RESUMO
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.
Assuntos
Microbiota , Bactérias/genética , Bases de Dados Genéticas , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota/genética , RNA Ribossômico 16S/genética , América do Sul , Microbiologia da ÁguaRESUMO
East African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components; however, protistan diversity is barely known. We investigated the community composition of small eukaryotes (<10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in 11 high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblages were associated with conductivity and productivity gradients, whereas depth had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (<90%) with reported sequences in public databases; these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.
Assuntos
Eucariotos , Estramenópilas , Biodiversidade , Ecossistema , Eucariotos/genética , Lagos , Filogenia , RNA Ribossômico 18S/genética , Estramenópilas/genéticaRESUMO
How diversity is structured has been a central goal of microbial ecology. In freshwater ecosystems, selection has been found to be the main driver shaping bacterial communities. However, its relative importance compared with other processes (dispersal, drift, diversification) may depend on spatial heterogeneity and the dispersal rates within a metacommunity. Still, a decrease in the role of selection is expected with increasing dispersal homogenization. Here, we investigate the main ecological processes modulating bacterial assembly in contrasting scenarios of environmental heterogeneity. We carried out a spatiotemporal survey in the floodplain system of the Paraná River. The bacterioplankton metacommunity was studied using both statistical inferences based on phylogenetic and taxa turnover as well as co-occurrence networks. We found that selection was the main process determining community assembly even at both extremes of environmental heterogeneity and homogeneity, challenging the general view that the strength of selection is weakened due to dispersal homogenization. The ecological processes acting on the community also determined the connectedness of bacterial networks associations. Heterogeneous selection promoted more interconnected networks increasing ß-diversity. Finally, spatiotemporal heterogeneity was an important factor determining the number and identity of the most highly connected taxa in the system. Integrating all these empirical evidences, we propose a new conceptual model that elucidates how the environmental heterogeneity determines the action of the ecological processes shaping the bacterial metacommunity.
Assuntos
Ecossistema , Rios , Organismos Aquáticos , Bactérias/genética , FilogeniaRESUMO
Ceratium furcoides is an invasive freshwater dinoflagellate that in the last three decades has expanded its geographic distribution in South America, being recently found in Paraná River floodplain (Argentina). Despite growing concern about the presence and impacts of this invader, information regarding genetic diversity in the Southern Hemisphere is missing. This work constitutes the first phylogenetic characterization of Ceratium populations of South America, particularly, from the Paraná system. After taxonomic identification as C. furcoides based on morphological traits, two sequencing-based approaches were applied using the ribosomal 18S gene: Sanger sequencing to isolated individuals and high-throughput amplicon sequencing (HTS) to environmental DNA. The sequence of C. furcoides obtained shared 100% identity to Asian sequences, and formed a highly supported clade in the constructed reference phylogenetic tree. HTS helped to recover low-frequency genetic variants suggesting the presence of different population of C. furcoides, and to alert potential invasion in its early stages.
Assuntos
Dinoflagellida , Argentina , Dinoflagellida/genética , Água Doce , Filogenia , Análise de Sequência de DNA , América do SulRESUMO
Trebouxiophyceae are a ubiquitous class of Chlorophyta encountered in aquatic and terrestrial environments. Most taxa are photosynthetic, and many acts as photobionts in symbiotic relationships, while others are free-living. Trebouxiophyceae have also been widely investigated for their use for biotechnological applications. In this work, we aimed at obtaining a comprehensive image of their diversity by compiling the information of 435 freshwater, soil and marine environmental DNA samples surveyed with Illumina sequencing technology in order to search for the most relevant environments for bioprospecting. Freshwater and soil were most diverse and shared more than half of all operational taxonomic units (OTUs), however, their communities were significantly distinct. Oceans hosted the highest genetic novelty, and did not share any OTUs with the other environments; also, marine samples host more diversity in warm waters. Symbiotic genera usually found in lichens such as Trebouxia, Myrmecia and Symbiochloris were also abundantly detected in the ocean, suggesting either free-living lifestyles or unknown symbiotic relationships with marine planktonic organisms. Altogether, our study opens the way to new prospection for trebouxiophycean strains, especially in understudied environments like the ocean.
Assuntos
Clorófitas/classificação , Clorófitas/genética , Líquens/citologia , Plâncton/citologia , Simbiose/fisiologia , Organismos Aquáticos/fisiologia , Água Doce , Sequenciamento de Nucleotídeos em Larga Escala , Oceanos e Mares , FilogeniaRESUMO
BACKGROUND: Flow cytometry (FCM) is one of the most commonly used technologies for analysis of numerous biological systems at the cellular level, from cancer cells to microbial communities. Its high potential and wide applicability led to the development of various analytical protocols, which are often not interchangeable between fields of expertise. Environmental science in particular faces difficulty in adapting to non-specific protocols, mainly because of the highly heterogeneous nature of environmental samples. This variety, although it is intrinsic to environmental studies, makes it difficult to adjust analytical protocols to maintain both mathematical formalism and comprehensible biological interpretations, principally for questions that rely on the evaluation of differences between cytograms, an approach also termed cytometric diversity. Despite the availability of promising bioinformatic tools conceived for or adapted to cytometric diversity, most of them still cannot deal with common technical issues such as the integration of differently acquired datasets, the optimal number of bins, and the effective correlation of bins to previously known cytometric populations. RESULTS: To address these and other questions, we have developed flowDiv, an R language pipeline for analysis of environmental flow cytometry data. Here, we present the rationale for flowDiv and apply the method to a real dataset from 31 freshwater lakes in Patagonia, Argentina, to reveal significant aspects of their cytometric diversities. CONCLUSIONS: flowDiv provides a rather intuitive way of proceeding with FCM analysis, as it combines formal mathematical solutions and biological rationales in an intuitive framework specifically designed to explore cytometric diversity.
Assuntos
Biodiversidade , Citometria de Fluxo/métodos , Software , Humanos , Lagos , Microbiota , Análise de Componente Principal , Estatísticas não ParamétricasRESUMO
Photosynthetic picoeukaryotes (PPE) are key components of primary production in marine and freshwater ecosystems. In contrast with those of marine environments, freshwater PPE groups have received little attention. In this work, we used flow cytometry cell sorting, microscopy and metabarcoding to investigate the composition of small photosynthetic eukaryote communities from six eutrophic shallow lakes in South America, Argentina. We compared the total molecular diversity obtained from PPE sorted populations as well as from filtered total plankton samples (FTP). Most reads obtained from sorted populations belonged to the classes: Trebouxiophyceae, Chlorophyceae and Bacillariophyceae. We retrieved sequences from non-photosynthetic groups, such as Chytridiomycetes and Ichthyosporea which contain a number of described parasites, indicating that these organisms were probably in association with the autotrophic cells sorted. Dominant groups among sorted PPEs were poorly represented in FTP and their richness was on average lower than in the sorted samples. A significant number of operational taxonomic units (OTUs) were exclusively found in sorting samples, emphasizing that sequences from FTP underestimate the diversity of PPE. Moreover, 22% of the OTUs found among the dominant groups had a low similarity (<95%) with reported sequences in public databases, demonstrating a high potential for novel diversity in these lakes.
Assuntos
Eucariotos/isolamento & purificação , Lagos/parasitologia , Argentina , Biodiversidade , Clorófitas/classificação , Clorófitas/citologia , Clorófitas/genética , Clorófitas/metabolismo , Diatomáceas/classificação , Diatomáceas/genética , Diatomáceas/isolamento & purificação , Diatomáceas/metabolismo , Ecossistema , Eucariotos/classificação , Eucariotos/genética , Eucariotos/metabolismo , Citometria de Fluxo , Sequenciamento de Nucleotídeos em Larga Escala , Lagos/análise , Fotossíntese , FilogeniaRESUMO
High-throughput sequencing (HTS) of the 16S rRNA gene has been used successfully to describe the structure and dynamics of microbial communities. Picocyanobacteria are important members of bacterioplankton communities, and, so far, they have predominantly been targeted using universal bacterial primers, providing a limited resolution of the picocyanobacterial community structure and dynamics. To increase such resolution, the study of a particular target group is best approached with the use of specific primers. Here, we aimed to design and evaluate specific primers for aquatic picocyanobacterial genera to be used with high-throughput sequencing. Since the various regions of the 16S rRNA gene have different degrees of conservation in different bacterial groups, we therefore first determined which hypervariable region of the 16S rRNA gene provides the highest taxonomic and phylogenetic resolution for the genera Synechococcus, Prochlorococcus, and Cyanobium An in silico analysis showed that the V5, V6, and V7 hypervariable regions appear to be the most informative for this group. We then designed primers flanking these hypervariable regions and tested them in natural marine and freshwater communities. We successfully detected that most (97%) of the obtained reads could be assigned to picocyanobacterial genera. We defined operational taxonomic units as exact sequence variants (zero-radius operational taxonomic units [zOTUs]), which allowed us to detect higher genetic diversity and infer ecologically relevant information about picocyanobacterial community composition and dynamics in different aquatic systems. Our results open the door to future studies investigating picocyanobacterial diversity in aquatic systems.IMPORTANCE The molecular diversity of the aquatic picocyanobacterial community cannot be accurately described using only the available universal 16S rRNA gene primers that target the whole bacterial and archaeal community. We show that the hypervariable regions V5, V6, and V7 of the 16S rRNA gene are better suited to study the diversity, community structure, and dynamics of picocyanobacterial communities at a fine scale using Illumina MiSeq sequencing. Due to its variability, it allows reconstructing phylogenies featuring topologies comparable to those generated when using the complete 16S rRNA gene sequence. Further, we successfully designed a new set of primers flanking the V5 to V7 region whose specificity for picocyanobacterial genera was tested in silico and validated in several freshwater and marine aquatic communities. This work represents a step forward for understanding the diversity and ecology of aquatic picocyanobacteria and sets the path for future studies on picocyanobacterial diversity.
Assuntos
Cianobactérias/classificação , Cianobactérias/genética , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota , Filogenia , Argentina , Simulação por Computador , Cianobactérias/isolamento & purificação , Primers do DNA/genética , Primers do DNA/isolamento & purificação , Ecologia , Água Doce/microbiologia , Variação Genética , Prochlorococcus/classificação , Prochlorococcus/genética , Prochlorococcus/isolamento & purificação , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação , Água do Mar/microbiologia , Análise de Sequência de DNA , Synechococcus/classificação , Synechococcus/genética , Synechococcus/isolamento & purificaçãoRESUMO
The flagellated protozoan parasite Trichomonas vaginalis is the etiologic agent of trichomoniasis, the most common non-viral sexually transmitted infection worldwide. As an obligate extracellular pathogen, adherence to epithelial cells is critical for parasite survival within the human host and a better understanding of this process is a prerequisite for the development of therapies to combat infection. In this sense, recent work has shown S-acylation as a key modification that regulates pathogenesis in different protozoan parasites. However, there are no reports indicating whether this post-translational modification is a mechanism operating in T. vaginalis In order to study the extent and function of S-acylation in T. vaginalis biology, we undertook a proteomic study to profile the full scope of S-acylated proteins in this parasite and reported the identification of 363 proteins involved in a variety of biological processes such as protein transport, pathogenesis related and signaling, among others. Importantly, treatment of parasites with the palmitoylation inhibitor 2-bromopalmitate causes a significant decrease in parasite: parasite aggregation as well as adherence to host cells suggesting that palmitoylation could be modifying proteins that are key regulators of Trichomonas vaginalis pathogenesis.
Assuntos
Lipoilação , Proteínas de Protozoários/metabolismo , Trichomonas vaginalis/metabolismo , Adesividade , Sequência de Aminoácidos , Ontologia Genética , Células HeLa , Humanos , Domínios Proteicos , Proteoma/metabolismo , Proteínas de Protozoários/química , Proteínas de Protozoários/isolamento & purificaçãoRESUMO
We analyzed the interplay between neutral and deterministic processes in maintaining contrasting alternative bacterioplankton communities through time in highly productive shallow lakes and evaluated the relevance of these processes when a regime shift from a clear to a turbid state occurred. We observed that local assembly is ruled primary deterministically, via local habitat filtering, with a secondary role of stochastic processes. We also found a hierarchy in the environmental sorting: while an unusual Verrucomicrobia dominance characterizes the three systems, local conditions limit within-bacterial community membership to closely phylogenetically related and ecologically similar taxa. These results indicate that bacterial abilities to establish in these lakes are strongly determined by their traits, and point toward special physiological adaptations to persist when these systems undergo a regime shift. Altogether, these results hint to a divergence in function among these alternative communities, mediated by major shifts in bacterial community trait structure, particularly regarding carbon use.