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3. Computational methods for differentially expressed gene analysis from RNA-Seq: an overview

Author

Costa-Silva, Juliana, Domingues, Douglas S., Menotti, David, Hungria, Mariangela, and Lopes, Fabricio M

Subjects
Quantitative Biology - Genomics, Computer Science - Computational Engineering, Finance, and Science
Abstract

The analysis of differential gene expression from RNA-Seq data has become a standard for several research areas mainly involving bioinformatics. The steps for the computational analysis of these data include many data types and file formats, and a wide variety of computational tools that can be applied alone or together as pipelines. This paper presents a review of differential expression analysis pipeline, addressing its steps and the respective objectives, the principal methods available in each step and their properties, bringing an overview in an organized way in this context. In particular, this review aims to address mainly the aspects involved in the differentially expressed gene (DEG) analysis from RNA sequencing data (RNA-Seq), considering the computational methods and its properties. In addition, a timeline of the evolution of computational methods for DEG is presented and discussed, as well as the relationships existing between the main computational tools are presented by an interaction network. A discussion on the challenges and gaps in DEG analysis is also highlighted in this review.

Published
2021

17. Increasing Application of Multifunctional Bacillus for Biocontrol of Pests and Diseases and Plant Growth Promotion: Lessons from Brazil.

Author

Vasques, Natalia Caetano, Nogueira, Marco Antonio, and Hungria, Mariangela

Subjects
ORGANIC farming, SUSTAINABILITY, PEST control, PLANT diseases, BIOLOGICAL pest control, PLANT growth, BIOLOGICAL pest control agents
Abstract

The microbial genus Bacillus inhabits a diverse range of environments and is widespread across all global biomes, with a significant presence in soil habitats. In agriculture, Bacillus strains play multifaceted roles, serving as biocontrol agents against pests and diseases, and promoting plant growth by facilitating nutrient availability and enhancing stress tolerance. Through mechanisms such as phosphate solubilization, ACC-deaminase activity, and synthesis of phytohormones and siderophores, Bacillus spp. contribute to soil health and crop productivity, in a new approach of regenerative agriculture. The ability of Bacillus spp. to solubilize phosphate makes essential nutrients more accessible to plants, while ACC-deaminase activity helps plants withstand environmental stresses. Additionally, the synthesis of phytohormones can stimulate plant growth and development, and siderophores may facilitate the uptake of nutrients such as iron by plants. As the agricultural industry embraces Bacillus-based formulations for pest management and crop enhancement, future research holds promising prospects for optimizing their applications and harnessing their full potential in agroecosystems. Continued exploration of Bacillus spp. diversity and their interactions with plants and soil microbiota will further advance sustainable agricultural practices. This review contributes to understanding how Bacillus strains can revolutionize agriculture by enhancing soil health, increasing crop productivity, and providing effective biological solutions against pests and diseases. The successful application of Bacillus-based technologies in millions of hectares in Brazilian agriculture demonstrates the synergy between the need for more sustainable agricultural practices and the use of bio-inputs. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield

Author

Moretti, Luiz Gustavo, Crusciol, Carlos Alexandre Costa, Leite, Marcio Fernandes Alves, Momesso, Letusa, Bossolani, João William, Costa, Ohana Yonara Assis, Hungria, Mariangela, Kuramae, Eiko Eurya, Moretti, Luiz Gustavo, Crusciol, Carlos Alexandre Costa, Leite, Marcio Fernandes Alves, Momesso, Letusa, Bossolani, João William, Costa, Ohana Yonara Assis, Hungria, Mariangela, and Kuramae, Eiko Eurya

Abstract

Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural prac

Published
2024

21. Soil macrofauna communities in Brazilian land-use systems

Author

Brown, George G., Demetrio, Wilian C., Gabriac, Quentin, Pasini, Amarildo, Korasaki, Vanesca, Oliveira, Lenita J., Dos Santos, Julia C.F., Torres, Eleno, Galerani, Paulo R., Gazziero, Dionisio L.P., Benito, Norton P., Nunes, Daiane H., Santos, Alessandra, Ferreira, Talita, Nadolny, Herlon S., Bartz, Marie, Maschio, Wagner, Dudas, Rafaela T., Zagatto, Mauricio R.G., Niva, Cintia C., Clasen, Lina, Sautter, Klaus D., Froufe, Luis C.M., Seoane, Carlos Eduardo S., De Moraes, Anibal, James, Samuel, Alberton, Odair, Brandão Júnior, Osvaldino, Saraiva, Odilon, Garcia, Antonio, Oliveira, Elma, César, Raul M., Corrêa-Ferreira, Beatriz S., Bruz, Lilianne S.M., da Silva, Elodie, Cardoso, Gilherme B.X., Lavelle, Patrick, Velasquez, Elena, Cremonesi, Marcus, Parron, Lucília M., Baggio, Amilton J., Neves, Edinelson, Hungria, Mariangela, Campos, Thiago A., da Silva, Wagner L., Reissmann, Carlos B., Conrado, Ana C., Bouillet, Jean-Pierre, Gonçalves, José Leonardo M., Brandani, Carolina B., Viani, Ricardo A.G., Paula, Ranieri Ribeiro, Laclau, Jean-Paul, et al., Brown, George G., Demetrio, Wilian C., Gabriac, Quentin, Pasini, Amarildo, Korasaki, Vanesca, Oliveira, Lenita J., Dos Santos, Julia C.F., Torres, Eleno, Galerani, Paulo R., Gazziero, Dionisio L.P., Benito, Norton P., Nunes, Daiane H., Santos, Alessandra, Ferreira, Talita, Nadolny, Herlon S., Bartz, Marie, Maschio, Wagner, Dudas, Rafaela T., Zagatto, Mauricio R.G., Niva, Cintia C., Clasen, Lina, Sautter, Klaus D., Froufe, Luis C.M., Seoane, Carlos Eduardo S., De Moraes, Anibal, James, Samuel, Alberton, Odair, Brandão Júnior, Osvaldino, Saraiva, Odilon, Garcia, Antonio, Oliveira, Elma, César, Raul M., Corrêa-Ferreira, Beatriz S., Bruz, Lilianne S.M., da Silva, Elodie, Cardoso, Gilherme B.X., Lavelle, Patrick, Velasquez, Elena, Cremonesi, Marcus, Parron, Lucília M., Baggio, Amilton J., Neves, Edinelson, Hungria, Mariangela, Campos, Thiago A., da Silva, Wagner L., Reissmann, Carlos B., Conrado, Ana C., Bouillet, Jean-Pierre, Gonçalves, José Leonardo M., Brandani, Carolina B., Viani, Ricardo A.G., Paula, Ranieri Ribeiro, Laclau, Jean-Paul, and et al.

Abstract

Background: Soil animal communities include more than 40 higher-order taxa, representing over 23% of all described species. These animals have a wide range of feeding sources and contribute to several important soil functions and ecosystem services. Although many studies have assessed macroinvertebrate communities in Brazil, few of them have been published in journals and even fewer have made the data openly available for consultation and further use. As part of ongoing efforts to synthesise the global soil macrofauna communities and to increase the amount of openly-accessible data in GBIF and other repositories related to soil biodiversity, the present paper provides links to 29 soil macroinvertebrate datasets covering 42 soil fauna taxa, collected in various land-use systems in Brazil. A total of 83,085 georeferenced occurrences of these taxa are presented, based on quantitative estimates performed using a standardised sampling method commonly adopted worldwide to collect soil macrofauna populations, i.e. the TSBF (Tropical Soil Biology and Fertility Programme) protocol. This consists of digging soil monoliths of 25 x 25 cm area, with handsorting of the macroinvertebrates visible to the naked eye from the surface litter and from within the soil, typically in the upper 0-20 cm layer (but sometimes shallower, i.e. top 0-10 cm or deeper to 0-40 cm, depending on the site). The land-use systems included anthropogenic sites managed with agricultural systems (e.g. pastures, annual and perennial crops, agroforestry), as well as planted forests and native vegetation located mostly in the southern Brazilian State of Paraná (96 sites), with a few additional sites in the neighbouring states of São Paulo (21 sites) and Santa Catarina (five sites). Important metadata on soil properties, particularly soil chemical parameters (mainly pH, C, P, Ca, K, Mg, Al contents, exchangeable acidity, Cation Exchange Capacity, Base Saturation and, infrequently, total N), particle size distrib

Published
2024

22. Guidelines for the description of rhizobial symbiovars

Author

Junta de Castilla y León, Fundação Araucária, Peix, Álvaro [0000-0001-5084-1586], Martinez-Romero, Esperanza, Peix, Álvaro, Hungria, Mariangela, Mousavi, Seyed Abdollah, Martinez-Romero, Julio, Young, Peter, Junta de Castilla y León, Fundação Araucária, Peix, Álvaro [0000-0001-5084-1586], Martinez-Romero, Esperanza, Peix, Álvaro, Hungria, Mariangela, Mousavi, Seyed Abdollah, Martinez-Romero, Julio, and Young, Peter

Abstract

Rhizobia are bacteria that form nitrogen-fixing nodules in legume plants. The sets of genes responsible for both nodulation and nitrogen fixation are carried in plasmids or genomic islands that are often mobile. Different strains within a species sometimes have different host specificities, while very similar symbiosis genes may be found in strains of different species. These specificity variants are known as symbiovars, and many of them have been given names, but there are no established guidelines for defining or naming them. Here, we discuss the requirements for guidelines to describe symbiovars, propose a set of guidelines, provide a list of all symbiovars for which descriptions have been published so far, and offer a mechanism to maintain a list in the future.

Published
2024

26. Soil macrofauna communities in Brazilian land-use systems

Author

Brown, George, primary, Demetrio, Wilian, additional, Gabriac, Quentin, additional, Pasini, Amarildo, additional, Korasaki, Vanesca, additional, Oliveira, Lenita, additional, dos Santos, Julio, additional, Torres, Eleno, additional, Galerani, Paulo, additional, Gazziero, Dionisio, additional, Benito, Norton, additional, Nunes, Daiane, additional, Santos, Alessandra, additional, Ferreira, Talita, additional, Nadolny, Herlon, additional, Bartz, Marie, additional, Maschio, Wagner, additional, Dudas, Rafaela, additional, Zagatto, Mauricio, additional, Niva, Cintia, additional, Clasen, Lina, additional, Sautter, Klaus, additional, Froufe, Luis, additional, Seoane, Carlos Eduardo, additional, de Moraes, Aníbal, additional, James, Samuel, additional, Alberton, Odair, additional, Brandão Júnior, Osvaldino, additional, Saraiva, Odilon, additional, Garcia, Antonio, additional, Oliveira, Elma, additional, César, Raul, additional, Corrêa-Ferreira, Beatriz, additional, Bruz, Lilianne, additional, Silva, Elodie, additional, Cardoso, Gilherme, additional, Lavelle, Patrick, additional, Velásquez, Elena, additional, Cremonesi, Marcus, additional, Parron, Lucília, additional, Baggio, Amilton, additional, Neves, Edinelson, additional, Hungria, Mariangela, additional, Campos, Thiago, additional, da Silva, Vagner, additional, Reissmann, Carlos, additional, Conrado, Ana, additional, Bouillet, Jean-Pierre, additional, Gonçalves, José, additional, Brandani, Carolina, additional, Viani, Ricardo, additional, Paula, Ranieri, additional, Laclau, Jean-Paul, additional, Peña-Venegas, Clara, additional, Peres, Carlos, additional, Decaëns, Thibaud, additional, Pey, Benjamin, additional, Eisenhauer, Nico, additional, Cooper, Miguel, additional, and Mathieu, Jérôme, additional

Published
2024
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31. The Complete Genome Sequence of Chromobacterium violaceum Reveals Remarkable and Exploitable Bacterial Adaptability

Author

de Almeida, Darcy F., Hungria, Mariangela, Guimarães, Claudia Teixeira, Antônio, Regina Vasconcellos, Almeida, Francisca Cunha, de Almeida, Rosana, Alves-Gomes, José Antonio, Andrade, Elizabeth Mazoni, Araripe, Julia, Astolfi-Filho, Spartaco, Azevedo, Vasco, Baptista, Alessandra Jorge, Beló, André, van den Berg, Cássio, Bogo, Maurício, Bonatto, Sandro, Bordignon, Juliano, Brigido, Marcelo Macedo, Brito, Cristiana Alves, Brocchi, Marcelo, Burity, Helio Almeida, Camargo, Anamaria Aranha, Carneiro, Newton Portilho, Carraro, Dirce Maria, Cavada, Benildo Sousa, Creczynski-Pasa, Tânia Beatriz, da Cunha-Junior, Nivaldo Costa, Fagundes, Nelson, Falcão, Clarissa Lima, Fantinatti, Fabiana, Farias, Izeni Pires, Ferrari, Lilian Pereira, Ferro, Jesus Aparecido, Franco, Gloria Regina, Furlan, Luiz Roberto, Gazzinelli, Ricardo Tostes, Gomes, Eliane Aparecida, Gonçalves, Pablo Rodrigues, Grangeiro, Thalles Barbosa, Grattapaglia, Dario, Grisard, Edmundo Carlos, Hanna, Ebert Seixas, Jardim, Sílvia Neto, Laurino, Jomar, Manfio, Gilson Paulo, Maranhão, Andrea Queiroz, Martins, Wellington Santos, Nicolás, Marisa Fabiana, Oliveira, Jaquelline Germano, Oliveira, Sergio Costa, Parente, Juliana Alves, Pereira, José Odair, Pereira, Maristela, Potrich, Deise Porto, Ramalho-Neto, Cicero Eduardo, Rigo, Liu Um, Rondinelli, Edson, Santos, Fabrício R., Seuanez, Hector N., Silva, Denise Wanderlei, Silva, Rosane, Simon, Daniel, Souza, Emanuel Maltempi, Souza, Rangel Celso, Steindel, Mário, Teixeira, Santuza Ribeiro, Urmenyi, Turan, Vettore, André, Wassem, Roseli, and Zaha, Arnaldo

Published
2003

42. Brazilian Microbiome Project: Revealing the Unexplored Microbial Diversity—Challenges and Prospects

Author

Pylro, Victor Satler, Roesch, Luiz Fernando Wurdig, Ortega, José Miguel, do Amaral, Alexandre Morais, Tótola, Marcos Rogério, Hirsch, Penny Ruth, Rosado, Alexandre Soares, Góes-Neto, Aristóteles, da Costa da Silva, Artur Luiz, Rosa, Carlos Augusto, Morais, Daniel Kumazawa, Andreote, Fernando Dini, Duarte, Gabriela Frois, de Melo, Itamar Soares, Seldin, Lucy, Lambais, Márcio Rodrigues, Hungria, Mariangela, Peixoto, Raquel Silva, Tsai, Ricardo Henrique Kruger Siu Mui, and Azevedo, Vasco

Published
2014

45. Pioneering Desmodiumspp. are nodulated by natural populations of stress-tolerant alpha- and beta-rhizobia

Author

Protachevicz, Ana Paolla, Paulitsch, Fabiane, Klepa, Milena Serenato, Hainosz, Jessica, Olchanheski, Luiz Ricardo, Hungria, Mariangela, and Stefania da Silva Batista, Jesiane

Abstract

The rhizobia-Desmodium(Leguminosae, Papilionoideae) symbiosis is generally described by its specificity with alpha-rhizobia, especially with Bradyrhizobium. Our study aimed to isolate rhizobia from root nodules of native D. barbatum, D. incanum, and D. discolor, collected in remnants of the biomes of Atlantic Forest and Cerrado in protected areas of the Paraná State, southern Brazil. Based on the 16S rRNA phylogeny, 18 out of 29 isolates were classified as Alphaproteobacteria (Bradyrhizobiumand Allorhizobium/Rhizobium) and 11 as Betaproteobacteria (Paraburkholderia). Phylogeny of the recAgene of the alpha-rhizobia resulted in ten main clades, of which two did not group with any described rhizobial species. In the 16S rRNA phylogeny of the beta-rhizobia, Paraburkholderiastrains from the same host and conservation unity occupied the same clade. Phenotypic characterization of representative strains revealed the ability of Desmodiumrhizobia to grow under stressful conditions such as high temperature, salinity, low pH conditions, and tolerance of heavy metals and xenobiotic compounds. Contrasting with previous reports, our results revealed that Brazilian native Desmodiumcan exploit symbiotic interactions with stress-tolerant strains of alpha- and beta-rhizobia. Stress tolerance can highly contribute to the ecological success of Desmodiumin this phytogeographic region, possibly relating to its pioneering ability in Brazil. We propose Desmodiumas a promising model for studies of plant-rhizobia interactions.

Published
2023
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50. Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense.

Author

Aparecida Ferrarezi, Jessica, Defant, Heloísa, Fonseca de Souza, Leandro, Lúcio Azevedo, João, Hungria, Mariangela, and Quecine, Maria Carolina

Subjects
AZOSPIRILLUM brasilense, PLANT breeding, AMINO acid metabolism, BACTERIAL metabolism, MICROBIAL products, RHIZOSPHERE
Abstract

Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10-3, 10-6, 10-9 and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10-3 +Ab-V5 and NS 10-6 Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10-3 + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab- V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The metaomics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products. [ABSTRACT FROM AUTHOR]

Published
2023
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