title: Comparison of bacterial  communities in the Solimões and Negro River tributaries of the Amazon River  based on small subunit rRNA gene sequences.
abstract: The  microbiota of the Amazon River basin has been little studied. We compared the  structure of bacterial communities of the Solimões and Negro Rivers, the main  Amazon River tributaries, based on analysis of 16S rRNA gene sequences. Water  was sampled with a 3-L Van Dorn collection bottle; samples were collected at  nine different points/depths totaling 27 L of water from each river. Total DNA  was extracted from biomass retained by a 0.22-μm filter after sequential filtration of  the water through 0.8- and 0.22-μm filters. The 16S rRNA gene was amplified by PCR,  cloned and sequenced, and the sequences were analyzed with the PHYLIP and DOTUR  programs to obtain the operational taxonomic units (OTUs) and to calculate the  diversity and richness indices using the SPADE program. Taxonomic affiliation  was determined using the naive Bayesian rRNA Classifier of the RDP II  (Ribosomal Database Project). We recovered 158 sequences from the Solimões  River grouped into 103 OTUs, and 197 sequences from the Negro River library  grouped into 90 OTUs by the DOTUR program. The Solimões River was found to have  a greater diversity of bacterial genera, and greater estimated richness of 446  OTUs, compared with 242 OTUs from the Negro River, as calculated by ACE  estimator. The Negro River has less bacterial diversity, but more 16S rRNA gene  sequences belonging to the bacterial genus Polynucleobacter were  detected; 56 sequences from this genus were found (about 30% of the total  sequences). We suggest that a more in-depth investigation be made to elucidate  the role played by these bacteria in the river environment. These differences  in bacterial diversity between Solimões and Negro Rivers could be explained by  differences in organic matter content and pH of the rivers.
authors.affiliation: Laboratório de Tecnologias do DNA, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Manaus, AM, Brasil.
authors.forename: J C C
authors.initials: JC
authors.lastname: Peixoto
authors.forename: L
authors.initials: L
authors.lastname: Leomil
authors.forename: J V
authors.initials: JV
authors.lastname: Souza
authors.forename: F B S
authors.initials: FB
authors.lastname: Peixoto
authors.forename: S
authors.initials: S
authors.lastname: Astolfi-Filho
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D001938:Brazil; D015723:Gene Library; D005798:Genes, Bacterial / Q000235:genetics*; D020459:Genes, rRNA / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics*; D054680:Ribosome Subunits, Small, Bacterial / Q000235:genetics*; D045483:Rivers / Q000382:microbiology*
chemical_list: D012335:RNA, Ribosomal