Sugarcane (Saccharum officinarum L.) is a strategic crop for the energy sector, but its intensive cultivation requires sustainable management practices. Plant growth-promoting bacteria (PGPB) such as Azospirillum brasilense and Nitrospirillum amazonense are known for their ability to fix atmospheric nitrogen and stimulate growth in grasses. This study evaluated the effects of inoculation with A. brasilense (Ab) and N. amazonense (Na), applied individually or in combination (Ab+Na), on sugarcane physiology, nitrogen use efficiency, root exudation, and rhizospheric microbial communities. The experiment was conducted under controlled greenhouse conditions with four treatments: Control (no inoculation), Ab, Na, and Ab+Na. The Ab+Na treatment promoted the highest photosynthetic rate, carboxylation efficiency, and water use efficiency. These physiological responses were associated with greater nitrogen accumulation in roots, rhizomes, and leaves, as well as increased total biomass and 15N fertilizer recovery. Nitrogen losses were significantly reduced in Ab and Ab+Na treatments. At the molecular level, rhizosphere soil analysis showed a reduced abundance of microbial functional genes related to nitrification and denitrification (amoA, nirK, and nosZ) in inoculated treatments, indicating a lower potential for nitrogen losses. However, gene abundances were higher in the Ab+Na than in the individual inoculations, likely due to greater organic acid exudation stimulating soil organic matter mineralization. Only Ab and Ab+Na increased nifH abundance, indicating enhanced biological nitrogen fixation, predominantly associated with A. brasilense. The Ab+Na treatment also led to a distinct rhizospheric microbial profile and promoted more uniform microbial community structure. These findings suggest that combining microbial inoculants improve plant nitrogen efficiency and modify rhizosphere functioning through coordinated physiological and microbial mechanisms. Foliar inoculation with compatible PGPB offers a promising strategy for sustainable sugarcane intensification.

Amazonian floodplain soils are highly dynamic and support diverse ecosystems, yet the influence of contrasting forest types on deep soil carbon storage and microbial functioning remains poorly understood. This study provides a depth-resolved comparison of soil fertility, carbon storage, and microbial functioning across five contrasting Amazonian floodplain forest types. We compared soil chemical, physical, and microbial characteristics to 200 cm depth in five forest types on Ilha das Cinzas in the Amazonian floodplain: a mangrove forest, lower and upper forests, a regenerated forest, and açaí agroforestry. The sampling design comprised 15 sampling sites (three sites per forest type), with soil collected at four depth intervals (0–50, 50–100, 100–150, and 150–200 cm). The analyses included chemical properties, soil organic carbon (SOC) and SOC stock (SOCS), microbial indicators (β-glucosidase activity, BG, and microbial biomass carbon, MBC), soil moisture, and bulk density. SOC and SOCS significantly differed among forest types and depths, with the highest values found in mangrove soils (2.18% and 52 Mg C ha⁻¹). SOC was positively associated with MBC (β = 0.567, p < 0.001), while pH showed a significant negative association with MBC (β = −0.341, p < 0.001). These findings indicate that forest type and soil depth are strongly associated with variation in carbon storage, nutrient availability, and microbial functioning across Amazonian floodplain soils. Mangrove soils consistently exhibited greater carbon storage than the other forest types. Ecologically, these results highlight the role of mangrove and other carbon-rich floodplain forests in maintaining deep soil carbon reservoirs and associated soil functions; from a management perspective, they support the conservation of mangroves, the protection of carbon-rich floodplain ecosystems, and the inclusion of deep soil horizons in carbon accounting, soil-fertility assessment, and ecosystem-management strategies across Amazonian estuarine landscapes.

The application of organic fertilizers is a fundamental practice in organic farming. However, its effects on the interaction between colonization by native arbuscular mycorrhizal fungi (AMF; referred to here as those originating from non-isolated field soil inoculum) and microbial enzyme-mediated phosphorus mineralization, two key strategies for plant phosphorus acquisition, are largely unknown in the cultivation of jambu (Acmella oleracea (L.) R. K. Jansen). Here, using two genetic accessions of jambu (“Yellow Flower” and “Purple Flower”) and three commonly employed organic fertilizers (cattle manure, vermicompost, and poultry litter), we show that the application of these inputs did not affect native AMF colonization (%MC) in “Yellow Flower” plants but reduced it in “Purple Flower” plants - possibly due to differences in mycorrhizal plasticity associated with accession-specific traits. In contrast, organic fertilizers increased acid phosphatase activity (A-PHO), easily extractable glomalin-related soil proteins (EE-GRSP) and plant yield, although the effect size varied by source and plant access. Notably, we found a decoupling between %MC and A-PHO driven by “Yellow Flower” jambu, suggesting a potential functional trade-off between these phosphorus acquisition strategies. Together, our findings indicate that organic fertilizers (especially vermicompost and poultry litter) can enhance soil biological attributes and improve jambu yield, while also providing evidence for a potential decoupling between AMF colonization and microbial enzyme-mediated phosphorus mineralization.

Oil palm-based agroforestry systems (AFS) can promote soil organic carbon (SOC) sequestration, but the pathways through AFS shape SOC persistence and its interactions with microbial communities and environmental factors remain only partially understood. Here, using long-term AFS plots and oil palm (Elaeis guineensis) monocultures in the Amazon, we show that AFS enhances microbial activity and assembles distinct microbial communities, while shaping microbial trait-based strategies related to substrate versatility and growth rate. These changes are accompanied by increases in particulate (POM-C; up to ~300%) and mineralassociated (MAOM-C; up to ~200%) SOC, with effects primarily dependent on plant species composition and soil depth. Microbial necromass carbon (MNC) accumulation in AFS demonstrated similar increase and it was dominated by fungal necromass (~64%) vs. bacterial necromass (~36%). However, the contribution of MNC to SOC was decoupled from increases in MNC contents, accounting for a maximum of ~27% of the bulk SOC in AFS (while ~25% in monoculture), challenging the prevailing paradigm that multi-species plant cultivation and high microbial activity (a proxy for microbial turnover) are major drivers of MNC contributions to SOC. These findings highlight ecosystem-level interactions as determinants of SOC sequestration and offer the first insights into MNC accumulation pathways in Amazonian agricultural systems.

Topographic and soil depth controls on soil carbon-linked biochemical processes shall be interpreted to forecast ecosystem processes in the Brazilian Amazon Forest. This research focused on the combined effects of topographic heterogeneity, soil depth, and soil chemistry on (3-glucosidase (BG), a fundamental enzyme controlling soil organic carbon (SOC) decomposition and microbial carbon turnover. Soil (N = 36) was sampled at three depths (0-5, 5-10, and 25-30 cm) along three slope positions (lower position, 2-5%; middle position, 5-10%; and upper position, 10-15%) over a 153.4 ha area. The result showed that SOC, total nitrogen (TN), and BG activity were strongly affected by the slope position. On the surface layer, the content of SOC on upper position (0.35%) was lower than that on lower position (1.63%), while that of TN ranged from 52.5 to 147 mg L- 1. In contrast, BG activity rose from 6.43 to 26.83 mu mol pNP g- 1 h- 1. The SOC was positively correlated with TN (r = 0.90) and BG activity (r = 0.87). Results of the analysis showed that SOC had the greatest positive direct effect on BG ((3 = 0.52) and that Fe had the worst ((3 = -0.26). Relative importance analysis showed that SOC (25.3%), pH (15. 2%), and TN (10.5%) accounted for a major proportion of the prediction. In general, the lower positions represent BG hot spots that promote SOC storage, nutrient cycling, and microbial metabolism. Microbial biomass and soil properties should be considered in future research.

The adoption of cover crops in no-tillage (NT) systems is a fundamental practice to improve soil quality and promote sustainable agricultural development. However, it is still not fully understood to what extent the legacy effect of these plants influences the structure of microbial communities in subsequent soybean cultivation. Thus, we analyzed a long-term field experiment (16 years), conducted during the 2021/2022 and 2022/2023 growing seasons, to evaluate soil fertility, enzymatic activity, and soybean yield, as well as the structure, diversity, composition, and networks of bacterial and fungal communities in a soybean-maize succession system. The study assessed the influence of different off-season cover crops, including a grass species (Ruzigrass), a legume (Sunn hemp), their combination (Mix), and a no-cover treatment (Fallow), using high-throughput sequencing techniques. Cover crops increased soil chemical attributes, stimulated beta-glucosidase activity, and enhanced soybean yield. We also observed differentiation in the structure of the soil fungal community and increases in the abundance of microbial groups related to nutrient cycling, plant growth promotion, and pathogen biocontrol. In addition, the network analysis revealed greater complexity and changes in the structure of keystone species in the soybean rhizosphere, especially in the Ruzigrass treatment. Our results highlight that the legacy effect of cover crops in NT systems acts not only on improving soil fertility and soybean yield but also on modulating the microbiome, establishing ecological interactions relevant to soil quality and the sustainability of the agricultural system.

Silicate rock powders can enhance nutrient availability through rhizosphere-mediated mineral weathering. Although organic acids mediate this process, how soil fertility shapes their interactions with rhizosphere microbial communities and nutrient release remains poorly understood. He, we evaluated how contrasting soil fertility influences rhizosphere organic acids, microbial communities, and nutrient release from silicate rock powders in tropical soils. A 10-month greenhouse experiment was conducted with Urochloa brizantha cv. Marandu grown in low- and high-fertility tropical soils amended with phonolite, diabase, or granite. Rhizosphere organic acids, soil chemistry, plant nutrient uptake, and bacterial and fungal communities were assessed using chemical analyses, high-throughput DNA sequencing, and partial least squares path modeling. In low-fertility soil, rock powder reshaped rhizosphere organic acid profiles, increasing their concentrations and improving soil fertility. Organic acids were positively associated with soil fertility indicators and nutrient availability. Path modeling identified organic acids as a central mediator linking rhizosphere biological attributes to improved soil fertility (path coefficient = 0.597, P < 0.01), and plant nutrient uptake (0.671, P < 0.01), whereas fungal community positively influenced organic acid concentrations (0.540, P < 0.05). By contrast, these relationships were substantially weaker in the high-fertility soil, where associations among organic acids, soil properties, and nutrient uptake were reduced, and organic acid concentrations were higher in the control than in rock powder-amended soils. Rock powder effectiveness was governed by rhizosphere-mediated processes driven by organic acids, microbial communities, and plant nutrient demand, with the strongest responses occurring in nutrient-limited tropical soils.

This brief communication analyzes five critical aspects of soil ecotoxicological testing protocols and their applicability to tropical and subtropical conditions, particularly in Brazil: tropical artificial soil (TAS) composition, natural soil variability, pH dynamics, organic matter content, and soil clay mineralogy. While standardized artificial soil testing has been fundamental for generating comparable data across regions, significant differences exist between TAS and natural Brazilian soils. Standard artificial soil, as specified in ecotoxicity protocols, contains 10% organic matter and has a pH of 6.0 ± 0.5, whereas natural soils typically contain 1.5-3.0% organic matter and are more acidic (pH 4.8-5.6). Additionally, while TAS primarily contains kaolinite clay and quartz, many natural soils are also characterized by iron oxides and gibbsite, which significantly influence contaminant retention and bioavailability. The TAS adaptation, using coconut husk fiber instead of peat moss, represents an improvement but still may not fully reflect local conditions. Brazil's extensive pedo-mineralogical diversity presents important challenges for establishing representative ecotoxicological testing conditions and validity criteria based on natural soils. These differences can significantly affect contaminant mobility, bioavailability, and toxicity, potentially leading to different outcomes compared with standardized artificial soil tests. This analysis highlights the need for future methodological and regulatory discussions aimed at improving the environmental representativeness of tropical soil ecotoxicology while preserving the benefits of standardization. A promising perspective involves the development of tiered testing frameworks that combine standardized artificial soils for screening and inter-laboratory harmonization with representative natural tropical soils for higher-tier ecological assessments. Such approaches could enhance the ecological realism of risk assessments by integrating biological responses with key physicochemical and mineralogical soil characteristics, ultimately supporting more robust and regionally relevant ecotoxicological evaluations in tropical and subtropical regions.

Plant roots can modify the stability of soil aggregates in the rhizosphere and the surrounding bulk soil. Italian ryegrass (Lolium multiflorum) is known to improve soil aggregation through processes related to microbial activity, but these dynamics vary throughout the crop cycle. This study aims to correlate microbial activity with soil aggregate stability, determined by turbidimetry (readily-dispersible clay and mechanically-dispersible clay), in the rhizosphere and bulk soil of Italian ryegrass at 86, 113, 141, and 168 days after sowing. Results showed that the rhizosphere soil was significantly more stable, with 85-154 % lower dispersed clay than the bulk soil. Furthermore, aggregate stability increased (i.e., dispersed clay decreased) throughout the crop cycle, in tandem with a general increase in microbial parameters such as beta-glucosidase, acid phosphatase, and glomalin-related soil protein. Aggregate stability was strongly correlated (R-2 = 0.17-0.53; p<0.01) with these microbial parameters. In conclusion, Italian ryegrass effectively enhances soil aggregation and microbial activity, particularly in the rhizosphere, making it a valuable crop for improving soil health.

Agricultural development and productivity under sustainable practices depend on plant-soil-microorganism interactions in the rhizosphere, a central interface in environmental microbiology and microbial ecology. Although the influence of soybean phenological stages on the rhizosphere microbiome has been reported, studies addressing the legacy effects of off-season cover crops on microbial dynamics throughout soybean development remain scarce. We conducted a greenhouse experiment to evaluate the structure, diversity, composition, and network connections of bacterial and fungal communities in the soybean rhizosphere at different plant stages (V4, R1, and R5) under the influence of off-season cover crops, including a grass species (Ruzigrass), a legume (Sunn hemp), their combination (Mix), and a no-cover treatment (Fallow), using high-throughput sequencing. We found that differentiation in bacterial and fungal community structure in the soybean rhizosphere across plant development is modulated by the legacy effect of cover crops during the no-tillage off-season. Specific microbial groups were highlighted, including the bacterial phyla Pseudomonadota, Bacteroidota, and Actinomycetota, which showed differential relative abundance among soybean growth stages under cover crop treatments, as well as symbiotic arbuscular mycorrhizal fungal genera, such as Gigaspora, Dominikia, Paraglomus, and Glomus, which were more abundant during reproductive stages in the soybean rhizosphere. In addition, we observed variations in ecological interactions within bacterial and fungal networks according to the legacy effect of each cover crop, with greater network complexity under the Ruzigrass and Mix treatments. These results demonstrate that cover crop legacy is a key factor shaping microbial dynamics in the soybean rhizosphere, with implications for sustainable crop management.

Improving soil productivity in the Brazilian semi-arid region remains a major challenge. Integrated livestock–forest (ILF) systems represent a promising strategy for agricultural intensification with lower environmental impacts, as they enhance soil microbial functioning and support soil organic carbon (SOC) stocks accumulation. However, studies on how ILF systems affect soil biological properties and SOC dynamics in tropical semi-arid regions, particularly in the Caatinga biome, remain scarce. This study assessed soil microbiological properties in ILF systems established for six years in the Brazil’s semi-arid region. Four ILF systems were evaluated, each cultivated with sorghum (ILFSo), forage cactus (ILFFc), massai grass (ILFMg), and buffel grass (ILFBg), at spacings of 7 m (S7), 14 m (S14), and 28 m (S28) between strips of native trees. A native vegetation (NV) area served as a reference. Soil analyses included microbial biomass carbon (MBC), basal respiration, β-glucosidase activity, easily extractable glomalin (EEG), and SOC. ILFMg and ILFBg were the most effective systems for maintaining microbial biomass, activity, and SOC levels. ILFFc and ILFSo increased MBC but did not promote SOC accumulation. The spacing S7 resulted in the highest MBC, microbial quotient, and SOC, and the lowest metabolic quotient. ILFSo and NV showed the highest β-glucosidase activity at 0–10 cm, while ILFFc had the lowest. At 10–20 cm, β-glucosidase activity was greatest in ILFMg and ILFBg. EEG activity was similar among systems in the surface layer, whereas in the 10–20 cm layer the highest values occurred in ILFSo and ILFBg, and the lowest in ILFFc. Overall, ILF systems with grasses demonstrated superior soil microbiological activity and SOC accumulation, indicating that high-biomass forage crops should be prioritized in Brazil’s semi-arid region.

Phosphorus availability determines whether single or consortium PGPB maximize tomato performance, demonstrating that rational inoculant design should prioritize functional complementarity over increasing microbial complexity. Phosphorus (P) availability is a major constraint for crop development and productivity, and beneficial bacteria are increasingly proposed to enhance plant P-acquisition efficiency. However, their comparative performance remains variable across studies and experimental contexts. This study investigated whether single plant growth-promoting bacteria (PGPB) strains and a defined bacterial consortium differentially modulate P nutrition and early growth of tomato under contrasting P availability. Tomato plants were grown hydroponically in a factorial design combining single-strain inoculations (Azospirillum brasilense, Pantoea agglomerans, Priestia aryabhattai), a defined consortium, and a non-inoculated control under five P regimes differing in concentration and chemical form (soluble vs. insoluble). Plant growth and root architecture traits were evaluated alongside ionomics and targeted expression analysis of SlPHT1 transporters, thus linking plant performance with nutrient status and regulation. Results indicated that P. agglomerans showed the most stable benefits under soluble P, while A. brasilense strongly promoted adaptive root and transporter responses under moderate limitation. P. aryabhattai induced subtler growth effects but reshaped nutrient associations, particularly with insoluble P. By contrast, the consortium did not consistently outperform single strains and showed clear advantages only when insoluble P was the sole source. Overall, these findings demonstrate that the effectiveness of single versus multi-strain inoculation is strongly context-dependent and emerges from the interaction between P availability, strain identity, and plant response integration. Accordingly, effective consortia should be designed based on functional complementarity and balance, rather than on increasing inoculant complexity, as overlapping PGP traits may lead to non-additive or even counterproductive effects.

Changes in the soil microbial community for studies of different novel communities can be promoted by different methodologies, among which soil autoclaving stands out as a quick and readily available tool. However, this procedure may also directly or indirectly alter nitrogen (N) and phosphorus (P) dynamics. The purposes of this study were as follows: (i) to characterize microbial activity after soil autoclaving through microbial 14CO2-respiration; and (ii) to evaluate the effect of microbial manipulation and autoclaving on soil N and 33P dynamics. For this, two sets of soil samples from two areas (forest and cultivated area) were used in the laboratory. Firstly, 14C-glucose was added to the soils and after 24 h five soil microbiomes were generated: AS (autoclaved soil), and AS re-inoculated with serial dilutions (w/v) prepared by successive mixing of soil suspensions in sterile deionized water obtaining 10−1, 10−3, and 10−6, which generated the treatments AS + 10−1, AS + 10−3, and AS + 10−6; and the treatment NS (non-autoclaved control), all incubated for 28 d. 14CO2 emission was used to characterize microbial activity; additionally, N dynamics were assessed at the end of incubation. In a second assay, 33P was applied to the soil before autoclaving and re-inoculation. Following further incubation (14 d), a 33P chemical fractionation was performed. The following are based on the results: (i) 14CO2 emission: microbial activity in the autoclaved soil is null, but after a reinoculation of AS + 10−1 and AS + 10−3 soil dilution suspension, the 14CO2-respiration is higher than in an NS. (ii) regarding the N dynamics, in autoclaved soils, the microbial levels increased N-NH4+ concentration, with an evident increase in the AS + 10−3 and AS + 10−1, and a reduction in the N-NO3− concentration in comparison to the NS. For 33P, the autoclaving procedure itself reduced the 33P lability, regardless of the levels of microbial community reinoculated.

Tropical rainforests such as the Amazon are of high importance as a global carbon sink. Due to its well-known nutrient limitation, the Amazon rainforest relies heavily on rapid microbial decomposition of biomass to release freshly available nutrients for plant growth. Despite the fundamental importance of decomposers for this ecosystem, little is known about the biodiversity of such microbiomes, their functional activity, and spatial and seasonal variability. We used 16S rDNA and ITS rDNA sequencing to analyze the microbial communities of the Amazon’s terra firme and the much drier white-sand ecosystems during the dry and wet seasons in 2022. Bacterial microbiomes differed significantly between seasons, displaying lower bacterial species richness and diversity in response to seasonal drought. In contrast, fungal richness and diversity differed strongly between sites, but were less affected by seasonal variation, suggesting their hyphae network and associations with plants as potential protectors against drought effects. Fungal and bacterial communities alike showed lower abundance of taxa involved in organic matter decomposition following seasonal drought. These changes were also reflected at the functional level, with samples collected during the dry season and at white-sand sites featuring lower abundances of decomposition and denitrification pathways. Soil hydro-chemical data also emphasizes how prolonged drought may limit soil nutrient supply via local microbiomes. Our results suggest that the reduced nutrient availability and soil connectivity during drought and within the white-sand ecosystem lower microbial activity and functional redundancy, henceforth demonstrating a strong impact of ecosystem type and drought on tropical microbiomes and their functional capacities. Our results further highlight that the observed increase in droughts in the Amazon rainforest may additionally limit nutrient supply through the microbial community, limiting carbon sequestration in the ecosystem with negative consequences for the global climate system.

Sugarcane (Saccharum spp.) is a globally important crop, and strategies to minimize the negative impacts of its cultivation and enhance its development are highly relevant. Plant growth-promoting bacteria (PGPB) can sustainably foster plant growth in agricultural systems and mitigate adverse effects of stress on plants. This is the first study to investigate the combined use of Azospirillum brasilense (Ab) and Nitrospirillum amazonense (Na), two microorganisms widely applied in agricultural systems, aiming to elucidate their effects on the nutritional status, biochemical responses, and productive parameters of sugarcane. Greenhouse experiments were conducted under controlled water and temperature conditions with four treatments: application of Ab, Na, or Ab + Na (Mix) or no PGPB application (control). Sugarcane was cultivated until the middle of the rapid growth stage. To validate the results, the greenhouse trials were replicated under field conditions at two sites (Maracaí-SP and Pradópolis-SP). The results showed that the inoculation of sugarcane with plant growth-promoting bacteria (PGPB), particularly Ab and Mix, enhanced nutritional aspects, especially N content. These increases were significant under greenhouse (p ≤ 0.05) and field conditions (p ≤ 0.10). Additionally, inoculation reduced oxidative stress and improved photosynthetic parameters, such as net photosynthetic rate, water use efficiency, and carboxylation efficiency. These cascading effects contributed to significant gains in crop productivity, with an average increase in stalk yield of 10.9 % for Ab and 12.2 % for Mix across both environments. Similarly, there was an increase in sugar yield per hectare, with gains of 13.3 % for Ab and 13.7 % for Mix compared to the control. These findings highlight the potential of PGPB as a sustainable strategy to enhance crop productivity and resilience, contributing to environmentally balanced agricultural systems. Although the benefits of PGPB were evident, differences between Ab and Mix were not pronounced. Therefore, additional studies are needed to explore the potential of these combinations under adverse conditions, when their effects could be more pronounced.

Plants growing in volcanic scoria soils face severe edaphic challenges, including nutrient scarcity, high porosity, and marked seasonal variability. This study explores the structural and functional stability, microbial interactions, and plant growth-promoting capacities of rhizosphere bacterial communities associated with Gaultheria mucronata (L. f.) Hook. & Arn. (Ericaceae), a native shrub adapted to extreme environments in southern Chile. Rhizosphere and bulk soil samples were collected in contrasting seasons (summer and winter) across two volcanic scoria sites. By employing 16S rRNA metabarcoding, functional inference, microbial isolation, and plant-beneficial trait assays, we demonstrated that rhizosphere bacterial communities maintain structural stability and distinct functional profiles, significantly differentiated from bulk soils despite seasonal fluctuations in soil nutrient availability. Network co-occurrence analyses revealed season-dependent patterns, with higher complexity and balanced interactions in winter. Functional predictions highlighted enrichment in rhizosphere processes related to nutrient mobilization, organic matter degradation, and antioxidant mechanisms. Arthrobacter sp. emerged as a keystone taxon with consistent high abundance, central network positioning, and multiple plant growth promoting traits, including phosphate solubilization, siderophore production, and ammonia synthesis. Our findings demonstrate that rhizosphere bacterial communities associated with Gaultheria mucronata maintain structural stability and exhibit functional plasticity across contrasting seasons in nutrientpoor volcanic scoria soils. These traits reflect the resistance of rhizobacteria to seasonal variability and suggest a role in supporting plant adaptation to extreme edaphic environments.

The Cerrado and Atlantic Rainforest are two geographically distinct biomes in Brazil that have undergone significant land-use change due to soybean cultivation. These biomes differ greatly in their edaphic and climatic characteristics, driving below-ground biodiversity patterns that remain poorly understood. To address this knowledge gap, 152 soil samples were collected from major soybean-producing areas in the Brazilian Cerrado and Atlantic Rainforest biomes between January and May 2021. This study explored the effect of soybean cultivation on nematode and bacterial communities across both biomes using 18S rRNA and 16S rRNA amplicon sequencing. The results revealed that bacterial diversity did not differ between the biomes, indicating possible biotic homogenization driven by agricultural practices. However, bacterial community composition varied, with the Cerrado having a higher relative abundance of Bacillota, whereas the Atlantic Rainforest had a greater relative abundance of Acidobacteriota. Redundancy analysis (RDA) indicated that bacterial communities were primarily influenced by soil clay content, regardless of biome. In contrast, nematode community structure had distinct patterns between the biomes, with a higher relative abundance of fungivorous nematodes associated with the Cerrado and bacterivorous and omnivorous nematodes associated with the Atlantic Rainforest. RDA also revealed that nematode communities were strongly influenced by mean air temperature, which differed significantly between the biomes. Network analyses highlighted greater complexity in the Cerrado, with both positive and negative correlations between bacteria and nematode trophic groups. In contrast, in the Atlantic Rainforest interactions were limited to negative correlations. This is the first study to consider both the bacterial and nematode communities of Brazilian soils at national scale.

Manure applications in agricultural soils are a major driver of antibiotic resistance gene (ARG) dissemination, yet long-term effects of composted manure applications under tropical real field conditions remain unclear. This study assessed how successive composted manure applications influence soil physicochemical attributes, bacteriome and resistome profiles in the Brazilian Cerrado, including one site with naturally high heavy metal content. Across all sites, multidrug resistance genes were most abundant, followed by macrolide-lincosamide-streptogramin (MLS), tetracycline, β-lactam and glycopeptides resistance, aligning with predominance of Actinomycetota and Pseudomonadota as key ARG hosts. Manure increased soil pH and available phosphorus (P), with pH significantly shaping bacterial communities and pH and P the resistome in uncontaminated sites (2 and 3). However, in the metal-rich site (1), Cu was the dominant driver. Manure increased ARG richness and changed resistome structure but did not affect clinically relevant genes or resistome diversity. Metal resistance genes (MRGs), particularly for Cu and Zn, strongly influenced resistome dynamics, highlighting co-selection. Integrons integrase genes (intl) abundance increased in metal-depleted but not in metal-rich soils. While composting appears to mitigate ARG spread, particularly for clinically relevant genes, the high antibiotic use in livestock, large manure volumes, and potential for ARG persistence in tropical soils highlight the need for further research on manure treatment strategies and ARG fate in these environments. Environmental Implication. Our study highlights the environmental risks of antibiotic resistance gene (ARG) dissemination in tropical agricultural soils, emphasizing the role of manure application and heavy metal contamination in shaping soil resistome. While composted manure increased bacterial diversity and ARG richness, it did not significantly impact clinically relevant genes and resistome diversity, suggesting that composting may help mitigate ARG spread but does not eliminate it. Metals were the dominant drivers of ARG selection in the contaminated site, underscoring the role of co-selection mechanisms in maintaining resistance. However, manure applications increased integrons abundance, raising concerns about horizontal gene transfer and potential ARG proliferation into pathogens. These findings stress the urgent need for improved manure management policies in Brazil, where high antibiotic use in livestock and large manure volumes pose significant environmental and public health risks. Developing sustainable manure treatment strategies and monitoring ARG persistence are essential to limit antibiotic resistance proliferation in tropical agricultural ecosystems.

Soil microbial diversity plays a crucial role in plant health, influencing pathogen suppression and biocontrol efficacy. This study investigated how soil microbial diversity modulates interactions between the pathogen Bipolaris sorokiniana and the biocontrol bacterium Pseudomonas inefficax in the wheat rhizosphere. Using a dilution-to-extinction method, we established five soil microbial diversity levels: natural soil, dilutions at 10-1, 10-3, 10-6, and fully autoclaved soil. This gradient allowed us to evaluate disease severity, plant growth, and rhizosphere microbiome shifts. Inoculation with Pseudomonas inefficax significantly reduced disease severity caused by Bipolaris sorokiniana, particularly in low-diversity soils, emphasizing the effectiveness of P. inefficax in these simplified environments where microbial competition is reduced. Despite higher pathogen abundance in low-diversity soils, P. inefficax effectively mitigated disease severity, likely through direct antagonistic activity. Alpha diversity indices confirmed a reduction in microbial diversity across the gradient, while beta diversity analyses revealed distinct shifts among treatments. Although Chitinophaga, Pseudomonas and Dyadobacter were significantly enriched in natural soils with inoculation of the P. inefficax, statistically significant disease suppression was not observed under these higher-diversity conditions. On the other hand, in low-diverse soils (autoclaved soil), where disease is suppressed with P. inefficax inoculation, Fluviicola showed a significant enrichment when compared with the treatment inoculated only with the pathogen, suggesting that this bacterial taxon can play a role in disease suppression along with the inoculant. These findings underscore the critical role of the soil microbial diversity in shaping the success of biocontrol interventions.