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Cunha IDCMD, Silva AVRD, Boleta EHM, Pellegrinetti TA, Zagatto LFG, Zagatto SDSS, Chaves MGD, Mendes R, Patreze CM, Tsai SM, Mendes LW. The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype. Microbiol Res 2024; 283:127706. [PMID: 38574431 DOI: 10.1016/j.micres.2024.127706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.
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Affiliation(s)
- Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Luiz de Queiroz College of Agriculture ESALQ, University of São Paulo USP, Piracicaba, SP 13418-900, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Eduardo Henrique Marcandalli Boleta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Luis Felipe Guandalin Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Department of Terrestrial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen NL-6700 AB, the Netherlands
| | - Solange Dos Santos Silva Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna 18020-000, Brazil
| | - Camila Maistro Patreze
- Institute of Biosciences, Federal University of the State of Rio de Janeiro, Rio de Janeiro, RJ 22290-240, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil.
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2
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Soares MB, Pedrinho A, Ferreira JR, Mendes LW, Colzato M, Alleoni LRF. Redox conditions and biochar pyrolysis temperature affecting As and Pb biogeochemical cycles and bacterial community of sediment from mining tailings. J Hazard Mater 2024; 471:134303. [PMID: 38669921 DOI: 10.1016/j.jhazmat.2024.134303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/17/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Despite the widespread use of biochar for soil and sediment remediation, little is known about the impact of pyrolysis temperature on the biogeochemistry of arsenic (As) and lead (Pb) and microorganisms in sediment under reducing conditions. In this study, we investigated the effects of pyrolysis temperature and the addition of glucose on the release and transformation of As and Pb, as well as their potential effects on the bacterial community in contaminated sediments. The addition of biochar altered the geochemical cycle of As, as it favors specific bacterial groups capable of changing species from As(V) to As(III) through fermentation, sulfate respiration and nitrate reduction. The carbon quality and content of N and S in solution shaped the pH and redox potential in a way that changed the microbial community, favoring Firmicutes and reducing Proteobacteria. This change played a fundamental role in the reductive dissolution of As and Pb minerals. The addition of biochar was the only efficient way to remove Pb, possibly as a function of its sorption and precipitation mechanisms. Such insights could contribute to the production or choice of high-efficiency biochar for the remediation of sediments subjected to redox conditions.
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Affiliation(s)
- Matheus Bortolanza Soares
- Department of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), 13418900 Piracicaba, SP, Brazil.
| | - Alexandre Pedrinho
- Department of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), 13418900 Piracicaba, SP, Brazil
| | - José Roberto Ferreira
- Environmental Science, São Paulo's Agency for Agribusiness Technology (APTA/SAA), 13412050, Piracicaba, Brazil; Analytical Chemistry Department, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), 13416000, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), 13416000 Piracicaba, SP, Brazil
| | - Marina Colzato
- Department of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), 13418900 Piracicaba, SP, Brazil
| | - Luís Reynaldo Ferracciú Alleoni
- Department of Soil Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), 13418900 Piracicaba, SP, Brazil
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3
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Mamangkey J, Mendes LW, Mustopa AZ, Hartanto A. Endophytic Aspergillii and Penicillii from medicinal plants: a focus on antimicrobial and multidrug resistant pathogens inhibitory activity. BioTechnologia (Pozn) 2024; 105:83-95. [PMID: 38633888 PMCID: PMC11020150 DOI: 10.5114/bta.2024.135644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 04/19/2024] Open
Abstract
The rise of multidrug resistance among microorganisms, where they develop resistance against formerly efficacious drugs, has led to increased disease prevalence and mortality rates, posing a growing challenge. Globally, antibiotic resistance has made a significant impact, causing millions of fatalities each year. Endophytic fungi have gained considerable attention in research due to their potential to produce a wide variety of secondary metabolites, including natural substances with antimicrobial capabilities. The genera Aspergillus and Penicillium stand out as the most prevalent species of endophytic fungi. Filamentous fungi, such as these are responsible for the production of 45% of known microbial metabolites. This review focuses on exploring the bioactive substances produced by endophytic fungi from these two genera, particularly in conjunction with medicinal plants. Emphasis is placed on their antimicrobial activity and their ability to inhibit multidrug-resistant pathogens. As the need for alternative treatments to combat drug-resistant infections continues to grow, endophytic fungi have the potential to provide a valuable source of bioactive molecules for medical applications.
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Affiliation(s)
- Jendri Mamangkey
- Department of Biology Education, Faculty of Education and Teacher Training, Universitas Kristen Indonesia, Jakarta, Indonesia
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Cibinong, Bogor, Indonesia
| | - Adrian Hartanto
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, Indonesia
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4
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Silva DEO, Costa RM, Campos JR, Rocha SMB, de Araujo Pereira AP, Melo VMM, Oliveira FAS, de Alcantara Neto F, Mendes LW, Araujo ASF. Short-term restoration practices change the bacterial community in degraded soil from the Brazilian semiarid. Sci Rep 2024; 14:6845. [PMID: 38514851 PMCID: PMC10957980 DOI: 10.1038/s41598-024-57690-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/20/2024] [Indexed: 03/23/2024] Open
Abstract
Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | - Ademir Sergio Ferreira Araujo
- Soil Microbial Ecology Group, Federal University of Piauí, Teresina, PI, Brazil.
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil.
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5
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Paes da Costa D, das Graças Espíndola da Silva T, Sérgio Ferreira Araujo A, Prudêncio de Araujo Pereira A, William Mendes L, Dos Santos Borges W, Felix da França R, Alberto Fragoso de Souza C, Alves da Silva B, Oliveira Silva R, Valente de Medeiros E. Soil fertility impact on recruitment and diversity of the soil microbiome in sub-humid tropical pastures in Northeastern Brazil. Sci Rep 2024; 14:3919. [PMID: 38365962 PMCID: PMC10873301 DOI: 10.1038/s41598-024-54221-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Soil fertility is key point to pastures systems and drives the microbial communities and their functionality. Therefore, an understanding of the interaction between soil fertility and microbial communities can increase our ability to manage pasturelands and maintain their soil functioning and productivity. This study probed the influence of soil fertility on microbial communities in tropical pastures in Brazil. Soil samples, gathered from the top 20 cm of twelve distinct areas with diverse fertility levels, were analyzed via 16S rRNA sequencing. The soils were subsequently classified into two categories, namely high fertility (HF) and low fertility (LF), using the K-Means clustering. The random forest analysis revealed that high fertility (HF) soils had more bacterial diversity, predominantly Proteobacteria, Nitrospira, Chloroflexi, and Bacteroidetes, while Acidobacteria increased in low fertility (LF) soils. High fertility (HF) soils exhibited more complex network interactions and an enrichment of nitrogen-cycling bacterial groups. Additionally, functional annotation based on 16S rRNA varied between clusters. Microbial groups in HF soil demonstrated enhanced functions such as nitrate reduction, aerobic ammonia oxidation, and aromatic compound degradation. In contrast, in the LF soil, the predominant processes were ureolysis, cellulolysis, methanol oxidation, and methanotrophy. Our findings expand our knowledge about how soil fertility drives bacterial communities in pastures.
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Affiliation(s)
- Diogo Paes da Costa
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil.
| | | | | | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Wisraiane Dos Santos Borges
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | - Rafaela Felix da França
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | | | - Bruno Alves da Silva
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | - Renata Oliveira Silva
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
| | - Erika Valente de Medeiros
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, Garanhuns, PE, 55292-270, Brazil
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6
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Pellegrinetti TA, de Cássia Mesquita da Cunha I, Chaves MGD, Freitas ASD, Passos GS, Silva AVRD, Cotta SR, Tsai SM, Mendes LW. Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths. Braz J Microbiol 2024:10.1007/s42770-024-01268-3. [PMID: 38358421 DOI: 10.1007/s42770-024-01268-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.
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Affiliation(s)
- Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Piracicaba, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Gabriel Schimmelpfeng Passos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Simone Raposo Cotta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil.
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Araujo ASF, de Medeiros EV, da Costa DP, Pereira APDA, Mendes LW. From desertification to restoration in the Brazilian semiarid region: Unveiling the potential of land restoration on soil microbial properties. J Environ Manage 2024; 351:119746. [PMID: 38071918 DOI: 10.1016/j.jenvman.2023.119746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 11/10/2023] [Accepted: 11/29/2023] [Indexed: 01/14/2024]
Abstract
Land desertification poses a significant challenge in the Brazilian semiarid region, encompassing a substantial portion of the country. Within this region, the detrimental effects of human activities, particularly unsuitable anthropic actions, have resulted in diminished vegetation cover and an accelerated rate of soil erosion. Notably, practices such as overgrazing and the conversion of native forests into pasturelands have played a pivotal role in exacerbating the process of land desertification. Ultimately, land desertification results in significant losses of soil organic matter and microbial diversity. To address this pressing issue and contribute to the existing literature, various land restoration practices, such as grazing exclusion, cover crops, and terracing, have been implemented in the Brazilian semiarid. These practices have shown promising results in terms of enhancing soil fertility and restoring microbial properties. Nonetheless, their effectiveness in improving soil microbial properties in the Brazilian semiarid region remains a subject of ongoing study. Recent advances in molecular techniques have improved our understanding of microbial communities in lands undergoing desertification and restoration. In this review, we focus on assessing the effectiveness of these restoration practices in revitalizing soil microbial properties, with a particular emphasis on the soil microbiome and its functions. Through a critical assessment of the impact of these practices on soil microbial properties, our research aims to provide valuable insights that can help mitigate the adverse effects of desertification and promote sustainable development in this ecologically sensitive region.
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Affiliation(s)
| | | | - Diogo Paes da Costa
- Federal University of the Agreste of Pernambuco, Garanhuns, Pernambuco, Brazil
| | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
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8
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Pellegrinetti TA, da Cunha IDCM, de Chaves MG, de Freitas AS, da Silva AVR, Tsai SM, Mendes LW. Draft genome sequences of representative Paenibacillus polymyxa, Bacillus cereus, Fictibacillus sp., and Brevibacillus agri strains isolated from Amazonian dark earth. Microbiol Resour Announc 2023; 12:e0057423. [PMID: 37811974 PMCID: PMC10652921 DOI: 10.1128/mra.00574-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 10/10/2023] Open
Abstract
Here, we report 10 distinct bacterial genomes from Amazonian dark earths, including six identified as Paenibacillus polymyxa, while the remaining four were unique representatives of Paenibacillus vini, Bacillus cereus, Brevibacillus agri, and Fictibacillus sp., respectively. Each strain exhibited antagonistic activity against Fusarium oxysporum, underscoring their potential as sustainable agriculture resources.
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Affiliation(s)
- Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Izadora De Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
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9
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Bieluczyk W, Asselta FO, Navroski D, Gontijo JB, Venturini AM, Mendes LW, Simon CP, Camargo PBD, Tadini AM, Martin-Neto L, Bendassolli JA, Rodrigues RR, van der Putten WH, Tsai SM. Linking above and belowground carbon sequestration, soil organic matter properties, and soil health in Brazilian Atlantic Forest restoration. J Environ Manage 2023; 344:118573. [PMID: 37459811 DOI: 10.1016/j.jenvman.2023.118573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/27/2023] [Accepted: 07/02/2023] [Indexed: 09/17/2023]
Abstract
Forest restoration mitigates climate change by removing CO2 and storing C in terrestrial ecosystems. However, incomplete information on C storage in restored tropical forests often fails to capture the ecosystem's holistic C dynamics. This study provides an integrated assessment of C storage in above to belowground subsystems, its consequences for greenhouse gas (GHG) fluxes, and the quantity, quality, and origin of soil organic matter (SOM) in restored Atlantic forests in Brazil. Relations between SOM properties and soil health indicators were also explored. We examined two restorations using tree planting ('active restoration'): an 8-year-old forest with green manure and native trees planted in two rounds, and a 15-year-old forest with native-planted trees in one round without green manure. Restorations were compared to reformed pasture and primary forest sites. We measured C storage in soil layers (0-10, 10-20, and 20-30 cm), litter, and plants. GHG emissions were assessed using CH4 and CO2 fluxes. SOM quantity was evaluated using C and N, quality using humification index (HLIFS), and origin using δ13C and δ15N. Nine soil health indicators were interrelated with SOM attributes. The primary forest presented the highest C stocks (107.7 Mg C ha-1), followed by 15- and 8-year-old restorations and pasture with 69.8, 55.5, and 41.8 Mg C ha-1, respectively. Soil C stocks from restorations and pasture were 20% lower than primary forest. However, 8- and 15-year-old restorations stored 12.3 and 28.3 Mg ha-1 more aboveground C than pasture. The younger forest had δ13C and δ15N values of 2.1 and 1.7‰, respectively, lower than the 15-year-old forest, indicating more C derived from C3 plants and biological N fixation. Both restorations and pasture had at least 34% higher HLIFS in deeper soil layers (10-30 cm) than primary forest, indicating a lack of labile SOM. Native and 15-year-old forests exhibited higher soil methane influx (141.1 and 61.9 μg m-2 h-1). Forests outperformed pasture in most soil health indicators, with 69% of their variance explained by SOM properties. However, SOM quantity and quality regeneration in both restorations approached the pristine forest state only in the top 10 cm layer, while deeper soil retained agricultural degradation legacies. In conclusion, active restoration of the Atlantic Forest is a superior approach compared to pasture reform for GHG mitigation. Nonetheless, the development of restoration techniques to facilitate labile C input into deeper soil layers (>10 cm) is needed to further improve soil multifunctionality and long-term C storage.
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Affiliation(s)
- Wanderlei Bieluczyk
- University of São Paulo, Center for Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil; University of São Paulo, Center for Nuclear Energy in Agriculture, Isotopic Ecology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Fernanda Ometto Asselta
- University of São Paulo, Center for Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Deisi Navroski
- University of São Paulo, Center for Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Júlia Brandão Gontijo
- University of São Paulo, Center for Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Andressa Monteiro Venturini
- Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, USA; Department of Biology, Stanford University, Stanford, CA, USA.
| | - Lucas William Mendes
- University of São Paulo, Center for Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Carla Penha Simon
- University of São Paulo, Center for Nuclear Energy in Agriculture, Isotopic Ecology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Plínio Barbosa de Camargo
- University of São Paulo, Center for Nuclear Energy in Agriculture, Isotopic Ecology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Amanda Maria Tadini
- Brazilian Agricultural Research Corporation, Embrapa Instrumentation, 1452 XV de Novembro Street, São Carlos, SP, 13560-970, Brazil.
| | - Ladislau Martin-Neto
- Brazilian Agricultural Research Corporation, Embrapa Instrumentation, 1452 XV de Novembro Street, São Carlos, SP, 13560-970, Brazil.
| | - José Albertino Bendassolli
- University of São Paulo, Center for Nuclear Energy in Agriculture, Stable Isotope Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
| | - Ricardo Ribeiro Rodrigues
- University of São Paulo, "Luiz de Queiroz" College of Agriculture, Laboratory of Ecology and Forest Restoration, 11 Pádua Dias Avenue, Piracicaba, SP, 13418-900, Brazil.
| | - Wim H van der Putten
- Netherlands Institute of Ecology, NIOO-KNAW, Department of Terrestrial Ecology, 6708, PB, Wageningen, Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700, ES, Wageningen, the Netherlands.
| | - Siu Mui Tsai
- University of São Paulo, Center for Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP, 13416-000, Brazil.
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10
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Dutra AF, Leite MRL, Melo CCDF, Amaral DS, da Silva JLF, Prado RDM, Piccolo MDC, Miranda RDS, da Silva Júnior GB, Sousa TKDSA, Mendes LW, Araújo ASF, Zuffo AM, de Alcântara Neto F. Soil and foliar Si fertilization alters elemental stoichiometry and increases yield of sugarcane cultivars. Sci Rep 2023; 13:16040. [PMID: 37749306 PMCID: PMC10519947 DOI: 10.1038/s41598-023-43351-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023] Open
Abstract
Silicon (Si) fertilization is widely recognized to improve the development of crops, especially in tropical soils and cultivation under dryland management. Herein, our working hypothesis was that Si stoichiometry favors the efficient use of carbon (C), nitrogen (N), and phosphorus (P) in sugarcane plants. Therefore, a field experiment was carried out using a 3 × 3 factorial scheme consisting of three cultivars (RB92579, RB021754 and RB036066) and three forms of Si application (control without Si; sodium silicate spray at 40 mmol L-1 in soil during planting; sodium silicate spray at 40 mmol L-1 on leaves at 75 days after emergence). All Si fertilizations altered the elemental C and P stoichiometry and sugarcane yield, but silicon-induced responses varied depending on sugarcane cultivar and application method. The most prominent impacts were found in the leaf Si-sprayed RB92579 cultivar, with a significant increase of 7.0% (11 Mg ha-1) in stalk yield, 9.0% (12 Mg ha-1) in total recoverable sugar, and 20% (4 Mg ha-1) in sugar yield compared to the Si-without control. In conclusion, our findings clearly show that silicon soil and foliar fertilization alter C:N:P stoichiometry by enhancing the efficiency of carbon and phosphorus utilization, leading to improved sugarcane production and industrial quality.
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Affiliation(s)
| | | | | | - Danilo Silva Amaral
- Postgraduate Program in Agronomy, São Paulo State University, Jaboticabal, 14884-900, Brazil
| | | | - Renato de Mello Prado
- Laboratory of Plant Nutrition, São Paulo State University, Jaboticabal, 14884-900, Brazil
| | - Marisa de Cássia Piccolo
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, 13416-000, Brazil
| | - Rafael de Souza Miranda
- Plant Science Department, Federal University of Piauí, Teresina, 64049-550, Brazil
- Postgraduate Program in Agricultural Sciences, Federal University of Piauí, Bom Jesus, 64900-000, Brazil
| | - Gabriel Barbosa da Silva Júnior
- Plant Science Department, Federal University of Piauí, Teresina, 64049-550, Brazil
- Postgraduate Program in Agricultural Sciences, Federal University of Piauí, Bom Jesus, 64900-000, Brazil
| | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, 13416-000, Brazil
| | | | - Alan Mario Zuffo
- Department of Agronomy, State University of Maranhão, Balsas, MA, 65800-000, Brazil
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11
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Mendes LW, Raaijmakers JM, de Hollander M, Sepo E, Gómez Expósito R, Chiorato AF, Mendes R, Tsai SM, Carrión VJ. Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome. Environ Microbiome 2023; 18:68. [PMID: 37537681 PMCID: PMC10401788 DOI: 10.1186/s40793-023-00524-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. RESULTS Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. CONCLUSION Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.
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Affiliation(s)
- Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP, 13416-000, Brazil.
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.
| | - Jos M Raaijmakers
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mattias de Hollander
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Edis Sepo
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Ruth Gómez Expósito
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Alisson Fernando Chiorato
- Centro de Análises e Pesquisa Tecnológica do Agronegócio dos Grãos e Fibras, Instituto Agronômico IAC, Campinas, 130001-970, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna, 18020-000, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP, 13416-000, Brazil
| | - Victor J Carrión
- Departament of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.
- Institute of Biology, Leiden University, Leiden, the Netherlands.
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain.
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12
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Araujo ASF, Pertile M, Costa RM, Costa MKL, de Aviz RO, Mendes LW, de Medeiros EV, da Costa DP, Melo VMM, Pereira APDA. Short-term responses of plant growth-promoting bacterial community to the herbicides imazethapyr and flumioxazin. Chemosphere 2023; 328:138581. [PMID: 37019406 DOI: 10.1016/j.chemosphere.2023.138581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Imazethapyr and flumioxazin are widely recommended herbicides for soybean fields due to their broad-spectrum effects. However, although both herbicides present low persistence, their potential impact on the community of plant growth-promoting bacteria (PGPB) is unclear. To address this gap, this study assessed the short-term effect of imazethapyr, flumioxazin, and their mixture on the PGPB community. Soil samples from soybean fields were treated with these herbicides and incubated for 60 days. We extracted soil DNA at 0, 15, 30, and 60 days and sequenced the 16S rRNA gene. In general, the herbicides presented temporary and short-term effects on PGPB. The relative abundance of Bradyrhizobium increased, while Sphingomonas decreased on the 30th day with the application of all herbicides. Both herbicides increased the potential function of nitrogen fixation at 15th days and decreased at 30th and 60th days of incubation. The proportions of generalists were similar (∼42%) comparing each herbicide and the control, while the proportion of specialists increased (varying from 24.9% to 27.6%) with the application of herbicides. Imazethapyr, flumioxazin and their mixture did not change the complexity and interactions of the PGPB network. In conclusion, this study showed that, in the short term, the application of imazethapyr, flumioxazin, and their mixture, at the recommended field rates, does not negatively affect the community of plant growth-promoting bacteria.
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Affiliation(s)
| | - Mariane Pertile
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI Brazil
| | - Romário Martins Costa
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI Brazil
| | | | - Rhaiana Oliveira de Aviz
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo CENA-USP, Piracicaba, SP Brazil
| | - Erika Valente de Medeiros
- Laboratory of Microbiology and Enzymology-LEMA, Federal University of Agreste Pernambuco, Garanhuns 55292-270, Brazil
| | - Diogo Paes da Costa
- Laboratory of Microbiology and Enzymology-LEMA, Federal University of Agreste Pernambuco, Garanhuns 55292-270, Brazil
| | - Vania Maria Maciel Melo
- Laboratório de Ecologia Microbiana e Biotecnologia, Federal University of Ceara, Fortaleza, CE Brazil
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13
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Araujo FF, Salvador GLO, Lupatini GC, Pereira APDA, Costa RM, de Aviz RO, de Alcantara Neto F, Mendes LW, Araujo ASF. Exploring the diversity and composition of soil microbial communities in different soybean-maize management systems. Microbiol Res 2023; 274:127435. [PMID: 37331053 DOI: 10.1016/j.micres.2023.127435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/20/2023]
Abstract
Soybean-maize are cultivated in different management systems, such as no-tillage and pastures, which presents potential to add organic residues, and it can potentially impacts the soil microbial community present in these systems. Thus, this study aimed to examine the effects of different soybean-maize management practices on the diversity and composition of soil microbial communities. Specifically, 16 S rRNA amplicon sequencing was used to investigate whether the use of pasture species in a fallowing system influences microbial communities in a soybean-maize rotation system, as compared to conventional tillage and no-tillage systems. The results indicate that the inclusion of the pasture species Urochloa brizantha in soybean-maize management systems leads to distinct responses within the soil microbial community. It was found that different soybean-maize management systems, particularly those with U. brizantha, affected the microbial community, likely due to the management applied to this pasture species. The system with 3 years of fallowing before soybean-maize showed the lowest microbial richness (∼2000 operational taxonomic units) and diversity index (∼6.0). Proteobacteria (∼30%), Acidobacteria (∼15%), and Verrucomicrobia (∼10%) were found to be the most abundant phyla in the soil under tropical native vegetation, while soils under cropland had an increased abundance of Firmicutes (∼30% to ∼50%) and Actinobacteria (∼30% to ∼35%). To summarize, this study identified the impacts of various soybean-maize management practices on the soil microbial community and emphasized the advantages of adding U. brizantha as a fallow species.
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14
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Bieluczyk W, Merloti LF, Cherubin MR, Mendes LW, Bendassolli JA, Rodrigues RR, de Camargo PB, van der Putten WH, Tsai SM. Forest restoration rehabilitates soil multifunctionality in riparian zones of sugarcane production landscapes. Sci Total Environ 2023; 888:164175. [PMID: 37201828 DOI: 10.1016/j.scitotenv.2023.164175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
Brazilian sugarcane plays a vital role in the production of both sugar and renewable energy. However, land use change and long-term conventional sugarcane cultivation have degraded entire watersheds, including a substantial loss of soil multifunctionality. In our study, riparian zones have been reforested to mitigate these impacts, protect aquatic ecosystems, and restore ecological corridors within the sugarcane production landscapes. We examined (i) how forest restoration enables rehabilitation of the soil's multifunctionality after long-term sugarcane cultivation and (ii) how long it takes to regain ecosystem functions comparable to those of a primary forest. We investigated a time series of riparian forests at 6, 15, and 30 years after starting restoration by planting trees (named 'active restoration') and determined soil C stocks, δ13C (indicative of C origin), as well as measures indicative of soil health. A primary forest and a long-term sugarcane field were used as references. Eleven soil physical, chemical, and biological indicators were used for a structured soil health assessment, calculating index scores based on soil functions. Forest-to-cane conversion reduced 30.6 Mg ha-1 of soil C stocks, causing soil compaction and loss of cation exchange capacity, thus degrading soil's physical, chemical, and biological functions. Forest restoration for 6-30 years recovered 16-20 Mg C ha-1 stored in soils. In all restored sites, soil functions such as supporting root growth, aerating the soil, nutrient storage capacity, and providing C energy for microbial activity were gradually recovered. Thirty years of active restoration was sufficient to reach the primary forest state in overall soil health index, multifunctional performance, and C sequestration. We conclude that active forest restoration in sugarcane-dominated landscapes is an effective way to restore soil multifunctionality approaching the level of the native forest in approximately three decades. Moreover, the C sequestration in the restored forest soils will help to mediate global warming.
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Affiliation(s)
- Wanderlei Bieluczyk
- University of São Paulo, Center of Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP 13416-000, Brazil.
| | - Luis Fernando Merloti
- Netherlands Institute of Ecology, NIOO-KNAW, Department of Terrestrial Ecology, 6708, PB, Wageningen, Netherlands
| | - Maurício Roberto Cherubin
- University of São Paulo, "Luiz de Queiroz" College of Agriculture, Soil Health & Management Research Laboratory, 11 Pádua Dias Avenue, Piracicaba, SP 13418-900, Brazil
| | - Lucas William Mendes
- University of São Paulo, Center of Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP 13416-000, Brazil
| | - José Albertino Bendassolli
- University of São Paulo, Center of Nuclear Energy in Agriculture, Stable Isotope Laboratory, 303 Centenário Avenue, Piracicaba, SP 13416-000, Brazil
| | - Ricardo Ribeiro Rodrigues
- University of São Paulo, "Luiz de Queiroz" College of Agriculture, Laboratory of Ecology and Forest Restoration, 11 Pádua Dias Avenue, Piracicaba, SP 13418-900, Brazil
| | - Plínio Barbosa de Camargo
- University of São Paulo, Center of Nuclear Energy in Agriculture, Isotopic Ecology Laboratory, 303 Centenário Avenue, Piracicaba, SP 13416-000, Brazil
| | - Wim H van der Putten
- Netherlands Institute of Ecology, NIOO-KNAW, Department of Terrestrial Ecology, 6708, PB, Wageningen, Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700, ES, Wageningen, Netherlands
| | - Siu Mui Tsai
- University of São Paulo, Center of Nuclear Energy in Agriculture, Cell and Molecular Biology Laboratory, 303 Centenário Avenue, Piracicaba, SP 13416-000, Brazil
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15
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Martins GL, de Souza AJ, Mendes LW, Gontijo JB, Rodrigues MM, Coscione AR, Oliveira FC, Regitano JB. Physicochemical and bacterial changes during composting of vegetable and animal-derived agro-industrial wastes. Bioresour Technol 2023; 376:128842. [PMID: 36898559 DOI: 10.1016/j.biortech.2023.128842] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/01/2023] [Accepted: 03/04/2023] [Indexed: 06/18/2023]
Abstract
This study investigates the impact of different agro-industrial organic wastes (i.e., sugarcane filter cake, poultry litter, and chicken manure) on the bacterial community and their relationship with physicochemical attributes during composting. Integrative analysis was performed by combining high-throughput sequencing and environmental data to decipher changes in the waste microbiome. The results revealed that animal-derived compost stabilized more carbon and mineralized a more organic nitrogen than vegetable-derived compost. Composting enhanced bacterial diversity and turned the bacterial community structure similar among all wastes, reducing Firmicutes abundance in animal-derived wastes. Potential biomarkers indicating compost maturation were Proteobacteria and Bacteroidota phyla, Chryseolinea genus and Rhizobiales order. The waste source influenced the final physicochemical attributes, whereas composting enhanced the complexity of the microbial community in the order of poultry litter > filter cake > chicken manure. Therefore, composted wastes, mainly the animal-derived ones, seem to present more sustainable attributes for agricultural use, despite their losses of C, N, and S.
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Affiliation(s)
- Guilherme Lucio Martins
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil; Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Adijailton José de Souza
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Júlia Brandão Gontijo
- Center for Nuclear Energy in Agriculture (CENA), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Mayra Maniero Rodrigues
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Aline Renée Coscione
- Center of Soil and Agroenviromental Resources, Instituto Agronômico de Campinas (IAC), Campinas, SP, Brazil
| | | | - Jussara Borges Regitano
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil.
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16
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da Silva JL, Mendes LW, Rocha SMB, Antunes JEL, Oliveira LMDS, Melo VMM, Oliveira FAS, Pereira APDA, Costa GDN, da Silva VB, Gomes RLF, de Alcantara Neto F, Lopes ACDA, Araujo ASF. Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere. Microb Ecol 2023; 85:1423-1433. [PMID: 35525854 DOI: 10.1007/s00248-022-02028-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/26/2022] [Indexed: 05/10/2023]
Abstract
Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.
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Affiliation(s)
- Josieli Lima da Silva
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | - Sandra Mara Barbosa Rocha
- Soil Microbial Ecology Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | | | | | - Vania Maria Maciel Melo
- Laboratório de Ecologia Microbiana E Biotecnologia, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | | | - Gérson do Nascimento Costa
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Veronica Brito da Silva
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | - Regina Lucia Ferreira Gomes
- Plant Genetic Resource Group, Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
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17
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Araujo ASF, de Araujo Pereira AP, Melo VMM, de Medeiros EV, Mendes LW. Environmental DNA Sequencing to Monitor Restoration Practices on Soil Bacterial and Archaeal Communities in Soils Under Desertification in the Brazilian Semiarid. Microb Ecol 2023; 85:1072-1076. [PMID: 35633375 DOI: 10.1007/s00248-022-02048-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/18/2022] [Indexed: 05/04/2023]
Abstract
Soils from Brazilian semiarid regions are highly vulnerable to desertification due to their geology, climate, human actions, and intensive land use that contribute to desertification. Therefore, areas under desertification have increased in the Brazilian semiarid region and it has negatively changed the soil bacterial and archaeal communities and their functionality. On the other hand, although restoration strategies are expensive and there are few soils restoration programs, some practices have been applied to restore these soils under desertification. For instance, conservationist practices and grazing exclusion have been strategically implemented, and they created a new altered soil condition for soil microbial communities, boosting soil microbial diversity. Here, we discuss the potential of these restoration strategies to recover the richness and diversity of soil bacterial and archaeal communities that were described through environmental DNA (eDNA) sequencing of soil samples. eDNA sequencing results show that areas where restoration strategies have been applied in regions under desertification in the Brazilian semiarid have increased species richness, diversity, and structure of the bacterial and archaeal community. In addition, network connectivity and functionality of the soil microorganisms have been improved over time. Altogether, we show that management strategies for soil restoration have positive effects on soil microbial communities and these effects can be monitored using the eDNA sequencing approach.
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Affiliation(s)
| | | | | | | | - Lucas William Mendes
- Centro de Energia Nuclear Na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
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18
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Obregon Alvarez D, Fonseca de Souza L, Mendes LW, de Moraes MT, Tosi M, Venturini AM, Meyer KM, Barbosa de Camargo P, Bohannan BJM, Mazza Rodrigues JL, Dunfield KE, Tsai SM. Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin. Mol Ecol 2023. [PMID: 36896778 DOI: 10.1111/mec.16912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.
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Affiliation(s)
- Dasiel Obregon Alvarez
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | | | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Kyle M Meyer
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | | | | | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California-Davis, Davis, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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19
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Araujo ASF, Jia X, Miranda ARL, Pereira APDA, Melo VMM, Rocha SMB, Costa RM, Saraiva TCDS, Mendes LW, Salles JF. Changes in the bacterial rare biosphere after permanent application of composted tannery sludge in a tropical soil. Chemosphere 2023; 313:137487. [PMID: 36521745 DOI: 10.1016/j.chemosphere.2022.137487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/21/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Composted tannery sludge (CTS) promotes shifts in soil chemical properties, affecting microbial communities. Although the effect of CTS application on the bacterial community has been studied, it is unclear whether this impact discriminates between the dominant and rare species. This present study investigated how the dominant and rare bacterial communities respond over time to different concentrations of CTS application (0, 2.5, 5, 10, and 20 tons/ha) for 180 days. The richness of operational taxonomic units (OTU) was 30-fold higher in the rare than in the dominant biosphere. While some phyla shifted their relative abundance differently in the dominant and rare biosphere, some genera increased their relative abundance under higher CTS concentrations, such as Nocardioides (∼100%), Rubrobacter (∼300%), and Nordella (∼400%). Undominated processes largely governed the dominant biosphere (76.97%), followed by homogeneous (12.51%) and variable (8.03%) selection, and to a lesser extent, the dispersal limitation (2.48%). The rare biosphere was driven by the CTS application as evidenced by the exclusively homogeneous selection (100%). This study showed that the rare biosphere was more sensitive to changes in soil chemical parameters due to CTS application, which evidences the importance explore this portion of the bacterial community for its biotechnological use in contaminated soils.
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Affiliation(s)
| | - Xiu Jia
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747AG, the Netherlands
| | | | | | | | | | | | | | - Lucas William Mendes
- Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, Piracicaba, SP Brazil
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747AG, the Netherlands
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Araujo ASF, Miranda ARL, Pereira APDA, de Melo WJ, Melo VMM, Ventura SH, Brito Junior ES, de Medeiros EV, Araujo FF, Mendes LW. Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination. Chemosphere 2023; 313:137417. [PMID: 36460149 DOI: 10.1016/j.chemosphere.2022.137417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/18/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg-1 Cr) and Cr-contaminated soils (∼250 mg kg-1 Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.
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Affiliation(s)
| | | | | | - Wanderley José de Melo
- Universidade Estadual Paulista (Unesp), Faculdade de Agronomia e Veterinaria, Jaboticabal, Brazil
| | | | | | | | | | | | - Lucas William Mendes
- Centro de Energia Nuclear Na Agricultura, Universidade de Sao Paulo, Piracicaba, SP, Brazil
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21
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Araujo ASF, de Araujo Pereira AP, Mendes LW. Applications of Cr-rich composted tannery sludge in the soil decrease microbial biomass and select specific bacterial groups. Environ Sci Pollut Res Int 2022; 29:75113-75118. [PMID: 36085223 DOI: 10.1007/s11356-022-22933-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
The tannery industries generate a solid waste known as tannery sludge, which is composed of organic and inorganic compounds, mainly chromium (Cr). When Cr is not removed from the tannery sludge, this solid waste is metal-rich and its application could affect the soil microorganisms. Alternatively, the composting of the tannery sludge can contribute to decreasing the concentration of Cr in the composted tannery sludge (CTS). However, in some cases, the concentration of Cr remains high in the CTS. During the last 10 years, the Cr-rich CTS has been successively applied in the soil, and its effect on soil microbial properties was verified. Here, we discuss the effect of successive applications of Cr-rich CTS on soil microbes. Interestingly, the findings have shown that successive applications of Cr-rich CTS selected specific soil microbial groups with potential functions. In addition, the studies added a new focus to further research evaluating the potential effect of successive applications of Cr-rich CTS on the rare microbial community.
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Affiliation(s)
| | | | - Lucas William Mendes
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, Brazil
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22
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Fonseca de Souza L, Alvarez DO, Domeignoz-Horta LA, Gomes FV, de Souza Almeida C, Merloti LF, Mendes LW, Andreote FD, Bohannan BJM, Mazza Rodrigues JL, Nüsslein K, Tsai SM. Maintaining grass coverage increases methane uptake in Amazonian pastures, with a reduction of methanogenic archaea in the rhizosphere. Sci Total Environ 2022; 838:156225. [PMID: 35623507 DOI: 10.1016/j.scitotenv.2022.156225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Cattle ranching is the largest driver of deforestation in the Brazilian Amazon. The rainforest-to-pasture conversion affects the methane cycle in upland soils, changing it from sink to source of atmospheric methane. However, it remains unknown if management practices could reduce the impact of land-use on methane cycling. In this work, we evaluated how pasture management can regulate the soil methane cycle either by maintaining continuous grass coverage on pasture soils, or by liming the soil to amend acidity. Methane fluxes from forest and pasture soils were evaluated in moisture-controlled greenhouse experiments with and without grass cover (Urochloa brizantha cv. Marandu) or liming. We also assessed changes in the soil microbial community structure of both bare (bulk) and rhizospheric pasture soils through high throughput sequencing of the 16S rRNA gene, and quantified the methane cycling microbiota by their respective marker genes related to methane generation (mcrA) or oxidation (pmoA). The experiments used soils from eastern and western Amazonia, and concurrent field studies allowed us to confirm greenhouse data. The presence of a grass cover not only increased methane uptake by up to 35% in pasture soils, but also reduced the abundance of the methane-producing community. In the grass rhizosphere this reduction was up to 10-fold. Methane-producing archaea belonged to the genera Methanosarcina sp., Methanocella sp., Methanobacterium sp., and Rice Cluster I. Further, we showed that soil liming to increasing pH compromised the capacity of forest and pasture soils to be a sink for methane, and instead converted formerly methane-consuming forest soils to become methane sources in only 40-80 days. Liming reduced the relative abundance of Beijerinckiacea family in forest soils, which account for many known methanotrophs. Our results demonstrate that pasture management that maintains grass coverage can mitigate soil methane emissions, compared to bare (bulk) pasture soil.
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Affiliation(s)
- Leandro Fonseca de Souza
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil; Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
| | - Dasiel Obregon Alvarez
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil; Applied Soil Ecology Lab, School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Luiz A Domeignoz-Horta
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA; Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Fabio Vitorino Gomes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | | | - Luis Fernando Merloti
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
| | | | | | | | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
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Goss-Souza D, Tsai SM, Rodrigues JLM, Klauberg-Filho O, Sousa JP, Baretta D, Mendes LW. Biogeographic responses and niche occupancy of microbial communities following long-term land-use change. Antonie Van Leeuwenhoek 2022; 115:1129-1150. [DOI: 10.1007/s10482-022-01761-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/29/2022] [Indexed: 10/17/2022]
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24
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Costa DPD, Araujo ASF, Pereira APDA, Mendes LW, França RFD, Silva TDGED, Oliveira JBD, Araujo JS, Duda GP, Menezes RSC, Medeiros EVD. Dataset for effects of the transition from dry forest to pasture on diversity and structure of bacterial communities in Northeastern Brazil. Data Brief 2022; 41:107842. [PMID: 35128002 PMCID: PMC8804183 DOI: 10.1016/j.dib.2022.107842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/06/2022] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
The data included in this article supplement the research article titled “Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga (manuscript ID: STOTEN-D-21-19067R1)”. This data article included the analysis of 18 chemical variables in 36 composite samples (included 4 replicates) of soils from the Microregion of Garanhuns (Northeast Brazil) and also partial 16S rRNA gene sequences from genomic DNA extracted from 27 of these samples (included 3 best quality replicates) for paired-end sequencing (up to 2 × 300 bp) in Illumina MiSeq platform (NCBI - BioProject accession: PRJNA753707). Soils were collected in August 2018 in a tropical subhumid region from the Brazilian Caatinga, along with 27 composite samples from the aboveground part of pastures to determine nutritional quality based on leaf N content. The analysis of variance (ANOVA) and post-hoc tests of environmental data and the main alpha-diversity indices based on linear mixed models (LMM) were represented in the tables. In this case, the collection region (C1 – Brejão, C2 – Garanhuns, and C3 – São João) was the random-effect variable and adjacent habitats formed by a forest (FO) and two pastures (PA and PB succeeded by this forest) composed the fixed-effect variable (land cover), both nested within C. In addition, a table with similarity percentages breakdown (SIMPER) was also shown, a procedure to assess the average percent contribution of individual phyla and bacterial classes. The figures showed the details of the study location, sampling procedure, vegetation status through the Normalized Difference Vegetation Index (NDVI), in addition to the general abundance and composition of the main bacterial phyla.
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Affiliation(s)
- Diogo Paes da Costa
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil
- Corresponding author.
| | | | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, 13400-970 Piracicaba, SP, Brazil
| | - Rafaela Felix da França
- Department of Soils, Federal Rural University of Rio de Janeiro, 23890-000 Seropédica, RJ, Brazil
| | | | - Julyana Braga de Oliveira
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil
| | - Jenifer Sthephanie Araujo
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil
| | - Gustavo Pereira Duda
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil
| | | | - Erika Valente de Medeiros
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil
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Costa DPD, Araujo ASF, Pereira APDA, Mendes LW, França RFD, Silva TDGED, Oliveira JBD, Araujo JS, Duda GP, Menezes RSC, Medeiros EVD. Forest-to-pasture conversion modifies the soil bacterial community in Brazilian dry forest Caatinga. Sci Total Environ 2022; 810:151943. [PMID: 34864020 DOI: 10.1016/j.scitotenv.2021.151943] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/21/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Soils comprise a huge fraction of the world's biodiversity, contributing to several crucial ecosystem functions. However, how the forest-to-pasture conversion impact soil bacterial diversity remains poorly understood, mainly in the Caatinga biome, the largest tropical dry forest of the world. Here, we hypothesized that forest-to-pasture conversion would shape the microbial community. Thus, the soil bacterial community was assessed using the 16S rRNA gene sequencing into the Illumina MiSeq platform. Then, we analyzed ecological patterns and correlated the bacterial community with environmental parameters in forest, and two distinct pastures areas, one less productive and another more productive. The variation in soil properties in pastures and forest influenced the structure and diversity of the bacterial community. Thus, the more productive pasture positively influenced the proportion of specialists and the co-occurrence network compared to the less productive pasture. Also, Proteobacteria, Acidobacteria, and Verrucomicrobia were abundant under forest, while Actinobacteria, Firmicutes, and Chloroflexi were abundant under pastures. Also, the more productive pasture presented a higher bacterial diversity, which is important since that a more stable and connected bacterial community could benefit the agricultural environment and enhance plant performance, as can be observed by the highest network complexity in this pasture. Together, our findings elucidate a significant shift in soil bacterial communities as a consequence of forest-to-pasture conversion and bring important information for the development of preservation strategies.
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Affiliation(s)
- Diogo Paes da Costa
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | | | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, 13400-970 Piracicaba, SP, Brazil.
| | - Rafaela Felix da França
- Department of Soils, Federal Rural University of Rio de Janeiro, 23890-000 Seropédica, RJ, Brazil.
| | | | - Julyana Braga de Oliveira
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | - Jenifer Sthephanie Araujo
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | - Gustavo Pereira Duda
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
| | | | - Erika Valente de Medeiros
- Microbiology and Enzimology Lab., Federal University of Agreste Pernambuco, 55292-270 Garanhuns, PE, Brazil.
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Corrêa PS, Jimenez CR, Mendes LW, Rymer C, Ray P, Gerdes L, da Silva VO, De Nadai Fernandes EA, Abdalla AL, Louvandini H. Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems. Front Microbiol 2021; 12:768480. [PMID: 34956130 PMCID: PMC8692951 DOI: 10.3389/fmicb.2021.768480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 01/10/2023] Open
Abstract
The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (13C) and nitrogen (15N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Carolina Rodriguez Jimenez
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Caroline Rymer
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Luciana Gerdes
- Reference Laboratory on Classification and Evaluation of Animal Products, Institute of Zootechnics, Nova Odessa, Brazil
| | - Vagner Ovani da Silva
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | | | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, São Paulo, Brazil
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Araujo ASF, de Pereira APDA, Antunes JEL, Oliveira LMDS, de Melo WJ, Rocha SMB, do Amorim MR, Araujo FF, Melo VMM, Mendes LW. Dynamics of bacterial and archaeal communities along the composting of tannery sludge. Environ Sci Pollut Res Int 2021; 28:64295-64306. [PMID: 34304356 DOI: 10.1007/s11356-021-15585-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The process of composting has been proposed as a biological alternative to improve the quality of tannery sludge (TS) by the action of microbial communities. However, there is limited knowledge about the dynamic of these microbial communities during the composting process. This study assessed the responses of bacterial and archaeal communities during TS composting using the 16S rRNA sequencing. The composting process occurred within 90 days, and samples of compost were collected on day 7 (d7; mesophilic stage), 30 (d30; thermophilic stage), 60 (d60; cooling stage), and 90 (d90; maturation stage). The results showed a succession of microbial phyla during the composting with enrichment of Synergistetes, WS1, and Euryarchaeota at the mesophilic stage, while at the thermophilic stage, there was an enrichment of Hydrogenedentes, WPS-2, Chloroflexi, and Deinococcus-Thermus. At the cooling stage, there was an enrichment of Kiritimatiellaeota, and at the maturation stage, there was an enrichment of Entotheonellaeota, Dadabacteria, Nitrospirae, Dependiatiae, and Fibrobacteres. When analyzing the drivers influencing microbial communities, Cr and pH presented more negative correlations with general phyla. In contrast, S, C, K, temperature, and N presented more positive correlations, while Ni, Cd, and P showed fewer correlations. According to niche occupancy, we observed a decreased proportion of generalists with a consequently increased proportion of specialists following the composting process. This study showed that different stages of the composting present a specific microbial community structure and dynamics, which are related to some specific composting characteristics.
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Affiliation(s)
| | | | | | | | - Wanderley José de Melo
- Technology Department, São Paulo State University, Jaboticabal, SP, Brazil
- Graduate Program in Environmental Science, Campus of Descalvado, Brazil University, Descalvado, SP, Brazil
| | | | | | | | - Vania Maria Maciel Melo
- Laboratory of Microbial Ecology and Biotechnology, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Lucas William Mendes
- Cellular and Molecular Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, Brazil
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28
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Moro MS, Wu X, Wei W, Mendes LW, Allen KC, Pinheiro JB, Clough SJ, Zucchi MI. Characterization and Comparison of Intestinal Bacterial Microbiomes of Euschistus heros and Piezodorus guildinii Collected in Brazil and the United States. Front Microbiol 2021; 12:769965. [PMID: 34777323 PMCID: PMC8579040 DOI: 10.3389/fmicb.2021.769965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Herbivorous insects are one of the main biological threats to crops. One such group of insects, stink bugs, do not eat large amounts of tissue when feeding on soybean, but are damaging to the quality of the seed yield as they feed on green developing seeds leading to poorly marketable harvests. In addition to causing physical damage during sucking-feeding activities, the insects can also transmit microbial pathogens, leading to even greater yield loss. Conducting surveys of the insect intestinal microbiome can help identify possible pathogens, as well as detail what healthy stink bug digestive systems have in common. Methods: We used the conserved V4 region of the 16S rRNA gene to characterize the bacterial microbiome of the red-banded stink bug Piezodorus guildinii collected in Brazil and the United States, as well as the neotropical brown stink bug Euschistus heros collected in Brazil. Results: After quality filtering of the data, 192 samples were kept for analyses: 117 samples from P. guildinii covering three sites in Brazil and four sites in the United States, and 75 samples for E. heros covering 10 sites in Brazil. The most interesting observations were that the diversity and abundance of some bacterial families were different in the different ecoregions of Brazil and the United States. Conclusion: Some families, such as Acetobacteraceae, Bacillaceae, Moraxellaceae, Enterobacteriaceae, and Rhodocyclaceae, may be related to the better adaptation in some localities in providing nutrients, break down cellulose, detoxify phytochemicals, and degrade organic compounds, which makes it difficult to control these species.
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Affiliation(s)
- Matheus Sartori Moro
- Genetics and Molecular Biology - Biology Institute, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Genetics and Genomics Conservation Laboratory (UNICAMP), Piracicaba, Brazil
| | - Xing Wu
- Department of Crop Science, University of Illinois, Urbana, IL, United States
| | - Wei Wei
- Department of Crop Science, University of Illinois, Urbana, IL, United States
| | | | - Kerry Clint Allen
- United States Department of Agriculture-Agricultural Research Services, Southern Insect Management Research, Stoneville, MS, United States
| | - José Baldin Pinheiro
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Steven J Clough
- Department of Crop Science, University of Illinois, Urbana, IL, United States.,United States Department of Agriculture-Agricultural Research Services, Soybean/Maize Germplasm, Pathology and Genetics Research, Urbana, IL, United States
| | - Maria Imaculada Zucchi
- Genetics and Genomics Conservation Laboratory (UNICAMP), Piracicaba, Brazil.,São Paulo Agency of Agribusiness Technology (APTA), Piracicaba, Brazil
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29
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Corrêa PS, Mendes LW, Lemos LN, Sampaio ACK, Issakowicz J, McManus CM, Tsai SM, Faciola AP, Abdalla AL, Louvandini H. The effect of Haemonchus contortus and Trichostrongylus colubriforms infection on the ruminal microbiome of lambs. Exp Parasitol 2021; 231:108175. [PMID: 34740587 DOI: 10.1016/j.exppara.2021.108175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 09/14/2021] [Accepted: 10/31/2021] [Indexed: 12/16/2022]
Abstract
We evaluated Haemonchus contortus (HC) and Trichostrongylus colubriformis (TC) infection on the ruminal microbial community of Santa Ines lambs to better understand the pathophysiology of parasite infections and the interactions among gastrointestinal nematodes and gut resident microbiota. In this study, 18 six months of age lambs were maintained for 34 days in individual pens divided into three treatments that included animals infected with HC and TC, and control (infection-free). Haematological, ruminal parameter and microbial nitrogen absorbed by pune derivatives, as well as enteric methane emission (CH4), were analysed, and the rumen microbial taxonomic and functional profile assessed by shotgun metagenomics. The analysis showed that total protein, albumin, urea, and butyrate level were lower in animals infected by both parasites, while HC infection also decreased the haemoglobin level. Both infected groups (TC and HC) increased the enteric methane emission (CH4). TC and HC infections increased the diversity and richness of functional microbial genes. Most alterations in the rumen microbiome composition of infected groups are associated with the suppression of microbes involved in microbial homeostasis maintenance and expansion of the archaeal community in the infected animals. Infection led to an increased abundance of nitrogen, amino acid, protein, and energy metabolism genes. Overall, TC and HC infection increased the enteric methane emission, negatively affected taxon's responsible for maintenance de rumen homeostasis and modulated some important genes related to protein and energy metabolism.
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Affiliation(s)
- Patricia Spoto Corrêa
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Laboratory of Animal Nutrition, Piracicaba, SP, 13400-970, Brazil; University of Florida, Department of Animal Sciences, United States of America, Gainesville, FL, 32611, USA.
| | - Lucas William Mendes
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Laboratory of Molecular Cell Biology, Piracicaba, SP, 13400-970, Brazil
| | - Leandro Nascimento Lemos
- Department of Bioinformatics, National Laboratory of Scientific Computing, Petrópolis, RJ, 25651-076, Brazil
| | - Ana Claudia Koki Sampaio
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Laboratory of Animal Nutrition, Piracicaba, SP, 13400-970, Brazil
| | - Juliano Issakowicz
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Laboratory of Animal Nutrition, Piracicaba, SP, 13400-970, Brazil
| | | | - Siu Mui Tsai
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Laboratory of Molecular Cell Biology, Piracicaba, SP, 13400-970, Brazil
| | - Antonio Pinheiro Faciola
- University of Florida, Department of Animal Sciences, United States of America, Gainesville, FL, 32611, USA
| | - Adibe Luiz Abdalla
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Laboratory of Animal Nutrition, Piracicaba, SP, 13400-970, Brazil
| | - Helder Louvandini
- University of São Paulo, Centre for Nuclear Energy in Agriculture, Laboratory of Animal Nutrition, Piracicaba, SP, 13400-970, Brazil; University of Florida, Department of Animal Sciences, United States of America, Gainesville, FL, 32611, USA
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Ishimoto CK, Aono AH, Nagai JS, Sousa H, Miranda ARL, Melo VMM, Mendes LW, Araujo FF, de Melo WJ, Kuroshu RM, Esposito E, Araujo ASF. Microbial co-occurrence network and its key microorganisms in soil with permanent application of composted tannery sludge. Sci Total Environ 2021; 789:147945. [PMID: 34051496 DOI: 10.1016/j.scitotenv.2021.147945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
Soil microbial communities act on important environmental processes, being sensitive to the application of wastes, mainly those potential contaminants, such as tannery sludge. Due to the microbiome complexity, graph-theoretical approaches have been applied to represent model microbial communities interactions and identify important taxa, mainly in contaminated soils. Herein, we performed network and statistical analyses into microbial 16S rRNA gene sequencing data from soil samples with the application of different levels of composted tannery sludge (CTS) to assess the most connected nodes and the nodes that act as bridges to identify key microbes within each community. The network analysis revealed hubs belonging to Proteobacteria in soil with lower CTS rates, while active degraders of recalcitrant and pollutant chemical hubs belonging to Proteobacteria and Actinobacteria were found in soils under the highest CTS rates. The majority of classified connectors belonged to Actinobacteria, but similarly to hubs taxa, they shifted from metabolic functional profile to taxa with abilities to degrade toxic compounds, revealing a soil perturbation with the CTS application on community organization, which also impacted the community modularity. Members of Actinobacteria and Acidobacteria were identified as both hub and connector suggesting their role as keystone groups. Thus, these results offered us interesting insights about crucial taxa, their response to environmental alterations, and possible implications for the ecosystem.
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Affiliation(s)
| | - Alexandre Hild Aono
- Institute of Science and Technology, Universidade Federal de São Paulo, Brazil
| | - James Shiniti Nagai
- Institute of Science and Technology, Universidade Federal de São Paulo, Brazil
| | - Hério Sousa
- Institute of Science and Technology, Universidade Federal de São Paulo, Brazil
| | | | - Vania Maria Maciel Melo
- Laboratório de Ecologia Microbiana e Biotecnologia, Federal University of Ceara, Fortaleza, CE, (Brazil)
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, SP, (Brazil)
| | | | - Wanderley José de Melo
- Universidade Estadual Paulista, Campus de Jaboticabal, Jaboticabal, SP, Brazil; Universidade Brasil, Descalvado, SP, Brazil
| | | | - Elisa Esposito
- Institute of Science and Technology, Universidade Federal de São Paulo, Brazil
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Virginio Junior GF, Reis ME, da Silva AP, de Toledo AF, Cezar AM, Mendes LW, Greco L, Montenegro H, Coutinho LL, Bittar CMM. Does algae β-glucan affect the fecal bacteriome in dairy calves? PLoS One 2021; 16:e0258069. [PMID: 34591937 PMCID: PMC8483308 DOI: 10.1371/journal.pone.0258069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
β-glucans has been reported to be associated with many health-promoting and improvements in animal performance, however, information about their effects on the bacterial community remains unknown. This study aimed to investigate how the addition of β-glucans can affect the fecal bacterial community with possible consequences on animal growth and health. For this, newborn Holstein calves (n = 14) were individually housed in tropical shelters and blocked according to sex, date, and weight at birth and randomly assigned to one of the following treatments: (1) Control: milk replacer (14% solids, 24% CP, 18.5% fat); (2) β-glucans: milk replacer supplemented with β-glucans (2 g/d). All calves were bucket fed 6 L/d of milk replacer and received water and starter concentrate ad libitum starting on d 2. To evaluate the bacteriome, fecal samples were collected at weeks 1, 2, 4, and 8. The bacterial community was assessed through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. No differences for Shannon and Chao1 indexes were observed for treatments, but both indexes increased with age (P < 0.001). There were dissimilarities in the structure of the bacterial community during the pre-weaning period (P = 0.01). In a deeper taxonomic level, Collinsella (Actinobacteriota), Prevotella (Bacteroidota), and Lactobacillus (Firmicutes) were the most abundant genera (9.84, 9.54, and 8.82% of the sequences, respectively). β-glucans promoted a higher abundance of Alloprevotella and Holdemanella, which may indicate a beneficial effect of supplementation on dairy calves. The bacterial community was highly correlated with the fecal score at weeks 1 and 2 and with starter concentrate intake at week 8. In conclusion, algae β-glucan supplementation could be beneficial to fecal bacteriome and consequently to the health and performance of dairy calves.
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Affiliation(s)
- Gercino Ferreira Virginio Junior
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (GFVJ); (CMMB)
| | - Maria Eduarda Reis
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Ana Paula da Silva
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Ariany Faria de Toledo
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Amanda Moelemberg Cezar
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Leandro Greco
- Kemin Animal Nutrition and Health Division South America, Valinhos, São Paulo, Brazil
| | - Horácio Montenegro
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Carla Maris Machado Bittar
- Department of Animal Science, “Luiz de Queiroz” College of Agriculture, University of Sao Paulo, Piracicaba, São Paulo, Brazil
- * E-mail: (GFVJ); (CMMB)
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Bendia AG, Lemos LN, Mendes LW, Signori CN, Bohannan BJM, Pellizari VH. Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica. Environ Microbiol 2021; 23:4054-4073. [PMID: 34245102 DOI: 10.1111/1462-2920.15649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 11/27/2022]
Abstract
Active volcanoes in Antarctica have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers and active fumaroles, which creates steep gradients that have been shown to affect microbial diversity. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore the metabolic potentials and survival strategies of microbial communities along an extreme temperature gradient in fumarole and glacier sediments on Deception Island. We observed that communities from a 98 °C fumarole were significantly enriched in genes related to hyperthermophilic (e.g. reverse gyrase, GroEL/GroES and thermosome) and oxidative stress responses, as well as genes related to sulfate reduction, ammonification and carbon fixation. Communities from <80 °C fumaroles possessed more genes related osmotic, cold- and heat-shock responses, and diverse metabolic potentials, such as those related to sulfur oxidation and denitrification, while glacier communities showed abundant metabolic potentials mainly related to heterotrophy. Through the reconstruction of genomes, we were able to reveal the metabolic potentials and different survival strategies of underrepresented taxonomic groups, especially those related to Nanoarchaeota, Pyrodictiaceae and thermophilic ammonia-oxidizing archaeal lineages.
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Affiliation(s)
- Amanda Gonçalves Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
| | - Leandro Nascimento Lemos
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Avenida Centenário 303, Piracicaba, SP, CEP 13416-00, Brazil
| | - Lucas William Mendes
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Avenida Centenário 303, Piracicaba, SP, CEP 13416-00, Brazil
| | - Camila Negrão Signori
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
| | - Brendan J M Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Vivian Helena Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo (USP), Praça do Oceanográfico, 191, São Paulo, SP, CEP 05508-120, Brazil
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Mamangkey J, Suryanto D, Munir E, Mustopa AZ, Sibero MT, Mendes LW, Hartanto A, Taniwan S, Ek-Ramos MJ, Harahap A, Verma A, Trihatmoko E, Putranto WS, Pardosi L, Rudia LOAP. Isolation and enzyme bioprospection of bacteria associated to Bruguiera cylindrica, a mangrove plant of North Sumatra, Indonesia. Biotechnol Rep (Amst) 2021; 30:e00617. [PMID: 34026573 PMCID: PMC8121877 DOI: 10.1016/j.btre.2021.e00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 11/05/2020] [Accepted: 04/08/2021] [Indexed: 11/30/2022]
Abstract
Mangrove-associated bacteria are of industrial interest due to their diverse and versatile enzyme properties. This study investigates the culturable bacteria from a wide range of habitat in a Bruguiera cylindrica mangrove ecosystem in North Sumatra. Screening of extracellular hydrolytic enzymes showed multiple potential traits in amylase, cellulase, chitinase, phosphatase, protease, and urease production by bacterial isolates. Molecular identification based on 16S rDNA region of a potential strain, Vibrio alginolyticus Jme3-20 is then reported as a newly proteolytic agent. The strain also showed a stable growth under salinity (NaCl) stress with considerable phosphate solubilization activities. Protease activity was enhanced by optimizing the 0.5 % (w/v) sucrose and soy peptone in the fermentation medium. SDS-PAGE and zymogram analysis showed the presence of a 35-kDa MW protease. Hence, our study revealed important insights into the bacterial diversity and activity in mangrove ecosystems, evidencing the importance of microbial exploration in this ecosystem.
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Affiliation(s)
- Jendri Mamangkey
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Dwi Suryanto
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Erman Munir
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Apon Zaenal Mustopa
- Research Center for Biotechnology, Indonesian Institute of Science, Jl. Raya Bogor Km. 46, Cibinong, West Java, 16911, Indonesia
| | - Mada Triandala Sibero
- Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Jl. Prof. Soedarto S.H., Tembalang, Semarang, 50275, Central Java, Indonesia
- Natural Product Laboratory, Integrated Laboratory for Research and Services, Universitas Diponegoro, Jl. Prof. Soedarto S.H., Tembalang, Semarang, 50275, Central Java, Indonesia
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Adrian Hartanto
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sumatera Utara, Medan, 20155, Indonesia
| | - Steven Taniwan
- Department of Agricultural Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Maria Julissa Ek-Ramos
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, Mexico
| | - Arman Harahap
- Faculty of Teacher Training and Education, Universitas Labuhanbatu, Rantauprapat, Indonesia
| | - Amit Verma
- Department of Biochemistry, College of Basic Science and Humanities, SD Agricultural University, Gujarat, 385506, India
| | - Edy Trihatmoko
- Department of Geography, Universitas Negeri Semarang, Semarang, 50229, Indonesia
| | | | - Lukas Pardosi
- Biology Study Program, Faculty of Agriculture, Universitas Timor, Kefamenanu, 85613, Indonesia
| | - La Ode Adi Parman Rudia
- Faculty of Mathematics and Natural Sciences, Halu Oleo University, Jalan H.E.A. Mokodompit, Kampus Baru, Kampus Hijau Bumi Tridharma Anduonohu, Kendari, 93232, Indonesia
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Lemos LN, Mendes LW, Baldrian P, Pylro VS. Genome-Resolved Metagenomics Is Essential for Unlocking the Microbial Black Box of the Soil. Trends Microbiol 2021; 29:279-282. [PMID: 33551270 DOI: 10.1016/j.tim.2021.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 01/20/2023]
Abstract
Despite several efforts to unravel the microbial diversity of soil, most microbes are still unknown. A recent large-scale effort based on genome-resolved metagenomics by Nayfach et al. has demonstrated how this approach can expand our understanding of novel bacterial lineages, including those from soils. Genomic catalogs of soil microbiomes are now enabling a deeper investigation of the evolutionary and functional role of high-complex soil microbiomes, promoting new knowledge from the reuse and sharing of multi-omics data.
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Affiliation(s)
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Victor Satler Pylro
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic; Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Brazil.
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35
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Navarrete AA, de Cássia Bonassi R, Américo-Pinheiro JHP, Vazquez GH, Mendes LW, de Souza Loureiro E, Kuramae EE, Tsai SM. Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops. Methods Mol Biol 2021; 2232:251-263. [PMID: 33161552 DOI: 10.1007/978-1-0716-1040-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here we describe a suite of methods to identify potential taxonomic and functional soil microbial indicators of soil quality and plant health in biofuel crops in various areas and land types. This approach draws on tools to assess microbial diversity, greenhouse gas fluxes, and soil physicochemical properties in bioenergy cropping systems. Integrative statistical models are then used to identify potential microbial indicators for sustainable management of bioenergy crops.
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Affiliation(s)
- Acacio Aparecido Navarrete
- Graduate Program in Agronomy, Federal University of Mato Grosso do Sul, Chapadão do Sul, MS, Brazil.
- Graduate Program in Environmental Sciences, Brazil University (Universidade Brasil), Fernandópolis, SP, Brazil.
| | - Rita de Cássia Bonassi
- Graduate Program in Environmental Sciences, Brazil University (Universidade Brasil), Fernandópolis, SP, Brazil
| | | | - Gisele Herbst Vazquez
- Graduate Program in Environmental Sciences, Brazil University (Universidade Brasil), Fernandópolis, SP, Brazil
| | - Lucas William Mendes
- Cell and Molecular Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | | | - Eiko Eurya Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Siu Mui Tsai
- Cell and Molecular Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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Nascimento Lemos L, Manoharan L, William Mendes L, Monteiro Venturini A, Satler Pylro V, Tsai SM. Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils. Environ Microbiol Rep 2020; 12:651-655. [PMID: 32815317 DOI: 10.1111/1758-2229.12880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 05/10/2023]
Abstract
Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.
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Affiliation(s)
- Leandro Nascimento Lemos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Lokeshwaran Manoharan
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- National Bioinformatics Infrastructure Sweden (NBIS), Lund University, Lund, Sweden
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Andressa Monteiro Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
| | - Victor Satler Pylro
- Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
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Corrêa PS, Mendes LW, Lemos LN, Crouzoulon P, Niderkorn V, Hoste H, Costa-Júnior LM, Tsai SM, Faciola AP, Abdalla AL, Louvandini H. Tannin supplementation modulates the composition and function of ruminal microbiome in lambs infected with gastrointestinal nematodes. FEMS Microbiol Ecol 2020; 96:5735434. [PMID: 32053145 DOI: 10.1093/femsec/fiaa024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
This study was carried out to evaluate the effects of tannin supplementation on ruminal microbiota of sixteen lambs infected and non-infected with Haemonchus contortus and Trichostrongylus colubriformis. Animals were fed with hay, concentrate and supplemented with Acacia mearnsii (A. mearnsii). The animals were divided into four treatments: two control groups without infection, either receiving A. mearnsii (C+) or not (C-), and two infected groups, one with A. mearnsii (I+) and another without A. mearnsii (I-). Ruminal short-chain fatty acids (SCFA) and metagenome sequencing of ruminal microbiota were used to evaluate the effect of tannin and infection on ruminal microbiome. For SCFA, differences were observed only with A. mearnsii. Total SCFA and acetate molar percentage were decreased in C+ and I+ (P<0.05). Butyrate, valerate and isovalerate were higher in lambs that received A. mearnsii in the diet (P<0.05). The infection changed the microbiome structure and decreased the abundance of butyrate-producing microorganisms. In addition, A. mearnsii supplementation also affected the structure the microbial community, increasing the diversity and abundance of the butyrate-producing and probiotics bacteria, amino acid metabolic pathways, purine, pyrimidine and sphingolipid metabolism. Together, our findings indicate that A. mearnsii supplementation modulates important groups related to nitrogen, amino acid, purine and pyrimidine metabolism, in rumen microbiome, affected by gastrointestinal nematodes infection in lambs.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil.,Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil.,Department of Animal Sciences, University of Florida, Gainesville 32611, United States
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Leandro Nascimento Lemos
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Pierre Crouzoulon
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Vincent Niderkorn
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès Champanelle, France
| | - Hervé Hoste
- INRAE, UMR, Chemin des Capelles - BP 87614 - 31 076 - Toulouse, France
| | - Livio Martins Costa-Júnior
- Biological and Health Center, Federal University of Maranhao, Avenida dos Portugueses, 1966 - Vila Bacanga, 65080-805, São Luís - Maranhao, Brazil
| | - Siu Mui Tsai
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | | | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 13400-970, Piracicaba, SP, Brazil.,Department of Animal Sciences, University of Florida, Gainesville 32611, United States
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Pedrinho A, Mendes LW, Merloti LF, Andreote FD, Tsai SM. The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region. FEMS Microbiol Ecol 2020; 96:5876346. [DOI: 10.1093/femsec/fiaa149] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/23/2020] [Indexed: 12/18/2022] Open
Abstract
ABSTRACT
We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.
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Affiliation(s)
- Alexandre Pedrinho
- Soil Microbiology Laboratory, Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Avenida Padua Dias 11, Piracicaba, Sao Paulo 13418-900, Brazil
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Luis Fernando Merloti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Fernando Dini Andreote
- Soil Microbiology Laboratory, Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Avenida Padua Dias 11, Piracicaba, Sao Paulo 13418-900, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
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Pertile M, Antunes JEL, Araujo FF, Mendes LW, Van den Brink PJ, Araujo ASF. Responses of soil microbial biomass and enzyme activity to herbicides imazethapyr and flumioxazin. Sci Rep 2020; 10:7694. [PMID: 32376948 PMCID: PMC7203139 DOI: 10.1038/s41598-020-64648-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/15/2020] [Indexed: 01/22/2023] Open
Abstract
The use of herbicides is important for controlling weeds in crops. However, they can present impacts on soil properties, such as biological properties. In this study, we evaluated the responses of soil microbial biomass and enzymes activity to the application of the herbicides imazethapyr and flumioxazin and their mixture in an experiment under laboratory conditions, using soils with a different history of use. Soil microbial biomass C (MBC) decreased, while microbial biomass N (MBN) was not affected after the application of the herbicides as compared to the control. Soil respiration, respiratory quotient, and dehydrogenase (DHA) activity increased significantly after the application of the herbicides compared to the control. The hydrolysis of fluorescein diacetate (FDA) was not significantly different between the control and the herbicide treatments. The principal response curve showed the largest initial effects for the flumioxazin, followed by imazethapyr and their mixture. Flumioxazin had a different influence on soil respiration and respiratory quotient than imazethapyr and their mixture. Finally, the effects of herbicides on soil microbial biomass and enzymes are short-term as we observed recovery in the biological parameters over time.
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Affiliation(s)
- Mariane Pertile
- Soil Quality Lab., Agricultural Science Center, Federal University of Piauí, Teresina, PI, Brazil
| | | | | | | | - Paul J Van den Brink
- Wageningen Environmental Research, Wageningen, The Netherlands.,Aquatic Ecology and Water Quality Management Group, Wageningen University, Wageningen, The Netherlands
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Goss-Souza D, Mendes LW, Rodrigues JLM, Tsai SM. Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion. Microb Ecol 2020; 79:110-122. [PMID: 31250077 DOI: 10.1007/s00248-019-01401-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/11/2019] [Indexed: 05/25/2023]
Abstract
Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.
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Affiliation(s)
- Dennis Goss-Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA, 95616, USA
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, SC, 88523-000, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil.
| | - Jorge Luiz Mazza Rodrigues
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA, 95616, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
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Mendes LW, de Chaves MG, Fonseca MDC, Mendes R, Raaijmakers JM, Tsai SM. Resistance Breeding of Common Bean Shapes the Physiology of the Rhizosphere Microbiome. Front Microbiol 2019; 10:2252. [PMID: 31632370 PMCID: PMC6779718 DOI: 10.3389/fmicb.2019.02252] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/17/2019] [Indexed: 12/05/2022] Open
Abstract
The taxonomically diverse rhizosphere microbiome contributes to plant nutrition, growth and health, including protection against soil-borne pathogens. We previously showed that breeding for Fusarium-resistance in common bean changed the rhizosphere microbiome composition and functioning. Here, we assessed the impact of Fusarium-resistance breeding in common bean on microbiome physiology. Combined with metatranscriptome data, community-level physiological profiling by Biolog EcoPlate analyses revealed that the rhizosphere microbiome of the Fusarium-resistant accession was distinctly different from that of the Fusarium-susceptible accession, with higher consumption of amino acids and amines, higher metabolism of xylanase and sialidase, and higher expression of genes associated with nitrogen, phosphorus and iron metabolism. The resistome analysis indicates higher expression of soxR, which is involved in protecting bacteria against oxidative stress induced by a pathogen invasion. These results further support our hypothesis that breeding for resistance has unintentionally shaped the assembly and activity of the rhizobacterial community toward a higher abundance of specific rhizosphere competent bacterial taxa that can provide complementary protection against fungal root infections.
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Affiliation(s)
- Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo, Piracicaba, Brazil.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo, Piracicaba, Brazil
| | - Mariley de Cassia Fonseca
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo, Piracicaba, Brazil
| | | | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo, Piracicaba, Brazil
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Miranda ARL, Mendes LW, Lemos LN, Antunes JEL, Amorim MR, Melo VMM, de Melo WJ, Van den Brink PJ, Araujo ASF. Dynamics of archaeal community in soil with application of composted tannery sludge. Sci Rep 2019; 9:7347. [PMID: 31089146 PMCID: PMC6517401 DOI: 10.1038/s41598-019-43478-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/25/2019] [Indexed: 01/08/2023] Open
Abstract
Application of composted tannery sludge (CTS) could promote a shift in the structure of soil microbial communities. Although the effect of CTS on bacterial community has been studied, it is unclear how the composition and diversity of archaeal community respond to CTS amendment and which environmental factors drive the community over time. Here, we hypothesize that the Archaea structure and composition respond to CTS amendment over the time. CTS had been previously applied annually along 6 years and this assessment occurred for 180 days following the application in the 7th year by using different rates (0, 2.5, 5, 10 and 20 ton ha−1). We used amplicon 16S rRNA sequencing to assess the changes in the structure of the archaeal community. Thaumarchaeota and Euryarchaeota were the most abundant phyla found in soils with application of CTS, with Thaumarchaeota dominating the sequences in all samples with relative abundances of >98%. We observed a decreasing trend on the archaeal diversity over the time with increasing CTS application rate, together with an increase in the community similarity. The redundancy analyses (RDA) explained 43% of the total variation in operational taxonomic units and identified Na, pH, Cr and P as the main drivers of the archaeal community over time after application of highest CTS rates. CTS application changes the structure of Archaea community, with significant increase of Thaumarchaeota and Aenigmarchaeota groups, which can be further explored for its biotechnological use in contaminated soils.
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Affiliation(s)
- Ana Roberta Lima Miranda
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil.
| | | | | | - Jadson Emanuel Lopes Antunes
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | - Marineide Rodrigues Amorim
- Federal University of Piauí, Department of Agricultural Engineering and Soil Science, Teresina, 64049-550, Brazil
| | | | - Wanderley Jose de Melo
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Path of Access Prof. Paulo Donato Castellane, Km 5, Postal Code: 14884-900, Jaboticabal, SP, Brazil.,University of Brazil: University campus Descalvado - Hilário da Silva Passos Avenue, 950 - University park, Descalvado, SP, Brazil
| | - Paul J Van den Brink
- Wageningen University, Aquatic Ecology and Water Quality Management Group, P.O. Box 47, 6700 AA, Wageningen, The Netherlands.,Wageningen Environmental Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
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Goss-Souza D, Mendes LW, Borges CD, Rodrigues JLM, Tsai SM. Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept. FEMS Microbiol Ecol 2019; 95:fiz009. [PMID: 30715365 DOI: 10.1093/femsec/fiz009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/31/2019] [Indexed: 12/17/2023] Open
Abstract
The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due to liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till cropping culminated in a decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in the rhizosphere than in bulk soil, regardless of the time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense, while functions related to nucleic acids metabolism increased. Functions in the soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that the soybean root system selects microbial taxa via trade-offs, to maintain functional resilience in the rhizosphere microbiome over time.
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Affiliation(s)
- Dennis Goss-Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
- Department of Soils and Natural Resources, Santa Catarina State University, Lages, SC 88523-000, Brazil
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Clovis Daniel Borges
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jorge L M Rodrigues
- Department of Land, Air and Water Resources, University of California - Davis, Davis, CA 95616, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400-970, Brazil
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Pedrinho A, Mendes LW, Merloti LF, da Fonseca MDC, Cannavan FDS, Tsai SM. Forest-to-pasture conversion and recovery based on assessment of microbial communities in Eastern Amazon rainforest. FEMS Microbiol Ecol 2018; 95:5245175. [DOI: 10.1093/femsec/fiy236] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/12/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alexandre Pedrinho
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Luis Fernando Merloti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Mariley de Cassia da Fonseca
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Fabiana de Souza Cannavan
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
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Suleiman AKA, Lourenço KS, Pitombo LM, Mendes LW, Roesch LFW, Pijl A, Carmo JB, Cantarella H, Kuramae EE. Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N 2O emissions. Sci Total Environ 2018; 631-632:1089-1099. [PMID: 29727935 DOI: 10.1016/j.scitotenv.2018.03.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/10/2018] [Accepted: 03/10/2018] [Indexed: 06/08/2023]
Abstract
Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N2O) emissions. The experimental sugarcane field had the following treatments: (I) control with nitrogen, phosphorus, and potassium (NPK), (II) sugarcane straw with NPK, (III) vinasse (by-product of ethanol industry) with NP, and (IV) vinasse plus sugarcane straw with NP. Soil samples were collected on days 1, 3, 6, 11, 24 and 46 of the experiment for DNA extraction and metagenome sequencing. N2O emissions were also measured. Treatments with straw and vinasse residues induced changes in soil microbial composition and potential functions. The change in the microbial community was highest in the treatments with straw addition with functions related to decomposition of different ranges of C-compounds overrepresented while in vinasse treatment, the functions related to spore-producing microorganisms were overrepresented. Furthermore, all additional residues increased microorganisms related to the nitrogen metabolism and vinasse with straw had a synergetic effect on the highest N2O emissions. The results highlight the importance of residues and fertiliser management in sustainable agriculture.
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Affiliation(s)
- Afnan Khalil Ahmad Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil; Institute of Biology Leiden, Leiden University, Netherlands
| | - Leonardo Machado Pitombo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), Rod. João Leme dos Santos Km 110, 18052-780 Sorocaba, SP, Brazil
| | - Lucas William Mendes
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Luiz Fernando Wurdig Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, 97300-000 São Gabriel, Brazil
| | - Agata Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Janaína Braga Carmo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), Rod. João Leme dos Santos Km 110, 18052-780 Sorocaba, SP, Brazil
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.
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46
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Mendes LW, Raaijmakers JM, de Hollander M, Mendes R, Tsai SM. Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME J 2018; 12:212-224. [PMID: 29028000 PMCID: PMC5739014 DOI: 10.1038/ismej.2017.158] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 06/21/2017] [Accepted: 06/24/2017] [Indexed: 01/16/2023]
Abstract
The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance. Pseudomonadaceae, bacillaceae, solibacteraceae and cytophagaceae were more abundant in the rhizosphere of the Fox-resistant cultivar. Network analyses showed a modular topology of the rhizosphere microbiome of the Fox-resistant cultivar, suggesting a more complex and highly connected bacterial community than in the rhizosphere of the Fox-susceptible cultivar. Metagenome analyses further revealed that specific functional traits such as protein secretion systems and biosynthesis genes of antifungal phenazines and rhamnolipids were more abundant in the rhizobacterial community of the Fox-resistant cultivar. Our findings suggest that breeding for Fox resistance in common bean may have co-selected for other unknown plant traits that support a higher abundance of specific beneficial bacterial families in the rhizosphere with functional traits that reinforce the first line of defense.
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Affiliation(s)
- Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
| | | | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, Brazil
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47
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Goss-Souza D, Mendes LW, Borges CD, Baretta D, Tsai SM, Rodrigues JLM. Soil microbial community dynamics and assembly under long-term land use change. FEMS Microbiol Ecol 2017; 93:4102335. [DOI: 10.1093/femsec/fix109] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/31/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Dennis Goss-Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
- Applied Ecology Graduate Program, Luiz de Queiroz School of Agriculture, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
- Department of Land, Air and Water Resources, University of California – Davis, Davis, CA 95616, USA
| | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
| | - Clovis Daniel Borges
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
- Applied Ecology Graduate Program, Luiz de Queiroz School of Agriculture, University of São Paulo, Piracicaba, SP, 13418–900, Brazil
| | - Dilmar Baretta
- Department of Soils and Sustainability, Santa Catarina State University, Chapecó, SC, 89815-630, Brazil
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13400–970, Brazil
| | - Jorge L. M. Rodrigues
- Department of Land, Air and Water Resources, University of California – Davis, Davis, CA 95616, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Mendes LW, Braga LPP, Navarrete AA, Souza DGD, Silva GGZ, Tsai SM. Using Metagenomics to Connect Microbial Community Biodiversity and Functions. Curr Issues Mol Biol 2017; 24:103-118. [PMID: 28686570 DOI: 10.21775/cimb.024.103] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Microbes constitute about a third of the Earth's biomass and are composed by an enormous genetic diversity. In a majority of environments the microbial communities play crucial roles for the ecosystem functioning, where a drastic biodiversity alteration or loss could lead to negative effects on the environment and sustainability. A central goal in microbiome studies is to elucidate the relation between microbial diversity to functions. A better understanding of the relation diversity-function would increase the ability to manipulate that diversity to improve plant and animal health and also setting conservation priorities. The recent advances in genomic methodologies in microbial ecology have provide means to assess highly complex communities in detail, making possible the link between diversity and the functions performed by the microbes. In this work we first explore some advances in bioinformatics tools to connect the microbial community biodiversity to their potential metabolism and after present some examples of how this information can be useful for a better understanding of the microbial role in the environment.
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Affiliation(s)
- Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
| | - Lucas Peres Palma Braga
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
| | - Acacio Aparecido Navarrete
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
| | - Dennis Goss de Souza
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
| | | | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of São Paulo USP, Piracicaba, SP, Brazil
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Val-Moraes SP, de Macedo HS, Kishi LT, Pereira RM, Navarrete AA, Mendes LW, de Figueiredo EB, La Scala N, Tsai SM, de Macedo Lemos EG, Alves LMC. Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil. Antonie Van Leeuwenhoek 2016; 109:1643-1654. [PMID: 27629424 DOI: 10.1007/s10482-016-0764-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/31/2016] [Indexed: 01/12/2023]
Abstract
Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.
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Affiliation(s)
- Silvana Pompeia Val-Moraes
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil.
| | - Helena Suleiman de Macedo
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Luciano Takeshi Kishi
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Rodrigo Matheus Pereira
- Faculdade de Ciências Biológicas e Ambientais FCBA, Universidade Federal da Grande Dourados UFGD, Rodovia Dourados, Itahum, Km 12 - Unidade II, Caixa Postal: 364, Dourados, MS, CEP 79804-970, Brazil
| | - Acacio Aparecido Navarrete
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Av. Centenário, 303, Caixa Postal 96, Piracicaba, SP, CEP 13400-970, Brazil
| | - Lucas William Mendes
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Av. Centenário, 303, Caixa Postal 96, Piracicaba, SP, CEP 13400-970, Brazil
| | - Eduardo Barretto de Figueiredo
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Newton La Scala
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Siu Mui Tsai
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Av. Centenário, 303, Caixa Postal 96, Piracicaba, SP, CEP 13400-970, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil
| | - Lúcia Maria Carareto Alves
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinária FCAV, Univ. Estadual Paulista UNESP, Acesso Prof. Dr. Paulo Donato Castellane, S/N, Jaboticabal, SP, 14884-900, Brazil.
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Tripathi BM, Edwards DP, Mendes LW, Kim M, Dong K, Kim H, Adams JM. The impact of tropical forest logging and oil palm agriculture on the soil microbiome. Mol Ecol 2016; 25:2244-57. [PMID: 26994316 DOI: 10.1111/mec.13620] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/19/2015] [Accepted: 01/19/2016] [Indexed: 01/30/2023]
Abstract
Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.
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Affiliation(s)
- Binu M Tripathi
- Department of Biological Science, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.,Arctic Research Center, Korea Polar Research Institute, Incheon, 406-840, Korea
| | - David P Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo - USP. Av. Centenário, 303, CEP 13400-970 Piracicaba (SP), Brazil.,Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen 6708 PB, The Netherlands
| | - Mincheol Kim
- Arctic Research Center, Korea Polar Research Institute, Incheon, 406-840, Korea
| | - Ke Dong
- Department of Biological Science, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea
| | - Hyoki Kim
- Celemics Inc., 19F, Bldg. A, BYC High city, 131, Gasandigital 1-ro, Geumcheon-gu, Seoul, 153-718, Korea
| | - Jonathan M Adams
- Department of Biological Science, College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea
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