Free-living diazotrophs drive castor bean nitrogen input in tropical semiarid soils / Diazotróficas de vida livre conduzem a entrada de nitrogênio em solos cultivados com mamona no semiárido

There are few studies of microbial diversity in castor bean soils in tropical semiarid environmental. Castor bean products have been widely used around the world justifying the commercial importance of ricinoculture in Brazil’ northeastern semiarid. There is no fertilization or maintenance of litter on the soils from the present study, so we hypothesized that the free-living diazotrophs microorganisms drive the nitrogen (N) input into these soils. We evaluated the communities’ structure and diversity of diazotrophs in tropical semiarid soils with i-Castor bean 50 years of cultivation intercropping with maize (CB-50); ii-Only Castor bean 10 years of cultivation (CB-10) and iii-soil under Caatinga vegetation (CAA). Nitrogenase enzyme activity was performed by the acetylene reduction assay (ARA) and the community profile of nifH gene was separated by denaturing gradient gel polyacrylamide electrophoresis (DGGE). Diazotrophs diversity was estimated by the Shannon (H’) and Simpson (D) indexes. Based on the maintenance of soil N stocks and N-microbial biomass over time, the activity of free-living diazotrophs was determinant in the N-input into these soils. The nifH gene was present and its profiles grouped the CB-50 with CAA treatments, so it reinforced the N-fixing by diazotrophs, which presented a greater diversity in the cultivated soils, even after the land use change for the castor bean implementation.

Existem poucos estudos sobre a diversidade microbiana em solos de mamona no ambiente semiárido tropical. Os produtos de mamona têm sido amplamente utilizados em todo o mundo e justificam a importância comercial da ricinocultura no semiárido nordestino brasileiro. Como não há qualquer tipo de fertilização, ou manutenção de resíduos da cultura nos solos de mamona do presente estudo, presume-se que a comunidade de diazotróficas forneça o nitrogênio (N) nesses solos. Avaliou-se a estrutura e diversidade de comunidades de diazotróficas em solos de mamona do semiárido tropical em: i-Mamona com 50 anos de cultivo, consorciada com milho (CB-50); ii-Mamona com 10 anos de cultivo sem consórcio (CB-10) e iii-solo sob vegetação de Caatinga preservada (CAA). Realizou-se avaliação de redução do acetileno a etileno (ARA) e o perfil do gene nifH foi separado por eletroforese em gel de poliacrilamida com gradiente desnaturante (DGGE). A diversidade de diazotróficas foi estimada pelos índices de Shannon (H’) e Simpson (D). Com base na manutenção dos estoques de nitrogênio no solo e da biomassa microbiana ao longo do tempo, a atividade dos diazotróficos de vida livre foi determinante na entrada de N nesses solos. O gene nifH esteve presente e seus perfis agruparam os tratamentos CB-50 com CAA, reforçando a fixação de N pelos diazotróficos, os quais apresentaram maior diversidade nos solos cultivados, mesmo após a mudança de uso da terra para o plantio de mamona.

Free-living diazotrophs drive castor bean nitrogen input in tropical semiarid soils / Diazotróficas de vida livre conduzem a entrada de nitrogênio em solos cultivados com mamona no semiárido

There are few studies of microbial diversity in castor bean soils in tropical semiarid environmental. Castor bean products have been widely used around the world justifying the commercial importance of ricinoculture in Brazil northeastern semiarid. There is no fertilization or maintenance of litter on the soils from the present study, so we hypothesized that the free-living diazotrophs microorganisms drive the nitrogen (N) input into these soils. We evaluated the communities structure and diversity of diazotrophs in tropical semiarid soils with i-Castor bean 50 years of cultivation intercropping with maize (CB-50); ii-Only Castor bean 10 years of cultivation (CB-10) and iii-soil under Caatinga vegetation (CAA). Nitrogenase enzyme activity was performed by the acetylene reduction assay (ARA) and the community profile of nifH gene was separated by denaturing gradient gel polyacrylamide electrophoresis (DGGE). Diazotrophs diversity was estimated by the Shannon (H) and Simpson (D) indexes. Based on the maintenance of soil N stocks and N-microbial biomass over time, the activity of free-living diazotrophs was determinant in the N-input into these soils. The nifH gene was present and its profiles grouped the CB-50 with CAA treatments, so it reinforced the N-fixing by diazotrophs, which presented a greater diversity in the cultivated soils, even after the land use change for the castor bean implementation.(AU)

Existem poucos estudos sobre a diversidade microbiana em solos de mamona no ambiente semiárido tropical. Os produtos de mamona têm sido amplamente utilizados em todo o mundo e justificam a importância comercial da ricinocultura no semiárido nordestino brasileiro. Como não há qualquer tipo de fertilização, ou manutenção de resíduos da cultura nos solos de mamona do presente estudo, presume-se que a comunidade de diazotróficas forneça o nitrogênio (N) nesses solos. Avaliou-se a estrutura e diversidade de comunidades de diazotróficas em solos de mamona do semiárido tropical em: i-Mamona com 50 anos de cultivo, consorciada com milho (CB-50); ii-Mamona com 10 anos de cultivo sem consórcio (CB-10) e iii-solo sob vegetação de Caatinga preservada (CAA). Realizou-se avaliação de redução do acetileno a etileno (ARA) e o perfil do gene nifH foi separado por eletroforese em gel de poliacrilamida com gradiente desnaturante (DGGE). A diversidade de diazotróficas foi estimada pelos índices de Shannon (H) e Simpson (D). Com base na manutenção dos estoques de nitrogênio no solo e da biomassa microbiana ao longo do tempo, a atividade dos diazotróficos de vida livre foi determinante na entrada de N nesses solos. O gene nifH esteve presente e seus perfis agruparam os tratamentos CB-50 com CAA, reforçando a fixação de N pelos diazotróficos, os quais apresentaram maior diversidade nos solos cultivados, mesmo após a mudança de uso da terra para o plantio de mamona.(AU)

Arbuscular mycorrhizal fungal communities in the rhizosphere of a continuous cropping soybean system at the seedling stage

Abstract Arbuscular mycorrhizae (AM) fungi play a crucial role in the growth of soybean; however, the planting system employed is thought to have an effect on AM fungal communities in the rhizosphere. This study was performed to explore the influence of continuous soybean cropping on the diversity of Arbuscular mycorrhizal (AM) fungi, and to identify the dominant AM fungus during the seedling stage. Three soybean cultivars were planted under two and three years continuous cropping, respectively. The diversity of AM fungi in the rhizosphere soil at the seedling stage was subsequently analyzed using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). The results showed that an increase in cropping years improved the colonization rate of AM in all three soybean cultivars. Moreover, the dominant species were found to be Funneliformis mosseae and Glomus species. The results of cluster analysis further confirmed that the number of years of continuous cropping significantly affected the composition of rhizospheric AM fungal communities in different soybean cultivars.

Arbuscular mycorrhizal fungal communities in the rhizosphere of a continuous cropping soybean system at the seedling stage

Arbuscular mycorrhizae (AM) fungi play a crucial role in the growth of soybean; however, the planting system employed is thought to have an effect on AM fungal communities in the rhizosphere. This study was performed to explore the influence of continuous soybean cropping on the diversity of Arbuscular mycorrhizal (AM) fungi, and to identify the dominant AM fungus during the seedling stage. Three soybean cultivars were planted under two and three years continuous cropping, respectively. The diversity of AM fungi in the rhizosphere soil at the seedling stage was subsequently analyzed using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). The results showed that an increase in cropping years improved the colonization rate of AM in all three soybean cultivars. Moreover, the dominant species were found to be Funneliformis mosseae and Glomus species. The results of cluster analysis further confirmed that the number of years of continuous cropping significantly affected the composition of rhizospheric AM fungal communities in different soybean cultivars.(AU)

Bacterial degradation of dissolved organic matter released by Planktothrix agardhii (Cyanobacteria)

Abstract Although Planktothrix agardhii often produces toxic blooms in eutrophic water bodies around the world, little is known about the fate of the organic matter released by these abundant Cyanobacteria. Thus, this study focused in estimating the bacterial consumption of the DOC and DON (dissolved organic carbon and dissolved organic nitrogen, respectively) produced by axenic P. agardhii cultures and identifying some of the bacterial OTUs (operational taxonomic units) involved in the process. Both P. agardhii and bacterial inocula were sampled from the eutrophic Barra Bonita Reservoir (SP, Brazil). Two distinct carbon degradation phases were observed: during the first three days, higher degradation coefficients were calculated, which were followed by a slower degradation phase. The maximum value observed for particulate bacterial carbon (POC) was 11.9 mg L-1, which consisted of 62.5% of the total available DOC, and its mineralization coefficient was 0.477 day-1 (t½ = 1.45 days). A similar pattern of degradation was observed for DON, although the coefficients were slightly different. Changes in the OTUs patterns were observed during the different steps of the degradation. The main OTUs were related to the classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) and Gammaproteobacteria (3 OTUs). The genus Acinetobacter was the only identified organism that occurred during the whole process. Bacterial richness was higher at the slower degradation phase, which could be related to the small amounts of DOM (dissolved organic matter) available, particularly carbon. The kinetics of the bacterial degradation of P. agardhii-originated DOM suggests minimal loss of DOM from the Barra Bonita reservoir.

Resumo Embora Planktothrix agardhii frequentemente forme florações tóxicas em corpos dágua pelo mundo, pouco ainda se sabe sobre o destino da matéria orgânica liberada por essa abundante Cyanobacteria. Assim, este estudo foi focado na estimativa do consumo bacteriano do carbono orgânico dissolvido (DOC) e nitrogênio orgânico dissolvido (DON) produzido por culturas axênicas de P. agardhii e identificação de algumas das unidades taxonômicas operacionais (OTUs) bacterianas envolvidas no processo. Ambos a linhagem de P. agardhii e o inóculo bacteriano foram amostrados do reservatório eutrófico de Barra Bonita (SP, Brasil). Foram observadas duas fases distintas da degradação do DOC: durante os três primeiros dias, coeficientes mais altos de degradação foram calculados, que foram então seguidos por uma fase mais lenta da degradação do carbono. O valor máximo calculado para o carbono bacteriano particulado (POC) foi de 11,9 mgL-1, o que equivale a aproximadamente 62,5% do DOC disponível para consumo, e o seu coeficiente de mineralização foi de 0,477 dia-1 (t1/2 = 1,45 dias). Um padrão similar de degradação foi observado para DON, embora os coeficientes sejam ligeiramente diferentes. Foram observadas mudanças nos padrões de OTUs durante os diferentes passos da degradação. As principais OTUs foram relacionadas às classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) e Gammaproteobacteria (3 OTUs). O gênero Acinetobacter foi o único organismo identificado que ocorreu durante todo o processo. A maior riqueza bacteriana foi observada durante a fase lenta de degradação, o que pode estar relacionado às pequenas quantidades de matéria orgânica dissovida (DOM) disponíveis, particularmente o carbono. A cinética da degradação bacteriana da MOD de P. agardhii, quando comparada ao tempo de retenção do reservatório, sugere que existe uma perda mínima após sua liberação em Barra Bonita.

Bacterial degradation of dissolved organic matter released by Planktothrix agardhii (Cyanobacteria)

Abstract Although Planktothrix agardhii often produces toxic blooms in eutrophic water bodies around the world, little is known about the fate of the organic matter released by these abundant Cyanobacteria. Thus, this study focused in estimating the bacterial consumption of the DOC and DON (dissolved organic carbon and dissolved organic nitrogen, respectively) produced by axenic P. agardhii cultures and identifying some of the bacterial OTUs (operational taxonomic units) involved in the process. Both P. agardhii and bacterial inocula were sampled from the eutrophic Barra Bonita Reservoir (SP, Brazil). Two distinct carbon degradation phases were observed: during the first three days, higher degradation coefficients were calculated, which were followed by a slower degradation phase. The maximum value observed for particulate bacterial carbon (POC) was 11.9 mg L-1, which consisted of 62.5% of the total available DOC, and its mineralization coefficient was 0.477 day-1 (t½ = 1.45 days). A similar pattern of degradation was observed for DON, although the coefficients were slightly different. Changes in the OTUs patterns were observed during the different steps of the degradation. The main OTUs were related to the classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) and Gammaproteobacteria (3 OTUs). The genus Acinetobacter was the only identified organism that occurred during the whole process. Bacterial richness was higher at the slower degradation phase, which could be related to the small amounts of DOM (dissolved organic matter) available, particularly carbon. The kinetics of the bacterial degradation of P. agardhii-originated DOM suggests minimal loss of DOM from the Barra Bonita reservoir.

Resumo Embora Planktothrix agardhii frequentemente forme florações tóxicas em corpos dágua pelo mundo, pouco ainda se sabe sobre o destino da matéria orgânica liberada por essa abundante Cyanobacteria. Assim, este estudo foi focado na estimativa do consumo bacteriano do carbono orgânico dissolvido (DOC) e nitrogênio orgânico dissolvido (DON) produzido por culturas axênicas de P. agardhii e identificação de algumas das unidades taxonômicas operacionais (OTUs) bacterianas envolvidas no processo. Ambos a linhagem de P. agardhii e o inóculo bacteriano foram amostrados do reservatório eutrófico de Barra Bonita (SP, Brasil). Foram observadas duas fases distintas da degradação do DOC: durante os três primeiros dias, coeficientes mais altos de degradação foram calculados, que foram então seguidos por uma fase mais lenta da degradação do carbono. O valor máximo calculado para o carbono bacteriano particulado (POC) foi de 11,9 mgL-1, o que equivale a aproximadamente 62,5% do DOC disponível para consumo, e o seu coeficiente de mineralização foi de 0,477 dia-1 (t1/2 = 1,45 dias). Um padrão similar de degradação foi observado para DON, embora os coeficientes sejam ligeiramente diferentes. Foram observadas mudanças nos padrões de OTUs durante os diferentes passos da degradação. As principais OTUs foram relacionadas às classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) e Gammaproteobacteria (3 OTUs). O gênero Acinetobacter foi o único organismo identificado que ocorreu durante todo o processo. A maior riqueza bacteriana foi observada durante a fase lenta de degradação, o que pode estar relacionado às pequenas quantidades de matéria orgânica dissovida (DOM) disponíveis, particularmente o carbono. A cinética da degradação bacteriana da MOD de P. agardhii, quando comparada ao tempo de retenção do reservatório, sugere que existe uma perda mínima após sua liberação em Barra Bonita.

Bacterial degradation of dissolved organic matter released by Planktothrix agardhii (Cyanobacteria) / Degradação bacteriana da matéria orgânica dissolvida liberada porPlanktothrix agardhii (Cyanobacteria)

Although Planktothrix agardhii often produces toxic blooms in eutrophic water bodies around the world, little is known about the fate of the organic matter released by these abundant Cyanobacteria. Thus, this study focused in estimating the bacterial consumption of the DOC and DON (dissolved organic carbon and dissolved organic nitrogen, respectively) produced by axenic P. agardhii cultures and identifying some of the bacterial OTUs (operational taxonomic units) involved in the process. Both P. agardhii and bacterial inocula were sampled from the eutrophic Barra Bonita Reservoir (SP, Brazil). Two distinct carbon degradation phases were observed: during the first three days, higher degradation coefficients were calculated, which were followed by a slower degradation phase. The maximum value observed for particulate bacterial carbon (POC) was 11.9 mg L-1, which consisted of 62.5% of the total available DOC, and its mineralization coefficient was 0.477 day-1 (t½ = 1.45 days). A similar pattern of degradation was observed for DON, although the coefficients were slightly different. Changes in the OTUs patterns were observed during the different steps of the degradation. The main OTUs were related to the classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) and Gammaproteobacteria (3 OTUs). The genus Acinetobacter was the only identified organism that occurred during the whole process. Bacterial richness was higher at the slower degradation phase, which could be related to the small amounts of DOM (dissolved organic matter) available, particularly carbon. The kinetics of the bacterial degradation of P. agardhii-originated DOM suggests minimal loss of DOM from the Barra Bonita reservoir.(AU)

Embora Planktothrix agardhii frequentemente forme florações tóxicas em corpos dágua pelo mundo, pouco ainda se sabe sobre o destino da matéria orgânica liberada por essa abundante Cyanobacteria. Assim, este estudo foi focado na estimativa do consumo bacteriano do carbono orgânico dissolvido (DOC) e nitrogênio orgânico dissolvido (DON) produzido por culturas axênicas de P. agardhii e identificação de algumas das unidades taxonômicas operacionais (OTUs) bacterianas envolvidas no processo. Ambos a linhagem de P. agardhii e o inóculo bacteriano foram amostrados do reservatório eutrófico de Barra Bonita (SP, Brasil). Foram observadas duas fases distintas da degradação do DOC: durante os três primeiros dias, coeficientes mais altos de degradação foram calculados, que foram então seguidos por uma fase mais lenta da degradação do carbono. O valor máximo calculado para o carbono bacteriano particulado (POC) foi de 11,9 mgL-1, o que equivale a aproximadamente 62,5% do DOC disponível para consumo, e o seu coeficiente de mineralização foi de 0,477 dia-1 (t1/2 = 1,45 dias). Um padrão similar de degradação foi observado para DON, embora os coeficientes sejam ligeiramente diferentes. Foram observadas mudanças nos padrões de OTUs durante os diferentes passos da degradação. As principais OTUs foram relacionadas às classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) e Gammaproteobacteria (3 OTUs). O gênero Acinetobacter foi o único organismo identificado que ocorreu durante todo o processo. A maior riqueza bacteriana foi observada durante a fase lenta de degradação, o que pode estar relacionado às pequenas quantidades de matéria orgânica dissovida (DOM) disponíveis, particularmente o carbono. A cinética da degradação bacteriana da MOD de P. agardhii, quando comparada ao tempo de retenção do reservatório, sugere que existe uma perda mínima após sua liberação em Barra Bonita.(AU)

Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE

Abstract Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM) to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) profiles indicated that a strain of Pediococcus acidilactici (band 9) is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process.

Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE

Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM) to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) profiles indicated that a strain of Pediococcus acidilactici (band 9) is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process.(AU)

The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure.(AU)

Bacterial degradation of dissolved organic matter released by Planktothrix agardhii (Cyanobacteria)

Abstract Although Planktothrix agardhii often produces toxic blooms in eutrophic water bodies around the world, little is known about the fate of the organic matter released by these abundant Cyanobacteria. Thus, this study focused in estimating the bacterial consumption of the DOC and DON (dissolved organic carbon and dissolved organic nitrogen, respectively) produced by axenic P. agardhii cultures and identifying some of the bacterial OTUs (operational taxonomic units) involved in the process. Both P. agardhii and bacterial inocula were sampled from the eutrophic Barra Bonita Reservoir (SP, Brazil). Two distinct carbon degradation phases were observed: during the first three days, higher degradation coefficients were calculated, which were followed by a slower degradation phase. The maximum value observed for particulate bacterial carbon (POC) was 11.9 mg L-1, which consisted of 62.5% of the total available DOC, and its mineralization coefficient was 0.477 day-1 (t½ = 1.45 days). A similar pattern of degradation was observed for DON, although the coefficients were slightly different. Changes in the OTUs patterns were observed during the different steps of the degradation. The main OTUs were related to the classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) and Gammaproteobacteria (3 OTUs). The genus Acinetobacter was the only identified organism that occurred during the whole process. Bacterial richness was higher at the slower degradation phase, which could be related to the small amounts of DOM (dissolved organic matter) available, particularly carbon. The kinetics of the bacterial degradation of P. agardhii-originated DOM suggests minimal loss of DOM from the Barra Bonita reservoir.

Resumo Embora Planktothrix agardhii frequentemente forme florações tóxicas em corpos dágua pelo mundo, pouco ainda se sabe sobre o destino da matéria orgânica liberada por essa abundante Cyanobacteria. Assim, este estudo foi focado na estimativa do consumo bacteriano do carbono orgânico dissolvido (DOC) e nitrogênio orgânico dissolvido (DON) produzido por culturas axênicas de P. agardhii e identificação de algumas das unidades taxonômicas operacionais (OTUs) bacterianas envolvidas no processo. Ambos a linhagem de P. agardhii e o inóculo bacteriano foram amostrados do reservatório eutrófico de Barra Bonita (SP, Brasil). Foram observadas duas fases distintas da degradação do DOC: durante os três primeiros dias, coeficientes mais altos de degradação foram calculados, que foram então seguidos por uma fase mais lenta da degradação do carbono. O valor máximo calculado para o carbono bacteriano particulado (POC) foi de 11,9 mgL-1, o que equivale a aproximadamente 62,5% do DOC disponível para consumo, e o seu coeficiente de mineralização foi de 0,477 dia-1 (t1/2 = 1,45 dias). Um padrão similar de degradação foi observado para DON, embora os coeficientes sejam ligeiramente diferentes. Foram observadas mudanças nos padrões de OTUs durante os diferentes passos da degradação. As principais OTUs foram relacionadas às classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) e Gammaproteobacteria (3 OTUs). O gênero Acinetobacter foi o único organismo identificado que ocorreu durante todo o processo. A maior riqueza bacteriana foi observada durante a fase lenta de degradação, o que pode estar relacionado às pequenas quantidades de matéria orgânica dissovida (DOM) disponíveis, particularmente o carbono. A cinética da degradação bacteriana da MOD de P. agardhii, quando comparada ao tempo de retenção do reservatório, sugere que existe uma perda mínima após sua liberação em Barra Bonita.

Bacterial degradation of dissolved organic matter released by Planktothrix agardhii (Cyanobacteria)

Abstract Although Planktothrix agardhii often produces toxic blooms in eutrophic water bodies around the world, little is known about the fate of the organic matter released by these abundant Cyanobacteria. Thus, this study focused in estimating the bacterial consumption of the DOC and DON (dissolved organic carbon and dissolved organic nitrogen, respectively) produced by axenic P. agardhii cultures and identifying some of the bacterial OTUs (operational taxonomic units) involved in the process. Both P. agardhii and bacterial inocula were sampled from the eutrophic Barra Bonita Reservoir (SP, Brazil). Two distinct carbon degradation phases were observed: during the first three days, higher degradation coefficients were calculated, which were followed by a slower degradation phase. The maximum value observed for particulate bacterial carbon (POC) was 11.9 mg L-1, which consisted of 62.5% of the total available DOC, and its mineralization coefficient was 0.477 day-1 (t½ = 1.45 days). A similar pattern of degradation was observed for DON, although the coefficients were slightly different. Changes in the OTUs patterns were observed during the different steps of the degradation. The main OTUs were related to the classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) and Gammaproteobacteria (3 OTUs). The genus Acinetobacter was the only identified organism that occurred during the whole process. Bacterial richness was higher at the slower degradation phase, which could be related to the small amounts of DOM (dissolved organic matter) available, particularly carbon. The kinetics of the bacterial degradation of P. agardhii-originated DOM suggests minimal loss of DOM from the Barra Bonita reservoir.

Resumo Embora Planktothrix agardhii frequentemente forme florações tóxicas em corpos dágua pelo mundo, pouco ainda se sabe sobre o destino da matéria orgânica liberada por essa abundante Cyanobacteria. Assim, este estudo foi focado na estimativa do consumo bacteriano do carbono orgânico dissolvido (DOC) e nitrogênio orgânico dissolvido (DON) produzido por culturas axênicas de P. agardhii e identificação de algumas das unidades taxonômicas operacionais (OTUs) bacterianas envolvidas no processo. Ambos a linhagem de P. agardhii e o inóculo bacteriano foram amostrados do reservatório eutrófico de Barra Bonita (SP, Brasil). Foram observadas duas fases distintas da degradação do DOC: durante os três primeiros dias, coeficientes mais altos de degradação foram calculados, que foram então seguidos por uma fase mais lenta da degradação do carbono. O valor máximo calculado para o carbono bacteriano particulado (POC) foi de 11,9 mgL-1, o que equivale a aproximadamente 62,5% do DOC disponível para consumo, e o seu coeficiente de mineralização foi de 0,477 dia-1 (t1/2 = 1,45 dias). Um padrão similar de degradação foi observado para DON, embora os coeficientes sejam ligeiramente diferentes. Foram observadas mudanças nos padrões de OTUs durante os diferentes passos da degradação. As principais OTUs foram relacionadas às classes Alphaproteobacteria (8 OTUs), Betaproteobacteria (2 OTUs) e Gammaproteobacteria (3 OTUs). O gênero Acinetobacter foi o único organismo identificado que ocorreu durante todo o processo. A maior riqueza bacteriana foi observada durante a fase lenta de degradação, o que pode estar relacionado às pequenas quantidades de matéria orgânica dissovida (DOM) disponíveis, particularmente o carbono. A cinética da degradação bacteriana da MOD de P. agardhii, quando comparada ao tempo de retenção do reservatório, sugere que existe uma perda mínima após sua liberação em Barra Bonita.

Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices

Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices (arenite, shale and polyurethane foam) as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM), Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA gene libraries in order to compare the microbial biomass yield, DNA recovery efficiency and diversity among the enrichments. The DNA from microbial communities in petroleum enrichments was purified according to a protocol established in this work and used for 16S rRNA amplification with bacterial generic primers. The PCR products were cloned, and positive clones were screened by Amplified Ribosomal DNA Restriction Analysis (ARDRA). Sequencing and phylogenetic analyses revealed that the bacterial community was mostly represented by members of the genera Petrotoga, Bacillus, Pseudomonas, Geobacillus and Rahnella. The use of different support materials in the enrichments yielded an increase in microbial biomass and biofilm formation, indicating that these materials may be employed for efficient biomass recovery from petroleum reservoir samples. Nonetheless, the most diverse microbiota were recovered from the biodegraded petroleum sample using polyurethane foam cubes as support material.(AU)

Bacaba beverage produced by Umutina Brazilian Amerindians: Microbiological and chemical characterization

Bacaba chicha is a beverage prepared by the indigenous Umutina people from the bacaba fruit (Oenocarpus bacaba), a purple berry that is rich in fat and carbohydrates, as well as a source of phenolic compounds. In this study, samples of bacaba chicha beverage were collected, and the microbial community was assessed using culture-dependent and -independent techniques. The nutritional composition and metabolite profiles were analyzed, and species belonging to lactic acid bacteria (LAB) and yeasts were detected. The LAB group detected by culture-dependent analysis included Enterococcus hormaechei and Leuconostoc lactis. Polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) detected additional Propionibacterium avidum, Acetobacter spp., and uncultured bacteria. Pichia caribbica and Pichia guilliermondii were detected in a culture-dependent method, and Pichia caribbica was confirmed by PCR-DGGE analysis. The pH value of the beverage was 6.2. The nutritional composition was as follows: 16.47 ± 0.73 g 100 mL-1 dry matter, 2.2 ± 0.0 g 100 mL-1 fat, 3.36 ± 0.44 g 100 mL-1 protein, and 10.87 ± 0.26 g 100 mL-1 carbohydrate. The metabolites detected were 2.69 g L-1 succinic acid, 0.9 g L-1 acetic acid, 0.49 g L-1 citric acid, 0.52 g L-1 ethanol, and 0.4 g L-1 glycerol. This is the first study to identify microbial diversity in bacaba chicha spontaneous fermentation. This study is also the starting step in the immaterial record of this Brazilian indigenous beverage prepared from bacaba fruit.(AU)

Characterization of pectinase activity for enology from yeasts occurring in Argentine Bonarda grape

Pectinolytic enzymes are greatly important in winemaking due to their ability to degrade pectic polymers from grape, contributing to enhance process efficiency and wine quality. This study aimed to analyze the occurrence of pectinolytic yeasts during spontaneous fermentation of Argentine Bonarda grape, to select yeasts that produce extracellular pectinases and to characterize their pectinolytic activity under wine-like conditions. Isolated yeasts were grouped using PCR-DGGE and identified by partial sequencing of 26S rRNA gene. Isolates comprised 7 genera, with Aureobasidium pullulans as the most predominant pectinolytic species, followed by Rhodotorula dairenensis and Cryptococcus saitoi. No pectinolytic activity was detected among ascomycetous yeasts isolated on grapes and during fermentation, suggesting a low occurrence of pectinolytic yeast species in wine fermentation ecosystem. This is the first study reporting R. dairenensis and Cr. saitoi species with pectinolytic activity. R. dairenensis GM-15 produced pectinases that proved to be highly active at grape pH, at 12 °C, and under ethanol and SO2 concentrations usually found in vinifications (pectinase activity around 1.1 U/mL). This strain also produced cellulase activity at 12 °C and pH 3.5, but did not produce β-glucosidase activity under these conditions. The strain showed encouraging enological properties for its potential use in low-temperature winemaking. (AU)

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit MiniprepTM (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit MiniprepTM (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.(AU)

UTILIZAÇÃO DE MICRORGANISMOS ISOLADOS DE TILÁPIA-DO-NILO (Oreochromis niloticus) COMO PROBIÓTICO EM PEIXES

O uso de sistemas intensivos de produção na piscicultura faz-se necessário para atender a demanda crescente por pescado, e como consequência negativa, possibilita o surgimento de surtos de doenças bacterianas, afetando a produtividade, a sobrevivência e o bem-estar dos animais, assim como a sua qualidade. A utilização de aditivos como os probióticos pode ser uma alternativa viável para a prevenção de agentes patogênicos, além de melhorar o crescimento dos animais. Portanto, o objetivo deste trabalho foi avaliar bactérias previamente testadas in vitro com potencial probiótico no desempenho zootécnico e o sistema imunológico inato de tilápia-do-nilo (Oreochromis niloticus), equilíbrio homeostático, fisiológico e microbiológico. Para esta finalidade, foi realizado um ensaio de desempenho de crescimento (duração de 81 dias), seguindo o delineamento experimental inteiramente casualizado, com sete tratamentos e três repetições (21 unidades experimentais), sendo: T0 controle, T1 Bacillus velezensis na ração, T2 Bacillus pumilus na ração, T3 Bacillus subtilis na ração, T4 Probiótico Enterococcus hirae na ração, T5 Enterococcus faecium na ração e T6 Mix de todas as bactérias dos outros tratamentos na ração. Ao final do período experimental, as variáveis de desempenho zootécnico de crescimento, DGGE (Denaturing gradient gel electrophoresis), hematologia, lactato, lisozima e burst respiratório de fagócitos foram avaliadas. A inclusão das bactérias B. pumilus (T2) e o mix (T6), em dietas para a tilápia-do-nilo, proporcionaram o aumento da biomassa total final de peixes em relação ao controle e aos outros tratamentos. O uso destes microrganismos não afetou a saúde e o bem-estar dos peixes, sendo que os índices hematológicos, exceto basófilos e trombócitos, níveis glicêmicos e de lactato foram semelhantes com o grupo controle. As análises de DGGE demonstraram a odulação dos microrganismos presentes no intestino dos peixes Conclui-se que as bactérias isoladas e pré-selecionadas do intestino e muco de tilápias-do-nilo do grupo T2 (B. pumilus) e T6 (B. velezensis, B. pumilus, B. subtilis, E. hirae e E. faecium), melhoram o desempenho de crescimento, além de modular a microbiota intestinal e podem ser usadas como probióticos para tilápia.

The use of intensive production system in fish farming is necessary to supply the increased demand for fish products, and consequently, enable the emergence bacterial diseases outbreaks, and negatively affect the productivity, survival rates and well-fare animals, and the flesh quality. The probiotics use may be a viable alternative to prevent the diseases and improves the animal growth performance. The development of specific probiotics for Nile tilapia could be interesting since may also promotes weight gain and other performance variables. This project aimed to evaluate the capacity of potential probiotic microorganisms, in diets, to improve the performance of Nile tilapia (Oreochromis niloticus), promote equilibrium balance of homeostasis, physiology, microbiology and upgrade the innate immunology system of the host. For this purpose, the growth performance assay (81 days of duration) was done, following the randomized experiment design with seven treatments and three replicates (21 experimental units): T0 control group, T1 Bacillus velezensis, T2 Bacillus pumilus, T3 Bacillus subtilis, T4 Enterococcus hirae T5 Enterococcus faecium and T6 Mix of bacteria strains belonged to other treatments. The following variables were analyzed: growth performance, DGGE (Denaturing gradient gel electrophoresis), respiratory burst activity from phagocytes, hematology and histology. As relevant result, the bacteria strains B. pumilus (T2) and mix (T6), included in diet for Nile tilapia, promoted better biomass values, with similar feed conversion rate of control group. Apparently, the use of these microorganisms does not affect the heath and well-fare of the fish, since the hematology indices, except for basophils and thrombocytes, glycemia and lactate level were similar to control group. We concluded that the isolated and pre-selected bacteria from the intestine and mucus of group T2 (B. pumilus) and T6 (B. velezensis, B. pumilus, B. subtilis, E. hirae and E. faecium), improve growth performance and can be used as probiotics for tilapia.

Tank bromeliad water: similar or distinct environments for research of bacterial bioactives?

The Atlantic Rainforest does not have a uniform physiognomy, its relief determines different environmental conditions that define the composition of its flora and fauna. Within this ecosystem, bromeliads that form tanks with their leaves hold water reservoirs throughout the year, maintaining complex food chains, based mainly on autotrophic and heterotrophic bacteria. Some works concluded that the water held by tank bromeliads concentrate the microbial diversity of their ecosystem. To investigate the bacterial diversity and the potential biotechnology of these ecosystems, tank bromeliads of the Neoregelia cruenta species from the Atlantic Rainforest in Brazil were used as models for this research. Bacteria isolated from these models were tested for production of bioactive compounds. DGGE of the water held by tank bromeliads was performed in different seasons, locations and sun exposure to verify whether these environmental factors affect bacterial communities. The DGGE bands profile showed no grouping of bacterial community by the environmental factors tested. Most of the isolates demonstrated promising activities in the tests performed. Collectively, these results suggest that tank bromeliads of the N. cruenta species provide important habitats for a diverse microbial community, suggesting that each tank forms a distinct micro-habitat. These tanks can be considered excellent sources for the search for new enzymes and/or new bioactive composites of microbial origin.

Tank bromeliad water: similar or distinct environments for research of bacterial bioactives?

The Atlantic Rainforest does not have a uniform physiognomy, its relief determines different environmental conditions that define the composition of its flora and fauna. Within this ecosystem, bromeliads that form tanks with their leaves hold water reservoirs throughout the year, maintaining complex food chains, based mainly on autotrophic and heterotrophic bacteria. Some works concluded that the water held by tank bromeliads concentrate the microbial diversity of their ecosystem. To investigate the bacterial diversity and the potential biotechnology of these ecosystems, tank bromeliads of the Neoregelia cruenta species from the Atlantic Rainforest in Brazil were used as models for this research. Bacteria isolated from these models were tested for production of bioactive compounds. DGGE of the water held by tank bromeliads was performed in different seasons, locations and sun exposure to verify whether these environmental factors affect bacterial communities. The DGGE bands profile showed no grouping of bacterial community by the environmental factors tested. Most of the isolates demonstrated promising activities in the tests performed. Collectively, these results suggest that tank bromeliads of the N. cruenta species provide important habitats for a diverse microbial community, suggesting that each tank forms a distinct micro-habitat. These tanks can be considered excellent sources for the search for new enzymes and/or new bioactive composites of microbial origin.(AU)