Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA

Edwards, Ulrike; Rogall, Till; Blöcker, Helmut; Emde, Monica; Böttger, Erik C.

doi:10.1093/nar/17.19.7843

Cited by 2,394 publications

(1,476 citation statements)

References 25 publications

(22 reference statements)

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“…PCR products were purified with the QIAquick PCR purification kit (Qiagen) and sequenced (GATC, Konstanz, Germany) with the following primers: 27F (Edwards et al, 1989) (59-AGA GTT TGA TCC TGG CTC AG-39), 1492R (Weisburg et al, 1991) (59-TAC GGY TAC CTT GTT ACG ACT T-39), 907R (Lane et al, 1985) (59-CCC GTC AAT TCM TTT GAG TTT-39) and 533F (Weisburg et al, 1991) (59-GTG CCA GCA GCC GCG GTA A-39). Sequences were aligned using DNASTAR (http://www.dnastar.com) and corrected manually.…”

Section: Methodsmentioning

confidence: 99%

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17

2010

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In anaerobic enrichment cultures for phototrophic nitrite-oxidizing bacteria from different freshwater sites, two different cell types, i.e. non-motile cocci and motile, rod-shaped bacteria, always outnumbered all other bacteria. Most-probable-number (MPN) dilution series with samples from two freshwater sites yielded only low numbers (¡3¾10 3 cm "3 ) of phototrophic nitrite oxidizers. Slightly higher numbers (about 10 4 cm "3 ) were found in activated sewage sludge. Anaerobic phototrophic oxidation of nitrite was studied with two different isolates, the phototrophic sulfur bacterium strain KS1 and the purple nonsulfur bacterium strain LQ17, both of which were isolated from activated sludge collected from the municipal sewage treatment plant in Konstanz, Germany. Strain KS1 converted 1 mM nitrite stoichiometrically to nitrate with concomitant formation of cell matter within 2-3 days, whereas strain LQ17 oxidized only up to 60 % of the given nitrite to nitrate within several months with the concomitant formation of cell biomass. Nitrite oxidation to nitrate was strictly light-dependent and required the presence of molybdenum in the medium. Nitrite was oxidized in both the presence and absence of oxygen. Nitrite inhibited growth at concentrations higher than 2 mM. Hydroxylamine and hydrazine were found to be toxic to the phototrophs in the range 5-50 mM and did not stimulate phototrophic growth. Based on morphology, substrate-utilization pattern, in vivo absorption spectra, and 16S rRNA gene sequence similarity, strain KS1 was assigned to the genus Thiocapsa and strain LQ17 to the genus Rhodopseudomonas. Also, Thiocapsa roseopersicina strains DSM 217 and DSM 221 were found to oxidize nitrite to nitrate with concomitant growth. We conclude that the ability to use nitrite phototrophically as electron donor is widespread in nature, but low MPN counts indicate that its contribution to nitrite oxidation in the studied habitats is rather limited.

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Section: Methodsmentioning

confidence: 99%

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17

2010

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“…the region between 20 and 80 % activity of PP1 enzyme. (Edwards et al, 1989) and B23S with PCR cycling as described by Lepère et al (2000). For amplification of over 500 bp of rpoB, primers (rpobF, rpoBR, rpoBF2 and rpoBR2) and PCR cycling conditions described by Rajaniemi et al (2005) were used.…”

Section: Methodsmentioning

confidence: 99%

Benthic cyanobacteria of the genus Nodularia are non-toxic, without gas vacuoles, able to glide and genetically more diverse than planktonic Nodularia

Lyra

Laamanen²,

Lehtimäki

et al. 2005

International Journal of Systematic and Evolutionary Microbiology

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Diversity and ecological features of cyanobacteria of the genus Nodularia from benthic, periphytic and soil habitats are less well known than those of Nodularia from planktonic habitats. Novel benthic Nodularia strains were isolated from the Baltic Sea and their morphology, the presence of gas vacuoles, nodularin production, gliding, 16S rRNA gene sequences, rpoB, rbcLX and ndaF genes, and gvpA-IGS regions were examined, as well as short tandemly repeated repetitive sequence fingerprints. Strains were identified as Nodularia spumigena, Nodularia sphaerocarpa or Nodularia harveyana on the basis of the size and shape of the different types of cells and the presence or absence of gas vacuoles. The planktonic strains of N. spumigena mostly had gas vacuoles and produced nodularin, whereas the benthic strains of N. sphaerocarpa and N. harveyana lacked gas vacuoles and did not produce nodularin (except for strain PCC 7804). The benthic strains were also able to glide on surfaces. In the genetic analyses, the planktonic N. spumigena and benthic N. sphaerocarpa formed monophyletic clusters, but the clusters were very closely related. Benthic strains determined as N. harveyana formed the most diverse and distant group of strains. In addition to phylogenetic analyses, the lack of the gvpA-IGS region and ndaF in N. sphaerocarpa and N. harveyana distinguished these species from the planktonic N. spumigena. Therefore, ndaF can be considered as a potential diagnostic tool for detecting and quantifying Baltic Sea bloom-forming, nodularin-producing N. spumigena strains. The data confirm that only one morphologically and genetically distinct planktonic species of Nodularia, N. spumigena, and at least two benthic species, N. sphaerocarpa and N. harveyana, exist in the Baltic Sea.

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“…The gene encoding 16S rRNA from selected isolates was amplified by PCR using universal primer pair pA (5 0 -AGA GTT TGA TCC TGG CTC AG-3 0 ) and pH (5 0 -AAG GAG GTG ATC CAG CCG CA-3 0 ) [15]. Approximately 1 lg of PCRamplified 16S rDNA gene fragments were cleaved with endonucleases DdeI, and TaqI (Fermentas, USA) separately at 37°C for overnight and resolved by electrophoresis in 2.5 % agarose.…”

Section: Identification Of Bacterial Isolatesmentioning

confidence: 99%

Influence of Long Term Irrigation with Pulp and Paper Mill Effluent on the Bacterial Community Structure and Catabolic Function in Soil

et al. 2013

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Microbial communities play a vital role in maintaining soil health. A multiphasic approach to assess the effect of pulp and paper mill effluent on both the structure and function of microbial soil communities is taken. Bacterial communities from agricultural soils irrigated with pulp and paper mill effluent were compared to communities form soils irrigated with well water. Samples were taken from fields in the state of Uttarakhand, India, where pulp and paper mill effluent has been used for irrigation for over 25 years.

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Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA

Cited by 2,394 publications

References 25 publications

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17

Benthic cyanobacteria of the genus Nodularia are non-toxic, without gas vacuoles, able to glide and genetically more diverse than planktonic Nodularia

Influence of Long Term Irrigation with Pulp and Paper Mill Effluent on the Bacterial Community Structure and Catabolic Function in Soil

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