Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth.
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ABSTRACT:
SUBMITTER: Baalsrud HT
PROVIDER: S-EPMC5554263 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundCyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.MethodologyWe examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.ResultsPicyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.ConclusionsPicocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.
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Project description:The Mandarin vole (Lasiopodomys mandarinus), a typical subterranean rodent, has undergone hematological adaptations to tolerate the hypoxic/hypercapnic underground environment. Hemoglobin (Hb) genes encode respiratory proteins functioning principally in oxygen binding and transport to various tissues and organs. To investigate the evolution of α- and β-hemoglobin (Hb) in subterranean rodent species, we sequenced Hb genes of the Mandarin vole and the related aboveground Brandt's vole (L. brandtii). Sequencing showed that in both voles, α-globin was encoded by a cluster of five functional genes in the following linkage order: HBZ, HBA-T1, HBQ-T1, HBA-T2, and HBQ-T2; among these, HBQ-T2 is a pseudogene in both voles. The β-globin gene cluster in both voles also included five functional genes in the following linkage order: HBE, HBE/HBG, HBG, HBB-T1, and HBB-T2. Phylogenetic analysis revealed that the Mandarin vole underwent convergent evolution with its related aboveground species (Brandt's vole) but not with other subterranean rodent species. Selection pressure analyses revealed that α- and β-globin genes are under strong purifying selection (ω < 1), and branch-site analyses identified positive selection sites on HBAT-T1 and HBB-T1 in different subterranean rodent species. This suggests that the adaptive evolution of these genes enhanced the ability of Hb to store and transport oxygen in subterranean rodent species. Our findings highlight the critical roles of Hb genes in the evolution of hypoxia tolerance in subterranean rodent species.
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Project description:Although bioluminescent bacteria are the most abundant and widely distributed of all light-emitting organisms, the biological role and evolutionary history of bacterial luminescence are still shrouded in mystery. Bioluminescence has so far been observed in the genomes of three families of Gammaproteobacteria in the form of canonical lux operons that adopt the CDAB(F)E(G) gene order. LuxA and luxB encode the two subunits of bacterial luciferase responsible for light-emission. Our deep exploration of public marine environmental databases considerably expands this view by providing a catalog of new lux homolog sequences, including 401 previously unknown luciferase-related genes. It also reveals a broader diversity of the lux operon organization, which we observed in previously undescribed configurations such as CEDA, CAED and AxxCE. This expanded operon diversity provides clues for deciphering lux operon evolution and propagation within the bacterial domain. Leveraging quantitative tracking of marine bacterial genes afforded by planetary scale metagenomic sampling, our study also reveals that the novel lux genes and operons described herein are more abundant in the global ocean than the canonical CDAB(F)E(G) operon.
| S-EPMC7671414 | biostudies-literature
Project description:Different from the existing global ocean climatological datasets of isothermal layer (ITL) depth (h), a global ocean synoptic dataset of h along with other parameters has been established from temperature profiles of the National Centers for Environmental Information (NCEI) world ocean database 1961-2017. The exponential leap-forward gradient method was used to identify h and thermocline gradient (G) from each temperature profile measured by expendable bathythermograph (XBT) and conductivity, temperature, depth (CTD) instruments. Due to quality and vertical resolution of the profiling data, the numbers of (G, h) pairs are 446,811 out of 964,942 CTD profiles and 755,086 out of 2,303,433 XBT profiles. With the given h, other parameters such as ITL heat content (HITL), sea surface temperature (SST), temperature below ITL (Tm), and quality measures (Q, I) indices are provided. Altogether, the dataset contains 1,201,897 temporally and horizontally varying sets of (G, h, HITL, SST, Tm, Q-index, I-index). Note that we added 200° to the longitude. This synoptic dataset is located on the NCEI website for public use.
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Project description:The LFY transcription factor gene family are important in the promotion of cell proliferation and floral development. Understanding their evolution offers an insight into floral development in plant evolution. Though a promiscuous transition intermediate and a gene duplication event within the LFY family had been identified previously, the early evolutionary path of this family remained elusive. Here, we reconstructed the LFY family phylogeny using maximum-likelihood and Bayesian inference methods incorporating LFY genes from all major lineages of streptophytes. The well-resolved phylogeny unveiled a high-confidence duplication event before the functional divergence of types I and II LFY genes in the ancestry of liverworts, mosses and tracheophytes, supporting sub-functionalization of an ancestral promiscuous gene. The identification of promiscuous genes in Osmunda suggested promiscuous LFY genes experienced an ancient transient duplication. Genomic synteny comparisons demonstrated a deep genomic positional conservation of LFY genes and an ancestral lineage-specific transposition activity in grasses.
| S-EPMC6588583 | biostudies-literature
Project description:For over 50 years, ocean scientists have oddly represented ocean oxygen consumption rates as a function of depth but not temperature in most biogeochemical models. This unique tradition or tactic inhibits useful discussion of climate change impacts, where specific and fundamental temperature-dependent terms are required. Tracer-based determinations of oxygen consumption rates in the deep sea are nearly universally reported as a function of depth in spite of their well-known microbial basis. In recent work, we have shown that a carefully determined profile of oxygen consumption rates in the Sargasso Sea can be well represented by a classical Arrhenius function with an activation energy of 86.5 kJ mol-1, leading to a Q10 of 3.63. This indicates that for 2°C warming, we will have a 29% increase in ocean oxygen consumption rates, and for 3°C warming, a 47% increase, potentially leading to large-scale ocean hypoxia should a sufficient amount of organic matter be available to microbes. Here, we show that the same principles apply to a worldwide collation of tracer-based oxygen consumption rate data and that some 95% of ocean oxygen consumption is driven by temperature, not depth, and thus will have a strong climate dependence. The Arrhenius/Eyring equations are no simple panacea and they require a non-equilibrium steady state to exist. Where transient events are in progress, this stricture is not obeyed and we show one such possible example.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.
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Project description:Evolution in the chronic cold of the Southern Ocean has had a profound influence on the physiology of cryonotothenioid fishes. However, the suite of genetic changes underlying the physiological gains and losses in these fishes is still poorly surveyed. By identifying the genomic signatures of selection, this study aims to identify the functional classes of genes that have been changed following two major physiological transitions: the onset of freezing temperatures and the loss of hemoproteins. Looking at the changes that followed the onset of freezing temperatures, positive selective pressure was found among a set of broadly acting gene regulatory factors, suggesting a route through which cryonotothenioid gene expression has been retooled for life in the cold. Further, genes related to the cell cycle and cellular adhesion were found under positive selection suggesting that both present key challenges to life in freezing waters. By contrast, genes showing signatures of the relaxation of selective pressure showed a narrower biological impact, acting on genes related to mitochondrial function. Finally, although chronic cold-water temperatures appear correlated with substantial genetic change, the loss of hemoproteins resulted in little observable change in protein-coding genes relative to their red-blooded relatives. Combined, the influence of positive and relaxed selection shows that long-term exposure to cold has led to profound changes in cryonotothenioid genomes that may make it challenging for them to adapt to a rapidly changing climate.
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Project description:Oxygenation of Earth's oceans and atmosphere through time has consequences for subducted surface signatures that are now stored in the mantle. Here, we report significant mass-dependent selenium isotope variations in modern hot spot-influenced oceanic lavas. These variations are correlated with tracers of mantle source enrichment, which can only be explained by incorporation of abyssal pelagic sediments subducted from a redox-stratified mid-Proterozoic ocean. Selenium geochemical signatures of these sediments have mostly been preserved during long-term recycling and may therefore complement the global surface sediment record as ancient oxygen archives. Combined deep mantle and surface perspectives, together with emerging models for atmospheric oxygen based on selenium systematics, further imply a significantly oxygenated ocean-atmosphere system throughout the mid-Proterozoic.
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Project description:The surface mixed layer of the world ocean regulates global climate by controlling heat and carbon exchange between the atmosphere and the oceanic interior1-3. The mixed layer also shapes marine ecosystems by hosting most of the ocean's primary production4 and providing the conduit for oxygenation of deep oceanic layers. Despite these important climatic and life-supporting roles, possible changes in the mixed layer during an era of global climate change remain uncertain. Here we use oceanographic observations to show that from 1970 to 2018 the density contrast across the base of the mixed layer increased and that the mixed layer itself became deeper. Using a physically based definition of upper-ocean stability that follows different dynamical regimes across the global ocean, we find that the summertime density contrast increased by 8.9 ± 2.7 per cent per decade (10-6-10-5 per second squared per decade, depending on region), more than six times greater than previous estimates. Whereas prior work has suggested that a thinner mixed layer should accompany a more stratified upper ocean5-7, we find instead that the summertime mixed layer deepened by 2.9 ± 0.5 per cent per decade, or several metres per decade (typically 5-10 metres per decade, depending on region). A detailed mechanistic interpretation is challenging, but the concurrent stratification and deepening of the mixed layer are related to an increase in stability associated with surface warming and high-latitude surface freshening8,9, accompanied by a wind-driven intensification of upper-ocean turbulence10,11. Our findings are based on a complex dataset with incomplete coverage of a vast area. Although our results are robust within a wide range of sensitivity analyses, important uncertainties remain, such as those related to sparse coverage in the early years of the 1970-2018 period. Nonetheless, our work calls for reconsideration of the drivers of ongoing shifts in marine primary production, and reveals stark changes in the world's upper ocean over the past five decades.
| S-EPMC7610469 | biostudies-literature