The maturation profile triggers differential expression of sugar metabolism genes in melon fruits.

Melons are commercially important crops that requires specific quality attributes for successful commercialization, including accumulation of sugars, particularly sucrose. This trait can be influenced by various factors, such as the type of ripening. Cucumis melo L. is an ideal species for studying sugar metabolism because it has both climacteric and non-climacteric cultivars. Thus, this study aimed to examine the gene expression of sucrose metabolism candidates using RT-qPCR, in conjunction with postharvest physiological analyzes and high-performance liquid chromatography-based sugar quantification, in the melon cultivars 'Gaúcho' (climacteric) and 'Eldorado' (non-climacteric). The results showed that sucrose synthase 1 played a role in the synthesis and accumulation of sucrose in both cultivars, whereas sucrose synthase 2 was more highly expressed in 'Gaúcho', contributing to lower hexose content. Invertase inhibitor 1 was more highly expressed in 'Eldorado' and may be involved in sugar-induced maturation. Neutral α-galactosidase had distinct functions, playing a role in substrate synthesis for the growth of young 'Eldorado' fruits, whereas in mature 'Gaúcho' fruits it participated in the metabolism of raffinose family oligosaccharides for sucrose accumulation. The expression of trehalose-6-phosphate synthase genes indicated a greater involvement of these enzymes in the sugar regulation in 'Gaúcho' melons. These findings shed light on the intraspecific differences related to fruit quality attributes in different types of maturation and contribute to a deeper understanding of the underlying molecular mechanisms involved in the metabolism of sugars in melons, which can inform breeding programs aimed at improving fruit quality attributes in this crop.

The new Ribopeaks (RPK-II): Updated and enlarged tool for bacterial classification based on r-protein m/z data.

Ribopeaks is a rapid, sensitive, and economic web tool for bacterial identification based on m/z data from MALDI-TOF MS. To provide greater accuracy and robustness in the Ribopeaks analyzes we present an updated bacterial identification tool version, called Ribopeaks II (RPK-II). RPK-II contains a larger database, with r-protein data from fully sequenced bacterial genomes and optimized algorithms. Furthermore, this new version provides additional information about the identified bacterium, regarding antibiotic resistance.

Molecular Techniques to Study Microbial Wastewater Communities

Abstract wastewater treatment (WT) is of major importance on modern cities, removing wastewater pollutants resultant from anthropogenic activities. The unique abilities of microbes to degrade organic matter, remove nutrients and transform toxic compounds into harmless products make them essential players in waste treatment. The microbial diversity determines the metabolic pathways that may occur in WT and quality of treated wastewater. Therefore, understanding WT microbial community structure, distribution, and metabolic functioning is essential for development and optimization of efficient microbial engineering systems. Since cultivation methods can only detect a small fraction of the microbial diversity, the use of culture-independent molecular methods has circumvented this issue, allowing unprecedented access to genes and genomes used for microbial composition and function evaluation. Traditional approaches like RAPD, DGGE, ARDRA, RISA, SSCP, T-RFLP, and FISH and modern approaches like microarray, qPCR, and metagenomics are essential techniques for identifying and depicting the total microbial community structure and their interaction with environmental and biotic factors. Thus, this review describes traditional and state of the art molecular techniques which provide insights into phylogenetic and functional activities of microbial assemblages in a WT system.

Transcriptome profiling of non-climacteric 'yellow' melon during ripening: insights on sugar metabolism.

BACKGROUND: The non-climacteric 'Yellow' melon (Cucumis melo, inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related pathways can contribute to the development of new field management and post-harvest practices, making it possible to deliver better quality fruits to consumers. RESULTS: The RNA-seq associated with RT-qPCR analyses of four maturation stages were performed to identify important enzymes and pathways that are involved in the ripening profile of non-climacteric 'Yellow' melon fruit focusing on sugar metabolism. We identified 895 genes 10 days after pollination (DAP)-biased and 909 genes 40 DAP-biased. The KEGG pathway enrichment analysis of these differentially expressed (DE) genes revealed that 'hormone signal transduction', 'carbon metabolism', 'sucrose metabolism', 'protein processing in endoplasmic reticulum' and 'spliceosome' were the most differentially regulated processes occurring during melon development. In the sucrose metabolism, five DE genes are up-regulated and 12 are down-regulated during fruit ripening. CONCLUSIONS: The results demonstrated important enzymes in the sugar pathway that are responsible for the sucrose content and maturation profile in non-climacteric 'Yellow' melon. New DE genes were first detected for melon in this study such as invertase inhibitor LIKE 3 (CmINH3), trehalose phosphate phosphatase (CmTPP1) and trehalose phosphate synthases (CmTPS5, CmTPS7, CmTPS9). Furthermore, the results of the protein-protein network interaction demonstrated general characteristics of the transcriptome of young and full-ripe melon and provide new perspectives for the understanding of ripening.

Multiple Effect of Different Plant Growth Promoting Microorganisms on Beans (Phaseolus vulgaris L. ) Crop

Abstract We evaluated the effect of combined Rhizobium tropici, Trichoderma asperellum and plant growth-promoting rhizobacteria (PGPR) in beans crop. The hypothesis that strains of T. asperullum, R. tropici and PGPR combined could improve growth, biomass accumulation and beans yield was tested under greenhouse and field conditions. The treatments consisted of control, mineral nitrogen application and inoculation, isolated and associated with the following microorganisms: Rhizobium tropici, Bacillus subtilis, Trichoderma asperellum and Burkholderia sp. 10N6. Results were evaluated by shoot dry weight (SDW) and root dry weight (RDW), number of nodules and yield components. In greenhouse environment all the microorganisms behaved similarly, and the treatments inoculated with Burkholderia sp. 10N6 (IBu) and R. tropici (IR) stood out regarding the production components. In field conditions the treatments IR and IRTBa presented the highest values of SDW and RDW. Our results suggest that inoculation with R. tropici, T. asperellum and PGPR may promote beans growth and bring benefits to shoot and root accumulation, increase the number of nodules as well as improve yield components, contributing to a sustainable agriculture.

Liming and Nitrogen Fertilization Effects on Soil Microbial Community in Long Term No-till

Abstract Soil management influences organic matter decomposition rates as well soil microbial community functional behavior. No-till (NT) is the most used management system by farmers due to its conservation practices and high productivity. The main objective of this study was to evaluate the impact of surface-applied lime, nitrogen (N) application, and black oat residues on soil microbial community of a Typic Hapludox under continuous NT. Therefore, soil chemical attributes, microbial biomass carbon, basal respiration, metabolic quotient, most probable number of diazotrophs, as well as bacterial functional analysis were performed. The effect of liming and N fertilization amendments inputs were saw in soil respiration and metabolic quotient measurements, showing them to be good indicators of soil quality. Further studies should be carried out in order to molecularly identify microbial communities present in soils with different liming and N fertilization management to evaluate the behavior of specific bacterial taxa under such conditions.

Ribopeaks: a web tool for bacterial classification through m/z data from ribosomal proteins.

Summary: MALDI-TOF MS is a rapid, sensitive and economic tool for bacterial identification. Highly abundant bacterial proteins are detected by this technique, including ribosomal proteins (r-protein), and the generated mass spectra are compared with a MALDI-TOF MS spectra database. Currently, it allows mainly the classification of clinical bacteria due to the limited number of environmental bacteria included in the spectra database. We present a wide-ranging bacterium classifier tool, called Ribopeaks, which was created based on r-protein data from the Genbank. The Ribopeaks database has more than 28 500 bacterial taxonomic records. It compares the incoming m/z data from MALDI-TOF MS analysis with models stored in the Ribopeaks database created by machine learning and then taxonomically classifies the bacteria. Availability and implementation: The software is available at http://www.ribopeaks.com. Supplementary information: Supplementary data are available at Bioinformatics online.

Labeled Azospirillum brasilense wild type and excretion-ammonium strains in association with barley roots.

Soil bacteria colonization in plants is a complex process, which involves interaction between many bacterial characters and plant responses. In this work, we labeled Azospirillum brasilense FP2 (wild type) and HM053 (excretion-ammonium) strains by insertion of the reporter gene gusA-kanamycin into the dinitrogenase reductase coding gene, nifH, and evaluated bacteria colonization in barley (Hordeum vulgare). In addition, we determined inoculation effect based on growth promotion parameters. We report an uncommon endophytic behavior of A. brasilense Sp7 derivative inside the root hair cells of barley and highlight the promising use of A. brasilense HM053 as plant growth-promoting bacterium.

Quinolone resistance and ornithine decarboxylation activity in lactose-negative Escherichia coli.

Quinolones and fluoroquinolones are widely used to treat uropathogenic Escherichia coli infections. Bacterial resistance to these antimicrobials primarily involves mutations in gyrA and parC genes. To date, no studies have examined the potential relationship between biochemical characteristics and quinolone resistance in uropathogenic E. coli strains. The present work analyzed the quinolone sensitivity and biochemical activities of fifty-eight lactose-negative uropathogenic E. coli strains. A high percentage of the isolates (48.3%) was found to be resistant to at least one of the tested quinolones, and DNA sequencing revealed quinolone resistant determining region gyrA and parC mutations in the multi-resistant isolates. Statistical analyses suggested that the lack of ornithine decarboxylase (ODC) activity is correlated with quinolone resistance. Despite the low number of isolates examined, this is the first study correlating these characteristics in lactose-negative E. coli isolates.

Quinolone resistance and ornithine decarboxylation activity in lactose-negative Escherichia coli

Quinolones and fluoroquinolones are widely used to treat uropathogenic Escherichia coli infections. Bacterial resistance to these antimicrobials primarily involves mutations in gyrA and parC genes. To date, no studies have examined the potential relationship between biochemical characteristics and quinolone resistance in uropathogenic E. coli strains. The present work analyzed the quinolone sensitivity and biochemical activities of fifty-eight lactose-negative uropathogenic E. coli strains. A high percentage of the isolates (48.3%) was found to be resistant to at least one of the tested quinolones, and DNA sequencing revealed quinolone resistant determining region gyrA and parC mutations in the multi-resistant isolates. Statistical analyses suggested that the lack of ornithine decarboxylase (ODC) activity is correlated with quinolone resistance. Despite the low number of isolates examined, this is the first study correlating these characteristics in lactose-negative E. coli isolates.

Multiple gene sequence analysis using genes of the bacterial DNA repair pathway

The ability to recognize and repair abnormal DNA structures is common to all forms of life. Physiological studies and genomic sequencing of a variety of bacterial species have identified an incredible diversity of DNA repair pathways. Despite the amount of available genes in public database, the usual method to place genomes in a taxonomic context is based mainly on the 16S rRNA or housekeeping genes. Thus, the relationships among genomes remain poorly understood. In this work, an approach of multiple gene sequence analysis based on genes of DNA repair pathway was used to compare bacterial genomes. Housekeeping and DNA repair genes were searched in 872 completely sequenced bacterial genomes. Seven DNA repair and housekeeping genes from distinct metabolic pathways were selected, aligned, edited and concatenated head-to-tail to form a super-gene. Results showed that the multiple gene sequence analysis using DNA repair genes had better resolution at class level than the housekeeping genes. As housekeeping genes, the DNA repair genes were advantageous to separate bacterial groups at low taxonomic levels and also sensitive to genes derived from horizontal transfer.

Seasonal changes in dominant bacterial taxa from acidic peatlands of the Atlantic Rain Forest.

The acidic peatlands of southern Brazil are essential for maintenance of the Atlantic Rain Forest, one of the 25 hot-spots of biodiversity in the world. While these ecosystems are closely linked to conservation issues, their microbial community ecology and composition remain unknown. In this work, histosol samples were collected from three acidic peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Culturing and culture-independent approaches based on SSU rRNA gene pyrosequencing were used to survey the bacterial community and to identify environmental factors affecting the biodiversity and microbial metabolic potential of the Brazilian peatlands. All acidic peatlands were dominated by the Acidobacteria phylum (56-22%) followed by Proteobacteria (28-12%). The OTU richness of these phyla and the abundance of their Gp1, Gp2, Gp3, Gp13, Rhodospirillales and Caulobacteriales members varied according to the period of collection and significantly correlated with the rainy season. However, despite changes in acidobacterial and proteobacterial communities, rainfall did not affect the microbial metabolic potential of the southern Brazilian Atlantic Rain Forest peatlands, as judged by the metabolic capabilities of the microbial community.

Ardra profiles of bacteria and archaea in mangrove sediments with different levels of contamination in the estuarine complex of Paranaguá, Brazil

The mangrove's sediments from the coastal areas under human activities may contain significant contaminations by hydrocarbons, even when there are no visual evidences of it. The microorganisms are essential to these ecosystems, especially in the control of their chemical environment. Sediment samples were collected in two regions under different environment conditions (pristine and contaminated) of the Paranaguá Estuarine Complex (Paranaguá Bay and Laranjeiras Bay), Brazil. Aliphatic hydrocarbons were determined by the GC-FID to assess the status of contamination of the studied areas. The total DNA was extracted from these samples. The 16S rRNA gene was amplified by the PCR reactions with the pair of primers 21F and 958R for the archaeal domain, and 27F and 1492R for the bacterial domain. Comparisons of communities were made by the ARDRA technique, using the HinfI restriction enzyme. The phosphate concentration showed significant differences between the two regions. The aliphatic hydrocarbons analysis showed the presence of unresolved complex mixture (UCM), an indicator of oil contamination, in the samples from the Paranaguá Bay, which was corroborated by the concentration of total aliphatic hydrocarbons. The ARDRA profile indicated that the structure of archaeal and bacterial communities of the sampled areas was very similar. Therefore, the anthropogenic influences in the Paranaguá Bay showed to be not sufficient to produce disturbances in the prokaryotic dominant groups.