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Lyra MDOCCPDE, Taketani RG, Freitas ADSDE, Silva CERSE, Mergulhão ACES, Silva MLRBDA, Antunes JELS, Araújo ASFDE, Giachetto PF. Structure and diversity of bacterial community in semiarid soils cultivated with prickly-pear cactus (Opuntia ficus-indica (L.) Mill.). AN ACAD BRAS CIENC 2021; 93:e20190183. [PMID: 34161510 DOI: 10.1590/0001-3765202120190183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 07/05/2019] [Indexed: 11/22/2022] Open
Abstract
Studies evaluating the structure and diversity of bacterial communities in arid environments including the rhizosphere of local and adapted plant species are important. Therefore, we used a sequencing of the 16S ribosomal RNA gene for describing the structure and diversity of soil bacterial community in three zones: Agreste, Transition and Sertão. The bacterial community was clustered in 9,838 OTUs in Agreste, 8,388 OTUs in the transition, and 14,849 OTUs for Sertão. Among the most abundant phyla, Proteobacteria and Acidobacteria were abundant in Agreste and Sertão, respectively, while Actinobacteria were abundant in Transition and Sertão. Specific taxa of Proteobacteria, in Agreste, and Actinobacteria, in Sertão, exhibited differences according to biotic and abiotic conditions. Thus, the structure and diversity of bacterial community were different in these areas and were influenced by environmental and soil conditions.
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Affiliation(s)
- Maria DO Carmo C P DE Lyra
- Instituto Agronômico de Pernambuco/IPA, Laboratório de Genômica, Avenida General San Martin, 1371, Bongi, 50761-000 Recife, PE, Brazil
| | - Rodrigo G Taketani
- EMBRAPA Meio Ambiente, Rodovia SP-340, Km 127,5, Tanquinho Velho, Caixa Postal 69, 13820-000 Jaguariúna, SP, Brazil
| | - Ana Dolores S DE Freitas
- Universidade Federal Rural de Pernambuco/UFRPE, Laboratório de Microbiologia, Rua Dom Manoel de Medeiros, s/n, Dois irmãos, 52171-900 Recife, PE, Brazil
| | - Carolina E R S E Silva
- Universidade Federal Rural de Pernambuco/UFRPE, Laboratório de Microbiologia, Rua Dom Manoel de Medeiros, s/n, Dois irmãos, 52171-900 Recife, PE, Brazil
| | - Adália C E S Mergulhão
- Instituto Agronômico de Pernambuco/IPA, Laboratório de Genômica, Avenida General San Martin, 1371, Bongi, 50761-000 Recife, PE, Brazil
| | - Maria Luiza R B DA Silva
- Instituto Agronômico de Pernambuco/IPA, Laboratório de Genômica, Avenida General San Martin, 1371, Bongi, 50761-000 Recife, PE, Brazil
| | - Jadson E L S Antunes
- Universidade Federal do Piauí, Centro de Ciências Agrárias, Rua Dirce de Oliveira, 3579, Campus da Soccopo, 64049-550 Teresina, PI, Brazil
| | - Ademir S F DE Araújo
- Universidade Federal do Piauí, Centro de Ciências Agrárias, Rua Dirce de Oliveira, 3579, Campus da Soccopo, 64049-550 Teresina, PI, Brazil
| | - Poliana F Giachetto
- EMBRAPA Informática Agropecuária, Av. Dr. André Tosello, 209, Cidade Universitária, 13083-886 Campinas, SP, Brazil
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Silva JBTD, Marques E, Menezes JE, Silva JPD, Mello SCMD. Population density of Trichoderma fungi in natural environments and agrosystems of a Cerrado area. BIOTA NEOTROPICA 2020. [DOI: 10.1590/1676-0611-bn-2020-1048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Soil microorganisms present a great diversity, involving taxonomically distinct groups that play a role in the decomposition of organic matter, nutrient cycling, soil aggregation, among others. In this diversity, the fungi of the genus Trichoderma have been successful plant pathogen biocontrol agents, as plant growth promoters and as inducers of plant resistance to diseases. In addition, they are important in the sustainability of natural ecosystems. Aiming to verify the population density of Trichoderma fungi in natural environments and agroecosystems, in Cerrado area, samples of soils and roots from native vegetation and agroecological production system were collected in the Federal District, Brazil. The collection points were randomly selected, and each soil or root sample was individually wrapped. The soil adhered to the roots was removed for evaluations. Serial sample dilutions and number of Colony Forming Units (CFUs) of Trichoderma isolates were performed. The results showed that the number of CFU varied depending on the plant and location evaluated. The replacement of native vegetation by organic farming systems did not result in a significant reduction in this number.
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López-Lozano NE, Echeverría Molinar A, Ortiz Durán EA, Hernández Rosales M, Souza V. Bacterial Diversity and Interaction Networks of Agave lechuguilla Rhizosphere Differ Significantly From Bulk Soil in the Oligotrophic Basin of Cuatro Cienegas. FRONTIERS IN PLANT SCIENCE 2020; 11:1028. [PMID: 32765547 PMCID: PMC7378863 DOI: 10.3389/fpls.2020.01028] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 06/23/2020] [Indexed: 05/05/2023]
Abstract
Due to the environmental conditions presented in arid zones, it is expected to have a high influence of deterministic processes over the community assemblages. Symbiotic interactions with microorganisms could increase colonization and survival of plants in difficult conditions, independent of the plants physiological and morphological characteristics. In this context, the microbial communities associated to plants that inhabit these types of areas can be a good model to understand the community assembly processes. We investigated the influence of stochastic and deterministic processes in the assemblage of rhizosphere microbial communities of Agave lechuguilla and bulk soil on the Cuatro Cienegas Basin, a site known for its oligotrophic conditions. We hypothesize that rhizospheric microbial communities of A. lechuguilla differ from those of bulk soil as they differ in physicochemical properties of soil and biotic interactions, including not only the plant, but also their microbial co-occurrence networks, it is expected that microbial species usually critical for plant growth and health are more common in the rhizosphere, whereas in the bulk soil microbial species related to the resistance to abiotic stress are more abundant. In order to confirm this hypothesis, 16S rRNA gene was sequenced by Illumina from rhizospheric and bulk soil samples in two seasons, also the physicochemical properties of the soil were determined. Our results showed differences in bacterial diversity, community composition, potential functions, and interaction networks between the rhizosphere samples and the ones from bulk soil. Although community structure arises from a complex interplay between deterministic and stochastic forces, our results suggest that A. lechuguilla recruits specific rhizospheric microbes with functional traits that benefits the plant through growth promotion and nutrition. This selection follows principally a deterministic process that shapes the rhizospheric microbial communities, directed by the plant modifications around the roots but also subjected to the influence of other environmental variables, such as seasonality and soil properties. Interestingly, keystone taxa in the interactions networks, not necessarily belong to the most abundant taxonomic groups, but they have an important role by their functional traits and keeping the connections on the community network.
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Affiliation(s)
- Nguyen E. López-Lozano
- CONACyT-División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), San Luis Potosí, Mexico
- *Correspondence: Nguyen E. López-Lozano,
| | - Andrea Echeverría Molinar
- CONACyT-División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICyT), San Luis Potosí, Mexico
| | | | | | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Lacerda-Júnior GV, Noronha MF, Cabral L, Delforno TP, de Sousa STP, Fernandes-Júnior PI, Melo IS, Oliveira VM. Land Use and Seasonal Effects on the Soil Microbiome of a Brazilian Dry Forest. Front Microbiol 2019; 10:648. [PMID: 31024471 PMCID: PMC6461016 DOI: 10.3389/fmicb.2019.00648] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 12/21/2022] Open
Abstract
Drylands occupy approximately 41% of the Earth's terrestrial surface. Climate change and land use practices are expected to affect biogeochemical cycling by the soil microbiome in these ecosystems. Understanding how soil microbial community might respond to these drivers is extremely important to mitigate the processes of land degradation and desertification. The Caatinga, an exclusively Brazilian biome composed of an extensive seasonal tropical dry forest, is exposed to variable spatiotemporal rainfall patterns as well as strong human-driven pressures. Herein, an integrated analysis of shotgun metagenomics approach coupled to meteorological data was employed to unravel the impact of seasonality and land use change on soil microbiome from preserved and agriculture-affected experimental fields in Caatinga drylands. Multivariate analysis suggested that microbial communities of preserved soils under seasonal changes were shaped primarily by water deficit, with a strong increase of Actinobacteria and Proteobacteria members in the dry and rainy seasons, respectively. In contrast, nutrient availability notably played a critical role in driving the microbial community in agriculture-affected soils. The strong enrichment of bacterial genera belonging to the poorly-known phylum Acidobacteria ('Candidatus Solibacter' and 'Candidatus Koribacter') in soils from dry season affected by ferti-irrigation practices presupposes a contrasting copiotrophic lifestyle and ecological role in mitigating the impact of chemical fertilization. Functional analyses identify overrepresented genes related to osmotic stress response (synthesis of osmoprotectant compounds, accumulation of potassium ions) and preferential carbon and nitrogen utilization when comparing the microbiome of preserved soils under seasonal changes, reflecting differences in the genetic potential for nutrient cycling and C acquisition in the environment. However, the prevalence of nitrosative stress and denitrification functions in irrigation/fertilization-affected soils of the dry season clearly suggest that nutrient input and disruption of natural water regime may impact biogeochemical cycles linked to the microbial processes, with potential impacts on the ecosystem functionality. These findings help to better understand how natural seasonality and agricultural management differentially affect soil microbial ecology from dry forests, providing support for the development of more sustainable land management in dryland ecosystems.
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Affiliation(s)
- Gileno V. Lacerda-Júnior
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, Brazil
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Melline F. Noronha
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Lucélia Cabral
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Tiago P. Delforno
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | - Sanderson Tarciso Pereira de Sousa
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
| | | | - Itamar S. Melo
- Brazilian Agricultural Research Corporation, Embrapa Meio Ambiente, Jaguariúna, Brazil
| | - Valéria M. Oliveira
- Division of Microbial Resources (DRM), Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), Campinas State University (UNICAMP), Campinas, Brazil
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Bacci G, Cerri M, Lastrucci L, Ferranti F, Ferri V, Foggi B, Gigante D, Venanzoni R, Viciani D, Mengoni A, Reale L, Coppi A. Applying predictive models to decipher rhizobacterial modifications in common reed die-back affected populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:708-722. [PMID: 29913366 DOI: 10.1016/j.scitotenv.2018.06.066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/06/2018] [Accepted: 06/06/2018] [Indexed: 05/03/2023]
Abstract
The microbiota inhabiting the soil, as well as the rhizosphere, represents a key determinant of several plant functions. Like for humans, dysbiosis of the plant-associated microbiota may be a co-causal agent in disease with still obscure eziology. In the last decades, the common reed Phragmites australis has been deeply studied for its disappearance from natural stands, but no clear causative agents have been identified and no laboratory models of such "reed die-back syndrome" (RDBS) have been developed. In this study, we try to shed light on the RDBS, by comparing the rhizosphere microbiota of five Italian P. australis populations with different degrees of decline. Results obtained showed a biogeographical meaningful pattern of rhizosphere microbiota, coupled with an impact of RDBS. Obtained data allowed to construct a two-steps predictive model which enabled the prediction of the plant health status from the microbiota taxonomic composition, independently from their geographic location. In conclusion, this study represents one of the first overviews that statistically links RDBS to alteration of rhizosphere microbiota and suggests a model for the analysis of plant-bacteria relationships in nature.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy.
| | - Martina Cerri
- Department of Agriculture, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | | | - Francesco Ferranti
- Department of Agriculture, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Valentina Ferri
- Department of Agriculture, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Bruno Foggi
- Department of Biology, University of Florence, Florence, Italy
| | - Daniela Gigante
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Roberto Venanzoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Daniele Viciani
- Department of Biology, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Lara Reale
- Department of Agriculture, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Andrea Coppi
- Department of Biology, University of Florence, Florence, Italy
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Taketani RG, Lançoni MD, Kavamura VN, Durrer A, Andreote FD, Melo IS. Dry Season Constrains Bacterial Phylogenetic Diversity in a Semi-Arid Rhizosphere System. MICROBIAL ECOLOGY 2017; 73:153-161. [PMID: 27558787 DOI: 10.1007/s00248-016-0835-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/09/2016] [Indexed: 06/06/2023]
Abstract
The rhizosphere is viewed as a deterministic environment led by the interaction between plants and microorganisms. In the case of semi-arid plants, this interaction is strengthened by the harshness of the environment. We tested the hypothesis that dry season represents a constraint on the bacterial diversity of the rhizosphere from semi-arid plants. To accomplish this, we sampled two leguminous species at five locations during the dry and rainy seasons in the Caatinga biome and characterised bacterial community structures using qPCR and 16S rRNA sequencing. We found that the main differences between seasons were due to reduced phylogenetic diversity caused by dryness. Variation partitioning indicated that environmental characteristics significant impacts in β-diversity. Additionally, distance decay relationship and taxa area relationship indicate a higher spatial turnover at the rainy season. During the dry season, decreased bacterial abundance is likely due to the selection of resistant or resilient microorganisms; with the return of the rain, the sensitive populations start to colonise the rhizosphere by a process that is strongly influenced by environmental characteristics. Thus, we propose that the reduction of PD and strong influence of environmental parameters on the assemblage of these communities make them prone to functional losses caused by climatic disturbances.
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Affiliation(s)
- Rodrigo Gouvêa Taketani
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Rodovia SP-340 km 127,5, Jaguariúna, SP, 13820-000, Brazil.
| | - Milena Duarte Lançoni
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Rodovia SP-340 km 127,5, Jaguariúna, SP, 13820-000, Brazil
| | - Vanessa Nessner Kavamura
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Rodovia SP-340 km 127,5, Jaguariúna, SP, 13820-000, Brazil
| | - Ademir Durrer
- Soil Science Department, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Fernando Dini Andreote
- Soil Science Department, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Rodovia SP-340 km 127,5, Jaguariúna, SP, 13820-000, Brazil
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Archaea in Natural and Impacted Brazilian Environments. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1259608. [PMID: 27829818 PMCID: PMC5086508 DOI: 10.1155/2016/1259608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 11/26/2022]
Abstract
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.
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Coleman‐Derr D, Desgarennes D, Fonseca‐Garcia C, Gross S, Clingenpeel S, Woyke T, North G, Visel A, Partida‐Martinez LP, Tringe SG. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. THE NEW PHYTOLOGIST 2016; 209:798-811. [PMID: 26467257 PMCID: PMC5057366 DOI: 10.1111/nph.13697] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 08/31/2015] [Indexed: 05/18/2023]
Abstract
Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared with native agaves, although no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.
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Affiliation(s)
- Devin Coleman‐Derr
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Plant Gene Expression CenterUSDA‐ARSAlbanyCA94710USA
| | - Damaris Desgarennes
- Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios AvanzadosIrapuato36821Mexico
| | - Citlali Fonseca‐Garcia
- Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios AvanzadosIrapuato36821Mexico
| | - Stephen Gross
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Scott Clingenpeel
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Tanja Woyke
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Gretchen North
- Department of BiologyOccidental CollegeLos AngelesCA90041USA
| | - Axel Visel
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- School of Natural SciencesUniversity of CaliforniaMercedCA95343USA
| | - Laila P. Partida‐Martinez
- Departamento de Ingeniería GenéticaCentro de Investigación y de Estudios AvanzadosIrapuato36821Mexico
| | - Susannah G. Tringe
- Department of EnergyJoint Genome InstituteWalnut CreekCA94598USA
- Genomics DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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Taketani RG, Kavamura VN, Mendes R, Melo IS. Functional congruence of rhizosphere microbial communities associated to leguminous tree from Brazilian semiarid region. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:95-101. [PMID: 25870877 DOI: 10.1111/1758-2229.12187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Semiarid environments are characterized by the uneven spread of rain throughout the year. This leads to the establishment of a biota that can go through long periods without rain. In order to understand the dynamics of rhizosphere microbial communities across these contrasting seasons in Caatinga, we used the Ion Torrent platform to sequence the metagenome of the rhizosphere of a native leguminous plant (Mimosa tenuiflora). The annotation indicated that most abundant groups detected were the Actinobacteria and Proteobacteria, and the dominant functional groups were carbohydrate and protein metabolisms, and that in the wet season, the communities carried carbohydrate and amino acid metabolisms.The major differences observed between seasons were higher abundance of genes related to carbohydrate and amino acid metabolisms in the rainy season, indicating that the populations present might be better adapted to a higher abundance of organic matter. Besides, no clear separation of samples was detected based on their taxonomic composition whereas the functional composition indicates that samples from the rain season are more related. Altogether, our results indicate that there is al arge functional stability in these communities mostly due to the selection of features that aid the biota to endure the dry season and blossom during rain.
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Affiliation(s)
- Rodrigo Gouvêa Taketani
- Laboratory of Environmental Microbiology, Embrapa Environment, Brazilian Agricultural Research Corporation-EMBRAPA, Jaguariuna, São Paulo, Brazil.
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Nessner Kavamura V, Taketani RG, Lançoni MD, Andreote FD, Mendes R, Soares de Melo I. Water regime influences bulk soil and Rhizosphere of Cereus jamacaru bacterial communities in the Brazilian Caatinga biome. PLoS One 2013; 8:e73606. [PMID: 24069212 PMCID: PMC3775785 DOI: 10.1371/journal.pone.0073606] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/19/2013] [Indexed: 11/19/2022] Open
Abstract
We used the T-RFLP technique combined with Ion Torrent (PGM) sequencing of 16S rRNA and multivariate analysis to study the structure of bulk soil and rhizosphere bacterial communities of a cactus, Cereus jamacaru, from the Brazilian Caatinga biome, which is unique to Brazil. The availability of water shapes the rhizosphere communities, resulting in different patterns during the rainy and dry seasons. Taxonomic approaches and statistical analysis revealed that the phylum Actinobacteria strongly correlated with the dry season, while samples from the rainy season exhibited a strong correlation with the phylum Proteobacteria for rhizosphere samples and with the phyla Bacteroidetes, Firmicutes, Lentisphaerae, and Tenericutes for bulk soil samples. The STAMP software also indicated that the phylum Bacteroidetes, as well as two classes in the Proteobacteria phylum (γ and δ), were the most significant ones during the rainy season. The average abundance of the phylum Actinobacteria and the genus Bacillus was significantly greater during the dry season. Some significant genera found during the dry season might reflect their tolerance to the extreme conditions found in the Caatinga biome. They may also indicate the ecological function that microorganisms play in providing plants with some degree of tolerance to water stress or in assisting in their development through mechanisms of growth promotion. Alterations in microbial communities can be due to the different abilities of native microorganisms to resist and adapt to environmental changes.
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Affiliation(s)
- Vanessa Nessner Kavamura
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, São Paulo, Brazil
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- * E-mail:
| | - Rodrigo Gouvêa Taketani
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, São Paulo, Brazil
| | - Milena Duarte Lançoni
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, São Paulo, Brazil
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, São Paulo, Brazil
| | - Itamar Soares de Melo
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, São Paulo, Brazil
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