Biology subjects

Flores-Uribe, J.

Publications and source records attributed to Flores-Uribe, J..

8 recordsLinked to original sources

bioRxiv2021

Characterization of the Chlamydomonas reinhardtii phycosphere reveals conserved features of the plant microbiota

Microscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model alga Chlamydomonas reinhardtii and reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Reconstitution experiments using synthetic communities derived from C. reinhardtii and Arabidopsis thaliana show that phycosphere and root bacteria assemble into taxonomically equivalent communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggests that the microbiota of photosynthetic organisms, including green algae and flowering plants, assembles according to core ecological principles.

microbiology↗

bioRxiv2020

Rising through the Ranks: Seasonal and Diel Patterns of Marine Viruses

Virus-microbe interactions have been studied in great molecular details for many years in cultured model systems, yielding a plethora of knowledge on how viruses use and manipulate host machinery. Since the advent of molecular techniques and high-throughput sequencing, viruses have been deemed the most abundant organisms on earth and methods such as co-occurrence, nucleotide composition and other statistical frameworks have been widely used to infer virus-microbe interactions, overcoming the limitations of culturing methods. However, their accuracy and relevance is still debatable, as co-occurrence does not necessarily mean interaction. Here, we introduce an ecological perspective of marine viral communities and potential interaction with their hosts, using analyses that make no prior assumptions on specific virus-host pairs. By size fractioning water samples into "free viruses" and "microbes" (i.e. also viruses inside or attached to their hosts) and looking at how viral groups abundance changes over time along both fractions, we show that the viral community is undergoing a change in rank abundance across seasons, suggesting a seasonal succession of viruses in the Red Sea. We use abundance patterns in the different size fractions to classify viral populations, indicating potential diverse interactions with their hosts and potential differences in life history traits between major viral groups. Finally, we show hourly resolved variations of intracellular abundance of similar viral groups, which might indicate differences in their infection cycles or metabolic capacities.

microbiology↗

bioRxiv2019

MerMAIDs: A novel family of metagenomically discovered, marine, anion-conducting and intensely desensitizing channelrhodopsins.

Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. ChRs desensitize under continuous bright-light illumination, resulting in a significant decline of photocurrents. We describe a novel, metagenomically identified family of phylogenetically distinct anion-conducting ChRs (designated MerMAIDs). MerMAIDs almost completely desensitize during continuous illumination due to accumulation of a late non-conducting photointermediate that disrupts the ion permeation pathway. MerMAID desensitization can be fully explained by a single photocycle in which a long-lived desensitized state follows the short-lived conducting state. A conserved cysteine is the critical factor in desensitization, as its mutation results in recovery of large stationary photocurrents. The rapid desensitization of MerMAIDs enables their use as optogenetic silencers for transient suppression of individual action potentials without affecting subsequent spiking during continuous illumination. Our results could facilitate the development of further novel optogenetic tools from metagenomic databases and enhance general understanding of ChR function.

biophysics↗

bioRxiv2018

Uncultured marine cyanophages encode for active NblA, phycobilisome proteolysis adaptor protein

Phycobilisomes (PBS) are large water-soluble membrane-associated complexes in cyanobacteria and some chloroplasts that serve as a light-harvesting antennas for the photosynthetic apparatus. When short of nitrogen or sulfur, cyanobacteria readily degrade their phycobilisomes allowing the cell to replenish the vanishing nutrients. The key regulator in the degradation process is NblA, a small protein (~6 kDa) which recruits proteases to the PBS. It was discovered previously that not only do cyanobacteria possess nblA genes but also that they are encoded by genomes of some freshwater cyanophages. A recent study, using assemblies from oceanic metagenomes, revealed genomes of a novel uncultured marine cyanophage lineage which contain genes coding for the PBS degradation protein. Here, we examine the functionality of nblA-like genes from these marine cyanophages by testing them in a freshwater model cyanobacterial nblA knockout. One of the viral NblA variants could complement the non-bleaching phenotype and restore PBS degradation. Our findings reveal a functional NblA from a novel marine cyanophage lineage. Furthermore, we shed new light on the distribution of nblA genes in cyanobacteria and cyanophages.\n\nOriginality-Significance StatementThis is the first study to examine the distribution and function of nblA genes of marine cyanophage origin. We describe as well the distribution of nblA-like genes in marine cyanobacteria using bioinformatic methods.

microbiology↗

bioRxiv2018

Heliorhodopsins are absent in diderm (Gram-negative) bacteria: Some thoughts and possible implications for activity

Microbial heliorhodopsins are a new type of rhodopsins with an opposite membrane topology compared to type-1 and -2 rhodopsins, currently believed to engage in light sensing. We determined their presence/absence is monoderms and diderms representatives from the Tara Oceans and freshwater 25 lakes metagenomes. Heliorhodopsins were absent in diderms, confirming our previous observations in cultured Proteobacteria. Based on these observations, we speculate on the putative role of heliorhodopsins in light-driven transport of amphiphilic molecules.

microbiology↗

bioRxiv2018

A novel oceanic uncultured temperate cyanophage lineage

Marine cyanobacteria are important contributors to primary production in the ocean and their viruses (cyanophages) affect the ocean microbial communities. Despite reports of lysogeny in marine cyanobacteria, the genome sequence of such temperate cyanophages remains unknown although genomic analysis indicate potential for lysogeny in certain marine cyanophages. Using assemblies from Red Sea and Tara Oceans metagenomes, we recovered genomes of a novel uncultured marine cyanophage lineage, which contain, in addition to common cyanophage genes, a phycobilisome degradation protein NblA, an integrase and a split DNA polymerase. The DNA polymerase forms a monophyletic clade with a DNA polymerase from a genomic island in Synechococcus WH8016. The island contains a relic prophage that does not resemble any previously reported cyanophage but shares several genes with the newly identified cyanophages reported here. Metagenomic recruitment indicates that the novel cyanophages are widespread, albeit at low abundance. Here we describe a novel potentially lysogenic cyanophage family, their abundance and distribution in the marine environment.\n\nOriginality-Significance StatementMarine cyanobacteria are major contributors to primary production in the ocean. Despite reports of lysogeny in marine cyanobacteria, genomes from lysogenic marine cyanophages have not been reported yet. Using metagenomics assemblies, we recovered complete genomes of a novel uncultured marine cyanophage lineage. Remarkably, the DNA polymerase of these uncultured phages forms a monophyletic clade with the DNA polymerase from a genomic island in Synechococcus WH8016. The genomic island contains a putative relic prophage that does not resemble any known cultured cyanophage but shares several genes with the newly identified cyanophage family. These findings provide both phylogenomic and abundance estimates that are missing from current ecological models of this important group of marine viruses.

microbiology↗

bioRxiv2017

Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function

Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood. Here we report a novel, widespread cyanophage AMG, encoding a fatty acid desaturase (FAD), found in two genotypes with distinct geographical distribution. FADs are capable of modulating the fluidity of the hosts membrane, a fundamental stress response in living cells. We show that both viral fatty acid desaturases (vFADs) families are {Delta}9 lipid desaturases, catalyzing the desaturation at carbon 9 in C16 fatty acid chains. In addition, we present the first fatty acid profiling for marine cyanobacteria, which suggests a unique desaturation pathway of medium to long chain fatty acids no longer than C16, in accordance to the vFADs activity. Our findings suggest that cyanophages fiddle with the infected hosts cell, leading to increased photoprotection and potentially enhancing viral-encoded photosynthetic proteins, resulting in a new viral metabolic network.

microbiology↗

bioRxiv2017

Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota Identified by Genome-Centric Metagenomics

Marine Group II Euryarchaeota (MGII) are among the most abundant microbes in the oceanic surface waters. So far, however, representatives of MGII have not been cultivated, and no viruses infecting these organisms have been described. Here we present complete genomes for 3 distinct groups of viruses assembled from metagenomic sequence datasets highly enriched for MGII. These novel viruses, which we denote Magroviruses, possess double-stranded DNA genomes of 65 to 100 kilobase in size that encode a structural module characteristic of head-tailed viruses and, unusually for archaeal and bacterial viruses, a nearly complete replication apparatus of apparent archaeal origin. The newly identified Magroviruses are widespread and abundant, and therefore are likely to be major ecological agents.

microbiology↗