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Ying
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Ying
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ArticleImpacts of Arctic sea ice on cold season atmospheric variability and trends estimated from observations and a multimodel large ensemble(American Meteorological Society, 2021-09-24) Liang, Yu-Chiao ; Frankignoul, Claude ; Kwon, Young-Oh ; Gastineau, Guillaume ; Manzini, Elisa ; Danabasoglu, Gokhan ; Suo, Lingling ; Yeager, Stephen G. ; Gao, Yongqi ; Attema, Jisk J. ; Cherchi, Annalisa ; Ghosh, Rohit ; Matei, Daniela ; Mecking, Jennifer V. ; Tian, Tian ; Zhang, YingTo examine the atmospheric responses to Arctic sea ice variability in the Northern Hemisphere cold season (from October to the following March), this study uses a coordinated set of large-ensemble experiments of nine atmospheric general circulation models (AGCMs) forced with observed daily varying sea ice, sea surface temperature, and radiative forcings prescribed during the 1979–2014 period, together with a parallel set of experiments where Arctic sea ice is substituted by its climatology. The simulations of the former set reproduce the near-surface temperature trends in reanalysis data, with similar amplitude, and their multimodel ensemble mean (MMEM) shows decreasing sea level pressure over much of the polar cap and Eurasia in boreal autumn. The MMEM difference between the two experiments allows isolating the effects of Arctic sea ice loss, which explain a large portion of the Arctic warming trends in the lower troposphere and drive a small but statistically significant weakening of the wintertime Arctic Oscillation. The observed interannual covariability between sea ice extent in the Barents–Kara Seas and lagged atmospheric circulation is distinguished from the effects of confounding factors based on multiple regression, and quantitatively compared to the covariability in MMEMs. The interannual sea ice decline followed by a negative North Atlantic Oscillation–like anomaly found in observations is also seen in the MMEM differences, with consistent spatial structure but much smaller amplitude. This result suggests that the sea ice impacts on trends and interannual atmospheric variability simulated by AGCMs could be underestimated, but caution is needed because internal atmospheric variability may have affected the observed relationship.
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ArticleVariation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100(Microbiology Society, 2019-12-01) Williams, Laura E. ; Cullen, Nicole ; DeGiorgis, Joseph A. ; Martinez, Karla J. ; Mellone, Justina ; Oser, Molly ; Wang, Jing ; Zhang, YingDefining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a ‘core genome’ of 778 protein-coding genes and identified four protein-coding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.
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ArticlePan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria(Frontiers Media, 2014-03-19) Zhang, Ying ; Sievert, Stefan M.The rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. Using the class Epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. Models were constructed to extrapolate the expansion of pan-genomes at three different taxonomic levels. The results show that, for Epsilonproteobacteria the seemingly large genome variations among strains of the same species are less noticeable when compared with groups at higher taxonomic ranks, indicating that genome stability is imposed by the potential existence of taxonomic boundaries. The analyses of pan-genomes has also defined a set of universally conserved core genes, based on which a phylogenetic tree was constructed to confirm that thermophilic species from deep-sea hydrothermal vents represent the most ancient lineages of Epsilonproteobacteria. Moreover, by comparing the flexible genome of a chemoautotrophic deep-sea vent species to (1) genomes of species belonging to the same genus, but inhabiting different environments, and (2) genomes of other vent species, but belonging to different genera, we were able to delineate the relative importance of lineage-specific versus niche-specific genes. This result not only emphasizes the overall importance of phylogenetic proximity in shaping the variable part of the genome, but also highlights the adaptive functions of niche-specific genes. Overall, by modeling the expansion of pan-genomes and analyzing core and flexible genes, this study provides snapshots on how the complex processes of gene acquisition, conservation, and removal affect the evolution of different species, and contribute to the metabolic diversity and versatility of Epsilonproteobacteria.
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ArticleThe FGGY carbohydrate kinase family : insights into the evolution of functional specificities(Public Library of Science, 2011-12-22) Zhang, Ying ; Zagnitko, Olga ; Rodionova, Irina ; Osterman, Andrei ; Godzik, AdamFunction diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS) of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB) evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose). Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.
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ArticleAddendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)(Frontiers Media, 2018-04-18) Waite, David W. ; Vanwonterghem, Inka ; Rinke, Christian ; Parks, Donovan H. ; Zhang, Ying ; Takai, Ken ; Sievert, Stefan M. ; Simon, Jörg ; Campbell, Barbara J. ; Hanson, Thomas E. ; Woyke, Tanja ; Klotz, Martin G. ; Hugenholtz, Philip
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ArticleMultiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments(American Association for the Advancement of Science, 2021-05-26) Gomaa, Fatma ; Utter, Daniel R. ; Powers, Christopher ; Beaudoin, David J. ; Edgcomb, Virginia P. ; Filipsson, Helena L. ; Hansel, Colleen M. ; Wankel, Scott D. ; Zhang, Ying ; Bernhard, Joan M.Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom’s plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among “typical” eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.
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ArticleComparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.)(Frontiers Media, 2017-04-24) Waite, David W. ; Vanwonterghem, Inka ; Rinke, Christian ; Parks, Donovan H. ; Zhang, Ying ; Takai, Ken ; Sievert, Stefan M. ; Simon, Jörg ; Campbell, Barbara J. ; Hanson, Thomas E. ; Woyke, Tanja ; Klotz, Martin G. ; Hugenholtz, PhilipThe Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
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ArticleArctic troposphere warming driven by external radiative forcing and modulated by the Pacific and Atlantic(American Geophysical Union, 2022-12-04) Suo, Lingling ; Gao, Yongqi ; Gastineau, Guillaume ; Liang, Yu‐Chiao ; Ghosh, Rohit ; Tian, Tian ; Zhang, Ying ; Kwon, Young‐Oh ; Matei, Daniela ; Otterå, Odd Helge ; Yang, ShutingDuring the past decades, the Arctic has experienced significant tropospheric warming, with varying decadal warming rates. However, the relative contributions from potential drivers and modulators of the warming are yet to be further quantified. Here, we utilize a unique set of multi‐model large‐ensemble atmospheric simulations to isolate the respective contributions from the combined external radiative forcing (ERF‐AL), interdecadal Pacific variability (IPV), Atlantic multidecadal variability (AMV), and Arctic sea‐ice concentration changes (ASIC) to the warming during 1979–2013. In this study, the ERF‐AL impacts are the ERF impacts directly on the atmosphere and land surface, excluding the indirect effects through SST and SIC feedback. The ERF‐AL is the primary driver of the April–September tropospheric warming during 1979–2013, and its warming effects vary at decadal time scales. The IPV and AMV intensify the warming during their transitioning periods to positive phases and dampen the warming during their transitioning periods to negative phases. The IPV impacts are prominent in winter and spring and are stronger than AMV impacts on 1979–2013 temperature trends. The warming impacts of ASIC are generally restricted to below 700 hPa and are strongest in autumn and winter. The combined effects of these factors reproduce the observed accelerated and step‐down Arctic warming in different decades, but the intensities of the reproduced decadal variations are generally weaker than in the observed.
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ArticleTwo canonically aerobic foraminifera express distinct peroxisomal and mitochondrial metabolisms(Frontiers Media, 2022-12-02) Powers, Christopher ; Gomaa, Fatma ; Billings, Elizabeth B. ; Utter, Daniel R. ; Beaudoin, David J. ; Edgcomb, Virginia P. ; Hansel, Colleen M. ; Wankel, Scott D. ; Filipsson, Helena L. ; Zhang, Ying ; Bernhard, Joan M.Certain benthic foraminifera thrive in marine sediments with low or undetectable oxygen. Potential survival avenues used by these supposedly aerobic protists include fermentation and anaerobic respiration, although details on their adaptive mechanisms remain elusive. To better understand the metabolic versatility of foraminifera, we studied two benthic species that thrive in oxygen-depleted marine sediments. Here we detail, via transcriptomics and metatranscriptomics, differential gene expression of Nonionella stella and Bolivina argentea , collected from Santa Barbara Basin, California, USA, in response to varied oxygenation and chemical amendments. Organelle-specific metabolic reconstructions revealed these two species utilize adaptable mitochondrial and peroxisomal metabolism. N. stella, most abundant in anoxia and characterized by lack of food vacuoles and abundance of intracellular lipid droplets, was predicted to couple the putative peroxisomal beta-oxidation and glyoxylate cycle with a versatile electron transport system and a partial TCA cycle. In contrast, B. argentea , most abundant in hypoxia and contains food vacuoles, was predicted to utilize the putative peroxisomal gluconeogenesis and a full TCA cycle but lacks the expression of key beta-oxidation and glyoxylate cycle genes. These metabolic adaptations likely confer ecological success while encountering deoxygenation and expand our understanding of metabolic modifications and interactions between mitochondria and peroxisomes in protists.
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ArticleSimulated contribution of the interdecadal Pacific oscillation to the west Eurasia cooling in 1998–2013(IOP Publishing, 2022-08-30) Suo, Lingling ; Gastineau, Guillaume ; Gao, Yongqi ; Liang, Yu-Chiao ; Ghosh, Rohit ; Tian, Tian ; Zhang, Ying ; Kwon, Young-Oh ; Otterå, Odd Helge ; Yang, Shuting ; Matei, DanielaLarge ensemble simulations with six atmospheric general circulation models involved are utilized to verify the interdecadal Pacific oscillation (IPO) impacts on the trend of Eurasian winter surface air temperatures (SAT) during 1998–2013, a period characterized by the prominent Eurasia cooling (EC). In our simulations, IPO brings a cooling trend over west-central Eurasia in 1998–2013, about a quarter of the observed EC in that area. The cooling is associated with the phase transition of the IPO to a strong negative. However, the standard deviation of the area-averaged SAT trends in the west EC region among ensembles, driven by internal variability intrinsic due to the atmosphere and land, is more than three times the isolated IPO impacts, which can shadow the modulation of the IPO on the west Eurasia winter climate.
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ArticleObserved winter Barents Kara Sea ice variations induce prominent sub-decadal variability and a multi-decadal trend in the warm Arctic cold Eurasia pattern(IOP Publishing, 2024-01-25) Ghosh, Rohit ; Manzini, Elisa ; Gao, Yongqi ; Gastineau, Guillaume ; Cherchi, Annalisa ; Frankignoul, Claude ; Liang, Yu-Chiao ; Kwon, Young-Oh ; Suo, Lingling ; Tyrlis, Evangelos ; Mecking, Jennifer V. ; Tian, Tian ; Zhang, Ying ; Matei, DanielaThe observed winter Barents-Kara Sea (BKS) sea ice concentration (SIC) has shown a close association with the second empirical orthogonal function (EOF) mode of Eurasian winter surface air temperature (SAT) variability, known as Warm Arctic Cold Eurasia (WACE) pattern. However, the potential role of BKS SIC on this WACE pattern of variability and on its long-term trend remains elusive. Here, we show that from 1979 to 2022, the winter BKS SIC and WACE association is most prominent and statistically significant for the variability at the sub-decadal time scale for 5–6 years. We also show the critical role of the multi-decadal trend in the principal component of the WACE mode of variability for explaining the overall Eurasian winter temperature trend over the same period. Furthermore, a large multi-model ensemble of atmosphere-only experiments from 1979 to 2014, with and without the observed Arctic SIC forcing, suggests that the BKS SIC variations induce this observed sub-decadal variability and the multi-decadal trend in the WACE. Additionally, we analyse the model simulated first or the leading EOF mode of Eurasian winter SAT variability, which in observations, closely relates to the Arctic Oscillation (AO). We find a weaker association of this mode to AO and a statistically significant positive trend in our ensemble simulation, opposite to that found in observation. This contrasting nature reflects excessive hemispheric warming in the models, partly contributed by the modelled Arctic Sea ice loss.
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ArticleForcing and impact of the Northern Hemisphere continental snow cover in 1979–2014(European Geosciences Union, 2023-05-23) Gastineau, Guillaume ; Frankignoul, Claude ; Gao, Yongqi ; Liang, Yu-Chiao ; Kwon, Young-Oh ; Cherchi, Annalisa ; Ghosh, Rohit ; Manzini, Elisa ; Matei, Daniela ; Mecking, Jennifer ; Suo, Lingling ; Tian, Tian ; Yang, Shuting ; Zhang, YingThe main drivers of the continental Northern Hemisphere snow cover are investigated in the 1979–2014 period. Four observational datasets are used as are two large multi-model ensembles of atmosphere-only simulations with prescribed sea surface temperature (SST) and sea ice concentration (SIC). A first ensemble uses observed interannually varying SST and SIC conditions for 1979–2014, while a second ensemble is identical except for SIC with a repeated climatological cycle used. SST and external forcing typically explain 10 % to 25 % of the snow cover variance in model simulations, with a dominant forcing from the tropical and North Pacific SST during this period. In terms of the climate influence of the snow cover anomalies, both observations and models show no robust links between the November and April snow cover variability and the atmospheric circulation 1 month later. On the other hand, the first mode of Eurasian snow cover variability in January, with more extended snow over western Eurasia, is found to precede an atmospheric circulation pattern by 1 month, similar to a negative Arctic oscillation (AO). A decomposition of the variability in the model simulations shows that this relationship is mainly due to internal climate variability. Detailed outputs from one of the models indicate that the western Eurasia snow cover anomalies are preceded by a negative AO phase accompanied by a Ural blocking pattern and a stratospheric polar vortex weakening. The link between the AO and the snow cover variability is strongly related to the concomitant role of the stratospheric polar vortex, with the Eurasian snow cover acting as a positive feedback for the AO variability in winter. No robust influence of the SIC variability is found, as the sea ice loss in these simulations only drives an insignificant fraction of the snow cover anomalies, with few agreements among models.