Editorial Genomic and Postgenomic Approaches to Understand Environmental Microorganisms María-Eugenia Guazzaroni , 1 Raul Alberto Platero , 2 and Rafael Silva-Rocha 3 1 Faculty of Philosophy, Sciences and Letters at Ribeirao Preto, Ribeirao Preto, Brazil 2 Clemente Estable Biological Research Institute, Montevideo, Uruguay 3 Ribeirao Preto Medical School, Ribeirao Preto, Brazil Correspondence should be addressed to Rafael Silva-Rocha; [email protected] Received 4 September 2018; Accepted 4 September 2018; Published 24 October 2018 Copyright © 2018 María-Eugenia Guazzaroni et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The introduction of new high-throughput technologies has profoundly impacted the development of modern science outside the gene-centered understanding perceived in the earlier genomic era [1, 2]. Thus, low-cost platforms known as Next Generation Sequencing (NGS) technologies can pro- duce millions of sequences of DNA molecules with different yields and sequence lengths, having displayed a considerable reduction in cost along the last decade and a lustrum [3]. At the same time, microorganisms are the most abun- dant organisms on Earth, playing elemental roles in bio- geochemical, biomedical, and biotechnological processes. In this sense, novel problem-solving techniques involving systems and synthetic biology approaches have emerged to give significant insights into the comprehension of the molecular mechanisms related to microbial function. Moreover, this knowledge can be extended to our under- standing of microbial processes, allowing the exploration of environmental microorganisms—including bacteria and fungi—as cell factories. In this context, this special issue attempts to explore how postgenomic approaches have allowed to take advantage of the abundance of the genetic and biochemical information currently being produced from the fields of (meta)genomics, (meta)transcriptomics or tran- scriptome profiling, and (meta)proteomics and how large amounts of data generated by these methodologies are inte- grated to engineer microbes for relevant applications. Accordingly, the current special issue includes two origi- nal researches and three review articles, comprising different aspects of the selected topics. For example, in one article, L. F. Ribeiro et al. review the current strategies applied to over- come the limitations of Cas9 protein (CRISPR-associated protein 9) to generate robust and efficient tools for cus- tomized DNA manipulation using protein engineering approaches. Application of revised techniques in diverse biological processes should permit the optimization of gene therapy, metabolic flux, and synthetic gene networks. In another revision, L. de Fátima Alves et al. focus on how metagenomics has contributed to gain scientific under- standing in diverse areas of knowledge. In this framework, main milestones in the metagenomic field are presented over the last 30 years, since the first published metage- nomic experiment. The article is oriented in a philosophi- cal manner, providing perceptions into potentialities and current challenges of metagenomic approaches, presenting the field as a promoter of new concepts in microbial sci- ence. The revision article authored by R. G. de Paula et al. discusses new perspectives about control of secretion and cellulase expression based on RNA-seq and functional characterization data of the filamentous fungi Trichoderma reesei, one of the most well-studied cellulolytic microor- ganisms. In one research article, A. Sanches-Medeiros et al. report a new method to calibrate transcriptional activity using constitutive synthetic promoters in the bac- terium Escherichia coli. In this article, authors demonstrate that simple experimental techniques involving the use of a single fluorescent reporter and plasmids are sufficient to provide robust characterization of transcriptional elements, which is fundamental to proper construction of complex Hindawi International Journal of Genomics Volume 2018, Article ID 4915348, 2 pages https://doi.org/10.1155/2018/4915348
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EditorialGenomic and Postgenomic Approaches to UnderstandEnvironmental Microorganisms
María-Eugenia Guazzaroni ,1 Raul Alberto Platero ,2 and Rafael Silva-Rocha 3
1Faculty of Philosophy, Sciences and Letters at Ribeirao Preto, Ribeirao Preto, Brazil2Clemente Estable Biological Research Institute, Montevideo, Uruguay3Ribeirao Preto Medical School, Ribeirao Preto, Brazil
Correspondence should be addressed to Rafael Silva-Rocha; [email protected]
Received 4 September 2018; Accepted 4 September 2018; Published 24 October 2018
Copyright © 2018 María-Eugenia Guazzaroni et al. This is an open access article distributed under the Creative CommonsAttribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original workis properly cited.
The introduction of new high-throughput technologies hasprofoundly impacted the development of modern scienceoutside the gene-centered understanding perceived in theearlier genomic era [1, 2]. Thus, low-cost platforms knownas Next Generation Sequencing (NGS) technologies can pro-duce millions of sequences of DNA molecules with differentyields and sequence lengths, having displayed a considerablereduction in cost along the last decade and a lustrum [3].
At the same time, microorganisms are the most abun-dant organisms on Earth, playing elemental roles in bio-geochemical, biomedical, and biotechnological processes.In this sense, novel problem-solving techniques involvingsystems and synthetic biology approaches have emergedto give significant insights into the comprehension of themolecular mechanisms related to microbial function.Moreover, this knowledge can be extended to our under-standing of microbial processes, allowing the exploration ofenvironmental microorganisms—including bacteria andfungi—as cell factories. In this context, this special issueattempts to explore how postgenomic approaches haveallowed to take advantage of the abundance of the geneticand biochemical information currently being produced fromthe fields of (meta)genomics, (meta)transcriptomics or tran-scriptome profiling, and (meta)proteomics and how largeamounts of data generated by these methodologies are inte-grated to engineer microbes for relevant applications.
Accordingly, the current special issue includes two origi-nal researches and three review articles, comprising differentaspects of the selected topics. For example, in one article, L. F.
Ribeiro et al. review the current strategies applied to over-come the limitations of Cas9 protein (CRISPR-associatedprotein 9) to generate robust and efficient tools for cus-tomized DNA manipulation using protein engineeringapproaches. Application of revised techniques in diversebiological processes should permit the optimization ofgene therapy, metabolic flux, and synthetic gene networks.In another revision, L. de Fátima Alves et al. focus on howmetagenomics has contributed to gain scientific under-standing in diverse areas of knowledge. In this framework,main milestones in the metagenomic field are presentedover the last 30 years, since the first published metage-nomic experiment. The article is oriented in a philosophi-cal manner, providing perceptions into potentialities andcurrent challenges of metagenomic approaches, presentingthe field as a promoter of new concepts in microbial sci-ence. The revision article authored by R. G. de Paulaet al. discusses new perspectives about control of secretionand cellulase expression based on RNA-seq and functionalcharacterization data of the filamentous fungi Trichodermareesei, one of the most well-studied cellulolytic microor-ganisms. In one research article, A. Sanches-Medeiroset al. report a new method to calibrate transcriptionalactivity using constitutive synthetic promoters in the bac-terium Escherichia coli. In this article, authors demonstratethat simple experimental techniques involving the use of asingle fluorescent reporter and plasmids are sufficient toprovide robust characterization of transcriptional elements,which is fundamental to proper construction of complex
HindawiInternational Journal of GenomicsVolume 2018, Article ID 4915348, 2 pageshttps://doi.org/10.1155/2018/4915348
http://orcid.org/0000-0002-4657-3731http://orcid.org/0000-0001-5331-1396http://orcid.org/0000-0001-6319-631Xhttps://creativecommons.org/licenses/by/4.0/https://creativecommons.org/licenses/by/4.0/https://doi.org/10.1155/2018/4915348
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synthetic circuits. Finally, in another research article, C.Mareque et al. evaluate how different levels of N fertiliza-tion affect the structure of total and diazotrophic endo-phytic bacterial microbiota associated with field-grownSorghum bicolor. The data obtained by the authors con-tribute to the understanding of how agronomical practicesimpact the plant-associated microbiota, an essential steptoward the design of new sustainable agricultural produc-tion systems based on plant growth-promoting bacteria.
Thus, in our opinion, gathered articles in this specialissue would allow us to explore novel methodologicalapproaches to understand the molecular mechanisms associ-ated to microbial function. We hope that these materials willhelp to inspire readers to perform novel studies capitalizingthe unlimited biological potential of environmental microor-ganisms, probably bringing important profits in areas ofagriculture, industry, pharmacy, and biotechnology.
Conflicts of Interest
The authors declare that they have no conflicts of interest.
María-Eugenia GuazzaroniRaul Alberto PlateroRafael Silva-Rocha
References
[1] E. L. van Dijk, H. Auger, Y. Jaszczyszyn, and C. Thermes, “Tenyears of next-generation sequencing technology,” Trends inGenetics, vol. 30, no. 9, pp. 418–426, 2014.
[2] L. Perbal, “The case of the gene: postgenomics betweenmodernity and postmodernity,” EMBO Reports, vol. 16,no. 7, pp. 777–781, 2015.
[3] A. Sanchez-Flores and C. Abreu-Goodger, “A practical guide tosequencing genomes and transcriptomes,” Current Topics inMedicinal Chemistry, vol. 14, no. 3, pp. 398–406, 2014.
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