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Detection of integron integrase genes on King George Island, Antarctica

Advances in Polar Science 2015年第1期26卷 30-37页

作者： Verónica Antelo Héctor Romero Silvia Batista Unidad de Microbiología Molecular Biogem Instituto de Investigaciones Biológicas Clemente Estable (MEC) Departamento de Ecología y Evolución Facultad de Ciencias UDeLaR Montevideo C.P.11400 Uruguay

The presence and diversity of class 1 integrase gene （intl） sequences were evaluated by PCR using previously designed primers. Two clone libraries were constructed from DNA in sediment and microbial mat samples collected on Fildes Peninsula, King George Island, *** libraries constructed from samples collected at Halfthree Point （HP） and Norma Cove （NC） contained 62 and 36 partial intl sequences, respectively. These sequences clustered into 10 different groups with 〈 95% amino acid identity. Alignment of the deduced amino acid sequences with those from recognized integron-encoded integrases demonstrated the presence of highly conserved motifs characteristic of intl integrases. The HP library contained 42 nucleotide sequences identical to the class 1 intl gene found in a collection of trimethoprim-resistant （Tmpr） Antarctic Enterobacter sp. isolates, previously collected in the same area. These integrons, located on plasmids, had a genetic organization similar to that of pKOX105 from Klebsiella oxytoca. The 20 remaining HP and NC library sequences were similar to integrase sequences previously determined in a metagenomic analysis of environmental samples. We have demonstrated the presence of integron integrase genes in Antarctic sediment samples. About half these genes were very similar to the class 1 integrons found in human- associated microbiota, suggesting that they originated from human-dominated ecosystems. The remaining integrase genes were probably associated with endemic bacteria.

关键词： integrase amplicon library maritime Antarctica

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Evaluation of Molecular Techniques in Characterization of Deep Terrestrial Biosphere

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Open Journal of Ecology 2014年第8期4卷 468-487页

作者： Malin Bomberg Mari Nyyssonen Aura Nousiainen Jenni Hultman Lars Paulin Petri Auvinen Merja Itavaara VTT Technical Research Centre of Finland EspooFinland Faculty of Veterinary Medicine University of HelsinkiHelsinkiFinland Institute of Biotechnology University of HelsinkiHelsinkiFinland

A suite of molecular methods targeting 16S rRNA genes (i.e., DGGE, clone and high-throughput [HTP] amplicon library sequencing) was used to profile the microbial communities in deep Fennoscandian crystalline bedrock fracture fluids. Variation among bacterial 16S rRNA genes was examined with two commonly used primer pairs: P1/P2 and U968f/U1401r. DGGE using U968f/ U1401r mostly detected β-, γ-proteobacteria and Firmicutes, while P1/P2 primers additionally detected other proteobacterial clades and candidate divisions. However, in combination with clone libraries the U968f/U1401r primers detected a higher bacterial diversity than DGGE alone. HTP amplicon sequencing with P1/P2 revealed an abundance of the DGGE bacterial groups as well as many other bacterial taxa likely representing minor components of these communities. Archaeal diversity was investigated via DGGE or HTP amplicon sequencingusing primers A344F/ 519RP. The majority of archaea detected with HTP amplicon sequencing belonged to uncultured Thermoplasmatales and Pendant 33/DHVE3, 4, 6 groups. DGGE of the same samples detected mostly SAGMEG and Methanosarcinales archaea, but almost none of those were revealed by HTP amplicon sequencing. Overall, our results show that the inferred diversity and composition of microbial communities in deep fracture fluids is highly dependent on analytical technique and that the method should be carefully selected with this in mind.

关键词： DGGE 16S rRNA Gene amplicon library Sequencing Deep Subsurface

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