Abstract
The aim of the present study was to isolate and evaluate the diversity of rhizobial and endophytic bacterial strains from undisturbed native rainforests within an iron ore mining site of the Serra Norte de Carajás in the Eastern Brazilian Amazon region to assess their biotechnological utility in reclamation of areas. Experiments were conducted to capture strains from samples of the soil of these forests at the sites Arenito II, Noroeste II, and Sul IV using Macroptilium atropurpureum and Mimosa acutistipula var. ferrea as trap host plants. Only M. atropurpureum nodulated, and the different bacterial strains were isolated from its nodules. There was no difference in the number of nodules among the areas, but the Arenito II bacterial community was the most efficient, indicated by the aboveground biomass production and suitable shoot mass/root mass ratio. Fifty-two (52) bacterial isolates were obtained, distributed in five groups, including nodulating and endophytic bacteria: 32 from Arenito II, 12 from Noroeste II, and 8 from Sul IV. The nodulating Bradyrhizobium genus was common to the three areas, whereas Paraburkholderia was found only in Arenito II. The nodD1 gene was amplified in all the strains of both nodulating genera. Strains of the nodulating genus Methylobacterium were also isolated from the three areas; however, they did not nodulate the host of origin, and their nodD1 gene was not amplified. Endophytic strains were also isolated from the genera Paenibacillus, Pantoea, and Leifsonia in Arenito II, Leifsonia in Noroeste I, and Paenibacillus in Sul IV. The greater nodulation and rhizobial and endophytic bacterial diversity observed in Arenito II were probably due to the more suitable edaphic properties of the area. The isolated strains were incorporated in the collection of the Department of Soil Science of UFLA and will be investigated in relation to their symbiotic characteristics with native host plants, as well as their ability to perform other biological processes.
Similar content being viewed by others
Availability of data and materials
Sequence data that support the findings of this study have been deposited in GenBank with accession codes from MK848616 to MK848687.
References
Moreira FMS, Siqueira JO (eds) (2006) Microbiologia e Bioquímica do Solo, 2nd edn. Lavas: UFLA
Madigan MT, Martinko JM, Bender KS, Buckley DH, & Stahl DA (Eds.) (2015) Brock biology of microorganisms (14th ed.). Pearson Education, Inc
Moreira FMS (2006) Nitrogen-fixing Leguminosae nodulating bacteria. In: Moreira FMS et al. (Eds) Soil Biodiversity in Amazonian and Other Brazilian Ecosystems (pp. 237–270). CABI Publishing
Sadowsky MJ, Graham PH, & Sugawara M (2013) Root and stem nodule bacteria of legumes. In: Rosenberg E et al (Eds) The Prokaryotes-Prokaryotic Biology and Symbiotic Associations (401–425). Springer
Marra LM, Oliveira SMD, Soares CRFS, Moreira FMDS (2011) Solubilisation of inorganic phosphates by inoculant strains from tropical legumes. Scientia Agricola 68(5):603–609. https://doi.org/10.1590/S0103-90162011000500015
Longatti SMDO, Marra LM, Moreira FMDS (2013) Evaluation of plant growth-promoting traits of Burkholderia and Rhizobium strains isolated from Amazon soils for their co-inoculation in common bean. Afr J Microbiol Res 7(11):948–959. https://doi.org/10.5897/AJMR12.1055
Rogers NJ, Carson KC, Glenn AR, Dilworth MJ, Hughes MN, Poole RK (2001) Alleviation of aluminum toxicity to Rhizobium leguminosarum bv. viciae by the hydroxamate siderophore vicibactin. Biometals 14(1):59–66. https://doi.org/10.1023/A:1016691301330
Schalk IJ, Hannauer M, Braud A (2011) New roles for bacterial siderophores in metal transport and tolerance. Environ Microbiol 13(11):2844–2854. https://doi.org/10.1111/j.1462-2920.2011.02556.x
Hesse E, O’Brien S, Tromas N, Bayer F, Luján AM, van Veen EM et al (2018) Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination. Ecol Lett 21(1):117–127. https://doi.org/10.1111/ele.12878
Sistani NR, Kaul H-P, Desalegn G, Wienkoop S (2017) Rhizobium impacts on seed productivity, quality, and protection of Pisum sativum upon disease stress caused by Didymella pinodes: phenotypic, proteomic, and metabolomic traits. Front Plant Sci 8:1961. https://doi.org/10.3389/fpls.2017.01961
Zahir ZA, Shah MK, Naveed M, Akhter MJ (2010) Substrate-dependent auxin production by Rhizobium phaseoli improves the growth and yield of Vigna radiata L. under salt stress conditions. J Microbiol Biotechnol 20(9):1288–1294. https://doi.org/10.4014/jmb.1002.02010
De Meyer SE, Beuf KD, Vekeman B, Willems A (2015) A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium). Soil Biol Biochem 83:1–11. https://doi.org/10.1016/j.soilbio.2015.01.002
Ferreira LVM, De Carvalho F, Andrade JFC, Oliveira DP, De Medeiros FHV, Moreira FMS (2020) Co-inoculation of selected nodule endophytic rhizobacterial strains with Rhizobium tropici promotes plant growth and controls damping off in common bean. Pedosphere 30(1):98–108. https://doi.org/10.1016/S1002-0160(19)60825-8
Wall DH, Bardgett RD, Behan-Pelletier V, Herrick JE, Jones TH, Ritz K, et al (Eds) (2012) Soil ecology and ecosystem services. Oxford University Press
MMA/SBF (2002) Avaliação e identificação de áreas e ações prioritárias para conservação, utilização sustentável e repartição dos benefícios da biodiversidade nos biomas brasileiros. Brasilia
Myers N (1988) Threatened biotas: “hot spots” in tropical forests. Environmentalist 8(3):187–208. https://doi.org/10.1007/BF02240252
Ducke A, & Black GA (1954) Notas sobre a fitogeografia da Amazônia Brasileira. Boletin Técnico do Instituto Agronômico do Norte
Silva MF, Carreira LMM, Tavares AS, Ribeiro IC, Jardim MAG, Lobo MGA, et al (1989) Leguminosas da Amazônia brasileira: Lista prévia. Anais Congresso Nacional De Botânica, Sociedade Brasileira de Botância (pp. 193–237). Belém
ter Steege H, & ATDN (Amazon Tree Diversity Network: collective author) and RAINFOR (The Amazon Forest Inventory Network: collective author). Contribution of current and historical processes to patterns of tree diversity and composition of the Amazon (2010) In: Hoorn C, & Wesselingh FP (Eds) Amazonia: Landscape and Species Evolution: A Look into the Past (pp. 346–359). Willey Blackwell
Magalhães FMM, Silva MF (1987) Associações Rhizobium - Leguminosas no Estado de Rondônia. Acta Amazon 17(1):7–18. https://doi.org/10.1590/1809-43921987175017
Moreira FMDS, Silva MFD, Faria SMD (1992) Occurrence of nodulation in legume species in the Amazon region of Brazil. New Phytol 121:563–570. https://doi.org/10.1111/j.1469-8137.1992.tb01126.x
Gehring C, Vlek PLG, Souza LAGD, Denich M (2005) Biological nitrogen fixation in secondary regrowth and mature rainforest of central Amazonia. Agr Ecosyst Environ 111:237–252. https://doi.org/10.1016/j.agee.2005.06.009
Faria SMD, Diedhiou AG, Lima HCD, Ribeiro RD, Galiana A, Castilho AF et al (2010) Evaluating the nodulation status of leguminous species from the Amazonian forest of Brazil. J Exp Bot 61(11):3119–3127. https://doi.org/10.1093/jxb/erq142
Moreira FMS, Gillis M, Pot B, Kersters K, Franco AA (1993) Characterization of rhizobia isolated from different divergence groups of tropical Leguminosae by comparative polyacrylamide gel electrophoresis of their total proteins. Syst Appl Microbiol 16(1):135–146. https://doi.org/10.1016/S0723-2020(11)80258-4
Moreira FMS, Haukka K, Young JPW (1998) Biodiversity of rhizobia isolated from a wide range of forest legumes in Brazil. Mol Ecol 7:889–895. https://doi.org/10.1046/j.1365-294x.1998.00411.x
Jesus EC, Moreira FMDS, Florentino LA, Rodrigues MID, Oliveira MSD (2005) Diversidade de bactérias que nodulam siratro em três sistemas de uso da terra da Amazônia Ocidental. Pesq Agrop Brasileira 40(8):769–776. https://doi.org/10.1590/S0100-204X2005000800006
Lima AS, Nóbrega RSA, Barberi A, Silva KD, Ferreira DF, Moreira FMDS (2009) Nitrogen-fixing bacteria communities occurring in soils under different uses in the Western Amazon Region as indicated by nodulation of siratro (Macroptilium atropurpureum). Plant Soil 319:127–145. https://doi.org/10.1007/s11104-008-9855-2
Guimarães AA, Jaramillo PMD, Nóbrega RSA, Florentino LA, Silva KB, Moreira FMDS (2012) Genetic and symbiotic diversity of nitrogen-fixing bacteria isolated from agricultural soils in the Western Amazon by using cowpea as the trap plant. Appl Environ Microbiol 78(18):6726–6733. https://doi.org/10.1128/AEM.01303-12
Jaramillo PMD, Guimarães AA, Florentino LA, Silva KB, Nóbrega RSA, Moreira FMS (2013) Symbiotic nitrogen-fixing bacterial populations trapped from soils under agroforestry systems in the Western Amazon. Scientia Agricola 70(6):397–404. https://doi.org/10.1590/S0103-90162013000600004
Borges WL, Prin Y, Ducousso M, Roux CL, Faria SMD (2016) Rhizobial characterization in revegetated areas after bauxite mining. Braz J Microbiol 4(7):314–321. https://doi.org/10.1016/j.bjm.2016.01.009
Carmo FFD, & Kamino LHY (Eds) (2015) Geossistemas Ferruginosos Do Brasil Áreas Prioritárias Para Conservação Da Diversidade Geológica E Biológica, Patrimônio Cultural E Serviços Ambientais. Belo Horizonte
ICMBio (2016) Plano De Manejo Da Floresta Nacional De Carajás: Volume II - Planejamento: Ministério do Meio Ambiente, Instituto Chico Mendes de Conservação da Biodiversidade
IBAMA (2003) Plano De Manejo Para Uso Múltiplo Da Floresta Nacional De Carajás: Instituto Brasileiro de Meio Ambiente e dos Recursos Naturais Renováveis
Alvarez VH, Novais RF, Barros NF, Cantarutti RB, & Lopes AS (1999) Interpretação dos resultados das análises de solos. In: Ribeiro AC et al (Eds) Comissão de Fertilidade do Solo do Estado de Minas Gerais-Recomendações para o uso de corretivos e fertilizantes 1999 em Minas Gerais - 5ª Aproximação. Viçosa
Moreira FMS (2008) Nitrogen-fixing Leguminosae nodulating bacteria. In: Moreira FMS et al (Eds) A Handbook of Tropical Soil Biology. Sampling and Characterization of Below-ground Biodiversity (pp. 107–129). Earthscan
Sprent JI (2009) Legume nodulation: a global perspective. Wiley-Blackwell
CNCFlora (2012) Mimosa acutistipula var. ferrea in Lista Vermelha da flora brasileira versão 2012.2 Centro Nacional de Conservação da Flora. http://cncflora.jbrj.gov.br/portal/pt-br/profile/Mimosa acutistipula var. ferrea. Accessed on 4 Jan 2019
Pires RDC, dos Reis Junior FB, Zill JE, Fischer D, Hofmann A, James EK et al (2018) Soil characteristics determine the rhizobia in association with different species of Mimosa in central Brazil. Plant Soil 423:411–428. https://doi.org/10.1007/s11104-017-3521-5
Assis Júnior RND, Almeida RTD, Vasconcelos I (1986) Testes Preliminares De Inoculação Cruzada Em Leguminosas Arbóreas Do Ceará. Ciência Agronômica 17(2):107–111
Ferreira PAA, Bomfeti CA, Júnior RDS, Soares BL, Soares CRFS, Moreira FMDS (2012) Eficiência simbiótica de estirpes de Cupriavidus necator tolerantes a zinco, cádmio, cobre e chumbo. Pesq Agrop Brasileira 47(1):85–95. https://doi.org/10.1590/S0100-204X2012000100012
Hoagland DR, & Arnon DL (1950) The water culture methods for growing plants without soil. Bulletin 347 (pp. 32). Berkeley: California Agriculture Experiment Station
Araújo KS, Carvalho FD, Moreira FMDS (2017) Burkholderia strains promote Mimosa spp. growth but not Macroptilium atropurpureum. Revista Ciência Agronômica 48(1):41–48
Schepers JS, Blackmer TM, Francis DD (1998) Chlorophyll meter method for estimating nitrogen content in plant tissue. In: Kalra YP (ed) Handbook of reference methods for plant analysis. Boca Raton Boston London New York Washington DC: CRC Press, pp 129–135
Fred EB, Waksman SA (1928) Laboratory manual of general microbiology, with special reference to the microorganisms of the soil. New York: McGraw-Hill
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, & Goodfellow MM (Eds) Nucleic Acid Techniques in Bacterial Systematics 5:115–175
Niemann S, Pühler A, Tichy HV, Simon R, Selbitschka W (1997) Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 82(4):477–484. https://doi.org/10.1046/j.1365-2672.1997.00141.x
Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51:263–273. https://doi.org/10.1101/SQB.1986.051.01.032
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors (DNA polymerase/nucleotide sequences/bacteriophage 4X174). Proc Natl Acad Sci USA 74(12):5463–5467. https://doi.org/10.1073/pnas.74.12.5463
Wright ES, Yilmaz LS, Noguera DR (2012) DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78(3):717–725. https://doi.org/10.1128/AEM.06516-11
Altschul SF, Gish W, Miller W, Myers EW, & Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(403–410). https://doi.org/10.1016/S0022-2836(05)80360-2
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J et al (2013) GenBank. Nucleic Acids Res 41(Database issue):D36–D42. https://doi.org/10.1093/nar/gks1195
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797. https://doi.org/10.1093/nar/gkh340
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10(3):512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023
Avontuur JR, Palmer M, Beukes CW, Chana WY, Coetzee MPA, Blom J et al (2019) Genome-informed Bradyrhizobium taxonomy: where to from here? Syst Appl Microbiol. https://doi.org/10.1016/j.syapm.2019.03.006
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42(2):182–192. https://doi.org/10.1093/sysbio/42.2.182
Sterner JP, Parker MA (1999) Diversity and relationships of Bradyrhizobia from Amphicarpaea bracteata based on partial nod and ribosomal sequences. Syst Appl Microbiol 22:387–392. https://doi.org/10.1016/S0723-2020(99)80047-2
Magurran AE (1988) Ecological diversity and its measurement. Princeton University Press
Chen W-M, Faria SMD, Chou J-H, James EK, Elliott GN, Sprent JI et al (2008) Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia. Int J Syst Evol Microbiol 58:2174–2179. https://doi.org/10.1099/ijs.0.65816-0
Silva JR, Gastauer M, Ramos SJ, Mitre SK, Furtini Neto AE, Siqueira JO et al (2018) Initial growth of Fabaceae species: combined effects of topsoil and fertilizer application for mineland revegetation. Flora 246–247:109–117. https://doi.org/10.1016/j.flora.2018.08.001
Andrews M, & Andrews ME (2017) Specificity in legume-rhizobia symbioses. Int J Mol Sci 18(705). https://doi.org/10.3390/ijms18040705
Minchin FR, & Witty JF (2005) Respiratory/carbon costs of symbiotic nitrogen fixation in legumes. In: Lambers H & Ribas-Carbo M (Eds) Plant Respiration (pp. 195–205). Springer
Zilli JE, Baraúna AC, Silva KD, Meyer SED, Farias ENC, Kaminski PE et al (2014) Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense. Int J Syst Evol Microbiol 64:3950–3957. https://doi.org/10.1099/ijs.0.065458-0
Sawana A, Adeoluand M, & Gupta RS (2014) Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 5. https://doi.org/10.3389/fgene.2014.00429
Estrada-de los Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET, Briscoe L, et al (2018) Whole genome analyses suggests that Burkholderia sensu lato contains two additional novel genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): implications for the evolution of diazotrophy and nodulation in the Burkholderiaceae. Genes 9(389). https://doi.org/10.3390/genes9080389
Sy A, Giraud E, Jourand P, Garcia N, Willems A, Lajudie PD et al (2001) Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183(1):214–220. https://doi.org/10.1128/JB.183.1.214-220.2001
Yates RJ, Howieson JG, Reeve WG, Nandasena KG, Law IJ, Brau L et al (2007) Lotononis angolensis forms nitrogen fixing, lupinoid nodules with phylogenetically unique, fast-growing, pink-pigmented bacteria, which do not nodulate L. bainesii or L. listii. Soil Biol Biochem 39:1680–1688. https://doi.org/10.1016/j.soilbio.2007.01.025
Ferguson BJ (2017) Rhizobia and legume nodulation genes. Ref Module Life Sci. https://doi.org/10.1016/b978-0-12-809633-8.07071-0
Moreira FMS, Franco AA (1994) Rhizobia-host interactions in tropical ecosystems in Brazil. In: Sprent JI, McKey D (Eds) Advances in legume Systematics: The Nitrogen factor. 1ªed.Kew: The Royal Botanic Gardens (5):63–74
Hedin LO, Brookshire ENJ, Menge DNL, Barron AR (2009) The nitrogen paradox in tropical forest ecosystems. Ann Rev Ecol Evol Syst 40:613–635. https://doi.org/10.1146/annurev.ecolsys.37.091305.110246
Reed SC, Townsend AR, Cleveland CC, Nemergut DR (2010) Microbial community shifts influence patterns in tropical forest nitrogen fixation. Oecologia 164:521–531. https://doi.org/10.1007/s00442-010-1649-6
Castro JLd, Souza MG, Rufini M, Guimarães AA, Rodrigues TL, & Moreira FMdS (2017) Diversity and efficiency of rhizobia communities from iron mining areas using cowpea as a trap plant. Rev Bras Ciênc Solo 41. https://doi.org/10.1590/18069657rbcs20160525
Silva AO, Guimarães AA, Costa AMd, Rodrigues TL, Carvalho TdS, Sales FR, et al (2020) Plant growth-promoting rhizobacterial communities from an area under the influence of iron mining and from the adjacent phytophysiognomies which have high genetic diversity. Land Degrad Dev 1-18. https://doi.org/10.1002/ldr.3593
Zgadzaj R, James EK, Kelly S, Kawaharada Y, de Jonge N, Jensen DB, et al (2015) A legume genetic framework controls infection of nodules by symbiotic and endophytic bacteria. PLOS Genet. https://doi.org/10.1371/journal.pgen.1005280
Ferreira LVM, de Carvalho F, Andrade JFC, Moreira FMS (2018) Growth promotion of common bean and genetic diversity of bacteria from Amazon pastureland. Scientia Agricola 75(6):461–469. https://doi.org/10.1590/1678-992x-2017-0049
Acknowledgements
Our thanks to the CAPES PEC-PG program (Programa de Estudantes-Convênio de Pós-Graduação da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) for the doctoral studies scholarship granted to the first author (no. 23038.005401/2016-08); to the CNPq (Conselho Nacional de Desenvolvimento. Científico e Tecnologia) for the research productivity fellowships granted to F.M.S Moreira, Marco A.C. Carneiro, and J.O. Siqueira; to CAPES-PROEX (Programa de Excelência Acadêmica da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) 593-2018; and to the ITV for funding this study. Our thanks also to the undergraduate studies research participant Daniela Pedroso for assistance in taking down the experiment.
Funding
CAPES PEC-PG Grant/Award No., 23038.005401/2016–08; CAPES-PROEX Grant/Award No., 593–2018; CNPq Grant/Award No., 304527/2016–5.
Author information
Authors and Affiliations
Contributions
FMSM and MACC conceived and designed the research. RMRR conducted the experiment and performed the assessments. RMRR, AAG, and JLC carried out the molecular data analysis. RMRR processed the data and wrote the manuscript with support from FMSM, MACC, and JOS. All authors revised and contributed to the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no competing interests.
Additional information
Responsible Editor: Acacio Aparecido Navarrete
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Rodríguez-Rodríguez, R.M., Guimarães, A.A., de Castro, J.L. et al. Rhizobia and endophytic bacteria isolated from rainforest fragments within an iron ore mining site of the Eastern Brazilian Amazon. Braz J Microbiol 52, 1461–1474 (2021). https://doi.org/10.1007/s42770-021-00524-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s42770-021-00524-0