The Evolutionary Kaleidoscope of Rhodopsins

Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through the conversion of electromagnetic radiation into physicochemical signals. As a result of an extensive survey of available genomic and metagenomic sequencing data, we reported the existence of novel clades and exotic sequence motifs scattered throughout the evolutionary radiations of both Type-1 and Type-3 rhodopsins that will likely enlarge the optogenetics toolbox. We expanded the typical rhodopsin blueprint by showing that a highly conserved and functionally important arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We proposed the umbrella term Alt-rhodopsins (AltRs) for all such proteins that departed Arg82 orthodoxy. Some AltRs formed novel clades in the rhodopsin phylogeny and were found in giant viruses. Some newly uncovered AltRs were phylogenetically close to heliorhodopsins, which allowed a closer examination of the phylogenetic border between Type-1 rhodopsins and heliorhodopsins. Comprehensive phylogenetic trees and ancestral sequence reconstructions allowed us to advance the hypothesis that proto-heliorhodopsins were a eukaryotic innovation before their subsequent diversification into the extant Type-3 rhodopsins. IMPORTANCE The rhodopsin scaffold is remarkably versatile and widespread, coupling light availability to energy production and other light-dependent cellular responses with minor alterations to critical residues. We described an unprecedented spectrum of substitutions at one of the most conserved amino acids in the rhodopsin fold, Arg82. We denoted such phylogenetically diverse rhodopsins with the umbrella name Alt-rhodopsins (AltR) and described a distinct branch of AltRs in giant viruses. Intriguingly, some AltRs were the closest phylogenetic neighbors to Heliorhodopsins (HeRs) whose origins have remained enigmatic. Our analyses of HeR origins in the light of AltRs led us to posit a most unusual evolutionary trajectory that suggested a eukaryotic origin for HeRs before their diversification in prokaryotes

Temporal patterns of picoplankton abundance and metabolism on the western coast of the equatorial Atlantic Ocean

Picoplankton are central global carbon (C) cycling players and often dominate the ocean plankton communities, especially in low latitudes. Therefore, evaluating picoplankton temporal dynamics is critical to understanding microbial stocks and C fluxes in tropical oceans. However, the lack of studies on low-latitude picoplankton communities translates into a common conception that there is an absence of seasonality. Herein, we studied the temporal variation in abundance (measured by flow cytometry), and carbon flux (taking bacterial production and respiration as proxies) of the picoplanktonic community for the first time, as well as their environmental drivers in a low-latitude (05° 59’ 20.7″S 035° 05’ 14.6″W) Atlantic coastal station. We performed monthly samplings between February 2013 and August 2016 in a novel microbial observatory – hereafter called the Equatorial Atlantic Microbial Observatory – established on the northeastern Brazilian Atlantic coast. Our results revealed stability in temporal dynamics of picoplankton, despite a considerable inter-annual variation, with some related to the El Niño (ENSO) event in 2015. However, weak environmental relationships found were not enough to explain the variation in picoplankton’s abundance, which suggests that other factors such as biological interactions may lead to picoplankton abundance variation over time. Heterotrophic bacteria dominated picoplankton during the entire study period and between photosynthetic counterparts, and Synechococcus showed greater relative importance than picoeukaryotes. These results bring a novel perspective that picoplankton may exhibit more pronounced fluctuations in the tropical region when considering inter-annual intervals, and is increasing prokaryotic contribution to carbon cycling towards the equator.Fil: Menezes, Maiara. Universidade Federal do Rio Grande do Norte; BrasilFil: Junger, Pedro C.. Universidade Federal do São Carlos; BrasilFil: Kavagutti, Vinicius S.. Universidade Federal do São Carlos; BrasilFil: Wanderley, Bruno. Universidade Federal do Rio Grande do Norte; BrasilFil: Cabral, Anderson de Souza. Universidade Federal do Rio de Janeiro; BrasilFil: Paranhos, Rodolfo. Universidade Federal do Rio de Janeiro; BrasilFil: Unrein, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Universidad Nacional de San Martin. Instituto Tecnologico de Chascomus. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - la Plata. Instituto Tecnologico de Chascomus.; ArgentinaFil: Amado, André M.. Universidade Federal do Rio Grande do Norte; Brasil. Universidade Federal de Juiz de Fora; BrasilFil: Sarmento, Hugo. Universidade Federal do São Carlos; Brasi

High-resolution metagenomic reconstruction of the freshwater spring bloom

Background The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce. Results We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation. Conclusion We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom

Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics

The persistent inertia in the ability to culture environmentally abundant microbes from aquatic ecosystems represents an obstacle in disentangling the complex web of ecological interactions spun by a diverse assortment of participants (pro- and eukaryotes and their viruses). In aquatic microbial communities, the numerically most abundant actors, the viruses, remain the most elusive, and especially in freshwaters their identities and ecology remain unknown. Here, using ultra-deep metagenomic sequencing from pelagic freshwater habitats, we recovered complete genomes of > 2000 phages, including small “miniphages” and large “megaphages” infecting iconic freshwater prokaryotic lineages. For instance, abundant freshwater Actinobacteria support infection by a very broad size range of phages (13–200 Kb). We describe many phages encoding genes that likely afford protection to their host from reactive oxygen species (ROS) in the aquatic environment and in the oxidative burst in protist phagolysosomes (phage-mediated ROS defense). Spatiotemporal abundance analyses of phage genomes revealed evanescence as the primary dynamic in upper water layers, where they displayed short-lived existences. In contrast, persistence was characteristic for the deeper layers where many identical phage genomes were recovered repeatedly. Phage and host abundances corresponded closely, with distinct populations displaying preferential distributions in different seasons and depths, closely mimicking overall stratification and mixis

ATLANTIC BATS: a data set of bat communities from the Atlantic Forests of South America

Made available in DSpace on 2018-12-11T17:35:03Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-12-01Bats are the second most diverse mammal order and they provide vital ecosystem functions (e.g., pollination, seed dispersal, and nutrient flux in caves) and services (e.g., crop pest suppression). Bats are also important vectors of infectious diseases, harboring more than 100 different virus types. In the present study, we compiled information on bat communities from the Atlantic Forests of South America, a species-rich biome that is highly threatened by habitat loss and fragmentation. The ATLANTIC BATS data set comprises 135 quantitative studies carried out in 205 sites, which cover most vegetation types of the tropical and subtropical Atlantic Forest: dense ombrophilous forest, mixed ombrophilous forest, semideciduous forest, deciduous forest, savanna, steppe, and open ombrophilous forest. The data set includes information on more than 90,000 captures of 98 bat species of eight families. Species richness averaged 12.1 per site, with a median value of 10 species (ranging from 1 to 53 species). Six species occurred in more than 50% of the communities: Artibeus lituratus, Carollia perspicillata, Sturnira lilium, Artibeus fimbriatus, Glossophaga soricina, and Platyrrhinus lineatus. The number of captures divided by sampling effort, a proxy for abundance, varied from 0.000001 to 0.77 individuals·h−1·m−2 (0.04 ± 0.007 individuals·h−1·m−2). Our data set reveals a hyper-dominance of eight species that together that comprise 80% of all captures: Platyrrhinus lineatus (2.3%), Molossus molossus (2.8%), Artibeus obscurus (3.4%), Artibeus planirostris (5.2%), Artibeus fimbriatus (7%), Sturnira lilium (14.5%), Carollia perspicillata (15.6%), and Artibeus lituratus (29.2%).Departamento de Ecologia Instituto de Biociências Universidade Estadual Paulista (UNESP)Department of Natural Resources Management and Museum Texas Tech University (TTU)Departamento de Biologia Animal Laboratório de Diversidade de Morcegos Instituto de Biologia Universidade Federal Rural do Rio de Janeiro (UFRRJ)Departamento de Biologia Geral Instituto de Ciências Biológicas Universidade Federal de Minas Gerais (UFMG)Departamento de Zoologia Instituto de Ciências Biológicas PPG-Zoologia Universidade Federal de Minas Gerais (UFMG)Departamento de Zoologia Universidade Federal do Paraná (UFPR)Laboratório de Ecologia Aplicada à Conservação Departamento de Ciências Biológicas Universidade Estadual de Santa Cruz (UESC)Laboratório de Vertebrados Departamento de Ecologia Instituto de Biologia Universidade Federal do Rio de Janeiro (UFRJ)School of Biological and Chemistry Sciences Queen Mary University of London (QMUL)Laboratório de Ecologia de Mamíferos Universidade do Estado do Rio de Janeiro (UERJ)Departamento de Zoologia Centro de Ciências Biológicas Universidade Federal de Pernambuco (UFPE)Centre for Virology Research School of Medicine of Ribeirão Preto University of São Paulo (USP)Programa de Pós-Graduação em Ecologia e Recursos Naturais Departamento de Hidrobiologia Universidade Federal de São Carlos (UFSCar)Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology (NTNU)Department of Microbiology Institute of Biomedical Sciences University of São Paulo (USP)Departamento de Ecologia Instituto de Biociências Universidade Estadual Paulista (UNESP