Luis Felipe Guandalin Zagatto

Amazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil’s most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.

Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (~15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.

Introduction: Deforestation of areas for agriculture and cattle breeding is the leading cause of ecological degradation and loss of biodiversity. The solution to mitigate these damages relies on techniques that improve soil health and the microbial quality of these degraded areas. Here, we demonstrate that the high nutrient and microbiological contents of Amazonian Dark Earths (ADE) can promote the development of trees used in ecological restoration projects. Methods: We used degraded soil from crops as control and ADE from the Central Amazon to conduct the experiment, using 20% of ADE as inoculum in degraded agricultural soil. Our goal was to assess whether a small amount of ADE could promote changes that improve plant development similar to its growth under a 100%ADE. We simulated conversion from pasture to forest restoration area by planting U. brizantha in all pots. After 60 days, we removed it and planted Cecropia pachystachya, Peltophorum dubium, and Cedrela fissilis. Results: Our results demonstrated that both 20%ADE and 100%ADE treatments increased pasture productivity and, consequently, soil carbon stock. Also, in these treatments, P. dubium and C. fissilis had better growth and development, with 20%ADE plants showing a performance similar to those planted in 100%ADE. Both 20%ADE and 100%ADE showed similar numbers of taxa, being significantly higher than in the control soil. Discussion: The 20%ADE was sufficient to increase significantly the microbial richness in the soil, providing several beneficial microorganisms to all tree species such as Pedomicrobium, Candidatus Nitrososphaera, and members of Paenebacillaceae. Nevertheless, C. pachystachya, a common pioneer tree in the Amazonian Forest showed a small response even to 100%ADE with a corresponding lower taxa number than the other two species. In conclusion, we point out that microbial structure remains very similar among plants but dissimilar among treatments, highlighting the role of ADE as an enhancer of plant development and beneficial microbiota enrichment in the rhizosphere. The use of 20%ADE was sufficient to alter the microbial community. Therefore, we believe our data could contribute to speeding up forest restoration programs by adopting new biotechnological approaches for forest restoration ecology.

Drought stress threatens global food security, highlighting the need for resilient crops. Harnessing rhizosphere microorganisms can improve plant performance in harsh conditions. Here, we investigated the rhizosphere microbiomes of drought-tolerant (BAT477, SEA5) and susceptible (IAC Milênio, IAC-Carioca 80SH) common bean cultivars (Phaseolus vulgaris L.) under contrasting water regimes in mesocosm experiments to assess microbiome functional modulation under drought. Analysis of plant growth, physiological responses, nutrient dynamics, and rhizosphere microbial functional diversity revealed that drought-tolerant cultivars exhibited greater water management, minimal growth reductions, and enrichment of beneficial microbial functions, including genes linked to drought tolerance. Notably, drought stress triggered differential abundance in 1864 microbial genes, highlighting a robust functional shift. Specifically, drought-tolerant cultivars showed an enrichment of genes related to osmotic response, photosynthetic efficiency (82–87 % reduction in photosynthesis in susceptible cultivars), oxidative stress mitigation, and osmoprotectant production, whereas susceptible cultivars relied more on genes associated with DNA repair and antioxidant defense, indicating a reactive rather than proactive stress response. Additionally, the rhizosphere microbiomes of drought-tolerant cultivars were enriched in functions related to biofilm formation, dormancy survival, and oxidative stress resistance. These cultivars also maintained higher photosynthetic activity and transpiration rates with more stable stomatal conductance. Upon rehydration, they partially restored physiological functions (e.g., 48–57 % recovery in photosynthesis), further demonstrating microbiome-conferred resilience. These findings underscore the potential of plant-microbiome interactions in adapting to water stress, suggesting that microbiome selection could be a promising strategy for developing drought-resilient crops and advancing sustainable agricultural practices.

Here, we report 27 metagenome-assembled bacterial genomes (MAGs) from litter samples of a secondary forest located in Brazil over an Amazonian Dark Earth pool. The data set includes members from the phyla Pseudomonadata (14 MAGs), Actinomycetota (7 MAGs), Bacteroidota (4 MAGs), Bacillota (1 MAG), and Bdellovibrionota (1 MAG).