326 results on '"Ghai, Rohit"'
Search Results
2. High-resolution metagenomic reconstruction of the freshwater spring bloom
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Kavagutti, Vinicius S., Bulzu, Paul-Adrian, Chiriac, Cecilia M., Salcher, Michaela M., Mukherjee, Indranil, Shabarova, Tanja, Grujčić, Vesna, Mehrshad, Maliheh, Kasalický, Vojtěch, Andrei, Adrian-Stefan, Jezberová, Jitka, Seďa, Jaromir, Rychtecký, Pavel, Znachor, Petr, Šimek, Karel, and Ghai, Rohit
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- 2023
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- View/download PDF
3. Isolation of phages infecting the abundant freshwater Actinobacteriota order ‘Ca. Nanopelagicales’
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Kavagutti, Vinicius S., Chiriac, Maria-Cecilia, Ghai, Rohit, Salcher, Michaela M., and Haber, Markus
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- 2023
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4. Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores
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Šimek, Karel, Mukherjee, Indranil, Szöke-Nagy, Tiberiu, Haber, Markus, Salcher, Michaela M., and Ghai, Rohit
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- 2023
- Full Text
- View/download PDF
5. Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR
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Chiriac, Maria-Cecilia, Bulzu, Paul-Adrian, Andrei, Adrian-Stefan, Okazaki, Yusuke, Nakano, Shin-ichi, Haber, Markus, Kavagutti, Vinicius Silva, Layoun, Paul, Ghai, Rohit, and Salcher, Michaela M.
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- 2022
- Full Text
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6. Uncovering the genomic basis of symbiotic interactions and niche adaptations in freshwater picocyanobacteria.
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Park, Hongjae, Bulzu, Paul‑Adrian, Shabarova, Tanja, Kavagutti, Vinicius S., Ghai, Rohit, Kasalický, Vojtěch, and Jezberová, Jitka
- Abstract
Background: Picocyanobacteria from the genera Prochlorococcus, Synechococcus, and Cyanobium are the most widespread photosynthetic organisms in aquatic ecosystems. However, their freshwater populations remain poorly explored, due to uneven and insufficient sampling across diverse inland waterbodies. Results: In this study, we present 170 high-quality genomes of freshwater picocyanobacteria from non-axenic cultures collected across Central Europe. In addition, we recovered 33 genomes of their potential symbiotic partners affiliated with four genera, Pseudomonas, Mesorhizobium, Acidovorax, and Hydrogenophaga. The genomic basis of symbiotic interactions involved heterotrophs benefiting from picocyanobacteria-derived nutrients while providing detoxification of ROS. The global abundance patterns of picocyanobacteria revealed ecologically significant ecotypes, associated with trophic status, temperature, and pH as key environmental factors. The adaptation of picocyanobacteria in (hyper-)eutrophic waterbodies could be attributed to their colonial lifestyles and CRISPR-Cas systems. The prevailing CRISPR-Cas subtypes in picocyanobacteria were I-G and I-E, which appear to have been acquired through horizontal gene transfer from other bacterial phyla. Conclusions: Our findings provide novel insights into the population diversity, ecology, and evolutionary strategies of the most widespread photoautotrophs within freshwater ecosystems. 62j11owDS1FAqTqkQkf7rC Video Abstract [ABSTRACT FROM AUTHOR]
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- 2024
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7. Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat
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Cabello-Yeves, Pedro J., Zemskaya, Tamara I., Zakharenko, Alexandra S., Sakirko, Mariya V., Ivanov, Vyacheslav G., Ghai, Rohit, and Rodriguez-Valera, Francisco
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- 2020
8. Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters
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National Science Centre (Poland), Czech Science Foundation, Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Villena-Alemany, Cristian, Mujaki, Izabela, Fecskeová, Livia K., Woodhouse, Jason, Auladell Martin, Adria, Dean, Jason, Hanusová, Martina, Gazulla, Carlota R., Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, Silva Kavagutti, Vinicius, Andrei, Adrian‑Ştefan, Grossart, Hans-Peter, Ghai, Rohit, Koblížek, Michal, Piwosz, Kasia, National Science Centre (Poland), Czech Science Foundation, Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72], Villena-Alemany, Cristian, Mujaki, Izabela, Fecskeová, Livia K., Woodhouse, Jason, Auladell Martin, Adria, Dean, Jason, Hanusová, Martina, Gazulla, Carlota R., Ruscheweyh, Hans-Joachim, Sunagawa, Shinichi, Silva Kavagutti, Vinicius, Andrei, Adrian‑Ştefan, Grossart, Hans-Peter, Ghai, Rohit, Koblížek, Michal, and Piwosz, Kasia
- Abstract
Background: Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite their substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across 3 years in a temperate, meso-oligotrophic freshwater lake. Results: AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM genes, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource, we demonstrated that the majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. AAP community presented an indigenous freshwater nature characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. Conclusions: Our findings highlight the substantial contribution of AAP bacteria to the carbon flow and ecological dynamics of lakes and unveil a recurrent and dynamic seasonal succession of the AAP community. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom. We suggest a potential role of AAP bacteria within the context of the PEG model and thei
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- 2024
9. Flexible genomic island conservation across freshwater and marine Methylophilaceae
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Layoun, Paul, primary, López-Pérez, Mario, additional, Haro-Moreno, Jose M, additional, Haber, Markus, additional, Thrash, J Cameron, additional, Henson, Michael W, additional, Kavagutti, Vinicius Silva, additional, Ghai, Rohit, additional, and Salcher, Michaela M, additional
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- 2024
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10. Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
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Vavourakis, Charlotte D, Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y, Tringe, Susannah G, Hugenholtz, Philip, and Muyzer, Gerard
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Microbiology ,Biological Sciences ,Ecology ,Genetics ,Human Genome ,soda lake brines ,Nanohaloarchaea ,Halobacteria ,Bacteroidetes ,hydrolytics ,cellulase ,chitinase ,rhodopsin ,Environmental Science and Management ,Soil Sciences ,Medical microbiology - Abstract
Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral brines of similar salinities. We present the first "metagenomic snapshots" of microbial communities thriving in the brines of four shallow soda lakes from the Kulunda Steppe (Altai, Russia) covering a salinity range from 170 to 400 g/L. Both amplicon sequencing of 16S rRNA fragments and direct metagenomic sequencing showed that the top-level taxa abundance was linked to the ambient salinity: Bacteroidetes, Alpha-, and Gamma-proteobacteria were dominant below a salinity of 250 g/L, Euryarchaeota at higher salinities. Within these taxa, amplicon sequences related to Halorubrum, Natrinema, Gracilimonas, purple non-sulfur bacteria (Rhizobiales, Rhodobacter, and Rhodobaca) and chemolithotrophic sulfur oxidizers (Thioalkalivibrio) were highly abundant. Twenty-four draft population genomes from novel members and ecotypes within the Nanohaloarchaea, Halobacteria, and Bacteroidetes were reconstructed to explore their metabolic features, environmental abundance and strategies for osmotic adaptation. The Halobacteria- and Bacteroidetes-related draft genomes belong to putative aerobic heterotrophs, likely with the capacity to ferment sugars in the absence of oxygen. Members from both taxonomic groups are likely involved in primary organic carbon degradation, since some of the reconstructed genomes encode the ability to hydrolyze recalcitrant substrates, such as cellulose and chitin. Putative sodium-pumping rhodopsins were found in both a Flavobacteriaceae- and a Chitinophagaceae-related draft genome. The predicted proteomes of both the latter and a Rhodothermaceae-related draft genome were indicative of a "salt-in" strategy of osmotic adaptation. The primary catabolic and respiratory pathways shared among all available reference genomes of Nanohaloarchaea and our novel genome reconstructions remain incomplete, but point to a primarily fermentative lifestyle. Encoded xenorhodopsins found in most drafts suggest that light plays an important role in the ecology of Nanohaloarchaea. Putative encoded halolysins and laccase-like oxidases might indicate the potential for extracellular degradation of proteins and peptides, and phenolic or aromatic compounds.
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- 2016
11. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae
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Salcher, Michaela M., Schaefle, Daniel, Kaspar, Melissa, Neuenschwander, Stefan M., and Ghai, Rohit
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- 2019
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12. Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
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Andrei, Adrian-Ştefan, Salcher, Michaela M., Mehrshad, Maliheh, Rychtecký, Pavel, Znachor, Petr, and Ghai, Rohit
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- 2019
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13. Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
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Kavagutti, Vinicius S., Andrei, Adrian-Ştefan, Mehrshad, Maliheh, Salcher, Michaela M., and Ghai, Rohit
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- 2020
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14. The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling
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Mehrshad, Maliheh, Rodriguez-Valera, Francisco, Amoozegar, Mohammad Ali, López-García, Purificación, and Ghai, Rohit
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- 2018
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15. Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes
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Ngugi, David Kamanda, primary, Salcher, Michaela M., additional, Andrei, Adrian-Stefan, additional, Ghai, Rohit, additional, Klotz, Franziska, additional, Chiriac, Maria-Cecilia, additional, Ionescu, Danny, additional, Büsing, Petra, additional, Grossart, Hans-Peter, additional, Xing, Peng, additional, Priscu, John C., additional, Alymkulov, Salmor, additional, and Pester, Michael, additional
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- 2023
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16. Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes
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Ngugi, David Kamanda; https://orcid.org/0000-0002-0442-4279, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Klotz, Franziska, Chiriac, Maria-Cecilia; https://orcid.org/0000-0001-5130-5232, Ionescu, Danny; https://orcid.org/0000-0002-4658-8597, Büsing, Petra, Grossart, Hans-Peter; https://orcid.org/0000-0002-9141-0325, Xing, Peng; https://orcid.org/0000-0002-4917-5181, Priscu, John C; https://orcid.org/0000-0001-5807-6364, Alymkulov, Salmor, Pester, Michael; https://orcid.org/0000-0001-6296-4145, Ngugi, David Kamanda; https://orcid.org/0000-0002-0442-4279, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Klotz, Franziska, Chiriac, Maria-Cecilia; https://orcid.org/0000-0001-5130-5232, Ionescu, Danny; https://orcid.org/0000-0002-4658-8597, Büsing, Petra, Grossart, Hans-Peter; https://orcid.org/0000-0002-9141-0325, Xing, Peng; https://orcid.org/0000-0002-4917-5181, Priscu, John C; https://orcid.org/0000-0001-5807-6364, Alymkulov, Salmor, and Pester, Michael; https://orcid.org/0000-0001-6296-4145
- Abstract
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.
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- 2023
17. High-resolution metagenomic reconstruction of the freshwater spring bloom
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Kavagutti, Vinicius S, Bulzu, Paul-Adrian, Chiriac, Cecilia M, Salcher, Michaela M, Mukherjee, Indranil, Shabarova, Tanja, Grujčić, Vesna, Mehrshad, Maliheh, Kasalický, Vojtěch, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Jezberová, Jitka, Seďa, Jaromir, Rychtecký, Pavel, Znachor, Petr, Šimek, Karel, Ghai, Rohit, Kavagutti, Vinicius S, Bulzu, Paul-Adrian, Chiriac, Cecilia M, Salcher, Michaela M, Mukherjee, Indranil, Shabarova, Tanja, Grujčić, Vesna, Mehrshad, Maliheh, Kasalický, Vojtěch, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Jezberová, Jitka, Seďa, Jaromir, Rychtecký, Pavel, Znachor, Petr, Šimek, Karel, and Ghai, Rohit
- Abstract
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. Con
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- 2023
18. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
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Kavagutti, Vinicius S., Andrei, Adrian-Ştefan, Mehrshad, Maliheh, Salcher, Michaela M., and Ghai, Rohit
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- 2019
- Full Text
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19. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake
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Vavourakis, Charlotte D., Mehrshad, Maliheh, Balkema, Cherel, van Hall, Rutger, Andrei, Adrian-Ştefan, Ghai, Rohit, Sorokin, Dimitry Y., and Muyzer, Gerard
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- 2019
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20. The Evolutionary Kaleidoscope of Rhodopsins
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Bulzu, Paul-Adrian, Kavagutti, Vinicius S, Andrei, Adrian-Stefan, Ghai, Rohit, University of Zurich, and Bulzu, Paul-Adrian
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Rhodopsin ,1303 Biochemistry ,Physiology ,2404 Microbiology ,1314 Physiology ,580 Plants (Botany) ,Biochemistry ,Microbiology ,Computer Science Applications ,1105 Ecology, Evolution, Behavior and Systematics ,10126 Department of Plant and Microbial Biology ,1311 Genetics ,Modeling and Simulation ,Rhodopsins, Microbial ,1312 Molecular Biology ,1706 Computer Science Applications ,Genetics ,10211 Zurich-Basel Plant Science Center ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,2611 Modeling and Simulation - Abstract
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.
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- 2022
21. Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores
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Šimek, Karel, primary, Mukherjee, Indranil, additional, Szöke-Nagy, Tiberiu, additional, Haber, Markus, additional, Salcher, Michaela M., additional, and Ghai, Rohit, additional
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- 2022
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22. Hidden in plain sight—highly abundant and diverse planktonic freshwater Chloroflexi
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Mehrshad, Maliheh, Salcher, Michaela M, Okazaki, Yusuke, Nakano, Shin-ichi, Šimek, Karel, Andrei, Adrian-Stefan, and Ghai, Rohit
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- 2018
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23. A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments
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Vavourakis, Charlotte D., Andrei, Adrian-Stefan, Mehrshad, Maliheh, Ghai, Rohit, Sorokin, Dimitry Y., and Muyzer, Gerard
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- 2018
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24. The Evolutionary Kaleidoscope of Rhodopsins
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Bulzu, Paul-Adrian; https://orcid.org/0000-0002-5637-9940, Kavagutti, Vinicius S; https://orcid.org/0000-0002-1692-0042, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Bulzu, Paul-Adrian; https://orcid.org/0000-0002-5637-9940, Kavagutti, Vinicius S; https://orcid.org/0000-0002-1692-0042, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, and Ghai, Rohit; https://orcid.org/0000-0002-0591-6152
- Abstract
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
- Published
- 2022
25. Additional file 2 of Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR
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Chiriac, Maria-Cecilia, Bulzu, Paul-Adrian, Andrei, Adrian-Stefan, Okazaki, Yusuke, Nakano, Shin-ichi, Haber, Markus, Kavagutti, Vinicius Silva, Layoun, Paul, Ghai, Rohit, and Salcher, Michaela M.
- Abstract
Additional file 2: Supplementary Figure S1. Geographic location of the 17 freshwater lakes sampled in this study. Trophic state of each lake is marked by a different color. Supplementary Figure S2. Randomized Axelerated Maximum Likelihood (RAxML) tree of 16S rRNA genes of different classes of Patescibacteria. The tree was split in two subtrees with collapsed branches for better visibility. The 16S rRNA gene sequences recovered from MAGs generated in this study are shown in bold. Targets for eight newly designed oligonucleotide probes for CARD-FISH are indicated with different colors. Bootstrap values (100 bootstraps) are indicated as differently sized circles, the tree scale is given on top. Asterisks indicate sequences not targeted by probes pgri-99 and ABY1b-1343, # indicate one outgroup hit of probe adl2-134. Supplementary Figure S3. Abundance (%) of 16S rRNA gene sequences affiliated to different classes in CPR. Samples that had < 1% of total abundance in any CPR class were not added to the plot. Supplementary Figure S4. Epifluorescence microscopy images of ABY1 class members using the ABY1a-193 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S5. Epifluorescence microscopy images of ABY1 class members using the ABY1b-1343 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S6. Epifluorescence microscopy images of Paceibacteria class members using the Adl1-132 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S7A. Epifluorescence microscopy images of Paceibacteria class members using the Adl1-134 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S7B. Epifluorescence microscopy images of Paceibacteria class members using the Adl1-134 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S8. Epifluorescence microscopy images of Gracilibacteria class members using the Pgri-99 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S9. Epifluorescence microscopy images of Gracilibacteria class members using the Pgri-124 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S10. Epifluorescence microscopy images of Saccharimonadia class members using the SacA-77 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S11. Epifluorescence microscopy images of Paceibacteria class members using the ZE-1429 probe. Panels labeled with a. are the overlap of the probe (green), DAPI (blue) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S12. Positive control for the Saccharibacteria class members performed using the SacA-77 and EUB I-III probes. Panels labeled with a. are the overlap of DAPI (blue), the Sac-77 probe (green), the EUB I-III probe (orange) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S13. Positive control for the Gracilibacteria class members performed using the Pgri-124 and EUB I-III probes. Panels labeled with a. are the overlap of DAPI (blue), the Pgri-124 probe (green), the EUB I-III probe (orange) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S14a. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), the NON338 probe (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S14b. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), the NON338 probe (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S15a. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), CARD amplification (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S15b. Negative controls for filters used for FISH from different lakes. Panels labeled with a. are the overlap of DAPI (blue), CARD amplification (green) and autofluorescence (red) signal. The rest of the panels represent individual signals. Supplementary Figure S16. Boxplots for the length and width of individual CPR cells observed with the 8 FISH probed designed and tested in this study. L – Length, W – Width. Supplementary Figure S17. Percentage of genes in each KEGG module encoded by CPRs, free-living freshwater bacteria and symbionts. All representative CPR genomes from GTDB (>40% completeness
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- 2022
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26. Additional file 1 of Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR
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Chiriac, Maria-Cecilia, Bulzu, Paul-Adrian, Andrei, Adrian-Stefan, Okazaki, Yusuke, Nakano, Shin-ichi, Haber, Markus, Kavagutti, Vinicius Silva, Layoun, Paul, Ghai, Rohit, and Salcher, Michaela M.
- Subjects
viruses - Abstract
Additional file 1. Identification of phage defense mechanisms in CPRs.
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- 2022
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27. Isolation of phages infecting the abundant freshwater Actinobacteriotaorder ‘Ca. Nanopelagicales’
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Kavagutti, Vinicius S, Chiriac, Maria-Cecilia, Ghai, Rohit, Salcher, Michaela M, and Haber, Markus
- Abstract
Low-GC Actinobacteriotaof the order ‘Ca. Nanopelagicales’ (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of ‘Ca. Nanopelagicales’ we isolated a novel species of its genus ‘Ca. Planktophila’. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host’s metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting ‘Ca. Nanopelagicales’. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.
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- 2023
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28. Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms
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Bulzu, Paul-Adrian, primary, Kavagutti, Vinicius Silva, additional, Chiriac, Maria-Cecilia, additional, Vavourakis, Charlotte D., additional, Inoue, Keiichi, additional, Kandori, Hideki, additional, Andrei, Adrian-Stefan, additional, and Ghai, Rohit, additional
- Published
- 2021
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29. Quorum-Sensing Signals from Epibiont Mediate the Induction of Novel Microviridins in the Mat-Forming Cyanobacterial Genus Nostoc
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Saha, Subhasish, primary, Bulzu, Paul-Adrian, additional, Urajová, Petra, additional, Mareš, Jan, additional, Konert, Grzegorz, additional, Câmara Manoel, João, additional, Macho, Markéta, additional, Ewe, Daniela, additional, Hrouzek, Pavel, additional, Masojídek, Jiří, additional, Ghai, Rohit, additional, and Saurav, Kumar, additional
- Published
- 2021
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30. Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes
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Mujakić, Izabela, Andrei, Adrian-Stefan, Shabarova, Tanja, Fecskeová, Lívia Kolesár, Salcher, Michaela M, Piwosz, Kasia, Ghai, Rohit, Koblížek, Michal, University of Zurich, and Koblížek, Michal
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1105 Ecology, Evolution, Behavior and Systematics ,1303 Biochemistry ,10126 Department of Plant and Microbial Biology ,1311 Genetics ,2404 Microbiology ,1312 Molecular Biology ,1706 Computer Science Applications ,1314 Physiology ,580 Plants (Botany) ,2611 Modeling and Simulation - Published
- 2021
31. Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes
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Mujakić, Izabela; https://orcid.org/0000-0001-5602-7331, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Shabarova, Tanja; https://orcid.org/0000-0003-4526-3587, Fecskeová, Lívia Kolesár, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Piwosz, Kasia; https://orcid.org/0000-0002-3248-3364, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Koblížek, Michal; https://orcid.org/0000-0001-6938-2340, Mujakić, Izabela; https://orcid.org/0000-0001-5602-7331, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Shabarova, Tanja; https://orcid.org/0000-0003-4526-3587, Fecskeová, Lívia Kolesár, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Piwosz, Kasia; https://orcid.org/0000-0002-3248-3364, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, and Koblížek, Michal; https://orcid.org/0000-0001-6938-2340
- Abstract
Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota. They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes’ epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.
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- 2021
32. Heliorhodopsin Evolution Is Driven by Photosensory Promiscuity in Monoderms
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Bulzu, Paul-Adrian, Kavagutti, Vinicius Silva, Chiriac, Maria-Cecilia, Vavourakis, Charlotte D, Inoue, Keiichi, Kandori, Hideki, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Bulzu, Paul-Adrian, Kavagutti, Vinicius Silva, Chiriac, Maria-Cecilia, Vavourakis, Charlotte D, Inoue, Keiichi, Kandori, Hideki, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, and Ghai, Rohit; https://orcid.org/0000-0002-0591-6152
- Abstract
Rhodopsins are light-activated proteins displaying an enormous versatility of function as cation/anion pumps or sensing environmental stimuli and are widely distributed across all domains of life. Even with wide sequence divergence and uncertain evolutionary linkages between microbial (type 1) and animal (type 2) rhodopsins, the membrane orientation of the core structural scaffold of both was presumed universal. This was recently amended through the discovery of heliorhodopsins (HeRs; type 3), that, in contrast to known rhodopsins, display an inverted membrane topology and yet retain similarities in sequence, structure, and the light-activated response. While no ion-pumping activity has been demonstrated for HeRs and multiple crystal structures are available, fundamental questions regarding their cellular and ecological function or even their taxonomic distribution remain unresolved. Here, we investigated HeR function and distribution using genomic/metagenomic data with protein domain fusions, contextual genomic information, and gene coexpression analysis with strand-specific metatranscriptomics. We bring to resolution the debated monoderm/diderm occurrence patterns and show that HeRs are restricted to monoderms. Moreover, we provide compelling evidence that HeRs are a novel type of sensory rhodopsins linked to histidine kinases and other two-component system genes across phyla. In addition, we also describe two novel putative signal-transducing domains fused to some HeRs. We posit that HeRs likely function as generalized light-dependent switches involved in the mitigation of light-induced oxidative stress and metabolic circuitry regulation. Their role as sensory rhodopsins is corroborated by their photocycle dynamics and their presence/function in monoderms is likely connected to the higher sensitivity of these organisms to light-induced damage. IMPORTANCE Heliorhodopsins are enigmatic, novel rhodopsins with a membrane orientation that is opposite to all known rhod
- Published
- 2021
33. Prokaryotic taxonomic and metabolic diversity of an intermediate salinity hypersaline habitat assessed by metagenomics
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Fernández, Ana B., Ghai, Rohit, Martin-Cuadrado, Ana-Belen, Sánchez-Porro, Cristina, Rodriguez-Valera, Francisco, and Ventosa, Antonio
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- 2014
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34. Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes
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Mujakić, Izabela, primary, Andrei, Adrian-Ştefan, additional, Shabarova, Tanja, additional, Fecskeová, Lívia Kolesár, additional, Salcher, Michaela M., additional, Piwosz, Kasia, additional, Ghai, Rohit, additional, and Koblížek, Michal, additional
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- 2021
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35. A freshwater radiation of diplonemids
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Mukherjee, Indranil, Salcher, Michaela M, Andrei, Adrian-Stefan, Kavagutti, Vinicius Silva, Shabarova, Tanja, Grujčić, Vesna, Haber, Markus, Layoun, Paul, Hodoki, Yoshikuni, Nakano, Shin-ichi, Šimek, Karel, Ghai, Rohit, and University of Zurich
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10126 Department of Plant and Microbial Biology ,580 Plants (Botany) - Published
- 2020
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36. A freshwater radiation of diplonemids
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Mukherjee, Indranil; https://orcid.org/0000-0001-9831-0346, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Kavagutti, Vinicius Silva; https://orcid.org/0000-0002-1692-0042, Shabarova, Tanja; https://orcid.org/0000-0003-4526-3587, Grujčić, Vesna; https://orcid.org/0000-0002-3322-599X, Haber, Markus; https://orcid.org/0000-0003-2591-6210, Layoun, Paul; https://orcid.org/0000-0001-7608-9521, Hodoki, Yoshikuni, Nakano, Shin-ichi, Šimek, Karel; https://orcid.org/0000-0002-7058-9063, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Mukherjee, Indranil; https://orcid.org/0000-0001-9831-0346, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Kavagutti, Vinicius Silva; https://orcid.org/0000-0002-1692-0042, Shabarova, Tanja; https://orcid.org/0000-0003-4526-3587, Grujčić, Vesna; https://orcid.org/0000-0002-3322-599X, Haber, Markus; https://orcid.org/0000-0003-2591-6210, Layoun, Paul; https://orcid.org/0000-0001-7608-9521, Hodoki, Yoshikuni, Nakano, Shin-ichi, Šimek, Karel; https://orcid.org/0000-0002-7058-9063, and Ghai, Rohit; https://orcid.org/0000-0002-0591-6152
- Abstract
Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and CARD-FISH. We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to marine isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single cell genomes of marine diplonemids shows they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.
- Published
- 2020
37. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes
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Hain, Torsten, Steinweg, Christiane, Kuenne, Carsten Tobias, Billion, Andre, Ghai, Rohit, Chatterjee, Som Subhra, Domann, Eugen, Karst, Uwe, Goesmann, Alexander, Bekel, Thomas, Bartels, Daniela, Kaiser, Olaf, Meyer, Folker, Puhler, Alfred, Weisshaar, Bernd, Wehland, Jurgen, Liang, Chunguang, Dandekar, Thomas, Lampidis, Robert, Kreft, Jurgen, Goebel, Werner, and Chakraborty, Trinad
- Subjects
Listeria -- Genetic aspects ,Listeria -- Physiological aspects ,Nucleotide sequence -- Research ,Listeria monocytogenes -- Genetic aspects ,Listeria monocytogenes -- Physiological aspects ,Biological sciences - Abstract
We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading frames. Comparative genomic analysis of chromosomal regions between L. welshimeri, Listeria innocua, and Listeria monocytogenes shows strong overall conservation of synteny, with the exception of the translocation of an [F.sub.0][F.sub.1] ATP synthase. The smaller size of the L. weishimeri genome is the result of deletions in all of the genes involved in virulence and of 'fitness' genes required for intracellular survival, transcription factors, and LPXTG- and LRR-containing proteins as well as 55 genes involved in carbohydrate transport and metabolism. In total, 482 genes are absent from L. welshimeri relative to L. monocytogenes. Of these, 249 deletions are commonly absent in both L. welshimeri and L. innocua, suggesting similar genome evolutionary paths from an ancestor. We also identified 311 genes specific to L. welshimeri that are absent in the other two species, indicating gene expansion in L. welshimeri, including horizontal gene transfer. The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp.
- Published
- 2006
38. Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria
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Ghai, Rohit, Mizuno, Carolina Megumi, Picazo, Antonio, Camacho, Antonio, and Rodriguez-Valera, Francisco
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- 2013
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39. Expanded Diversity and Metabolic Versatility of Marine Nitrite-Oxidizing Bacteria Revealed by Cultivation- and Genomics-Based Approaches
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Park, Soo-Je, primary, Andrei, Adrian-Ştefan, additional, Bulzu, Paul-Adrian, additional, Kavagutti, Vinicius S., additional, Ghai, Rohit, additional, and Mosier, Annika C., additional
- Published
- 2020
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40. Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition (CARD-FISH)
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Salcher, Michaela M., primary, Andrei, Adrian-Ştefan, additional, Bulzu, Paul-Adrian, additional, Keresztes, Zsolt G., additional, Banciu, Horia L., additional, and Ghai, Rohit, additional
- Published
- 2020
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41. Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H + pumps
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Inoue, Keiichi, primary, Tsunoda, Satoshi P., additional, Singh, Manish, additional, Tomida, Sahoko, additional, Hososhima, Shoko, additional, Konno, Masae, additional, Nakamura, Ryoko, additional, Watanabe, Hiroki, additional, Bulzu, Paul-Adrian, additional, Banciu, Horia L., additional, Andrei, Adrian-Ştefan, additional, Uchihashi, Takayuki, additional, Ghai, Rohit, additional, Béjà, Oded, additional, and Kandori, Hideki, additional
- Published
- 2020
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42. Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat
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Cabello‐Yeves, Pedro J., primary, Zemskaya, Tamara I., additional, Zakharenko, Alexandra S., additional, Sakirko, Mariya V., additional, Ivanov, Vyacheslav G., additional, Ghai, Rohit, additional, and Rodriguez‐Valera, Francisco, additional
- Published
- 2019
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43. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake
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Vavourakis, Charlotte D. (author), Mehrshad, Maliheh (author), Balkema, Cherel (author), Van Hall, Rutger (author), Andrei, Adrian Ştefan (author), Ghai, Rohit (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author), Vavourakis, Charlotte D. (author), Mehrshad, Maliheh (author), Balkema, Cherel (author), Van Hall, Rutger (author), Andrei, Adrian Ştefan (author), Ghai, Rohit (author), Sorokin, Dimitry Y. (author), and Muyzer, Gerard (author)
- Abstract
Background: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here, we investigate dissimilatory sulfur cycling in the brine and sediments of a southwestern Siberian soda lake characterized by an extremely high pH and salinity, combining meta-omics analyses of its uniquely adapted highly diverse prokaryote communities with biogeochemical profiling to identify key microbial players and expand our understanding of sulfur cycling under haloalkaline conditions. Results: Peak microbial activity was found in the top 4 cm of the sediments, a layer with a steep drop in oxygen concentration and redox potential. The majority of sulfur was present as sulfate or iron sulfide. Thiosulfate was readily oxidized by microbes in the presence of oxygen, but oxidation was partially inhibited by light. We obtained 1032 metagenome-assembled genomes, including novel population genomes of characterized colorless sulfur-oxidizing bacteria (SOB), anoxygenic purple sulfur bacteria, heterotrophic SOB, and highly active lithoautotrophic sulfate reducers. Surprisingly, we discovered the potential for nitrogen fixation in a new genus of colorless SOB, carbon fixation in a new species of phototrophic Gemmatimonadetes, and elemental sulfur/sulfite reduction in the "Candidatus Woesearchaeota." Polysulfide/thiosulfate and tetrathionate reductases were actively transcribed by various (facultative) anaerobes. Conclusions: The recovery of over 200 genomes that encoded enzymes capable of catalyzing key reactions in the inorganic sulfur cycle indicates complete cycling between sulfate and sulfide at moderately hypersaline and extreme alkaline conditions. Our results suggest that more taxonomic groups are involved in sulfur dissimil, BT/Environmental Biotechnology
- Published
- 2019
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44. Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
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Kavagutti, Vinicius S, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Mehrshad, Maliheh, Salcher, Michaela M, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Kavagutti, Vinicius S, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Mehrshad, Maliheh, Salcher, Michaela M, and Ghai, Rohit; https://orcid.org/0000-0002-0591-6152
- Abstract
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.
- Published
- 2019
45. Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae
- Author
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Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Schaefle, Daniel, Kaspar, Melissa, Neuenschwander, Stefan M, Ghai, Rohit; https://orcid.org/0000-0002-0591-6152, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Schaefle, Daniel, Kaspar, Melissa, Neuenschwander, Stefan M, and Ghai, Rohit; https://orcid.org/0000-0002-0591-6152
- Abstract
The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (“Ca. Methylopumilus”) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2–3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.
- Published
- 2019
46. Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
- Author
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Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Mehrshad, Maliheh, Rychtecký, Pavel, Znachor, Petr, Ghai, Rohit, Andrei, Adrian-Stefan; https://orcid.org/0000-0003-1425-7168, Salcher, Michaela M; https://orcid.org/0000-0003-1063-6523, Mehrshad, Maliheh, Rychtecký, Pavel, Znachor, Petr, and Ghai, Rohit
- Abstract
Freshwater environments teem with microbes that do not have counterparts in culture collections or genetic data available in genomic repositories. Currently, our apprehension of evolutionary ecology of freshwater bacteria is hampered by the difficulty to establish organism models for the most representative clades. To circumvent the bottlenecks inherent to the cultivation-based techniques, we applied ecogenomics approaches in order to unravel the evolutionary history and the processes that drive genome architecture in hallmark freshwater lineages from the phylum Planctomycetes. The evolutionary history inferences showed that sediment/soil Planctomycetes transitioned to aquatic environments, where they gave rise to new freshwater-specific clades. The most abundant lineage was found to have the most specialised lifestyle (increased regulatory genetic circuits, metabolism tuned for mineralization of proteinaceous sinking aggregates, psychrotrophic behaviour) within the analysed clades and to harbour the smallest freshwater Planctomycetes genomes, highlighting a genomic architecture shaped by niche-directed evolution (through loss of functions and pathways not needed in the newly acquired freshwater niche).
- Published
- 2019
47. An Indian feast.
- Author
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Ghai, Rohit and Manfield, Christine
- Published
- 2022
48. Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes
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Hain Torsten, Ghai Rohit, Billion André, Kuenne Carsten, Steinweg Christiane, Izar Benjamin, Mohamed Walid, Mraheil Mobarak, Domann Eugen, Schaffrath Silke, Kärst Uwe, Goesmann Alexander, Oehm Sebastian, Pühler Alfred, Merkl Rainer, Vorwerk Sonja, Glaser Philippe, Garrido Patricia, Rusniok Christophe, Buchrieser Carmen, Goebel Werner, and Chakraborty Trinad
- Subjects
Listeria monocytogenes ,Lineage ,Comparative genomics ,Gene decay ,Comparative transcriptomics ,Flagella ,Prophage ,Monocin ,Isogenic deletion mutants ,Murine infection ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans. Results The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. Conclusion Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.
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- 2012
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49. New Halonotius Species Provide Genomics-Based Insights Into Cobalamin Synthesis in Haloarchaea
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Durán-Viseras, Ana, primary, Andrei, Adrian-Stefan, additional, Ghai, Rohit, additional, Sánchez-Porro, Cristina, additional, and Ventosa, Antonio, additional
- Published
- 2019
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- View/download PDF
50. Gram-positive pathogenic bacteria induce a common early response in human monocytes
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Ghai Rohit, Tchatalbachev Svetlin, Hossain Hamid, and Chakraborty Trinad
- Subjects
Microbiology ,QR1-502 - Abstract
Abstract Background We infected freshly isolated human peripheral monocytes with live bacteria of three clinically important gram-positive bacterial species, Staphylococcus aureus, Streptococcus pneumoniae and Listeria monocytogenes and studied the ensuing early transcriptional response using expression microarrays. Thus the observed response was unbiased by signals originating from other helper and effector cells of the host and was not limited to induction by solitary bacterial constituents. Results Activation of monocytes was demonstrated by the upregulation of chemokine rather than interleukin genes except for the prominent expression of interleukin 23, marking it as the early lead cytokine. This activation was accompanied by cytoskeleton rearrangement signals and a general anti-oxidative stress and anti-apoptotic reaction. Remarkably, the expression profiles also provide evidence that monocytes participate in the regulation of angiogenesis and endothelial function in response to these pathogens. Conclusion Regardless of the invasion properties and survival mechanisms of the pathogens used, we found that the early response comprised of a consistent and common response. The common response was hallmarked by the upregulation of interleukin 23, a rather unexpected finding regarding Listeria infection, as this cytokine has been linked primarily to the control of extracellular bacterial dissemination.
- Published
- 2010
- Full Text
- View/download PDF
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