Amazonian Dark Earth harbors multifunctional plant growth-promoting bacteria across soil horizonsABSTRACT
Amazonian Dark Earth (ADE) represents a unique anthropogenic soil system characterized by high fertility and remarkable microbial diversity, offering substantial potential for sustainable agriculture. This study investigated the culturable fraction of plant growth-promoting bacteria from a single ADE profile collected at the Jabuti archaeological site (Bragança, Eastern Amazon, Brazil). Using King’s B medium, 466 bacterial isolates were recovered from three soil horizons (A, B, and C) and evaluated for their functional and biotechnological traits. Among these isolates, 24.2% produced indole-3-acetic acid at concentrations up to 63.3 μg•mL-1, whereas 18% exhibited phosphate-solubilizing capacity. Siderophore production was comparatively limited (2.7%), likely reflecting the physicochemical conditions of ADE soils, where increased iron availability may reduce the ecological advantage associated with siderophore synthesis. Biological nitrogen fixation potential was broadly distributed: 86.1% of the pre-selected isolates exhibited diazotrophic behavior, although only 44.2% harbored the nifH gene. The acdS gene, associated with 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity and stress alleviation, was detected in 9.6% of the isolates. Molecular identification revealed the predominance of Bacillus (40%) and Pseudomonas (24.4%). Notably, Bacillus velezensis exhibited multifunctional traits, including nitrogen fixation potential and the presence of the acdS gene, highlighting its relevance as a promising candidate for bioinoculant development. Several isolates displayed < 97% similarity in 16S rRNA sequences, suggesting that ADE may harbor phylogenetically divergent or potentially novel bacterial taxa with unexplored biotechnological potential. Overall, ADE sustains functionally diverse bacterial communities throughout the soil profile, constituting a strategic microbial reservoir for the development of sustainable agricultural inputs.
Key words
plant growth-promoting bacteria; indole-3-acetic acid production; phosphate solubilization; diazotrophy
INTRODUCTION
The Amazonian Dark Earths (ADE), locally known as terra preta de índio, represent a unique class of anthropic soils formed through long-term human-induced pedogenetic processes (Schmidt et al. 2023). These soils originated from a specific pedogenetic pathway termed melanization, where the intense darkening of inorganic matrices resulted from the continuous deposition and stabilization of organic matter within the A-horizon (Macedo et al. 2017). Unlike typical Amazonian soils, which are predominantly characterized by low natural fertility, high acidity, and advanced weathering status (Silva et al. 2024), ADE profiles exhibit exceptional natural fertility, high cation exchange capacity, and a recalcitrant organic matter pool. Such attributes promote long-term nutrient buffering and create chemically stable microsites capable of sustaining microbial activity over extended periods. This distinct chemical architecture creates a specialized environment that has been associated with enhanced microbial activity and diverse microbial communities (Souza et al. 2025).
In the soil matrix, microorganisms act as major drivers of biogeochemical cycling, regulating organic matter decomposition, biological nitrogen fixation, phosphate solubilization, and the synthesis of phytohormones and siderophores (Thepbandit and Athinuwat 2024). Plant growth-promoting bacteria (PGPB) enhance plant performance through a coordinated interplay of direct and indirect mechanisms capable of substantially increasing crop productivity (Timofeeva et al. 2023). Direct mechanisms involve modulation of hormonal signaling and nutrient acquisition through the secretion of indolic compounds, iron-chelating siderophores, and metabolites capable of converting insoluble phosphorus into plant-available forms (Shahwar et al. 2023). Conversely, indirect mechanisms suppress phytopathogens by triggering induced systemic resistance, antibiotic synthesis, and the production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which lowers stress-induced ethylene levels and mitigates physiological damage under adverse environmental conditions (Kumar et al. 2022). Collectively, these mechanisms drive plant resilience and contribute to the stabilization of plant-soil interactions under environmental stress.
The strategic application of PGPB has been increasingly validated as an alternative to improve nutrient uptake efficiency while reducing the environmental dependence on inorganic fertilizers in staple crops such as maize, sorghum, soybean, and wheat (Aquino et al. 2021, Kumawat et al. 2022). Beyond nutritional benefits, these microorganisms also exert strong biocontrol activity against phytopathogens, as demonstrated in Piper nigrum cultivation (Lau et al. 2020). Recent studies by Araújo et al. (2020), Araújo et al. (2023), and Carvalho Neta et al. (2024) already demonstrated that microbial consortia can outperform single-strain inoculants by enhancing stress tolerance and improving plant performance under both controlled and field conditions. In particular, strains belonging to Streptomyces, Arthrobacter, and other PGPB have demonstrated the ability to alleviate abiotic stress through mechanisms associated with nutrient mobilization, hormonal regulation, and modulation of plant stress responses.
Despite the remarkable microbial richness associated with ADE, the functional prospecting of its culturable bacterial fraction remains comparatively underexplored. The phyla Bacillota and Pseudomonadota typically dominate the PGPB landscape, with genera such as Burkholderia, Enterobacter, Pseudomonas, Acinetobacter, and Bacillus representing important functional groups (Grzyb and Szulc 2024). Its unique anthropogenic origin may have favored bacterial communities with high biotechnological potential.
In this sense, ADE represents a strategic microbial reservoir for the development of next-generation bioinputs adapted to tropical environments. Investigating the vertical distribution of these bacteria may provide ecological insights and support the development of microbial-based strategies for improving soil functionality and advancing Sustainable Development Goals (SDGs) 2 and 12 (He et al. 2024, Sharma et al. 2024). Furthermore, identifying native strains harboring multifunctional traits, such as efficient phosphorus solubilization and ACC deaminase activity, may contribute to restoring degraded tropical soils while enhancing agricultural sustainability and food security (Shahid et al. 2023).
Based on the unique ecological conditions provided by the selected ADE profile, which was selected because it represents a recently characterized archaeological ADE with limited previous microbiological investigation and recognized potential for biotechnological prospecting, we hypothesized that these soils harbor specialized bacterial communities with high biotechnological potential and multifunctional plant growth-promotion traits maintained throughout the soil profile, including deeper horizons. Thus, this study aimed to isolate and morphologically characterize bacteria from the investigated profile, evaluate their in-vitro multifunctionality through key plant growth-promotion mechanisms, and identify the most promising strains via 16S rRNA gene sequencing to explore associations between taxonomy and plant growth-promotion potential.
METHODS
Sampling
Soil sampling was conducted at the Jabuti archaeological site, located in the Caeté-Taperaçu Marine Extractive Reserve, in Bragança, Pará, Brazil (46°40’19.8”W; 0°55’39.5”S). The study was conducted on a single previously established soil profile (Fig. 1), located in a recently characterized archaeological ADE within a heterogeneous landscape comprising saline fields, upland forest, and coastal environments. The surrounding area is predominantly covered by native vegetation, and no documented evidence of previous agroforestry management or cultivation with deep-rooted crops is available for the sampling site. The site has undergone previous archaeological and pedological characterization.
Geographic location of the sampling area in the municipality of Bragança, Pará state, Eastern Amazon, Brazil, and representative soil profile of Amazonian Dark Earth.
The soil was classified as a Gleysol, displaying an A-Cg horizon sequence according to the Brazilian Soil Classification System (Santos et al. 2018). The stratification included Horizon A (0–30-cm depth; hereafter referred to as HA), composed of authentic Amazonian Dark Earth; Horizon B (30–40-cm depth; hereafter referred to as HB), representing a transitional layer; and Horizon C (40–70-cm depth; hereafter referred to as HC).
Before sampling, the exposed profile face was cleaned by removing approximately 20–30 cm of soil to minimize edge effects (Fig. 1). Soil samples were collected using polyvinyl chloride (PVC) tubes (100 mm in diameter and 100 mm in length). Five biological replicates were collected from each soil horizon along the exposed profile face, after which samples were aseptically stored, transported on ice, and maintained at 4°C until microbiological analysis. Physical and chemical characterization was performed according to Teixeira et al. (2017), establishing the environmental background of each soil horizon (Table 1).
Bacterial isolation, characterization, and purification
Bacterial isolation was performed using a serial dilution procedure (10-1 to 10-4) with 10 g of soil suspended in 90 mL of sterile 0.85% NaCl solution. Aliquots were plated onto King B medium (King et al. 1954) and incubated at 30°C for 72 h. Pure cultures were obtained through successive subculturing based on distinct colony morphotypes. Isolates were preserved in King B broth supplemented with 25% glycerol at -20°C in triplicate.
Following purification, isolates were clustered according to phenotypic characteristics, including growth rate, colony morphology, transparency, pigmentation, and mucoid production, using the unweighted pair group method with arithmetic mean (UPGMA) method based on the Jaccard coefficient (Hammer et al. 2001) to group isolates sharing identical phenotypic profiles according to the evaluated descriptors. A total of 466 isolates were subsequently screened for plant growth-promotion traits.
In-vitro characterization of plant growth-promotion mechanisms
Quantitative indole-3-acetic acid (IAA) production was assessed according to Brick et al. (1991), with modifications proposed by Kuss et al. (2007). Cultures were grown in tryptone soya broth (TSB) supplemented with 5 mM∙L-1 tryptophan under dark conditions (48 h, 30°C, 150 rpm). All assays were performed in three technical replicates, and the mean values obtained for each isolate were used for the statistical analyses. After incubation, supernatants were reacted with Salkowski reagent (4:1), incubated for 15 min, and absorbance was measured at 530 nm using a calibration curve.
Siderophore production was evaluated qualitatively using the chrome azurol S (CAS) assay (Schwyn and Neilands 1987). After seven days of incubation in King B broth, supernatants were mixed (1:1) with CAS reagent. Siderophore production was considered positive based on the decolorization of the CAS complex. Calcium phosphate solubilization was evaluated on solid medium according to Verma et al. (2001). After 15 days of incubation at 28°C, the solubilization index (SI) was calculated as the ratio between total halo diameter and colony diameter.
The potential for biological nitrogen fixation was screened using nitrogen-free JNFB semi-solid medium (Dobereiner et al. 1995). Prior to inoculation, isolates were triple-washed in sterile 0.85% NaCl solution. Pellicle formation below the medium surface after seven days of incubation was considered an indicative qualitative phenotype associated with diazotrophic behavior rather than direct evidence of active nitrogen fixation.
Based on the results obtained from the in-vitro assays, isolates selected for downstream molecular analyses were prioritized based on high IAA production, phosphate-solubilizing capacity, siderophore production, or the simultaneous expression of multiple plant growth-promotion-associated traits.
Molecular identification
Molecular identification targeted the 16S rRNA gene. Genomic DNA was extracted using the PureLink microbiome DNA purification kit (Thermo Fisher Scientific). Polymerase chain reaction (PCR) amplification was performed using the universal primers 27F and 1492R (Lane 1991) under optimized thermal cycling conditions. Amplicons were sequenced by Macrogen (South Korea), and sequence similarity analyses were conducted using the EzBioCloud 16S-based identification platform (Yoon et al. 2017).
Phylogenetic trees were constructed using the Neighbor-Joining algorithm with the Kimura-2 parameter model in MEGA 6 (Tamura et al. 2013), based on 1,000 bootstrap replicates (Ünal 2024). The partial sequences were submitted to GenBank under access numbers PZ804964-PZ805001.
Quantitative polymerase chain reaction for functional genes
To investigate the genetic potential associated with biological nitrogen fixation and ethylene stress mitigation, quantitative polymerase chain reaction (qPCR) assays were performed targeting the nifH (nitrogenase) and acdS (ACC deaminase) genes. Reactions were conducted in duplicate using GoTaq® qPCR Master Mix (Promega). Primer specificity and amplification conditions are described in Table 2.
Primers and cycling conditions used to amplify quantitative polymerase chain reation target genes.
Although the analyses were based on the presence or absence of the target genes, qPCR was selected because of its higher analytical sensitivity, allowing the detection of target genes during the exponential amplification phase while minimizing potential interference from primer dimers commonly associated with endpoint conventional PCR. Isolates were considered positive when a specific amplification curve was detected during the qPCR assay. Gene amplification was interpreted as molecular evidence supporting the presence of genetic traits potentially associated with plant growth-promotion mechanisms.
Data analysis
Quantitative variables were evaluated for normality using the Shapiro-Wilk’s test before being subjected to analysis of variance (ANOVA). Means were compared using Tukey’s test at a 5% significance level using SISVAR version 5.1.
For IAA production and calcium phosphate solubilization analyses, isolates were grouped according to phenotypic similarity using the PAST3 software. Subsequently, representative isolates from each phenotypic group were subjected to Tukey’s multiple comparison test at the 5% significance level using SISVAR version 5.1.
RESULTS
Isolation and phenotypic and morphological diversity
A total of 466 bacterial isolates were recovered from the investigated profile—149 isolates from HA, 194 from HB, and 123 from HC. Most of the isolated bacteria showed morphological differences in color, shape, elevation, edges, and surface (Fig. 2). Phenotypic clustering generated 77, 115, and 73 distinct groups for HA, HB, and HC, respectively, revealing substantial morphophysiological diversity throughout the soil profile.
Morphological diversity of bacterial isolates obtained from different soil horizons of Amazonian Dark Earth cultivated on solid King’s B medium.
Indole-3-acetic acid and siderophore production
IAA production was detected in 24.2% of the isolates (113 isolates), with concentrations ranging from 4.35 to 63.03 μg∙mL-1. The highest individual IAA-producing isolates were recovered from the HC horizon. For descriptive purposes, IAA-producing isolates were classified according to their production levels. Among the IAA-producing isolates, 15.8% produced low concentrations (1–11 μg∙mL-1), whereas 7.5% exhibited intermediate production levels (11–50 μg∙mL-1). Only 0.85% of the isolates (four isolates) produced concentrations exceeding 50 μg∙mL-1 (Table 3).
In-vitro growth promotion mechanisms of isolates prospectively identified in the Amazonian Dark Earth soil<tfn href="tfn04">*</tfn>.
Siderophore production was detected in 2.7% of the isolates (13 isolates), based on the qualitative colorimetric shift observed in the CAS assay (Table 3).
Phosphate solubilization and biological nitrogen fixation
Phosphate solubilization was observed in 18% of the isolates, with SI values reaching 3.76 for isolate 269 and 4.46 for 402. For descriptive purposes, phosphate-solubilizing isolates were classified according to their SI values. Most phosphate-solubilizing isolates (15.6%) exhibited SI values below 2, whereas 2.3% showed moderate solubilization capacity (Table 3).
Regarding the screening for diazotrophic-associated phenotype, 86.1% of the 166 pre-selected isolates formed a subsurface pellicle in JNFB semi-solid medium. Among these isolates, 46.3% maintained neutral pH, while 27.7 and 12.1% promoted medium alkalization and acidification, respectively.
Occurrence of nifH and acdS genes
Qualitative molecular screening of the selected isolates revealed the presence of the nifH gene in 44.2% (23 isolates), whereas the acdS gene was detected in 9.6% (five isolates). Isolate 193, identified as Bacillus velezensis, was positive for both nifH and acdS genes (Table 3).
Molecular taxonomy and phylogeny
Molecular identification of representative isolates revealed the predominance of Bacillus (40 %) and Pseudomonas (24,4%). Isolates 126 and 104 exhibited high similarity with Paenibacillus contaminans (97.9%) and B. velezensis (96.7%), respectively. In contrast, several isolates displayed similarity values below 97%, including isolate 351A (76.6% similarity with Pseudomonas pisciculturae) and isolate 351B (76.7% similarity with B. velezensis), indicating the occurrence of phylogenetically divergent bacterial groups within the selected ADE profile (Table 4; Fig. 3).
Identification of isolates prospected in the Amazonian Dark Earth soil, based on EzBioCloud sequences.
Phylogenetic relationship of bacterial isolates obtained from soil horizons of Amazonian Dark Earth based on partial 16S rRNA gene sequences. The scale bar at the bottom indicates the number of differences in base composition among the sequences.
DISCUSSION
This study assessed the culturable fraction of PGPB across an ADE profile, establishing a collection of 466 isolates distributed along the A, B, and C horizons. Phenotypic clustering performed independently within each horizon generated 77, 115, and 73 groups, respectively, revealing substantial phenotypic diversity within each soil layer.
Although the clustering approach was not designed to compare the occurrence of identical strains among horizons, the observed phenotypic diversity suggests that the ADE profile provides a wide range of ecological conditions capable of supporting a functionally diverse culturable bacterial community. These findings are consistent with metagenomic studies reporting enhanced microbial diversity and metabolic versatility in ADE compared to adjacent soils (Lima et al. 2014, Pellegrinetti et al. 2024). In addition, the relatively high frequency of isolates expressing plant growth-promoting traits reinforces the ecological relevance of ADE-associated microbial communities.
IAA production was detected in 24.2% of the isolates, reaching values of up to 63.03 μg∙mL-1, indicating that a considerable portion of the culturable community may contribute to plant developmental processes. Bacterial-derived IAA has been associated with lateral root formation and root hair proliferation, which can increase the absorptive surface and improve nutrient and water acquisition under limiting conditions (Gong et al. 2025). Notably, the highest IAA-producing isolates were predominantly recovered from the HC horizon, suggesting that deeper microbial communities retain metabolically active populations even under comparatively reduced inputs of labile organic substrates. This pattern may reflect shifts in ecological competition and resource availability along the soil profile, favoring microorganisms adapted to oligotrophic conditions (Yin et al. 2024). Moreover, acidic conditions observed throughout the profile (pH 4.1–5.6) may also contribute to the selection of acid-tolerant bacterial groups capable of maintaining phytohormone-related metabolism under restrictive conditions (Çakmakçi et al. 2010).
Siderophore production was detected in only 2.7% of the isolates, suggesting that this trait may be less selectively favored under the physicochemical conditions of ADE. In highly acidic environments, increased Fe3+ solubility may partially reduce the ecological advantage associated with siderophore-mediated iron acquisition (Tamariz-Angeles et al. 2021). Furthermore, the energetic costs associated with siderophore biosynthesis may favor alternative nutrient acquisition strategies in these systems. In contrast, phosphate solubilization was observed in 18% of the isolates and is commonly associated with the secretion of low-molecular-weight organic acids capable of releasing phosphorus bound to mineral fractions (Wei et al. 2018). The greater occurrence of phosphate-solubilizing isolates in surface horizons may be associated with higher organic matter inputs and intensified rhizosphere-derived carbon availability (Ahmad et al. 2018). In addition, the co-occurrence of phosphate solubilization and IAA production in some isolates suggests the existence of complementary traits potentially associated with nutrient acquisition and root development.
The occurrence of pellicle formation in JNFB medium among 86.1% of the pre-selected isolates indicates that diazotrophic-associated phenotypes were widely distributed throughout the investigated profile. However, only 44.2% of the evaluated isolates carried the nifH gene, reinforcing the limitations of exclusively phenotypic screening approaches and highlighting the importance of molecular validation, since pellicle formation may also be linked to other metabolic responses (Li et al. 2017). The simultaneous occurrence of traits associated with nitrogen metabolism, phytohormone production, and ACC deaminase-related genes suggests that several isolates harbor multifunctional characteristics potentially relevant for plant-microbe interactions under stressful environmental conditions (Maheshwari et al. 2020). Such multifunctionality may be particularly advantageous in tropical soils, where nutrient limitation and abiotic stress frequently overlap.
The predominance of Bacillus and Pseudomonas agrees with previous reports describing these genera as recurrent members of plant-associated microbial communities due to their metabolic versatility and ecological adaptability. Bacillus species are recognized for their capacity to persist under adverse environmental conditions through endospore formation and secondary metabolite production (Abuhena et al. 2024). In the present study, isolate 193, identified as B. velezensis, harbored both nifH and acdS genes, suggesting the coexistence of traits potentially associated with nitrogen metabolism and stress alleviation. ACC deaminase activity has been widely associated with reductions in stress-induced ethylene accumulation, which may indirectly favor root development and plant tolerance under abiotic stress conditions (Shahid et al. 2023). Additionally, the detection of isolates displaying < 97% similarity in 16S rRNA sequences indicates the occurrence of phylogenetically divergent bacterial groups within the investigated ADE profile, reinforcing its biotechnological relevance.
Bacillus velezensis has been increasingly recognized as an important plant-associated bacterium because of its multifunctional plant growth-promoting and biocontrol potential (Rabbee et al. 2023). Previous studies have associated this species with auxin production, ACC deaminase activity, nutrient mobilization, and enhanced tolerance to abiotic stresses, supporting its relevance for sustainable agriculture. Although these traits were not directly evaluated in the present study, the identification of a B. velezensis isolate harboring both nifH and acdS genes reinforces its potential as a candidate for future bioinoculant development.
The uneven distribution of plant growth-promoting traits across soil horizons suggests that edaphic factors, including pH, organic matter content, and nutrient availability, may act as ecological filters shaping microbial assemblages along the profile. From an applied perspective, microbial prospecting in ADE reinforces the potential of these soils as reservoirs of agriculturally relevant microorganisms. In particular, the identification of isolates combining traits associated with phosphate solubilization, phytohormone production, and stress-related genes may support the future development of multifunctional microbial consortia adapted to tropical agricultural systems (Araújo et al. 2023, Carvalho Neta et al. 2024). In addition to supporting the development of microbial bioinputs, the ecological characteristics observed in the investigated ADE profile also reinforce the importance of agroecological management practices that promote soil organic matter accumulation, biological activity, and habitat diversification. Such practices may contribute to the long-term establishment of functionally diverse microbial communities capable of enhancing soil health and ecosystem functioning.
Overall, the ADE evaluated in this study harbored a diverse culturable bacterial community exhibiting multiple plant growth-promoting traits throughout the analyzed soil profile, highlighting its potential as a source of microorganisms for sustainable agriculture. Nevertheless, greenhouse and field-scale studies remain necessary to validate the ecological performance and agronomic consistency of these isolates under natural conditions.
CONCLUSION
The ADE evaluated in this study harbored a diverse culturable bacterial community exhibiting multiple plant growth-promoting traits distributed throughout the analyzed soil profile. The recovery of 466 isolates across distinct soil horizons, combined with their pronounced phenotypic variability, indicates that the investigated ADE profile supports complex microbial assemblages even in deeper layers.
The occurrence of plant growth-promoting traits, including IAA production, phosphate solubilization, diazotrophic-associated phenotype, and the detection of nifH and acdS genes, demonstrates that ADE-associated bacteria possess a broad repertoire of characteristics potentially relevant for nutrient cycling, stress mitigation, and plant-microbe interactions. In addition, the predominance of Bacillus and Pseudomonas reinforces the ecological importance of these genera within tropical soil environments.
The study hypothesis was supported, since bacterial isolates exhibiting plant growth-promoting traits were detected throughout the investigated profile, including deeper horizons. Moreover, the identification of multifunctional isolates, together with the occurrence of phylogenetically divergent strains displaying low 16S rRNA similarity values, highlights the ecological and biotechnological relevance of the investigated ADE profile.
Overall, the present study demonstrates that the ADE constitutes a strategic reservoir of culturable bacteria with potential applications in sustainable agriculture and bioinput development. Nevertheless, further greenhouse, plant-based, and field-scale studies remain necessary to validate the functional stability and agronomic performance of these isolates under field conditions.
ACKNOWLEDGEMENTS
Not applicable.
How to cite:
FUNDING
DECLARATION OF USE OF INTELLIGENCE ARTIFICIAL TOOLS
DATA AVAILABILITY STATEMENT
The data are available at GenBank under access numbers PZ804964-PZ805001.
REFERENCES
-
Abuhena, M., Zhakypbek, Y., Uteyev, Y., Aben, A., Kamarkhan, Z., Allakhverdiev, S. I., Assemgul, S. K., Al Rashid, J., Karim, M. D., Kuanysh, T. T., Belkozhayev, A. M. and Kossalbayev, B. D. (2024). An overview of Bacillus species in agriculture for growth promotion, biocontrol and dry tolerance. ES Food and Agroforestry, 18, 1321. https://doi.org/10.30919/esfaf1321
» https://doi.org/10.30919/esfaf1321 -
Ahmad, M., Ahmad, I., Hilger, T. H., Nadeem, S. M., Akhtar, M. F., Jamil, M., Hussain, A. and Zahir, Z. A. (2018). Preliminary study on phosphate solubilizing Bacillus subtilis strain Q3 and Paenibacillus sp. strain Q6 for improving cotton growth under alkaline conditions. PeerJ, 6, e5122. https://doi.org/10.7717/peerj.5122
» https://doi.org/10.7717/peerj.5122 -
Aquino, J. P. A., Antunes, J. E. L., Bonifácio, A., Rocha, S. M. B., Amorim, M. R., Alcântara Neto, F. and Araujo, A. S. F. (2021). Plant growth-promoting bacteria improve growth and nitrogen metabolism in maize and sorghum. Theoretical and Experimental Plant Physiology, 33, 249-260. https://doi.org/10.1007/s40626-021-00209-x
» https://doi.org/10.1007/s40626-021-00209-x -
Araújo, V. L. V. P., Fracetto, G. G. M., Silva, A. M. M., Pereira, A. P. A., Freitas, C. C. G., Barros, F. M. R., Santana, M. C., Feiler, H. P., Matteoli, F. P., Fracetto, F. J. C. and Cardoso, E. J. B. N. (2023). Potential of growth-promoting bacteria in maize (Zea mays L.) varies according to soil moisture. Microbiological Research, 271, 127352. https://doi.org/10.1016/j.micres.2023.127352
» https://doi.org/10.1016/j.micres.2023.127352 -
Araújo, V. L. V. P., Lira Júnior, M. A., Souza Júnior, V. S., Araújo Filho, J. C., Fracetto, F. J. C., Andreote, F. D., Pereira, A. P. A., Mendes Júnior, J. P., Barros, F. M. R. and Fracetto, G. G. M. (2020). Bacteria from tropical semiarid temporary ponds promote maize growth under hydric stress. Microbiological Research, 240, 126564. https://doi.org/10.1016/j.micres.2020.126564
» https://doi.org/10.1016/j.micres.2020.126564 -
Brick, J. M., Bostock, R. M. and Silverstone, S. E. (1991). Rapid in situ assay for indoleacetic acid production by bacteria immobilized on a nitrocellulose membrane. Applied and Environmental Microbiology, 57, 535-538. https://doi.org/10.1128/aem.57.2.535-538.1991
» https://doi.org/10.1128/aem.57.2.535-538.1991 -
Çakmakçi, R., Dönmez, M. F., Ertürk, Y., Erat, M., Haznedar, A. and Sekban, R. (2010). Diversity and metabolic potential of culturable bacteria from the rhizosphere of Turkish tea grown in acidic soils. Plant and Soil, 332, 299-318. https://doi.org/10.1007/s11104-010-0295-4
» https://doi.org/10.1007/s11104-010-0295-4 -
Carvalho Neta, S. J., Araújo, V. L. V. P., Fracetto, F. J. C., Silva, C. C. G., Souza, E. R., Silva, W. R., Lumini, E. and Fracetto, G. G. M. (2024). Growth-promoting bacteria and arbuscular mycorrhizal fungus enhance maize tolerance to saline stress. Microbiological Research, 284, 127708. https://doi.org/10.1016/j.micres.2024.127708
» https://doi.org/10.1016/j.micres.2024.127708 - Dobereiner, J., Baldani, J. I. and Baldani, V. L. D. (1995). Como isolar e identificar bactérias diazotróficas de plantas não leguminosas. Brasília: EMBRAPA.
-
Gong, Y., Arif, M. A., Xu, X., Lei, M., Uwamungu, J. Y., Wang, S. and Wang, H. (2025). Insights into asexual propagation techniques and molecular mechanisms underlying adventitious root formation in apple rootstocks. Horticulturae, 11, 1366. https://doi.org/10.3390/horticulturae11111366
» https://doi.org/10.3390/horticulturae11111366 -
Grzyb, T. and Szulc, J. (2024). Deciphering molecular mechanisms and diversity of plant holobiont bacteria: Microhabitats, community ecology, and nutrient acquisition. International Journal of Molecular Sciences, 25, 13601. https://doi.org/10.3390/ijms252413601
» https://doi.org/10.3390/ijms252413601 -
Hammer, Ø., Harper, D. A. and Ryan, P. D. (2001). PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4, 1-9. Available at: http://palaeo-electronica.org/2001_1/past/issue1_01.htm Accessed on: Oct. 6, 2026.
» http://palaeo-electronica.org/2001_1/past/issue1_01.htm -
He, S., Li, L., Lv, M., Wang, R., Wang, L., Yu, S., Gao, Z. and Li, X. (2024). PGPR: key to enhancing crop productivity and achieving sustainable agriculture. Current Microbiology, 81, 377. https://doi.org/10.1007/s00284-024-03893-5
» https://doi.org/10.1007/s00284-024-03893-5 -
Jaya, D. K., Giyanto, G., Nurhidayat, N. and Antonius, S. (2019). Isolation, identification, and detection of acc deaminase gene-encoding rhizobacteria from rhizosphere of stressed pineapple. Indonesian Journal of Biotechnology, 24, 17-25. https://doi.org/10.22146/ijbiotech.39018
» https://doi.org/10.22146/ijbiotech.39018 - King, E. O., Ward, M. K. and Raney, D. E. (1954). Two simple media for the demonstration of pyocyanin and fluorescin. Journal of Laboratory and Clinical Medicine, 44, 301-307.
-
Kumar, M., Poonam, Ahmad, S. and Singh, R. P. (2022). Plant growth promoting microbes: Diverse roles for sustainable and ecofriendly agriculture. Energy Nexus, 7, 100133. https://doi.org/10.1016/j.nexus.2022.100133
» https://doi.org/10.1016/j.nexus.2022.100133 -
Kumawat, K. C., Singh, I., Nagpal, S., Sharma, P., Gupta, R. K. and Sirari, A. (2022). Co-inoculation of indigenous Pseudomonas oryzihabitans and Bradyrhizobium sp. modulates the growth, symbiotic efficacy, nutrient acquisition, and grain yield of soybean. Pedosphere, 32, 438-451. https://doi.org/10.1016/S1002-0160(21)60085-1
» https://doi.org/10.1016/S1002-0160(21)60085-1 -
Kuss, A. V., Kuss, V. V., Lovato, T. and Flôres, M. L. (2007). Fixação de nitrogênio e produção de ácido indolacético in vitro por bactérias diazotróficas endofíticas. Pesquisa Agropecuária Brasileira, 42, 1459-1465. https://doi.org/10.1590/S0100-204X2007001000013
» https://doi.org/10.1590/S0100-204X2007001000013 - Lane, D. J. (1991). 16S/23S rRNA Sequencing. In E. Stackebrandt and M. Goodfellow (Eds.), Nucleic acid techniques in bacterial systematic (p. 115-175). John Wiley and Sons.
-
Lau, E. T., Tani, A., Khew, C. Y., Chua, Y. Q. and San Hwang, S. (2020). Plant growth-promoting bacteria as potential bio-inoculants and biocontrol agents to promote black pepper plant cultivation. Microbiological Research, 240, 126549. https://doi.org/10.1016/j.micres.2020.126549
» https://doi.org/10.1016/j.micres.2020.126549 -
Li, H. B., Singh, R. K., Singh, P., Song, Q. Q., Xing, Y. X., Yang, L. T. and Li, Y. R. (2017). Genetic diversity of nitrogen-fixing and plant growth promoting Pseudomonas species isolated from sugarcane rhizosphere. Frontiers in Microbiology, 8, 1268. https://doi.org/10.3389/fmicb.2017.01268
» https://doi.org/10.3389/fmicb.2017.01268 -
Lima, A. B., Muniz, A. W. and Dumont, M. G. (2014). Activity and abundance of methane-oxidizing bacteria in secondary forest and manioc plantations of Amazonian Dark Earth and their adjacent soils. Frontiers in Microbiology, 5, 550. https://doi.org/10.3389/fmicb.2014.00550
» https://doi.org/10.3389/fmicb.2014.00550 -
Macedo, R. S., Teixeira, W. G., Corrêa, M. M., Martins, G. C. and Vidal-Torrado, P. (2017). Pedogenetic processes in anthrosols with pretic horizon (Amazonian Dark Earth) in Central Amazon, Brazil. PLoS One, 12, e0178038. https://doi.org/10.1371/journal.pone.0178038
» https://doi.org/10.1371/journal.pone.0178038 -
Maheshwari, R., Bhutani, N. and Suneja, P. (2020). Isolation and characterization of ACC deaminase producing endophytic Bacillus mojavensis PRN2 from Pisum sativum. Iranian Journal of Biotechnology, 18, e2308. https://doi.org/10.30498/IJB.2020.137279.2308
» https://doi.org/10.30498/IJB.2020.137279.2308 -
Pellegrinetti, T. A., Cunha, I. C. M., Chaves, M. G., Freitas, A. S., Passos, G. S., Silva, A. V. R., Cotta, S. R., Tsai, S. M. and Mendes, L. W. (2024). Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian dark earths. Brazilian Journal of Microbiology, 55, 1817-1828. https://doi.org/10.1007/s42770-024-01268-3
» https://doi.org/10.1007/s42770-024-01268-3 -
Poly, F., Monrozier, L. J. and Bally, R. (2001). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Research in Microbiology, 152, 95-103. https://doi.org/10.1016/S0923-2508(00)01172-4
» https://doi.org/10.1016/S0923-2508(00)01172-4 -
Rabbee, M. F., Hwang, B. S. and Baek, K. H. (2023). Bacillus velezensis: a beneficial biocontrol agent or facultative phytopathogen for sustainable agriculture. Agronomy, 13, 840. https://doi.org/10.3390/agronomy13030840
» https://doi.org/10.3390/agronomy13030840 - Santos, H. G., Jacomine, P. K. T., Anjos, L. H. C., Oliveira, V. A., Lumbreras, J. F., Coelho, M. R., Almeida, J. Á., Araujo Filho, J. C., Oliveira, J. B. and Cunha, T. J. F. (2018). Sistema Brasileiro de Classificação de Solos. Brasília: EMBRAPA.
-
Schmidt, M. J., Goldberg, S. L., Heckenberger, M., Fausto, C., Franchetto, B., Watling, J., Lima, H., Moraes, B., Dorshow, W. B., Toney, J., Kuikuro, Y., Waura, K., Kuikuro, H., Kuikuro, T. W., Kuikuro, T., Kuikuro, Y., Kuikuro, A., Teixeira, W., Rocha, B., Honorato, V., Tavares, H., Magalhães, M., Barbosa, C. A., Fonseca, J. A., Mendes, K., Alleoni, L. R. F., Cerri, C. E. P., Arroyo-Kalin, M., Neves, E. and Perron, J. T. (2023). Intentional creation of carbon-rich dark earth soils in the Amazon. Science Advances, 9, eadh8499. https://doi.org/10.1126/sciadv.adh8499
» https://doi.org/10.1126/sciadv.adh8499 -
Schwyn, B. and Neilands, J. (1987). Universal chemical assay for the detection and determination of siderophores. Analytical Biochemistry, 160, 47-56. https://doi.org/10.1016/0003-2697(87)90612-9
» https://doi.org/10.1016/0003-2697(87)90612-9 -
Shahid, M., Singh, U. B., Khan, M. S., Singh, P., Kumar, R., Singh, R. N., Kumar, A. and Singh, H. V. (2023). Bacterial ACC deaminase: Insights into enzymology, biochemistry, genetics, and potential role in amelioration of environmental stress in crop plants. Frontiers in Microbiology, 14, 1132770. https://doi.org/10.3389/fmicb.2023.1132770
» https://doi.org/10.3389/fmicb.2023.1132770 -
Shahwar, D., Mushtaq, Z., Mushtaq, H., Alqarawi, A. A., Park, Y., Alshahrani, T. S. and Faizan, S. (2023). Role of microbial inoculants as bio-fertilizers for improving crop productivity: A review. Heliyon, 9, e16134. https://doi.org/10.1016/j.heliyon.2023.e16134
» https://doi.org/10.1016/j.heliyon.2023.e16134 -
Sharma, P., Sharma, P. and Thakur, N. (2024). Sustainable farming practices and soil health: A pathway to achieving SDGs and prospects. Discover Sustainability, 5, 250. https://doi.org/10.1007/s43621-024-00447-4
» https://doi.org/10.1007/s43621-024-00447-4 -
Silva, R. N. P., Mateus, N. S., Santos, C. R. C., Costa, M. G., Ferreira, E. V. O. and Viégas, I. J. M. (2024). Impact of changes in soil attributes and composition following anthropization related to agricultural practices in the Amazon Region. Journal of Soil Science and Plant Nutrition, 24, 2898-2909. https://doi.org/10.1007/s42729-024-01716-x
» https://doi.org/10.1007/s42729-024-01716-x -
Simonet, P., Grosjean, M. C., Misra, A. K., Nazaret, S., Cournoyer, B. and Normand, P. (1991). Frankia genus-specific characterization by polymerase chain reaction. Applied and Environmental Microbiology, 57, 3278-3286. https://doi.org/10.1128/aem.57.11.3278-3286.1991
» https://doi.org/10.1128/aem.57.11.3278-3286.1991 -
Souza, J. G., Alcaina-Mateos, J., Lancelotti, C., Vidal-Torrado, P., Calegari, M. R., Teixeira, W. G., Macedo, G. R. S. and Madella, M. (2025). Spatial analysis of Amazonian Dark Earth formation supports an anthropic origin at the Caldeirao site, Brazil. Journal of Archaeological Science, 176, 106169. https://doi.org/10.1016/j.jas.2025.106169
» https://doi.org/10.1016/j.jas.2025.106169 -
Tamariz-Angeles, C., Huamán, G. D., Palacios-Robles, E., Olivera-Gonzales, P. and Castañeda-Barreto, A. (2021). Characterization of siderophore-producing microorganisms associated to plants from high-Andean heavy metal polluted soil from Callejón de Huaylas (Ancash, Perú). Microbiological Research, 250, 126811. https://doi.org/10.1016/j.micres.2021.126811
» https://doi.org/10.1016/j.micres.2021.126811 -
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013). MEGA 6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
» https://doi.org/10.1093/molbev/mst197 - Teixeira, P. C., Donagemma, G. K., Fontana, A. and Teixeira, W. G. (2017). Manual de método de análise do solo (3 ed.). Brasília: EMBRAPA.
-
Thepbandit, W. and Athinuwat, D. (2024). Rhizosphere microorganisms supply availability of soil nutrients and induce plant defense. Microorganisms, 12, 558. https://doi.org/10.3390/microorganisms12030558
» https://doi.org/10.3390/microorganisms12030558 -
Timofeeva, A. M., Galyamova, M. R. and Sedykh, S. E. (2023). Plant growth-promoting soil bacteria: nitrogen fixation, phosphate solubilization, siderophore production, and other biological activities. Plants, 12, 4074. https://doi.org/10.3390/plants12244074
» https://doi.org/10.3390/plants12244074 -
Ünal, F. (2024). Phylogenetic analysis of Microdochium spp. associated with turfgrass and their pathogenicity in cereals. PeerJ, 12, e16837. https://doi.org/10.7717/peerj.16837
» https://doi.org/10.7717/peerj.16837 -
Verma, S. C., Ladha, J. K. and Tripathi, A. K. (2001). Evaluation of plant growth promoting and colonization ability of endophytic diazotrophs from deep water rice. Journal of Biotechnology, 91, 127-141. https://doi.org/10.1016/S0168-1656(01)00333-9
» https://doi.org/10.1016/S0168-1656(01)00333-9 -
Wei, Y., Zhao, Y., Shi, M., Cao, Z., Lu, Q., Yang, T., Fan, Y. and Wei, Z. (2018). Effect of organic acids production and bacterial community on the possible mechanism of phosphorus solubilization during composting with enriched phosphate-solubilizing bacteria inoculation. Bioresource Technology, 247, 190-199. https://doi.org/10.1016/j.biortech.2017.09.092
» https://doi.org/10.1016/j.biortech.2017.09.092 -
Yin, Q., He, K., Collins, G., De Vrieze, J. and Wu, G. (2024). Microbial strategies driving low-concentration substrate degradation for sustainable remediation solutions. npj Clean Water, 7, 52. https://doi.org/10.1038/s41545-024-00348-z
» https://doi.org/10.1038/s41545-024-00348-z -
Yoon, S., Ha, S., Kwon, S., Lim, J., Kim, Y., Seo, H. and Chun, J. (2017). Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology, 67, 1613. https://doi.org/10.1099/ijsem.0.001755
» https://doi.org/10.1099/ijsem.0.001755
HA: horizon A; HB: horizon B; HC: horizon C.
