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Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to a morphology-based approach for peritrich ciliate determinations, its most abundant group. We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera Epistylis and Vorticella being the most abundant and showing a clear succession at both sites. Other ciliates were morphologically identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure of both prokaryotic and eukaryotic components of periphyton was not different, while the turnover dynamics differed between the two sites, in spite of their adjacent locations and similar abiotic properties. This indicates that the establishment of these communities can vary even on a local scale within a lake ecosystem.

To investigate patterns of biotic community composition at different spatial scales and biological contexts, we used environmental DNA metabarcoding to characterize eukaryotic and prokaryotic assemblages present in the phytotelmata of three bromeliad species (Aechmea gamosepala, Vriesea friburgensis, and Vriesea platynema) at a single Atlantic Forest site in southern Brazil. We sampled multiple individuals per species and multiple tanks from each individual, totalizing 30 samples. We observed very high levels of diversity in these communities, and remarkable variation across individuals and even among tanks from the same individual. The alpha diversity was higher for prokaryotes than eukaryotes, especially for A. gamosepala and V. platynema samples. Some biotic components appeared to be species-specific, while most of the biota was shared among species, but varied substantially in frequency among samples. Interestingly, V. friburgensis communities (which were sampled at nearby locations) tended to be more heterogeneous across samples, for both eukaryotes and prokaryotes. The opposite was true for V. platynema, whose samples were more broadly spaced but whose communities were more similar to each other. Our results indicate that additional attention should be devoted to within-individual heterogeneity when assessing bromeliad phytotelmata biodiversity, and highlight the complexity of the biotic assemblages gathered in these unique habitats.

Periphyton communities in freshwater systems play an essential role in biogeochemical processes, but knowledge of their structure and dynamics lags far behind other environments. We used eDNA metabarcoding of 16S and 18S rRNA markers to investigate the formation and establishment of a periphytic community, in addition to morphology-based analyses of its most abundant group (peritrich ciliates). We sampled two nearby sites within a large Neotropical lake at four time points, aiming to assess whether periphyton establishment can be replicated on this local scale. Producers and denitrifiers were abundant in the community, illustrating the relevant role of biofilms in freshwater nutrient recycling. Among microeukaryotes, peritrich ciliates dominated the community, with genera Epistylis and Vorticella being the most abundant and showing a clear succession at both sites. Other ciliates were identified and, in some cases, their occurrence was strongly related to bacterial abundance. The structure and succession dynamics of both prokaryotic and eukaryotic components of periphyton differed between the two sites, in spite of their adjacent locations and similar abiotic properties, indicating that the establishment of these communities can vary even on a local scale within a lake ecosystem.

Conspicuous physicochemical vertical stratification in the deep sea is one of the main forces driving microbial diversity in the oceans. Oxygen and sunlight availability are key factors promoting microbial diversity throughout the water column. Ocean currents also play a major role in the physicochemical stratification, carrying oxygen down to deeper zones as well as moving deeper water masses up towards shallower depths. Water samples within a 50-km radius in a pockmark location of the southwestern Atlantic Ocean were collected and the prokaryotic communities from different water depths - chlorophyll maximum, oxygen minimum and deep-sea bottom (down to 1355 m) - were described. At phylum level, Proteobacteria were the most frequent in all water depths, Cyanobacteria were statistically more frequent in chlorophyll maximum zone, while Thaumarchaeota were significantly more abundant in both oxygen minimum and bottom waters. The most frequent microorganism in the chlorophyll maximum and oxygen minimum zones was a Pelagibacteraceae operational taxonomic unit (OTU). At the bottom, the most abundant genus was the archaeon Nitrosopumilus. Beta diversity analysis of the 16S rRNA gene sequencing data uncovered in this study shows high spatial heterogeneity among water zones communities. Our data brings important contribution for the characterisation of oceanic microbial diversity, as it consists of the first description of prokaryotic communities occurring in different oceanic water zones in the southwestern Atlantic Ocean.

As the depth increases and the light fades in oceanic cold seeps, a variety of chemosynthetic-based benthic communities arise. Previous assessments reported polychaete annelids belonging to the family Siboglinidae as part of the fauna at cold seeps, with the 'Vestimentifera' clade containing specialists that depend on microbial chemosynthetic endosymbionts for nutrition. Little information exists concerning the microbiota of the external portion of the vestimentiferan trunk wall. We employed 16S rDNA-based metabarcoding to describe the external microbiota of the chitin tubes from the vestimentiferan Escarpia collected from a chemosynthetic community in a cold seep area at the southwestern Atlantic Ocean. The most abundant operational taxonomic unit (OTU) belonged to the family Pirellulaceae (phylum Planctomycetes), and the second most abundant OTU belonged to the order Methylococcales (phylum Proteobacteria), composing an average of 21.1 and 15.4% of the total reads on tubes, respectively. These frequencies contrasted with those from the surrounding environment (sediment and water), where they represent no more than 0.1% of the total reads each. Moreover, some taxa with lower abundances were detected only in Escarpia tube walls. These data constitute on the first report of an epibiont microbial community found in close association with external surface of a cold-seep metazoan, Escarpia sp., from a chemosynthetic community in the southwestern Atlantic Ocean.

Bromeliads are a diverse group of plants that includes many species whose individuals are capable of retaining water, forming habitats called phytotelmata. These habitats harbor a diversity of organisms including prokaryotes, unicellular eukaryotes, metazoans, and fungi. Among single-celled eukaryotic organisms, ciliates are generally the most abundant. In the present study, we used Illumina DNA sequencing to survey the eukaryotic communities, especially ciliates, inhabiting the tanks of the bromeliads Aechmea gamosepala and Vriesea platynema in the Atlantic Forest of southern Brazil. Filtered sequences were clustered into distinct OTUs using a 99% identity threshold, and then assigned to phylum and genus using a BLAST-based approach (implemented in QIIME) and the SILVA reference database. Both bromeliad species harbored very diverse eukaryotic communities, with Arthropoda and Ciliophora showing the highest abundance (as estimated by the number of sequence reads). The ciliate genus Tetrahymena was the most abundant among single-celled organisms, followed by apicomplexan gregarines and the ciliate genus Glaucoma. Another interesting finding was the presence and high abundance of Trypanosoma in these bromeliad tanks, demonstrating their occurrence in this type of environment. The results presented here demonstrate a hidden diversity of eukaryotes in bromeliad tank waters, opening up new avenues for their in-depth characterization.

Waste disposal from paper and pulp industry is of great environmental concern. Sludge from recycled paper mills favors colonization with different microbial species due to its chemical composition. In this environment, the microbiota can express enzymes that hydrolyze celluloses and hemicelluloses, such as cellulases, β-glucosidases, and xylanases. Understanding microbiota living in such disposal may give directions to what kind of enzymes or bioproducts may be possible to obtain from this microorganism and how to deal with the waste during the process. We have accessed microbial community associated with two steps in the recycled paper sludge generation by high-throughput DNA sequencing: fibrous residue, and wastewater sludge. Bacteroidetes, Proteobacteria and Firmicutes phyla represented more than 96% of the total. From the eukaryote perspective, Vorticella was the most frequent in fibrous residue samples while Acanthamoeba was the most common on wastewater sludge samples. Among the isolates cellulase activity was detectable only from fungi isolates. Half of the bacterial isolates presented xylanase activity, and most of them in high level of activity. Both a metabarcoding and culturing approaches are valuable tools for enzymatic screening in industrial waste disposal.

The ecology of complex microhabitats remains poorly characterized in most tropical and subtropical biomes, and holds potential to help understand the structure and dynamics of different biodiversity components in these ecosystems. We assessed nutritional and metabolic parameters of two bromeliad species (Aechmea gamosepala and Vriesea platynema) at an Atlantic Forest site and used 16S rDNA metabarcoding to survey the microbial communities inhabiting their tanks. We observed that levels of some nutrients (e.g., nitrogen) varied across seasons consistently in both species, while others (e.g., phenolic compounds) presented considerable differences between the two bromeliads. In contrast, patterns of tank microbial diversity did not follow a similar temporal trend. There was extensive variation in microbial composition among samples, which included intra-specific differences but also some consistent differences between the two bromeliads. For example, Citrobacter, Klebsiella and Pantoea presented significantly different abundances in the two species. Interestingly, the dominant bacterial genera in both species included Pseudomonas and Enterobacter, which have been reported to include plant-beneficial species. Overall, our data contribute to the characterization of the nutritional status of Atlantic Forest bromeliads and the composition of their prokaryotic communities, laying the foundation for detailed investigations targeting the ecological interactions between these plants and their associated microbes.

Chemosynthetic communities have been described from a variety of deep-sea environments across the world's oceans. They constitute very interesting biological systems in terms of their ecology, evolution and biogeography, and also given their potential as indicators of the presence and abundance of consistent hydrocarbon-based nutritional sources. Up to now such peculiar biotic assemblages have not been reported for the western South Atlantic Ocean, leaving this large region undocumented with respect to the presence, composition and history of such communities. Here we report on the presence of a chemosynthetic community off the coast of southern Brazil, in an area where high-levels of methane and the presence of gas hydrates have been detected. We performed metagenomic analyses of the microbial community present at this site, and also employed molecular approaches to identify components of its benthic fauna. We conducted phylogenetic analyses comparing the components of this assemblage to those found elsewhere in the world, which allowed a historical assessment of the structure and dynamics of these systems. Our results revealed that the microbial community at this site is quite diverse, and contains many components that are very closely related to lineages previously sampled in ecologically similar environments across the globe. Anaerobic methanotrophic (ANME) archaeal groups were found to be very abundant at this site, suggesting that methane is indeed an important source of nutrition for this community. In addition, we document the presence at this site of a vestimentiferan siboglinid polychaete and the bivalve Acharax sp., both of which are typical components of deep-sea chemosynthetic communities. The remarkable similarity in biotic composition between this area and other deep-sea communities across the world supports the interpretation that these assemblages are historically connected across the global oceans, undergoing colonization from distant sites and influenced by local ecological features that select a stereotyped suite of specifically adapted organisms.

The peritrich ciliate Epistylis portoalegrensis n. sp. was found in two bodies of freshwater located in Porto Alegre, Southern Brazil. Morphological features were investigated using live and protargol-stained specimens. The zooids presented a vase to cylindrical shape narrowed at the scopula, and a mean size of 131 × 37 μm in vivo. A C-shaped macronucleus lay in the middle of the cell close to a single contractile vacuole. The oral infraciliature was typical for the genus, with all infundibular polykineties composed by three distinct rows of kinetosomes. Colonies are often nonbranched with no lateral stalk, carrying several zooids stemming from a single point. Specimens from the two sampling sites showed identical arrangement of the infraciliature, similar morphometry, identical 18S rDNA sequences, and a single nucleotide difference across the more variable ITS regions. Molecular phylogenetic analyses placed E. portoalegrensis in a well-supported clade containing other Epistylis species, within the order Vorticellida.

The consortium between the colonial stramenopile Solenicola setigera and the centric chain-forming diatom Leptocylindrus mediterraneus is cosmopolitan throughout the world ocean yet rarely abundant. However, the nature of the association remains enigmatic. A mutualistic symbiosis requires a live diatom host, but the frustule of L. mediterraneus is apparently empty, lacking protoplasm and plastids. The parasitism requires free-living host cells to be infected, but there is no evidence of populations of the free-living diatom. During experiments attempting to culture the heterotrophic S. setigera, we successfully obtained a strain of the host diatom. In the small-subunit (SSU) rDNA phylogeny, L. mediterraneus was closely related to Dactyliosolen blavyanus and to a new sequence of Dactyliosolen sp. while distantly related to the genus Leptocylindrus. We proposed the reinstatement of L. mediterraneus in the genus Dactyliosolen as D. mediterraneus. Even under optimal growth conditions, the frustule wa...

We have generated 18S rRNA sequences for peritrichs collected in Brazil, including four Opercularia species, two different populations of Epistylis plicatilis (one epibiont and another free-living), and one additional Epistylis species. Our Opercularia species clustered with the previously available Opercularia microdiscum, corroborating the monophyly of this genus. The Epistylis sampled here clustered with previously sequenced species of this genus. The two populations of E. plicatilis collected in Brazil clustered closely together despite their different ecological contexts, whereas both were very divergent from the sample assigned to the same species previously sampled in China. If affirmed by additional morphological corroboration of species assignment, this observation would indicate that samples from different continents morphologically allocated in the same species may in fact belong to distant evolutionary lineages. More broadly, our results support the recognition of two major clades within Peritrichia. Given the robustness of their support, we suggest that these two clades should be formally recognized as orders, and propose the names Vorticellida and Operculariida to designate them. Furthermore, Epistylis species occurred in both orders, tending to occupy basal positions. This suggests that characters used to define this genus may be plesiomorphic for Peritrichia, so that Epistylis may in fact represent an assemblage of basal species retaining ancestral features.

Phytotelmata are vegetal structures that hold water from the rain, and organic matter from the forest and the soil, resulting in small, compartmentalized bodies of water, which provide an essential environment for the establishment and development of many organisms. These microenvironments generally harbor endemic species, but many organisms that are found in lakes and rivers, are also present. Here, we report, for the first time, the occurrence of the ciliate genus Paramecium in the tank of the bromeliad species Aechmaea distichantha. The identification of the Paramecium species was performed based on live observations, protargol impregnation, scanning electronic microscopy, and sequencing of the 18s rRNA. The absence of Paramecium from bromeliad tank water was highlighted in several earlier investigations, and may be due to the fact that this species is unable to make cysts. The occurrence of Paramecium multimicronucleatum in our samples may be explained by the proximity between the bromeliads and the river, a potential source of the species. Further, we also believe that the counting methodology used in our study provides a more accurate analysis of the species diversity, since we investigated all samples within a maximum period of 6 h after sampling, allowing minimum loss of specimens.

Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

We have generated 18S rRNA sequences for peritrichs collected in Brazil, including four Opercularia species, two different populations of Epistylis plicatilis (one epibiont and another free-living), and one additional Epistylis species. Our Opercularia species clustered with the previously available Opercularia microdiscum, corroborating the monophyly of this genus. The Epistylis sampled here clustered with previously sequenced species of this genus. The two populations of E. plicatilis collected in Brazil clustered closely together despite their different ecological contexts, whereas both were very divergent from the sample assigned to the same species previously sampled in China. If affirmed by additional morphological corroboration of species assignment, this observation would indicate that samples from different continents morphologically allocated in the same species may in fact belong to distant evolutionary lineages. More broadly, our results support the recognition of two major clades within Peritrichia. Given the robustness of their support, we suggest that these two clades should be formally recognized as orders, and propose the names Vorticellida and Operculariida to designate them. Furthermore, Epistylis species occurred in both orders, tending to occupy basal positions. This suggests that characters used to define this genus may be plesiomorphic for Peritrichia, so that Epistylis may in fact represent an assemblage of basal species retaining ancestral features.