Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

MOTIVATION: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked. RESULTS: More than 1 million hyper-variable internal transcribed spacer 1 (ITS1) sequences of fungal origin have been analyzed. The ITS1 sequences were first properly extracted from 454 reads using generalized profiles. Then, otupipe, cd-hit-454, ESPRIT-Tree and DBC454, a new algorithm presented here, were used to analyze the sequences. A numerical assay was developed to measure the reproducibility and robustness of these algorithms. DBC454 was the most robust, closely followed by ESPRIT-Tree. DBC454 features density-based hierarchical clustering, which complements the other methods by providing insights into the structure of the data. AVAILABILITY: An executable is freely available for non-commercial users at ftp://ftp.vital-it.ch/tools/dbc454. It is designed to run under MPI on a cluster of 64-bit Linux machines running Red Hat 4.x, or on a multi-core OSX system. CONTACT: dbc454@vital-it.ch or nicolas.guex@isb-sib.ch.

An ultrastructural approach to analogies between fungal structures and needle fibre calcite

Needle fiber calcite (NFC) is an ubiquitous terrestrial secondary calcium carbonate mineral often associated with calcitic nanofibers. NFC's origin has been debated for a long time and a fungal origin is often proposed. Fungi are known to be involved in mineral weathering and production of metal oxalate, but little information exists regarding the genesis of other minerals, such as calcite. In this study, a comparison of similar ultrastructural characteristics of fungal hyphae and NFC has been performed to highlight analogies between both features. These analogies clearly demonstrate the probable close relationship between fungal filaments (hyphae and rhizomorphs) and NFC and its associated nanofibers.

The ecological significance of arbuscular mycorrhizal fungal effects on clonal reproduction in plants

The population ecology of clonal plants depends on the number and distribution of ramets formed during growth. Variation in clonal reproduction has previously been explained by variation in effects of abiotic resource heterogeneity and by plant genotypic variation. Different co-occurring species of the mutualistic arbuscular mycorrhizal fungi (AMF) have been shown to differentially alter growth traits of Prunella vulgaris which we hypothesize would lead to changes in clonal reproduction. Two experiments were carried out to test whether different co-occurring mycorrhizal fungi significantly influence clonal reproduction of P. vulgaris whether this effect also occurs when P. vulgaris is growing in an artificial plant community and how the effects compare with plant genotype effects on clonal growth of P. vulgaris. In the first experiment the number of ramets of P. vulgaris growing in a plant community of simulated calcareous grassland was significantly affected by inoculation with different mycorrhizal fungi. The number of ramets produced by P. vulgaris differed by a factor of up to 1.8 with different mycorrhizal fungi. The fungal effects on the number of new ramets were independent of their effects on the biomass of P. vulgaris. In a second experiment 17 different genotypes of P. vulgaris were inoculated with different mycorrhizal fungi. There were significant main effects of genotypes and mycorrhizal fungi on clonal reproduction of P. vulgaris. The effect of different mycorrhizal fungi contributed more than the effect of plant genotype to variation in size and ramet production. However mean stolon length and spacer length which determine the spatial arrangement of ramets were only significantly affected by plant genotype. There were no mycorrhizal fungal X plant genotype interactions on clonal growth of P. vulgaris indicating that there is no obvious evidence that selection pressures would favor further coevolution between P. vulgaris and mycorrhizal fungal species. In natural communities plants can be colonized by several different AMF at the same time. The effect of the mixed AMF treatment on the growth and clonal reproduction of P. vulgaris could not be predicted from the responses of the plants to the single AMF To what extent however the patterns of colonization by different AMF differ among plants in a natural community is unknown. Since the effects of AMF on growth and clonal reproduction occur on a population of P. vulgaris in a microcosm plant community and because the effects are also as great as those caused by plant genotypic variation we conclude that the effects are strong enough to potentially affect population size and variation of clonal plants in communities.

Comparative Genomics Suggests that the Fungal Pathogen Pneumocystis Is an Obligate Parasite Scavenging Amino Acids from Its Host's Lungs.

Pneumocystis jirovecii is a fungus causing severe pneumonia in immuno-compromised patients. Progress in understanding its pathogenicity and epidemiology has been hampered by the lack of a long-term in vitro culture method. Obligate parasitism of this pathogen has been suggested on the basis of various features but remains controversial. We analysed the 7.0 Mb draft genome sequence of the closely related species Pneumocystis carinii infecting rats, which is a well established experimental model of the disease. We predicted 8'085 (redundant) peptides and 14.9% of them were mapped onto the KEGG biochemical pathways. The proteome of the closely related yeast Schizosaccharomyces pombe was used as a control for the annotation procedure (4'974 genes, 14.1% mapped). About two thirds of the mapped peptides of each organism (65.7% and 73.2%, respectively) corresponded to crucial enzymes for the basal metabolism and standard cellular processes. However, the proportion of P. carinii genes relative to those of S. pombe was significantly smaller for the "amino acid metabolism" category of pathways than for all other categories taken together (40 versus 114 against 278 versus 427, P<0.002). Importantly, we identified in P. carinii only 2 enzymes specifically dedicated to the synthesis of the 20 standard amino acids. By contrast all the 54 enzymes dedicated to this synthesis reported in the KEGG atlas for S. pombe were detected upon reannotation of S. pombe proteome (2 versus 54 against 278 versus 427, P<0.0001). This finding strongly suggests that species of the genus Pneumocystis are scavenging amino acids from their host's lung environment. Consequently, they would have no form able to live independently from another organism, and these parasites would be obligate in addition to being opportunistic. These findings have implications for the management of patients susceptible to P. jirovecii infection given that the only source of infection would be other humans.

Materiales para una flora de las algas del NE de España. I. Zygnemales

Posteriormente a la publicación de mi primera contribución a la flora algológica de nuestras aguas dulces (1944), he dado preferencia a la preparación de trabajos de carácter local y ecológico, por entender que éstos podían conducir más rápidamente al planteamiento, y quizá a la resolución, de problemas de interés superior al puramente taxonómico. Pero el estudio de muchos centenares de muestras de algas, procedentes de localidades dispersas de Cataluña y de comarcas limítrofes, ha ido prosiguiendo independientemente, permitiendo reunir una cantidad considerable de datos inéditos. Eáta nota es la primera de una serie de contribuciones taxonómicas a nuestra flora algológica, que tendrán como base el material no utilizado en otros trabajos de limnología regional o local.

Materiales para una flora de las algas del NE de España. II, Chrysophyceae, Heterocontae, Dinophyceae, Euglenineae

En este segundo artículo (véase Coüecianea Botánica, vol. I, n.' 9) se estudian grupos de particular interés; varios de ellos requieren trabajar con material vivo y son menos conocidos que el resto de las algas. Se da cuenta de especies que no fueron citadas anteriormente, de rectificaciones y de diversos datos sobre especies ya mencionadas en nuestra flora. Varias formas, posiblemente especies nuevas, que no han podido ser completamente estudiadas, son también tenidas en consideración. Numerosas nuevas citas de las especies menos raras se encontrarán en otro trabajo: sobre la vegetación, todavía no publicado.

Materiales para una flora de las algas del NE de España, III a, Euchlorophyceae

Al presente artículo pueden referirse también las advertencias generales que encabezan los que le precedieron (véase Collectanea Botánica, vol. I, pág. 107, y vol. 11, pág. 99). En éste se citan 122 formas, más de la mitad de las cuales son mencionadas por primera vez de Cataluña.

Materiales para una flora de las algas del NE. de España, IV a, Cyanophyceae

La peculiar estructura celular de las cianofíceas puede explicar las dificultades que su sistemática ofrece, notablemente superiores a las que presentan los otros grupos de algas, donde los tipos específicos se suelen mostrar mucho más constantes y caracterizables. Basta una experiencia mediana para darse cuenta de la existencia de un elevado número de razas más o menos distintas dentro de cada «especie» de cianofícea ; consecuencia de la forma de transmitirse los materiales de herencia y de la ausencia de anfimixis...

Materiales para una flora de las algas del NE de España, V a, Bacillariophyta

En las páginas siguientes se estudian las diatomeas contenidas en una serie de recolecciones que no han sido utilizadas en la preparación de trabajos de tipo regional publicados anteriormente, aunque una parte de estos materiales inéditos se aprovechó para un estudio sobre la vegetación de las aguas dulces de Cataluña (Vegetatio, vol. i, págs. 258-284, 1949), en el que se pueden encontrar algunas referencias complementarias sobre ecología y biocenología de las especies.

Materiales para una Flora de las algas del NE de España, VI, Desmidiales, Phodophyceae

Como en anteriores trabajos de esta serie, se reunen en el presente cierto número de datos inéditos sobre especies observadas en recolecciones un tanto esporádicas. La representación de las desmidiales y de las rodofíceas en las tierras bajas de Cataluña es pobre; en conjunto, en la siguiente enumeración no figuran más que ochenta y cuatro nombres.

Materiales para una flora de las algas del NE. de España, VII suplemento

En esta nota adicional se reúnen datos sobre 140 especies, la mayor parte de ellas nuevas para la flora de las tierras bajas catalanas; se han incluido referencias inéditas sobre alguuas pocas formas ya citadas, pero que son raras o que no se encuentran fructificadas habitualmente (edogoniales, zignemales). La clorofícea Thamniochaete frutex se describe como especie nueva; una heteroconta no denominada representa verosímilmente un género nuevo, que deberá recibir nombre cuando pueda disponerse de mejor material.

Aportación a la Flora Bentónica de las Islas Baleares, V.

Los numerosos trabajos sobre fitobentos marino de las islas Baleares fueron recopilados en los catálogos florísticos de RIBERA & GÓMEZ (Collect. Bot. (Barcelona) 15: 377-406. 1984; Collect. Bot. (Barcelona) 16:25-41.1985). Posteriormente, debido a la realización de numerosos estudios bentónicos de la zona, se han publicado adiciones a dicho catálogo (PERICAS, Boll. Soc. Hist. Nat. Balears: 139-146.1984; BALLESTEROS, Bull. Inst. Cat. Hist. Nat. 51 (See. Bot, 5): 31-33. 1984; BALLESTEROS, Fol. Bot. Mise. 6: 65-70. 1989; RULL LLUCH, GÓMEZ GARRETA and RIBERA Collect. Bot. (Barcelona) 15: 377-406. 1987; CREMADES Anales Jard. Bot. Madrid 46 (1): 149-152. 1989; CREMADES A nales Jard. Bot. Madrid 46 (1): 341-343. 1989).