Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations

Locating Pleistocene Refugia: Comparing Phylogeographic and Ecological Niche Model Predictions

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution

Networking the microbial diversity information

The Internet, the electronic global network of computers, has expanded significantly over the last few years, connecting segments from academia, industry and the private sector, The use of the Internet by researchers has diversified substantially from the primordial exchange of electronic messages to the current use of highly developed graphic interfaces capable of accessing images, sounds and retrieving information from databases in different computers around the world, The reduced costs for data storage and ease of connection to the net have nourished a steady exponential growth in the number of sites, Microbiologists now benefit from a wealth of databases and Web sites with microbiological information, ranging from culture collection data, information on microbial diversity, taxonomic and phylogenetic data, biotechnological applications and taxonomic expertise. Efforts are required to stimulate the integration of complex molecular and image databases with more traditional information resources, such as bibliographic, strain data, compendia of species descriptions and metabolic products databases. Coordinating and linking mechanisms are needed in order to promote the development of protocols, guidelines and minimal standards to ensure data quality, Future challenges to the scientific use of Internet resources include the setting up of clearing-house mechanisms and virtual libraries for the organization of the microbiological resources on the network.174179549850

SCREENING OF LIGNIN-DEGRADING FUNGI FOR REMOVAL OF COLOR FROM KRAFT MILL WASTE-WATER WITH NO ADDITIONAL EXTRA CARBON-SOURCE

A screening of 51 ligninolytic strains of fungi to examine their ability to decolorized phenolic industrial effluent was carried out. The selection showed that Lentinus edodes (UEC-2019) strain removed 73% of colour in 5 days, without any additional carbon sources. Under these conditions, L. edodes was more efficient than the known Phanerochaete chrysosporium (BKM-F-1767) strain (e.g. COD reductions were 60% and 26%, respectively).13857157

Characterization of selected strains of Mucorales using fatty acid profiles

The fatty acid profiles of several fungi of the order Mucorales (Zygomycetes), including Backusella lamprospora (Lendner) Benny and R.K. Benj., Benjaminiella youngii P.M. Kirk, Circinella simplex van Tieghem, Cunninghamella blakesleeana Lendner, Mortierella ramanniana (Moller) Linnem., Mucor circinelloides f. janssenii (Lendner) Schipper, Mycotypha microspora Fenner, Rhizomucor miehei (Cooney and R. Emerson) Schipper and Rhizomucor pusillus (Lindt) Schipper, and of Volutella sp. Fr., from the class Ascomycetes, were qualitatively analysed by gas-liquid chromatography in order to determine the taxonomic value of these chemotaxonomic markers. The fatty acids present in all strains were palmitic (16:0), oleic (18:1), linoleic (18:2) and gamma-linolenic (18:3) acid, with the exception that the latter was not found in Volutella sp. Chemotaxonomic markers for some species and genera were obtained, including a non-identified fatty acid, FAME8 (minimum and maximum retention times of 27.92 and 28.28 minutes) for Rhizomucor miehei CCT 2236 and Rhizomucor pusillus CCT 4133, and FAME3 (minimum and maximum of 16.53 and 16.61 minutes) for Benjaminiella youngii CCT 4121. The chemotaxonomic marker of the order Mucorales was the fatty acid 18:3 omega 6, confirming previous data from literature. The results of the present study suggest that qualitative fatty acid analysis can be an important chemotaxonomic tool for the classification of fungi assigned to the order Mucorales (Zygomycetes).29427628

CHARACTERIZATION OF BACILLUS-THURINGIENSIS AND RELATED BACTERIA BY RIBOSOMAL-RNA GENE RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISMS

Ribosomal RNA gene restriction patterns have been determined for 43 strains of Bacillus thuringiensis representing 10 serovars and eight reference strains of B. anthracis, B. cereus and B. mycoides. Strains within a B. thuringiensis serovar produced highly related or identical ribotype patterns: in particular, 12 strains of serovar israelensis, five strains of serovar kurstaki, two strains of serovar galleriae and three strains of serovar aizawa produced ribotype patterns consistent with serotype designations. Moreover, variety tenebrionis (serotype 8a8b). a coleopteran pathogen, could be distinguished from the more common lepidopteran pathogens of this serotype (serovar morrisoni) by ribotyping. The correlation of ribotype patterns with serotype suggests a clonal population structure for B. thuringiensis.14051015102

CHARACTERIZATION BY POLYACRYLAMIDE-GEL ELECTROPHORESIS OF WHOLE-CELL PROTEINS OF SOME BACILLUS-THURINGIENSIS SUBSP ISRAELENSIS STRAINS ISOLATED IN BRAZIL

Of 14 strains of Bacillus thuringiensis selected from 956 isolates from soil samples from Brazil, 12 were toxic to larvae of Aedes fluviatilis and two were nontoxic. Nine of the 14 strains were serotyped as subspecies israelensis (serotype 14), one as subspecies kurstaki (serotype 3a 3b) one as subspecies morrisoni (serotype 8a 8b) and three did not agglutinate any antisera. Electrophoresis of whole cell proteins showed that all subsp. israelensis strains formed a homogeneous group which included two non-typable toxic strains, and could be readily distinguished from reference strains toxic for lepidoptera or coleoptera.17110410

PHENOLOXIDASES AND HYDROLASES FROM PYCNOPORUS-SANGUINEUS (UEC-2050 STRAIN) - APPLICATIONS

The basidiomycete, Pycnoporus sanguineus, possess lignin peroxidase, Mn-peroxidase, phenoloxidases, xylanase and beta-glucosidase activities when grown on malt extract. A large induction, mainly in laccase activity with malt extract/E1 effluent (46 U l-1), malt extract (100 U l-1) and malt extract/Eucalyptus grandis wood (61 U l-1) as carbon sources was found. The phenoloxidase capacity along with the presence of beta-glucosidase P. sanguineus led us investigate its use in effluent treatment. This fungus was efficient not only in chromophore group transformations but also in the reduction of phenols, biochemical and chemical oxygen demands, and toxicity.29321922

Metabolism of aromatic hydrocarbons by the filamentous fungus Cyclothyrium sp.

The metabolism of biphenyl, naphthalene, anthracene, phenanthrene, pyrene and benzo[a]pyrene by Cyclothyrium sp. CBS 109850, a coelomycete isolated for the first time in Brazil from industrially polluted estuarine sediment, was studied. The metabolites were extracted and separated by high performance liquid chromatography (HPLC) and characterized by UV spectral analyses and mass, and proton nuclear magnetic resonance (H-1 NMR) spectrometry. Cyclothyrium sp. transformed biphenyl to 4-hydroxybiphenyl and anthracene to anthracene trans-1,2-dihydrodiol. This isolate metabolized 90% of [9-C-14] phenanthrene, producing phenanthrene trans-9,10-dihydrodiol as a major metabolite, phenanthrene trans-3,4-dihydrodiol, 1-hydroxyphenanthrene, 3-hydroxyphenanthrene, 4-hydroxyphenanthrene, and a novel metabolite, 2-hydroxy-7-methoxyphenanthrene. Circular dichroism spectra analyses indicated that the major enantiomers of phenanthrene trans-9, 10-dihydrodiol, phenanthrene trans-3,4-dihydrodiol and pyrene trans-4,5-dihydrodiol, a pyrene metabolite produced previously by Cyclothyrium sp. CBS 109850, were predominantly in the (R,R) configuration, revealing a high stereoselectivity for initial monooxygenation and enzymatic hydration of phenanthrene and pyrene by Cyclothyrium sp. CBS109850. The results also show a high regioselectivity since the K-regions of phenanthrene and pyrene were the major sites of metabolism. (C) 2004 Elsevier Ltd. All rights reserved.57894395

Screening filamentous fungi isolated from estuarine sediments for the ability to oxidize polycyclic aromatic hydrocarbons

Nineteen. lamentous fungi, isolated from estuarine sediments in Brazil, were screened for degradation of polycyclic aromatic hydrocarbons (PAH). The fungal isolates were incubated with pyrene. The cultures were extracted and metabolites in the extracts were detected by high performance liquid chromatography (HPLC) and u.v. spectral analyses. Six fungi were selected for further studies using [4,5,9,10-C-14] pyrene. Cyclothyrium sp., Penicillium simplicissimum, Psilocybe sp., and a sterile mycelium demonstrated the ability to transform pyrene. Cyclothyrium sp. was the most efficient fungus, transforming 48% of pyrene to pyrene trans-4,5-dihydrodiol, pyrene-1,6-quinone, pyrene-1,8-quinone and 1-hydroxypyrene. This fungus was also evaluated with a synthetic mixture of PAH. After 192 h of incubation, Cyclothyrium sp. was able to degrade simultaneously 70, 74, 59 and 38% of phenanthrene, pyrene, anthracene and benzo[a]pyrene, respectively.19439940