Spatial Distribution of Total, Ammonia-Oxidizing, and Denitrifying Bacteria in Biological Wastewater Treatment Reactors for Bioregenerative Life Support

Sakano, Yuko; Pickering, Karen D.; Strom, Peter F.; Kerkhof, Lee J.

doi:10.1128/aem.68.5.2285-2293.2002

Cited by 58 publications

(30 citation statements)

References 30 publications

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“…For TRFLP analysis, a fluorescent dye was incorporated on the 5Ј primer for 16S rRNA genes (27). Fluorescently labeled PCR products (20 l) were purified with the Geneclean kit II (Qbiogene, Inc., Carlsbad, Calif.) and were digested for 6 h at 37°C with MnlI (New England Biolabs, Beverly, Mass.).…”

Section: Methodsmentioning

confidence: 99%

“…DNA was extracted from whole sponge tissues and enrichment cultures by using a UltraClean Soil DNA isolation kit (MO BIO, Solana Beach, Calif.). For 16S rDNA gene amplification, genomic DNA was amplified with bacterial universal primers 27F and 1525R (16), as described previously (27). PCR amplification parameters were as follows: 94°C and 5 min of initial melt; 30 amplification cycles of 94°C, 30 s; 55°C, 30 s; and 72°C, 1.3 min; and a final extension at 72°C for 10 min in a Perkin-Elmer Gene-AMP PCR system 2400 thermal cycler (Perkin-Elmer, Foster City, Calif.).…”

Section: Methodsmentioning

confidence: 99%

“…We used specific PCR primers designed for the detection of reductive dehalogenase genes (26) to demonstrate the presence of putative dehalogenase gene motifs in sponge tissue and associated bacteria. To determine the microbial community enriched on each substrate and to identify sponge-associated microorganisms involved in dehalogenation, two community analysis techniques, denaturing gradient gel electrophoresis (DGGE) (28,39) and terminal restriction fragment length polymorphism (TRFLP) (15,27), were used (41).…”

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confidence: 99%

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Reductive Dehalogenation of Brominated Phenolic Compounds by Microorganisms Associated with the Marine Sponge Aplysina aerophoba

Ahn¹,

Rhee

Fennell

et al. 2003

Appl Environ Microbiol

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122

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Marine sponges are natural sources of brominated organic compounds, including bromoindoles, bromophenols, and bromopyrroles, that may comprise up to 12% of the sponge dry weight. Aplysina aerophoba sponges harbor large numbers of bacteria that can amount to 40% of the biomass of the animal. We postulated that there might be mechanisms for microbially mediated degradation of these halogenated chemicals within the sponges. The capability of anaerobic microorganisms associated with the marine sponge to transform haloaromatic compounds was tested under different electron-accepting conditions (i.e., denitrifying, sulfidogenic, and methanogenic). We observed dehalogenation activity of sponge-associated microorganisms with various haloaromatics. 2-Bromo-, 3-bromo-, 4-bromo-, 2,6-dibromo-, and 2,4,6-tribromophenol, and 3,5-dibromo-4-hydroxybenzoate were reductively debrominated under methanogenic and sulfidogenic conditions with no activity observed in the presence of nitrate. Monochlorinated phenols were not transformed over a period of 1 year. Debromination of 2,4,6-tribromophenol, and 2,6-dibromophenol to 2-bromophenol was more rapid than the debromination of the monobrominated phenols. Ampicillin and chloramphenicol inhibited activity, suggesting that dehalogenation was mediated by bacteria. Characterization of the debrominating methanogenic consortia by using terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis analysis indicated that different 16S ribosomal DNA (rDNA) phylotypes were enriched on the different halogenated substrates. Sponge-associated microorganisms enriched on organobromine compounds had distinct 16S rDNA TRFLP patterns and were most closely related to the ␦ subgroup of the proteobacteria. The presence of homologous reductive dehalogenase gene motifs in the sponge-associated microorganisms suggested that reductive dehalogenation might be coupled to dehalorespiration.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Reductive Dehalogenation of Brominated Phenolic Compounds by Microorganisms Associated with the Marine Sponge Aplysina aerophoba

Ahn¹,

Rhee

Fennell

et al. 2003

Appl Environ Microbiol

Self Cite

122

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“…A selection of environmental nosZ clones from marine sediment (Scala & Kerkof 1999, Mills et al 2008, soils (Stres et al 2004, Horn et al 2006, wastewater (Sakano et al 2002) and coastal seawater (unpublished, Accession #AB089825, AB089829 and AB089832) were chosen to cover the greatest possible sequence variation. The tree was reconstructed using sequences of partial gene fragments (1137-bp) with Neighbor Joining and Maximum Likelihood method integrated in the Bosque program.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Structure of denitrifying communities reducing N2O at suboxic waters off northern Chile and Perú

Castro-González

Ulloa

2015

Rev. biol. mar. oceanogr.

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Resumen.-El gen nosZ, el cual codifica para la reducción de N 2 O a N 2 , fue usado para estudiar la estructura de las comunidades desnitrificantes en la zona de mínimo oxígeno frente a las costas de Chile y Perú, a través del polimorfismo de los fragmentos largos de restricción terminal (PFLRT) y clonamiento de los genes nosZ. El análisis del PFLRT mostró poca diversidad de genes nosZ en las profundidades subóxicas (núcleo de la zona de mínimo oxígeno-ZMO) comparado con las profundidades donde el O 2 varío ampliamente (límite superior de la zona de mínimo oxígeno o LSZMO). Las comunidades desnitrificantesnosZ presentaron diferencias en su estructura entre localidades geográficas y tiempo de muestreo sugiriendo asociación con la variación en las condiciones ambientales. El análisis de correspondencia canónica indicó que los parámetros ambientales seleccionados como variables predictoras (N 2 O, O 2 , NH 4 + y NO 2 -) explicaron bien las diferencias en la composición de la comunidad nosZ entre sitios de muestreo. El análisis filogenético mostró poca diversidad de secuencias nosZ y agrupó el 81% de los clones cerca al clúster de secuencias de sedimentos del Pacífico. Las secuencias no se relacionaron con ninguna secuencia nosZ reportada en agua de mar, o de bacterias desnitrificantes conocidas, demostrando la novedad de los filotipos encontrados en esta área. Palabras clave: Pacífico sur este, gen nosZ, zona de mínimo oxígenoAbstract.-The nosZ gene, which encodes for N 2 O reduction to N 2 , was used to study the structure of denitrifying communities in the oxygen minimum zone off Chilean and Peruvian coast throughout terminal restriction fragment length polymorphism (TRFLP) and cloning of nosZ genes. TRFLP analysis showed little diversity of nosZ genes at suboxic depths (Oxygen Minimum Zone´s core) compared with depths where O 2 largely varied (upper limit of OMZ or ULOMZ). The nosZ-denitrifying communities showed differences in its structure between geographical locations and time sampling suggesting an association with the shift in the environmental conditions. The canonical correspondence analysis showed that the environmental parameters selected as predictor variables (N 2 O, O 2 , NH 4 + and NO 2 -) explained well the differences in nosZ-denitrifying community composition among sampling sites. The phylogenetic analysis showed little nosZ sequence diversity and grouped 81% of nosZ-clones near the cluster of sediments sequences from Pacific. Our sequences did not branch with any known denitrifying bacteria or seawater nosZ-sequences available, demonstrating the novelty of phylotypes founded in this area.

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“…In several ecosystems, these techniques have proven to be valuable for the comparison of the structures of complex microbial communities and for monitoring their dynamics in relation to environmental factors (Bernard et al 2000, Scala & Kerkhof 2000, Hollibaugh et al 2002, Sakano et al 2002, Freitag & Prosser 2003, Jasti et al 2005. Denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphisms (T-RFLP), have been applied in the study of microbial ecology community structure and dynamics, detecting differences in the nucleotide sequence of 16S rRNA genes that belong to different genotypes (Heuer et al 1997, Bernard et al 2000, Scala & Kerkhof 2000.…”

Section: Introductionmentioning

confidence: 99%

Diversity of the marine picocyanobacteria Prochlorococcus and Synechococcus assessed by terminal restriction fragment length polymorphisms of 16S-23S rRNA internal transcribed spacer sequences

Lavín¹,

Gómez²,

Gonzále

et al. 2008

Rev. chil. hist. nat.

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In order to assess the appropriateness of the use of internal transcribed spacer (ITS) sequences for the study of population genetics of marine cyanobacteria, we amplified and cloned the 16S rRNA gene plus the 16S-23S ITS regions of six strains of Prochlorococcus and Synechococcus. We analyzed them by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphisms (T-RFLP). When using the standard application of these techniques, we obtained more than one band or terminal restriction fragment (T-RF) per strain or cloned sequence. Reports in literature have suggested that these anomalies can result from the formation of secondary structures. Secondary structures of the ITS sequences of Prochlorococcus and Synechococcus strains were computationally modelled at the different temperatures that were used during the polymerase chain reaction (PCR). Modelling results predicted the existence of hairpin loops that would still be present at the extension temperature; it is likely that these loops produced incomplete and single stranded PCR products. We modified the standard T-RFLP procedure by adding the labelled ITS primer in the last two cycles of the PCR reaction; this resulted, in most cases, in only one T-RF per ribotype. Application of this technique to a natural picoplankton community in marine waters off northern Chile, showed that it was possible to identify the presence, and determine the relative abundance, of several phylogenetic lineages within the genera Prochlorococcus and Synechococcus inhabiting the euphotic zone. Phylogenetic analysis of ITS sequences obtained by cloning and sequencing DNA from the same sample confirmed the presence of the different genotypes. With the proposed modification, T-RFLP profiles should therefore be suitable for studying the diversity of natural populations of cyanobacteria, and should become an important tool to study the factors influencing the genetic structure and distribution of these organisms.Key words: cyanobacteria, DGGE, T-RFLP, ITS, secondary structure. RESUMENCon el fin de evaluar la utilización de secuencias del espaciador interno transcrito (ITS) en estudios de genética de población de cianobacterias marinas, se amplificó y clonó la secuencia del gen ARNr 16S junto a la región espaciadora 16S-23S ARNr de seis cepas de Prochlorococcus y Synechococcus. Se analizaron los amplicones del ITS por electroforesis en gel de gradiente de desnaturalización (DGGE) y por polimorfismos de longitud de fragmentos de restricción terminal (T-RFLP). Al aplicar los métodos estándares de estas técnicas, se obtuvo más de una banda o fragmento de restricción terminal (T-RF) por cepa o secuencia clonada. Informes en la literatura han sugerido que estas anomalías podrían ser atribuidas a la formación de estructuras secundarias. Por consiguiente, la estructura secundaria de las secuencias de ITS de las cepas de Prochlorococcus y Synechococcus fue modelada a las diferentes temperaturas que se utilizaron durante la reacción en cadena de polimera...

show abstract

Spatial Distribution of Total, Ammonia-Oxidizing, and Denitrifying Bacteria in Biological Wastewater Treatment Reactors for Bioregenerative Life Support

Cited by 58 publications

References 30 publications

Reductive Dehalogenation of Brominated Phenolic Compounds by Microorganisms Associated with the Marine Sponge Aplysina aerophoba

Reductive Dehalogenation of Brominated Phenolic Compounds by Microorganisms Associated with the Marine Sponge Aplysina aerophoba

Structure of denitrifying communities reducing N2O at suboxic waters off northern Chile and Perú

Diversity of the marine picocyanobacteria Prochlorococcus and Synechococcus assessed by terminal restriction fragment length polymorphisms of 16S-23S rRNA internal transcribed spacer sequences

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