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<p>The Amazon rainforest represents nearly 40% of the world’s tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites (<i>R</i> = 0.942), whereas phages communities exhibited no significant variation. Pasture soils—particularly those under fertilization—showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and <i>Pycsar</i> systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.</p>

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Characterization of defensome genes and mobile genetic Elements in different types of pasture soil agroecosystems from the Brazilian Amazon

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年5月19日

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  • Luan Filipe de Souza Pereira,
  • Taynara Cristina Santos Tavares,
  • David Tavares Martins,
  • Carlos Willian Dias Dantas,
  • Fernanda Olivia Rodrigues de Souza,
  • Maria Clara Coelho Prazeres,
  • Cristian Faturi,
  • Hervé Louis Ghislain Rogez,
  • Rommel Thiago Jucá Ramos,
  • Oscar Victor Cardenas Alegria,
  • Adriana Ribeiro Carneiro Nunes

摘要

The Amazon rainforest represents nearly 40% of the world’s tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites (R = 0.942), whereas phages communities exhibited no significant variation. Pasture soils—particularly those under fertilization—showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and Pycsar systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.