Quantitative analysis of Terminal Restriction Fragment Length Polymorphism (T-RFLP) microbial community profiles: peak height data showed to be more reproducible than peak area

Caffaro-Filho, Roberto A.; Fantinatti-Garboggini, Fabiana; Durrant, Lúcia Regina

doi:10.1590/s1517-83822007000400027

Cited by 5 publications

(3 citation statements)

References 16 publications

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“…The determination of microbial load was carried out by following the terminal restriction fragment length polymorphism (T-RFLP) method described by Caffaro-Filho et al [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

Effect of Dietary Supplementation of Immunobiotic Lactiplantibacillusplantarum N14 Fermented Rakkyo (Allium chinense) Pickled Juice on the Immunocompetence and Production Performance of Pigs

Islam

Hashiguchi²,

Kober

et al. 2021

Animals

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Rakkyo (Allium chinense), is a Japanese leek that is primarily used to make a popular sweet or sour pickled dish. Lactic acid bacteria are often involved in the preparation steps of fermented pickles, which helps in the effective preservation of the natural bioactive compounds of fruits and vegetable, and thereby exert several health benefits including immunomodulation and growth performance. This work aimed to evaluate the in vivo effects of adding Lactiplantibacillus plantarum N14 fermented rakkyo pickled juice as feed supplement on the immunocompetence and production performance of pigs. We first analyzed the nutritional composition, which revealed that the proportion of protein, lipid, and water-soluble fiber content were estimated as of 4%, 5%, and 5% in rakkyo residual liquid or juice, while 22%, 15% and 14%, respectively, were estimated in rakkyo residual powder. For the in vivo feeding trials, three groups of pigs were treated either with 5%, 20%, or 40% mixture (v/v) of fermented rakkyo pickled juice and the grinded residual liquid supplemented in the drinking water in addition to standard feed. The results of the feeding trials showed that the administration of a juice mixture of 5% or 20% (fermented pickled juice and residual liquid) had a similar trend of effects in improving the complement activity, phagocytic activity and leucocytes counts in the peripheral blood when compared to pigs fed with 40% mixture or untreated controls. Those changes were related to an improved resistance to enteric infections. Moreover, animals receiving a mixture of fermented pickled juice and fermented rakkyo residues had a higher growth rate and carcass quality than controls. The results suggested that the use of 5% mixture of fermented rakkyo pickled juice and the residual liquid through drinking water could be a cost-effective approach to promote the immune-health and production performance of pigs. This approach would contribute not only to the sustainable management of food wastes but also to the application of a value-added feed supplement for the promotion of animal health and production.

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“…The determination of microbial load was carried out by following the terminal restriction fragment length polymorphism (T-RFLP) method described by Caffaro-Filho et al [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

Effect of Dietary Supplementation of Immunobiotic Lactiplantibacillusplantarum N14 Fermented Rakkyo (Allium chinense) Pickled Juice on the Immunocompetence and Production Performance of Pigs

Islam

Hashiguchi²,

Kober

et al. 2021

Animals

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“…All sub-subplots had a part without application of glyphosate to follow the aerial biomass production of CC up to the grain-filling phenological stage. The space between main plots represents an internal path of the experiment enzyme inactivation by heating for 15 min at 65 C, samples were sent to Macrogen, Korea, for the GeneScan Service using the GS1200LIZ DNA fragment length standard (Applied Biosystems™) to assess the length of fluorescently labelled terminal restriction fragments (T-RFs) (Caffaro-Filho, Fantinatti-Garboggini, & Durrant, 2007;Cooper & Rao, 2006).…”

Section: Analysis Of Structural Diversitymentioning

confidence: 99%

Impact of management of cover crop–soybean agroecosystems on rhizosphere microbial communities

Ortega

Vásquez²,

Alba³

et al. 2020

European J Soil Science

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Knowledge of the rhizosphere and use of quality microbial bioinputs are tools to achieve agricultural sustainability. The impact of management of cover crop–soybean agroecosystems on rhizosphere microbial communities was evaluated. A field experiment in a randomized complete block design with factorial arrangement in sub‐divided plots was performed. Effects of fertilization (0 and 45 kg·ha−1), oats, rye and control without cover crops, plant growth promoting rhizobacteria (PGPR) co‐inoculation of Azospirillum brasilense and Pseudomonas fluorescens, and three sampling times on microbial counts, community‐level physiological profiles (CLPP) and terminal restriction fragment length polymorphism (T‐RLFP) were studied. CLPP were drastically changed at three sampling times: before glyphosate, after glyphosate and at soybean harvest. Before glyphosate application, the interaction between PGPR inoculation and coverage treatments modified the functional and structural profiles of the rhizosphere microbial communities. Furthermore, the highest microbial counts and the greatest functional diversity indices were observed before glyphosate application but significantly decayed after glyphosate application and at soybean harvest, showing a permanent impact of glyphosate application on the rhizosphere microbial community functionality, which was confirmed with several statistical analyses. For the cover crop–soybean agroecosystems, we can conclude that the rhizosphere microbial communities showed high sensitivity to glyphosate. PGPR inoculation only increased the aerial biomass of rye at the jointing and grain‐filling stages. Inoculated plants without fertilization and non‐inoculated plants with fertilization showed similar aerial biomass production of this crop. This work demonstrates that different management decisions can change plant–microorganism relationships in the rhizospheres of cover crops and impact aboveground biomass production. A better understanding of microbial ecology will allow the sustainable use of available resources.Highlights A field experiment was conducted using oats and rye as cover crops in succession with soybean. Management decisions changed plant–microorganism relationships and impact on microbial ecology. Management of cover crops with glyphosate had negative impacts on rhizosphere microbial communities. Co‐inoculation with Azospirillum brasilense and Pseudomonas fluorescens increased the aerial biomass production of rye.

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“…Recentemente, métodos moleculares, também chamados de independentes de cultivo, têm sido utilizados no estudo da ecologia microbiana por permitir a comparação rápida e eficiente das estruturas das comunidades microbianas presentes em amostras de solos (CAFFARO-FILHO et al, 2007).…”

Section: Introdução Geralunclassified

Atributos microbiológicos de solos cultivados com café (>i<Coffea arábica>/i< L.)

Simon¹

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Dedico aos meus pais, senhor João Carlos Simon e a senhora Neuza Maria da Silva Simon, com amor, admiração e gratidão pela compreensão, carinho e apoio ao longo do período de elaboração deste trabalho. Obrigada! 4 AGRADECIMENTOS À Deus, por sempre guiar meus passos e por colocar boas pessoas no meu caminho. Aos meus pais, a senhora Neuza Maria da Silva Simon e o senhor João Carlos Simon, pelo incentivo na realização do curso de doutorado, principalmente a minha mãe por ter acreditado mais em mim do que eu mesma. Ao Prof. Dr. Fernando Dini Andreote, pela atenção, paciência e apoio durante o processo de definição e orientação. Professor, com você aprendi a olhar para os defeitos dos nossos colegas com mais tolerância, consegui diminuir meu nível de ansiedade e compreendi que não podemos ser escravos do trabalho. Obrigada de coração, hoje vejo o quanto isso faz diferença na vida pessoal e profissional. Ao grupo DaTerra Coffee, representados pela Isabela Pascoal Becker e seus familiares. É com imensa satisfação que defendo essa tese sabendo que o grupo DaTerra sempre esteve compromissado com atividade de ensino e pesquisa, abrindo as portas da propriedade e assumindo o compromisso para com a área acadêmica. Em especial, agradeço ao Leo (in memorian), que nos deixou marcados pela sua competência, experiência e fascinação pela cafeicultura e pela ciência. Ao Prof. Dr. Sebastião Ferreira de Lima, que nos anos de convivência durante o mestrado e no período do curso de doutorado sempre esteve presente e muito me ensinou, contribuindo para meu crescimento científico, intelectual, profissional e pessoal. A minha amiga Marianna Carde Peccinelii pelo companheirismo, pela parceria, pela alegria e simpatia compartilhada. O que seria de mim sem você na ESALQ/USP? À equipe do Laboratório de Microbiologia do Solo, em especial a Denise de Lourdes Colombo Mescolotti, Sonia Pires Moraes e ao Luiz Fernando Baldesin pelo carinho, companheirismo e confiança! Às minhas irmãs Carla da Penha Simon e Camila da Conceição Simon! Às amizades construídas dentro da Pós-Graduação, em especial ao Guilherme Nacata,

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Quantitative analysis of Terminal Restriction Fragment Length Polymorphism (T-RFLP) microbial community profiles: peak height data showed to be more reproducible than peak area

Cited by 5 publications

References 16 publications

Effect of Dietary Supplementation of Immunobiotic Lactiplantibacillusplantarum N14 Fermented Rakkyo (Allium chinense) Pickled Juice on the Immunocompetence and Production Performance of Pigs

Effect of Dietary Supplementation of Immunobiotic Lactiplantibacillusplantarum N14 Fermented Rakkyo (Allium chinense) Pickled Juice on the Immunocompetence and Production Performance of Pigs

Impact of management of cover crop–soybean agroecosystems on rhizosphere microbial communities

Atributos microbiológicos de solos cultivados com café (>i<Coffea arábica>/i< L.)

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