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| Brown, Mark V.; Lauro, Federico M.; Demaere, Matthew Z.; Muir, Les; Wilkins, David; Thomas, Torsten; Riddle, Martin J.; Fuhrman, Jed A.; Andrews-pfannkoch, Cynthia; Hoffman, Jeffrey M.; Mcquaid, Jeffrey B.; Allen, Andrew; Rintoul, Stephen R.; Cavicchioli, Ricardo. |
| The ubiquitous SAR11 bacterial clade is the most abundant type of organism in the world’s oceans, but the reasons for its success are not fully elucidated. We analysed 128 surface marine metagenomes, including 37 new Antarctic metagenomes. The large size of the data set enabled internal transcribed spacer (ITS) regions to be obtained from the Southern polar region, enabling the first global characterization of the distribution of SAR11, from waters spanning temperatures −2 to 30°C. Our data show a stable co-occurrence of phylotypes within both ‘tropical’ (>20°C) and ‘polar’ (<10°C) biomes, highlighting ecological niche differentiation between major SAR11 subgroups. All phylotypes display transitions in abundance that are strongly correlated with... |
| Tipo: Text |
Palavras-chave: Adaptive radiation; Antarctica; Metagenome; Pelagibacter; Phylotype distribution. |
| Ano: 2012 |
URL: https://archimer.ifremer.fr/doc/00140/25132/23242.pdf |
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| Zapata-perez, Ruben; Garcia-saura, Antonio G.; Jebbar, Mohamed; Golyshin, Peter N.; Sanchez-ferrer, Alvaro. |
| Nicotinamidases catalyze the hydrolysis of the amide bond in nicotinamide (NAM) to produce ammonia and nicotinic acid (NA). These enzymes are an essential component of the NAD(+) salvage pathway and are implicated in the viability of several pathogenic organisms. Its absence in humans makes them a promising drug target. In addition, although they are key analytical biocatalysts for screening modulators in relevant biomedical enzymes, such as sirtuins and poly-ADP-ribosyltransferases, no commercial sources are available. Surprisingly, the finding of an affordable source of nicotinamidase from metagenomic libraries is hindered by the absence of a suitable and fast screening method. In this manuscript, we describe the development of two new whole-cell methods... |
| Tipo: Text |
Palavras-chave: Amidohydrolases; Nicotinamidase; Functional screening; Metagenome; Library; High-throughput screening assays. |
| Ano: 2016 |
URL: http://archimer.ifremer.fr/doc/00362/47269/47232.pdf |
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| LUVIZOTTO,DANICE M.; ARAUJO,JULIANA E.; SILVA,MICHELE DE CÁSSIA P.; DIAS,ARMANDO C. F.; KRAFT,BEATE; TEGETMEYE,HALINA; STROUS,MARC; ANDREOTE,FERNANDO D.. |
| Abstract Mangroves are ecosystems located in the transition zone between land and sea, characterized by periodic flooding that confer to its unique characteristics. Little is known about the transformation of nutrients that occur during the organic matter degradation in this system. In this study, we monitor the nitrogen transformations in soils from three mangroves with distinct levels of contamination using labeled 15NO3-. We also screened the mangroves metagenomes for the presence of genes that encode enzymes involved in denitrification (nirS, nirK, nosZ, norB and narG), anaerobic oxidation of ammonia (anammox) (hh, hao and hzo) and dissimilatory nitrate reduction to ammonium (DNRA) (nrfA). The transformations of 15NO3- indicated the balance of... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: N cycling; Anaerobiosis; Metagenome; Environmental contamination. |
| Ano: 2019 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652019000200503 |
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| Pereira,Rodrigo Matheus; Silveira,Érico Leandro da; Scaquitto,Denilson César; Pedrinho,Eliamar Aparecida Nascimbém; Val-Moraes,Silvana Pompéia; Wickert,Ester; Carareto-Alves,Lúcia Maria; Lemos,Eliana Gertrudes de Macedo. |
| Until recently, few studies were carried out in Brazil about diversity of bacterial soil communities. Aiming to characterize the bacterial population in the soil through 16S rRNA analysis, two types of soil have been analyzed: one of them characterized by intensive use where tomato, beans and corn were cultivated (CS); the other analyzed soil was under forest (FS), unchanged by man; both located in Guaíra, São Paulo State, Brazil. Using specific primers, 16S rRNA genes from metagenomic DNA in both soils were amplified by PCR, amplicons were cloned and 139 clones from two libraries were partially sequenced. The use of 16S rRNA analysis allowed identification of several bacterial populations in the soil belonging to the following phyla: Acidobacteria,... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Metagenome; Microbial diversity; 16S rRNA. |
| Ano: 2006 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822006000400007 |
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| Souza,Renata Carolini; Cantão,Maurício Egídio; Nogueira,Marco Antonio; Vasconcelos,Ana Tereza Ribeiro; Hungria,Mariangela. |
| ABSTRACT The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases > laccases > cellulases > proteases > amylases > pectinases. Statistically significant differences were attributed to the... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Metagenome; Microbiome; Soil enzymes; Soil management; No-tillage. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000400723 |
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