Comparison of bacterial communities in the Solimões and Negro River tributaries of the Amazon River based on small subunit rRNA gene sequences

Abstract

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.

Bacterial Biogeography across the Amazon River-Ocean Continuum

“…Actinobacteria and Betaproteobacteria dominated all river communities, but the Amazon and Tapajós rivers had higher proportions of Chloroflexi, Acidobacteria, Nitrospirae, and Deltaproteobacteria than other rivers, and a much lower proportion of Flavobacteriia and other Bacteroidetes ( Figure 5B ). Bacteroidetes were detected in the tropical Paraná River, but these taxa did not include Flavobacteriia (Lemke et al, 2009), and Bacteroidetes were not detected in a small survey of bacteria in the tropical Solimões and Negro River tributaries of the Amazon (Peixoto et al, 2011). A small fraction of sequences from an Amazon River metagenome mapped to Bacteroidetes, but it is not clear whether those taxa were Flavobacteriia (Ghai et al, 2011).…”

Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River

“…Many studies describing microbial communities have focused on water environments, such as estuaries101112, rivers1314, lakes151617, and oceans1819. Although researchers have also evaluated bacterioplankton communities within these water environments, few studies of planktonic archaeal communities in freshwater habitats have been performed, particularly in fluvial ecosystems20.…”

Biodiversidad bacteriana en un riachuelo con vertido continuo de efluentes de hidrocarburos

“…En un estudio realizado para analizar la diversidad microbiana presente en el río Negro (afluente del Amazonas, Brasil), se identificó como filo predominante (81 %) Proteobacteria (Neves, 2013). Igualmente, el filo Proteobacteria fue el más abundante en todas las muestras de ríos y lagos de la región amazónica de Brasil (Peixoto et al, 2011;Rodrigues, 2011;Toyama, 2012), el cual es característico de ambientes de agua dulce (Zwart et al, 2002).…”

“…Ciertas estimaciones indican que aproximadamente 99 % de los microorganismos presentes en muchos ambientes naturales, no son cultivables en laboratorio mediante técnicas tradicionales de cultivo (Amann et al, 1995). Los avances recientes en biología molecular, especialmente en la tecnología de secuenciación del ácido desoxirribonucleico (DNA, según sus siglas en inglés), han brindado más oportunidades para estudios exhaustivos de microorganismos en diversos ecosistemas (Parmar et al, 2019), específicamente realizando análisis metagenómico (genomas secuenciados directamente de la muestra ambiental, sin necesidad de cultivo y aislamiento de microorganismos en laboratorio), para determinar de manera más realista la diversidad bacteriana (Peixoto et al, 2011).…”