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

Autor(es)

Perez Braga, Lucas Palma ^[1] ; Pereira, Roberta Verciano ^[1] ; Martins, Layla Farage ^[1] ; Silva Moura, Livia Maria ^{[1, 2]} ; Sanchez, Fabio Beltrame ^{[1, 2]} ; Leister Patane, Jose Salvatore ^[3] ; da Silva, Aline Maria ^[1] ; Setubal, Joao Carlos ^[1]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Inst Quim, Dept Bioquim, Sao Paulo - Brazil

^[2] Univ Sao Paulo, Programa Posgrad Interunidades Bioinformat, Sao Paulo - Brazil

^[3] Inst Butantan, Lab Especial Ciclo Celular, Sao Paulo, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: BMC Genomics; v. 22, n. 1 SEP 10 2021.
• Citações Web of Science: 0

Resumo

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, O-2 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. (AU)

• Processo FAPESP: 11/50870-6 - Estudos da diversidade microbiana no Parque Zoológico do Estado de São Paulo
• Beneficiário: João Carlos Setubal
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOTA - Temático
• Processo FAPESP: 18/19247-0 - Desvendando o papel dos vírus na evolução de rizobactérias benéficas e patogênicas
• Beneficiário: Lucas Palma Perez Braga
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado