Biology subjects

Sharon, I.

Publications and source records attributed to Sharon, I..

4 recordsLinked to original sources

bioRxiv2018

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

The metabolic machinery from which microbial aerobic respiration evolved is tightly linked to the origins of oxygenic Cyanobacteria (Oxyphotobacteria). Even though the majority of Oxyphotobacteria are photoautotrophs and can use carbohydrates with oxygen (O2) as the electron acceptor, all are fermenters under dark anoxic conditions. Studies suggest that the ancestor of Oxyphotobacteria may have used hydrogen (H2) as an electron donor and that two types of NiFe hydrogenases are essential for its oxidation. Melainabacteria and Sericytochromatia, close phylogenetic neighbors to Oxyphotobacteria comprise fermentative and aerobic representatives, or organisms capable of both. Margulisbacteria (candidate divisions RBX-1 and ZB3) and Saganbacteria (candidate division WOR-1), a novel cluster of bacteria phylogenetically related to Melainabacteria, Sericytochromatia and Oxyphotobacteria may further constrain the metabolic platform in which oxygenic photosynthesis and aerobic respiration arose. Here, we predict the metabolisms of Margulisbacteria and Saganbacteria from new and published metagenome-assembled genomes (MAGs) and single amplified genomes (SAGs), and compare them to their phylogenetic neighbors. Sediment-associated Margulisbacteria are predicted to have a fermentation-based metabolism featuring a variety of hydrogenases, a nitrogenase for nitrogen (N2) fixation, and electron bifurcating complexes involved in cycling of ferredoxin and NAD(P)H. Overall, the genomic features suggest the capacity for metabolic fine-tuning under strictly anoxic conditions. In contrast, the genomes of Margulisbacteria from the ocean ecosystem encode an electron transport chain that supports aerobic growth. Similarly, some Saganbacteria genomes encode various hydrogenases, and others may have the ability to use O2 under certain conditions via a putative novel type of heme copper O2 reductase. Like Melainabacteria and Sericytochromatia, Margulisbacteria and Saganbacteria have diverse energy metabolisms capable of fermentation, and aerobic or anaerobic respiration. In summary, our findings support the hypothesis that the ancestor of these groups was an anaerobe in which fermentation and H2 metabolism were central metabolic features. Our genomic data also suggests that contemporary lineages sibling to the Oxyphotobacteria may have acquired the ability to use O2 as a terminal electron acceptor under certain environmental conditions.

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↗