Microbial communities in an anammox reactor treating municipal wastewater at mainstream conditions : Practical implications of different molecular approaches

Altres ajuts: Acord transformatiu CRUE-CSICBiases on molecular techniques used to study microbial communities in the anammox process are not always considered. This work aimed to evaluate different molecular approaches to study bacterial communities in an anammox reactor treating real urban wastewater at mainstream conditions. 16S rRNA amplicon sequencing with different primer sets, metagenomics, and qPCR were evaluated. An enriched anammox reactor feed with synthetic wastewater was used as a positive control. We reported that, despite its in silico coverage, the universal primers 515F-909R had, in fact, very low coverage (1%) of the Planctomycetota phylum. The functional genes approach showed a taxonomic resolution at the species level, although genomic database updates are a bias to be considered. From the phylogenetic analysis, coherence among the approaches was obtained. Primers targeting anammox 16S rRNA and hydrazine synthase genes in qPCR showed consistency in the quantification, making them useful for comparing similar investigations. According to the results, recommendations on the biomolecular approach to be used were outlined

Evolução dos pacientes com condrossarcoma grau I em relação ao tipo de tratamento cirúrgico

PURPOSE: To evaluate the oncological outcome of patients with grade I chondrosarcomas according to the type of surgical treatment performed, since there is still controversy regarding the need for aggressive resections to reach a successful outcome. MATERIALS AND METHODS: The records of 23 patients with grade I chondrosarcomas were reviewed. The mean age was 38.4 years, ranging from 11 to 70 years; 52% were men and 48% were women. The femur was the site of 13 tumors. The tumors were staged as IA (17, 74%) and IB (6, 26%). Regarding tumor location, 74% (17) were medullary, 22% (5) were peripheral, and 4% (1) was indeterminate. Tumor size ranged from 2 to 25 cm, mean 7.9 cm. Regarding the surgical procedure, 11 patients underwent intralesional resection, 9 patients underwent wide resection, and 3 underwent radical resection. The follow-up period ranged from 24 to 192 months. RESULTS: None of the patients developed local recurrence or metastases; 7 patients had other general complications. CONCLUSIONS: This data supports the use of less aggressive procedures for treatment of low-grade chondrosarcomas.OBJETIVO: Avaliar a evolução oncológica de portadores de condrossarcomas grau I de acordo com o tipo de tratamento cirúrgico efetuado. Existe controvérsia em relação à necessidade de ressecções agressivas para obtenção de uma evolução clínica favorável. MATERIAIS E MÉTODOS: Os prontuários de 23 portadores de condrossarcoma grau I foram analisados. A idade dos pacientes variou de 11 a 70 anos com média de 38,4 anos, 52% eram homens e 48% mulheres. O local mais acometido foi o fêmur com 13 pacientes. Dezessete lesões (74%) foram classificadas como IA e seis (26%) como IB. Setenta e quatro por cento dos tumores eram medulares, 22% eram periféricas e uma lesão indeterminada. O tamanho dos tumores variou de 2 a 25 cm, média de 7,9 cm. Onze pacientes foram submetidos a ressecção intralesional, nove a ressecção ampla e três a ressecção radical. O seguimento variou de 24 a 192 meses. RESULTADOS: Complicações não oncológicas ocorreram em sete pacientes. Nenhum dos pacientes apresentou recidiva local ou metástase. Estes dados sugerem que os procedimentos cirúrgicos menos agressivos são seguros para o tratamento dos pacientes com condrossarcoma grau I

Metagenómica y metatranscriptómica aplicadas al estudio de Chloroflexota en sistemas de tratamiento de aguas residuales escala real

El filo Chloroflexota es uno de los grupos predominantes en sistemas de tratamiento de aguas residuales aerobios (lodos activados) y anaerobios (metanogénicos). Dentro de este filo, la clase Anaerolineae representa más del 80%, sin embargo, su rol en estos sistemas aún sigue sin conocerse. Esto se debe principalmente a las dificultades para asilarlos en cultivo puro. Los pocos representantes cultivados son capaces de fermentar, se caracterizan por tener crecimiento lento y morfología filamentosa. Se ha postulado que están involucrados en la formación de gránulos en reactores anaerobios y flóculos en reactores de lodos activados, pero su crecimiento excesivo se ha relacionado problemas de sedimentación de la biomasa (bulking). Las condiciones que favorecen el crecimiento excesivo de estas bacterias siguen siendo desconocidas. Expandir el conocimiento sobre este grupo es esencial para controlar su sobrecrecimiento y prevenir episodios de bulking. Para determinar la morfología, diversidad y expresión génica de organismos del filo Chloroflexota, se aplicaron diversas técnicas de biología molecular como hibridación in situ fluorescente, secuenciación de amplicones, metagenómica y metatranscriptómica en dos reactores de lodos activados y dos reactores metanogénicos que trataban distintas aguas residuales industriales. El filo Chloroflexota fue uno de los 5 filos más abundantes en todos los reactores y presentó diversas morfologías filamentosas. Se ensamblaron 17 genomas de especies nuevas de la clase Anaerolineae y un genoma de la clase Dehalococcoidia. Mediante el análisis de las vías metabólicas obtenidas mediante metagenómica se determinó que todos los genomas presentaron varias vías de fermentación, que incluían la producción de lactato, acetato, formiato y acetoína. Los genomas obtenidos de sistemas aerobios presentaron el potencial de respirar anaeróbicamente utilizando nitrito y nitrato reductasas como aceptores de electrones. Estas funciones metabólicas fueron confirmadas mediante el análisis de los metatranscriptomas. Por lo tanto, las especies del filo Chloroflexota detectadas en estos sistemas de tratamiento juegan un rol fundamental en la remoción de la materia en sistemas aerobios y anaerobios, y particularmente en sistemas de lodos activados, colaboran en la remoción del nitrogeno de las aguas residuales.Agencia Nacional de Investigación e Innovació

Proposal for a new classification of a deep branching bacterial phylogenetic lineage: Transfer of Coprothermobacter proteolyticus and Coprothermobacter platensis to Coprothermobacteraceae fam. nov., within Coprothermobacterales ord. nov., Coprothermobacteria classis nov. and Coprothermobacterota phyl. nov. and emended description of the family Thermodesulfobiaceae

The genus Coprothermobacter (initially named Thermobacteroides) is currently placed within the phylum Firmicutes. Early 16S rRNA gene based phylogenetic studies pointed out the great differences between Coprothermobacter and other members of the Firmicutes, revealing that it constitutes a new deep branching lineage. Over the years, several studies based on 16S rRNA gene and whole genome sequences have indicated that Coprothermobacter is very distant phylogenetically to all other bacteria, supporting its placement in a distinct deeply rooted novel phylum. In view of this, we propose its allocation to the new family Coprothermobacteraceae within the novel order Coprothermobacterales, the new class Coprothermobacteria, and the new phylum Coprothermobacterota, and an emended description of the family Thermodesulfobiaceae.Fil: Pavan, Maria Elisa. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Pavan, Esteban E.. Politecnico di Milano; ItaliaFil: Glaeser, Stefanie P.. Universitat Giessen; AlemaniaFil: Etchebehere, Claudia. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Kämpfer, Peter. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Pettinari, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; ArgentinaFil: López, Nancy Irene. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentin

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Microbial communities are responsible for biological wastewater treatment, but our knowledge of their diversity and function is still poor. Here, we sequence more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and use the sequences to construct the ‘MiDAS 4’ database. MiDAS 4 is an amplicon sequence variant resolved, full-length 16S rRNA gene reference database with a comprehensive taxonomy from domain to species level for all sequences. We use an independent dataset (269 WWTPs) to show that MiDAS 4, compared to commonly used universal reference databases, provides a better coverage for WWTP bacteria and an improved rate of genus and species level classification. Taking advantage of MiDAS 4, we carry out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting regions of the 16S rRNA gene, revealing how environmental conditions and biogeography shape the activated sludge microbiota. We also identify core and conditionally rare or abundant taxa, encompassing 966 genera and 1530 species that represent approximately 80% and 50% of the accumulated read abundance, respectively. Finally, we show that for well-studied functional guilds, such as nitrifiers or polyphosphate-accumulating organisms, the same genera are prevalent worldwide, with only a few abundant species in each genus.Fil: Dueholm, Morten Kam Dahl. Aalborg University; DinamarcaFil: Nierychlo, Marta. Aalborg University; DinamarcaFil: Andersen, Kasper Skytte. Aalborg University; DinamarcaFil: Rudkjøbing, Vibeke. Aalborg University; DinamarcaFil: Knutsson, Simon. Aalborg University; DinamarcaFil: Arriaga, Sonia. Instituto Potosino de Investigación Científica y Tecnológica; MéxicoFil: Bakke, Rune. University College of Southeast Norway; NoruegaFil: Boon, Nico. University of Ghent; BélgicaFil: Bux, Faizal. Durban University of Technology; SudáfricaFil: Christensson, Magnus. Veolia Water Technologies Ab; SueciaFil: Chua, Adeline Seak May. University Malaya; MalasiaFil: Curtis, Thomas P.. University of Newcastle; Reino UnidoFil: Cytryn, Eddie. Agricultural Research Organization Of Israel; IsraelFil: Erijman, Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires; ArgentinaFil: Etchebehere, Claudia. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Fatta Kassinos, Despo. University of Cyprus; ChipreFil: Frigon, Dominic. McGill University; CanadáFil: Garcia Chaves, Maria Carolina. Universidad de Antioquia; ColombiaFil: Gu, April Z.. Cornell University; Estados UnidosFil: Horn, Harald. Karlsruher Institut Für Technologie; AlemaniaFil: Jenkins, David. David Jenkins & Associates Inc; Estados UnidosFil: Kreuzinger, Norbert. Tu Wien; AustriaFil: Kumari, Sheena. Durban University of Technology; SudáfricaFil: Lanham, Ana. University of Bath; Reino UnidoFil: Law, Yingyu. Singapore Centre For Environmental Life Sciences Engineering; SingapurFil: Leiknes, TorOve. King Abdullah University of Science and Technology; Arabia SauditaFil: Morgenroth, Eberhard. Eth Zürich; SuizaFil: Muszyński, Adam. Politechnika Warszawska; PoloniaFil: Petrovski, Steve. La Trobe University; AustraliaFil: Pijuan, Maite. Catalan Institute For Water Research; EspañaFil: Pillai, Suraj Babu. Va Tech Wabag Ltd; IndiaFil: Reis, Maria A. M.. Universidade Nova de Lisboa; PortugalFil: Rong, Qi. Chinese Academy of Sciences; ChinaFil: Rossetti, Simona. Istituto Di Ricerca Sulle Acque (irsa) ; Consiglio Nazionale Delle Ricerche;Fil: Seviour, Robert. La Trobe University; AustraliaFil: Tooker, Nick. University of Massachussets; Estados UnidosFil: Vainio, Pirjo. Espoo R&D Center; FinlandiaFil: van Loosdrecht, Mark. Delft University of Technology; Países BajosFil: Vikraman, R.. VA Tech Wabag, Philippines Inc; FilipinasFil: Wanner, Jiří. University of Chemistry And Technology; República ChecaFil: Weissbrodt, David. Delft University of Technology; Países BajosFil: Wen, Xianghua. Tsinghua University; ChinaFil: Zhang, Tong. The University of Hong Kong; Hong KongFil: Nielsen, Per H.. Aalborg University; DinamarcaFil: Albertsen, Mads. Aalborg University; DinamarcaFil: Nielsen, Per Halkjær. Aalborg University; Dinamarc

Presence of Two Different Active nirS Nitrite Reductase Genes in a Denitrifying Thauera sp. from a High-Nitrate-Removal-Rate Reactor

The nirS nitrite reductase genes were studied in two strains (strains 27 and 28) isolated from two denitrifying reactors and characterized as Thauera according to their 16S rRNA gene sequences. Strain 28 contains a single nirS sequence, which is related to the nirS of Thauera mechernichensis, and strain 27 contains two nirS sequences; one is similar to the nirS sequence from Thauera mechernichensis (gene 2), but the second one (gene 8) is from a separate clade with nirS from Pseudomonas stutzeri, Azoarcus species, Alcaligenes faecalis, and other Thauera species. Both genes were expressed, but gene 8 was constitutively expressed while gene 2 was positively regulated by nitrate

Editorial: Meta-omic Approaches to the Complex Anaerobic Communities in Wastewater Treatment Plants and Digesters

none4openErijman L.; Campanaro S.; Etchebehere C.; Varesche M.B.A.Erijman, L.; Campanaro, S.; Etchebehere, C.; Varesche, M. B. A

Correlations between molecular and operational parameters in continuous lab-scale anaerobic reactors

In this study, the microbial community characteristics in continuous lab-scale anaerobic reactors were correlated to reactor functionality using the microbial resource management (MRM) approach. Two molecular techniques, denaturing gradient gel electrophoresis (DGGE) and terminal-restriction fragment length polymorphism (T-RFLP), were applied to analyze the bacterial and archaeal communities, and the results obtained have been compared. Clustering analyses showed a similar discrimination of samples with DGGE and T-RFLP data, with a clear separation between the meso- and thermophilic communities. Both techniques indicate that bacterial and mesophilic communities were richer and more even than archaeal and thermophilic communities, respectively. Remarkably, the community composition was highly dynamic for both Bacteria and Archaea, with a rate of change between 30% and 75% per 18 days, also in stable performing periods. A hypothesis to explain the latter in the context of the converging metabolism in anaerobic processes is proposed. Finally, a more even and diverse bacterial community was found to be statistically representative for a well-functioning reactor as evidenced by a low Ripley index and high biogas production

Desarrollo de una técnica de bioprospección de hidrocarburos basada en la detección del gen bmoX

En la última década, el gobierno de Uruguay ha comenzado a incorporar fuentes de energía renovables en la matriz energética del país. Sin embargo, el uso de los hidrocarburos continúa dominando, principalmente en el área del transporte. Actualmente, Uruguay no es un país productor de hidrocarburos pero recientemente se han realizado actividades de exploración onshore y offshore. La bioprospección se basa en la detección de algunos grupos de microorganismos indicadores de reservas de petróleo o gas. Uno de estos grupos son las bacterias oxidadoras de butano. Estas bacterias se encuentran enriquecidas en los suelos ubicados encima de las reservas de hidrocarburos debido a que el gas butano presente en las reservas difunde hacia la superficie generando zonas de alta concentración de gas butano y por lo tanto, estimulando el crecimiento de dichas bacterias. En el presente trabajo nos enfocamos en desarrollar un método molecular fiable y validado que permita detectar bacterias oxidadoras de butano. Esto es relevante para ANCAP ya que los métodos que han utilizado hasta el momento son dependientes de cultivo y no han dado resultados confiables. Se decidió poner a punto la técnica de real-time PCR específica para el gen bmoX utilizando los primers bmoX-F y bmoX-R diseñados por Zhang et al., 2013 . Este gen codifica para la subunidad alfa de la butano hidroxilasa, una proteína capaz de hidrolizar el butano. Para la puesta a punto utilizamos como control positivo Thauera butanivorans DSM2080 que contiene el gen bmoX. Con dicha cepa se realizará la curva estándar. La técnica será probada en suelos positivos obtenidos de un pozo petrolero de Argentina y suelos negativos uruguayos utilizados para fines agronómicos. Para conocer el límite de detección de la técnica se mezclarán concentraciones conocidas de la cepa T. butanivorans con suelos negativos y se realizará la técnica de real time PCR. Finalmente, se aplicará la técnica sobre suelos uruguayos de sitios donde ya se utilizó la técnica de bioprospección utilizando métodos tradicionales de cultivo. Hasta el momento se puso a punto un ensayo de PCR a tiempo final del gen bmoX utilizando la cepa T. butanivorans. Se logró amplificar el gen del tamaño esperado de 419 pb. Además, se confirmó la presencia del gen en algunas muestras de suelos positivos. Actualmente nos encontramos poniendo a punto el ensayo de real-time PCR. Los resultados obtenidos contribuirán al desarrollo de metodologías novedosas y aportan métodos confiables para la bioprospección de petróleo por parte de ANCAP.Agencia Nacional de Investigación e Innovació

Relationship between surgical procedure and outcome for patients with grade I chondrosarcomas Evolução dos pacientes com condrossarcoma grau I em relação ao tipo de tratamento cirúrgico

PURPOSE: To evaluate the oncological outcome of patients with grade I chondrosarcomas according to the type of surgical treatment performed, since there is still controversy regarding the need for aggressive resections to reach a successful outcome. MATERIALS AND METHODS: The records of 23 patients with grade I chondrosarcomas were reviewed. The mean age was 38.4 years, ranging from 11 to 70 years; 52% were men and 48% were women. The femur was the site of 13 tumors. The tumors were staged as IA (17, 74%) and IB (6, 26%). Regarding tumor location, 74% (17) were medullary, 22% (5) were peripheral, and 4% (1) was indeterminate. Tumor size ranged from 2 to 25 cm, mean 7.9 cm. Regarding the surgical procedure, 11 patients underwent intralesional resection, 9 patients underwent wide resection, and 3 underwent radical resection. The follow-up period ranged from 24 to 192 months. RESULTS: None of the patients developed local recurrence or metastases; 7 patients had other general complications. CONCLUSIONS: This data supports the use of less aggressive procedures for treatment of low-grade chondrosarcomas.<br>OBJETIVO: Avaliar a evolução oncológica de portadores de condrossarcomas grau I de acordo com o tipo de tratamento cirúrgico efetuado. Existe controvérsia em relação à necessidade de ressecções agressivas para obtenção de uma evolução clínica favorável. MATERIAIS E MÉTODOS: Os prontuários de 23 portadores de condrossarcoma grau I foram analisados. A idade dos pacientes variou de 11 a 70 anos com média de 38,4 anos, 52% eram homens e 48% mulheres. O local mais acometido foi o fêmur com 13 pacientes. Dezessete lesões (74%) foram classificadas como IA e seis (26%) como IB. Setenta e quatro por cento dos tumores eram medulares, 22% eram periféricas e uma lesão indeterminada. O tamanho dos tumores variou de 2 a 25 cm, média de 7,9 cm. Onze pacientes foram submetidos a ressecção intralesional, nove a ressecção ampla e três a ressecção radical. O seguimento variou de 24 a 192 meses. RESULTADOS: Complicações não oncológicas ocorreram em sete pacientes. Nenhum dos pacientes apresentou recidiva local ou metástase. Estes dados sugerem que os procedimentos cirúrgicos menos agressivos são seguros para o tratamento dos pacientes com condrossarcoma grau I