Exploring tRNA gene cluster in archaea

BACKGROUND Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain. OBJECTIVE Explore the occurrence of tRNA gene clusters in archaea. METHODS In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements. FINDINGS We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer. MAIN CONCLUSIONS tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.

Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota

Abstract In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.

Methanogenic toxicity evaluation of chlortetracycline hydrochloride

Background Anaerobic digestion is a technology applied successfully to converting organic matter into biogas. However, the presence of inhibitory compounds such as antibiotics can adversely affect methane production. The aim of this study is to evaluate the toxic effect of chlortetracycline hydrochloride (CLOR) on the methanogenic bacteria. In order to study the methanogenic toxicity of CLOR, different concentrations of CLOR (10, 50, 100, 200 mg L- 1) were evaluated by methanogenic toxicity assays using three feedings. Results Maximum methane production was obtained for the assays with 10 mg CLOR L- 1, the values obtained were 277 ± 4.07; 193 ± 11.31 and 166 ± 7.07 mL for the first, second and third feedings, respectively. The average values for acetic, propionic and butyric acid at start of the experiments were 2104 ± 139; 632 ± 7.6; 544 ± 26 mg L- 1, respectively. The VFA values obtained finally of the experiment were dependent on the evaluated antibiotic concentrations, indicating that the efficiency of methanogenesis is directly affected by the CLOR concentration. Conclusions CLOR is an effective methanogenic bacteria inhibitor. Moreover, the results show that CLOR has a bactericidal effect on methanogenic activity given that methane production did not recover during the third feeding. This study shows that the 50% inhibitory concentration (IC50) for methanogenic bacteria in 10 mg L- 1.

Búsqueda intencionada y reclasificación de muertes maternas en México: el efecto en la distribución de las causas / Intentional search and reclassification of maternal deaths in Mexico: The effect on the distribution of causes

Objetivo. Corregir la mala clasificación y mejorar la calidad de la información sobre la mortalidad materna en México. Material y métodos. A través de los registros clínicos y autopsias verbales, se estudiaron todas las defunciones certificadas como maternas y una selección de defunciones de mujeres en edad fértil, cuyas causas fueron consideradas como sospechosas de encubrir una muerte materna; todas ocurridas durante 2011 en México. Resultados. La búsqueda intencionada y reclasificación de muertes maternas permitió rescatar más de 100 muertes que no habían sido registradas ni codificadas inicialmente como maternas y se ratificaron o rectificaron las causas anotadas en los certificados de defunción. Este procedimiento también permitió reclasificar como muertes maternas 297 defunciones de la base preliminar del Instituto Nacional de Estadística y Geografía. Conclusiones. La Búsqueda Intencionada y Reclasificación de Muertes Maternas es un procedimiento muy útil para mejorar la calidad de la información sobre la mortalidad materna.

Objective. To correct the misclassification and improve the quality of information on maternal mortality in Mexico. Materials and methods. Using clinical records and verbal autopsies, we studied all deaths certified as maternal deaths as well as a selection of deaths of women of childbearing age whose causes were considered as suspected of hiding a maternal death, all of which occurred during 2011 within Mexico. Results. The deliberate search of maternal deaths and reclassification allowed the rescue of just over 100 deaths that were not originally registered or coded as maternal and confirmed or corrected the causes of death recorded on death certificates as confirmed maternal deaths. This procedure also allowed the reclassification of 297 maternal deaths of women in the groundwork of the National Institute of Statistics and Geography. Conclusions. International Search and Reclassification of Maternal Deaths is a very useful procedure for improving the classification of cases that were not classified as maternal deaths and the effect was greater with the coding of indirect obstetric deaths.

Prokaryotic communities of acidic peatlands from the southern Brazilian Atlantic Forest

The acidic peatlands of southern Brazil are ecosystems essential for the maintenance of the Atlantic Forest, one of the 25 hot-spots of biodiversity in the world. In this work, we investigated the composition of prokaryotic communities in four histosols of three acidic peatland regions by constructing small-subunit (SSU) rRNA gene libraries and sequencing. SSU rRNA gene sequence analysis showed the prevalence of Acidobacteria (38.8%) and Proteobacteria (27.4%) of the Bacteria domain and Miscellaneous (58%) and Terrestrial (24%) groups of Crenarchaeota of the Archaea domain. As observed in other ecosystems, archaeal communities showed lower richness than bacterial communities. We also found a limited number of Euryarchaeota and of known methanotrophic bacteria in the clone libraries.

Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia

Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the a subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95 percent similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified -the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean mcrα observed in the present study varied little, and presented approximately 70 percent identity in comparison with the mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

Purification and characterization of an extreme halothermophilic protease from a halophilic bacterium Chromohalobacter sp. TVSP101

An extreme halophilic bacterium was isolated from solar saltern samples and identified based on biochemical tests and 16S r RNA sequencing as Chromohalobacter sp. strain TVSP101. The halophilic protease was purified using ultrafiltration, ethanol precipitation, hydrophobic interaction column chromatography and gel permeation chromatography to 180 fold with 22% yield. The molecular mass of the protease determined by SDS PAGE was 66 kDa. The purified enzyme was salt dependent for its activity and stability with an optimum of 4.5 M NaCl. The optimum temperature for maximum protease activity was 75ºC. The protease was optimally active at pH 8 and retained more than 80% of its activity in the range of pH 7-10. Sucrose and glycine at 10% (w/v) were the most effective osmolytes, retained 100% activity in the absence of NaCl. The activity was completely inhibited by ZnCl2 (2 mM), 0.1% SDS and PMSF (1mM). The enzyme was not inhibited by 1mM of pepstatin, EDTA and PCMB. The protease was active and retained 100% it activity in 10% (v/v) DMSO, DMF, ethanol and acetone.

Avaliação da biodegradabilidade anaeróbia de lixiviados de aterro sanitários / Evaluate of the anaerobic biodegradability of landfill leachate

Os objetivos deste artigo foram investigar as condições ambientais e operacionais favoráveis ao desenvolvimento do teste de biodegradabilidade anaeróbia para lixiviados de aterro sanitário. As condições avaliadas foram a relação alimento/microrganismo (A/M), aclimatação do lodo, e toxicidade devido à alta concentração de amônia. Os resultados indicaram que a relação A/M equivalente a 0,45 apresentou-se como a mais favorável à realização do teste, e que o lodo empregado apresentou boa capacidade de adaptação ao lixiviado, não demandando aclimatação prévia. O lixiviado em questão apresentou relativamente baixa biodegradabilidade anaeróbia, associado aos resultados de estudos de biodegradabilidade aeróbia anteriores que sugerem que uma significativa fração de matéria orgânica é refratária mesmo ao metabolismo aeróbio,indica que o tratamento físico-químico deve ser utilizado como forma de pré ou pós-tratamento.

The objectives of this article were to investigate the favorable environment and operational conditions to the development of the anaerobic biodegradability test for landfill leachate. The evaluated conditions were the relation food/microrganismo (A/M), seed acclimatization, and toxicity due to high ammonia concentration. The results indicated that A/M relation equivalent to 0,45 was presented as most favorable to the accomplishment of the test, and that the seed used presented good capacity of adaptation to the leachate, not demanding previous acclimatization. The leachate in question presented relatively low anaerobic biodegradability, and associated to the results of previous studies of aerobic biodegradability suggest that a significant fraction of organic substance is refractory to the aerobic and anaerobic metabolism, indicating that the physical-chemical treatment must be used as form of pre or post-treatment.