Structure and Dynamics of Periphyton in a Neotropical Freshwater Lake, with Emphasis on Ciliates and Their Relationships with Bacterial Taxa.

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.

Remarkably Complex Microbial Community Composition in Bromeliad Tank Waters Revealed by eDNA Metabarcoding.

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.

Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water.

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.

Epistylis portoalegrensis n. sp. (Ciliophora, Peritrichia): A New Freshwater Ciliate Species from Southern Brazil.

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.

Multiple lines of evidence shed light on the occurrence of paramecium (ciliophora, oligohymenophorea) in bromeliad tank water.

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.

Expanded phylogenetic representation of genera Opercularia and Epistylis sheds light on the evolution and higher-level taxonomy of peritrich ciliates (Ciliophora: Peritrichia).

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.

Characterization of ciliate diversity in bromeliad tank waters from the Brazilian Atlantic Forest.

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.

Functional analysis of conserved cysteine residues in the catalytic subunit of the yeast vacuolar H(+)-ATPase.

The A subunit of the yeast vacuolar ATPase contains three highly conserved cysteines: Cys-261, Cys-284, and Cys-538. Cys-261 is located within the nucleotide-binding P-loop. Each of the conserved cysteines, and one nonconserved cysteine, Cys-254, were altered to serine by site-directed mutagenesis, and the effects on growth at pH 7.5 were determined. The Cys-254-->Ser, Cys-261-->Ser and the double mutants all grew at pH 7.5 and contained nitrate- and bafilomycin-sensitive ATPase activity. However, the ATPase activities of the Cys-261-->Ser and the double mutants were insensitive to the sulfhydryl group inhibitor, N-ethylmaleimide, demonstrating that Cys-261 is the site of inhibition by N-ethylmaleimide. Changing either Cys-284 or Cys-538 to serine prevented growth at pH 7.5. Cys-284 and Cys-538 thus appear to be essential cysteine residues which are required either for assembly or catalysis.

A New Vertical Mesh Transfer Technique for Metal-Tolerance Studies in Arabidopsis (Ecotypic Variation and Copper-Sensitive Mutants).

A new vertical mesh transfer (VMT) technique has been developed to facilitate the rapid isolation of plant metal-tolerance mutants. The technique is quantitative, allowing comparisons of the growth responses of different strains or ecotypes. Using the VMT technique, we have characterized the dose responses of 10 ecotypes of Arabidopsis thaliana to Cu2+, Zn2+, Ni2+, Cr3+, Cd2+, and Al3+. Ecotypic variations in the highest concentration causing no inhibition and the lowest concentration causing complete inhibition for the six metals were observed. Two ecotypes, Ws and Enkheim, exhibited an inducible tolerance mechanism in response to copper. Pretreatment of Ws with the highest concentration causing no inhibition for copper resulted in a shifting of the lowest concentration causing complete inhibition to a higher value. Partial cross-induction and cross-tolerance between Cu2+ and Zn2+ were demonstrated. In addition, ethyl methanesulfonate-mutagenized Columbia seeds were screened for copper-sensitive (cus) mutants using the VMT procedure. Thus far, 59 putative cus mutants have survived retesting to the M4 or M5 generation. When grown on gellan gum supplemented with 30 [mu]M CuCl2, cus mutants develop marked toxicity symptoms. A copper dose-response curve of the cus1 mutant showed that the metal-sensitive phenotype is specific for the lower concentration range.

Gene duplication as a means for altering H+/ATP ratios during the evolution of FoF1 ATPases and synthases.

In the evolution of the FoF1 family of proton-translocating membrane complexes, two reversals in function appear to have occurred, first changing it from an ATPase to an ATP synthase and then back again to an ATPase. Here we suggest that with each change in function, the ratio of protons transported per ATP hydrolyzed or synthesized (H+/ATP) was altered in order for the complex to better adapt to its new role. We propose that this was accomplished by gene duplication with partial loss in the number of functional catalytic sites (to increase H+/ATP) or functional proton channels (to decrease H+/ATP). This method of changing the H+/ATP ratio preserved overall structural features of the complex essential to energy coupling.

The H+ ATPase regulatory subunit of Methanococcus thermolithotrophicus: amplification of an 800 bp fragment by polymerase chain reaction.

An 800 bp fragment of Methanococcus thermolithotrophicus genomic DNA was amplified by the polymerase chain reaction method using primers designed from conserved regions of the V-type H+ ATPase regulatory subunits from the archaebacterium Sulfolobus, and several eukaryotes. Although more than one product was obtained, only one of them had the expected size and was exclusively amplified in the presence of the left and right primers. The DNA and the deduced protein sequences of the putative Methanococcus H+ ATPase subunit revealed homology to the corresponding sequences in Sulfolobus and eukaryotes (about 60% identical residues) and a less evident homology to the eubacterial F1-ATPase alpha-subunit (22% identical residues with E. coli).

THE PLANT VACUOLE.

Plant cells are unique in containing large acidic vacuoles which occupy most of the cell volume. The vacuolar H+-ATPase (V-ATPase) is the enzyme responsible for acidifying the central vacuole, although it is also present on Golgi and coated vesicles. Many secondary transport processes are driven by the proton-motive force generated by the V-ATPase, including reactions required for osmoregulation, homeostasis, storage, plant defense and many other functions. However, a second proton pump, the V-PPase, serves as a potential back-up system and may, in addition, pump potassium. The plant V-ATPase is structurally similar to other eukaryotic V-ATPases and its subunits appear to be encoded by small multigene families. These multigene families may play important roles in the regulation of gene expression and in the sorting of V-ATPase isoforms to different organelles.

Molecular evolution of H+-ATPases. I. Methanococcus and Sulfolobus are monophyletic with respect to eukaryotes and Eubacteria.

The classification of methanogenic bacteria as archaebacteria based on 16 s rRNA sequence analysis is currently in dispute. To provide an alternative molecular marker, the polymerase chain reaction technique was used to amplify a 930 bp fragment of Methanococcus thermolithotrophicus genomic DNA corresponding to the catalytic domain of the membrane H+-ATPase. The deduced amino acid sequence was 54-58% identical to the approximately 70 kDa subunits of Sulfolobus acidocaldarius and the eukaryotic vacuolar-type H+-ATPase, and only 29% identical to the beta subunit of the eubacterial-type F0F1-ATPases. Interestingly, a highly conserved aspartate residue in the phosphorylation domain of E1E2-ATPases (P-type) is conserved in the Methanococcus sequence, but is absent from all other known vacuolar and F0F1-ATPases. This suggests that the H+-ATPase of M. thermolithotrophicus, like that of M. voltae, may have a phosphorylated intermediate, despite belonging to the vacuolar-type class of proton pumps. Phylogenetic analysis using Felsenstein's maximum likelihood method and Lake's evolutionary parsimony method confirmed that the H+-ATPases of the two archaebacteria, Methanococcus and Sulfolobus, when compared to eukaryotic vacuolar-type ATPases and eubacterial F0F1-ATPases, form a monophyletic group.

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification.

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.

Phenotypic characterization of lettuce dwarf mutants and their response to applied gibberellins.

Four monogenic, recessive dwarf mutants of lettuce (Lactuca sativa L.), previously isolated from a population induced by ethyl methanesulfonate, were compared with the normal genotype (E-1) for plant height, weight, leaf area, as well as hypocotyl length and root length. These nonallelic dwarfs (dwf1, dwf2, and dwf3) exhibited reduced hypocotyl length, smaller, dark green leaves, and reduced stem length. Another mutant, dwf2, allelic with dwf2, exhibited an intermediate phenotype. Epidermal cells on hypocotyls and mature leaves were counted for both normal E-1 and dwf2 plants. The total number of epidermal cells per unit area for hypocotyls and for leaves from these plants was very similar, implying the dwarf's smaller size was due to an inhibition of cell expansion and not due to decreased cell divisions. Both dwarf and normal hypocotyls elongated normally in response to exogenous gibberellin A(3) (GA(3)). In the rosette stage, only E-1 and dwf2 responded similarly to lower concentrations of GA(3), while the other dwarfs required higher concentrations to respond. Hypocotyls of dwf2 and E-1 elongated equally with applied ent-kaurenol, ent-kaurenoic acid, GA(53)-aldehyde, GA(53), GA(19), GA(20), and GA(1) indicating that the biochemical block in dwf2 occurs at a very early step in the GA-biosynthetic pathway.

Characterization of the subunit structure of the maize tonoplast ATPase. Immunological and inhibitor binding studies.

Gradient purified preparations of the maize 400-kDa tonoplast ATPase are enriched in two major polypeptides, 72 and 62 kDa. Polyclonal antibodies were prepared against these two putative subunits after elution from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel slices and against the solubilized native enzyme. Antibodies to both the 72- and 62-kDa polypeptides cross-reacted with similar bands on immunoblots of a tonoplast-enriched fraction from barley, while only the 72-kDa antibodies cross-reacted with tonoplast and tonoplast ATPase preparations from Neurospora. Antibodies to the 72-kDa polypeptide and the native enzyme both strongly inhibited enzyme activity, but the 62-kDa antibody was without effect. The identity and function of the subunits was further probed using radiolabeled covalent inhibitors of the tonoplast ATPase, 7-chloro-4-nitro[14C]benzo-2-oxa-1,3-diazole ([14C]NBD-Cl) and N,N'-[14C]dicyclohexylcarbodiimide ([14C]DCCD). [14C]NBD-Cl preferentially labeled the 72-kDa polypeptide, and labeling was prevented by ATP. [14C]DCCD, an inhibitor of the proton channel portion of the mitochondrial ATPase, bound to a 16-kDa polypeptide. Venturicidin blocked binding to the mitochondrial 8-kDa polypeptide but did not affect binding to the tonoplast 16-kDa polypeptide. Taken together, the results implicate the 72-kDa polypeptide as the catalytic subunit of the tonoplast ATPase. The DCCD-binding 16-kDa polypeptide may comprise the proton channel. The presence of nucleotide-binding sites on the 62-kDa polypeptide suggests that it may function as a regulatory subunit.

Comparison of metallothionein gene expression and nonprotein thiols in ten Arabidopsis ecotypes. Correlation with copper tolerance.

Seedlings of 10 Arabidopsis ecotypes were compared with respect to copper tolerance, expression of two metallothionein genes (MT1 and MT2), and nonprotein thiol levels. MT1 was uniformly expressed in all treatments, and MT2 was copper inducible in all 10 ecotypes. MT1 and MT2 mRNA levels were compared with various growth parameters for the 10 ecotypes in the presence of 40 microM Cu2+. The best correlation (R = 0.99) was obtained between MT2 mRNA and the rate of root extension. MT2 mRNA levels also paralleled the recovery phase following inhibition by copper. Induction of MT2 mRNA was initiated at copper concentrations below the threshold for growth inhibition. In cross-induction experiments, Ag+, Cd2+, Zn2+, Ni2+, and heat shock all induced significant levels of MT2 gene expression, whereas Al3+ and salicylic acid did not. The correlation between copper tolerance and nonprotein thiol levels in the 10 ecotypes was not statistically significant. However, 2 ecotypes, Ws and Enkheim, previously shown to exhibit an acclimation response, had the highest levels of nonprotein thiols. We conclude that MT2 gene expression may be the primary determinant of ecotypic differences in the copper tolerance of nonpretreated Arabidopsis seedlings.

Vanadate inhibition of auxin-enhanced H secretion and elongation in pea epicotyls and oat coleoptiles.

In experiments carried out to investigate the acid secretion theory of auxin action, we utilized sodium orthovanadate, an agent found to be a selective inhibitor of a plasma membrane-associated H(+)-pumping ATPase in Neurospora [Bowman, B. J. & Slayman, C. W. (1979) J. Biol. Chem. 245, 2928-2934]. At 1 mM, vanadate inhibited auxin-enhanced medium acidification by pea epicotyl segments within 5 min, whether added 0.5 or 2.5 hr after auxin. Inhibition of acidification was total after 10-15 min but could be reversed within 10 min after vanadate removal. When given as a 40-min pretreatment, vanadate completely prevented any auxin-enhanced acidification. Vanadate inhibition of medium acidification by oat coleoptile segments was also total and reversible, but both inhibition and reversal occurred after longer lag times than in pea. Inhibitory effects of vanadate on elongation in pea and oat tissue closely paralleled its effects on acidification, and the inhibitory effect of vanadate on elongation could be reversed by an acidic buffer. Vanadate did not inhibit respiration or protein synthesis in pea epicotyl segments, although it strongly inhibited L-[(14)C]leucine uptake. These results indicate the importance of cell wall acidification for short- and long-term auxin-enhanced growth and suggest the participation in wall acidification of a plasma membrane-associated ATPase acting as an H(+) pump.

Immunocytochemical Localization of the Vacuolar H-ATPase in Maize Root Tip Cells.

The vacuolar H(+)-ATPase of maize (Zea mays L.) root tip cells has been localized at the EM level using rabbit polyclonal antibodies to the 69 kilodalton subunit and protein A-colloidal gold. Intracellular gold particles were detected mainly on the tonoplast and Golgi membranes. Only about 27% of the vacuoles were labeled above background. The absence of gold particles on the majority of vacuoles suggests either that the tonoplast H(+)-ATPase is degraded during tissue preparation or that the small vacuoles of root tip cells are specialized with respect to H(+)-ATP ase activity. The pattern of gold particles on the labeled vacuoles ranged from uniform to patchy. Virtually all of the Golgi bodies were labeled by the antibody, but the particle densities were too low to determine whether the H(+)-ATPase was associated with specific regions, such as the trans-face. Cell wall-labeling was also observed which could be partially prevented by the inclusion of gelatin as a blocking agent. The immunocytochemical results confirm previous biochemical studies with isolated membrane fractions (A Chanson, L Taiz 1985 Plant Physiol 78: 232-240).