49605 T to the genus Streptomyces. Strain TRM 49605 T shows high sequence similarities to Streptomyces roseolilacinus NBRC 12815 T (98.62 %), Streptomyces flavovariabilis NRRL B-16367 T (98.45 %) and Streptomyces variegatus NRRL B-16380 T (98.45 %). Whole cell hydrolysates of strain TRM 49605 T were found to contain LL-diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, xylose and mannose as the major whole cell sugars. The major fatty acids in strain TRM 49605 T were identified as iso C 16:0 , anteiso C 15:0 , C 16:0 and Summed Feature 5 as defined by MIDI. The main menaquinones were identified as MK-9(H 4 ), MK-9(H 6 ), MK-9(H 8 ) and MK-10(H 6 ). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The G+C content of the genomic DNA was determined to be 71.2 %. The DNA-DNA relatedness between strain TRM 49605 T and the phylogenetically related strain S. roseolilacinus NBRC 12815 T was 60.12 ± 0.06 %, which is lower than the 70 % threshold value for delineation of genomic prokaryotic species. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain TRM 49605 T (=CCTCC AA2015026 T  = KCTC 39666 T ) should be designated as the type strain of a novel species of the genus

Membrane-acting bacteriocin purified from a soil isolate Pediococcus pentosaceus LB44 shows broad host-range.

PubMed

Kaur, Ramanjeet; Tiwari, Santosh Kumar

2018-04-15

Bacteriocin LB44 was purified from cell-free supernatant (CFS) of Pediococcus pentosaceus LB44 using activity-guided chromatography techniques. It was stable up to 121 °C, pH 2.0-6.0, sensitive to proteinase K, papain and trypsin, and retained complete activity in the presence of organic solvents tested. The molecular weight of bacteriocin was ∼6 kDa and initial ten amino acid residues (GECGMCXECG) suggested a new compound. The loss in viable cell count and K + ion efflux of target cells of Micrococcus luteus suggested bactericidal activity. The cell membrane of bacteriocin-treated cells was found to be ruptured which was further confirmed by Fourier Transform Infrared (FTIR) analysis suggesting interaction of bacteriocin with phospholipids in cell membrane. It showed broad host-range and inhibited the growth of Lactobacillus delbrueckii NRRL B-4525, L. plantarum NRRL B-4496, L. acidophilus NRRL B-4495, Enterococcus hirae LD3, Weissella confusa LM85, Staphylococcus aureus, Salmonella typhi ATCC 13311, Serratia marcescens ATCC 27137, Pseudomonas aeruginosa ATCC 27853, Proteus vulgaris ATCC 29905, Haloferax larsenii HA1, HA3, HA8, HA9 and HA10. These properties suggested a new bacteriocin from soil isolate P. pentosaceus LB44 which may offers possible applications in food-safety and therapeutics. Copyright © 2018 Elsevier Inc. All rights reserved.

Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees.

PubMed

Kwong, Waldan K; Moran, Nancy A

2016-03-01

Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29-31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T).

Tsukamurella spongiae sp. nov., a novel actinomycete isolated from a deep-water marine sponge.

PubMed

Olson, Julie B; Harmody, Dedra K; Bej, Asim K; McCarthy, Peter J

2007-07-01

A Gram-positive, rod-shaped, non-spore-forming bacterium (strain K362(T)) was isolated from a deep-water marine sponge collected off the coast of Curaçao in the Netherlands Antilles. On the basis of 16S rRNA gene sequence similarities, strain K362(T) was shown to belong to the genus Tsukamurella, being most closely related to Tsukamurella pulmonis (99.2 %), Tsukamurella tyrosinosolvens (98.9 %), Tsukamurella strandjordii (98.8 %), Tsukamurella pseudospumae (98.8 %) and Tsukamurella spumae (98.8 %). A combination of the substrate utilization patterns, the fatty acid and mycolic acid profiles and the DNA-DNA hybridization results supported the affiliation of strain K362(T) to the genus Tsukamurella and enabled the genotypic and phenotypic differentiation of strain K362(T) from the seven recognized Tsukamurella species. Strain K362(T) therefore represents a novel species of the genus Tsukamurella, for which the name Tsukamurella spongiae sp. nov. is proposed. The type strain is K362(T) (=DSM 44990(T)=NRRL B-24467(T)).

DNA–DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov

PubMed Central

Holmes, B.; Steigerwalt, A. G.; Nicholson, A. C.

2015-01-01

The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA–DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indoleproducing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530T=CCUG 60564T=CDC G229T), Chryseobacterium carnis sp. nov. (type strain NCTC 13525T=CCUG 60559T=CDC G81T), Chryseobacterium lactis sp. nov. (type strain NCTC 11390T=CCUG 60566T=CDC KC1864T) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529T=CCUG 60563T=CDC G41T). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490T=X-65T=CCTCC AB 208154T=NRRL B-51322T) is also proposed to accommodate the reclassified Planobacterium taklimakanense. PMID:23934253

Description of Kribbella italica sp. nov., isolated from a Roman catacomb.

PubMed

Everest, Gareth J; Curtis, Sarah M; De Leo, Filomena; Urzì, Clara; Meyers, Paul R

2015-02-01

A novel actinobacterium, strain BC637(T), was isolated from a biodeteriogenic biofilm sample collected in 2009 in the Saint Callixstus Roman catacomb. The strain was found to belong to the genus Kribbella by analysis of the 16S rRNA gene. Phylogenetic analysis using the 16S rRNA gene and the gyrB, rpoB, relA, recA and atpD concatenated gene sequences showed that strain BC637(T) was most closely related to the type strains of Kribbella lupini and Kribbella endophytica. DNA-DNA hybridization experiments confirmed that strain BC637(T) is a genomic species that is distinct from its closest phylogenetic relatives, K. endophytica DSM 23718(T) (63 % DNA relatedness) and K. lupini LU14(T) (63 % DNA relatedness). Physiological comparisons showed that strain BC637(T) is phenotypically distinct from the type strains of K. endophytica and K. lupini. Thus, strain BC637(T) represents the type strain of a novel species, for which the name Kribella italica sp. nov. is proposed ( = DSM 28967(T) = NRRL B-59155(T)). © 2015 IUMS.

Endangered Species

EPA Pesticide Factsheets

EPA's Endangered Species Protection Program helps promote recovery of listed species. The ESPP determines if pesticide use in a geographic area may affect any listed species. Find needed limits on pesticide use in Endangered Species Protection Bulletins.

The nuclear question: rethinking species importance in multi-species animal groups.

PubMed

Srinivasan, Umesh; Raza, Rashid Hasnain; Quader, Suhel

2010-09-01

1. Animals group for various benefits, and may form either simple single-species groups, or more complex multi-species associations. Multi-species groups are thought to provide anti-predator and foraging benefits to participant individuals. 2. Despite detailed studies on multi-species animal groups, the importance of species in group initiation and maintenance is still rated qualitatively as 'nuclear' (maintaining groups) or 'attendant' (species following nuclear species) based on species-specific traits. This overly simplifies and limits understanding of inherently complex associations, and is biologically unrealistic, because species roles in multi-species groups are: (i) likely to be context-specific and not simply a fixed species property, and (ii) much more variable than this dichotomy indicates. 3. We propose a new view of species importance (measured as number of inter-species associations), along a continuum from 'most nuclear' to 'least nuclear'. Using mixed-species bird flocks from a tropical rainforest in India as an example, we derive inter-species association measures from randomizations on bird species abundance data (which takes into account species 'availability') and data on 86 mixed-species flocks from two different flock types. Our results show that the number and average strength of inter-species associations covary positively, and we argue that species with many, strong associations are the most nuclear. 4. From our data, group size and foraging method are ecological and behavioural traits of species that best explain nuclearity in mixed-species bird flocks. Parallels have been observed in multi-species fish shoals, in which group size and foraging method, as well as diet, have been shown to correlate with nuclearity. Further, the context in which multi-species groups occur, in conjunction with species-specific traits, influences the role played by a species in a multi-species group, and this highlights the importance of extrinsic factors in

Cloning, sequencing and characterization of lipase genes from a polyhydroxyalkanoate- (PHA-) synthesizing Pseudomonas resinovorans

USDA-ARS?s Scientific Manuscript database

Lipase (lip) and lipase-specific foldase (lif) genes of a biodegradable polyhydroxyalkanoate- (PHA-) synthesizing Pseudomonas resinovorans NRRL B-2649 were cloned using primers based on consensus sequences, followed by PCR-based genome walking. Sequence analyses showed a putative Lip gene-product (...

Bioabatement with hemicellulase supplementation to reduce enzymatic hydrolysis inhibitors

USDA-ARS?s Scientific Manuscript database

Removal of inhibitory compounds by bioabatement, combined with xylan hydrolysis, enables effective cellulose hydrolysis of pretreated corn stover, for fermentation of the sugars to fuel ethanol or other products. The fungus Coniochaeta ligniaria NRRL30616 eliminates most enzyme and fermentation inhi...

Bioabatement with xylanase supplementation to reduce enzymatic hydrolysis inhibitors

USDA-ARS?s Scientific Manuscript database

Bioabatement, using the fungus Coniochaeta ligniaria NRRL30616 can effectively eliminate enzyme inhibitors from pretreated biomass hydrolysis. However, our recent research suggested that bioabatement had no beneficial effect on removing xylo-oligomers which were identified as strong inhibitors to ce...

Production of xylitol from biomass using an inhibitor-tolerant fungal strain

USDA-ARS?s Scientific Manuscript database

Inhibitory compounds arising from physical–chemical pretreatment of biomass feedstock can interfere with fermentation of biomass sugars to product. A fungus, Coniochaeta ligniaria NRRL30616 improves fermentability of biomass sugars by metabolizing a variety of microbial inhibitors including furan al...

A new beta-glucosidase producing yeast for lower-cost cellulosic ethanol production from xylose-extracted corncob residues by simultaneous saccharification and fermentation

USDA-ARS?s Scientific Manuscript database

Conventional cellulose-to-ethanol conversion by simultaneous saccharification and fermentation (SSF)requires enzymatic saccharification using both cellulase and ß-glucosidase allowing cellulose utilization by common ethanologenic yeast. Here we report a new yeast strain of Clavispora NRRL Y-50464 th...

Production of xylitol by a Coniochaeta ligniaria strain tolerant of inhibitors and defective in xylose metabolism

USDA-ARS?s Scientific Manuscript database

In conversion of biomass to fuels or chemicals, inhibitory compounds arising from physical-chemical pretreatment of the feedstock can interfere with fermentation of the sugars to product. Fungal strain Coniochaeta ligniaria NRRL30616, metabolizes the furan aldehydes furfural and 5-hydroxymethylfurfu...

Biological abatement of inhibitors in rice hull hydrolyzate and fermentation to ethanol using conventional and engineered microbes

USDA-ARS?s Scientific Manuscript database

Microbial inhibitors arise from lignin, hemicellulose, and degraded sugar during pretreatment of lignocellulosic biomass. The fungus Coniochaeta ligniaria NRRL30616 has native ability to metabolize a number of these compounds, including furan and aromatic aldehydes known to act as inhibitors toward...

ConSpeciFix: Classifying prokaryotic species based on gene flow.

PubMed

Bobay, Louis-Marie; Ellis, Brian Shin-Hua; Ochman, Howard

2018-05-16

Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML. ljbobay@uncg.edu.

Estimating Effects of Species Interactions on Populations of Endangered Species.

PubMed

Roth, Tobias; Bühler, Christoph; Amrhein, Valentin

2016-04-01

Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

Confronting species distribution model predictions with species functional traits.

PubMed

Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

2016-02-01

Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum

PubMed Central

Alvarado-Sizzo, Hernán; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC. PMID:29342184

Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum.

PubMed

Alvarado-Sizzo, Hernán; Casas, Alejandro; Parra, Fabiola; Arreola-Nava, Hilda Julieta; Terrazas, Teresa; Sánchez, Cristian

2018-01-01

The Stenocereus griseus species complex (SGSC) has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

Bacillus odysseyi sp. nov., a round-spore-forming bacillus isolated from the Mars Odyssey spacecraft

NASA Technical Reports Server (NTRS)

La Duc, Myron T.; Satomi, Masataka; Venkateswaran, Kasthuri

2004-01-01

A round-spore-forming Bacillus species that produces an exosporium was isolated from the surface of the Mars Odyssey spacecraft. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA-DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus and is a Gram-positive, aerobic, rod-shaped, endospore-forming eubacterium. Ultrathin sections of the spores showed the presence of an exosporium, spore coat, cortex and core. 16S rDNA sequence similarities between this strain, Bacillus fusiformis and Bacillus silvestris were approximately 96% and DNA-DNA reassociation values with these two bacilli were 23 and 17%, respectively. Spores of the novel species were resistant to desiccation, H2O2 and UV and gamma radiation. Of all strains tested, the spores of this strain were the most consistently resistant and survived all of the challenges posed, i.e. exposure to conditions of desiccation (100% survival), H2O2 (26% survival), UV radiation (10% survival at 660 J m(-2)) and gamma radiation (0.4% survival). The name proposed for this novel bacterium is Bacillus odysseyi sp. nov.; the type strain is 34hs-1T (=ATCC PTA-4993T=NRRL B-30641T=NBRC 100172T).

Paenibacillus methanolicus sp. nov., a xylanolytic, methanol-utilizing bacterium isolated from the phyllosphere of bamboo (Pseudosasa japonica).

PubMed

Madhaiyan, Munusamy; Poonguzhali, Selvaraj; Saravanan, Venkatakrishnan Sivaraj; Pragatheswari, Dhandapani; Duraipandiyan, Veeramuthu; Al-Dhabi, Naif Abdullah; Santhanakrishnan, Palani

2016-11-01

Strain BL24T, isolated from bamboo phyllosphere collected in Coimbatore, India, was studied for taxonomic classification. Cells of the strain were aerobic, Gram-stain-positive, motile, catalase- and oxidase-positive rods and grew on media containing methanol. In 16S rRNA gene sequence analysis, strain BL24Tshowed the highest sequence similarities with Paenibacillus phyllosphaeraeKACC 11473T (97.8 %) and Paenibacillus sacheonensisSY01 (95.1 %). DNA-DNA hybridization with P. phyllosphaerae KACC 11473T, phylogenetically the most closely related species, was 21.6 %; this value showed that strain BL24Tbelonged to a different species. The cell-wall peptidoglycan was found to possess meso-diaminopimelic acid and the G+C content of genomic DNA was 52.1 mol %. It contained menaquinone (MK)-7 as the predominant respiratory quinone and the major cellular fatty acids are C16 : 0, anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0. Based on the molecular and chemotaxonomic markers and physiological properties, strain BL24T (=NRRL B-51698T=CCM 7577T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillusmethanolicusis proposed.

Biological deammonification of livestock effluents after anaerobic digestion using specialized bacterial cultures

USDA-ARS?s Scientific Manuscript database

We investigated a deammonification process for the removal of ammonia from anaerobi digestion (AD) effluents. This process is autotrophic and removes N without carbon. Instant deammonification reaction was obtained by mixing a high performance nitrifying sludge (HPNS) (NRRL B-50298) with anammox slu...

Reduction of Fusarium head blight using prothioconazole and prothioconazole-tolerant variants of the Fusarium head blight antagonist Cryptococcus flavescens OH 182.9

USDA-ARS?s Scientific Manuscript database

Integrated disease management strategies utilize a range of measures to prevent or reduce plant diseases. Combining the biological control agent Cryptococcus flavescens OH 182.9 (NRRL Y-30216) with a triazole fungicide such as prothioconazole has potential for significantly contributing to the redu...

Efficient utilization of crude glycerol as fermentation substrate in the synthesis of poly(3-hydroxybutyrate) biopolymers

USDA-ARS?s Scientific Manuscript database

One refined and 2 crude glycerol samples were utilized to produce poly(3-hydroxybutyrate) (PHB) by Pseudomonas oleovorans NRRL B-14682. Fermentation conditions were determined to efficiently utilize glycerol while maintaining PHB yields. A batch culture protocol including 1% glycerol and an aerati...

Save Our Species: Protecting Endangered Species from Pesticides.

ERIC Educational Resources Information Center

Environmental Protection Agency, Washington, DC.

This full-size poster profiles 11 wildlife species that are endangered. Color illustrations of animals and plants are accompanied by narrative describing their habitats and reasons for endangerment. The reverse side of the poster contains information on the Endangered Species Act, why protecting endangered and threatened species is important, how…

Single-species versus multiple-species approaches for management

Treesearch

William M. Block; Deborah M. Finch; Leonard A. Brennan

1995-01-01

Neotropical migratory birds are major components of the avifauna in most North American terrestrial ecosystems. Over 150 species of Neotropical migratory birds are known to breed in North America (Finch 1991a). Given the large number of species, developing effective management strategies for Neotropical migratory birds is a monumental task because each species exploits...

Estimating species richness and accumulation by modeling species occurrence and detectability

USGS Publications Warehouse

Dorazio, R.M.; Royle, J. Andrew; Soderstrom, B.; Glimskarc, A.

2006-01-01

A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.

Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil.

PubMed

Lee, Hyo-Jin; Whang, Kyung-Sook

2016-09-01

Three novel isolates belonging to the genus Streptomyces, designated JR-35T, JR-46 and WH-9T, were isolated from bamboo forest soil in Damyang, Korea. The 16S rRNA gene sequences of strains JR-35T and JR-46 showed highest similarities with Streptomyces olivochromogenes NBRC 3178T (99.1 %), Streptomyces siamensis KC-038T (98.9 %), Streptomyces chartreusis NBRC 12753T (98.9 %), Streptomyces resistomycificus NRRL ISP-5133T (98.9 %) and Streptomyces bobili JCM 4627T (98.8 %), and strain WH-9Tshowed highest sequence similarities with Streptomyces. bobili JCM 4627T (99.2 %), Streptomyces phaeoluteigriseus NRRL ISP-5182T (99.2 %), Streptomyces alboniger NBRC 12738T (99.2 %), Streptomyces galilaeus JCM 4757T (99.1 %) and Streptomyces pseudovenezuelae NBRC 12904T (99.1 %). The predominant menaquinones were MK-9 (H6) and MK-9 (H8). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C14 : 0 and iso-C15 : 0 for strains JR-35T and JR-46 and anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 for strain WH-9T. The G+C content of the genomic DNA of strains JR-35T, JR-46 and WH-9T were 69.4, 74.4 and 74.1 mol%, respectively. Based on the phenotypic and genotypic data, the three strains are assigned to two novel species of the genus Streptomyces, for which the names Streptomyces rhizosphaerihabitans sp. nov. (type stain JR-35T=KACC 17181T=NBRC 109807T) and Streptomyces adustus sp. nov. (type strain WH-9T=KACC 17197T=NBRC 109810T) are proposed.

Rare species contribute disproportionately to the functional structure of species assemblages

PubMed Central

Zuanon, Jansen; Williams, Stephen E.; Baraloto, Christopher; Mendonça, Fernando P.

2016-01-01

There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions. PMID:27053754

Analysis of the Surface Properties of Wheat Spikelet Components and Their Role in Colonization by the Biocontrol Antagonist Cryptococcus flavescens OH 182.9

USDA-ARS?s Scientific Manuscript database

Cryptococcus flavescens OH 182.9 (NRRL Y-30216) is a biocontrol antagonist which has been shown to be effective in managing Fusarium head blight in wheat. Cryptococcus flavescens works by colonizing the wheat spikelet and competing with potential pathogens for the limited resources available. Know...

Colonization of Wheat Heads by Fusarium Head Blight Antagonist Cryptococcus flavescens OH 182.9 when Applied Alone or in Combination with Prothioconazole and the Treatment Effect on FHB Disease Development in Field-Grown Whea

USDA-ARS?s Scientific Manuscript database

The use of yeast biological control agent Cyptococcus flavescens OH 182.9 (NRRL Y-30216) as part of an integrated management strategy against Fusarium head blight (FHB) of wheat is understudied yet has considerable potential for significantly contributing to the reduction of FHB and deoxynivalenol (...

Glycerine and levulinic acid: renewable co-substrates for the fermentative synthesis of short-chain poly(hydroxyalkanoate) biopolymers

USDA-ARS?s Scientific Manuscript database

Glycerine and levulinic acid were used alone and in combination for the fermentative synthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB/V) biopolymers. Shake-flask cultures of Pseudomonas oleovorans NRRL B-14682 containing different glycerine:levulinic acid ratios (1%, w/v total carbon ...

Tolerant industrial yeast Saccharomyces cerevisiae posses a more robust cell wall integrity signaling pathway against 2-furaldehyde and 5-(hydroxymethyl)-2-furaldehyde

USDA-ARS?s Scientific Manuscript database

Cell wall integrity signaling pathway in Saccharomyces cerevisiae is a conserved function for detecting and responding to cell stress conditions but less understood for industrial yeast. We dissected gene expression dynamics for a tolerant industrial yeast strain NRRL Y-50049 in response to challeng...

The ARS Culture Collection and Developments in Biotechnology

USDA-ARS?s Scientific Manuscript database

The ARS Culture Collection (NRRL) has played a prominent role in the development of biotechnology since its founding in 1940 when the Northern Regional Research Laboratory opened. Early discoveries included selection of production strains for penicillin, dextran blood extender, xanthan gum and the v...

Terrestrial animals as invasive species and as species at risk from invasions

Treesearch

Deborah M. Finch; Dean Pearson; Joseph Wunderle; Wayne Arendt

2010-01-01

Including terrestrial animal species in the invasive species strategy plan is an important step in invasive species management. Invasions by nonindigenous species threaten nearly 50 percent of imperiled native species in the United States and are the Nation's second leading cause of species endangerment. Invasion and conversion of native habitats by exotic species...

Rare species contribute disproportionately to the functional structure of species assemblages.

PubMed

Leitão, Rafael P; Zuanon, Jansen; Villéger, Sébastien; Williams, Stephen E; Baraloto, Christopher; Fortunel, Claire; Mendonça, Fernando P; Mouillot, David

2016-04-13

There is broad consensus that the diversity of functional traits within species assemblages drives several ecological processes. It is also widely recognized that rare species are the first to become extinct following human-induced disturbances. Surprisingly, however, the functional importance of rare species is still poorly understood, particularly in tropical species-rich assemblages where the majority of species are rare, and the rate of species extinction can be high. Here, we investigated the consequences of local and regional extinctions on the functional structure of species assemblages. We used three extensive datasets (stream fish from the Brazilian Amazon, rainforest trees from French Guiana, and birds from the Australian Wet Tropics) and built an integrative measure of species rarity versus commonness, combining local abundance, geographical range, and habitat breadth. Using different scenarios of species loss, we found a disproportionate impact of rare species extinction for the three groups, with significant reductions in levels of functional richness, specialization, and originality of assemblages, which may severely undermine the integrity of ecological processes. The whole breadth of functional abilities within species assemblages, which is disproportionately supported by rare species, is certainly critical in maintaining ecosystems particularly under the ongoing rapid environmental transitions. © 2016 The Author(s).

Microbiological and chemical transformations of argentatin B.

PubMed

Maatooq, Galal T

2003-01-01

Argentatin B is a naturally occurring tetracyclic triterpene isolated from Parthenium argentatum x P. tomentosa. It was microbiologically transformed to 16, 24-epoxycycloartan-3alpha, 25-diol, (isoargentatin D), by Nocardia corallina var. taoka ATCC 31338, Mycobacterium species NRRL B3683 and Septomyxa affinis ATCC 6737. The later microbe also produced 16, 24-epoxycycloartan-3beta, 25-diol (argentatin D) and 1, 2-didehydroargentatin B, (isoargentatin D). Sodium hydroxide converted argentatin B to argentatin D and isoargentatin D. Hydrochloric acid treatment gave cycloartan-25-ol-3, 24-dione. Cerium sulfate/sulfuric acid/aqueous methanol induced scission of the isopropanol moiety and provided an isomeric mixture of 24-methoxy-25-27-trinorargentatin B. Oxidation of this isomeric mixture with pyridinium chlorochromate, selectively, attacked the isomer with the equatorial proton at position-24 to give the corresponding lactone, 24-oxo-25-27-trinorargentatin B. The produced compounds were characterized by spectroscopic methods.

Effect of specific amino acids on growth and aflatoxin production by Aspergillus parasiticus and Aspergillus flavus in defined media.

PubMed Central

Payne, G A; Hagler, W M

1983-01-01

Four amino acids were used as sole nitrogen sources or as supplements to ammonium sulfate, and casein and ammonium sulfate were used as sole nitrogen sources to examine their effects on aflatoxin production by Aspergillus parasiticus NRRL 2999 and Aspergillus flavus 3357 grown on synthetic liquid media. In general, when proline, asparagine, casein, and ammonium sulfate were used as sole nitrogen sources, they supported more growth and toxin production than tryptophan or methionine. However, proline stimulated more toxin production per gram of mycelium in stationary cultures than the other nitrogen sources, including the amino acid asparagine, which is generally recognized as supporting good aflatoxin production. The exact responses to individual nitrogen sources were influenced by the species of fungus and whether cultures were stationary or shaken. In shake cultures, but not in stationary cultures, increased growth was generally associated with increased toxin production. PMID:6416168

Identification of molecular species of polyol oils produced from soybean oil by Pseudomonas aeruginosa e03-12 nrrl b-59991

USDA-ARS?s Scientific Manuscript database

The objective of this study is to develop a bioprocess for the production of polyol oils directly from soybean oil. We reported earlier methods for microbial screening and production of polyol oils from soybean oil (Hou and Lin, 2013). The polyol oil produced by Acinetobacter haemolyticus A01-35 (NR...

Conserving rare species can have high opportunity costs for common species.

PubMed

Neeson, Thomas M; Doran, Patrick J; Ferris, Michael C; Fitzpatrick, Kimberly B; Herbert, Matthew; Khoury, Mary; Moody, Allison T; Ross, Jared; Yacobson, Eugene; McIntyre, Peter B

2018-04-13

Conservation practitioners face difficult choices in apportioning limited resources between rare species (to ensure their existence) and common species (to ensure their abundance and ecosystem contributions). We quantified the opportunity costs of conserving rare species of migratory fishes in the context of removing dams and retrofitting road culverts across 1,883 tributaries of the North American Great Lakes. Our optimization models show that maximizing total habitat gains across species can be very efficient in terms of benefits achieved per dollar spent, but disproportionately benefits common species. Conservation approaches that target rare species, or that ensure some benefits for every species (i.e., complementarity) enable strategic allocation of resources among species but reduce aggregate habitat gains. Thus, small habitat gains for the rarest species necessarily come at the expense of more than 20 times as much habitat for common ones. These opportunity costs are likely to occur in many ecosystems because range limits and conservation costs often vary widely among species. Given that common species worldwide are declining more rapidly than rare ones within major taxa, our findings provide incentive for triage among multiple worthy conservation targets. © 2018 John Wiley & Sons Ltd.

Response of tree growth and species coexistence to density and species evenness in a young forest plantation with two competing species.

PubMed

Collet, Catherine; Ningre, François; Barbeito, Ignacio; Arnaud, Anthony; Piboule, Alexandre

2014-03-01

There is considerable evidence for the presence of positive species diversity-productivity relationships in plant populations, but the population parameters determining the type and strength of the relationship are poorly defined. Relationships between species evenness and tree survival or species coexistence are not well established. The objective of this study was to quantify the joint effects of density and species evenness on tree productivity and species coexistence. A 12-year-old experimental tree plantation mixing two species according to a double gradient of density and species proportion was used. A neighbourhood approach was employed and descriptors of local competition were used to model individual tree growth. Fagus sylvatica and Acer pseudoplatanus were used as model species, as they can be considered as ecologically equivalent in their young stages. Density and tree size were primary factors determining individual growth and stand productivity. Species identity had a significant, but less pronounced, role. Stand productivity was highest when species evenness was close to 1 and slightly lower in uneven mixtures. The reduction in stand productivity when species evenness decreased was of similar magnitude irrespective of which species became dominant, indicating symmetric effects for the two species. When examining individual tree growth in response to species proportion for each species separately, it was observed for both species that individual trees exhibited greater growth in uneven mixtures in which the other species was more frequent. The results suggest that mixtures of these two functionally similar species have the highest production at maximum evenness, indicating a complementary effect between them. The presence of a mixture combines both stabilizing mechanisms (individuals from both species show higher growth when surrounded by individuals from the other species) and equalizing mechanisms (the two species have very similar growth curves

50 CFR Table 2c to Part 679 - Species Codes: FMP Forage Fish Species (all species of the following families)

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Species Codes: FMP Forage Fish Species (all species of the following families) 2c Table 2c to Part 679 Wildlife and Fisheries FISHERY...: FMP Forage Fish Species (all species of the following families) Species Description Code Bristlemouths...

50 CFR Table 2c to Part 679 - Species Codes: FMP Forage Fish Species (all species of the following families)

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Species Codes: FMP Forage Fish Species (all species of the following families) 2c Table 2c to Part 679 Wildlife and Fisheries FISHERY...: FMP Forage Fish Species (all species of the following families) Species Description Code Bristlemouths...

50 CFR Table 2c to Part 679 - Species Codes: FMP Forage Fish Species (all species of the following families)

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Species Codes: FMP Forage Fish Species (all species of the following families) 2c Table 2c to Part 679 Wildlife and Fisheries FISHERY...: FMP Forage Fish Species (all species of the following families) Species Description Code Bristlemouths...

50 CFR Table 2c to Part 679 - Species Codes: FMP Forage Fish Species (all species of the following families)

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Species Codes: FMP Forage Fish Species (all species of the following families) 2c Table 2c to Part 679 Wildlife and Fisheries FISHERY...: FMP Forage Fish Species (all species of the following families) Species Description Code Bristlemouths...

50 CFR Table 2c to Part 679 - Species Codes: FMP Forage Fish Species (all species of the following families)

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Species Codes: FMP Forage Fish Species (all species of the following families) 2c Table 2c to Part 679 Wildlife and Fisheries FISHERY...: FMP Forage Fish Species (all species of the following families) Species Description Code Bristlemouths...

Core-satellite species hypothesis and native versus exotic species in secondary succession

USGS Publications Warehouse

Martinez, Kelsey A.; Gibson, David J.; Middleton, Beth A.

2015-01-01

A number of hypotheses exist to explain species’ distributions in a landscape, but these hypotheses are not frequently utilized to explain the differences in native and exotic species distributions. The core-satellite species (CSS) hypothesis predicts species occupancy will be bimodally distributed, i.e., many species will be common and many species will be rare, but does not explicitly consider exotic species distributions. The parallel dynamics (PD) hypothesis predicts that regional occurrence patterns of exotic species will be similar to native species. Together, the CSS and PD hypotheses may increase our understanding of exotic species’ distribution relative to natives. We selected an old field undergoing secondary succession to study the CSS and PD hypotheses in conjunction with each other. The ratio of exotic to native species (richness and abundance) was observed through 17 years of secondary succession. We predicted species would be bimodally distributed and that exotic:native species ratios would remain steady or decrease through time under frequent disturbance. In contrast to the CSS and PD hypotheses, native species occupancies were not bimodally distributed at the site, but exotic species were. The exotic:native species ratios for both richness (E:Nrichness) and abundance (E:Ncover) generally decreased or remained constant throughout supporting the PD hypothesis. Our results suggest exotic species exhibit metapopulation structure in old field landscapes, but that metapopulation structures of native species are disrupted, perhaps because these species are dispersal limited in the fragmented landscape.

A New Species from Athous (Orthathous) acutangulus Species Group from Turkey

PubMed Central

Kabalak, Mahmut; Sert, Osman

2012-01-01

A new Elateridae species, Athous (Orthathous) cagatayae n. sp., is presented from Ankara, Turkey. The morphology of the new species is described. Photographs of imago and aedeagus, aedeagi drawings of the new species, and identification key are given. The new species is discussed with species of acutangulus group, with a differential diagnosis. PMID:23448209

Incorporating Context Dependency of Species Interactions in Species Distribution Models.

PubMed

Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

2017-07-01

Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

The Importance of Species Traits for Species Distribution on Oceanic Islands

PubMed Central

Vazačová, Kristýna; Münzbergová, Zuzana

2014-01-01

Understanding species' ability to colonize new habitats is a key knowledge allowing us to predict species' survival in the changing landscapes. However, most studies exploring this topic observe distribution of species in landscapes which are under strong human influence being fragmented only recently and ignore the fact that the species distribution in these landscapes is far from equilibrium. Oceanic islands seem more appropriate systems for studying the relationship between species traits and its distribution as they are fragmented without human contribution and as they remained unchanged for a long evolutionary time. In our study we compared the values of dispersal as well as persistence traits among 18 species pairs from the Canary Islands differing in their distribution within the archipelago. The data were analyzed both with and without phylogenetic correction. The results demonstrate that no dispersal trait alone can explain the distribution of the species in the system. They, however, also suggest that species with better dispersal compared to their close relatives are better colonizers. Similarly, abundance of species in the archipelago seems to be an important predictor of species colonization ability only when comparing closely related species. This implies that analyses including phylogenetic correction may provide different insights than analyses without such a correction and both types of analyses should be combined to understand the importance of various plant traits for species colonization ability. PMID:25003737

77 FR 56237 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-12

... use commercially available, freeze-dried marine bacterium, Vibrio fisheri, NRRL B-11177, for experimental use at the Crary Science and Engineering Center (CSEC) at McMurdo Station. This bacterium is used... bacterium is used with a reconstituting reagent to determine toxicity levels. All laboratory plastic-ware...

Cloning, sequencing and characterization of lipase from a polyhydroxyalkanoate- (PHA-) synthesizing Pseudomonas resinovorans

USDA-ARS?s Scientific Manuscript database

Lipase gene (lip) of a biodegradable polyhydroxyalkanoate- (PHA-) synthesizing bacterium P. resinovorans NRRL B-2649 was cloned, sequenced and characterized by using consensus primers and PCR-based genome walking method. The ORF of the putative Lip (314 amino acids) and its active site (Ser111, Asp...

75 FR 6576 - Exemption from the Requirement of a Tolerance; Technical Amendment

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-10

... the requirement of a tolerance is established for residues of Aspergillus flavus NRRL 21882 on corn, field, forage; corn, field, grain; corn, field, stover; corn, field, aspirated grain fractions; corn, sweet, kernel plus cob with husk removed; corn, sweet, forage; corn, sweet, stover; corn, pop, grain...

Cellobiose fermenting yeast produces varied forms of native ß-glucosidase

USDA-ARS?s Scientific Manuscript database

The rapid growing yeast strain NRRL Y-50464 is robust to environmental stress and resistant to 2-furaldehyde (furfural) and 5-[hydroxymethyl]-2-furaldehyde (HMF). It is able to utilize cellobiose as its sole source of carbon and produces ethanol from lignocellulosic biomass by simultaneous saccharif...

Antagonist cryptococcus flavescens OH 182.9 3C colonization of wheat heads when applied with triazole fungicides and the effect on scab

USDA-ARS?s Scientific Manuscript database

Integrated pest management (IPM) is the best available approach for reducing Fusarium head blight (FHB; caused by Fusarium graminearum) and the mycotoxin deoxynivalenol (DON) in wheat grain. Utilizing FHB biological control agent Cryptococcus flavescens OH 182.9 (NRRL Y-30216) as part ...

Isolation of Xanthomegnin from Penicillium viridicatum by Preparative High-Pressure Liquid Chromatography

PubMed Central

Peterson, R. E.; Grove, M. D.

1983-01-01

A method was developed for the production and purification of xanthomegnin from Penicillium viridicatum (NRRL 6430) cultured on rice at 15°C for 29 days. Liquid-liquid extraction followed by high-pressure liquid chromatography afforded 440 mg of crystalline xanthomegnin per kg of rice. PMID:6881966

Microbial lipid production from SPORL-pretreated Douglas fir by Mortierella isabellina

Treesearch

S.M. Harde; Z. Wang; M. Horne; Junyong Zhu; X. Pan

2016-01-01

The solid substrate and spent liquo robtained after SPORL pretreatment of Douglas fir residues were evaluated as substrates for the production of intracellular microbial lipid by Mortierella isabellina NRRL 1757. The production of lipid was investigated in a batch fermentation using different strategies viz. separate hydrolysis...

Response of tree growth and species coexistence to density and species evenness in a young forest plantation with two competing species

PubMed Central

Collet, Catherine; Ningre, François; Barbeito, Ignacio; Arnaud, Anthony; Piboule, Alexandre

2014-01-01

Background and Aims There is considerable evidence for the presence of positive species diversity–productivity relationships in plant populations, but the population parameters determining the type and strength of the relationship are poorly defined. Relationships between species evenness and tree survival or species coexistence are not well established. The objective of this study was to quantify the joint effects of density and species evenness on tree productivity and species coexistence. Methods A 12-year-old experimental tree plantation mixing two species according to a double gradient of density and species proportion was used. A neighbourhood approach was employed and descriptors of local competition were used to model individual tree growth. Fagus sylvatica and Acer pseudoplatanus were used as model species, as they can be considered as ecologically equivalent in their young stages. Key Results Density and tree size were primary factors determining individual growth and stand productivity. Species identity had a significant, but less pronounced, role. Stand productivity was highest when species evenness was close to 1 and slightly lower in uneven mixtures. The reduction in stand productivity when species evenness decreased was of similar magnitude irrespective of which species became dominant, indicating symmetric effects for the two species. When examining individual tree growth in response to species proportion for each species separately, it was observed for both species that individual trees exhibited greater growth in uneven mixtures in which the other species was more frequent. Conclusions The results suggest that mixtures of these two functionally similar species have the highest production at maximum evenness, indicating a complementary effect between them. The presence of a mixture combines both stabilizing mechanisms (individuals from both species show higher growth when surrounded by individuals from the other species) and equalizing mechanisms

DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov.

PubMed

Holmes, B; Steigerwalt, A G; Nicholson, A C

2013-12-01

The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA-DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indole-producing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530(T) = CCUG 60564(T) = CDC G229(T)), Chryseobacterium carnis sp. nov. (type strain NCTC 13525(T) = CCUG 60559(T) = CDC G81(T)), Chryseobacterium lactis sp. nov. (type strain NCTC 11390(T) = CCUG 60566(T) = CDC KC1864(T)) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529(T) = CCUG 60563(T) = CDC G41(T)). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490(T) = X-65(T) = CCTCC AB 208154(T) = NRRL B-51322(T)) is also proposed to accommodate the reclassified Planobacterium taklimakanense.

Cryptococcus cyanovorans sp. nov., a basidiomycetous yeast isolated from cyanide-contaminated soil.

PubMed

Motaung, Thabiso E; Albertyn, Jacobus; Kock, Johan L F; Pohl, Carolina H

2012-05-01

Eighteen yeast strains were isolated and identified from cyanide-contaminated soil in South Africa. According to sequence-based analyses using the D1/D2 region of the large ribosomal subunit and ITS region, three of these strains were found to be identical and represent a novel species. Phylogenetic analysis based on the combined dataset of the D1/D2 and ITS regions revealed a grouping with Cryptococcus curvatus, representing a defined clade (Curvatus) in the order Trichosporonales. The three strains were demarcated from Cryptococcus curvatus by standard physiological tests such as assimilation of lactose, xylitol, 5-keto-D-gluconate, succinate and citrate as well as growth on media containing 10 % (w/v) NaCl and 5 % (w/v) glucose. In addition, it was established that these strains could utilize up to 10 mM NaCN as sole carbon source on solid media and as sole nitrogen source in liquid media. On the basis of these findings, it is suggested that the three strains represent a novel species for which the name Cryptococcus cyanovorans sp. nov. is given (type strain CBS 11948(T) = NRRL Y-48730(T)).

Aeromicrobium ginsengisoli sp. nov., isolated from a ginseng field.

PubMed

Kim, Myung Kyum; Park, Min-Ju; Im, Wan-Taek; Yang, Deok-Chun

2008-09-01

Strain Gsoil 098(T), a Gram-positive, non-spore-forming, non-motile coccus, was isolated from soil from a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Gsoil 098(T) belongs to the family Nocardioidaceae, and the highest degrees of sequence similarity were found with Aeromicrobium marinum T2(T) (99.0%), A. panaciterrae Gsoil 161(T) (98.9%), A. alkaliterrae KSL-107(T) (98.4%), A. fastidiosum KCTC 9576(T) (98.1%) and A. erythreum NRRL B-3381(T) (97.5%). Chemotaxonomic analysis revealed that strain Gsoil 098(T) possesses menaquinone MK-9(H(4)) and predominant fatty acids C(16 : 0), 10-methyl C(18:0) and C(18:0). DNA-DNA hybridization results and physiological and biochemical tests clearly demonstrated that strain Gsoil 098(T) represents a distinct species. Based on these data, Gsoil 098(T) (=KCTC 19207(T) =JCM 14732(T) =GBS 39(T)) should be classified as the type strain of a novel Aeromicrobium species, for which the name Aeromicrobium ginsengisoli sp. nov. is proposed.

Investigating species co-occurrence patterns when species are detected imperfectly

USGS Publications Warehouse

MacKenzie, D.I.; Bailey, L.L.; Nichols, J.D.

2004-01-01

1. Over the last 30 years there has been a great deal of interest in investigating patterns of species co-occurrence across a number of locations, which has led to the development of numerous methods to determine whether there is evidence that a particular pattern may not have occurred by random chance. 2. A key aspect that seems to have been largely overlooked is the possibility that species may not always be detected at a location when present, which leads to 'false absences' in a species presence/absence matrix that may cause incorrect inferences to be made about co-occurrence patterns. Furthermore, many of the published methods for investigating patterns of species co-occurrence do not account for potential differences in the site characteristics that may partially (at least) explain non-random patterns (e.g. due to species having similar/different habitat preferences). 3. Here we present a statistical method for modelling co-occurrence patterns between species while accounting for imperfect detection and site characteristics. This method requires that multiple presence/absence surveys for the species be conducted over a reasonably short period of time at most sites. The method yields unbiased estimates of probabilities of occurrence, and is practical when the number of species is small (< 4). 4. To illustrate the method we consider data collected on two terrestrial salamander species, Plethodonjordani and members of the Plethodon glutinosus complex, collected in the Great Smoky Mountains National Park, USA. We find no evidence that the species do not occur independently at sites once site elevation has been allowed for, although we find some evidence of a statistical interaction between species in terms of detectability that we suggest may be due to changes in relative abundances.

Two-species occupancy modeling accounting for species misidentification and nondetection

USGS Publications Warehouse

Chambert, Thierry; Grant, Evan H. Campbell; Miller, David A. W.; Nichols, James; Mulder, Kevin P.; Brand, Adrianne B,

2018-01-01

In occupancy studies, species misidentification can lead to false‐positive detections, which can cause severe estimator biases. Currently, all models that account for false‐positive errors only consider omnibus sources of false detections and are limited to single‐species occupancy.However, false detections for a given species often occur because of the misidentification with another, closely related species. To exploit this explicit source of false‐positive detection error, we develop a two‐species occupancy model that accounts for misidentifications between two species of interest. As with other false‐positive models, identifiability is greatly improved by the availability of unambiguous detections at a subset of site x occasions. Here, we consider the case where some of the field observations can be confirmed using laboratory or other independent identification methods (“confirmatory data”).We performed three simulation studies to (1) assess the model's performance under various realistic scenarios, (2) investigate the influence of the proportion of confirmatory data on estimator accuracy and (3) compare the performance of this two‐species model with that of the single‐species false‐positive model. The model shows good performance under all scenarios, even when only small proportions of detections are confirmed (e.g. 5%). It also clearly outperforms the single‐species model.We illustrate application of this model using a 4‐year dataset on two sympatric species of lungless salamanders: the US federally endangered Shenandoah salamander Plethodon shenandoah, and its presumed competitor, the red‐backed salamander Plethodon cinereus. Occupancy of red‐backed salamanders appeared very stable across the 4 years of study, whereas the Shenandoah salamander displayed substantial turnover in occupancy of forest habitats among years.Given the extent of species misidentification issues in occupancy studies, this modelling approach should help

75 FR 44291 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-28

... available, freeze- dried marine bacterium, Vibrio fisher, NRRL B-11177, for experimental use at the McMurdo Station Crary Science and Engineering Center (CSEC). This bacterium is used as one of the reagents for the Microtox toxicity analyzer, Azur Environmental model 500, 0073486. The bacterium are used with a...

Reclassification of "Dactylosporangium variesporum" as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev.

USDA-ARS?s Scientific Manuscript database

In the course of a polyphasic study it was observed that “Dactylosporangium variesporum” NRRL B-16296 is misclassified as a member of the genus Dactylosporangium becasuse it exhibits properties consistent with its assignment to the genus Saccharothrix. Phylogenetic analyses based on 16S rRNA gene se...

Haenamindole and fumiquinazoline analogs from a fungicolous isolate of Penicillium lanosum

USDA-ARS?s Scientific Manuscript database

Two new amino acid-derived compounds, lanosindole (1) and 2'-epi-fumiquinazoline C (2), were isolated from cultures of a fungicolous isolate of Penicillium lanosum (MYC 1813 = NRRL 66231), together with 2'-epi-fumiquinazoline D (3), previously reported only as a product of an in vitro enzymatic step...

High temperature dilute phosphoric acid pretreatment of corn stover for furfural and ethanol production

USDA-ARS?s Scientific Manuscript database

Furfural was produced from corn stover by one stage pretreatment process using dilute H3PO4 and solid residues following furfural production were used for ethanol production by Saccharomyces cerevisiae NRRL- Y2034. A series of experiments were conducted at varied temperatures (140-200 oC) and acid ...

Novel technologies for enhanced production of ethanol: impact of high productivity on process economics

USDA-ARS?s Scientific Manuscript database

In these studies Saccharomyces cerevisiae NRRL Y-566 was used to produce ethanol from a concentrated glucose (250-300 gL-1) solution. When fermentation media were supplemented with CaCO3 and CaCl2, ethanol concentrations, yield, and productivities were improved significantly. In control batch fermen...

Effect of sexual recombination on population diversity in aflatoxin production by Aspergillus flavus

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus is the major producer of carcinogenic aflatoxins (AFs) in crops worldwide. Recent efforts to reduce AF concentrations in crops have focused on the use of two non-aflatoxigenic A. flavus strains, AF36 and NRRL 21882 (Afla-Guard), as biological control agents. These products are a...

Mating-type heterokaryosis and population shifts in Aspergillus flavus

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus is a fungal pathogen of many agronomically important crops worldwide. We sampled A. flavus strains from a cornfield in Rocky Mount, NC. This field was planted in 2010 and plots were inoculated at tasselling with either AF36 or NRRL 21882 (=Afla-Guard) biocontrol strains, both of...

Population shifts and mating-type heterokaryosis in Aspergillus flavus

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus is a fungal pathogen of many agronomically important crops worldwide. We sampled A. flavus strains from a cornfield in Rocky Mount, NC. This field was planted in 2010 and plots were inoculated at tasselling with either AF36 or NRRL 21882 (=Afla-Guard) biocontrol strains, both of...

Aspergillus flavus genetic diversity of corn fields treated with non-toxigenic strain afla-guard in the southern U.S

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus genetic diversity of corn fields treated with the non-toxigenic strain Afla-Guard (NRRL 21882) was determined for 384 A. flavus isolates from 14 locations within 6 states in the southern U.S. ELISA test has determined low levels of toxigenic strains (only 91 positive). Nearly hal...

L-Asparaginase Synthesis by Erwinia aroideae

PubMed Central

Liu, F. S.; Zajic, J. E.

1972-01-01

Maximum L-asparaginase activity was obtained when 1.0% lactose and 1.5% yeast extract were supplied as carbon and nitrogen sources, respectively. Glucose inhibited the enzyme formation. The diauxie phenomenon was observed with Erwinia aroideae NRRL B-138 grown in a medium containing glucose and lactose. PMID:5021978

Polysaccharide Production Benefits Dry Storage Survival of the Biocontrol Agent Pseudomonas fluorescens S11:P:12 Effective Against Several Maladies of Stored Potatoes

USDA-ARS?s Scientific Manuscript database

Pseudomonas fluorescens S11:P:12 (NRRL B-21133) is a biological control agent able to suppress several potato diseases and sprouting. Notably, it produces a polysaccharide during liquid cultivation; and the objective of this work was to determine the role of this material in the bio-control process...

Use of green fluorescent protein to monitor fungal growth in biomass hydrolysate

USDA-ARS?s Scientific Manuscript database

Green Fluorescent Protein (GFP) was introduced into the Ascomycete Coniochaeta ligniaria NRRL30616, and fluorescence of cultures was monitored as a measure of cell growth. Fluorescence in the GFP-expressing strain was measured during growth of cells in defined and complex media as well as in the liq...

Isolation of Gregatin A from Phialophora gregata by Preparative High-Pressure Liquid Chromatography

PubMed Central

Taylor, Scott L.; Peterson, Robert E.; Gray, Lynn E.

1985-01-01

A method was developed for the production and purification of gregatin A from Phialophora gregata NRRL 13198 cultured on rice at 20°C for 28 days. Liquid extraction followed by high-pressure liquid chromatography afforded 247.0 mg of crystalline gregatin A per kg of rice. PMID:16346936

Delineating generalized species boundaries from species distribution data and a species distribution model

Treesearch

Matthew P. Peters; Stephen N. Matthews; Louis R. Iverson; Anantha M. Prasad

2013-01-01

Species distribution models (SDM) are commonly used to provide information about species ranges or extents, and often are intended to represent the entire area of potential occupancy or suitable habitat in which individuals occur. While SDMs can provide results over various geographic extents, they normally operate within a grid and cannot delimit distinct, smooth...

In defense of species.

PubMed

LaPorte, Joseph

2007-03-01

In this paper, I address the charge that the category species should be abandoned in biological work. The widespread appeal to species in scientific discourse provides a presumption in favor of the category's usefulness, but a defeasible presumption. Widely acknowledged troubles attend species: these troubles might render the concept unusable by showing that 'species' is equivocal or meaningless or in some similar way fatally flawed. Further, there might be better alternatives to species. I argue that the presumption in favor of species is not defeated on these scores. Troubles attending species, which arise on account of contextual variation attending the use of 'species', do not indicate that the concept is unusable. And alternatives to the use of 'species', which have been proposed in connection with rank-free systematics and in connection with conservation efforts, fail to provide a proper replacement for species.

Use of species-specific PCR for the identification of 10 sea cucumber species

NASA Astrophysics Data System (ADS)

Wen, Jing; Zeng, Ling

2014-11-01

We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

Cluster Analysis of Longidorus Species (Nematoda: Longidoridae), a New Approach in Species Identification

PubMed Central

Ye, Weimin; Robbins, R. T.

2004-01-01

Hierarchical cluster analysis based on female morphometric character means including body length, distance from vulva opening to anterior end, head width, odontostyle length, esophagus length, body width, tail length, and tail width were used to examine the morphometric relationships and create dendrograms for (i) 62 populations belonging to 9 Longidorus species from Arkansas, (ii) 137 published Longidorus species, and (iii) 137 published Longidorus species plus 86 populations of 16 Longidorus species from Arkansas and various other locations by using JMP 4.02 software (SAS Institute, Cary, NC). Cluster analysis dendograms visually illustrated the grouping and morphometric relationships of the species and populations. It provided a computerized statistical approach to assist by helping to identify and distinguish species, by indicating morphometric relationships among species, and by assisting with new species diagnosis. The preliminary species identification can be accomplished by running cluster analysis for unknown species together with the data matrix of known published Longidorus species. PMID:19262809

Population dynamics of the fusarium head blight biocontrol agent cryptococcus flavescens OH182.9 on wheat anthers and heads

USDA-ARS?s Scientific Manuscript database

Cryptococcus flavescens OH 182.9 (NRRL Y-30216) reduces Fusarium head blight (FHB) incited by Fusarium graminearum and DON contamination of grain in greenhouse and field settings. Yet little is known about the population dynamics of OH 182.9 on wheat heads and anthers from the time of inoculating he...

The yajC gene from Lactobacillus buchneri and Escherichia coli and its role in ethanol tolerance

USDA-ARS?s Scientific Manuscript database

The yajC gene (Lbuc_0921)from Lactobacillus buchneri NRRL B-30929 was identified from proteomics analyses in response to ethanol treatment. This protein’s expression level was increased by 15 fold in response to 10% vs 0% ethanol. The yajC encodes the smaller subunit of the preprotein translocase co...

Isolation of Chromanone and Isobenzofuran Derivatives from a Fungicolous Isolate of Epiccocum purpurascens

USDA-ARS?s Scientific Manuscript database

Chemical studies of an organic extract of Epicoccum purpurascens NRRL 37031, isolated from a wood decay fungus in Florida, led to the isolation of two new metabolites, 7-methoxy-4-oxo-chroman-5-carboxylic acid methyl ester (1) and 1,3-dihydro-5-methoxy-7-methylisobenzofuran (2). Two known isobenzof...

Assessment of biocontrol strains for reduction of mycotoxins (aflatoxin and CPA) in maize

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus strains K49, NRRL 21882 (from Afla-Guard®) and AF36 are being developed as biocontrol agents for the control of aflatoxin in maize. In this study, the three non-aflatoxigenic strains were compared to evaluate which is most effective in reducing aflatoxin. Also, we tested these st...

Screening Saccharomyces cerevisiae Distillery Strains in Industrial Media

USDA-ARS?s Scientific Manuscript database

Twenty-four distillery yeast strains were obtained from the ARS Culture Collection (NRRL) in Peoria, IL, and screened for ethanol production at 30 and 35°C using industrial media. The medium used in the tests consisted of corn mash prepared by combining coarse ground corn, water, and stillage from a...

Population dynamics of Aspergillus flavus following biocontrol treatment of corn

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus is a fungal pathogen of many agronomically important crops worldwide. We sampled A. flavus strains from a cornfield in Rocky Mount, North Carolina, over a period of two years. The field was planted in 2010 and plots were inoculated at tasselling with either AF36 or NRRL 21882 (=Af...

Population structure of Aspergillus flavus before and after biocontrol treatment

USDA-ARS?s Scientific Manuscript database

Aspergillus flavus is a fungal pathogen of many important crops worldwide. We sampled A. flavus strains from a cornfield in Rocky Mount, North Carolina, over a period of two years. Plots were inoculated at tasselling with either AF36 or NRRL 21882 (=Afla-Guard) biocontrol strains, both of which are ...

Production of polyol oils from soybean oil by bioprocess and Philippines edible medicinal wild mushrooms

USDA-ARS?s Scientific Manuscript database

We have been trying to develop a bioprocess for the production of polyol oils directly from soybean oil. We reported earlier the polyol products produced from soybean oil by Acinetobacter haemolyticus A01-35 (NRRL B-59985) (Hou and Lin, 2013). The objective of this study is to identify the chemical ...

Diversity of cuticular wax among Salix species and Populus species hybrids.

PubMed

Cameron, Kimberly D; Teece, Mark A; Bevilacqua, Eddie; Smart, Lawrence B

2002-08-01

The leaf cuticular waxes of three Salix species and two Populus species hybrids, selected for their ability to produce high amounts of biomass, were characterized. Samples were extracted in CH(2)Cl(2) three times over the growing season. Low kV SEM was utilized to observe differences in the ultrastructure of leaf surfaces from each clone. Homologous series of wax components were classified into organic groups, and the variation in wax components due to clone, sample time, and their interaction was identified. All Salix species and Populus species hybrids showed differences in total wax load at each sampling period, whereas the pattern of wax deposition over time differed only between the Salix species. A strong positive relationship was identified between the entire homologous series of alcohols and total wax load in all clones. Similarly strong relationships were observed between fatty acids and total wax load as well as fatty acids and alcohols in two Salix species and one Populus species hybrid. One Salix species, S. dasyclados, also displayed a strong positive relationship between alcohols and alkanes. These data indicate that species grown under the same environmental conditions produce measurably different cuticular waxes and that regulation of wax production appears to be different in each species. The important roles cuticular waxes play in drought tolerance, pest, and pathogen resistance, as well as the ease of wax extraction and analysis, strongly suggest that the characteristics of the cuticular wax may prove to be useful selectable traits in a breeding program.

Scale dependence in species turnover reflects variance in species occupancy.

PubMed

McGlinn, Daniel J; Hurlbert, Allen H

2012-02-01

Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

A globally-distributed alien invasive species poses risks to United States imperiled species.

PubMed

McClure, Meredith L; Burdett, Christopher L; Farnsworth, Matthew L; Sweeney, Steven J; Miller, Ryan S

2018-03-28

In the midst of Earth's sixth mass extinction event, non-native species are a driving factor in many imperiled species' declines. One of the most widespread and destructive alien invasive species in the world, wild pigs (Sus scrofa) threaten native species through predation, habitat destruction, competition, and disease transmission. We show that wild pigs co-occur with up to 87.2% of imperiled species in the contiguous U.S. identified as susceptible to their direct impacts, and we project increases in both the number of species at risk and the geographic extent of risks by 2025. Wild pigs may therefore present a severe threat to U.S. imperiled species, with serious implications for management of at-risk species throughout wild pigs' global distribution. We offer guidance for efficient allocation of research effort and conservation resources across species and regions using a simple approach that can be applied to wild pigs and other alien invasive species globally.

Anopheles species associations in Southeast Asia: indicator species and environmental influences.

PubMed

Obsomer, Valérie; Dufrene, Marc; Defourny, Pierre; Coosemans, Marc

2013-05-04

Southeast Asia presents a high diversity of Anopheles. Environmental requirements differ for each species and should be clarified because of their influence on malaria transmission potential. Monitoring projects collect vast quantities of entomological data over the whole region and could bring valuable information to malaria control staff but collections are not always standardized and are thus difficult to analyze. In this context studying species associations and their relation to the environment offer some opportunities as they are less subject to sampling error than individual species. Using asymmetrical similarity coefficients, indirect clustering and the search of indicator species, this paper identified species associations. Environmental influences were then analysed through canonical and discriminant analysis using climatic and topographic data, land cover in a 3 km buffer around villages and vegetation indices. Six groups of sites characterized the structure of the species assemblage. Temperature, rainfall and vegetation factors all play a role. Four out of the six groups of sites based on species similarities could be discriminated using environmental information only. Vegetation indices derived from satellite imagery proved very valuable with one variable explaining more variance of the species dataset than any other variable. The analysis could be improved by integrating seasonality in the sampling and collecting at least 4 consecutive days.

Program SimAssem: software for simulating species assemblages and estimating species richness

Treesearch

Gordon C. Reese; Kenneth R. Wilson; Curtis H. Flather

2013-01-01

1. Species richness, the number of species in a defined area, is the most frequently used biodiversity measure. Despite its intuitive appeal and conceptual simplicity, species richness is often difficult to quantify, even in well surveyed areas, because of sampling limitations such as survey effort and species detection probability....

Assessing Species Boundaries Using Multilocus Species Delimitation in a Morphologically Conserved Group of Neotropical Freshwater Fishes, the Poecilia sphenops Species Complex (Poeciliidae)

PubMed Central

Bagley, Justin C.; Alda, Fernando; Breitman, M. Florencia; Bermingham, Eldredge; van den Berghe, Eric P.; Johnson, Jerald B.

2015-01-01

Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including ‘non-adaptive radiations’ containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial ‘major-lineages’ diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of

Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae).

PubMed

Bagley, Justin C; Alda, Fernando; Breitman, M Florencia; Bermingham, Eldredge; van den Berghe, Eric P; Johnson, Jerald B

2015-01-01

Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for

Species-barrier-independent prion replication in apparently resistant species

NASA Astrophysics Data System (ADS)

Hill, Andrew F.; Joiner, Susan; Linehan, Jackie; Desbruslais, Melanie; Lantos, Peter L.; Collinge, John

2000-08-01

Transmission of prions between mammalian species is thought to be limited by a "species barrier," which depends on differences in the primary structure of prion proteins in the infecting inoculum and the host. Here we demonstrate that a strain of hamster prions thought to be nonpathogenic for conventional mice leads to prion replication to high levels in such mice but without causing clinical disease. Prions pathogenic in both mice and hamsters are produced. These results demonstrate the existence of subclinical forms of prion infection with important public health implications, both with respect to iatrogenic transmission from apparently healthy humans and dietary exposure to cattle and other species exposed to bovine spongiform encephalopathy prions. Current definitions of the species barrier, which have been based on clinical end-points, need to be fundamentally reassessed.

Incorporation of Chlorine-36 into Ochratoxin A

PubMed Central

Wei, Ru-Dong; Strong, F. M.; Smalley, E. B.

1971-01-01

Incubation of Aspergillus ochraceus NRRL 3174 in a medium containing Na36Cl incorporated 36Cl into ochratoxin A. The highest incorporation (0.75 and 0.70%, respectively) was obtained when the radioactive chloride was added to the medium by the 2nd or 3rd day of incubation. Images PMID:5119199

Data on the fungal species consumed by mammal species in Australia.

PubMed

Nuske, S J; Vernes, K; May, T W; Claridge, A W; Congdon, B C; Krockenberger, A; Abell, S E

2017-06-01

The data reported here support the manuscript Nuske et al. (2017) [1]. Searches were made for quantitative data on the occurrence of fungi within dietary studies of Australian mammal species. The original location reported in each study was used as the lowest grouping variable within the dataset. To standardise the data and compare dispersal events from populations of different mammal species that might overlap, data from locations were further pooled and averaged across sites if they occurred within 100 km of a random central point. Three locations in Australia contained data on several (>7) mycophagous mammals, all other locations had data on 1-3 mammal species. Within these three locations, the identity of the fungi species was compared between mammal species' diets. A list of all fungi species found in Australian mammalian diets is also provide along with the original reference and fungal synonym names.

Species climate range influences hydraulic and stomatal traits in Eucalyptus species.

PubMed

Bourne, Aimee E; Creek, Danielle; Peters, Jennifer M R; Ellsworth, David S; Choat, Brendan

2017-07-01

Plant hydraulic traits influence the capacity of species to grow and survive in water-limited environments, but their comparative study at a common site has been limited. The primary aim of this study was to determine whether selective pressures on species originating in drought-prone environments constrain hydraulic traits among related species grown under common conditions. Leaf tissue water relations, xylem anatomy, stomatal behaviour and vulnerability to drought-induced embolism were measured on six Eucalyptus species growing in a common garden to determine whether these traits were related to current species climate range and to understand linkages between the traits. Hydraulically weighted xylem vessel diameter, leaf turgor loss point, the water potential at stomatal closure and vulnerability to drought-induced embolism were significantly ( P < 0·05) correlated with climate parameters from the species range. There was a co-ordination between stem and leaf parameters with the water potential at turgor loss, 12 % loss of conductivity and the point of stomatal closure significantly correlated. The correlation of hydraulic, stomatal and anatomical traits with climate variables from the species' original ranges suggests that these traits are genetically constrained. The conservative nature of xylem traits in Eucalyptus trees has important implications for the limits of species responses to changing environmental conditions and thus for species survival and distribution into the future, and yields new information for physiological models. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Multiple mechanisms enable invasive species to suppress native species.

PubMed

Bennett, Alison E; Thomsen, Meredith; Strauss, Sharon Y

2011-07-01

Invasive plants represent a significant threat to ecosystem biodiversity. To decrease the impacts of invasive species, a major scientific undertaking of the last few decades has been aimed at understanding the mechanisms that drive invasive plant success. Most studies and theories have focused on a single mechanism for predicting the success of invasive plants and therefore cannot provide insight as to the relative importance of multiple interactions in predicting invasive species' success. We examine four mechanisms that potentially contribute to the success of invasive velvetgrass Holcus lanatus: direct competition, indirect competition mediated by mammalian herbivores, interference competition via allelopathy, and indirect competition mediated by changes in the soil community. Using a combination of field and greenhouse approaches, we focus on the effects of H. lanatus on a common species in California coastal prairies, Erigeron glaucus, where the invasion is most intense. We found that H. lanatus had the strongest effects on E. glaucus via direct competition, but it also influenced the soil community in ways that feed back to negatively influence E. glaucus and other native species after H. lanatus removal. This approach provided evidence for multiple mechanisms contributing to negative effects of invasive species, and it identified when particular strategies were most likely to be important. These mechanisms can be applied to eradication of H. lanatus and conservation of California coastal prairie systems, and they illustrate the utility of an integrated set of experiments for determining the potential mechanisms of invasive species' success.

Palpi aplenty: New species in the Chrysotus longipalpus species group (Diptera: Dolichopodidae)

Treesearch

Justin B. Runyon; Renato S. Capellari

2018-01-01

Four new Nearctic species belonging to the Chrysotus longipalpus species group are described: Chrysotus keyensis sp. nov. (Florida), Chrysotus mccreadiei sp. nov. (Alabama), Chrysotus mystax sp. nov. (Alabama), and Chrysotus plumarista sp. nov. (Alabama). This brings the number of known species in this group to twelve. A key to species of males of the C. longipalpus...

Species recovery in the United States: Increasing the effectiveness of the Endangered Species Act

Treesearch

Daniel M. Evans; Judy P. Che-Castaldo; Deborah Crouse; Frank W. Davis; Rebecca Epanchin-Niell; Curtis H. Flather; R. Kipp Frohlich; Dale D. Goble; Ya-Wei Li; Timothy D. Male; Lawrence L. Master; Matthew P. Moskwik; Maile C. Neel; Barry R. Noon; Camille Parmesan; Mark W. Schwartz; J. Michael Scott; Byron K. Williams

2016-01-01

The Endangered Species Act (ESA) has succeeded in shielding hundreds of species from extinction and improving species recovery over time. However, recovery for most species officially protected by the ESA - i.e., listed species - has been harder to achieve than initially envisioned. Threats to species are persistent and pervasive, funding has been insufficient...

Invasive forest species

Treesearch

Barbara L. Illman

2006-01-01

Nonnative organisms that cause a major change to native ecosystems-once called foreign species, biological invasions, alien invasives, exotics, or biohazards–are now generally referred to as invasive species or invasives. invasive species of insects, fungi, plants, fish, and other organisms present a rising threat to natural forest ecosystems worldwide. Invasive...

Ecology of Caenorhabditis species.

PubMed Central

Kiontke, Karin; Sudhaus, Walter

2006-01-01

Although several Caenorhabditis species are now studied in laboratories in great detail, the knowledge of the ecology of most Caenorhabditis species is scarce. In this chapter we present data on the habitat, animal associations, and geographical distribution of the eighteen described and five undescribed Caenorhabditis species currently known to science. The habitats of these species are very diverse, ranging from rotting cactus tissue to inflamed auditory canals of zebu cattle. Some species, including C. elegans, have only been isolated from anthropogenic habitats. Consequently, their natural habitat is unknown. All Caenorhabditis species are colonizers of nutrient- and bacteria-rich substrates and none of them is a true soil nematode. Dauer juveniles of many Caenorhabditis species were shown to be associated with terrestrial arthropods or gastropods. An association with invertebrates is also likely for the remaining species. The type of association is either phoresy (for transport to a new habitat) or necromeny (to secure the body of the associated animal as a future food source). There are also some records of Caenorhabditis species associated with vertebrates. The Caenorhabditis stem species was probably a colonizer of nutrient-rich substrates and was phoretic on arthropods. Some evolutionary trends within the taxon are discussed. PMID:18050464

Phylogenetic species recognition and hybridisation in Lasiodiplodia: A case study on species from baobabs.

PubMed

Cruywagen, Elsie M; Slippers, Bernard; Roux, Jolanda; Wingfield, Michael J

2017-04-01

Lasiodiplodia species (Botryosphaeriaceae, Ascomycota) infect a wide range of typically woody plants on which they are associated with many different disease symptoms. In this study, we determined the identity of Lasiodiplodia isolates obtained from baobab (Adansonia species) trees in Africa and reviewed the molecular markers used to describe Lasiodiplodia species. Publicly available and newly produced sequence data for some of the type strains of Lasiodiplodia species showed incongruence amongst phylogenies of five nuclear loci. We conclude that several of the previously described Lasiodiplodia species are hybrids of other species. Isolates from baobab trees in Africa included nine species of Lasiodiplodia and two hybrid species. Inoculation trials with the most common Lasiodiplodia species collected from these trees produced significant lesions on young baobab trees. There was also variation in aggressiveness amongst isolates from the same species. The apparently widespread tendency of Lasiodiplodia species to hybridise demands that phylogenies from multiple loci (more than two and preferably four or more) are compared for congruence prior to new species being described. This will avoid hybrids being incorrectly described as new taxa, as has clearly occurred in the past. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Estimation of species extinction: what are the consequences when total species number is unknown?

PubMed

Chen, Youhua

2014-12-01

The species-area relationship (SAR) is known to overestimate species extinction but the underlying mechanisms remain unclear to a great extent. Here, I show that when total species number in an area is unknown, the SAR model exaggerates the estimation of species extinction. It is proposed that to accurately estimate species extinction caused by habitat destruction, one of the principal prerequisites is to accurately total the species numbers presented in the whole study area. One can better evaluate and compare alternative theoretical SAR models on the accurate estimation of species loss only when the exact total species number for the whole area is clear. This presents an opportunity for ecologists to simulate more research on accurately estimating Whittaker's gamma diversity for the purpose of better predicting species loss.

Invasive non-native species' provision of refugia for endangered native species.

PubMed

Chiba, Satoshi

2010-08-01

The influence of non-native species on native ecosystems is not predicted easily when interspecific interactions are complex. Species removal can result in unexpected and undesired changes to other ecosystem components. I examined whether invasive non-native species may both harm and provide refugia for endangered native species. The invasive non-native plant Casuarina stricta has damaged the native flora and caused decline of the snail fauna on the Ogasawara Islands, Japan. On Anijima in 2006 and 2009, I examined endemic land snails in the genus Ogasawarana. I compared the density of live specimens and frequency of predation scars (from black rats [Rattus rattus]) on empty shells in native vegetation and Casuarina forests. The density of land snails was greater in native vegetation than in Casuarina forests in 2006. Nevertheless, radical declines in the density of land snails occurred in native vegetation since 2006 in association with increasing predation by black rats. In contrast, abundance of Ogasawarana did not decline in the Casuarina forest, where shells with predation scars from rats were rare. As a result, the density of snails was greater in the Casuarina forest than in native vegetation. Removal of Casuarina was associated with an increased proportion of shells with predation scars from rats and a decrease in the density of Ogasawarana. The thick and dense litter of Casuarina appears to provide refugia for native land snails by protecting them from predation by rats; thus, eradication of rats should precede eradication of Casuarina. Adaptive strategies, particularly those that consider the removal order of non-native species, are crucial to minimizing the unintended effects of eradication on native species. In addition, my results suggested that in some cases a given non-native species can be used to mitigate the impacts of other non-native species on native species.

Production of phytase by Mucor racemosus in solid-state fermentation.

PubMed

Bogar, Barbara; Szakacs, George; Pandey, Ashok; Abdulhameed, Sabu; Linden, James C; Tengerdy, Robert P

2003-01-01

Phytase production was studied by three Mucor and eight Rhizopus strains by solid-state fermentation (SSF) on three commonly used natural feed ingredients (canola meal, coconut oil cake, wheat bran). Mucor racemosus NRRL 1994 (ATCC 46129) gave the highest yield (14.5 IU/g dry matter phytase activity) on coconut oil cake. Optimizing the supplementation of coconut oil cake with glucose, casein and (NH(4))(2)SO(4), phytase production in solid-state fermentation was increased to 26 IU/g dry matter (DM). Optimization was carried out by Plackett-Burman and central composite experimental designs. Using the optimized medium phytase, alpha-amylase and lipase production of Mucor racemosus NRRL 1994 was compared in solid-state fermentation and in shake flask (SF) fermentation. SSF yielded higher phytase activity than did SF based on mass of initial substrate. Because this particular isolate is a food-grade fungus that has been used for sufu fermentation in China, the whole SSF material (crude enzyme, in situ enzyme) may be used directly in animal feed rations with enhanced cost efficiency.

The constituents of essential oil: antimicrobial and antioxidant activity of Micromeria congesta Boiss. & Hausskn. ex Boiss. from East Anatolia.

PubMed

Herken, Emine Nur; Celik, Ali; Aslan, Mustafa; Aydınlık, Nilüfer

2012-09-01

The chemical composition, antimicrobial activity, total phenol content, total antioxidant activity, and total oxidant status of the essential oil from Micromeria congesta Boiss. & Hausskn. ex Boiss. were investigated. Steam distillation was used to obtain the essential oil, and the chemical analyses were performed by gas chromatography-mass spectrometry. The antimicrobial activity was tested by an agar disc diffusion method against the tested microorganisms: Bacillus subtilis NRRL B-744, Bacillus cereus NRRL B-3711, Staphylococcus aureus ATCC 12598, S. aureus ATCC 25923, S. aureus ATCC 25933, Escherichia coli 0157H7, E. coli ATCC25922, Micrococcus luteus NRLL B-4375, Enterococcus faecalis ATCC 19433, Proteus vulgaris RSKK 96026, and Yersinia enterecolitica RSKK 1501. The major compounds found in volatiles of M. congesta were piperitone oxide, linalool oxide, veratrole, pulegone, dihydro carvone, naphthalene, iso-menthone, para-menthone, and cyclohexanone. Compared to that of reference antibiotics, the antibacterial activity of the essential oil is considered as significant. Results showed that M. congesta has the potential for being used in food and medicine depending on its antioxidant and antibacterial activity.

Species Composition (SC)

Treesearch

John F. Caratti

2006-01-01

The FIREMON Species Composition (SC) method is used to provide ocular estimates of cover and height measurements for plant species on a macroplot. The SC method provides plant species composition and coverage estimates to describe a stand or plant community and can be used to document changes over time. It is suited for a wide variety of vegetation types and is...

Invasive Species Science Branch: research and management tools for controlling invasive species

USGS Publications Warehouse

Reed, Robert N.; Walters, Katie D.

2015-01-01

Invasive, nonnative species of plants, animals, and disease organisms adversely affect the ecosystems they enter. Like “biological wildfires,” they can quickly spread and affect nearly all terrestrial and aquatic ecosystems. Invasive species have become one of the greatest environmental challenges of the 21st century in economic, environmental, and human health costs, with an estimated effect in the United States of more than $120 billion per year. Managers of the Department of the Interior and other public and private lands often rank invasive species as their top resource management problem. The Invasive Species Science Branch of the Fort Collins Science Center provides research and technical assistance relating to management concerns for invasive species, including understanding how these species are introduced, identifying areas vulnerable to invasion, forecasting invasions, and developing control methods. To disseminate this information, branch scientists are developing platforms to share invasive species information with DOI cooperators, other agency partners, and the public. From these and other data, branch scientists are constructing models to understand and predict invasive species distributions for more effective management. The branch also has extensive herpetological and population biology expertise that is applied to harmful reptile invaders such as the Brown Treesnake on Guam and Burmese Python in Florida.

Evaluating species richness: biased ecological inference results from spatial heterogeneity in species detection probabilities

USGS Publications Warehouse

McNew, Lance B.; Handel, Colleen M.

2015-01-01

Accurate estimates of species richness are necessary to test predictions of ecological theory and evaluate biodiversity for conservation purposes. However, species richness is difficult to measure in the field because some species will almost always be overlooked due to their cryptic nature or the observer's failure to perceive their cues. Common measures of species richness that assume consistent observability across species are inviting because they may require only single counts of species at survey sites. Single-visit estimation methods ignore spatial and temporal variation in species detection probabilities related to survey or site conditions that may confound estimates of species richness. We used simulated and empirical data to evaluate the bias and precision of raw species counts, the limiting forms of jackknife and Chao estimators, and multi-species occupancy models when estimating species richness to evaluate whether the choice of estimator can affect inferences about the relationships between environmental conditions and community size under variable detection processes. Four simulated scenarios with realistic and variable detection processes were considered. Results of simulations indicated that (1) raw species counts were always biased low, (2) single-visit jackknife and Chao estimators were significantly biased regardless of detection process, (3) multispecies occupancy models were more precise and generally less biased than the jackknife and Chao estimators, and (4) spatial heterogeneity resulting from the effects of a site covariate on species detection probabilities had significant impacts on the inferred relationships between species richness and a spatially explicit environmental condition. For a real dataset of bird observations in northwestern Alaska, the four estimation methods produced different estimates of local species richness, which severely affected inferences about the effects of shrubs on local avian richness. Overall, our results

Species-to-species rate coefficients for the H3+ + H2 reacting system

NASA Astrophysics Data System (ADS)

Sipilä, O.; Harju, J.; Caselli, P.

2017-10-01

Aims: We study whether or not rotational excitation can make a large difference to chemical models of the abundances of the H3+ isotopologs, including spin states, in physical conditions corresponding to starless cores and protostellar envelopes. Methods: We developed a new rate coefficient set for the chemistry of the H3+ isotopologs, allowing for rotational excitation, using previously published state-to-state rate coefficients. These new so-called species-to-species rate coefficients are compared with previously-used ground-state-to-species rate coefficients by calculating chemical evolution in variable physical conditions using a pseudo-time-dependent chemical code. Results: We find that the new species-to-species model produces different results to the ground state-to-species model at high density and toward increasing temperatures (T> 10 K). The most prominent difference is that the species-to-species model predicts a lower H3+ deuteration degree at high density owing to an increase of the rate coefficients of endothermic reactions that tend to decrease deuteration. For example at 20 K, the ground-state-to-species model overestimates the abundance of H2D+ by a factor of about two, while the abundance of D3+ can differ by up to an order of magnitude between the models. The spin-state abundance ratios of the various H3+ isotopologs are also affected, and the new model better reproduces recent observations of the abundances of ortho and para H2D+ and D2H+. The main caveat is that the applicability regime of the new rate coefficients depends on the critical densities of the various rotational transitions which vary with the abundances of the species and the temperature in dense clouds. Conclusions: The difference in the abundances of the H3+ isotopologs predicted by the species-to-species and ground state-to-species models is negligible at 10 K corresponding to physical conditions in starless cores, but inclusion of the excited states is very important in studies

Use of Endophytic and Rhizosphere Actinobacteria from Grapevine Plants To Reduce Nursery Fungal Graft Infections That Lead to Young Grapevine Decline

PubMed Central

Álvarez-Pérez, José Manuel; González-García, Sandra; Cobos, Rebeca; Olego, Miguel Ángel; Ibañez, Ana; Díez-Galán, Alba; Garzón-Jimeno, Enrique

2017-01-01

ABSTRACT Endophytic and rhizosphere actinobacteria isolated from the root system of 1-year-old grafted Vitis vinifera plants were evaluated for their activities against fungi that cause grapevine trunk diseases. A total of 58 endophytic and 94 rhizosphere isolates were tested. Based on an in vitro bioassay, 15.5% of the endophytic isolates and 30.8% of the rhizosphere isolates exhibited antifungal activity against the fungal pathogen Diplodia seriata, whereas 13.8% of the endophytic isolates and 16.0% of the rhizosphere isolates showed antifungal activity against Dactylonectria macrodidyma (formerly Ilyonectria macrodidyma). The strains which showed the greatest in vitro efficacy against both pathogens were further analyzed for their ability to inhibit the growth of Phaeomoniella chlamydospora and Phaeoacremonium minimum (formerly Phaeoacremonium aleophilum). Based on their antifungal activity, three rhizosphere isolates and three endophytic isolates were applied on grafts in an open-root field nursery in a 3-year trial. The field trial led to the identification of one endophytic strain, Streptomyces sp. VV/E1, and two rhizosphere isolates, Streptomyces sp. VV/R1 and Streptomyces sp. VV/R4, which significantly reduced the infection rates produced by the fungal pathogens Dactylonectria sp., Ilyonectria sp., P. chlamydospora, and P. minimum, all of which cause young grapevine decline. The VV/R1 and VV/R4 isolates also significantly reduced the mortality level of grafted plants in the nursery. This study shows that certain actinobacteria could represent a promising new tool for controlling fungal trunk pathogens that infect grapevine plants through the root system in nurseries. IMPORTANCE Grapevine trunk diseases are a major threat to the wine and grape industry worldwide. They cause a significant reduction in yields as well as in grape quality, and they can even cause plant death. Trunk diseases are caused by fungal pathogens that enter through pruning wounds and

Use of Endophytic and Rhizosphere Actinobacteria from Grapevine Plants To Reduce Nursery Fungal Graft Infections That Lead to Young Grapevine Decline.

PubMed

Álvarez-Pérez, José Manuel; González-García, Sandra; Cobos, Rebeca; Olego, Miguel Ángel; Ibañez, Ana; Díez-Galán, Alba; Garzón-Jimeno, Enrique; Coque, Juan José R

2017-12-15

Endophytic and rhizosphere actinobacteria isolated from the root system of 1-year-old grafted Vitis vinifera plants were evaluated for their activities against fungi that cause grapevine trunk diseases. A total of 58 endophytic and 94 rhizosphere isolates were tested. Based on an in vitro bioassay, 15.5% of the endophytic isolates and 30.8% of the rhizosphere isolates exhibited antifungal activity against the fungal pathogen Diplodia seriata , whereas 13.8% of the endophytic isolates and 16.0% of the rhizosphere isolates showed antifungal activity against Dactylonectria macrodidyma (formerly Ilyonectria macrodidyma ). The strains which showed the greatest in vitro efficacy against both pathogens were further analyzed for their ability to inhibit the growth of Phaeomoniella chlamydospora and Phaeoacremonium minimum (formerly Phaeoacremonium aleophilum ). Based on their antifungal activity, three rhizosphere isolates and three endophytic isolates were applied on grafts in an open-root field nursery in a 3-year trial. The field trial led to the identification of one endophytic strain, Streptomyces sp. VV/E1, and two rhizosphere isolates, Streptomyces sp. VV/R1 and Streptomyces sp. VV/R4, which significantly reduced the infection rates produced by the fungal pathogens Dactylonectria sp., Ilyonectria sp., P. chlamydospora , and P. minimum , all of which cause young grapevine decline. The VV/R1 and VV/R4 isolates also significantly reduced the mortality level of grafted plants in the nursery. This study shows that certain actinobacteria could represent a promising new tool for controlling fungal trunk pathogens that infect grapevine plants through the root system in nurseries. IMPORTANCE Grapevine trunk diseases are a major threat to the wine and grape industry worldwide. They cause a significant reduction in yields as well as in grape quality, and they can even cause plant death. Trunk diseases are caused by fungal pathogens that enter through pruning wounds and/or the

The Neotropical species of Atractodes (Hymenoptera, Ichneumonidae, Cryptinae), II: the A. pleuripunctatus species-group.

PubMed

Bordera, Santiago; Mazón, Marina; Sääksjärvi, Ilari E

2016-09-06

We describe three new species of parasitoid wasps of the genus Atractodes (Ichneumonidae: Cryptinae) from South America: A. colchaguensis sp. nov. from Chile, and A. pleuripunctatus sp. nov. and A. saragurensis sp. nov. from Ecuador. These species are all characterized by a densely and strongly punctate mesopleuron. The Atractodes pleuripunctatus species-group is defined to accommodate the new species. In addition, the second part of the key to species of the Neotropical Atractodes including this species-group is given.

Proctolaelaps species (Acari: Mesostigmata: Melicharidae) from Egypt, with description of a new species and complementary descriptions of other five species.

PubMed

Abo-Shnaf, Reham I A; Moraes, Gilberto J De

2016-09-12

The objective of this paper is to provide a taxonomic appraisal of the melicharids from Egypt, based on specimens previously collected by different authors and on specimens newly collected by the first author of this paper, all belonging to the genus Proctolaelaps Berlese. A new species, Proctolaelaps gizaensis n. sp., is described, thus raising to six the number of Proctolaelaps species recorded from Egypt. Complementary descriptions of the following species are also provided: Proctolaelaps aegyptiacus Nasr, 1986; Proctolaelaps holoventris Moraes, Britto, Mineiro & Halliday, 2016; Proctolaelaps pygmaeus (Müller, 1859); Proctolaelaps drosophilae Karg, Baker & Jenkinson, 1995 and Proctolaelaps regalis De Leon, 1963. The latter two species were not found in Egypt, but they are related to the new species described here. They were re-described based on the type specimens from Europe and North America. A dichotomous key is given to help the separation of the Proctolaelaps species concluded to be found in Egypt.

Draft Genome Sequence of the d-Xylose-Fermenting Yeast Spathaspora arborariae UFMG-HM19.1AT

PubMed Central

Lobo, Francisco P.; Gonçalves, Davi L.; Alves, Sergio L.; Gerber, Alexandra L.; de Vasconcelos, Ana Tereza R.; Basso, Luiz C.; Franco, Glória R.; Soares, Marco A.; Cadete, Raquel M.; Rosa, Carlos A.

2014-01-01

The draft genome sequence of the yeast Spathaspora arborariae UFMG-HM19.1AT (CBS 11463 = NRRL Y-48658) is presented here. The sequenced genome size is 12.7 Mb, consisting of 41 scaffolds containing a total of 5,625 predicted open reading frames, including many genes encoding enzymes and transporters involved in d-xylose fermentation. PMID:24435867

Selecting focal species as surrogates for imperiled species using relative sensitivities derived from occupancy analysis

USGS Publications Warehouse

Silvano, Amy; Guyer, Craig; Steury, Todd; Grand, James B.

2017-01-01

Most imperiled species are rare or elusive and difficult to detect, which makes gathering data to estimate their response to habitat restoration a challenge. We used a repeatable, systematic method for selecting focal species using relative sensitivities derived from occupancy analysis. Our objective was to select suites of focal species that would be useful as surrogates when predicting effects of restoration of habitat characteristics preferred by imperiled species. We developed 27 habitat profiles that represent general habitat relationships for 118 imperiled species. We identified 23 regularly encountered species that were sensitive to important aspects of those profiles. We validated our approach by examining the correlation between estimated probabilities of occupancy for species of concern and focal species selected using our method. Occupancy rates of focal species were more related to occupancy rates of imperiled species when they were sensitive to more of the parameters appearing in profiles of imperiled species. We suggest that this approach can be an effective means of predicting responses by imperiled species to proposed management actions. However, adequate monitoring will be required to determine the effectiveness of using focal species to guide management actions.

Paenibacillus profundus sp. nov., a deep sediment bacterium that produces isocoumarin and peptide antibiotics.

PubMed

Romanenko, Lyudmila A; Tanaka, Naoto; Svetashev, Vassilii I; Kalinovskaya, Natalia I

2013-04-01

A novel bacterial strain Sl 79(T) was isolated from a deep surface sediment sample obtained from the Sea of Japan and investigated by phenotypic and molecular methods. The bacterium Sl 79(T) was Gram-positive, facultatively anaerobic, spore-forming, motile and able to form two different types of colonies. It contained the major menaquinone MK-7 and anteiso-C(15:0) followed by iso-C(15:0) as predominant fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Sl 79(T) belonged to the genus Paenibacillus where it clustered to Paenibacillus apiarius NRRL NRS-1438(T) with a sequence similarity of 97.7 % and sharing sequence similarities below than 96.7 % to other validly named Paenibacillus species. Strain Sl 79(T) was found to possess a remarkable inhibitory activity against indicatory microorganisms. On the basis of combined spectral analyses, strain Paenibacillus sp. Sl 79(T) was established to produce isocoumarin and novel peptide antibiotics. On the basis of DNA-DNA relatedness, phenotypic and phylogenetic data obtained, it was concluded that strain Sl 79(T) represents a novel species, Paenibacillus profundus sp. nov. with the type strain Sl 79(T) = KMM 9420(T) = NRIC 0885(T).

Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete.

PubMed

Linos, Alexandros; Berekaa, Mahmoud M; Steinbüchel, Alexander; Kim, Kwang Kyu; Sproer, Cathrin; Kroppenstedt, Reiner M

2002-07-01

A cis-1,4-polyisoprene-degrading bacterium (strain Kb2T) was isolated from foul water taken from the inside of a deteriorated automobile tyre found on a farmer's field in Westfalia, Germany. The strain was aerobic, Gram-positive, exhibited orange smooth and rough colonies on complex nutrient agar, produced elementary branching hyphae that fragmented into rod/coccus-like elements and showed chemotaxonomic markers which were consistent with its classification within the genus Gordonia, i.e. the presence of mesodiaminopimelic acid, arabinose and galactose in whole-cell hydrolysates (cell-wall chemotype IV), N-glycolylmuramic acid in the peptidoglycan wall, a fatty-acid pattern composed of unbranched saturated and monounsaturated fatty acids plus tuberculostearic acid, mycolic acids comprising 56-60 carbon atoms and MK-9(H2) as the only menaquinone. The 16S rDNA sequence of strain Kb2T was found to be most similar to the 16S rDNA sequences of the type strains of Gordonia alkanivorans (DSM 44369T) and Gordonia nitida (KCTC 0605BPT). However, DNA-DNA relatedness data showed that strain Kb2T ( =DSM 44215T NRRL B-24152T) could be distinguished from these two species and represented a new species within the genus Gordonia, for which the name Gordonia westfalica is proposed.

Kribbella albertanoniae sp. nov., isolated from a Roman catacomb, and emended description of the genus Kribbella.

PubMed

Everest, Gareth J; Curtis, Sarah M; De Leo, Filomena; Urzì, Clara; Meyers, Paul R

2013-10-01

A novel actinobacterium, strain BC640(T), was isolated from a biofilm sample collected in 2009 in the Saint Callistus Roman catacombs. Analysis of the 16S rRNA gene sequence showed that the strain belonged to the genus Kribbella. Phylogenetic analysis using the 16S rRNA gene and concatenated gyrB, rpoB, relA, recA and atpD gene sequences showed that strain BC640(T) was most closely related to the type strains of Kribbella yunnanensis and Kribbella sandramycini. Based on gyrB genetic distance analysis, strain BC640(T) was shown to be distinct from all Kribbella type strains. DNA-DNA hybridization experiments confirmed that strain BC640(T) represents a genomic species distinct from its closest phylogenetic relatives, K. yunnanensis DSM 15499(T) (53.5±7.8 % DNA relatedness) and K. sandramycini DSM 15626(T) (33.5±5.0 %). Physiological comparisons further showed that strain BC640(T) is phenotypically distinct from the type strains of K. yunnanensis and K. sandramycini. Strain BC640(T) ( = DSM 26744(T) = NRRL B-24917(T)) is thus presented as the type strain of a novel species, for which the name Kribbella albertanoniae sp. nov. is proposed.

Pseudomonas aestus sp. nov., a plant growth-promoting bacterium isolated from mangrove sediments.

PubMed

Vasconcellos, Rafael L F; Santos, Suikinai Nobre; Zucchi, Tiago Domingues; Silva, Fábio Sérgio Paulino; Souza, Danilo Tosta; Melo, Itamar Soares

2017-10-01

Strain CMAA 1215 T , a Gram-reaction-negative, aerobic, catalase positive, polarly flagellated, motile, rod-shaped (0.5-0.8 × 1.3-1.9 µm) bacterium, was isolated from mangrove sediments, Cananéia Island, Brazil. Analysis of the 16S rRNA gene sequences showed that strain CMAA 1215 T forms a distinct phyletic line within the Pseudomonas putida subclade, being closely related to P. plecoglossicida ATCC 700383 T , P. monteilii NBRC 103158 T , and P. taiwanensis BCRC 17751 T of sequence similarity of 98.86, 98.73, and 98.71%, respectively. Genomic comparisons of the strain CMAA 1215 T with its closest phylogenetic type strains using average nucleotide index (ANI) and DNA:DNA relatedness approaches revealed 84.3-85.3% and 56.0-63.0%, respectively. A multilocus sequence analysis (MLSA) performed concatenating 16S rRNA, gyrB and rpoB gene sequences from the novel species was related with Pseudomonas putida subcluster and formed a new phylogenetic lineage. The phenotypic, physiological, biochemical, and genetic characteristics support the assignment of CMAA 1215 T to the genus Pseudomonas, representing a novel species. The name Pseudomonas aestus sp.nov. is proposed, with CMAA 1215 T (=NRRL B-653100 T  = CBMAI 1962 T ) as the type strain.

Effects of Hydrogen Peroxide on Different Toxigenic and Atoxigenic Isolates of Aspergillus flavus

PubMed Central

Fountain, Jake C.; Scully, Brian T.; Chen, Zhi-Yuan; Gold, Scott E.; Glenn, Anthony E.; Abbas, Hamed K.; Lee, R. Dewey; Kemerait, Robert C.; Guo, Baozhu

2015-01-01

Drought stress in the field has been shown to exacerbate aflatoxin contamination of maize and peanut. Drought and heat stress also produce reactive oxygen species (ROS) in plant tissues. Given the potential correlation between ROS and exacerbated aflatoxin production under drought and heat stress, the objectives of this study were to examine the effects of hydrogen peroxide (H2O2)-induced oxidative stress on the growth of different toxigenic (+) and atoxigenic (−) isolates of Aspergillus flavus and to test whether aflatoxin production affects the H2O2 concentrations that the isolates could survive. Ten isolates were tested: NRRL3357 (+), A9 (+), AF13 (+), Tox4 (+), A1 (−), K49 (−), K54A (−), AF36 (−), and Aflaguard (−); and one A. parasiticus isolate, NRRL2999 (+). These isolates were cultured under a H2O2 gradient ranging from 0 to 50 mM in two different media, aflatoxin-conducive yeast extract-sucrose (YES) and non-conducive yeast extract-peptone (YEP). Fungal growth was inhibited at a high H2O2 concentration, but specific isolates grew well at different H2O2 concentrations. Generally the toxigenic isolates tolerated higher concentrations than did atoxigenic isolates. Increasing H2O2 concentrations in the media resulted in elevated aflatoxin production in toxigenic isolates. In YEP media, the higher concentration of peptone (15%) partially inactivated the H2O2 in the media. In the 1% peptone media, YEP did not affect the H2O2 concentrations that the isolates could survive in comparison with YES media, without aflatoxin production. It is interesting to note that the commercial biocontrol isolates, AF36 (−), and Aflaguard (−), survived at higher levels of stress than other atoxigenic isolates, suggesting that this testing method could potentially be of use in the selection of biocontrol isolates. Further studies will be needed to investigate the mechanisms behind the variability among isolates with regard to their degree of oxidative stress

SPECIES - EVALUATING THERMODYNAMIC PROPERTIES, TRANSPORT PROPERTIES & EQUILIBRIUM CONSTANTS OF AN 11-SPECIES AIR MODEL

NASA Technical Reports Server (NTRS)

Thompson, R. A.

1994-01-01

Accurate numerical prediction of high-temperature, chemically reacting flowfields requires a knowledge of the physical properties and reaction kinetics for the species involved in the reacting gas mixture. Assuming an 11-species air model at temperatures below 30,000 degrees Kelvin, SPECIES (Computer Codes for the Evaluation of Thermodynamic Properties, Transport Properties, and Equilibrium Constants of an 11-Species Air Model) computes values for the species thermodynamic and transport properties, diffusion coefficients and collision cross sections for any combination of the eleven species, and reaction rates for the twenty reactions normally occurring. The species represented in the model are diatomic nitrogen, diatomic oxygen, atomic nitrogen, atomic oxygen, nitric oxide, ionized nitric oxide, the free electron, ionized atomic nitrogen, ionized atomic oxygen, ionized diatomic nitrogen, and ionized diatomic oxygen. Sixteen subroutines compute the following properties for both a single species, interaction pair, or reaction, and an array of all species, pairs, or reactions: species specific heat and static enthalpy, species viscosity, species frozen thermal conductivity, diffusion coefficient, collision cross section (OMEGA 1,1), collision cross section (OMEGA 2,2), collision cross section ratio, and equilibrium constant. The program uses least squares polynomial curve-fits of the most accurate data believed available to provide the requested values more quickly than is possible with table look-up methods. The subroutines for computing transport coefficients and collision cross sections use additional code to correct for any electron pressure when working with ionic species. SPECIES was developed on a SUN 3/280 computer running the SunOS 3.5 operating system. It is written in standard FORTRAN 77 for use on any machine, and requires roughly 92K memory. The standard distribution medium for SPECIES is a 5.25 inch 360K MS-DOS format diskette. The contents of the

Ants Learn Aphid Species as Mutualistic Partners: Is the Learning Behavior Species-Specific?

PubMed

Hayashi, Masayuki; Nakamuta, Kiyoshi; Nomura, Masashi

2015-12-01

In ant-aphid associations, many aphid species provide ants with honeydew and are tended by ants, whereas others are never tended and are frequently preyed upon by ants. In these relationships, ants must have the ability to discriminate among aphid species, with mutualistic aphids being accepted as partners rather than prey. Although ants reportedly use cuticular hydrocarbons (CHCs) of aphids to differentiate between mutualistic and non-mutualistic species, it is unclear whether the ability to recognize mutualistic aphid species as partners is innate or involves learning. Therefore, we tested whether aphid recognition by ants depends on learning, and whether the learning behavior is species-specific. When workers of the ant Tetramorium tsushimae had previously tended the cowpea aphid, Aphis craccivora, they were less aggressive toward this species. In addition, ants also reduced their aggressiveness toward another mutualistic aphid species, Aphis fabae, after tending A. craccivora, whereas ants remained aggressive toward the non-mutualistic aphid, Acyrthosiphon pisum, regardless of whether or not they had previous experience in tending A. craccivora. When ants were offered glass dummies treated with CHCs of these aphid species, ants that had tended A. craccivora displayed reduced aggression toward CHCs of A. craccivora and A. fabae. Chemical analyses showed the similarity of the CHC profiles between A. craccivora and A. fabae but not with A. pisum. These results suggest that aphid recognition of ants involves learning, and that the learning behavior may not be species-specific because of the similarity of CHCs between different aphid species with which they form mutualisms.

Invading species in the Eel River, California: Successes, failures, and relationships with resident species

USGS Publications Warehouse

Brown, L.R.; Moyle, P.B.

1997-01-01

We examined invasions of non-native fishes into the Eel River, California. At least 16 species of fish have been introduced into the drainage which originally supported 12-14 fish species. Our study was prompted by the unauthorized introduction in 1979 of Sacramento squawfish, Ptychocheilus grandis, a large predatory cyprinid. From 1986 to 1990, we conducted growth and diet studies of squaw fish, conducted intensive surveys of the distribution and habitat associations of both native and introduced species, and examined the nature of species-habitat and interspecies relationships. We found no evidence for increased growth or expanded feeding habits, compared to native populations, of Sacramento squawfish as they invaded the Eel River drainage. Ten of the introduced species were well established, with four species limited to a reservoir and six species established in streams. The success or failure of introductions of stream species appeared to be a function of the ability of a species to survive the fluctuating, highly seasonal, flow regime. The present mixture of native and exotic species has not formed stable fish assemblages but it seems likely that four habitat-associated assemblages will develop. The overall effect of the successful species introductions has been to assemble a group of species, with some exceptions, that are native to and occur together in many California streams. The assemblages now forming are similar to those found in other California streams. The assemblage characterized by squawfish and suckers is likely to be resistant to invasion, in the absence of human caused habitat modifications.

The Species Delimitation Uncertainty Principle

PubMed Central

Adams, Byron J.

2001-01-01

If, as Einstein said, "it is the theory which decides what we can observe," then "the species problem" could be solved by simply improving our theoretical definition of what a species is. However, because delimiting species entails predicting the historical fate of evolutionary lineages, species appear to behave according to the Heisenberg Uncertainty Principle, which states that the most philosophically satisfying definitions of species are the least operational, and as species concepts are modified to become more operational they tend to lose their philosophical integrity. Can species be delimited operationally without losing their philosophical rigor? To mitigate the contingent properties of species that tend to make them difficult for us to delimit, I advocate a set of operations that takes into account the prospective nature of delimiting species. Given the fundamental role of species in studies of evolution and biodiversity, I also suggest that species delimitation proceed within the context of explicit hypothesis testing, like other scientific endeavors. The real challenge is not so much the inherent fallibility of predicting the future but rather adequately sampling and interpreting the evidence available to us in the present. PMID:19265874

Species accounts. Chapter 4

Treesearch

Margaret K. Trani; W. Mark Ford; Brian R., eds. Chapman

2007-01-01

Narrative accounts for each species are presented by several authors in a consistent format to convey specific information relative to that mammal. The orders are arranged phylogenetically; families and species are arranged alphabetically to facilitate finding a particular species.

Biodiversity in the cyclic competition system of three species according to the emergence of mutant species

NASA Astrophysics Data System (ADS)

Park, Junpyo

2018-05-01

Understanding mechanisms which promote or hinder existing ecosystems are important issues in ecological sciences. In addition to fundamental interactions such as competition and migration among native species, existing ecosystems can be easily disturbed by external factors, and the emergence of new species may be an example in such cases. The new species which does not exist in a current ecosystem can be regarded as either alien species entered from outside or mutant species born by mutation in existing normal species. Recently, as existing ecosystems are getting influenced by various physical/chemical external factors, mutation due to anthropogenic and environmental factors can occur more frequently and is thus attracting much attention for the maintenance of ecosystems. In this paper, we consider emergences of mutant species among self-competing three species in the cyclic dominance. By defining mutation as the birth of mutant species, we investigate how mutant species can affect biodiversity in the existing ecosystem. Through microscopic and macroscopic approaches, we have found that the society of existing normal species can be disturbed by mutant species either the society is maintained accompanying with the coexistence of all species or jeopardized by occupying of mutant species. Due to the birth of mutant species, the existing society may be more complex by constituting two different groups of normal and mutant species, and our results can be contributed to analyze complex ecosystems of many species. We hope our findings may propose a new insight on mutation in cyclic competition systems of many species.

Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov.

PubMed

Busarakam, Kanungnid; Brown, Ros; Bull, Alan T; Tan, Geok Yuan Annie; Zucchi, Tiago D; da Silva, Leonardo José; de Souza, Wallace Rafael; Goodfellow, Michael

2016-02-01

The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)).

ASPERGILLUS LUCHUENSIS , AN INDUSTRIALLY IMPORTANT BLACK ASPERGILLUS IN EAST ASIA

PubMed Central

Hong, Seung-Beom; Lee, Mina; Kim, Dae-Ho; Varga, Janos; Frisvad, Jens C.; Perrone, Giancarlo; Gomi, Katsuya; Yamada, Osamu; Machida, Masayuki; Houbraken, Jos; Samson, Robert A.

2013-01-01

Aspergilli known as black- and white-koji molds which are used for awamori, shochu, makgeolli and other food and beverage fermentations, are reported in the literature as A. luchuensis, A. awamori, A. kawachii, or A. acidus. In order to elucidate the taxonomic position of these species, available ex-type cultures were compared based on morphology and molecular characters. A. luchuensis, A. kawachii and A. acidus showed the same banding patterns in RAPD, and the three species had the same rDNA-ITS, β-tubulin and calmodulin sequences and these differed from those of the closely related A. niger and A. tubingensis. Morphologically, the three species are not significantly different from each other or from A. niger and A. tubingensis. It is concluded that A. luchuensis, A. kawachii and A. acidus are the same species, and A. luchuensis is selected as the correct name based on priority. Strains of A. awamori which are stored in National Research Institute of Brewing in Japan, represent A. niger (n = 14) and A. luchuensis (n = 6). The neotype of A. awamori (CBS 557.65 =  NRRL 4948) does not originate from awamori fermentation and it is shown to be identical with the unknown taxon Aspergillus welwitschiae. Extrolite analysis of strains of A. luchuensis showed that they do not produce mycotoxins and therefore can be considered safe for food and beverage fermentations. A. luchuensis is also frequently isolated from meju and nuruk in Korea and Puerh tea in China and the species is probably common in the fermentation environment of East Asia. A re-description of A. luchuensis is provided because the incomplete data in the original literature. PMID:23723998

Aspergillus luchuensis, an industrially important black Aspergillus in East Asia.

PubMed

Hong, Seung-Beom; Lee, Mina; Kim, Dae-Ho; Varga, Janos; Frisvad, Jens C; Perrone, Giancarlo; Gomi, Katsuya; Yamada, Osamu; Machida, Masayuki; Houbraken, Jos; Samson, Robert A

2013-01-01

Aspergilli known as black- and white-koji molds which are used for awamori, shochu, makgeolli and other food and beverage fermentations, are reported in the literature as A. luchuensis, A. awamori, A. kawachii, or A. acidus. In order to elucidate the taxonomic position of these species, available ex-type cultures were compared based on morphology and molecular characters. A. luchuensis, A. kawachii and A. acidus showed the same banding patterns in RAPD, and the three species had the same rDNA-ITS, β-tubulin and calmodulin sequences and these differed from those of the closely related A. niger and A. tubingensis. Morphologically, the three species are not significantly different from each other or from A. niger and A. tubingensis. It is concluded that A. luchuensis, A. kawachii and A. acidus are the same species, and A. luchuensis is selected as the correct name based on priority. Strains of A. awamori which are stored in National Research Institute of Brewing in Japan, represent A. niger (n = 14) and A. luchuensis (n = 6). The neotype of A. awamori (CBS 557.65 =  NRRL 4948) does not originate from awamori fermentation and it is shown to be identical with the unknown taxon Aspergillus welwitschiae. Extrolite analysis of strains of A. luchuensis showed that they do not produce mycotoxins and therefore can be considered safe for food and beverage fermentations. A. luchuensis is also frequently isolated from meju and nuruk in Korea and Puerh tea in China and the species is probably common in the fermentation environment of East Asia. A re-description of A. luchuensis is provided because the incomplete data in the original literature.

Do water quality criteria based on nonnative species provide appropriate protection for native species?

PubMed

Jin, Xiaowei; Wang, Zijian; Wang, Yeyao; Lv, Yibing; Rao, Kaifeng; Jin, Wei; Giesy, John P; Leung, Kenneth M Y

2015-08-01

The potential use of toxicity data for nonnative species to derive water quality criteria is controversial because it is sometimes questioned whether criteria based on species from one geographical region provide appropriate protection for species in a different region. However, this is an important concept for the development of Chinese water quality criteria or standards. Data were assembled on 38 chemicals for which values were available for both native and nonnative species. Sensitivities of these organisms were compared based on the 5% hazardous concentration values and the species sensitivity distribution from a literature review. Results of the present study's analysis showed that there is approximately 74% certainty that use of nonnative species to generate water quality criteria would be sufficiently protective of aquatic ecosystems in China. Without applying any assessment factor to the water quality criteria generated from nonnative species, the uncertainty would be 26% when the native Chinese species might be under protection. Applying an assessment factor of 10 would offer adequate protection to native Chinese species for approximately 90% of tested chemicals and thus reduce the uncertainty from 26% to 10%. © 2015 SETAC.

Boechera Species Exhibit Species-Specific Responses to Combined Heat and High Light Stress

PubMed Central

Gallas, Genna; Waters, Elizabeth R.

2015-01-01

As sessile organisms, plants must be able to complete their life cycle in place and therefore tolerance to abiotic stress has had a major role in shaping biogeographical patterns. However, much of what we know about plant tolerance to abiotic stresses is based on studies of just a few plant species, most notably the model species Arabidopsis thaliana. In this study we examine natural variation in the stress responses of five diverse Boechera (Brassicaceae) species. Boechera plants were exposed to basal and acquired combined heat and high light stress. Plant response to these stresses was evaluated based on chlorophyll fluorescence measurements, induction of leaf chlorosis, and gene expression. Many of the Boechera species were more tolerant to heat and high light stress than A. thaliana. Gene expression data indicates that two important marker genes for stress responses: APX2 (Ascorbate peroxidase 2) and HsfA2 (Heat shock transcription factor A2) have distinct species-specific expression patterns. The findings of species-specific responses and tolerance to stress indicate that stress pathways are evolutionarily labile even among closely related species. PMID:26030823

Attempted integration of multiple species of turaco into a mixed-species aviary.

PubMed

Valuska, Annie J; Leighty, Katherine A; Ferrie, Gina M; Nichols, Valerie D; Tybor, Cheryl L; Plassé, Chelle; Bettinger, Tamara L

2013-03-01

Mixed-species exhibits offer a variety of benefits but can be challenging to maintain due to difficulty in managing interspecific interactions. This is particularly true when little has been documented on the behavior of the species being mixed. This was the case when we attempted to house three species of turaco (family: Musophagidae) together with other species in a walk-through aviary. To learn more about the behavior of great blue turacos, violaceous turacos, and white-bellied gray go-away birds, we supplemented opportunistic keeper observations with systematic data collection on their behavior, location, distance from other birds, and visibility to visitors. Keepers reported high levels of aggression among turacos, usually initiated by a go-away bird or a violaceous turaco. Most aggression occurred during feedings or when pairs were defending nest sites. Attempts to reduce aggression by temporarily removing birds to holding areas and reintroducing them days later were ineffective. Systematic data collection revealed increased social behavior, including aggression, during breeding season in the violaceous turacos, as well as greater location fidelity. These behavioral cues may be useful in predicting breeding behavior in the future. Ultimately, we were only able to house three species of turaco together for a short time, and prohibitively high levels of conflict occurred when pairs were breeding. We conclude that mixing these three turaco species is challenging and may not be the most appropriate housing situation for them, particularly during breeding season. However, changes in turaco species composition, sex composition, or exhibit design may result in more compatible mixed-turaco species groups. © 2012 Wiley Periodicals, Inc.

Inferring species roles in metacommunity structure from species co-occurrence networks

PubMed Central

Borthagaray, Ana I.; Arim, Matías; Marquet, Pablo A.

2014-01-01

A long-standing question in community ecology is what determines the identity of species that coexist across local communities or metacommunity assembly. To shed light upon this question, we used a network approach to analyse the drivers of species co-occurrence patterns. In particular, we focus on the potential roles of body size and trophic status as determinants of metacommunity cohesion because of their link to resource use and dispersal ability. Small-sized individuals at low-trophic levels, and with limited dispersal potential, are expected to form highly linked subgroups, whereas large-size individuals at higher trophic positions, and with good dispersal potential, will foster the spatial coupling of subgroups and the cohesion of the whole metacommunity. By using modularity analysis, we identified six modules of species with similar responses to ecological conditions and high co-occurrence across local communities. Most species either co-occur with species from a single module or are connectors of the whole network. Among the latter are carnivorous species of intermediate body size, which by virtue of their high incidence provide connectivity to otherwise isolated communities playing the role of spatial couplers. Our study also demonstrates that the incorporation of network tools to the analysis of metacommunity ecology can help unveil the mechanisms underlying patterns and processes in metacommunity assembly. PMID:25143039

Modeling species-abundance relationships in multi-species collections

USGS Publications Warehouse

Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

2003-01-01

Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

PubMed Central

Lassalle, Florent; Campillo, Tony; Vial, Ludovic; Baude, Jessica; Costechareyre, Denis; Chapulliot, David; Shams, Malek; Abrouk, Danis; Lavire, Céline; Oger-Desfeux, Christine; Hommais, Florence; Guéguen, Laurent; Daubin, Vincent; Muller, Daniel; Nesme, Xavier

2011-01-01

The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species. PMID:21795751

Competition with wind-pollinated plant species alters floral traits of insect-pollinated plant species

PubMed Central

Flacher, Floriane; Raynaud, Xavier; Hansart, Amandine; Motard, Eric; Dajoz, Isabelle

2015-01-01

Plant traits related to attractiveness to pollinators (e.g. flowers and nectar) can be sensitive to abiotic or biotic conditions. Soil nutrient availability, as well as interactions among insect-pollinated plants species, can induce changes in flower and nectar production. However, further investigations are needed to determine the impact of interactions between insect-pollinated species and abiotically pollinated species on such floral traits, especially floral rewards. We carried out a pot experiment in which three insect-pollinated plant species were grown in binary mixtures with four wind-pollinated plant species, differing in their competitive ability. Along the flowering period, we measured floral traits of the insect-pollinated species involved in attractiveness to pollinators (i.e. floral display size, flower size, daily and total 1) flower production, 2) nectar volume, 3) amount of sucrose allocated to nectar). Final plant biomass was measured to quantify competitive interactions. For two out of three insect-pollinated species, we found that the presence of a wind-pollinated species can negatively impact floral traits involved in attractiveness to pollinators. This effect was stronger with wind-pollinated species that induced stronger competitive interactions. These results stress the importance of studying the whole plant community (and not just the insect-pollinated plant community) when working on plant-pollinator interactions. PMID:26335409

On the distribution of species occurrence

USGS Publications Warehouse

Buzas, Martin A.; Koch, Carl F.; Culver, Stephen J.; Sohl, Norman F.

1982-01-01

The distribution of species abundance (number of individuals per species) is well documented. The distribution of species occurrence (number of localities per species), however, has received little attention. This study investigates the distribution of species occurrence for five large data sets. For modern benthic foraminifera, species occurrence is examined from the Atlantic continental margin of North America, where 875 species were recorded 10,017 times at 542 localities, the Gulf of Mexico, where 848 species were recorded 18,007 times at 426 localities, and the Caribbean, where 1,149 species were recorded 6,684 times at 268 localities. For Late Cretaceous molluscs, species occurrence is examined from the Gulf Coast where 716 species were recorded 6,236 times at 166 localities and a subset of this data consisting of 643 species recorded 3,851 times at 86 localities.Logseries and lognormal distributions were fitted to these data sets. In most instances the logseries best predicts the distribution of species occurrence. The lognormal, however, also fits the data fairly well, and, in one instance, better. The use of these distributions allows the prediction of the number of species occurring once, twice, ..., n times.Species abundance data are also available for the molluscan data sets. They indicate that the most abundant species (greatest number of individuals) usually occur most frequently. In all data sets approximately half the species occur four or less times. The probability of noting the presence of rarely occurring species is small, and, consequently, such species must be used with extreme caution in studies requiring knowledge of the distribution of species in space and time.

Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine.

PubMed

Benardini, James N; Vaishampayan, Parag A; Schwendner, Petra; Swanner, Elizabeth; Fukui, Youhei; Osman, Sharif; Satomi, Masakata; Venkateswaran, Kasthuri

2011-06-01

A novel Gram-positive, motile, endospore-forming, aerobic bacterium was isolated from the NASA Phoenix Lander assembly clean room that exhibits 100 % 16S rRNA gene sequence similarity to two strains isolated from a deep subsurface environment. All strains are rod-shaped, endospore-forming bacteria, whose endospores are resistant to UV radiation up to 500 J m(-2). A polyphasic taxonomic study including traditional phenotypic tests, fatty acid analysis, 16S rRNA gene sequencing and DNA-DNA hybridization analysis was performed to characterize these novel strains. The 16S rRNA gene sequencing convincingly grouped these novel strains within the genus Paenibacillus as a separate cluster from previously described species. The similarity of 16S rRNA gene sequences among the novel strains was identical but only 98.1 to 98.5 % with their nearest neighbours Paenibacillus barengoltzii ATCC BAA-1209(T) and Paenibacillus timonensis CIP 108005(T). The menaquinone MK-7 was dominant in these novel strains as shown in other species of the genus Paenibacillus. The DNA-DNA hybridization dissociation value was <45 % with the closest related species. The novel strains had DNA G+C contents of 51.9 to 52.8 mol%. Phenotypically, the novel strains can be readily differentiated from closely related species by the absence of urease and gelatinase and the production of acids from a variety of sugars including l-arabinose. The major fatty acid was anteiso-C(15 : 0) as seen in P. barengoltzii and P. timonensis whereas the proportion of C(16 : 0) was significantly different from the closely related species. Based on phylogenetic and phenotypic results, it was concluded that these strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus phoenicis sp. nov. is proposed. The type strain is 3PO2SA(T) ( = NRRL B-59348(T)  = NBRC 106274(T)).

Complete Genome Sequences of 38 Gordonia sp. Bacteriophages

PubMed Central

Montgomery, Matthew T.; Bonilla, J. Alfred; Dejong, Randall; Garlena, Rebecca A.; Guerrero Bustamante, Carlos; Klyczek, Karen K.; Russell, Daniel A.; Wertz, John T.; Jacobs-Sera, Deborah; Hatfull, Graham F.

2017-01-01

ABSTRACT We report here the genome sequences of 38 newly isolated bacteriophages using Gordonia terrae 3612 (ATCC 25594) and Gordonia neofelifaecis NRRL59395 as bacterial hosts. All of the phages are double-stranded DNA (dsDNA) tail phages with siphoviral morphologies, with genome sizes ranging from 17,118 bp to 93,843 bp and spanning considerable nucleotide sequence diversity. PMID:28057748

No universal scale-dependent impacts of invasive species on native plant species richness.

PubMed

Stohlgren, Thomas J; Rejmánek, Marcel

2014-01-01

A growing number of studies seeking generalizations about the impact of plant invasions compare heavily invaded sites to uninvaded sites. But does this approach warrant any generalizations? Using two large datasets from forests, grasslands and desert ecosystems across the conterminous United States, we show that (i) a continuum of invasion impacts exists in many biomes and (ii) many possible species-area relationships may emerge reflecting a wide range of patterns of co-occurrence of native and alien plant species. Our results contradict a smaller recent study by Powell et al. 2013 (Science 339, 316-318. (doi:10.1126/science.1226817)), who compared heavily invaded and uninvaded sites in three biomes and concluded that plant communities invaded by non-native plant species generally have lower local richness (intercepts of log species richness-log area regression lines) but steeper species accumulation with increasing area (slopes of the regression lines) than do uninvaded communities. We conclude that the impacts of plant invasions on plant species richness are not universal.

Environmental responses, not species interactions, determine synchrony of dominant species in semiarid grasslands.

PubMed

Tredennick, Andrew T; de Mazancourt, Claire; Loreau, Michel; Adler, Peter B

2017-04-01

Temporal asynchrony among species helps diversity to stabilize ecosystem functioning, but identifying the mechanisms that determine synchrony remains a challenge. Here, we refine and test theory showing that synchrony depends on three factors: species responses to environmental variation, interspecific interactions, and demographic stochasticity. We then conduct simulation experiments with empirical population models to quantify the relative influence of these factors on the synchrony of dominant species in five semiarid grasslands. We found that the average synchrony of per capita growth rates, which can range from 0 (perfect asynchrony) to 1 (perfect synchrony), was higher when environmental variation was present (0.62) rather than absent (0.43). Removing interspecific interactions and demographic stochasticity had small effects on synchrony. For the dominant species in these plant communities, where species interactions and demographic stochasticity have little influence, synchrony reflects the covariance in species' responses to the environment. © 2017 by the Ecological Society of America.

Recovery of imperiled species under the Endangered Species Act: The need for a new approach

USGS Publications Warehouse

Scott, J.M.; Goble, D.D.; Wiens, J.A.; Wilcove, D.S.; Bean, M.; Male, T.

2005-01-01

The recovery (delisting) of a threatened or endangered species is often accompanied by the expectation that conservation management of the species will no longer be necessary. However, the magnitude and pace of human impacts on the environment make it unlikely that substantial progress will be made in delisting many species unless the definition of "recovery" includes some form of active management. Preventing delisted species from again being at risk of extinction may require continuing, species-specific management actions. We characterize such species as "conservation-reliant", and suggest that viewing "recovery" as a continuum of states rather than as a simple "recovered/not recovered" dichotomy may enhance our ability to manage such species within the framework of the Endangered Species Act. With ongoing loss of habitat, disruption of natural disturbance regimes, and the increasing impacts of non-native invasive species, it is probable that the number of conservation-reliant species will increase. We propose the development of "recovery management agreements", with legally and biologically defensible contracts that would provide for continu-ing conservation management following delisting. The use of such formalized agreements will facilitate shared management responsibilities between federal wildlife agencies and other federal agencies, and with state, local, and tribal governments, as well as with private entities that have demonstrated the capability to meet the needs of conservation-reliant species. ?? The Ecological Society of America.

The Earth's Vanishing Species.

ERIC Educational Resources Information Center

USA Today, 1981

1981-01-01

Elaborates on the problem of expanding human activity to the world's plant and animal species. Concludes that preserving an individual species is largely a waste of time and effort and that the best way to protect the most species of plants and animals is to save their environments over large tracts of land. (DB)

Consilience and a Hierarchy of Species Concepts: Advances Toward Closure on the Species Puzzle

PubMed Central

Mayden, Richard L.

1999-01-01

Numerous concepts exist for biological species. This diversity of ideas derives from a number of sources ranging from investigative study of particular taxa and character sets to philosophical aptitude and world view to operationalism and nomenclatorial rules. While usually viewed as counterproductive, in reality these varied concepts can greatly enhance our efforts to discover and understand biological diversity. Moreover, this continued "turf war" and dilemma over species can be resolved if the various concepts are viewed in a hierarchical system and each evaluated for its inherent level of consilience. Under this paradigm a theoretically appropriate, highly consilient concept of species capable of colligating the abundant types of species diversity offers the best guidance for developing and employing secondary operational concepts for identifying diversity. Of all the concepts currently recognized, only the non-operational Evolutionary Species Concept corresponds to the requisite parameters and, therefore, should serve as the theoretical concept appropriate for the category Species. As operational concepts, the remaining ideas have been incompatible with one another in their ability to encompass species diversity because each has restrictive criteria as to what qualifies as a species. However, the operational concepts can complement one another and do serve a vital role under the Evolutionary Species Concept as fundamental tools necessary for discovering diversity compatible with the primary theoretical concept. Thus, the proposed hierarchical system of primary and secondary concepts promises both the most productive framework for mutual respect for varied concepts and the most efficient and effective means for revealing species diversity. PMID:19270881

Species distribution modelling for plant communities: Stacked single species or multivariate modelling approaches?

Treesearch

Emilie B. Henderson; Janet L. Ohmann; Matthew J. Gregory; Heather M. Roberts; Harold S.J. Zald

2014-01-01

Landscape management and conservation planning require maps of vegetation composition and structure over large regions. Species distribution models (SDMs) are often used for individual species, but projects mapping multiple species are rarer. We compare maps of plant community composition assembled by stacking results from many SDMs with multivariate maps constructed...

Detecting the role of individual species for overyielding in experimental grassland communities composed of potentially dominant species.

PubMed

Roscher, Christiane; Schumacher, Jens; Weisser, Wolfgang W; Schmid, Bernhard; Schulze, Ernst-Detlef

2007-12-01

Several studies have shown that the contribution of individual species to the positive relationship between species richness and community biomass production cannot be easily predicted from species monocultures. Here, we used a biodiversity experiment with a pool of nine potentially dominant grassland species to relate the species richness-productivity relationship to responses in density, size and aboveground allocation patterns of individual species. Aboveground community biomass increased strongly with the transition from monocultures to two-species mixtures but only slightly with the transition from two- to nine-species mixtures. Tripartite partitioning showed that the strong increase shown by the former was due to trait-independent complementarity effects, while the slight increase shown by the latter was due to dominance effects. Trait-dependent complementarity effects depended on species composition. Relative yield total (RYT) was greater than 1 (RYT>1) in mixtures but did not increase with species richness, which is consistent with the constant complementarity effect. The relative yield (RY) of only one species, Arrhenatherum elatius, continually increased with species richness, while those of the other species studied decreased with species richness or varied among different species compositions within richness levels. High observed/expected RYs (RYo/RYe>1) of individual species were mainly due to increased module densities, whereas low observed/expected RYs (RYo/RYe<1) were due to more pronounced decreases in module density (species with stoloniferous or creeping growth) or module size (species with clearly-defined plant individuals). The trade-off between module density and size, typical for plant populations under the law of constant final yield, was compensated among species. The positive trait-independent complementarity effect could be explained by an increase in community module density, which reached a maximum at low species richness. In contrast

SEXUAL SPECIES ARE SEPARATED BY LARGER GENETIC GAPS THAN ASEXUAL SPECIES IN ROTIFERS

PubMed Central

Tang, Cuong Q; Obertegger, Ulrike; Fontaneto, Diego; Barraclough, Timothy G

2014-01-01

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra- and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation. PMID:24975991

Isohydric species are not necessarily more carbon limited than anisohydric species during drought.

PubMed

Garcia-Forner, N; Biel, C; Savé, R; Martínez-Vilalta, J

2017-04-01

Isohydry (i.e., strong regulation of leaf water potential, Ψl) is commonly associated with strict stomatal regulation of transpiration under drought, which in turn is believed to minimize hydraulic risk at the expense of reduced carbon assimilation. Hence, the iso/anisohydric classification has been widely used to assess drought resistance and mortality mechanisms across species, with isohydric species being hypothetically more prone to carbon starvation and anisohydric species more vulnerable to hydraulic failure. These hypotheses and their underlying assumptions, however, have rarely been tested under controlled, experimental conditions. Our objective is to assess the physiological mechanisms underlying drought resistance differences between two co-occurring Mediterranean forest species with contrasting drought responses: Phillyrea latifolia L. (anisohydric and more resistant to drought) and Quercus ilex L. (isohydric and less drought resistant). A total of 100 large saplings (50 per species) were subjected to repeated drought treatments for a period of 3 years, after which Q. ilex showed 18% mortality whereas no mortality was detected in P. latifolia. Relatively isohydric behavior was confirmed for Q. ilex, but higher vulnerability to cavitation in this species implied that estimated embolism levels were similar across species (12-52% in Q. ilex vs ~30% in P. latifolia). We also found similar seasonal patterns of stomatal conductance and assimilation between species. If anything, the anisohydric P. latifolia tended to show lower assimilation rates than Q. ilex under extreme drought. Similar growth rates and carbon reserves dynamics in both species also suggests that P. latifolia was as carbon-constrained as Q. ilex. Increasing carbon reserves under extreme drought stress in both species, concurrent with Q. ilex mortality, suggests that mortality in our study was not triggered by carbon starvation. Our results warn against making direct connections between �

Abundance of common species, not species richness, drives delivery of a real-world ecosystem service.

PubMed

Winfree, Rachael; Fox, Jeremy W; Williams, Neal M; Reilly, James R; Cariveau, Daniel P

2015-07-01

Biodiversity-ecosystem functioning experiments have established that species richness and composition are both important determinants of ecosystem function in an experimental context. Determining whether this result holds for real-world ecosystem services has remained elusive, however, largely due to the lack of analytical methods appropriate for large-scale, associational data. Here, we use a novel analytical approach, the Price equation, to partition the contribution to ecosystem services made by species richness, composition and abundance in four large-scale data sets on crop pollination by native bees. We found that abundance fluctuations of dominant species drove ecosystem service delivery, whereas richness changes were relatively unimportant because they primarily involved rare species that contributed little to function. Thus, the mechanism behind our results was the skewed species-abundance distribution. Our finding that a few common species, not species richness, drive ecosystem service delivery could have broad generality given the ubiquity of skewed species-abundance distributions in nature. © 2015 John Wiley & Sons Ltd/CNRS.

Two new species of the Phanaeus endymion species group (Coleoptera, Scarabaeidae, Scarabaeinae).

PubMed

Moctezuma, Victor; Sánchez-Huerta, José Luis; Halffter, Gonzalo

2017-01-01

Phanaeus bravoensis sp. n. is described from the coniferous-oak forests in the state of Guerrero, and P. huichol sp. n. from coniferous-oak forests and cloud forests in Jalisco and Nayarit. The new species are closely related to P. halffterorum and P. zoque respectively. Morphological trait combination, geographic distribution, and trophic habits show important differences among the studied species. A distribution map and an updated key to separate the species are included.

The application of species criteria in avian taxonomy and its implications for the debate over species concepts.

PubMed

Sangster, George

2014-02-01

The debate over species concepts has produced a huge body of literature on how species can, may or should be delimited. By contrast, very few studies have documented how species taxa are delimited in practice. The aims of the present study were to (i) quantify the use of species criteria in taxonomy, (ii) discuss its implications for the debate over species concepts and (iii) assess recent claims about the impact of different species concepts on taxonomic stability and the 'nature' of species. The application of six species criteria was examined in taxonomic studies of birds published between 1950 and 2009. Three types of taxonomic studies were included: descriptions of new species (N = 329), proposals to change the taxonomic rank of species and subspecies (N = 808) and the taxonomic recommendations of the American Ornithologists' Union Committee on Classification and Nomenclature (N = 176). In all three datasets, diagnosability was the most frequently applied criterion, followed by reproductive isolation and degree of difference. This result is inconsistent with the popular notion that the Biological Species Concept is the dominant species concept in avian taxonomy. Since the 1950s, avian species-level taxonomy has become increasingly pluralistic and eclectic. This suggests that taxonomists consider different criteria as complementary rather than as rival approaches to species delimitation. Application of diagnosability more frequently led to the elevation of subspecies to species rank than application of reproductive isolation, although the difference was small. Hypotheses based on diagnosability and reproductive isolation were equally likely to be accepted in a mainstream checklist. These findings contradict recent claims that application of the Phylogenetic Species Concept causes instability and that broader application of the Biological Species Concept can stabilise taxonomy. The criteria diagnosability and monophyly, which are commonly associated

DNA barcoding Australia's fish species

PubMed Central

Ward, Robert D; Zemlak, Tyler S; Innes, Bronwyn H; Last, Peter R; Hebert, Paul D.N

2005-01-01

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups—dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus—were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or ‘barcoding’, can be used to identify fish species. PMID:16214743

Bias correction in species distribution models: pooling survey and collection data for multiple species.

PubMed

Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A

2015-04-01

Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence-absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence-absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model's performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence-absence data for a given species is scarceIf we have only presence-only data and no presence-absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species' geographic range.

Redescription of four species of Mehdiella from Testudinidae, with a key to the species and discussion on the relationships among the species of this genus.

PubMed

Bouamer, S; Morand, S; Kara, M

2003-12-01

Four species of the genus Mehdiella Seurat, 1918 are redescribed: M. cristata Petter, 1966 and M. stylosa dollfusi Petter, 1966, parasite of Pyxix arachnoides Bell, 1827 from Madagascar, M. s. stylosa (Thapar, 1925) and M. uncinata (Drasche, 1884), parasite of Testudo graeca Linneaus, 1758, Testudo hermanni Gmelin, 1789 and Testudo horsfieldii (Gray, 1844) from Palaearctic region. Light microscopy and scanning electron microscopy (SEM) studies revealed new informations on the morphology of these species. On the basis of this morphological study, the sub-species Mehdiella stylosa dollfusi and M. s. stylosa are raised to level of species. The position of Mehdiella cristata among the species of the genus Mehdiella and the relationships among the species of the genus Mehdiella are discussed. A key to the eight valid species Mehdiella is given.

Species composition and abundance of Brevipalpus spp. on different citrus species in Mexican orchards.

PubMed

Salinas-Vargas, D; Santillán-Galicia, M T; Valdez-Carrasco, J; Mora-Aguilera, G; Atanacio-Serrano, Y; Romero-Pescador, P

2013-08-01

We studied the abundance of Brevipalpus spp. in citrus orchards in the Mexican states of Yucatan, Quintana Roo and Campeche. Mites were collected from 100 trees containing a mixture of citrus species where sweet orange was always the main species. Eight collections were made at each location from February 2010 to February 2011. Mites from the genus Brevipalpus were separated from other mites surveyed and their abundance and relationships with the different citrus species were quantified throughout the collection period. A subsample of 25% of the total Brevipalpus mites collected were identified to species level and the interaction of mite species and citrus species were described. Brevipalpus spp. were present on all collection dates and their relative abundance was similar on all citrus species studies. The smallest number of mites collected was during the rainy season. Brevipalpus phoenicis (Geijskes) and Brevipalpus californicus (Banks) were the only two species present and they were found in all locations except Campeche, where only B. phoenicis was present. Yucatan and Campeche are at greater risk of leprosis virus transmission than Quintana Roo because the main vector, B. phoenicis, was more abundant than B. californicus. The implications of our results for the design of more accurate sampling and control methods for Brevipalpus spp. are discussed.

The Species Problem and the Value of Teaching and the Complexities of Species

ERIC Educational Resources Information Center

Chung, Carl

2004-01-01

Discussions on species taxa directly refer to a range of complex biological phenomena. Given these phenomena, biologists have developed and continue to appeal to a series of species concepts and do not have a clear definition for it as each species concept tells us part of the story or helps the biologists to explain and understand a subset of…

Molecular species delimitation methods recover most song-delimited cicada species in the European Cicadetta montana complex.

PubMed

Wade, E J; Hertach, T; Gogala, M; Trilar, T; Simon, C

2015-12-01

Molecular species delimitation is increasingly being used to discover and illuminate species level diversity, and a number of methods have been developed. Here, we compare the ability of two molecular species delimitation methods to recover song-delimited species in the Cicadetta montana cryptic species complex throughout Europe. Recent bioacoustics studies of male calling songs (premating reproductive barriers) have revealed cryptic species diversity in this complex. Maximum likelihood and Bayesian phylogenetic analyses were used to analyse the mitochondrial genes COI and COII and the nuclear genes EF1α and period for thirteen European Cicadetta species as well as the closely related monotypic genus Euboeana. Two molecular species delimitation methods, general mixed Yule-coalescent (GMYC) and Bayesian phylogenetics and phylogeography, identified the majority of song-delimited species and were largely congruent with each other. None of the molecular delimitation methods were able to fully recover a recent radiation of four Greek species. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Eighteen new oleaginous yeast species.

PubMed

Garay, Luis A; Sitepu, Irnayuli R; Cajka, Tomas; Chandra, Idelia; Shi, Sandy; Lin, Ting; German, J Bruce; Fiehn, Oliver; Boundy-Mills, Kyria L

2016-07-01

Of 1600 known species of yeasts, about 70 are known to be oleaginous, defined as being able to accumulate over 20 % intracellular lipids. These yeasts have value for fundamental and applied research. A survey of yeasts from the Phaff Yeast Culture Collection, University of California Davis was performed to identify additional oleaginous species within the Basidiomycota phylum. Fifty-nine strains belonging to 34 species were grown in lipid inducing media, and total cell mass, lipid yield and triacylglycerol profiles were determined. Thirty-two species accumulated at least 20 % lipid and 25 species accumulated over 40 % lipid by dry weight. Eighteen of these species were not previously reported to be oleaginous. Triacylglycerol profiles were suitable for biodiesel production. These results greatly expand the number of known oleaginous yeast species, and reveal the wealth of natural diversity of triacylglycerol profiles within wild-type oleaginous Basidiomycetes.

Two new species of the Phanaeus endymion species group (Coleoptera, Scarabaeidae, Scarabaeinae)

PubMed Central

Moctezuma, Victor; Sánchez-Huerta, José Luis; Halffter, Gonzalo

2017-01-01

Abstract Phanaeus bravoensis sp. n. is described from the coniferous-oak forests in the state of Guerrero, and P. huichol sp. n. from coniferous-oak forests and cloud forests in Jalisco and Nayarit. The new species are closely related to P. halffterorum and P. zoque respectively. Morphological trait combination, geographic distribution, and trophic habits show important differences among the studied species. A distribution map and an updated key to separate the species are included. PMID:29118601

Phenotypic differentiation within a foundation grass species correlates with species richness in a subalpine community.

PubMed

Al Hayek, Patrick; Touzard, Blaise; Le Bagousse-Pinguet, Yoann; Michalet, Richard

2014-10-01

Few studies have examined consequences of ecotypic differentiation within alpine foundation species for community diversity and their feedbacks for the foundation species' fitness. Additionally, no study has quantified ecotypic differences in competitive effects in the field and in controlled conditions to disentangle genetic from plasticity effects in foundation/subordinate species interactions. We focused on a subalpine community of the French Pyrenees including two phenotypes of a cushion-forming species, Festuca gautieri: tight cushions in dry convex outcrops, and loose cushions (exhibiting high subordinate species richness) in wet concave slopes. We assessed, with field and shadehouse experiments, the genetic vs. plasticity basis of differences in: (1) cushion traits and (2) competitive effects on subordinates, and (3) quantified community feedbacks on foundation species' fitness. We found that trait differences across habitats had both genetic and plasticity bases, with stronger contribution of the latter. Field results showed higher competition within loose than tight phenotypes. In contrast, shadehouse results showed higher competitive ability for tight phenotypes. However, as changes in interactions across habitats were due to environmental effects without changes in cushion effects, we argue that heritable and plastic changes in competitive effects maintain high subordinate species diversity through decreasing competition. We showed high reproduction cost for loose cushions when hosting subordinates highlighting the occurrence of community feedbacks. These results suggest that phenotypic differentiation within foundation species may cascade on subordinate species diversity through heritable and plastic changes in the foundation species' competitive effects, and that community feedbacks may affect foundation species' fitness.

Novel angiotensin I-converting enzyme inhibitory peptides produced in fermented milk by specific wild Lactococcus lactis strains.

PubMed

Rodríguez-Figueroa, J C; González-Córdova, A F; Torres-Llanez, M J; Garcia, H S; Vallejo-Cordoba, B

2012-10-01

The ability of specific wild Lactococcus lactis strains to hydrolyze milk proteins to release angiotensin I-converting enzyme (ACE) inhibitory peptides was evaluated. The peptide profiles were obtained from the <3 kDa water-soluble extract and subsequently fractionated by reversed-phase HPLC. The fractions with the lowest half-maximal inhibitory concentration estimated values (peptide concentration necessary to inhibit ACE activity by 50%) were Lc. lactis NRRL B-50571 fraction (F)1 (0.034 ± 0.002 μg/mL; mean ± SD) and Lc. lactis NRRL B-50572B F 0005 (0.041 ± 0.003 μg/mL; mean ± SD). All peptide fractions were analyzed by reversed-phase HPLC tandem mass spectrometry. Twenty-one novel peptide sequences associated with ACE inhibitory (ACEI) activity were identified. Several novel ACEI peptides presented peptides encrypted with proven hypotensive activity. In conclusion, specific wild Lc. lactis strains were able to hydrolyze milk proteins to generate potent ACEI peptides. However, further studies are necessary to find out the relationship between Lc. lactis strain proteolytic systems and their ability to biogenerate hypotensive peptides. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

6-Methyl-1,2,4-benzenetriol, a new intermediate in penicillic acid biosynthesis in Penicillium cyclopium

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

Sekiguchi, J.; Katayama, S.; Yamada, Y.

1987-07-01

Penicillic acid-negative mutants were obtained from a color mutant derived from Penicillium cyclopium NRRL 1888 through N-methyl-N'-nitro-N-nitrosoguanidine treatment. One mutant (SK2N6) accumulated 6-methyl-1,2,4-benzenetriol, which was not previously known to be a metabolite of P. cyclopium, in addition to orsellinic acid and orcinol. The radioactivity of (1-/sup 14/C)acetic acid was rapidly incorporated into 6-methyl-1,2,4-benzenetriol in a culture of P. cyclopium SK2N6. Moreover, the radioactivity of (/sup 14/C)6-methyl-1,2,4-benzenetriol was efficiently incorporated into penicillic acid in a culture of P. cyclopium NRRL 1888. These data indicate that 6-methyl-1,2,4-benzenetriol is a precursor for penicillic acid biosynthesis. The results on the addition of 1,4-dihydroxy-6-methoxy-2-methylbenzene, 6-methoxy-2-methylbenzoquinonemore » (1,4), and 1-O-methylorcinol to a culture of P. cyclopium SK2N6 indicated that only the former two compounds are converted to penicillic acid. Thus, a new portion of the penicillic acid biosynthetic pathway is proposed.« less

Shelf life stability of lactobacilli encapsulated in raspberry powder: insights into non-dairy probiotics.

PubMed

Anekella, Kartheek; Orsat, Valérie

2014-06-01

Study the shelf-life quality changes in raspberry juice with encapsulated lactobacilli (Lactobacillus rhamnosus NRRL B-4495 and Lactobacillus acidophilus NRRL B-442) obtained by spray drying and understand the various factors involved. Raspberry powder was obtained from spray drying lactobacilli and raspberry juice with maltodextrin as an additive. Shelf life of the powder was analyzed over a period of 30 d. Acid and bile tolerance and antibiotic resistance was compared before and after spray drying. Water activity, survival, and scanning electron microscope images were also measured during the shelf life. A combination of processing conditions: inlet temperature (°C), maltodextrin to juice solids ratio and inlet feed rate (ml/min) during spray drying had a significant role on the survival of lactobacilli during shelf life. Refrigerated storage provided a higher shelf-life stability with regards to CFU/g (as high as 84% on day 0 and 98% retention by the end of 30 d) compared to room temperature storage. Probiotic properties during shelf life are affected by the processing conditions and encapsulated food matrix. Thus, understanding these aspects in vitro during shelf life gives us a brief insight into the future of non-dairy probiotics.

Optimization of high molecular weight pullulan production by Aureobasidium pullulans in batch fermentations.

PubMed

Gibson, Larry H; Coughlin, Robert W

2002-01-01

Of five strains of Aureobasidium pullulans studied, NRRL Y-2311-1 yielded the highest titer (26.2 g/L) of pullulan and formed the lowest amount of melanin-like pigment. Sucrose was superior to glucose as the carbon and energy source on the basis of yield and titer of pullulan produced. Pullulan titer was higher (26.2 vs 5.1 g/L), biomass concentration was lower (6.9 vs 12.7 g/L), and DO was lower (0 vs 60% of saturation) when the fermenter was agitated by a marine propeller compared to Rushton impellers. Pullulan produced by strain NRRL Y-2311-1 ranged in weight-average molar mass (M(w)) from 486 KDa and number-average molar mass (M(n)) from 220 Da on day 1 of growth to 390 KDa and 690 Da on day 6; M(w) declined by about 35% from day 1 to day 3, the day of maximum pullulan titer. For the other strains, the ranges of molar mass on the day of maximum pullulan titer were 338-614 KDa (M(w)) and 100-6820 Da (M(n)).

Production of xylitol by a Coniochaeta ligniaria strain tolerant of inhibitors and defective in growth on xylose.

PubMed

Nichols, Nancy N; Saha, Badal C

2016-05-01

In conversion of biomass to fuels or chemicals, inhibitory compounds arising from physical-chemical pretreatment of the feedstock can interfere with fermentation of the sugars to product. Fungal strain Coniochaeta ligniaria NRRL30616 metabolizes the furan aldehydes furfural and 5-hydroxymethylfurfural, as well as a number of aromatic and aliphatic acids and aldehydes. Use of NRRL30616 to condition biomass sugars by metabolizing the inhibitors improves their fermentability. Wild-type C. ligniaria has the ability to grow on xylose as sole source of carbon and energy, with no accumulation of xylitol. Mutants of C. ligniaria unable to grow on xylose were constructed. Xylose reductase and xylitol dehydrogenase activities were reduced by approximately two thirds in mutant C8100. The mutant retained ability to metabolize inhibitors in biomass hydrolysates. Although C. ligniaria C8100 did not grow on xylose, the strain converted a portion of xylose to xylitol, producing 0.59 g xylitol/g xylose in rich medium and 0.48 g xylitol/g xylose in corn stover dilute acid hydrolysate. 2016 American Institute of Chemical Engineers Biotechnol. Prog., 2016 © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:606-612, 2016. © 2016 American Institute of Chemical Engineers.

Growth, ethanol production, and inulinase activity on various inulin substrates by mutant kluyveromyces marxianus strains NRRL Y-50798 and NRRL Y-50799

USDA-ARS?s Scientific Manuscript database

Economically important plants contain large amounts of inulin. Disposal of waste resulting from their processing presents environmental issues. Finding microorganisms capable of converting inulin waste to biofuel and valuable co-products in a biorefinery at the processing site would have significant...

Growth, ethanol production, and inulinase activity on various inulin substrates by mutant Kluyveromyces marxianus strains NRRL Y-50798 and NRRL Y-50799.

PubMed

Galindo-Leva, Luz Ángela; Hughes, Stephen R; López-Núñez, Juan Carlos; Jarodsky, Joshua M; Erickson, Adam; Lindquist, Mitchell R; Cox, Elby J; Bischoff, Kenneth M; Hoecker, Eric C; Liu, Siqing; Qureshi, Nasib; Jones, Marjorie A

2016-07-01

Economically important plants contain large amounts of inulin. Disposal of waste resulting from their processing presents environmental issues. Finding microorganisms capable of converting inulin waste to biofuel and valuable co-products at the processing site would have significant economic and environmental impact. We evaluated the ability of two mutant strains of Kluyveromyces marxianus (Km7 and Km8) to utilize inulin for ethanol production. In glucose medium, both strains consumed all glucose and produced 0.40 g ethanol/g glucose at 24 h. In inulin medium, Km7 exhibited maximum colony forming units (CFU)/mL and produced 0.35 g ethanol/g inulin at 24 h, while Km8 showed maximum CFU/mL and produced 0.02 g ethanol/g inulin at 96 h. At 24 h in inulin + glucose medium, Km7 produced 0.40 g ethanol/g (inulin + glucose) and Km8 produced 0.20 g ethanol/g (inulin + glucose) with maximum CFU/mL for Km8 at 72 h, 40 % of that for Km7 at 36 h. Extracellular inulinase activity at 6 h for both Km7 and Km8 was 3.7 International Units (IU)/mL.

Introduced species as evolutionary traps

USGS Publications Warehouse

Schlaepfer, Martin A.; Sherman, P.W.; Blossey, B.; Runge, M.C.

2005-01-01

Invasive species can alter environments in such a way that normal behavioural decision-making rules of native species are no longer adaptive. The evolutionary trap concept provides a useful framework for predicting and managing the impact of harmful invasive species. We discuss how native species can respond to changes in their selective regime via evolution or learning. We also propose novel management strategies to promote the long-term co-existence of native and introduced species in cases where the eradication of the latter is either economically or biologically unrealistic.

Why some plant species are rare.

PubMed

Wieger Wamelink, G W; Wamelink, G W Weiger; Goedhart, Paul W; Frissel, Joep; Frissel, Josep Y

2014-01-01

Biodiversity, including plant species diversity, is threatened worldwide as a result of anthropogenic pressures such as an increase of pollutants and climate change. Rare species in particular are on the verge of becoming extinct. It is still unclear as to why some plant species are rare and others are not. Are they rare due to: intrinsic reasons, dispersal capacity, the effects of management or abiotic circumstances? Habitat preference of rare plant species may play an important role in determining why some species are rare. Based on an extensive data set of soil parameters we investigated if rarity is due to a narrow habitat preference for abiotic soil parameters. For 23 different abiotic soil parameters, of which the most influential were groundwater-table, soil-pH and nutrient-contents, we estimated species responses for common and rare species. Based on the responses per species we calculated the range of occurrence, the range between the 5 and 95 percentile of the response curve giving the habitat preference. Subsequently, we calculated the average response range for common and rare species. In addition, we designed a new graphic in order to provide a better means for presentation of the results. The habitat preferences of rare species for abiotic soil conditions are significantly narrower than for common species. Twenty of the twenty-three abiotic parameters showed on average significantly narrower habitat preferences for rare species than for common species; none of the abiotic parameters showed on average a narrower habitat preference for common species. The results have major implications for the conservation of rare plant species; accordingly management and nature development should be focussed on the maintenance and creation of a broad range of environmental conditions, so that the requirements of rare species are met. The conservation of (abiotic) gradients within ecosystems is particularly important for preserving rare species.

Species associations in a species-rich subtropical forest were not well-explained by stochastic geometry of biodiversity.

PubMed

Wang, Qinggang; Bao, Dachuan; Guo, Yili; Lu, Junmeng; Lu, Zhijun; Xu, Yaozhan; Zhang, Kuihan; Liu, Haibo; Meng, Hongjie; Jiang, Mingxi; Qiao, Xiujuan; Huang, Handong

2014-01-01

The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.

Species Associations in a Species-Rich Subtropical Forest Were Not Well-Explained by Stochastic Geometry of Biodiversity

PubMed Central

Wang, Qinggang; Bao, Dachuan; Guo, Yili; Lu, Junmeng; Lu, Zhijun; Xu, Yaozhan; Zhang, Kuihan; Liu, Haibo; Meng, Hongjie; Jiang, Mingxi; Qiao, Xiujuan; Huang, Handong

2014-01-01

The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure. PMID:24824996

Sexual species are separated by larger genetic gaps than asexual species in rotifers.

PubMed

Tang, Cuong Q; Obertegger, Ulrike; Fontaneto, Diego; Barraclough, Timothy G

2014-10-01

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra- and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Species pools, community completeness and invasion: disentangling diversity effects on the establishment of native and alien species.

PubMed

Bennett, Jonathan A; Riibak, Kersti; Kook, Ene; Reier, Ülle; Tamme, Riin; Guillermo Bueno, C; Pärtel, Meelis

2016-12-01

Invasion should decline with species richness, yet the relationship is inconsistent. Species richness, however, is a product of species pool size and biotic filtering. Invasion may increase with richness if large species pools represent weaker environmental filters. Measuring species pool size and the proportion realised locally (completeness) may clarify diversity-invasion relationships by separating environmental and biotic effects, especially if species' life-history stage and origin are accounted for. To test these relationships, we added seeds and transplants of 15 native and alien species into 29 grasslands. Species pool size and completeness explained more variation in invasion than richness alone. Although results varied between native and alien species, seed establishment and biotic resistance to transplants increased with species pool size, whereas transplant growth and biotic resistance to seeds increased with completeness. Consequently, species pools and completeness represent multiple independent processes affecting invasion; accounting for these processes improves our understanding of invasion. © 2016 John Wiley & Sons Ltd/CNRS.

Enzymatic degradation of oligosaccharides in pinto bean flour.

PubMed

Song, Danfeng; Chang, Sam K C

2006-02-22

The use of dry edible beans is limited due to the presence of flatulence factors, the raffinose oligosaccharides. Our objective was to investigate the process for the removal of oligosaccharides from pinto bean using enzymatic treatment and to compare it to removal by soaking and cooking methods. Crude enzyme preparation was produced by six fungal species on wheat bran- and okara-based substrates with soy tofu whey. The loss of raffinose oligosaccharides after soaking pinto beans for 16 h at the room temperature was 10%, after cooking for 90 min was 52%, and after autoclaving for 30 min was 58%. On the other hand, the treatment using crude alpha-galactosidase (60 U mL(-1)) produced by Aspergillus awamori NRRL 4869 from wheat bran-based substrate with soy tofu whey on pinto bean flour for 2 h completely hydrolyzed raffinose oligosaccharides. These results supported that the enzymatic treatment was the most effective among various processing methods tested for removing the raffinose oligosaccharides, and hence, crude alpha-galactosidases from fungi have potential use in the food industry.

Sympodiomycopsis lanaiensis sp. nov., a basidiomycetous yeast (Ustilaginomycotina: Microstromatales) from marine driftwood in Hawai‘i

PubMed Central

Mahdi, Leena E.; Statzell-Tallman, Adele; Fell, Jack W.; Brown, Mark V.; Donachie, Stuart P.

2009-01-01

A previously unknown basidiomycetous yeast is described for which the name Sympodiomycopsis lanaiensis is proposed. The type strain, LM418T, was isolated from driftwood collected on a beach on Lana‘i (Hawai‘i). On the basis of ribosomal DNA sequence analysis [large subunit (LSU), internal transcribed spacer (ITS) 1 & 2, and 18S], LM418T belongs to the order Microstromatales, which includes the genera Sympodiomycopsis, Rhodotorula, Microstroma, Volvocisporium and Quambalaria. The strain is described as a new species in the genus Sympodiomycopsis on the basis of morphological and physiological characteristics and the phylogenetic relationship to Sympodiomycopsis paphiopedili. Sexual reproduction was not observed in LM418T. GenBank accession numbers for nucleotide sequences of regions of the LSU, ITS and 18S regions of the ribosomal operon in LM418T are DQ990016, DQ990017 and DQ990018, respectively. LM418T has been deposited in the DSMZ as DSM 18755, in the ATCC as MYA-4092, in the Agricultural Research Service Culture Collection as NRRL Y-48466, and the Centraalbureau voor Schimmelcultures as CBS 10858. PMID:19054136

Putting the Biological Species Concept to the Test: Using Mating Networks to Delimit Species

PubMed Central

Lagache, Lélia; Leger, Jean-Benoist; Daudin, Jean-Jacques; Petit, Rémy J.; Vacher, Corinne

2013-01-01

Although interfertility is the key criterion upon which Mayr’s biological species concept is based, it has never been applied directly to delimit species under natural conditions. Our study fills this gap. We used the interfertility criterion to delimit two closely related oak species in a forest stand by analyzing the network of natural mating events between individuals. The results reveal two groups of interfertile individuals connected by only few mating events. These two groups were largely congruent with those determined using other criteria (morphological similarity, genotypic similarity and individual relatedness). Our study, therefore, shows that the analysis of mating networks is an effective method to delimit species based on the interfertility criterion, provided that adequate network data can be assembled. Our study also shows that although species boundaries are highly congruent across methods of species delimitation, they are not exactly the same. Most of the differences stem from assignment of individuals to an intermediate category. The discrepancies between methods may reflect a biological reality. Indeed, the interfertility criterion is an environment-dependant criterion as species abundances typically affect rates of hybridization under natural conditions. Thus, the methods of species delimitation based on the interfertility criterion are expected to give results slightly different from those based on environment-independent criteria (such as the genotypic similarity criteria). However, whatever the criterion chosen, the challenge we face when delimiting species is to summarize continuous but non-uniform variations in biological diversity. The grade of membership model that we use in this study appears as an appropriate tool. PMID:23818990

Species delimitation and biogeography of two fir species (Abies) in central China: cytoplasmic DNA variation.

PubMed

Wang, J; Abbott, R J; Peng, Y L; Du, F K; Liu, J-Q

2011-10-01

It remains unclear how speciation history might contribute to species-specific variation and affect species delimitation. We examined concordance between cytoplasmic genetic variation and morphological taxonomy in two fir species, Abies chensiensis and A. fargesii, with overlapping distributions in central China. Range-wide genetic variation was investigated using mitochondrial (mt) and plastid (pt) DNA sequences, which contrast in their rates of gene flow. Four mtDNA haplotypes were recovered and showed no obvious species' bias in terms of relative frequency. In contrast, a high level of ptDNA variation was recorded in both species with 3 common ptDNA haplotypes shared between them and 21 rare ptDNA haplotypes specific to one or other species. We argue that the lack of concordance between morphological and molecular variation between the two fir species most likely reflects extensive ancestral polymorphism sharing for both forms of cytoplasmic DNA variation. It is feasible that a relatively fast mutation rate for ptDNA contributed to the production of many species-specific ptDNA haplotypes, which remained rare due to insufficient time passing for their spread and fixation in either species, despite high levels of intraspecific ptDNA gene flow. Our phylogeographic analyses further suggest that polymorphisms in both organelle genomes most likely originated during and following glacial intervals preceding the last glacial maximum, when species distributions became fragmented into several refugia and then expanded in range across central China.

Rare Species (RS)

Treesearch

Steve Sutherland

2006-01-01

The FIREMON Rare Species (RS) method is used to assess changes in uncommon, perennial plant species when other monitoring methods are not effective. This method monitors individual plants and statistically quantifies changes in plant survivorship, growth, and reproduction over time. Plants are spatially located using distance along and from a permanent baseline, and...

No longer a circumtropical species: revision of the lizardfishes in the Trachinocephalus myops species complex, with description of a new species from the Marquesas Islands.

PubMed

Polanco F, A; Acero P, A; Betancur-R, R

2016-08-01

Trachinocephalus, a formerly monotypic and nearly circumtropical genus of lizardfishes, is split into three valid species. Trachinocephalus gauguini n. sp. is described from the Marquesas Islands and is distinguished from the two other species in the genus by having a shorter snout, a narrower interorbital space, larger eye and modally fewer anal-fin and pectoral-fin rays. The distribution of Trachinocephalus myops (type species) is restricted to the Atlantic Ocean and the name Trachinocephalus trachinus is resurrected for populations from the Indo-West Pacific Ocean. Principal component analyses and bivariate plots based on the morphometric data differentiated T. gauguini from the other two species, but a substantial overlap between T. myops and T. trachinus exists. Phylogenetic evidence based on mtDNA COI sequences unambiguously supports the recognition of at least three species in Trachinocephalus, revealing deep divergences between the Atlantic Ocean, Indo-West Pacific Ocean and Marquesas entities. Additional analyses of species delimitations using the generalized mixed Yule coalescent model and the Poisson tree processes model provide a more liberal assessment of species in Trachinocephalus, indicating that many more cryptic species may exist. Finally, a taxonomic key to identify the three species recognized here is provided. © 2016 The Fisheries Society of the British Isles.

Inference methods for spatial variation in species richness and community composition when not all species are detected

USGS Publications Warehouse

Nichols, J.D.; Boulinier, T.; Hines, J.E.; Pollock, K.H.; Sauer, J.R.

1998-01-01

Inferences about spatial variation in species richness and community composition are important both to ecological hypotheses about the structure and function of communities and to community-level conservation and management. Few sampling programs for animal communities provide censuses, and usually some species present. We present estimators useful for drawing inferences about comparative species richness and composition between different sampling locations when not all species are detected in sampling efforts. Based on capture-recapture models using the robust design, our methods estimate relative species richness, proportion of species in one location that are also found in another, and number of species found in one location but not in another. The methods use data on the presence or absence of each species at different sampling occasions (or locations) to estimate the number of species not detected at any occasions (or locations). This approach permits estimation of the number of species in the sampled community and in subsets of the community useful for estimating the fraction of species shared by two communities. We provide an illustration of our estimation methods by comparing bird species richness and composition in two locations sampled by routes of the North American Breeding Bird Survey. In this example analysis, the two locations (an associated bird communities) represented different levels of urbanization. Estimates of relative richness, proportion of shared species, and number of species present on one route but not the other indicated that the route with the smaller fraction of urban area had greater richness and a larer number of species that were not found on the more urban route than vice versa. We developed a software package, COMDYN, for computing estimates based on the methods. Because these estimation methods explicitly deal with sampling in which not all species are detected, we recommend their use for addressing questions about species

Seed dormancy in alpine species

PubMed Central

Schwienbacher, Erich; Navarro-Cano, Jose Antonio; Neuner, Gilbert; Erschbamer, Brigitta

2011-01-01

In alpine species the classification of the various mechanisms underlying seed dormancy has been rather questionable and controversial. Thus, we investigated 28 alpine species to evaluate the prevailing types of dormancy. Embryo type and water impermeability of seed coats gave an indication of the potential seed dormancy class. To ascertain the actual dormancy class and level, we performed germination experiments comparing the behavior of seeds without storage, after cold-dry storage, after cold-wet storage, and scarification. We also tested the light requirement for germination in some species. Germination behavior was characterized using the final germination percentage and the mean germination time. Considering the effects of the pretreatments, a refined classification of the prevailing dormancy types was constructed based on the results of our pretreatments. Only two out of the 28 species that we evaluated had predominantly non-dormant seeds. Physiological dormancy was prevalent in 20 species, with deep physiological dormancy being the most abundant, followed by non-deep and intermediate physiological dormancy. Seeds of four species with underdeveloped embryos were assigned to the morphophysiologial dormancy class. An impermeable seed coat was identified in two species, with no additional physiological germination block. We defined these species as having physical dormancy. Light promoted the germination of seeds without storage in all but one species with physiological dormancy. In species with physical dormancy, light responses were of minor importance. We discuss our new classification in the context of former germination studies and draw implications for the timing of germination in the field. PMID:24415831

Previously unknown species of Aspergillus.

PubMed

Gautier, M; Normand, A-C; Ranque, S

2016-08-01

The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care. Copyright © 2016 European Society of Clinical Microbiology and

Revision of the western Palaearctic species of Aleiodes Wesmael (Hymenoptera, Braconidae, Rogadinae). Part 1: Introduction, key to species groups, outlying distinctive species, and revisionary notes on some further species

PubMed Central

van Achterberg, Cornelis; Shaw, Mark R.

2016-01-01

Abstract Seven new species of the genus Aleiodes Wesmael, 1838 (Braconidae: Rogadinae) are described and illustrated: Aleiodes abraxanae sp. n., Aleiodes angustipterus sp. n., Aleiodes artesiariae sp. n., Aleiodes carminatus sp. n., Aleiodes diarsianae sp. n., Aleiodes leptofemur sp. n., and Aleiodes ryrholmi sp. n. A neotype is designated for each of Aleiodes circumscriptus (Nees, 1834) and Aleiodes pictus (Herrich-Schäffer, 1838), and both species are redescribed and illustrated. Aleiodes ochraceus Hellén, 1927 (not Aleiodes ochraceus (Curtis, 1834)) is renamed as Aleiodes curticornis nom. n. & stat. rev., and redescribed and illustrated. Aleiodes bistrigatus Roman, 1917, Aleiodes nigriceps Wesmael, 1838, and Aleiodes reticulatus (Noskiewicz, 1956), are re-instated as valid species. A lectotype is designated for Aleiodes bistrigatus Roman. An illustrated key is given to some distinctive species and the residual species groups along which further parts of an entire revision of western Palaearctic species of Aleiodes and Heterogamus will be organised. Biology, host associations and phenology are discussed for the keyed species (in addition to the above, Aleiodes albitibia (Herrich-Schäffer, 1838), Aleiodes apiculatus (Fahringer, 1932), Aleiodes arcticus (Thomson, 1892), Aleiodes cantherius (Lyle, 1919), Aleiodes esenbeckii (Hartig, 1834), Aleiodes jakowlewi (Kokujev, 1898), Aleiodes modestus (Reinhard, 1863), Aleiodes nigricornis Wesmael, 1838, Aleiodes pallidator (Thunberg, 1822), Aleiodes praetor (Reinhard, 1863), Aleiodes seriatus (Herrich- Schäffer, 1838) sensu lato, Aleiodes testaceus (Telenga, 1941), Aleiodes ungularis (Thomson, 1892), and Aleiodes varius (Herrich-Schäffer, 1838)) which are dealt with in full here (with the exception of Aleiodes seriatus s.l. which is, however, included in the key). The experimental methodology covering the revision as a whole, which involves some behavioural investigation, is outlined. PMID:28138281

Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae).

PubMed

Grummer, Jared A; Bryson, Robert W; Reeder, Tod W

2014-03-01

Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal-likelihood scores of competing species delimitation models, from which Bayes factor values were compared, were estimated with four different methods: harmonic mean estimation (HME), smoothed harmonic mean estimation (sHME), path-sampling/thermodynamic integration (PS), and stepping-stone (SS) analysis. We also performed model selection using a posterior simulation-based analog of the Akaike information criterion through Markov chain Monte Carlo analysis (AICM). Bayes factor species delimitation results from the empirical data were then compared with results from the reversible-jump MCMC (rjMCMC) coalescent-based species delimitation method Bayesian Phylogenetics and Phylogeography (BP&P). Simulation results show that HME and sHME perform poorly compared with PS and SS marginal-likelihood estimators when identifying the true species delimitation model. Furthermore, Bayes factor delimitation (BFD) of species showed improved performance when species limits are tested by reassigning individuals between species, as opposed to either lumping or splitting lineages. In the empirical data, BFD through PS and SS analyses, as well as the rjMCMC method, each provide support for the recognition of all scalaris group taxa as independent evolutionary lineages. Bayes factor species delimitation and BP&P also support the recognition of three previously undescribed lineages. In both simulated and empirical data sets, harmonic and smoothed harmonic mean marginal-likelihood estimators provided much higher marginal-likelihood estimates

Species coextinctions and the biodiversity crisis.

PubMed

Koh, Lian Pin; Dunn, Robert R; Sodhi, Navjot S; Colwell, Robert K; Proctor, Heather C; Smith, Vincent S

2004-09-10

To assess the coextinction of species (the loss of a species upon the loss of another), we present a probabilistic model, scaled with empirical data. The model examines the relationship between coextinction levels (proportion of species extinct) of affiliates and their hosts across a wide range of coevolved interspecific systems: pollinating Ficus wasps and Ficus, parasites and their hosts, butterflies and their larval host plants, and ant butterflies and their host ants. Applying a nomographic method based on mean host specificity (number of host species per affiliate species), we estimate that 6300 affiliate species are "coendangered" with host species currently listed as endangered. Current extinction estimates need to be recalibrated by taking species coextinctions into account.

Cerebellar Abiotrophy Across Domestic Species.

PubMed

Scott, Erica Yuki; Woolard, Kevin Douglas; Finno, Carrie J; Murray, James D

2018-06-01

Cerebellar abiotrophy (CA) is a neurodegenerative disorder affecting the cerebellum and occurs in multiple species. Although CA is well researched in humans and mice, domestic species such as the dog, cat, sheep, cow, and horse receive little recognition. This may be due to few studies addressing the mechanism of CA in these species. However, valuable information can still be extracted from these cases. A review of the clinicohistologic phenotype of CA in these species and determining the various etiologies of CA may aid in determining conserved and required pathways necessary for proper cerebellar development and function. This review outlines research approaches of studies of CA in domestic species, compared to the approaches used in mice, with the objective of comparing CA in domestic species while identifying areas for further research efforts.

Reproductive Impacts of Endocrine-Disrupting Chemicals on Wildlife Species: Implications for Conservation of Endangered Species.

PubMed

Tubbs, Christopher W; McDonough, Caitlin E

2018-02-15

Wildlife have proven valuable to our understanding of the potential effects of endocrine-disrupting chemicals (EDCs) on human health by contributing considerably to our understanding of the mechanisms and consequences of EDC exposure. But the threats EDCs present to populations of wildlife species themselves are significant, particularly for endangered species whose existence is vulnerable to any reproductive perturbation. However, few studies address the threats EDCs pose to endangered species owing to challenges associated with their study. Here, we highlight those barriers and review the available literature concerning EDC effects on endangered species. Drawing from other investigations into nonthreatened wildlife species, we highlight opportunities for new approaches to advance our understanding and potentially mitigate the effects of EDCs on endangered species to enhance their fertility.

The Neotropical species of Atractodes (Hymenoptera, Ichneumonidae, Cryptinae), I: the A. propodeator and A. altoandinus species-groups.

PubMed

Bordera, Santiago; Mazón, Marina; Sääksjärvi, Ilari E

2016-07-08

The Neotropical species of the cryptine genus Atractodes are studied, and four species-groups are proposed. In this paper, A. altoandinus and A. propodeator species-groups are diagnosed. The former species-group occurs from southern Mexico to Brazil and includes some of the largest Atractodes species ever found, all possessing a strongly sloped propodeum; the latter species-group is only known from the Chilean Andes and includes one of the smallest species of Atractodes, characterised by a very short and curved tergite I and short first flagellomere. Four species, A. altoandinus, A. propodeator, A. reijoi and A. verapacensis are described as new. An illustrated identification key to all species-groups and to species of the A. propodeator species-group is provided.

Ecological impacts of non-native species

USGS Publications Warehouse

Wilkinson, John W.

2012-01-01

Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae).

PubMed

Šašić, Ljiljana; Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods).

On the Domene species of China, with descriptions of four new species (Coleoptera, Staphylinidae).

PubMed

Feldmann, Benedikt; Peng, Zhong; Li, Li-Zhen

2014-01-01

Material of the paederine genus Domene Fauvel, 1873 from China is examined. Nine species were identified, four of them described previously, one unnamed (represented exclusively by females), and four are newly described: Domenecultrata sp. n. (Gansu, Hubei, Shaanxi); Domenecuspidata sp. n. (Gansu, Shaanxi, Sichuan); Domenechenae sp. n. (Guangxi); Domenereducta sp. n. (Sichuan). A lectotype is designated for Domenereitteri Koch, 1939; a neotype is designated for Domenechenpengi Li, 1990. Domenedersuuzalai Gusarov, 1992 is placed in synonymy with Domenechenpengi. Previous records of two Japanese species from China are most likely based on misidentifications and considered erroneous. Thus, the Domene fauna of China is currently composed of twelve described species. A key to the Domene species of China is provided. The distributions of eleven species are mapped.

Seasonal species interactions minimize the impact of species turnover on the likelihood of community persistence.

PubMed

Saavedra, Serguei; Rohr, Rudolf P; Fortuna, Miguel A; Selva, Nuria; Bascompte, Jordi

2016-04-01

Many of the observed species interactions embedded in ecological communities are not permanent, but are characterized by temporal changes that are observed along with abiotic and biotic variations. While work has been done describing and quantifying these changes, little is known about their consequences for species coexistence. Here, we investigate the extent to which changes of species composition impact the likelihood of persistence of the predator-prey community in the highly seasonal Białowieza Primeval Forest (northeast Poland), and the extent to which seasonal changes of species interactions (predator diet) modulate the expected impact. This likelihood is estimated extending recent developments on the study of structural stability in ecological communities. We find that the observed species turnover strongly varies the likelihood of community persistence between summer and winter. Importantly, we demonstrate that the observed seasonal interaction changes minimize the variation in the likelihood of persistence associated with species turnover across the year. We find that these community dynamics can be explained as the coupling of individual species to their environment by minimizing both the variation in persistence conditions and the interaction changes between seasons. Our results provide a homeostatic explanation for seasonal species interactions and suggest that monitoring the association of interactions changes with the level of variation in community dynamics can provide a good indicator of the response of species to environmental pressures.

Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers.

PubMed

Zhang, Defang; Xia, Tao; Yan, Maomao; Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

2014-01-01

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.

Two new species of nocturnal bees of the genus Megalopta (Hymenoptera: Halictidae) with keys to species.

PubMed

Gonzalez, Victor H; Griswold, Terry; Ayala, Ricardo

2010-03-01

Megalopta Smith, 1853, is a Neotropical genus of nocturnal or crepuscular bees. Two subgenera are recognized with most of its nearly 30 species placed in the nominate subgenus. Species of Megalopta s. str. are more commonly collected than species of Noctoraptor Engel et al. 1997, all presumably parasites of Megalopta s. str. Two new species of Megalopta are described here: M. (Megalopta) tetewana, n. sp., from Mexico and M. (Noctoraptor) huaoranii, n. sp., from Ecuador. Identification keys to the Central American species of Megalopta s. str. and the species of the parasitic subgenus Noctoraptor are presented.

A new species of Labidocera (Copepoda, Calanoida, Pontellidae) collected from Okinawa, southwestern Japan, with establishment of five Indo-West Pacific species groups in the L.detruncata species complex.

PubMed

Hirabayashi, Takeshi; Ohtsuka, Susumu

2014-01-01

Labidocerachuraumi sp. n. is described from Okinawa, southwestern Japan. The female of the new species differs from other congeners in genital compound somite with right postero-lateral and left antero-lateral processes. The male is distinguished from other congeners by the structure of the fifth leg. This new species is assigned to a newly proposed species group, the Labidoceramadurae species group, within the Labidoceradetruncata species complex. In this species complex five Indo-West Pacific species groups are recognized (cervi, detruncata, gangetica, madurae, and pavo) and defined on the basis of difference in sexual dimorphism.

78 FR 12702 - Endangered and Threatened Species; Proposed Rule To List 66 Reef-Building Coral Species; Proposed...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-25

... Endangered Species Act (ESA); Extension of Public Comment Period and Notice of Public Hearing AGENCY... RIN 0648-XT12 Endangered and Threatened Species; Proposed Rule To List 66 Reef- Building Coral Species... species as threatened or endangered under the ESA. We concluded that 12 of the petitioned coral species...

Bias correction in species distribution models: pooling survey and collection data for multiple species

PubMed Central

Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A.

2016-01-01

Summary Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence–absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence–absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model’s performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence–absence data for a given species is scarceIf we have only presence-only data and no presence–absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species’ geographic range. PMID:27840673

An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.

PubMed

Suatoni, Elizabeth; Vicario, Saverio; Rice, Sean; Snell, Terry; Caccone, Adalgisa

2006-10-01

Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.

Defining species-specific immunodominant B cell epitopes for molecular serology of Chlamydia species.

PubMed

Rahman, K Shamsur; Chowdhury, Erfan U; Poudel, Anil; Ruettger, Anke; Sachse, Konrad; Kaltenboeck, Bernhard

2015-05-01

Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Defining Species-Specific Immunodominant B Cell Epitopes for Molecular Serology of Chlamydia Species

PubMed Central

Rahman, K. Shamsur; Chowdhury, Erfan U.; Poudel, Anil; Ruettger, Anke; Sachse, Konrad

2015-01-01

Urgently needed species-specific enzyme-linked immunosorbent assays (ELISAs) for the detection of antibodies against Chlamydia spp. have been elusive due to high cross-reactivity of chlamydial antigens. To identify Chlamydia species-specific B cell epitopes for such assays, we ranked the potential epitopes of immunodominant chlamydial proteins that are polymorphic among all Chlamydia species. High-scoring peptides were synthesized with N-terminal biotin, followed by a serine-glycine-serine-glycine spacer, immobilized onto streptavidin-coated microtiter plates, and tested with mono-specific mouse hyperimmune sera against each Chlamydia species in chemiluminescent ELISAs. For each of nine Chlamydia species, three to nine dominant polymorphic B cell epitope regions were identified on OmpA, CT618, PmpD, IncA, CT529, CT442, IncG, Omp2, TarP, and IncE proteins. Peptides corresponding to 16- to 40-amino-acid species-specific sequences of these epitopes reacted highly and with absolute specificity with homologous, but not heterologous, Chlamydia monospecies-specific sera. Host-independent reactivity of such epitopes was confirmed by testing of six C. pecorum-specific peptides from five proteins with C. pecorum-reactive sera from cattle, the natural host of C. pecorum. The probability of cross-reactivity of peptide antigens from closely related chlamydial species or strains correlated with percent sequence identity and declined to zero at <50% sequence identity. Thus, phylograms of B cell epitope regions predict the specificity of peptide antigens for rational use in the genus-, species-, or serovar-specific molecular serology of Chlamydia spp. We anticipate that these peptide antigens will improve chlamydial serology by providing easily accessible assays to nonspecialist laboratories. Our approach also lends itself to the identification of relevant epitopes of other microbial pathogens. PMID:25761461

Species diversity and predation strategies in a multiple species predator-prey model

NASA Astrophysics Data System (ADS)

Mullan, Rory; Glass, David H.; McCartney, Mark

2015-08-01

A single predator, single prey ecological model, in which the behaviour of the populations relies upon two control parameters has been expanded to allow for multiple predators and prey to occupy the ecosystem. The diversity of the ecosystem that develops as the model runs is analysed by assessing how many predator or prey species survive. Predation strategies that dictate how the predators distribute their efforts across the prey are introduced in this multiple species model. The paper analyses various predation strategies and highlights their effect on the survival of the predators and prey species.

Drought responses by individual tree species are not often correlated with tree species diversity in European forests

DOE PAGES

Forrester, David I.; Bonal, Damien; Dawud, Seid; ...

2016-07-26

Drought frequency and intensity are predicted to increase in many parts of the Northern Hemisphere and the effects of such changes on forest growth and tree mortality are already evident in many regions around the world. Mixed-species forests and increasing tree species diversity have been put forward as important risk reduction and adaptation strategies in the face of climate change. But, little is known about whether the species interactions that occur in diverse forests will reduce drought susceptibility or water stress. In this study, we focused on the effect of drought on individual tree species (n = 16) within sixmore » regions of Europe and assessed whether this response was related to tree species diversity and stand density, and whether community-level responses resulted from many similar or contrasting species-level responses. For each species in each plot, we calculated the increase in carbon isotope composition of latewood from a wet to a dry year (Δδ13C) as an estimate of its drought stress level. Furthermore, when significant community-level relationships occurred (three of six regions), there was only one species within the given community that showed a significant relationship (three of 25 species–region combinations), showing that information about a single species can be a poor indicator of the response of other species or the whole community. There were many two-species mixtures in which both species were less water-stressed compared with their monocultures, but also many mixtures where both species were more stressed compared with their monocultures. Furthermore, a given species combination responded differently in different regions. Synthesis and applications. Our study shows that drought stress may sometimes be reduced in mixed-species forests, but this is not a general pattern, and even varies between sites for a given combination. The management or prediction of drought stress requires consideration of the physiological characteristics

Drought responses by individual tree species are not often correlated with tree species diversity in European forests

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

Forrester, David I.; Bonal, Damien; Dawud, Seid

Drought frequency and intensity are predicted to increase in many parts of the Northern Hemisphere and the effects of such changes on forest growth and tree mortality are already evident in many regions around the world. Mixed-species forests and increasing tree species diversity have been put forward as important risk reduction and adaptation strategies in the face of climate change. But, little is known about whether the species interactions that occur in diverse forests will reduce drought susceptibility or water stress. In this study, we focused on the effect of drought on individual tree species (n = 16) within sixmore » regions of Europe and assessed whether this response was related to tree species diversity and stand density, and whether community-level responses resulted from many similar or contrasting species-level responses. For each species in each plot, we calculated the increase in carbon isotope composition of latewood from a wet to a dry year (Δδ13C) as an estimate of its drought stress level. Furthermore, when significant community-level relationships occurred (three of six regions), there was only one species within the given community that showed a significant relationship (three of 25 species–region combinations), showing that information about a single species can be a poor indicator of the response of other species or the whole community. There were many two-species mixtures in which both species were less water-stressed compared with their monocultures, but also many mixtures where both species were more stressed compared with their monocultures. Furthermore, a given species combination responded differently in different regions. Synthesis and applications. Our study shows that drought stress may sometimes be reduced in mixed-species forests, but this is not a general pattern, and even varies between sites for a given combination. The management or prediction of drought stress requires consideration of the physiological characteristics

ARSENIC SPECIES CAUSE RELEASE OF IRON FROM FERRITIN GENERATING REACTIVE OXYGEN SPECIES

EPA Science Inventory

ARSENIC SPECIES CAUSE RELEASE OF IRON FROM FERRITIN GENERATING REACTIVE OXYGEN SPECIES

Arsenic-associated cancer (lung, bladder, skin, liver, kidney) remains a significant world- wide public health problem (e.g., Taiwan, Chile, Bangladesh, India, China and Thailand). Rece...

ARSENIC SPECIES CAUSE RELEASE OF IRON FROM FERRITIN GENERATING REACTIVIE OXYGEN SPECIES

EPA Science Inventory

ARSENIC SPECIES. CAUSE RELEASE OF IRON , FROM FERRITIN GENERATING REACTIVE OXYGEN SPECIES

Arsenic-associated cancer (lung, bladder, skin, liver, kidney) remains a significant world- wide public health problem (e.g., Taiwan, Chile, Bangladesh, India, China and Thailand). R...

Estimating species-specific suvival and movement when species identification is uncertain

USGS Publications Warehouse

Runge, J.P.; Hines, J.E.; Nichols, J.D.

2007-01-01

Incorporating uncertainty in the investigation of ecological studies has been the topic of an increasing body of research. In particular, mark?recapture methodology has shown that incorporating uncertainty in the probability of detecting individuals in populations enables accurate estimation of population-level processes such as survival, reproduction, and dispersal. Recent advances in mark?recapture methodology have included estimating population-level processes for biologically important groups despite the misassignment of individuals to those groups. Examples include estimating rates of apparent survival despite less than perfect accuracy when identifying individuals to gender or breeding state. Here we introduce a method for estimating apparent survival and dispersal in species that co-occur but that are difficult to distinguish. We use data from co-occurring populations of meadow voles (Microtus pennsylvanicus) and montane voles (M. montanus) in addition to simulated data to show that ignoring species uncertainty can lead to biased estimates of population processes. The incorporation of species uncertainty in mark?recapture studies should aid future research investigating ecological concepts such as interspecific competition, niche differentiation, and spatial population dynamics in sibling species.

On the Domene species of China, with descriptions of four new species (Coleoptera, Staphylinidae)

PubMed Central

Feldmann, Benedikt; Peng, Zhong; Li, Li-Zhen

2014-01-01

Abstract Material of the paederine genus Domene Fauvel, 1873 from China is examined. Nine species were identified, four of them described previously, one unnamed (represented exclusively by females), and four are newly described: Domene cultrata sp. n. (Gansu, Hubei, Shaanxi); Domene cuspidata sp. n. (Gansu, Shaanxi, Sichuan); Domene chenae sp. n. (Guangxi); Domene reducta sp. n. (Sichuan). A lectotype is designated for Domene reitteri Koch, 1939; a neotype is designated for Domene chenpengi Li, 1990. Domene dersuuzalai Gusarov, 1992 is placed in synonymy with Domene chenpengi. Previous records of two Japanese species from China are most likely based on misidentifications and considered erroneous. Thus, the Domene fauna of China is currently composed of twelve described species. A key to the Domene species of China is provided. The distributions of eleven species are mapped. PMID:25709524

Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae)

PubMed Central

Ačanski, Jelena; Vujić, Ante; Ståhls, Gunilla; Radenković, Snežana; Milić, Dubravka; Obreht Vidaković, Dragana; Đan, Mihajla

2016-01-01

The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods). PMID:27532618

Species Delimitation and Global Biosecurity

PubMed Central

Boykin, Laura M.; Armstrong, Karen F.; Kubatko, Laura; De Barro, Paul

2012-01-01

Species delimitation directly impacts on global biosecurity. It is a critical element in the decisions made by national governments in regard to the flow of trade and to the biosecurity measures imposed to protect countries from the threat of invasive species. Here we outline a novel approach to species delimitation, “tip to root”, for two highly invasive insect pests, Bemisia tabaci (sweetpotato whitefly) and Lymantria dispar (Asian gypsy moth). Both species are of concern to biosecurity, but illustrate the extremes of phylogenetic resolution that present the most complex delimitation issues for biosecurity; B. tabaci having extremely high intra-specific genetic variability and L. dispar composed of relatively indistinct subspecies. This study tests a series of analytical options to determine their applicability as tools to provide more rigorous species delimitation measures and consequently more defensible species assignments and identification of unknowns for biosecurity. Data from established DNA barcode datasets (COI), which are becoming increasingly considered for adoption in biosecurity, were used here as an example. The analytical approaches included the commonly used Kimura two-parameter (K2P) inter-species distance plus four more stringent measures of taxon distinctiveness, (1) Rosenberg’s reciprocal monophyly, (P(AB)),1 (2) Rodrigo’s (P(randomly distinct)),2 (3) genealogical sorting index, (gsi),3 and (4) General mixed Yule-coalescent (GMYC).4,5 For both insect datasets, a comparative analysis of the methods revealed that the K2P distance method does not capture the same level of species distinctiveness revealed by the other three measures; in B. tabaci there are more distinct groups than previously identified using the K2P distances and for L. dipsar far less variation is apparent within the predefined subspecies. A consensus for the results from P(AB), P(randomly distinct) and gsi offers greater statistical confidence as to where genetic limits

A new species of Labidocera (Copepoda, Calanoida, Pontellidae) collected from Okinawa, southwestern Japan, with establishment of five Indo-West Pacific species groups in the L. detruncata species complex

PubMed Central

Hirabayashi, Takeshi; Ohtsuka, Susumu

2014-01-01

Abstract Labidocera churaumi sp. n. is described from Okinawa, southwestern Japan. The female of the new species differs from other congeners in genital compound somite with right postero-lateral and left antero-lateral processes. The male is distinguished from other congeners by the structure of the fifth leg. This new species is assigned to a newly proposed species group, the Labidocera madurae species group, within the Labidocera detruncata species complex. In this species complex five Indo-West Pacific species groups are recognized (cervi, detruncata, gangetica, madurae, and pavo) and defined on the basis of difference in sexual dimorphism. PMID:25349514

Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China

PubMed Central

Zheng, Honglei; Fan, Liqiang; Milne, Richard I.; Zhang, Lei; Wang, Yaling; Mao, Kangshan

2017-01-01

Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to detect and test genetic clustering, morphological and habitat differentiation, and gene flow between/among putative species. The nSSR data and ENM suggested that there are two separately evolving meta-population lineages that correspond to P. davidiana (pd) and P. rotundifolia (pr). Furthermore, several lines of evidence supported a subdivision of P. davidiana into Northeastern (NEC) and Central-North (CNC) groups, yet they are still functioning as one species. CpDNA data revealed that five haplotype clades formed a pattern of [pdNEC, ((pdCNC, pr), (pdCNC, pr))], but most haplotypes are species-specific. Meanwhile, PCA based on morphology suggested a closer relationship between the CNC group (P. davidiana) and P. rontundifolia. Discrepancy of nSSR and ENM vs. cpDNA and morphology could have reflected a complex lineage divergence and convergence history. P. davidiana and P. rotundifolia can be regarded as a recently diverged species pair that experienced parapatric speciation due to ecological differentiation in the face of gene flow. Our findings highlight the importance of integrative surveys at population level, as we have undertaken, is an important approach to detect the boundary of a group of species that have experienced complex evolutionary

Evaluation of Central North American prairie management based on species diversity, life form, and individual species metrics.

PubMed

Brudvig, Lars A; Mabry, Catherine M; Miller, James R; Walker, Tracy A

2007-06-01

Reintroduction of fire and grazing, alone or in combination, has increasingly been recognized as central to the restoration of North American mixed-grass and tallgrass prairies. Although ecological studies of these systems are abundant, they have generally been observational, or if experimental, have focused on plant species diversity. Species diversity measures alone are not sufficient to inform management, which often has goals associated with life-form groups and individual species. We examined the effects of prescribed fire, light cattle grazing, and a combination of fire and grazing on three vegetation components: species diversity, groups of species categorized by life-form, and individual species. We evaluated how successful these three treatments were in achieving specific management goals for prairies in the Iowa Loess Hills (U.S.A.). The grazing treatment promoted the greatest overall species richness, whereas grazing and burning and grazing treatments resulted in the lowest cover by woody species. Burning alone best achieved the management goals of increasing the cover and diversity of native species and reducing exotic forb and (predominantly exotic) cool-season grass cover. Species-specific responses to treatments appeared idiosyncratic (i.e., within each treatment there existed a set of species attaining their highest frequency) and nearly half of uncommon species were present in only one treatment. Because all management goals were not achieved by any one treatment, we conclude that management in this region may need refining. We suggest that a mosaic of burning and grazing (alone and in combination) may provide the greatest landscape-level species richness; however, this strategy would also likely promote the persistence of exotic species. Our results support the need to consider multiple measures, including species-specific responses, when planning and evaluating management.

50 CFR 15.31 - Criteria for including species in the approved list for captive-bred species.

Code of Federal Regulations, 2012 CFR

2012-10-01

... approved list for captive-bred species. 15.31 Section 15.31 Wildlife and Fisheries UNITED STATES FISH AND..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Approved List of Species Listed... captive-bred species. The Director will periodically review the list of captive-bred exotic bird species...

50 CFR 15.31 - Criteria for including species in the approved list for captive-bred species.

Code of Federal Regulations, 2014 CFR

2014-10-01

... approved list for captive-bred species. 15.31 Section 15.31 Wildlife and Fisheries UNITED STATES FISH AND..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Approved List of Species Listed... captive-bred species. The Director will periodically review the list of captive-bred exotic bird species...

50 CFR 15.31 - Criteria for including species in the approved list for captive-bred species.

Code of Federal Regulations, 2011 CFR

2011-10-01

... approved list for captive-bred species. 15.31 Section 15.31 Wildlife and Fisheries UNITED STATES FISH AND..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Approved List of Species Listed... captive-bred species. The Director will periodically review the list of captive-bred exotic bird species...

50 CFR 15.31 - Criteria for including species in the approved list for captive-bred species.

Code of Federal Regulations, 2013 CFR

2013-10-01

... approved list for captive-bred species. 15.31 Section 15.31 Wildlife and Fisheries UNITED STATES FISH AND..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Approved List of Species Listed... captive-bred species. The Director will periodically review the list of captive-bred exotic bird species...

50 CFR 15.31 - Criteria for including species in the approved list for captive-bred species.

Code of Federal Regulations, 2010 CFR

2010-10-01

... approved list for captive-bred species. 15.31 Section 15.31 Wildlife and Fisheries UNITED STATES FISH AND..., EXPORTATION, AND IMPORTATION OF WILDLIFE AND PLANTS WILD BIRD CONSERVATION ACT Approved List of Species Listed... captive-bred species. The Director will periodically review the list of captive-bred exotic bird species...

CpDNA-based species identification and phylogeography: application to African tropical tree species.

PubMed

Duminil, J; Heuertz, M; Doucet, J-L; Bourland, N; Cruaud, C; Gavory, F; Doumenge, C; Navascués, M; Hardy, O J

2010-12-01

Despite the importance of the African tropical rainforests as a hotspot of biodiversity, their history and the processes that have structured their biodiversity are understood poorly. With respect to past demographic processes, new insights can be gained through characterizing the distribution of genetic diversity. However, few studies of this type have been conducted in Central Africa, where the identification of species in the field can be difficult. We examine here the distribution of chloroplast DNA (cpDNA) diversity in Lower Guinea in two tree species that are difficult to distinguish, Erythrophleum ivorense and Erythrophleum suaveolens (Fabaceae). By using a blind-sampling approach and comparing molecular and morphological markers, we first identified retrospectively all sampled individuals and determined the limits of the distribution of each species. We then performed a phylogeographic study using the same genetic data set. The two species displayed essentially parapatric distributions that were correlated well with the rainfall gradient, which indicated different ecological requirements. In addition, a phylogeographic structure was found for E. suaveolens and, for both species, substantially higher levels of diversity and allelic endemism were observed in the south (Gabon) than in the north (Cameroon) of the Lower Guinea region. This finding indicated different histories of population demographics for the two species, which might reflect different responses to Quaternary climate changes. We suggest that a recent period of forest perturbation, which might have been caused by humans, favoured the spread of these two species and that their poor recruitment at present results from natural succession in their forest formations. © 2010 Blackwell Publishing Ltd.

Revision of the Japanese species of Epicephala Meyrick with descriptions of seven new species (Lepidoptera, Gracillariidae)

PubMed Central

Kawakita, Atsushi; Kato, Makoto

2016-01-01

Abstract Epicephala moths are involved in obligate mutualisms with their Phyllanthaceae hosts, in which the female moths assure pollination and, in return, their progeny develop by consuming the seeds. Ecological, molecular and geographical data suggest that the genus includes several hundred species, but the majority remains to be formally described. Here we revise the Japanese species of Epicephala Meyrick, 1880. In addition to two previously named species, seven species are newly described: Epicephala anthophilia sp. n., Epicephala lanceolatella sp. n., Epicephala perplexa sp. n., Epicephala obovatella sp. n., Epicephala corruptrix sp. n., Epicephala parasitica sp. n. and Epicephala nudilingua sp. n. The first four are species involved in obligate pollination mutualism, while the fifth is a pollinating seed parasite and the last two are derived non-pollinating seed parasites of herbaceous Phyllanthus. Each of the nine Japanese Epicephela species is specialized to a single plant species in the genera Glochidion, Breynia or Phyllanthus, except for Epicephala obovatella and Epicephala corruptrix that each utilizes two closely related Glochidion species. Considerable variations are found in pollination and oviposition behaviors among species, which are reflected in their proboscis and ovipositor morphologies, respectively. Molecular phylogeny indicated that there have been repeated transitions in oviposition mode during the diversification of Epicephala, which were accompanied by changes in ovipositor morphology, as suggested by a correlation analysis. Keys to species are provided. PMID:27103875

Endangered Species. IUCN Special Report: How and Why We Should Conserve Species.

ERIC Educational Resources Information Center

IUCN Bulletin, 1987

1987-01-01

Contains articles addressing the need to protect endangered species. Includes an introductory article that stresses the relationships between the loss of species diversity and the future of the human society. Seventeen brief articles follow that deal with specific endangered plants and animals. (TW)

Streptomyces odonnellii sp. nov., a proteolytic streptomycete isolated from soil under cerrado (savanna) vegetation cover.

PubMed

Pereira, Pedro Henrique Freitas; Macrae, Andrew; Reinert, Fernanda; de Souza, Rodrigo Fonseca; Coelho, Rosalie Reed Rodrigues; Pötter, Gabrielle; Klenk, Hans-Peter; Labeda, David P

2017-12-01

A novel streptomycete, strain 594 T , isolated from Brazilian soil collected under cerrado (savanna) vegetation cover is described. Strain 594 T produced thermophilic chitinolytic proteases in assays containing feather meal and corn steep liquor as sole sources of carbon and nitrogen. The strain produced white to grey aerial mycelium and spiral chains of spiny-surfaced spores on the aerial mycelium and did not produce diffusible pigments. The ll-isomer of diaminopimelic acid was present in the cell wall and menaquinones were predominantly MK-9(H6) (52 %) and MK-9(H8) (30 %) with 6 % MK-9(H4) and slightly less than 1 % MK-9(H2). Polar lipids present were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major fatty acids were anteiso-C15 : 0, anteiso-C16 : 0, anteiso-C14 : 0 and anteiso-C17 : 0. The G+C content of the genomic DNA was 70.4 mol%. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence indicated that it differed from described Streptomyces species. Multilocus sequence analysis (MLSA) using five housekeeping genes (atpD, gyrB, rpoB, recA and trpB) comparing Streptomyces type strains showed that the MLSA distance of strain 594 T to the most closely related species was greater than the 0.007 threshold. The in silico DNA-DNA relatedness between the genome sequence of strain 594 T and that of the phylogenetically nearest species was well below the species level recommendation. There was thus multiple evidence justifying the description of this strain as representing a novel species, for which the name Streptomyces odonnellii sp. nov. is proposed. The type strain is 594 T (=IMPPG 594 T =DSM 41949 T =NRRL B-24891 T ).

The myth of plant species saturation

USGS Publications Warehouse

Stohlgren, Thomas J.; Barnett, David T.; Jarnevich, Catherine S.; Flather, Curtis; Kartesz, John

2008-01-01

Plant species assemblages, communities or regional floras might be termed ‘saturated’ when additional immigrant species are unsuccessful at establishing due to competitive exclusion or other inter-specific interactions, or when the immigration of species is off-set by extirpation of species. This is clearly not the case for state, regional or national floras in the USA where colonization (i.e. invasion by exotic species) exceeds extirpation by roughly a 24 to 1 margin. We report an alarming temporal trend in plant invasions in the Pacific Northwest over the past 100 years whereby counties highest in native species richness appear increasingly invaded over time. Despite the possibility of some increased awareness and reporting of native and exotic plant species in recent decades, historical records show a significant, consistent long-term increase in exotic species (number and frequency) at county, state and regional scales in the Pacific Northwest. Here, as in other regions of the country, colonization rates by exotic species are high and extirpation rates are negligible. The rates of species accumulation in space in multi-scale vegetation plots may provide some clues to the mechanisms of the invasion process from local to national scales.

Maintaining microendemic primate species along an environmental gradient - parasites as drivers for species differentiation.

PubMed

Sommer, Simone; Rakotondranary, Solofomalla Jacques; Ganzhorn, Jörg U

2014-12-01

Understanding the drivers of species adaptations to changing environments on the one hand and the limits for hybridization on the other hand is among the hottest questions in evolutionary biology. Parasites represent one of the major selective forces driving host evolution and at least those with free-living stages are at the same time dependent on the ecological conditions of their host's habitat. Local immunological adaptations of host species to varying parasite pressure are therefore expected and might represent the genetic basis for ecological speciation and the maintenance of recently diverged species. Madagascar provides one of the rare examples where two partially sympatric primate species (Microcebus griseorufus, M. murinus) and their hybrids, as well as an allopatric species (M. cf rufus) live in close proximity along a very steep environmental gradient ranging from southern dry spiny bush to gallery forest to evergreen eastern humid rain forest, thus mimicking the situation encountered during extensions and retreats of vegetation formations under changing climatic conditions. This system was used to study parasite infection and immune gene (MHC) adaptations to varying parasite pressure that might provide selective advantages to pure species over hybrids. Parasite burdens increased with increasing humidity. M. griseorufus, M. murinus, and their hybrids but not M. rufus shared the same MHC alleles, indicating either retention of ancestral polymorphism or recent gene flow. The hybrids had much higher prevalence of intestinal parasites than either of the parent species living under identical environmental conditions. The different representation of parasites can indicate a handicap for hybrids that maintains species identities.

Differences in time until dispersal between cryptic species of a marine nematode species complex.

PubMed

De Meester, Nele; Derycke, Sofie; Moens, Tom

2012-01-01

Co-occurrence of closely related species may be achieved in environments with fluctuating dynamics, where competitively inferior species can avoid competition through dispersal. Here we present an experiment in which we compared active dispersal abilities (time until first dispersal, number and gender of dispersive adults, and nematode densities at time of dispersal) in Litoditis marina, a common bacterivorous nematode species complex comprising four often co-occurring cryptic species, Pm I, II, III, and IV, as a function of salinity and food distribution. The experiment was conducted in microcosms consisting of an inoculation plate, connection tube, and dispersal plate. Results show species-specific dispersal abilities with Pm I dispersing almost one week later than Pm III. The number of dispersive adults at time of first dispersal was species-specific, with one dispersive female in Pm I and Pm III and a higher, gender-balanced, number in Pm II and Pm IV. Food distribution affected dispersal: in absence of food in the inoculation plate, all species dispersed after ca four days. When food was available Pm I dispersed later, and at the same time and densities irrespective of food conditions in the dispersal plate (food vs no food), suggesting density-dependent dispersal. Pm III dispersed faster and at a lower population density. Salinity affected dispersal, with slower dispersal at higher salinity. These results suggest that active dispersal in Litoditis marina is common, density-dependent, and with species, gender- and environment-specific dispersal abilities. These differences can lead to differential responses under suboptimal conditions and may help to explain temporary coexistence at local scales.

Endangered Species Protection Bulletins

EPA Pesticide Factsheets

Endangered Species Protection Bulletins set forth geographically specific pesticide use limitations for the protection of threatened and endangered (listed) species and their designated critical habitat. Find out how to get and use Bulletins.

Toward reassessing data-deficient species.

PubMed

Bland, Lucie M; Bielby, Jon; Kearney, Stephen; Orme, C David L; Watson, James E M; Collen, Ben

2017-06-01

One in 6 species (13,465 species) on the International Union for Conservation of Nature (IUCN) Red List is classified as data deficient due to lack of information on their taxonomy, population status, or impact of threats. Despite the chance that many are at high risk of extinction, data-deficient species are typically excluded from global and local conservation priorities, as well as funding schemes. The number of data-deficient species will greatly increase as the IUCN Red List becomes more inclusive of poorly known and speciose groups. A strategic approach is urgently needed to enhance the conservation value of data-deficient assessments. To develop this, we reviewed 2879 data-deficient assessments in 6 animal groups and identified 8 main justifications for assigning data-deficient status (type series, few records, old records, uncertain provenance, uncertain population status or distribution, uncertain threats, taxonomic uncertainty, and new species). Assigning a consistent set of justification tags (i.e., consistent assignment to assessment justifications) to species classified as data deficient is a simple way to achieve more strategic assessments. Such tags would clarify the causes of data deficiency; facilitate the prediction of extinction risk; facilitate comparisons of data deficiency among taxonomic groups; and help prioritize species for reassessment. With renewed efforts, it could be straightforward to prevent thousands of data-deficient species slipping unnoticed toward extinction. © 2016 Society for Conservation Biology.

Are trade-offs among species' ecological interactions scale dependent? A test using pitcher-plant inquiline species.

PubMed

Kneitel, Jamie M

2012-01-01

Trade-offs among species' ecological interactions is a pervasive explanation for species coexistence. The traits associated with trade-offs are typically measured to mechanistically explain species coexistence at a single spatial scale. However, species potentially interact at multiple scales and this may be reflected in the traits among coexisting species. I quantified species' ecological traits associated with the trade-offs expected at both local (competitive ability and predator tolerance) and regional (competitive ability and colonization rate) community scales. The most common species (four protozoa and a rotifer) from the middle trophic level of a pitcher plant (Sarracenia purpurea) inquiline community were used to link species traits to previously observed patterns of species diversity and abundance. Traits associated with trade-offs (competitive ability, predator tolerance, and colonization rate) and other ecological traits (size, growth rate, and carrying capacity) were measured for each of the focal species. Traits were correlated with one another with a negative relationship indicative of a trade-off. Protozoan and rotifer species exhibited a negative relationship between competitive ability and predator tolerance, indicative of coexistence at the local community scale. There was no relationship between competitive ability and colonization rate. Size, growth rate, and carrying capacity were correlated with each other and the trade-off traits: Size was related to both competitive ability and predator tolerance, but growth rate and carrying capacity were correlated with predator tolerance. When partial correlations were conducted controlling for size, growth rate and carrying capacity, the trade-offs largely disappeared. These results imply that body size is the trait that provides the basis for ecological interactions and trade-offs. Altogether, this study showed that the examination of species' traits in the context of coexistence at different scales

National invasive species program

Treesearch

Anna Rinick

2007-01-01

The structure and function of the National Invasive Species Council was presented below. The names and contact information for the USDA Invasive Species coordinators as of February 2006 were presented on the next page.

A Five-Species Jungle Game.

PubMed

Kang, Yibin; Pan, Qiuhui; Wang, Xueting; He, Mingfeng

2016-01-01

In this paper, we investigate the five-species Jungle game in the framework of evolutionary game theory. We address the coexistence and biodiversity of the system using mean-field theory and Monte Carlo simulations. Then, we find that the inhibition from the bottom-level species to the top-level species can be critical factors that affect biodiversity, no matter how it is distributed, whether homogeneously well mixed or structured. We also find that predators' different preferences for food affect species' coexistence.

A New Species of the Simulium (Simulium) striatum Species Group (Diptera: Simuliidae) from Thailand, and Its Differentiation from Two Related Species Based on a Fast-Evolving Nuclear Gene.

PubMed

Takaoka, Hiroyuki; Srisuka, Wichai; Low, Van Lun; Saeung, Atiporn

2018-05-04

Simulium (Simulium) phraense sp. nov. (Diptera: Simuliidae) is described from females, males, pupae, and larvae from Thailand. This new species is placed in the Simulium striatum species group and is most similar to Simulium (Simulium) nakhonense Takaoka & Suzuki (Diptera: Simuliidae) from Thailand among species of the same species group but is barely distinguished from the latter species by lacking annular ridges on the surface of the pupal gill filaments. The fast-evolving nuclear big zinc finger (BZF) gene has successfully differentiated this new species from its allies, S. (S.) nakhonense and Simulium (Simulium) chiangmaiense Takaoka & Suzuki (Diptera: Simuliidae) of the S. striatum species group. The BZF gene sequences show that this new species is more closely related to S. (S.) nakhonense than to S. (S.) chiangmaiense, further supporting its morphological classification.

75 FR 78974 - Endangered Species

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-17

...-XA086 Endangered Species AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... the Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.) and the regulations governing the taking, importing, and exporting of endangered and threatened species (50 CFR 222-226). Permit...

75 FR 78974 - Endangered Species

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-17

...-XA087 Endangered Species AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and.... SUPPLEMENTARY INFORMATION: The subject permit is requested under the authority of the Endangered Species Act of... exporting of endangered and threatened species (50 CFR 222-226). Mr. Savoy is seeking a permit enabling the...

Lactobacillus arizonensis sp. nov., isolated from jojoba meal.

PubMed

Swezey, J L; Nakamura, L K; Abbott, T P; Peterson, R E

2000-09-01

Five strains of simmondsin-degrading, lactic-acid-producing bacteria were isolated from fermented jojoba meal. These isolates were facultatively anaerobic, gram-positive, non-motile, non-spore-forming, homofermentative, rod-shaped organisms. They grew singly and in short chains, produced lactic acid but no gas from glucose, and did not exhibit catalase activity. Growth occurred at 15 and 45 degrees C. All strains fermented cellobiose, D-fructose, D-galactose, D-glucose, lactose, maltose, D-mannitol, D-mannose, melibiose, D-ribose, salicin, D-sorbitol, sucrose and trehalose. Some strains fermented L-(-)-arabinose and L-rhamnose. D-Xylose was not fermented and starch was not hydrolysed. The mean G+C content of the DNA was 48 mol%. Phylogenetic analyses of 16S rDNA established that the isolates were members of the genus Lactobacillus. DNA reassociation of 45% or less was obtained between the new isolates and the reference strains of species with G+C contents of about 48 mol%. The isolates were differentiated from other homofermentative Lactobacillus spp. on the basis of 16S rDNA sequence divergence, DNA relatedness, stereoisomerism of the lactic acid produced, growth temperature and carbohydrate fermentation. The data support the conclusion that these organisms represent strains of a new species, for which the name Lactobacillus arizonensis is proposed. The type strain of L. arizonensis is NRRL B-14768T (= DSM 13273T).

Biological species in the viral world.

PubMed

Bobay, Louis-Marie; Ochman, Howard

2018-06-05

Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

Cryptic Species Due to Hybridization: A Combined Approach to Describe a New Species (Carex: Cyperaceae)

PubMed Central

Escudero, Marcial

2016-01-01

Disappearance of diagnostic morphological characters due to hybridization is considered to be one of the causes of the complex taxonomy of the species-rich (ca. 2000 described species) genus Carex (Cyperaceae). Carex furva s.l. belongs to section Glareosae. It is an endemic species from the high mountains of the Iberian Peninsula (Spain and Portugal). Previous studies suggested the existence of two different, cryptic taxa within C. furva s.l. Intermediate morphologies found in the southern Iberian Peninsula precluded the description of a new taxa. We aimed to determine whether C. furva s.l. should be split into two different species based on the combination of morphological and molecular data. We sampled ten populations across its full range and performed a morphological study based on measurements on herbarium specimens and silica-dried inflorescences. Both morphological and phylogenetic data support the existence of two different species within C. furva s.l. Nevertheless, intermediate morphologies and sterile specimens were found in one of the southern populations (Sierra Nevada) of C. furva s.l., suggesting the presence of hybrid populations in areas where both supposed species coexist. Hybridization between these two putative species has blurred morphological and genetic limits among them in this hybrid zone. We have proved the utility of combining molecular and morphological data to discover a new cryptic species in a scenario of hybridization. We now recognize a new species, C. lucennoiberica, endemic to the Iberian Peninsula (Sierra Nevada, Central system and Cantabrian Mountains). On the other hand, C. furva s.s. is distributed only in Sierra Nevada, where it may be threatened by hybridization with C. lucennoiberica. The restricted distribution of both species and their specific habitat requirements are the main limiting factors for their conservation. PMID:27973589

Cryptic Species Due to Hybridization: A Combined Approach to Describe a New Species (Carex: Cyperaceae).

PubMed

Maguilla, Enrique; Escudero, Marcial

2016-01-01

Disappearance of diagnostic morphological characters due to hybridization is considered to be one of the causes of the complex taxonomy of the species-rich (ca. 2000 described species) genus Carex (Cyperaceae). Carex furva s.l. belongs to section Glareosae. It is an endemic species from the high mountains of the Iberian Peninsula (Spain and Portugal). Previous studies suggested the existence of two different, cryptic taxa within C. furva s.l. Intermediate morphologies found in the southern Iberian Peninsula precluded the description of a new taxa. We aimed to determine whether C. furva s.l. should be split into two different species based on the combination of morphological and molecular data. We sampled ten populations across its full range and performed a morphological study based on measurements on herbarium specimens and silica-dried inflorescences. Both morphological and phylogenetic data support the existence of two different species within C. furva s.l. Nevertheless, intermediate morphologies and sterile specimens were found in one of the southern populations (Sierra Nevada) of C. furva s.l., suggesting the presence of hybrid populations in areas where both supposed species coexist. Hybridization between these two putative species has blurred morphological and genetic limits among them in this hybrid zone. We have proved the utility of combining molecular and morphological data to discover a new cryptic species in a scenario of hybridization. We now recognize a new species, C. lucennoiberica, endemic to the Iberian Peninsula (Sierra Nevada, Central system and Cantabrian Mountains). On the other hand, C. furva s.s. is distributed only in Sierra Nevada, where it may be threatened by hybridization with C. lucennoiberica. The restricted distribution of both species and their specific habitat requirements are the main limiting factors for their conservation.

Status of endangered and threatened plant species on Nevada Test Site: a survey. Part 2. Threatened species

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

Rhoads, W.A.; Cochrane, S.A.; Williams, M.P.

This is the second of a two-part study of plant species on the Nevada Test Site (NTS) that are listed as possibly threatened or endangered by the U.S. Fish and Wildlife Service (FWS). This study was undertaken as a response by DOE to comply with the Endangered Species Act of 1973 (the Act). Part 1 treated species listed under terms of the Act as proposed endangered species. Part 2 primarily treats those species listed as threatened species candidates. Among the 15 species that grow on NTS and appeared in the Federal Register lists of candidate threatened species we report three:more » Astragalus funereus, Coryphantha vivipara var. rosea, and Gilia ripleyi, that should be considered as threatened. Two other species which occur on NTS and were not included on either the threatened or endangered lists should also be classified as threatened: Penstemon thurberi var. anestius and Sclerocactus polyancistrus. Of the 12 other species originally listed in the Federal Register, eight are of sufficient interest to warrant continued monitoring under a category we suggest as ''Plants of Special Concern.'' The other four do not appear to require any protective measures or surveillance at this time. We suggest critical habitats for those species recommended for threatened status and note that some suggested critical habitats may serve for more than one species and may also include habitats for some species of special concern. Updated information about species covered in Part 1 suggests that Trifolium andersonii var. beatleyae, earlier considered endangered, should now be recommended to be removed from endangered or threatened status because of more widespread distribution than was known to us at the time Part 1 was published.« less

Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding.

PubMed

Ghahramanzadeh, R; Esselink, G; Kodde, L P; Duistermaat, H; van Valkenburg, J L C H; Marashi, S H; Smulders, M J M; van de Wiel, C C M

2013-01-01

Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics. © 2012 Blackwell Publishing Ltd.

Maternal experience and soil origin influence interactions between resident species and a dominant invasive species.

PubMed

Stotz, Gisela C; Gianoli, Ernesto; Cahill, James F

2018-01-01

Invasive species dominance in invaded communities may not be long-lasting due to regulatory processes, such as plant-soil feedbacks and neighboring species adaptation. Further, the change in species competitive ability may be contingent upon neighbor identity (i.e., specialized response) or consistent across neighbors (i.e., generalized response). Specialized responses can facilitate overall coexistence, while generalized responses may result in competitive exclusion. We set up a greenhouse experiment to test, in three species, the effect of soil conditions (non-invaded vs. invaded soil) and maternal experience (offspring of maternal plants from invaded vs. non-invaded areas) on species competitive ability against the invader Bromus inermis and conspecifics. If changes in species competitive ability against B. inermis were also evident when interacting with conspecifics, it would suggest a generalized increased/decreased competitive ability. Maternal experience resulted in reduced suppression of B. inermis in the three species and no change in tolerance. On the other hand, tolerance to B. inermis was enhanced when plants grew in soil from invaded areas, compared to non-brome soil. Importantly, both the decreased suppression due to maternal experience with B. inermis and the increased tolerance in invaded soil appear to be invader specific, as no such effects were observed when interacting with conspecifics. Specialized responses should facilitate coexistence, as no individual/species is a weaker or stronger competitor against all other neighbors or under all local soil conditions. Further, the negative plant-soil feedback for B. inermis should facilitate native species recovery in invaded areas and result in lower B. inermis performance and dominance over time.

76 FR 2348 - Endangered Species

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-13

.... 15596] Endangered Species AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and... requested permit has been issued under the authority of the Endangered Species Act of 1973, as amended (ESA... endangered and threatened species (50 CFR parts 222-226). The North Carolina Aquarium at Fort Fisher has been...

Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula

PubMed Central

Schorr, G; Holstein, N; Pearman, P B; Guisan, A; Kadereit, J W

2012-01-01

The major intention of the present study was to investigate whether an approach combining the use of niche-based palaeodistribution modeling and phylo-geography would support or modify hypotheses about the Quaternary distributional history derived from phylogeographic methods alone. Our study system comprised two closely related species of Alpine Primula. We used species distribution models based on the extant distribution of the species and last glacial maximum (LGM) climate models to predict the distribution of the two species during the LGM. Phylogeographic data were generated using amplified fragment length polymorphisms (AFLPs). In Primula hirsuta, models of past distribution and phylogeographic data are partly congruent and support the hypothesis of widespread nunatak survival in the Central Alps. Species distribution models (SDMs) allowed us to differentiate between alpine regions that harbor potential nunatak areas and regions that have been colonized from other areas. SDMs revealed that diversity is a good indicator for nunataks, while rarity is a good indicator for peripheral relict populations that were not source for the recolonization of the inner Alps. In P. daonensis, palaeo-distribution models and phylogeographic data are incongruent. Besides the uncertainty inherent to this type of modeling approach (e.g., relatively coarse 1-km grain size), disagreement of models and data may partly be caused by shifts of ecological niche in both species. Nevertheless, we demonstrate that the combination of palaeo-distribution modeling with phylogeographical approaches provides a more differentiated picture of the distributional history of species and partly supports (P. hirsuta) and partly modifies (P. daonensis and P. hirsuta) hypotheses of Quaternary distributional history. Some of the refugial area indicated by palaeodistribution models could not have been identified with phylogeographic data. PMID:22833799

Hydraulics and life history of tropical dry forest tree species: coordination of species' drought and shade tolerance.

PubMed

Markesteijn, Lars; Poorter, Lourens; Bongers, Frans; Paz, Horacio; Sack, Lawren

2011-07-01

Plant hydraulic architecture has been studied extensively, yet we know little about how hydraulic properties relate to species' life history strategies, such as drought and shade tolerance. The prevailing theories seem contradictory. We measured the sapwood (K(s) ) and leaf (K(l) ) hydraulic conductivities of 40 coexisting tree species in a Bolivian dry forest, and examined associations with functional stem and leaf traits and indices of species' drought (dry-season leaf water potential) and shade (juvenile crown exposure) tolerance. Hydraulic properties varied across species and between life-history groups (pioneers vs shade-tolerant, and deciduous vs evergreen species). In addition to the expected negative correlation of K(l) with drought tolerance, we found a strong, negative correlation between K(l) and species' shade tolerance. Across species, K(s) and K(l) were negatively correlated with wood density and positively with maximum vessel length. Consequently, drought and shade tolerance scaled similarly with hydraulic properties, wood density and leaf dry matter content. We found that deciduous species also had traits conferring efficient water transport relative to evergreen species. Hydraulic properties varied across species, corresponding to the classical trade-off between hydraulic efficiency and safety, which for these dry forest trees resulted in coordinated drought and shade tolerance across species rather than the frequently hypothesized trade-off. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Identification and authentication of Rosa species through development of species-specific SCAR marker(s).

PubMed

Bashir, K M I; Awan, F S; Khan, I A; Khan, A I; Usman, M

2014-05-30

Roses (Rosa indica) belong to one of the most crucial groups of plants in the floriculture industry. Rosa species have special fragrances of interest to the perfume and pharmaceutical industries. The genetic diversity of plants based on morphological characteristics is difficult to measure under natural conditions due to the influence of environmental factors, which is why a reliable fingerprinting method was developed to overcome this problem. The development of molecular markers will enable the identification of Rosa species. In the present study, randomly amplified polymorphic DNA (RAPD) analysis was done on four Rosa species, Rosa gruss-an-teplitz (Surkha), Rosa bourboniana, Rosa centifolia, and Rosa damascena. A polymorphic RAPD fragment of 391 bp was detected in R. bourboniana, which was cloned, purified, sequenced, and used to design a pair of species-specific sequence-characterized amplified region (SCAR) primers (forward and reverse). These SCAR primers were used to amplify the specific regions of the rose genome. These PCR amplifications with specific primers are less sensitive to reaction conditions, and due to their high reproducibility, these species-specific SCAR primers can be used for marker-assisted selection and identification of Rosa species.

California Endangered Species Resource Guide.

ERIC Educational Resources Information Center

California State Dept. of Education, Los Angeles.

This document was developed in response to California Senate Bill No. 885, "The Endangered Species Education Project," that called for a statewide program in which schools adopt a local endangered species, research past and current efforts to preserve the species' habitat, develop and implement an action plan to educate the community…

Emergent neutrality drives phytoplankton species coexistence

PubMed Central

Segura, Angel M.; Calliari, Danilo; Kruk, Carla; Conde, Daniel; Bonilla, Sylvia; Fort, Hugo

2011-01-01

The mechanisms that drive species coexistence and community dynamics have long puzzled ecologists. Here, we explain species coexistence, size structure and diversity patterns in a phytoplankton community using a combination of four fundamental factors: organism traits, size-based constraints, hydrology and species competition. Using a ‘microscopic’ Lotka–Volterra competition (MLVC) model (i.e. with explicit recipes to compute its parameters), we provide a mechanistic explanation of species coexistence along a niche axis (i.e. organismic volume). We based our model on empirically measured quantities, minimal ecological assumptions and stochastic processes. In nature, we found aggregated patterns of species biovolume (i.e. clumps) along the volume axis and a peak in species richness. Both patterns were reproduced by the MLVC model. Observed clumps corresponded to niche zones (volumes) where species fitness was highest, or where fitness was equal among competing species. The latter implies the action of equalizing processes, which would suggest emergent neutrality as a plausible mechanism to explain community patterns. PMID:21177680

Tree species richness decreases while species evenness increases with disturbance frequency in a natural boreal forest landscape.

PubMed

Yeboah, Daniel; Chen, Han Y H; Kingston, Steve

2016-02-01

Understanding species diversity and disturbance relationships is important for biodiversity conservation in disturbance-driven boreal forests. Species richness and evenness may respond differently with stand development following fire. Furthermore, few studies have simultaneously accounted for the influences of climate and local site conditions on species diversity. Using forest inventory data, we examined the relationships between species richness, Shannon's index, evenness, and time since last stand-replacing fire (TSF) in a large landscape of disturbance-driven boreal forest. TSF has negative effect on species richness and Shannon's index, and a positive effect on species evenness. Path analysis revealed that the environmental variables affect richness and Shannon's index only through their effects on TSF while affecting evenness directly as well as through their effects on TSF. Synthesis and applications. Our results demonstrate that species richness and Shannon's index decrease while species evenness increases with TSF in a boreal forest landscape. Furthermore, we show that disturbance frequency, local site conditions, and climate simultaneously influence tree species diversity through complex direct and indirect effects in the studied boreal forest.

Molluscan indicator species and their potential use in ecological status assessment using species distribution modeling.

PubMed

Moraitis, Manos L; Tsikopoulou, Irini; Geropoulos, Antonios; Dimitriou, Panagiotis D; Papageorgiou, Nafsika; Giannoulaki, Marianna; Valavanis, Vasilis D; Karakassis, Ioannis

2018-05-24

Marine habitat assessment using indicator species through Species Distribution Modeling (SDM) was investigated. The bivalves: Corbula gibba and Flexopecten hyalinus were the indicator species characterizing disturbed and undisturbed areas respectively in terms of chlorophyll a concentration in Greece. The habitat suitability maps of these species reflected the overall ecological status of the area. The C. gibba model successfully predicted the occurrence of this species in areas with increased physical disturbance driven by chlorophyll a concentration, whereas the habitat map for F. hyalinus showed an increased probability of occurrence in chlorophyll-poor areas, affected mainly by salinity. We advocate the use of C. gibba as a proxy for eutrophication and the incorporation of this species in monitoring studies through SDM methods. For the Mediterranean Sea we suggest the use of F. hyalinus in SDM as an indicator of environmental stability and a possible forecasting tool for salinity fluctuations. Copyright © 2018 Elsevier Ltd. All rights reserved.

New species of Auritella (Inocybaceae) from Cameroon, with a worldwide key to the known species.

PubMed

Matheny, P Brandon; Henkel, Terry W; Séné, Olivier; Korotkin, Hailee B; Dentinger, Bryn T M; Aime, M Catherine

2017-12-01

Two new species in the genus Auritella ( Inocybaceae ) are described as new from tropical rainforest in Cameroon. Descriptions, photographs, line drawings, and a worldwide taxonomic key to the described species of Auritella are presented. Phylogenetic analysis of 28S rDNA and rpb2 nucleotide sequence data suggests at least five phylogenetic species that can be ascribed to Auritella occur in the region comprising Cameroon and Gabon and constitute a strongly supported monophyletic subgroup within the genus. Phylogenetic analysis of ITS data supports the conspecificity of numerous collections attributed to the two new species as well as the monophyly of Australian species of Auritella . This work raises the known number of described species of Auritella to thirteen worldwide, four of which occur in tropical Africa, one in tropical India, and eight in temperate and tropical regions of Australia. This is the first study to confirm an ectomycorrhizal status of Auritella using molecular data.

Two New Species of the Simulium (Simulium) variegatum Species-Group of Black Flies (Diptera: Simuliidae) From Thailand.

PubMed

Takaoka, Hiroyuki; Srisuka, Wichai; Saeung, Atiporn

2017-09-01

Two new species of black flies, Simulium (Simulium) srisukai and S. (S.) kiewmaepanense, are described from specimens collected in Thailand. Both species are assigned to the Simulium variegatum species-group of the subgenus Simulium (Simulium) Latreille. They are characterized by the darkened female femora and tibiae and six inflated pupal gill filaments, and the darkened female tibiae and six ordinary thread-like pupal gill filaments, respectively. Taxonomic notes are given to separate these new species from 10 related species among the group. These new species represent the third and fourth species of the S. variegatum species-group from Thailand. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com Version of Record, first published online May 15, 2017 with fixed content and layout in compliance with Art. 8.1.3.2 ICZN.

Measurement of Reactive Oxygen Species, Reactive Nitrogen Species, and Redox-Dependent Signaling in the Cardiovascular System

PubMed Central

Griendling, Kathy K.; Touyz, Rhian M.; Zweier, Jay L.; Dikalov, Sergey; Chilian, William; Chen, Yeong-Renn; Harrison, David G.; Bhatnagar, Aruni

2017-01-01

Reactive oxygen species and reactive nitrogen species are biological molecules that play important roles in cardiovascular physiology and contribute to disease initiation, progression, and severity. Because of their ephemeral nature and rapid reactivity, these species are difficult to measure directly with high accuracy and precision. In this statement, we review current methods for measuring these species and the secondary products they generate and suggest approaches for measuring redox status, oxidative stress, and the production of individual reactive oxygen and nitrogen species. We discuss the strengths and limitations of different methods and the relative specificity and suitability of these methods for measuring the concentrations of reactive oxygen and reactive nitrogen species in cells, tissues, and biological fluids. We provide specific guidelines, through expert opinion, for choosing reliable and reproducible assays for different experimental and clinical situations. These guidelines are intended to help investigators and clinical researchers avoid experimental error and ensure high-quality measurements of these important biological species. PMID:27418630

Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae)

PubMed Central

Bergsten, Johannes; Weingartner, Elisabeth; Hájek, Jiří

2017-01-01

Abstract The species status of Hyphydrus anatolicus Guignot, 1957 and H. sanctus Sharp, 1882, previously often confused with the widespread H. ovatus (Linnaeus, 1760), are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1) was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the three species with no other than the three species solution included in the confidence interval. A likelihood ratio test rejected the one-species null model. Important morphological characters distinguishing the species are provided and illustrated. New distributional data are given for the following species: Hyphydrus anatolicus from Slovakia and Ukraine, and H. aubei Ganglbauer, 1891, and H. sanctus from Turkey. PMID:28769697

Intraspecific variation and species coexistence.

PubMed

Lichstein, Jeremy W; Dushoff, Jonathan; Levin, Simon A; Pacala, Stephen W

2007-12-01

We use a two-species model of plant competition to explore the effect of intraspecific variation on community dynamics. The competitive ability ("performance") of each individual is assigned by an independent random draw from a species-specific probability distribution. If the density of individuals competing for open space is high (e.g., because fecundity is high), species with high maximum (or large variance in) performance are favored, while if density is low, species with high typical (e.g., mean) performance are favored. If there is an interspecific mean-variance performance trade-off, stable coexistence can occur across a limited range of intermediate densities, but the stabilizing effect of this trade-off appears to be weak. In the absence of this trade-off, one species is superior. In this case, intraspecific variation can blur interspecific differences (i.e., shift the dynamics toward what would be expected in the neutral case), but the strength of this effect diminishes as competitor density increases. If density is sufficiently high, the inferior species is driven to extinction just as rapidly as in the case where there is no overlap in performance between species. Intraspecific variation can facilitate coexistence, but this may be relatively unimportant in maintaining diversity in most real communities.

Incorporating climate science in applications of the US endangered species act for aquatic species.

PubMed

McClure, Michelle M; Alexander, Michael; Borggaard, Diane; Boughton, David; Crozier, Lisa; Griffis, Roger; Jorgensen, Jeffrey C; Lindley, Steven T; Nye, Janet; Rowland, Melanie J; Seney, Erin E; Snover, Amy; Toole, Christopher; VAN Houtan, Kyle

2013-12-01

Aquatic species are threatened by climate change but have received comparatively less attention than terrestrial species. We gleaned key strategies for scientists and managers seeking to address climate change in aquatic conservation planning from the literature and existing knowledge. We address 3 categories of conservation effort that rely on scientific analysis and have particular application under the U.S. Endangered Species Act (ESA): assessment of overall risk to a species; long-term recovery planning; and evaluation of effects of specific actions or perturbations. Fewer data are available for aquatic species to support these analyses, and climate effects on aquatic systems are poorly characterized. Thus, we recommend scientists conducting analyses supporting ESA decisions develop a conceptual model that links climate, habitat, ecosystem, and species response to changing conditions and use this model to organize analyses and future research. We recommend that current climate conditions are not appropriate for projections used in ESA analyses and that long-term projections of climate-change effects provide temporal context as a species-wide assessment provides spatial context. In these projections, climate change should not be discounted solely because the magnitude of projected change at a particular time is uncertain when directionality of climate change is clear. Identifying likely future habitat at the species scale will indicate key refuges and potential range shifts. However, the risks and benefits associated with errors in modeling future habitat are not equivalent. The ESA offers mechanisms for increasing the overall resilience and resistance of species to climate changes, including establishing recovery goals requiring increased genetic and phenotypic diversity, specifying critical habitat in areas not currently occupied but likely to become important, and using adaptive management. Incorporación de las Ciencias Climáticas en las Aplicaciones del

Herbaceous plant species invading natural areas tend to have stronger adaptive root foraging than other naturalized species

PubMed Central

Keser, Lidewij H.; Visser, Eric J. W.; Dawson, Wayne; Song, Yao-Bin; Yu, Fei-Hai; Fischer, Markus; Dong, Ming; van Kleunen, Mark

2015-01-01

Although plastic root-foraging responses are thought to be adaptive, as they may optimize nutrient capture of plants, this has rarely been tested. We investigated whether nutrient-foraging responses are adaptive, and whether they pre-adapt alien species to become natural-area invaders. We grew 12 pairs of congeneric species (i.e., 24 species) native to Europe in heterogeneous and homogeneous nutrient environments, and compared their foraging responses and performance. One species in each pair is a USA natural-area invader, and the other one is not. Within species, individuals with strong foraging responses, measured as plasticity in root diameter and specific root length, had a higher biomass. Among species, the ones with strong foraging responses, measured as plasticity in root length and root biomass, had a higher biomass. Our results therefore suggest that root foraging is an adaptive trait. Invasive species showed significantly stronger root-foraging responses than non-invasive species when measured as root diameter. Biomass accumulation was decreased in the heterogeneous vs. the homogeneous environment. In aboveground, but not belowground and total biomass, this decrease was smaller in invasive than in non-invasive species. Our results show that strong plastic root-foraging responses are adaptive, and suggest that it might aid in pre-adapting species to becoming natural-area invaders. PMID:25964790

Protectiveness of species sensitivity distribution hazard concentrations for acute toxicity used in endangered species risk assessment.

PubMed

Raimondo, Sandy; Vivian, Deborah N; Delos, Charles; Barron, Mace G

2008-12-01

A primary objective of threatened and endangered species conservation is to ensure that chemical contaminants and other stressors do not adversely affect listed species. Assessments of the ecological risks of chemical exposures to listed species often rely on the use of surrogate species, safety factors, and species sensitivity distributions (SSDs) of chemical toxicity; however, the protectiveness of these approaches can be uncertain. We comprehensively evaluated the protectiveness of SSD first and fifth percentile hazard concentrations (HC1, HC5) relative to the application of safety factors using 68 SSDs generated from 1,482 acute (lethal concentration of 50%, or LC50) toxicity records for 291 species, including 24 endangered species (20 fish, four mussels). The SSD HC5s and HCls were lower than 97 and 99.5% of all endangered species mean acute LC50s, respectively. The HC5s were significantly less than the concentrations derived from applying safety factors of 5 and 10 to rainbow trout (Oncorhynchus mykiss) toxicity data, and the HCls were generally lower than the concentrations derived from a safety factor of 100 applied to rainbow trout toxicity values. Comparison of relative sensitivity (SSD percentiles) of broad taxonomic groups showed that crustaceans were generally the most sensitive taxa and taxa sensitivity was related to chemical mechanism of action. Comparison of relative sensitivity of narrow fish taxonomic groups showed that standard test fish species were generally less sensitive than salmonids and listed fish. We recommend the use of SSDs as a distribution-based risk assessment approach that is generally protective of listed species.

[Yeast species in vulvovaginitis candidosa].

PubMed

Nemes-Nikodém, Éva; Tamási, Béla; Mihalik, Noémi; Ostorházi, Eszter

2015-01-04

Vulvovaginal candidiasis is the most common mycosis, however, the available information about antifungal susceptibilities of these yeasts is limited. To compare the gold standard fungal culture with a new molecular identification method and report the incidence of yeast species in vulvovaginitis candidosa. The authors studied 370 yeasts isolated from vulvovaginal candidiasis and identified them by phenotypic and molecular methods. The most common species was Candida albicans (85%), followed by Candida glabrata, and other Candida species. At present there are no recommendations for the evaluation of antifungal susceptibility of pathogenic fungal species occurring in vulvovaginal candidiasis and the natural antifungal resistance of the different species is known only. Matrix Assisted Laser Desorption Ionization Time of Flight identification can be used to differentiate the fluconazole resistant Candida dubliniensis and the sensitive Candida albicans strains.

SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.

PubMed

Töpel, Mats; Zizka, Alexander; Calió, Maria Fernanda; Scharn, Ruud; Silvestro, Daniele; Antonelli, Alexandre

2017-03-01

Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years. [ancestral area reconstruction; biodiversity

A framework for spatial risk assessments: Potential impacts of nonindigenous invasive species on native species

USGS Publications Warehouse

Allen, Craig R.; Johnson, A.R.; Parris, L.

2006-01-01

Many populations of wild animals and plants are declining and face increasing threats from habitat fragmentation and loss as well as exposure to stressors ranging from toxicants to diseases to invasive nonindigenous species. We describe and demonstrate a spatially explicit ecological risk assessment that allows for the incorporation of a broad array of information that may influence the distribution of an invasive species, toxicants, or other stressors, and the incorporation of landscape variables that may influence the spread of a species or substances. The first step in our analyses is to develop species models and quantify spatial overlap between stressor and target organisms. Risk is assessed as the product of spatial overlap and a hazard index based on target species vulnerabilities to the stressor of interest. We illustrate our methods with an example in which the stressor is the ecologically destructive nonindigenous ant, Solenopsis invicta, and the targets are two declining vertebrate species in the state of South Carolina, USA. A risk approach that focuses on landscapes and that is explicitly spatial is of particular relevance as remaining undeveloped lands become increasingly uncommon and isolated and more important in the management and recovery of species and ecological systems. Effective ecosystem management includes the control of multiple stressors, including invasive species with large impacts, understanding where those impacts may be the most severe, and implementing management strategies to reduce impacts. Copyright ?? 2006 by the author(s).

Cryptic diversity in a fig wasp community-morphologically differentiated species are sympatric but cryptic species are parapatric.

PubMed

Darwell, C T; Cook, J M

2017-02-01

A key debate in ecology centres on the relative importance of niche and neutral processes in determining patterns of community assembly with particular focus on whether ecologically similar species with similar functional traits are able to coexist. Meanwhile, molecular studies are increasingly revealing morphologically indistinguishable cryptic species with presumably similar ecological roles. Determining the geographic distribution of such cryptic species provides opportunities to contrast predictions of niche vs. neutral models. Discovery of sympatric cryptic species increases alpha diversity and supports neutral models, while documentation of allopatric/parapatric cryptic species increases beta diversity and supports niche models. We tested these predictions using morphological and molecular data, coupled with environmental niche modelling analyses, of a fig wasp community along its 2700-km latitudinal range. Molecular methods increased previous species diversity estimates from eight to eleven species, revealing morphologically cryptic species in each of the four wasp genera studied. Congeneric species pairs that were differentiated by a key morphological functional trait (ovipositor length) coexisted sympatrically over large areas. In contrast, morphologically similar species, with similar ovipositor lengths, typically showed parapatric ranges with very little overlap. Despite parapatric ranges, environmental niche models of cryptic congeneric pairs indicate large regions of potential sympatry, suggesting that competitive processes are important in determining the distributions of ecologically similar species. Niche processes appear to structure this insect community, and cryptic diversity may typically contribute mostly to beta rather than alpha diversity. © 2016 John Wiley & Sons Ltd.

Over-invasion by functionally equivalent invasive species.

PubMed

Russell, James C; Sataruddin, Nurul S; Heard, Allison D

2014-08-01

Multiple invasive species have now established at most locations around the world, and the rate of new species invasions and records of new invasive species continue to grow. Multiple invasive species interact in complex and unpredictable ways, altering their invasion success and impacts on biodiversity. Incumbent invasive species can be replaced by functionally similar invading species through competitive processes; however the generalized circumstances leading to such competitive displacement have not been well investigated. The likelihood of competitive displacement is a function of the incumbent advantage of the resident invasive species and the propagule pressure of the colonizing invasive species. We modeled interactions between populations of two functionally similar invasive species and indicated the circumstances under which dominance can be through propagule pressure and incumbent advantage. Under certain circumstances, a normally subordinate species can be incumbent and reject a colonizing dominant species, or successfully colonize in competition with a dominant species during simultaneous invasion. Our theoretical results are supported by empirical studies of the invasion of islands by three invasive Rattus species. Competitive displacement is prominent in invasive rats and explains the replacement of R. exulans on islands subsequently invaded by European populations of R. rattus and R. norvegicus. These competition outcomes between invasive species can be found in a broad range of taxa and biomes, and are likely to become more common. Conservation management must consider that removing an incumbent invasive species may facilitate invasion by another invasive species. Under very restricted circumstances of dominant competitive ability but lesser impact, competitive displacement may provide a novel method of biological control.

[New species and sympatric relations of the chigger mite species group Talmiensis (Trombiculidae, Neotrombicula)].

PubMed

Stekol'nikov, A A

2001-01-01

A revision of chigger mites species being closely related to Neotrombicula talmiensis (Schluger, 1955) has been performed. 2 new species are described: N. pontica sp. n. from Krasnodar Territory (Western Caucasus) and N. sympatrica sp. n. from Krasnodar Territory, Daghestan, Tuva, Armenia, Kirghizia and Turkey (Rize Province). N. pontica sp. n. is closely related to N. carpathica Schluger et Vysotzkaya, 1970 and differs from this species by the larger number of idiosomal setae (NDV = = 75-99 against 63-77), shorter legs (Ip = 782-847 against 844-920, TaIII = 67-74 against 70-80), lesser m-t (0.180 against 0.192), slightly lesser scutum and slightly longer setae. N. sympatrica sp. n. is closely related to N. carpathica and differs from this species by the longer scutal and idiosomal setae (PL = 67-78 against 57-69, H = 65-75 against 57-68, Dmin = 43-52 against 39-48, Dmax = 61-70 against 54-64), longer legs (Ip = 892-973 against 844-920, TaIII = = 77-86 against 70-80) and lesser m-t (0.168 against 0.192). N. carpathica is reported for the first time from Northern Caucasus (Karachai-Cherkess Republic, Kabardino-Balkaria, North Ossetia); N. talmiensis is reported for the first time from Khakasia. Data on joint occurrence of 3 species are reported. The 3 types of sympatric pairs of the species have been found in the Western Caucasus: 1) N. pontica sp. n. and N. sympatrica sp. n., 2) N. sympatrica sp. n., and N. carpathica, 3) N. pontica sp. n., and N. carpathica. Differences between species in that localities, where the joint occurrence was recorded, have been analysed. Sympatric relations between N. sympatrica sp. n. and N. carpathica are characterized by increased value of some general diagnostic characters of these species, such as the length of idiosomal setae and length of legs. Different characters play main distinguishing role in different sympatric localities. Besides that, some local features appear in certain species of sympatric pairs (narrow scutum in 3

Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics.

PubMed

Vitecek, Simon; Kučinić, Mladen; Previšić, Ana; Živić, Ivana; Stojanović, Katarina; Keresztes, Lujza; Bálint, Miklós; Hoppeler, Felicitas; Waringer, Johann; Graf, Wolfram; Pauls, Steffen U

2017-06-06

Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling.

PubMed

Wisz, Mary Susanne; Pottier, Julien; Kissling, W Daniel; Pellissier, Loïc; Lenoir, Jonathan; Damgaard, Christian F; Dormann, Carsten F; Forchhammer, Mads C; Grytnes, John-Arvid; Guisan, Antoine; Heikkinen, Risto K; Høye, Toke T; Kühn, Ingolf; Luoto, Miska; Maiorano, Luigi; Nilsson, Marie-Charlotte; Normand, Signe; Öckinger, Erik; Schmidt, Niels M; Termansen, Mette; Timmermann, Allan; Wardle, David A; Aastrup, Peter; Svenning, Jens-Christian

2013-02-01

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km(2) to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

PubMed Central

Wisz, Mary Susanne; Pottier, Julien; Kissling, W Daniel; Pellissier, Loïc; Lenoir, Jonathan; Damgaard, Christian F; Dormann, Carsten F; Forchhammer, Mads C; Grytnes, John-Arvid; Guisan, Antoine; Heikkinen, Risto K; Høye, Toke T; Kühn, Ingolf; Luoto, Miska; Maiorano, Luigi; Nilsson, Marie-Charlotte; Normand, Signe; Öckinger, Erik; Schmidt, Niels M; Termansen, Mette; Timmermann, Allan; Wardle, David A; Aastrup, Peter; Svenning, Jens-Christian

2013-01-01

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km2 to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally

Eighteen microsatellite loci in Salix arbutifolia (Salicaceae) and cross-species amplification in Salix and Populus species.

PubMed

Hoshikawa, Takeshi; Kikuchi, Satoshi; Nagamitsu, Teruyoshi; Tomaru, Nobuhiro

2009-07-01

Salix arbutifolia is a riparian dioecious tree species that is of conservation concern in Japan because of its highly restricted distribution. Eighteen polymorphic loci of dinucleotide microsatellites were isolated and characterized. Among these, estimates of the expected heterozygosity ranged from 0.350 to 0.879. Cross-species amplification was successful at 9-13 loci among six Salix species and at three loci in one Populus species. © 2009 Blackwell Publishing Ltd.

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia.

PubMed

DeBiasse, Melissa B; Hellberg, Michael E

2015-02-01

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia

PubMed Central

DeBiasse, Melissa B; Hellberg, Michael E

2015-01-01

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges. PMID:25691989

The influences of canopy species and topographic variables on understory species diversity and composition in coniferous forests.

PubMed

Huo, Hong; Feng, Qi; Su, Yong-hong

2014-01-01

Understanding the factors that influence the distribution of understory vegetation is important for biological conservation and forest management. We compared understory species composition by multi-response permutation procedure and indicator species analysis between plots dominated by Qinghai spruce (Picea crassifolia Kom.) and Qilian juniper (Sabina przewalskii Kom.) in coniferous forests of the Qilian Mountains, northwestern China. Understory species composition differed markedly between the forest types. Many heliophilous species were significantly associated with juniper forest, while only one species was indicative of spruce forest. Using constrained ordination and the variation partitioning model, we quantitatively assessed the relative effects of two sets of explanatory variables on understory species composition. The results showed that topographic variables had higher explanatory power than did site conditions for understory plant distributions. However, a large amount of the variation in understory species composition remained unexplained. Forward selection revealed that understory species distributions were primarily affected by elevation and aspect. Juniper forest had higher species richness and α-diversity and lower β-diversity in the herb layer of the understory plant community than spruce forest, suggesting that the former may be more important in maintaining understory biodiversity and community stability in alpine coniferous forest ecosystems.

Hierarchical species distribution models

USGS Publications Warehouse

Hefley, Trevor J.; Hooten, Mevin B.

2016-01-01

Determining the distribution pattern of a species is important to increase scientific knowledge, inform management decisions, and conserve biodiversity. To infer spatial and temporal patterns, species distribution models have been developed for use with many sampling designs and types of data. Recently, it has been shown that count, presence-absence, and presence-only data can be conceptualized as arising from a point process distribution. Therefore, it is important to understand properties of the point process distribution. We examine how the hierarchical species distribution modeling framework has been used to incorporate a wide array of regression and theory-based components while accounting for the data collection process and making use of auxiliary information. The hierarchical modeling framework allows us to demonstrate how several commonly used species distribution models can be derived from the point process distribution, highlight areas of potential overlap between different models, and suggest areas where further research is needed.

Two new species of Aulospongus Norman, 1878 with a key to the Atlantic species (Poecilosclerida; Demospongiae; Porifera).

PubMed

Cavalcanti, Thaynã; Santos, George Garcia; Pinheiro, Ulisses

2014-07-03

We describe two new species: Aulospongus trirhabdostylus sp. nov. and Aulospongus mandela sp. nov. from Potiguar Basin (Rio Grande do Norte State, Northeastern Brazil). Both species were compared with their congeners and an identification key for the Atlantic species of Aulospongus is provided. The genus Aulospongus now contains 16 species.

Systematics of the Dendropsophus leucophyllatus species complex (Anura: Hylidae): Cryptic diversity and the description of two new species

PubMed Central

Caminer, Marcel A.; Milá, Borja; Jansen, Martin; Fouquet, Antoine; Venegas, Pablo J.; Chávez, Germán; Lougheed, Stephen C.

2017-01-01

Genetic data in studies of systematics of Amazonian amphibians frequently reveal that purportedly widespread single species in reality comprise species complexes. This means that real species richness may be significantly higher than current estimates. Here we combine genetic, morphological, and bioacoustic data to assess the phylogenetic relationships and species boundaries of two Amazonian species of the Dendropsophus leucophyllatus species group: D. leucophyllatus and D. triangulum. Our results uncovered the existence of five confirmed and four unconfirmed candidate species. Among the confirmed candidate species, three have available names: Dendropsophus leucophyllatus, Dendropsophus triangulum, and Dendropsophus reticulatus, this last being removed from the synonymy of D. triangulum. A neotype of D. leucophyllatus is designated. We describe the remaining two confirmed candidate species, one from Bolivia and another from Peru. All confirmed candidate species are morphologically distinct and have much smaller geographic ranges than those previously reported for D. leucophyllatus and D. triangulum sensu lato. Dendropsophus leucophyllatus sensu stricto occurs in the Guianan region. Dendropsophus reticulatus comb. nov. corresponds to populations in the Amazon basin of Brazil, Ecuador, and Peru previously referred to as D. triangulum. Dendropsophus triangulum sensu stricto is the most widely distributed species; it occurs in Amazonian Ecuador, Peru and Brazil, reaching the state of Pará. We provide accounts for all described species including an assessment of their conservation status. PMID:28248998

Mating patterns and post-mating isolation in three cryptic species of the Engystomops petersi species complex.

PubMed

Trillo, Paula A; Narvaez, Andrea E; Ron, Santiago R; Hoke, Kim L

2017-01-01

Determining the extent of reproductive isolation in cryptic species with dynamic geographic ranges can yield important insights into the processes that generate and maintain genetic divergence in the absence of severe geographic barriers. We studied mating patterns, propensity to hybridize in nature and subsequent fertilization rates, as well as survival and development of hybrid F1 offspring for three nominal species of the Engystomops petersi species complex in Yasuní National Park, Ecuador. We found at least two species in four out of six locations sampled, and 14.3% of the wild pairs genotyped were mixed-species (heterospecific) crosses. We also found reduced fertilization rates in hybrid crosses between E. petersi females and E. "magnus" males, and between E. "magnus" females and E. "selva" males but not in the reciprocal crosses, suggesting asymmetric reproductive isolation for these species. Larval development times decreased in F1 hybrid crosses compared to same species (conspecific) crosses, but we did not find significant reduction in larval survival or early metamorph survival. Our results show evidence of post-mating isolation for at least two hybrid crosses of the cryptic species we studied. The general decrease in fertilization rates in heterospecific crosses suggests that sexual selection and reinforcement might have not only contributed to the pattern of call variation and behavioral isolation we see between species today, but they may also contribute to further signal divergence and behavioral evolution, especially in locations where hybridization is common and fertilization success is diminished.

METHYLATION INACTIVATES PENTAVALENT ARSENIC SPECIES BUT ACTIVATES TRIVALENT ARSENIC SPECIES TO POTENT GENOTOXICANTS

EPA Science Inventory

Methylation Inactivates Pentavalent Arsenic Species but Activates Trivalent Arsenic Species to Potent Genotoxicants

The sensitivity ofhumans to arsenic-induced cancer is thought to be related in part to the limited ability of humans to detoxify arsenic. Recently, methyl- ...

Four new species of frogs and one new species of snake from the Chapare region of Bolivia, with notes on other species

USGS Publications Warehouse

Reynolds, R.P.; Foster, M.S.

1992-01-01

We report on a collection of 74 frogs, 11 lots of frog eggs or tadpoles, and two snakes collected from the Chapare Region in the yungas of the eastern Andean Cordillera de Cochabamba, Bolivia. Collecting localities range from approximately 300 m to >3200 m in elevation. The specimens pertain to 23 species, probably 10 of which are undescribed. We describe four new species of frogs, one each in the genera Bufo, Centrolenella, Colostethus, and Hyla, and one new species of snake, genus Dipsas. We place Atelopus rugulosus in synonymy with A. tricolor.

The myth of plant species saturation

Treesearch

Thomas J. Stohlgren; David T. Barnett; Catherine S. Jarnevich; Curtis Flather; John Kartesz

2008-01-01

Plant species assemblages, communities or regional floras might be termed saturated when additional immigrant species are unsuccessful at establishing due to competitive exclusion or other inter-specific interactions, or when the immigration of species is off-set by extirpation of species. This is clearly not the case for state, regional or national floras in the USA...

Progress toward a general species concept.

PubMed

Hausdorf, Bernhard

2011-04-01

New insights in the speciation process and the nature of "species" that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species.

PubMed

Robins, Judith H; Tintinger, Vernon; Aplin, Ken P; Hingston, Melanie; Matisoo-Smith, Elizabeth; Penny, David; Lavery, Shane D

2014-01-01

The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and

Phylogenetic Species Identification in Rattus Highlights Rapid Radiation and Morphological Similarity of New Guinean Species

PubMed Central

Robins, Judith H.; Tintinger, Vernon; Aplin, Ken P.; Hingston, Melanie; Matisoo-Smith, Elizabeth; Penny, David; Lavery, Shane D.

2014-01-01

The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and

Deriving field-based species sensitivity distributions (f-SSDs) from stacked species distribution models (S-SDMs).

PubMed

Schipper, Aafke M; Posthuma, Leo; de Zwart, Dick; Huijbregts, Mark A J

2014-12-16

Quantitative relationships between species richness and single environmental factors, also called species sensitivity distributions (SSDs), are helpful to understand and predict biodiversity patterns, identify environmental management options and set environmental quality standards. However, species richness is typically dependent on a variety of environmental factors, implying that it is not straightforward to quantify SSDs from field monitoring data. Here, we present a novel and flexible approach to solve this, based on the method of stacked species distribution modeling. First, a species distribution model (SDM) is established for each species, describing its probability of occurrence in relation to multiple environmental factors. Next, the predictions of the SDMs are stacked along the gradient of each environmental factor with the remaining environmental factors at fixed levels. By varying those fixed levels, our approach can be used to investigate how field-based SSDs for a given environmental factor change in relation to changing confounding influences, including for example optimal, typical, or extreme environmental conditions. This provides an asset in the evaluation of potential management measures to reach good ecological status.

Development of Species-Specific SCAR Markers, Based on a SCoT Analysis, to Authenticate Physalis (Solanaceae) Species

PubMed Central

Feng, Shangguo; Zhu, Yujia; Yu, Chenliang; Jiao, Kaili; Jiang, Mengying; Lu, Jiangjie; Shen, Chenjia; Ying, Qicai; Wang, Huizhong

2018-01-01

Physalis is an important genus in the Solanaceae family. It includes many species of significant medicinal value, edible value, and ornamental value. However, many Physalis species are easily confused because of their similar morphological traits, which hinder the utilization and protection of Physalis resources. Therefore, it is necessary to create fast, sensitive, and reliable methods for the Physalis species authentication. Intended for that, in this study, species-specific sequence-characterized amplified region (SCAR) markers were developed for accurate identification of the closely related Physalis species P. angulata, P. minima, P. pubescens, and P. alkekengi var. franchetii, based on a simple and novel marker system, start codon targeted (SCoT) marker. A total of 34 selected SCoT primers yielded 289 reliable SCoT loci, of which 265 were polymorphic. Four species-specific SCoT fragments (SCoT3-1404, SCoT3-1589, SCoT5-550, and SCoT36-520) from Physalis species were successfully identified, cloned, and sequenced. Based on these selected specific DNA fragments, four SCAR primers pairs were developed and named ST3KZ, ST3MSJ, ST5SJ, and ST36XSJ. PCR analysis of each of these primer pairs clearly demonstrated a specific amplified band in all samples of the target Physalis species, but no amplification was observed in other Physalis species. Therefore, the species-specific SCAR primer pairs developed in this study could be used as powerful tools that can rapidly, effectively, and reliably identify and differentiate Physalis species.

New species of Bacuma Cameron (Hymenoptera: Braconidae: Braconinae) from Kenya and West Darfur with a key to species.

PubMed

Quicke, Donald L J; Guy, Travis J; Noort, Simon VAN; Broad, Gavin R; Butcher, Buntika A

2017-05-08

Three new species of the Afrotropical braconine wasp genus Bacuma are described, and biological observations (nectar feeding) by one of them are noted. The new species are: B. kayserae Quicke & Butcher sp. nov. from Kenya, B. madiensis Quicke & Butcher sp. nov. from Uganda and B. darfurensis Quicke & Butcher sp. nov. from Sudan. A group of four large nominal species with red metasomas and finely sculptured tergites (B. granulatus, B. maculipennis, B. rufa and B. whitei) may represent a single widespread species or a pair of species separated by mesoscutum colour, or four separate but morphologically very similar species. However, given the small number of specimens available for study and the poor condition of some of these, including the types, they are not formally synonymised here. A partial key to the species of Bacuma is presented, which recognizes those species that are clearly distinct, including three new species. Interactive Lucid dichotomous and matrix keys are available on www.waspweb.org.

Cryobanking of aquatic species.

PubMed

Martínez-Páramo, Sonia; Horváth, Ákos; Labbé, Catherine; Zhang, Tiantian; Robles, Vanesa; Herráez, Paz; Suquet, Marc; Adams, Serean; Viveiros, Ana; Tiersch, Terrence R; Cabrita, Elsa

2017-04-01

This review is focused on the applications of genome cryobanking of aquatic species including freshwater and marine fish, as well as invertebrates. It also reviews the latest advances in cryobanking of model species, widely used by the scientific community worldwide, because of their applications in several fields. The state of the art of cryopreservation of different cellular types (sperm, oocytes, embryos, somatic cells and primordial germ cells or early spermatogonia) is discussed focusing on the advantages and disadvantages of each procedure according to different applications. A special review on the need of standardization of protocols has also been carried out. In summary, this comprehensive review provides information on the practical details of applications of genome cryobanking in a range of aquatic species worldwide, including the cryobanks established in Europe, USA, Brazil, Australia and New Zealand, the species and type of cells that constitute these banks and the utilization of the samples preserved. This review compiles the last advances on germplasm cryobanking of freshwater and marine fish species and invertebrates, with high value for commercial aquaculture or conservation. It is reviewed the most promising cryopreservation protocols for different cell types, embryos and larvae that could be applied in programs for genetic improvement, broodstock management or conservation of stocks to guarantee culture production.

Theoretical ecology without species

NASA Astrophysics Data System (ADS)

Tikhonov, Mikhail

The sequencing-driven revolution in microbial ecology demonstrated that discrete ``species'' are an inadequate description of the vast majority of life on our planet. Developing a novel theoretical language that, unlike classical ecology, would not require postulating the existence of species, is a challenge of tremendous medical and environmental significance, and an exciting direction for theoretical physics. Here, it is proposed that community dynamics can be described in a naturally hierarchical way in terms of population fluctuation eigenmodes. The approach is applied to a simple model of division of labor in a multi-species community. In one regime, effective species with a core and accessory genome are shown to naturally appear as emergent concepts. However, the same model allows a transition into a regime where the species formalism becomes inadequate, but the eigenmode description remains well-defined. Treating a community as a black box that expresses enzymes in response to resources reveals mathematically exact parallels between a community and a single coherent organism with its own fitness function. This coherence is a generic consequence of division of labor, requires no cooperative interactions, and can be expected to be widespread in microbial ecosystems. Harvard Center of Mathematical Sciences and Applications;John A. Paulson School of Engineering and Applied Sciences.

Can species distribution models really predict the expansion of invasive species?

PubMed

Barbet-Massin, Morgane; Rome, Quentin; Villemant, Claire; Courchamp, Franck

2018-01-01

Predictive studies are of paramount importance for biological invasions, one of the biggest threats for biodiversity. To help and better prioritize management strategies, species distribution models (SDMs) are often used to predict the potential invasive range of introduced species. Yet, SDMs have been regularly criticized, due to several strong limitations, such as violating the equilibrium assumption during the invasion process. Unfortunately, validation studies-with independent data-are too scarce to assess the predictive accuracy of SDMs in invasion biology. Yet, biological invasions allow to test SDMs usefulness, by retrospectively assessing whether they would have accurately predicted the latest ranges of invasion. Here, we assess the predictive accuracy of SDMs in predicting the expansion of invasive species. We used temporal occurrence data for the Asian hornet Vespa velutina nigrithorax, a species native to China that is invading Europe with a very fast rate. Specifically, we compared occurrence data from the last stage of invasion (independent validation points) to the climate suitability distribution predicted from models calibrated with data from the early stage of invasion. Despite the invasive species not being at equilibrium yet, the predicted climate suitability of validation points was high. SDMs can thus adequately predict the spread of V. v. nigrithorax, which appears to be-at least partially-climatically driven. In the case of V. v. nigrithorax, SDMs predictive accuracy was slightly but significantly better when models were calibrated with invasive data only, excluding native data. Although more validation studies for other invasion cases are needed to generalize our results, our findings are an important step towards validating the use of SDMs in invasion biology.

Can species distribution models really predict the expansion of invasive species?