Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

Background Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. Results Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. Conclusions The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.

High-quality draft genome sequence of pantanalinema sp. GBBB05, a cyanobacterium from cerrado biome

Cyanobacteria comprise one of the oldest and most diverse phyla in the Bacteria domain and are recognized for their importance in the biosphere evolution. Members of this phylum can be found in a wide variety of environments reflecting their photosynthetic ability, adaptability to various environmental conditions, and diversified metabolism. Such characteristics make cyanobacteria one of the preferred targets for research on bioactive compounds and new enzymes (Schirrmeister et al., 2011; Dittmann et al., 2015). Pantanalinema was described as a new genus of the Leptolyngbyaceae cyanobacterial family by a polyphasic approach, which included morphological characteristics, 16S rRNA gene phylogeny, 16S-23S ITS rRNA secondary structures, and physiological characteristics such as adaptability to pH variations (Vaz et al., 2015). This genus has been described only in Brazilian biomes such as the Pantanal and the Amazon, the first isolates being found in a lake. These Pantanalinema isolates were characterized by their ability to grow over a wide pH range (pH 4 to 11) as well as to modify the culture medium pH around neutrality (pH 6 to 7.4). Due to these characteristics, it is thought that this genus can occupy a variety of ecological niches, such as alkaline or slightly acidic water bodies (Vaz et al., 2015; Genuário et al., 2017). Taxonomic classification of Pantanalinema isolates requires the use of molecular markers as this genus is morphologically very similar to the recently described genus Amazoninema, which, in turn, has comparable morphology to other genera of the Leptolyngbyaceae family (Genuário et al., 2018). In this work, we report the genome sequence of a new Pantanalinema strain, named GBBB05, which was isolated from the Brazilian Cerrado biome. This is the first genome assembly for the Pantanalinema genus, which, along with the analyses provided here, is expected to enhance our understanding of this genus’s metabolic potential

A comparative genomic analysis of Xanthomonas arboricola pv. juglandis strains reveal hallmarks of mobile genetic elements in the adaptation and accelerated evolution of virulence

Xanthomonas arboricola pv. juglandis (Xaj) is the most significant aboveground walnut bacterial pathogen. Disease management uses copper-based pesticides which induce pathogen resistance. We examined the genetic repertoire associated with adaptation and virulence evolution in Xaj. Comparative genomics of 32 Xaj strains reveal the possible acquisition and propagation of virulence factors via insertion sequences (IS). Fine-scale annotation revealed a Tn3 transposon (TnXaj417) encoding copper resistance genes acquired by horizontal gene transfer and associated with adaptation and tolerance to metal-based pesticides commonly used to manage pathogens in orchard ecosystems. Phylogenomic analysis reveals IS involvement in acquisition and diversification of type III effector proteins ranging from two to eight in non-pathogenic strains, 16 to 20 in pathogenic strains, besides six other putative effectors with a reduced identity degree found mostly among pathogenic strains. Yersiniabactin, xopK, xopAI, and antibiotic resistance genes are also located near ISs or inside genomic islands and structures resembling composite transposons.

High-quality draft genome sequence resources of eight Xylella fastidiosa strains isolated from citrus, coffee, plum and hibiscus in South America.

Xylella fastidiosa subsp. pauca , once confined to South America and infecting mainly citrus and coffee plants, has been found to be associated with other hosts and in other geographic regions. We present high-quality draft genome sequences of X. fastidiosa subsp. pauca strains J1a12, B111, U24D and XRB isolated from citrus plants in Brazil, strain Fb7 isolated from a citrus plant in Argentina and strains 3124, Pr8x and Hib4 isolated, respectively, from coffee, plum and hibiscus plants in Brazil. Sequencing was performed using Roche 454-GS FLX, MiSeq-Illumina or Pacific Biosciences platforms. These high-quality genome assemblies will be useful for further studies about the genomic diversity, evolution, and biology of X. fastidiosa.

High-quality draft genome sequence resources of eight Xylella fastidiosa strains isolated from citrus, coffee, plum and hibiscus in South America.

Xylella fastidiosa subsp. pauca , once confined to South America and infecting mainly citrus and coffee plants, has been found to be associated with other hosts and in other geographic regions. We present high-quality draft genome sequences of X. fastidiosa subsp. pauca strains J1a12, B111, U24D and XRB isolated from citrus plants in Brazil, strain Fb7 isolated from a citrus plant in Argentina and strains 3124, Pr8x and Hib4 isolated, respectively, from coffee, plum and hibiscus plants in Brazil. Sequencing was performed using Roche 454-GS FLX, MiSeq-Illumina or Pacific Biosciences platforms. These high-quality genome assemblies will be useful for further studies about the genomic diversity, evolution, and biology of X. fastidiosa.

O Acompanhante do Paciente Adulto Hospitalizado: percepção dos enfermeiros: uma abordagem qualitativa / El acompañante del paciente adulto hospitalizado; percepción de los enfermeros: una abordaje cualitativa / The Companion of the Adult Hospitalized Patient: nurses' perception: a qualitative boarding

This study, was aimed at analyzing the knowledge of nurse about institutional policies and its perceptions in relation to the stay of the companion of the hospitalized adult patient. 29 (100%) nurses that worked in the adult inpatient units, at a university-based philanthropic hospital institution from the city of São Paulo, of extra size and high complexity, associated to SUS. Most of the subjects were of the female sex with up to 10 years of post-graduation experience, did not know institucional policies established, however they had related to know the "Instruction Manual for Patients and Companions", of the Institution. The content analysis was used to study the perceptions of the nurses in relation to the stay of companions. This analysis permitted the identification of thematic units, from which analysis units emerged that led to the establishment of the categories. The categories analyzed with a basis on the theoretical principles of Peplau's Interpersonal Relations in Nursing in the following phases: Orientation, Identification, Exploration and Resolution. The participation of the nurse as an element capable of establishing a process of interaction in the relationship between the professional and the companion seeking integration between both parties, was understood as as result of the awareness of the nurse in relation to a competent practice in its intervention, in situations of assistance to the companion.

Este estudio tuvo como objetivo analizar el conocimiento del enfermero sobre las políticas institucionales y su percepción cuánto la permanencia del acompañante del paciente adulto hospitalizado. Incluyó 29 (100%) de los enfermeros que actuaban en las Unidades de Internación de Adultos, en una institución de hospital filantrópico, universitario, de la ciudad de San Pablo, Brasil, de porte extra, de alta complejidad, en convenio con el Sistema Único de Salud del Gobierno. Los sujetos era del sexo femenino con hasta 10 años de graduados, sobre el conocimiento de las políticas institucionales establecidas, la mayoría no las conocía. Con respecto a la percepción de los enfermeros sobre la permanencia de los acompañantes, se utilizó el análisis de contenido que posibilitó la identificación de unidades temáticas, de las cuales surgieron unidades de análisis que condujeron al establecimiento de las categorías analizadas con base en los principios teóricos de la Relación Interpersonal en Enfermería de Peplau en las fases de: Orientación, Identificación, Exploración y Resolución. La participación del enfermero, como elemento capaz de establecer un proceso de interacción en la relación entre el profesional y el acompañante, buscando la integración entre ambos, se entendió como resultante de la concientización del enfermero con relación a una práctica competente en su intervención en situaciones de asistencia al acompañante.

Este estudo teve como objetivo analisar o conhecimento do enfermeiro sobre as políticas adotadas pela Instituição e a sua percepção quanto a permanência dos acompanhantes junto ao paciente adulto hospitalizado. Participaram 29 (100%) enfermeiros que atuavam nas unidades de internação de adultos, de uma Instituição hospitalar filantrópica, universitária, da cidade São Paulo, de porte extra, de alta complexidade, conveniada com o Sistema Único de Saúde. Os sujeitos eram em maior número do sexo feminino, com até 10 anos de formados, não conheciam as políticas institucionais estabelecidas, porém referiram conhecer o “Manual de Orientação ao Paciente e Acompanhante”, da Instituição. Para analisar a percepção dos enfermeiros sobre a permanência dos acompanhantes utilizou-se a análise de conteúdo que possibilitou a identificação de unidades temáticas, das quais emergiram unidades de análise que conduziram ao estabelecimento das categorias. As categorias foram analisadas com base nos princípios teóricos do Relacionamento Interpessoal em Enfermagem de Peplau, nas fases de: Orientação, Identificação, Exploração e Resolução. A participação do enfermeiro como elemento capaz de estabelecer um processo de interação no relacionamento entre o profissional e o acompanhante buscando a integração entre ambos, entendeu-se como decorrente da conscientização desse profissional em relação a uma prática competente na sua intervenção, em situações de assistência ao acompanhante.

The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane

O sequenciamento de ESTs (etiquetas de seqüências transcritas) tem possibilitado a descoberta de muitos novos genes em uma ampla variedade de organismos. Um aumento do aproveitamento desta informaçäo pela comunidade científica tem sido possível graças ao desenvolvimento de base de dados contendo seqüências completamente anotadas. O trabalho aqui relatado teve como objetivo a identiflcaçäo de ESTs de cana de açúcar seqüenciadas através do projeto SUCEST (http://sucest.lad.ic.unicamp.br) que codificam para proteínas envolvidas em mecanismos de transduçäo de sinal. Nós também preparamos um catálogo dos componentes de transduçäo de sinal da cana de açúcar (SUCAST) englobando as principais categorias e vias conhecidas (http://sucest.lad.ic.unicamp.br/private/mining-reports/QG/QG-mining.htm). ESTs codificadoras de enzimas envolvidas nas rotas de biossíntese de hormônios (giberelinas, etileno, auxinas, ácido abscíssico, ácido jasmônico) foram encontradas e sua expressäo específica nos tecidos foi inferida a partir de seu enriquecimento nas diferentes bibliotecas. Quando possível, transmissores do sinal hormonal e da resposta a peptídeos produzidos pela planta foram associados a suas respectivas vias. Mais de 100 receptores foram encontrados na cana de açúcar, entre os quais uma grande família de receptores Ser/Thr quinase e também de fotoreceptores, receptores do tipo histidina quinase e seus respectivos reguladores da resposta. Proteínas G e GTPases pequenas foram também analisadas e comparadas com membros destas famílias já conhecidos em mamíferos e plantas. As vias principais que envolvem a participaçäo de proteínas quinases e fosfatases foram mapeadas, em especial as vias da quinase MAP quinase e do inositol que säo bem estudadas em plantas.