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Enright DJ, Frangioso KM, Isobe K, Rizzo DM, Glassman SI. Mega‐fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa that are Phylogenetically Conserved. Mol Ecol 2022; 31:2475-2493. [DOI: 10.1111/mec.16399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Dylan J. Enright
- Department of Microbiology and Plant Pathology University of California 3401 Watkins Drive Riverside CA 92521 USA
| | - Kerri M. Frangioso
- Department of Plant Pathology University of California 1 Shields Ave Davis CA 95616 USA
| | - Kazuo Isobe
- Department of Applied Biological Chemistry Graduate School of Agricultural and Life Sciences The University of Tokyo 1‐1‐1 Yayoi, Bunkyo‐ku Tokyo 113‐8657
| | - David M. Rizzo
- Department of Plant Pathology University of California 1 Shields Ave Davis CA 95616 USA
| | - Sydney I. Glassman
- Department of Microbiology and Plant Pathology University of California 3401 Watkins Drive Riverside CA 92521 USA
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Maquia IS, Fareleira P, Videira e Castro I, Brito DRA, Soares R, Chaúque A, Ferreira-Pinto MM, Lumini E, Berruti A, Ribeiro NS, Marques I, Ribeiro-Barros AI. Mining the Microbiome of Key Species from African Savanna Woodlands: Potential for Soil Health Improvement and Plant Growth Promotion. Microorganisms 2020; 8:E1291. [PMID: 32846974 PMCID: PMC7563409 DOI: 10.3390/microorganisms8091291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 01/19/2023] Open
Abstract
(1) Aims: Assessing bacterial diversity and plant-growth-promoting functions in the rhizosphere of the native African trees Colophospermum mopane and Combretum apiculatum in three landscapes of the Limpopo National Park (Mozambique), subjected to two fire regimes. (2) Methods: Bacterial communities were identified through Illumina Miseq sequencing of the 16S rRNA gene amplicons, followed by culture dependent methods to isolate plant growth-promoting bacteria (PGPB). Plant growth-promoting traits of the cultivable bacterial fraction were further analyzed. To screen for the presence of nitrogen-fixing bacteria, the promiscuous tropical legume Vigna unguiculata was used as a trap host. The taxonomy of all purified isolates was genetically verified by 16S rRNA gene Sanger sequencing. (3) Results: Bacterial community results indicated that fire did not drive major changes in bacterial abundance. However, culture-dependent methods allowed the differentiation of bacterial communities between the sampled sites, which were particularly enriched in Proteobacteria with a wide range of plant-beneficial traits, such as plant protection, plant nutrition, and plant growth. Bradyrhizobium was the most frequent symbiotic bacteria trapped in cowpea nodules coexisting with other endophytic bacteria. (4) Conclusion: Although the global analysis did not show significant differences between landscapes or sites with different fire regimes, probably due to the fast recovery of bacterial communities, the isolation of PGPB suggests that the rhizosphere bacteria are driven by the plant species, soil type, and fire regime, and are potentially associated with a wide range of agricultural, environmental, and industrial applications. Thus, the rhizosphere of African savannah ecosystems seems to be an untapped source of bacterial species and strains that should be further exploited for bio-based solutions.
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Affiliation(s)
- Ivete Sandra Maquia
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
- TropiKMan Doctoral Program, Nova School of Business & Economics (Nova SBE), 2775-405 Carcavelos, Portugal
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Paula Fareleira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Isabel Videira e Castro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Denise R. A. Brito
- Biotechnology Center, Eduardo Mondlane University, CP 257 Maputo, Mozambique;
| | - Ricardo Soares
- Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (P.F.); (I.V.eC.); (R.S.)
| | - Aniceto Chaúque
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - M. Manuela Ferreira-Pinto
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Erica Lumini
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Andrea Berruti
- Institute for Sustainable Plant Protection, National Research Council, I-10135 Turin, Italy; (E.L.); (A.B.)
| | - Natasha S. Ribeiro
- Faculty of Agronomy and Forest Engineering, Eduardo Mondlane University, CP 257 Maputo, Mozambique; (A.C.); (N.S.R.)
| | - Isabel Marques
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
| | - Ana I. Ribeiro-Barros
- Plant Stress & Biodiversity Lab—Forest Research Center (CEF), School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal; (I.S.M.); (M.M.F.-P.)
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The Soil Microbiome of the Laurel Forest in Garajonay National Park (La Gomera, Canary Islands): Comparing Unburned and Burned Habitats after a Wildfire. FORESTS 2019. [DOI: 10.3390/f10121051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The evergreen laurel forest is a relic of ancient subtropical/tropical forests, of which the best remnant in the Canary Islands is in Garajonay National Park, on La Gomera island. The soil microbiome associated with a mature undisturbed (unburned) laurel forest was characterized at two locations at different topographical positions on the mountain: The slope and the ridge crest. Given the unusual circumstance of an intense wildfire that severely affected part of this forest, the burned soils were also studied. The soil in undisturbed areas was relatively uniform. The bacterial community composition was dominated by bacteria from phyla Proteobacteria, Acidobacteria, and Actinobacteria. The wildfire changed the composition of the bacterial communities. The Acidobacteria, Actinobacteria, and Alphaproteobacteria (dominant class in unburned forests) significantly decreased in burned soils along with a parallel high increase in Betaproteobacteria, Bacteroidetes, and Firmicutes. We further showed the dramatic effect of a wildfire on the soil microbiome of the laurel forest, appearing as a loss of species richness and diversity, species dominance, and changes in the composition of the bacterial communities.
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Short-term response of the soil bacterial community to differing wildfire severity in Pinus tabulaeformis stands. Sci Rep 2019; 9:1148. [PMID: 30718899 PMCID: PMC6362210 DOI: 10.1038/s41598-019-38541-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/28/2018] [Indexed: 01/22/2023] Open
Abstract
In recent years, the investigation of fire disturbance of microbial communities has gained growing attention. However, how the bacterial community varies in response to different severities of fire at different soil depths is largely unknown. We utilized Illumina MiSeq sequencing to illustrate the changing patterns of the soil bacterial community following low-, moderate- and high-severity wildfire in the topsoil (0–10 cm) and subsoil (10–20 cm), 6 months after the fire. Acidobacteria, Proteobacteria, Actinobacteria, Verrucomicrobia and Chloroflexi were the dominant phyla among all samples. Bacterial alpha diversity (i.e. Shannon and Simpson indices) in the topsoil was significantly higher than that in the subsoil after a high-severity wildfire. Non-metric multidimensional scaling (NMDS) analysis and permutational multivariate analysis of variance (PERMANOVA) revealed significant differences in the bacterial community structure between the two soil layers. Soil pH, ammonium nitrogen (NH4+-N) and total nitrogen were the main factors in shaping the bacterial community structure, of which soil pH was the most robust in both soil layers. Our study reveals that wildfire results in short-term changes in soil bacterial community. However, a long-term monitoring of microbial variation after burning is also essential.
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The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils. Sci Rep 2017; 7:6008. [PMID: 28729641 PMCID: PMC5519729 DOI: 10.1038/s41598-017-06112-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 06/08/2017] [Indexed: 12/17/2022] Open
Abstract
After a forest wildfire, the microbial communities have a transient alteration in their composition. The role of the soil microbial community in the recovery of an ecosystem following such an event remains poorly understood. Thus, it is necessary to understand the plant-microbe interactions that occur in burned soils. By high-throughput sequencing, we identified the main bacterial taxa of burnt holm-oak rhizosphere, then we obtained an isolate collection of the most abundant genus and its growth promoting activities were characterised. 16S rRNA amplicon sequencing showed that the genus Arthrobacter comprised more than 21% of the total community. 55 Arthrobacter strains were isolated and characterized using RAPDs and sequencing of the almost complete 16S rRNA gene. Our results indicate that isolated Arthrobacter strains present a very high genetic diversity, and they could play an important ecological role in interaction with the host plant by enhancing aerial growth. Most of the selected strains exhibited a great ability to degrade organic polymers in vitro as well as possibly presenting a direct mechanism for plant growth promotion. All the above data suggests that Arthrobacter can be considered as an excellent PGP rhizobacterium that may play an important role in the recovery of burned holm-oak forests.
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Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest. Sci Rep 2014; 4:3829. [PMID: 24452061 PMCID: PMC3899593 DOI: 10.1038/srep03829] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 01/06/2014] [Indexed: 11/08/2022] Open
Abstract
Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20-100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4(+) content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties.
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