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Vilela CLS, Peixoto RS, Rachid CTCDC, Bassin JP. Assessing the impact of synthetic estrogen on the microbiome of aerated submerged fixed-film reactors simulating tertiary sewage treatment and isolation of estrogen-degrading consortium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140428. [PMID: 32763724 DOI: 10.1016/j.scitotenv.2020.140428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
17α-ethinylestradiol (EE2) is a synthetic estrogen that can cause harmful effects on animals, such as male feminization and infertility. However, the impact of the EE2 contamination on microbial communities and the potential role of bacterial strains as bioremediation agents are underexplored. The aim of this work was to evaluate the impact of EE2 on the microbial community dynamics of aerated submerged fixed-film reactors (ASFFR) simulating a polishing step downstream of a secondary sewage treatment. For this purpose, the reactors were fed with a synthetic medium with low COD content (around 50 mg l-1), supplemented (reactor H) or not (reactor C) with 1 μg l-1 of EE2. Sludge samples were periodically collected during the bioreactors operation to assess the bacterial profile over time by 16S rRNA gene amplicon sequencing or by bacterial isolation using culture-dependent approach. The results revealed that the most abundant phyla in both reactors were Proteobacteria and Bacteroidetes. At genus level, Chitinophagaceae, Nitrosomonas and Bdellovibrio predominated. Significant effects caused by EE2 treatment and bioreactors operating time were observed by non-metric multidimensional scaling. Therefore, even at low concentrations as 1 μg l-1, EE2 is capable of influencing the bioreactor microbiome. Culture-dependent methods showed that six bacterial isolates, closely related to Pseudomonas and Acinetobacter genera, could grow on EE2 as the sole carbon source under aerobic conditions. These organisms may potentially be used for the assembly of an EE2-degrading bacterial consortium and further exploited for bioremediation applications, including tertiary sewage treatment to remove hormone-related compounds not metabolized in secondary depuration stages.
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Affiliation(s)
- Caren Leite Spindola Vilela
- Department of General Microbiology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Department of General Microbiology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Caio Tavora Coelho da Costa Rachid
- Department of General Microbiology, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - João Paulo Bassin
- Chemical Engineering Program, COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Sarto MVM, Borges WLB, Bassegio D, Pires CAB, Rice CW, Rosolem CA. Soil microbial community, enzyme activity, C and N stocks and soil aggregation as affected by land use and soil depth in a tropical climate region of Brazil. Arch Microbiol 2020; 202:2809-2824. [PMID: 32747999 DOI: 10.1007/s00203-020-01996-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/28/2020] [Accepted: 07/22/2020] [Indexed: 11/24/2022]
Abstract
The impact of agricultural land-use on soil microbial community composition and enzyme activity has not been extensively investigated in Ultisols. We investigated soil health parameters by analyzing phospholipid fatty acids (PLFAs), extracellular enzyme activity, C and N stocks, and soil structure. Four land uses were established in a tropical climate region of Brazil: native Cerrado (savanna), monoculture pasture [Urochloa brizantha (Hochst. Ex A. Rich.) R. Webster 'Marandu'], an integrated crop-livestock system (ICLS), and maize (Zea mays)-fallow in a no-tillage system. Soil microbial biomass was 40% higher in the native Cerrado than in the monoculture pasture, ICLS, and no-tillage maize. Soil organic carbon was positively correlated with microbial community composition (MB; gram-; AC; AMF; Fungi; F: B ratio) and enzyme activity (bG, AP, NAG). Large macroaggregates were positively correlated with bG, AP, and AMF. In summary, the native Cerrado had a higher level of carbon at the soil surface and greater soil structure with increased microbial biomass, gram+ bacteria, AMF, fungi, and F:B ratio in a tropical region of Brazil. However, bG and AP enzyme activities were lower in the ICLS and no-till maize at the soil surface (0-5 cm) compared to the native Cerrado. The conversion of native Cerrado to agricultural systems shifted the soil microbial community composition, enzyme activity, C and N, and soil structure of this sandy soil of the Brazilian Cerrado.
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Affiliation(s)
- Marcos V M Sarto
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA. .,, 1712 Claflin Rd, Manhattan, KS, 66502, USA.
| | - Wander L B Borges
- Advanced Research Center of Rubber Tree and Agroforestry Systems, Agronomic Institute/IAC, Votuporanga, SP, Brazil
| | - Doglas Bassegio
- Western Parana State University, UNIOESTE, Cascavel, PR, CEP 85819-130, Brazil
| | - Carlos A B Pires
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Charles W Rice
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Ciro A Rosolem
- São Paulo State University, UNESP, Av. Universitária 3780, Botucatu, SP, CEP 18610-034, Brazil
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Short-term impacts of management practices on soil properties under maize cultivation in Akure, Ondo State, Nigeria. SCIENTIFIC AFRICAN 2019. [DOI: 10.1016/j.sciaf.2019.e00129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Armada E, Leite MFA, Medina A, Azcón R, Kuramae EE. Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome. FEMS Microbiol Ecol 2018; 94:4996783. [DOI: 10.1093/femsec/fiy092] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/13/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Elisabeth Armada
- Estación Experimental del Zaidín, CSIC, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Prof. Albareda 1, 18008, Granada, Spain
| | - Márcio F A Leite
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Leiden University, Department of Biology, Leiden, 2311 EZ, The Netherlands
- Maranhão State University (UEMA), department of Agroecology, São Luís, Brazil
| | - Almudena Medina
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Rosario Azcón
- Estación Experimental del Zaidín, CSIC, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Prof. Albareda 1, 18008, Granada, Spain
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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Peixoto RS, Rosado PM, Leite DCDA, Rosado AS, Bourne DG. Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience. Front Microbiol 2017; 8:341. [PMID: 28326066 PMCID: PMC5339234 DOI: 10.3389/fmicb.2017.00341] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental "probiotics" to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.
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Affiliation(s)
- Raquel S. Peixoto
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - Phillipe M. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | | | - Alexandre S. Rosado
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
- Instituto Museu Aquário Marinho do Rio de Janeiro-AquaRio (IMAM/AquaRio) – Rio de Janeiro Marine Aquarium Research CenterRio de Janeiro, Brazil
| | - David G. Bourne
- College of Science and Engineering, James Cook University, TownsvilleQLD, Australia
- Australian Institute of Marine Science, TownsvilleQLD, Australia
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Maxwel AA, Karina TMG, Andréia OS, Rosane FS. Microbial community structure and chemical composition from dark earth in a native archaeological site of the lower Amazon. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajmr2016.8218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Souza RC, Mendes IC, Reis-Junior FB, Carvalho FM, Nogueira MA, Vasconcelos ATR, Vicente VA, Hungria M. Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado? BMC Microbiol 2016; 16:42. [PMID: 26983403 PMCID: PMC4794851 DOI: 10.1186/s12866-016-0657-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/02/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. RESULTS Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. CONCLUSION High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most efficient for some functions. Our results highlight that underneath the rustic appearance of the Cerrado vegetation there is a fragile soil microbial community.
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Affiliation(s)
- Renata Carolini Souza
- />Embrapa Soja, Soil Biotechnology, C.P. 231, 86001-970 Londrina, PR Brazil
- />Department Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990 Curitiba, PR Brazil
| | - Iêda Carvalho Mendes
- />Embrapa Cerrado, Soil Microbiology, C.P. 08223, 73301-970 Planaltina, DF Brazil
| | | | | | | | | | - Vânia Aparecida Vicente
- />Department Microbiology, Universidade Federal do Paraná, C.P. 19031, 81531-990 Curitiba, PR Brazil
| | - Mariangela Hungria
- />Embrapa Soja, Soil Biotechnology, C.P. 231, 86001-970 Londrina, PR Brazil
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Rachid CTCC, Pires CA, Leite DCA, Coutinho HLC, Peixoto RS, Rosado AS, Salton J, Zanatta JA, Mercante FM, Angelini GAR, Balieiro FDC. Sugarcane trash levels in soil affects the fungi but not bacteria in a short-term field experiment. Braz J Microbiol 2016; 47:322-6. [PMID: 26991293 PMCID: PMC4874680 DOI: 10.1016/j.bjm.2016.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/10/2015] [Indexed: 11/29/2022] Open
Abstract
The sugarcane in Brazil is passing through a management transition that is leading to the abolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is generated, and there is a discussion regarding the utilization of this biomass in the industry versus keeping it in the field to improve soil quality. To study the effects of the trash removal on soil quality, we established an experimental sugarcane plantation with different levels of trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed the structure of the bacterial and fungal community as the bioindicators of impacts. The soil DNA was extracted, and the microbial community was screened by denaturing gradient gel electrophoresis in two different seasons. Our results suggest that there are no effects from the different levels of trash on the soil chemistry and soil bacterial community. However, the fungal community was significantly impacted, and after twelve months, the community presented different structures among the treatments.
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Affiliation(s)
- C T C C Rachid
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - C A Pires
- Embrapa Solos, Rio de Janeiro, Brazil; Federal Rural University of Rio de Janeiro, Seropédica, Brazil
| | - D C A Leite
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - R S Peixoto
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A S Rosado
- Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - J Salton
- Embrapa Agropecuária Oeste, Dourados, Brazil
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Pessoa-Filho M, Barreto CC, dos Reis Junior FB, Fragoso RR, Costa FS, de Carvalho Mendes I, de Andrade LRM. Microbiological functioning, diversity, and structure of bacterial communities in ultramafic soils from a tropical savanna. Antonie van Leeuwenhoek 2015; 107:935-49. [PMID: 25616909 DOI: 10.1007/s10482-015-0386-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 01/13/2015] [Indexed: 12/01/2022]
Abstract
Ultramafic soils are characterized by high levels of metals, and have been studied because of their geochemistry and its relation to their biological component. This study evaluated soil microbiological functioning (SMF), richness, diversity, and structure of bacterial communities from two ultramafic soils and from a non-ultramafic soil in the Brazilian Cerrado, a tropical savanna. SMF was represented according to simultaneous analysis of microbial biomass C (MBC) and activities of the enzymes β-glucosidase, acid phosphomonoesterase and arylsulfatase, linked to the C, P and S cycles. Bacterial community diversity and structure were studied by sequencing of 16S rRNA gene clone libraries. MBC and enzyme activities were not affected by high Ni contents. Changes in SMF were more related to the organic matter content of soils (SOM) than to their available Ni. Phylogeny-based methods detected qualitative and quantitative differences in pairwise comparisons of bacterial community structures of the three sites. However, no correlations between community structure differences and SOM or SMF were detected. We believe this work presents benchmark information on SMF, diversity, and structure of bacterial communities for a unique type of environment within the Cerrado biome.
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Lisboa FJG, Peres-Neto PR, Chaer GM, Jesus EDC, Mitchell RJ, Chapman SJ, Berbara RLL. Much beyond Mantel: bringing Procrustes association metric to the plant and soil ecologist's toolbox. PLoS One 2014; 9:e101238. [PMID: 24971901 PMCID: PMC4074130 DOI: 10.1371/journal.pone.0101238] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022] Open
Abstract
The correlation of multivariate data is a common task in investigations of soil biology and in ecology in general. Procrustes analysis and the Mantel test are two approaches that often meet this objective and are considered analogous in many situations especially when used as a statistical test to assess the statistical significance between multivariate data tables. Here we call the attention of ecologists to the advantages of a less familiar application of the Procrustean framework, namely the Procrustean association metric (a vector of Procrustean residuals). These residuals represent differences in fit between multivariate data tables regarding homologous observations (e.g., sampling sites) that can be used to estimate local levels of association (e.g., some groups of sites are more similar in their association between biotic and environmental features than other groups of sites). Given that in the Mantel framework, multivariate information is translated into a pairwise distance matrix, we lose the ability to contrast homologous data points across dimensions and data matrices after their fit. In this paper, we attempt to familiarize ecologists with the benefits of using these Procrustean residual differences to further gain insights about the processes underlying the association among multivariate data tables using real and hypothetical examples.
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Affiliation(s)
- Francy Junio Gonçalves Lisboa
- Soil Science Department, Agronomy Institute, Federal Rural University of Rio de Janeiro, Seropédica-RJ, Brazil
- The James Hutton Institute, Craigiebuckler, Aberdeen, United Kingdom
| | - Pedro R. Peres-Neto
- Canada Research Chair in Spatial Modelling and Biodiversity; Université du Québec à Montréal, Département des sciences biologiques, Québec, Canada
| | | | | | - Ruth Joy Mitchell
- The James Hutton Institute, Craigiebuckler, Aberdeen, United Kingdom
| | | | - Ricardo Luis Louro Berbara
- Soil Science Department, Agronomy Institute, Federal Rural University of Rio de Janeiro, Seropédica-RJ, Brazil
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Rampelotto PH, de Siqueira Ferreira A, Barboza ADM, Roesch LFW. Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems. MICROBIAL ECOLOGY 2013; 66:593-607. [PMID: 23624541 DOI: 10.1007/s00248-013-0235-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/15/2013] [Indexed: 05/10/2023]
Abstract
The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.
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Affiliation(s)
- Pabulo Henrique Rampelotto
- Universidade Federal do Pampa, Campus São Gabriel-Av. Antônio Trilha, no 1847, 97300-000, São Gabriel, RS, Brazil
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Jorquera MA, Martínez OA, Marileo LG, Acuña JJ, Saggar S, Mora ML. Effect of nitrogen and phosphorus fertilization on the composition of rhizobacterial communities of two Chilean Andisol pastures. World J Microbiol Biotechnol 2013; 30:99-107. [PMID: 23842756 DOI: 10.1007/s11274-013-1427-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 07/03/2013] [Indexed: 11/28/2022]
Abstract
The effect of nitrogen (N) and phosphorus (P) fertilization on composition of rhizobacterial communities of volcanic soils (Andisols) from southern Chile at molecular level is poorly understood. This paper investigates the composition of rhizobacterial communities of two Andisols under pasture after 1- and 6-year applications of N (urea) and P (triple superphosphate). Soil samples were collected from two previously established sites and the composition of rhizobacterial communities was determined by denaturing gradient gel electrophoresis (PCR-DGGE). The difference in the composition and diversity between rhizobacterial communities was assessed by nonmetric multidimensional scaling (MDS) analysis and the Shannon-Wiener index. In Site 1 (fertilized for 1 year), PCR-DGGE targeting 16S rRNA genes and MDS analysis showed that moderate N application (270 kg N ha(-1) year(-1)) without P significantly changed the composition of rhizobacterial communities. However, no significant community changes were observed with P (240 kg P ha(-1) year(-1)) and N-P application (270 kg N ha(-1) year(-1) plus 240 kg P ha(-1) year(-1)). In Site 2 (fertilized for 6 years with P; 400 kg P ha(-1) year(-1)), PCR-DGGE targeting rpoB, nifH, amoA and alkaline phosphatase genes and MDS analysis showed changes in rhizobacterial communities only at the highest rate of N application (600 kg N ha(-1) year(-1)). Quantitative PCR targeting 16S rRNA genes also showed higher abundance of bacteria at higher N application. In samples from both sites, the Shannon-Wiener index did not show significant difference in the diversity of rhizobacterial communities. The changes observed in rhizobacterial communities coincide in N fertilized pastures with lower soil pH and higher pasture yields. This study indicates that N-P application affects the soil bacterial populations at molecular level and needs to be considered when developing fertilizer practices for Chilean pastoral Andisols.
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Affiliation(s)
- Milko A Jorquera
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Ave. Francisco Salazar, 01145, Temuco, Chile,
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Ding GC, Piceno YM, Heuer H, Weinert N, Dohrmann AB, Carrillo A, Andersen GL, Castellanos T, Tebbe CC, Smalla K. Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem. PLoS One 2013; 8:e59497. [PMID: 23527207 PMCID: PMC3603937 DOI: 10.1371/journal.pone.0059497] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/14/2013] [Indexed: 12/31/2022] Open
Abstract
Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years) of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE) analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes) correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.
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Affiliation(s)
- Guo-Chun Ding
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Yvette M. Piceno
- Department of Ecology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Nicole Weinert
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
| | - Anja B. Dohrmann
- Institute for Biodiversity, Johann Heinrich von Thünen-Institut (TI), Braunschweig, Germany
| | - Angel Carrillo
- Centro de Investigaciones biologicas del Noroeste, S.C. La Paz, Mexico
| | - Gary L. Andersen
- Department of Ecology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | | | - Christoph C. Tebbe
- Institute for Biodiversity, Johann Heinrich von Thünen-Institut (TI), Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics - Federal Research Centre for Cultivated Plants (JKI), Braunschweig, Germany
- * E-mail:
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Brazilian Cerrado soil Actinobacteria ecology. BIOMED RESEARCH INTERNATIONAL 2013; 2013:503805. [PMID: 23555089 PMCID: PMC3595109 DOI: 10.1155/2013/503805] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 12/04/2012] [Accepted: 12/19/2012] [Indexed: 11/30/2022]
Abstract
A total of 2152 Actinobacteria strains were isolated from native Cerrado (Brazilian Savannah) soils located in Passos, Luminárias, and Arcos municipalities (Minas Gerais State, Brazil). The soils were characterised for chemical and microbiological analysis. The microbial analysis led to the identification of nine genera (Streptomyces, Arthrobacter, Rhodococcus, Amycolatopsis, Microbacterium, Frankia, Leifsonia, Nakamurella, and Kitasatospora) and 92 distinct species in both seasons studied (rainy and dry). The rainy season produced a high microbial population of all the aforementioned genera. The pH values of the soil samples from the Passos, Luminárias, and Arcos regions varied from 4.1 to 5.5. There were no significant differences in the concentrations of phosphorus, magnesium, and organic matter in the soils among the studied areas. Samples from the Arcos area contained large amounts of aluminium in the rainy season and both hydrogen and aluminium in the rainy and dry seasons. The Actinobacteria population seemed to be unaffected by the high levels of aluminium in the soil. Studies are being conducted to produce bioactive compounds from Actinobacteria fermentations on different substrates. The present data suggest that the number and diversity of Actinobacteria spp. in tropical soils represent a vast unexplored resource for the biotechnology of bioactives production.
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Araujo JF, de Castro AP, Costa MMC, Togawa RC, Júnior GJP, Quirino BF, Bustamante MMC, Williamson L, Handelsman J, Krüger RH. Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance. MICROBIAL ECOLOGY 2012; 64:760-770. [PMID: 22570118 DOI: 10.1007/s00248-012-0057-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 04/10/2012] [Indexed: 05/31/2023]
Abstract
The Brazilian Cerrado is the second largest biome in Brazil and is considered a biodiversity hotspot. In this work, we compared the bacterial communities in Cerrado soil associated with four types of native vegetation (Cerrado Denso, Cerrado sensu stricto, Campo Sujo, and Mata de Galeria) by ribosomal RNA intergenic spacer analysis, terminal fragment restriction length polymorphism and pyrosequencing. The fingerprinting results were very similar. The bacterial communities of Cerrado Denso and Cerrado sensu stricto grouped together and were distinct from those in Campo Sujo and Mata de Galeria. Pyrosequencing generated approximately 40,000 16S rRNA gene sequences per sample and allowed the identification of 17 phyla in soil samples under Cerrado vegetation. Acidobacteria were dominant in all areas studied with a relative frequency of 40-47 %, followed closely by Proteobacteria accounting for 34-40 % of the sequences. Results from all molecular techniques used suggested that the bacterial communities of Cerrado sensu stricto and Cerrado Denso are very similar to each other, while Campo Sujo forms a separate group, and Mata de Galeria is the most distinct with higher species richness. This is the first extensive study of native Cerrado soil microbiota, an important but endangered biome.
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Affiliation(s)
- Janaina F Araujo
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasilia, Federal District, Brazil
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Rachid CTCC, Piccolo MC, Leite DCA, Balieiro FC, Coutinho HLC, van Elsas JD, Peixoto RS, Rosado AS. Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems. BMC Microbiol 2012; 12:170. [PMID: 22873209 PMCID: PMC3438109 DOI: 10.1186/1471-2180-12-170] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 07/19/2012] [Indexed: 11/23/2022] Open
Abstract
Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.
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Affiliation(s)
- Caio T C C Rachid
- Center for Nuclear Energy in Agriculture, Universidade de São Paulo, Piracicaba, Brazil.
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dos Santos HF, Cury JC, do Carmo FL, dos Santos AL, Tiedje J, van Elsas JD, Rosado AS, Peixoto RS. Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution. PLoS One 2011; 6:e16943. [PMID: 21399677 PMCID: PMC3047533 DOI: 10.1371/journal.pone.0016943] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 01/17/2011] [Indexed: 11/30/2022] Open
Abstract
Background Mangroves are transitional coastal ecosystems in tropical and sub-tropical regions and represent biologically important and productive ecosystems. Despite their great ecological and economic importance, mangroves are often situated in areas of high anthropogenic influence, being exposed to pollutants, such as those released by oil spills. Methodology/Principal Findings A microcosm experiment was conducted, which simulated an oil spill in previously pristine mangrove sediment. The effect of the oil spill on the extant microbial community was studied using direct pyrosequencing. Extensive bacterial diversity was observed in the pristine mangrove sediment, even after oil contamination. The number of different OTUs only detected in contaminated samples was significantly higher than the number of OTUs only detected in non-contaminated samples. The phylum Proteobacteria, in particular the classes Gammaproteobacteria and Deltaproteobacteria, were prevalent before and after the simulated oil spill. On the other hand, the order Chromatiales and the genus Haliea decreased upon exposure to 2 and 5% oil, these are proposed as sensitive indicators of oil contamination. Three other genera, Marinobacterium, Marinobacter and Cycloclasticus increased their prevalence when confronted with oil. These groups are possible targets for the biomonitoring of the impact of oil in mangrove settings. Conclusions/Significance We suggest the use of sequences of the selected genera as proxies for oil pollution, using qPCR assessments. The quantification of these genera in distinct mangrove systems in relation to the local oil levels would permit the evaluation of the level of perturbance of mangroves, being useful in field monitoring. Considering the importance of mangroves to many other environments and the susceptibility of such areas to oil spills this manuscript will be of broad interest.
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Affiliation(s)
- Henrique Fragoso dos Santos
- Laboratory of Molecular Microbial Ecology, Departamento of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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