Microbiologia Agrícola
URI permanente para esta coleçãohttps://locus.ufv.br/handle/123456789/190
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Resultados da Pesquisa
Item The known unknowns: understanding slow-growing bacteria and their plant interaction through reverse ecology approaches(Universidade Federal de Viçosa, 2023-07-18) Gonçalves, Osiel Silva; Santana, Mateus Ferreira; http://lattes.cnpq.br/5810415406152941The cultivation of bacteria that exhibit slow growth rates has posed a longstanding challenge in microbiology, resulting in a significant number of unculturable bacterial species. This phenomenon, known as the "great plate count anomaly", represents one of the oldest unresolved topics in the field. Recent advancements in cultivation techniques have shown promise in overcoming this challenge. In addition, the study of slow-growing bacteria and their interactions with plants has gained significant attention due to their ecological importance and potential applications in agriculture. Genomics techniques have provided valuable insights into the genetic characteristics underlying microbe-plant interactions. In this context, by examining the in-cultivation techniques, genomics, and computational modeling, we seek to shed light on the slow-growing bacteria and uncover their contributions to ecosystem functioning and plant interaction. Our initial understanding was obtained through the study of 92 slow-growing bacteria isolated from the Brazilian Cerrado soil during a four week-long isolation period. These bacteria can thrive in low-water conditions, promote plant growth, and belong to a novel species group. Genome analysis of five strains revealed their potential in biogeochemical cycles, plant growth promotion, and biosynthesis of secondary metabolites. Next, we conducted greenhouse experiments to assess the efficacy of these bacteria in soybean cultivation, employing a carefully designed bacterial consortium based on our comprehensive understanding of microbial-microbe and plant-microbe interactions. The results showed promising outcomes for improving soybean productivity. In the third chapter of this thesis, we employed in-silico modeling to design a synthetic microbial community aimed at enhancing the yield of important crop plants. By selecting six hub species with essential plant growth-promoting traits from the dominant plant species found in the Campos rupestres, we aimed to optimize the plant-microbe interactions and maximize crop productivity. Lastly, our analysis of 758 metagenome- assembled genomes shed light on the global distribution of the Acidobacteriota phylum and its interactions with plants and biogeochemical processes. This exploration revealed distinct ecological roles for individual taxonomic groups within this phylum, providing valuable insights for future research. Overall, our thesis contributes to a better understanding of slow-growing bacteria, their ecological significance, and their potential applications in agriculture, offering insights into ecosystem functioning and plant interactions. Keywords: Agriculture. Slow-growing bacteria. Ecosystems. Genomics. Microbe-plant interactions. MicrobiologyItem On the move: Mobilome of the Ralstonia solanacearum Species Complex and its role in the fitness, pathogenicity and genome evolution(Universidade Federal de Viçosa, 2019-07-26) Gonçalves, Osiel Silva; Santana, Mateus Ferreira; http://lattes.cnpq.br/5810415406152941Ralstonia solanacearum is one of the most devastating plant pathogenic bacteria found all over the world, capable of infecting a wide diversity of hosts. This soil-borne pathogen is composed of a large-scale group of strains varying in geographical distribution and pathogenic behavior known as R. solanacearum Species Complex (RSSC). In this context, mobile genetic elements may play a significant role in shaping the genetic, and these elements may be important to the bacteria expand their ecological niche or colonize a new host since they promote genetic variability and often carry a cargo gene. In this context, we performed a genome mining in 106 RSSC and 15 Ralstonia spp. genomes and comparative genomic analysis based on Integrative and Conjugative Elements (ICEs), Genomic Islands (GIs), Insertion Sequences (ISs) and Transposons. Our results provided a collective dataset of 41 GIs and 12 ICEs in the RSSC. These elements represent an important fraction of the Ralstonia genomes (1-5%). Phylogenetic analysis showed that the elements are related to geographic origin and species, but there is evidence of genetic flux between isolates belonging to different countries from the Americas and Horizontal Gene Transfer between strains from Asia. ICEs and GIs carry a repertoire of genes with potential impact on Ralstonia fitness and pathogenicity such as stress response and candidate virulence genes as several type III effector proteins which may enable the bacteria to evolve rapidly and infect a wide range of hosts. In addition, we identified 2,957 IS elements in the genome of 59 representative RSSC strains and closely related Ralstonia spp. A unique set of 13 IS families were found highly conserved across the strains, suggesting their ancestral acquisition. We found four novel transposons sequences belong to Tn3 family carrying genes related to antibiotic resistance and avirulence protein as passenger genes. Numerous internal rearrangements events with a subset being associated with IS were demonstrated, indicating the impact of these elements on RSSC genome evolution. We also mapped numerous IS elements interrupting avirulence genes, which provides evidence that IS may be one of the driving forces of RSSC pathogenicity evolution. In conclusion, here we provide a dataset of the mobile genetic elements in one of the most important plant pathogens found all over the world. These data provide novel insights into the RSSC diversified adaptation, opening new paths to a better understanding of the impact of these elements on the genome evolution and pathogenicity of R. solanacearum. Keywords: Genome evolution. Phytopathogen. ICEs. Genomic islands. Insertion Sequence