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Bacteria are an essential biotic component in freshwater environments. A group of 262 bacterial strains of freshwater environments from an altitudinal gradient in the Eastern Cordillera of Colombia was identified using the 16S rRNA gene sequence analysis. Hill numbers and related diversity indices were calculated to know the bacteria diversity in this collection and environments. In addition, the Bray-Curtis index was also calculated to know the differences in genera composition between sampled localities and their relationship with altitudinal gradient. The identified bacterial strains were grouped into 7 major phylogenetic groups (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Flavobacteriia, Actinomycetes, Clostridia, and Bacilli), 38 genera, and 84 distinctive species. Diversity analysis based on Hill numbers showed that the diversity concerning bacteria inhabiting freshwater environments was consistently high. Dominant genera were Klebsiella, Serratia, and Pseudomonas, although other genera such as Bacillus, Lelliottia, and Obesumbacterium were well represented per locality. The highest bacterial diversity came from localities Cimitarra and El Carmen del Chucurí, while those originating from Santa Bárbara and Páramo del Almorzadero were relatively lower diverse. Differences in diversity were found to be mainly due to the spatial replacement of one genus by another and, to a lesser extent, to the loss or gain of taxa.

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RESUMEN En el trabajo se estudió un consorcio microbiano metanogénico de una mina de carbón de la cuenca de Bogotá en Colombia. Se establecieron cultivos de enriquecimiento de carbón ex situ para el crecimiento y la producción de gas de novo. El gas biogénico producido por los cultivos se analizó mediante cromatografía de gases con detectores de ionización de llama y conductividad térmica. Los cultivos se utilizaron para aislar estirpes microbianas y para generar bibliotecas del gene 16S rARN empleando de cebadores de bacteria y de arquea. El análisis de cromatografía de gases mostró producción de metano a 37 oC, pero no a 60 oC, donde el CO2 fue el componente principal del gas biogénico. El análisis de la secuencia del gen 16S rARN de estirpes microbianos y de las bibliotecas de clones, estableció que el consorcio microbiano metanogénico estuvo formado por especies de bacterias de los géneros Bacillus y Gracilibacter más la arquea del género Methanothermobacter. El consorcio microbiano metanogénico identificado es potencialmente responsable de la generación de gas biogénico en la mina de carbón La Ciscuda. Los resultados sugirieron que los metanógenos de este consorcio producían metano por vía hidrogenotrófica o de reducción de CO2.

ABSTRACT The work studied the methanogenic microbial consortium in a coal mine from the Bogotá basin in Colombia. Ex situ coal-enrichment cultures were established for in vitro growth and de novo gas production. Biogenic gas produced by cultures was analyzed by gas chromatography using thermal conductivity and flame ionization detectors. Cultures were used to isolate microbial specimens and to generate 16S rRNA gene libraries employing bacterial and archaeal primer sets. The gas chromatographic analysis showed methane production at 37 oC, but not at 60 oC, where CO2 was the major component of the biogenic gas. 16S rRNA gene sequence analysis of microbial isolates and clone libraries established that the methanogenic microbial consortium was formed by bacteria species from Bacillus and Gracilibacter genera plus archaea from the Methanothermobacter genus. This meth-anogenic microbial consortium was potentially responsible for biogenic gas generation in La Ciscuda coal mine. The results suggested that these methanogens produced methane by hydrogenotrophic or CO2 reduction pathways.

RESUMO

This is the first extensive report on the identification and characterization of Avibacterium paragallinarum (AVP) isolates obtained from outbreaks of infectious coryza (IC) in IC-vaccinated layer flocks from Sonora State in Mexico. Isolates obtained from IC outbreaks during the years 2007, 2014, 2015, 2017, and 2019 were identified by conventional PCR test and 16S rRNA gene analysis, serotyped by Page serotyping and genotyped by the recently described partial sequence analysis of the HPG2 region. Furthermore, antimicrobial susceptibility profiles were determined by a recently improved minimal inhibitory concentration (MIC) test. The conventional PCR test and the 16S rRNA analyses confirmed the isolates as AVP. Serotyping results showed the involvement of isolates belonging to serotypes A, B, and C in the IC outbreaks. Genotyping of the HPG2 region revealed the presence of sequence type (ST)1, ST4, and ST11, of which the latter has also been identified in Europe. The MIC susceptibility test showed that all tested isolates were susceptible for the majority of tested antimicrobials, including erythromycin and tetracycline, which are important antibiotics for the treatment of IC. The IC situation in Sonora State, Mexico, is complex because of the presence of serotypes A, B, and C. This finding emphasizes the importance of biosecurity in combination with the application of the most optimal vaccination programs in the control of IC in Sonora State, Mexico.

Nota de investigación­Análisis de secuencias de la región HPG2 y susceptibilidad antimicrobiana de aislamientos de Avibacterium paragallinarum obtenidos de brotes de coriza infecciosa en aves de postura comerciales en el estado de Sonora, México. Este es el primer informe extenso sobre la identificación y caracterización de aislamientos de Avibacterium paragallinarum (AVP) obtenidos de brotes de coriza infecciosa (IC) de parvadas de ponedoras vacunadas con coriza infecciosa en el estado de Sonora en México. Los aislamientos obtenidos de los brotes de coriza infecciosa durante los años 2007, 2014, 2015, 2017 y 2019 se identificaron mediante una prueba de PCR convencional y el análisis del gene de ARNr 16S, se serotipificaron mediante el método de Page y se genotipificaron mediante el análisis parcial de secuencias descrito recientemente de la región HPG2. Además, se determinaron los perfiles de susceptibilidad a los antimicrobianos mediante la prueba de concentración mínima inhibitoria (MIC) que ha sido mejorada recientemente. La prueba de PCR convencional y los análisis de secuencias del gene ARNr 16S confirmaron que los aislados eran A. paragallinarum. Los resultados de la serotipificación mostraron la participación de aislamientos pertenecientes a los serotipos A, B y C en los brotes de coriza infecciosa. La genotipificación de la región HPG2 reveló la presencia de secuencias del tipo (ST) 1, ST4 y ST11, de los cuales este último también ha sido identificada en Europa. La prueba de susceptibilidad por concentración mínima inhibitoria mostró que todos los aislados analizados eran susceptibles a la mayoría de los antimicrobianos analizados, incluida la eritromicina y la tetraciclina, que son antibióticos importantes para el tratamiento contra la coriza infecciosa. La situación de coriza infecciosa en el estado de Sonora, México, es compleja por la presencia de los serotipos A, B y C. Este hallazgo enfatiza la importancia de la bioseguridad en combinación con la aplicación de los programas de vacunación óptimos en el control de la coriza infecciosa en el estado de Sonora, México.

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Bovine digital dermatitis (BDD) is an infectious and contagious disease characterized by ulcerative and proliferative lesions affecting the skin on the bulbs of the heel or the interdigital cleft in dairy cattle, often associated with lameness. Evidences on the etiology of BDD indicate that it is multifactorial, involving environmental factors and multiple bacterial colonization. We isolated and identified microorganisms from BDD biopsy samples obtained from five Holstein Friesian and two Jersey cows by cultivation and molecular identification of bacterial isolates using 16S rRNA gene sequence analysis. We identified six bacterial species: Spirochetes as Treponema pedis and Leptospira broomi/L. fainei, L. licerasiae/L. wolffii; Corynebacterium appendicis, Cupriavidus gilardii and Enterococcus casseliflavus/E. gallinarum. It was quite surprising to have isolated and identified Leptospira species in three out of seven cultures, from different individual cows and two different farms. The species identified belong to the intermediate pathogenic clade, which is a group found to cause human and animal disease. Our findings indicate the need to further investigate the association of Leptospira of intermediate pathogenicity with BDD lesions and whether its presence would have any veterinary and medical significance both in Leptospirosis and with the pathogenesis of BDD lesions, especially in tropical countries.(AU)

Dermatite digital bovina (DDB) é uma doença infecciosa, contagiosa, caracterizada por lesões ulcerativas e proliferativas da região dos talões e/ou do espaço interdigital, frequentemente associada com claudicação. Evidências indicam que a etiologia da DDB é multifatorial, envolvendo fatores ambientais e colonização polimicrobiana. Relata-se aqui o isolamento e a identificação bacteriana em amostras de biópsias em lesões de DDB, obtidas de cinco vacas da raça Holandesa e duas da raça Jersey, por meio de cultivo e identificação molecular de isolados, com base na análise de sequências de genes 16S rRNA. São identificadas seis espécies bacterianas: as espiroquetas Treponema pedis e Leptospira broomi/L. fainei, L. licerasiae/L. wolffii; Corynebacterium appendicis, Cupriavidus gilardii e Enterococcus casseliflavus/E. gallinarum. O isolamento e a identificação de espécies de Leptospira surpreenderam, destacando-se sua presença em três dos sete cultivos obtidos em diferentes vacas, de duas fazendas distintas. As espécies identificadas pertencem ao grupo tipificado como de patogenicidade intermediária, causador de doenças em animais e no homem. Os resultados apresentados indicam a necessidade de maiores investigações sobre a associação entre Leptospira de patogenicidade intermediária e a patogênese das lesões DDB, investigando-se sua presença e significado nas medicinas veterinária e humana, especialmente em países tropicais.(AU)

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Bovine digital dermatitis (BDD) is an infectious and contagious disease characterized by ulcerative and proliferative lesions affecting the skin on the bulbs of the heel or the interdigital cleft in dairy cattle, often associated with lameness. Evidences on the etiology of BDD indicate that it is multifactorial, involving environmental factors and multiple bacterial colonization. We isolated and identified microorganisms from BDD biopsy samples obtained from five Holstein Friesian and two Jersey cows by cultivation and molecular identification of bacterial isolates using 16S rRNA gene sequence analysis. We identified six bacterial species: Spirochetes as Treponema pedis and Leptospira broomi/L. fainei, L. licerasiae/L. wolffii; Corynebacterium appendicis, Cupriavidus gilardii and Enterococcus casseliflavus/E. gallinarum. It was quite surprising to have isolated and identified Leptospira species in three out of seven cultures, from different individual cows and two different farms. The species identified belong to the intermediate pathogenic clade, which is a group found to cause human and animal disease. Our findings indicate the need to further investigate the association of Leptospira of intermediate pathogenicity with BDD lesions and whether its presence would have any veterinary and medical significance both in Leptospirosis and with the pathogenesis of BDD lesions, especially in tropical countries.(AU)

Dermatite digital bovina (DDB) é uma doença infecciosa, contagiosa, caracterizada por lesões ulcerativas e proliferativas da região dos talões e/ou do espaço interdigital, frequentemente associada com claudicação. Evidências indicam que a etiologia da DDB é multifatorial, envolvendo fatores ambientais e colonização polimicrobiana. Relata-se aqui o isolamento e a identificação bacteriana em amostras de biópsias em lesões de DDB, obtidas de cinco vacas da raça Holandesa e duas da raça Jersey, por meio de cultivo e identificação molecular de isolados, com base na análise de sequências de genes 16S rRNA. São identificadas seis espécies bacterianas: as espiroquetas Treponema pedis e Leptospira broomi/L. fainei, L. licerasiae/L. wolffii; Corynebacterium appendicis, Cupriavidus gilardii e Enterococcus casseliflavus/E. gallinarum. O isolamento e a identificação de espécies de Leptospira surpreenderam, destacando-se sua presença em três dos sete cultivos obtidos em diferentes vacas, de duas fazendas distintas. As espécies identificadas pertencem ao grupo tipificado como de patogenicidade intermediária, causador de doenças em animais e no homem. Os resultados apresentados indicam a necessidade de maiores investigações sobre a associação entre Leptospira de patogenicidade intermediária e a patogênese das lesões DDB, investigando-se sua presença e significado nas medicinas veterinária e humana, especialmente em países tropicais.(AU)

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ABSTRACT The goal of this investigation was to isolate competent polynuclear aromatic hydrocarbons degraders that can utilize polynuclear aromatic hydrocarbons of former industrial sites at McDoel Switchyard in Bloomington, Indiana. Using conventional enrichment method based on soil slurry, we isolated, screened and purified two bacterial species strains PB1 and PB2. Applying the ribotyping technique using the 16S rRNA gene analysis, the strains were assigned to the genus Pseudomonas (Pseudomonas plecoglossicida strain PB1 and Pseudomonas sp. PB2). Both isolates showed promising metabolic capacity on pyrene sprayed MS agar plates during the preliminary investigations. Using time course studies in the liquid cultures at calculated concentrations 123, 64, 97 and 94 ppm for naphthalene, chrysene, fluroanthene and pyrene, P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 showed partial utilization of the polynuclear aromatic hydrocarbons. Naphthalene was degraded between 26% and 40%, chrysene 14% and 16%, fluroanthene 5% and 7%; pyrene 8% and 13% by P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 respectively. Based on their growth profile, we developed a model R2 = 1 to predict the degradation rate of slow polynuclear aromatic hydrocarbon-degraders where all the necessary parameters are constant. From this investigation, we confirm that the former industrial site soil microbial communities may be explored for the biorestoration of the industrial site.

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RESUMO

The goal of this investigation was to isolate competent polynuclear aromatic hydrocarbons degraders that can utilize polynuclear aromatic hydrocarbons of former industrial sites at McDoel Switchyard in Bloomington, Indiana. Using conventional enrichment method based on soil slurry, we isolated, screened and purified two bacterial species strains PB1 and PB2. Applying the ribotyping technique using the 16S rRNA gene analysis, the strains were assigned to the genus Pseudomonas (Pseudomonas plecoglossicida strain PB1 and Pseudomonas sp. PB2). Both isolates showed promising metabolic capacity on pyrene sprayed MS agar plates during the preliminary investigations. Using time course studies in the liquid cultures at calculated concentrations 123, 64, 97 and 94 ppm for naphthalene, chrysene, fluroanthene and pyrene, P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 showed partial utilization of the polynuclear aromatic hydrocarbons. Naphthalene was degraded between 26% and 40%, chrysene 14% and 16%, fluroanthene 5% and 7%; pyrene 8% and 13% by P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 respectively. Based on their growth profile, we developed a model R2 = 1 to predict the degradation rate of slow polynuclear aromatic hydrocarbon-degraders where all the necessary parameters are constant. From this investigation, we confirm that the former industrial site soil microbial communities may be explored for the biorestoration of the industrial site.(AU)

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RESUMO

The goal of this investigation was to isolate competent polynuclear aromatic hydrocarbons degraders that can utilize polynuclear aromatic hydrocarbons of former industrial sites at McDoel Switchyard in Bloomington, Indiana. Using conventional enrichment method based on soil slurry, we isolated, screened and purified two bacterial species strains PB1 and PB2. Applying the ribotyping technique using the 16S rRNA gene analysis, the strains were assigned to the genus Pseudomonas (Pseudomonas plecoglossicida strain PB1 and Pseudomonas sp. PB2). Both isolates showed promising metabolic capacity on pyrene sprayed MS agar plates during the preliminary investigations. Using time course studies in the liquid cultures at calculated concentrations 123, 64, 97 and 94ppm for naphthalene, chrysene, fluroanthene and pyrene, P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 showed partial utilization of the polynuclear aromatic hydrocarbons. Naphthalene was degraded between 26% and 40%, chrysene 14% and 16%, fluroanthene 5% and 7%; pyrene 8% and 13% by P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 respectively. Based on their growth profile, we developed a model R(2)=1 to predict the degradation rate of slow polynuclear aromatic hydrocarbon-degraders where all the necessary parameters are constant. From this investigation, we confirm that the former industrial site soil microbial communities may be explored for the biorestoration of the industrial site.

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