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The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.

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In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable.

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Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.

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Protozooplankton is an important component of the aquatic microbial food webs and its composition, density, and distribution reflect the chemical, physical, and biological aspects of the environment. Considering the scarce literature on freshwater protozoans in Brazil and on protozoan ecology in subtropical environments, we listed the ciliates and amoebae taxa found in 13 water bodies in São Paulo State and analyzed their abundance in relation to the environmental variables. We collected two samples in each environment, fixed immediately with mercuric chloride and stained with bromophenol blue. After microscopical analysis, 74 protozoan genera were identified and the Ciliophora were dominant in the majority of the environments. The Stichotrichia, represented mostly by the genus Halteria, occurred in all environments, and was the dominant subclass in five of them. The canonic correspondence analysis of the most frequent genera and the environmental variables showed that nitrite and nitrate were the variables that better explained the distribution of Limnostrombidium, Urotricha, and Vorticella. The densities of the genera Halteria, Coleps, and of the species Cinetochilum margaritaceum were positively affected by increasing concentrations of dissolved oxygen, particulate phosphate, conductivity, and temperature. C. margaritaceum were also negatively affected by increasing concentrations of nitrite and nitrate. Considering that we made only one sampling in each environment, the richness was high compared to the mean diversity of lakes in the São Paulo State. The Diogo Lake, located in an ecological reserve, was the richest one, confirming the need of more research on the biodiversity of more preserved environments.

O protozooplâncton é um componente importante da rede trófica microbiana de ambientes aquáticos e sua composição, densidade e distribuição refletem os aspectos físicos, químicos e bióticos do ambiente. Considerando a escassa literatura sobre protozoários de água doce no Brasil e sobre sua ecologia em ambientes subtropicais, inventariamos os táxons de ciliados e amebas em 13 corpos d'água do Estado de São Paulo e analisamos a variação na abundância dos gêneros/espécies de maior incidência em relação às variáveis ambientais. Coletamos duas amostras por ambiente, fixando-as com cloreto de mercúrio e corando-as com azul de bromofenol para posterior quantificação e identificação em microscópio ótico. Identificamos 74 gêneros de ciliados e amebas, e os Ciliophora dominaram na maioria dos ambientes. A subclasse Stichotrichia ocorreu em todos os ambientes, predominando em cinco deles, especialmente pela ocorrência o gênero Halteria. A Análise de Correspondência Canônica mostrou que as concentrações de nitrito e nitrato são as principais variáveis que explicam a distribuição dos gêneros Limnostrombidium, Urotricha e Vorticella. O aumento na concentração de oxigênio dissolvido, condutividade, temperatura e concentração de fosfato particulado afetou positivamente a densidade dos gêneros Halteria e Coleps e da espécie Cinetochilum margaritaceum, que foi ainda influenciada negativamente pelo aumento nas concentrações de nitrito e nitrato. Considerando-se que foi realizada apenas uma coleta, a riqueza de espécies foi alta quando comparada à média de taxa encontrada para corpos d'água do Estado de São Paulo. O ambiente mais rico, Lagoa do Diogo, localiza-se em uma estação ecológica, confirmando a necessidade de mais pesquisas sobre a diversidade em ambientes menos impactados.