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4. Novel thermophilic genera Geochorda gen. nov. and Carboxydochorda gen. nov. from the deep terrestrial subsurface reveal the ecophysiological diversity in the class Limnochordia.

Author

Karnachuk, Olga V., Lukina, Anastasia P., Avakyan, Marat R., Kadnikov, Vitaly V., Begmatov, Shahjahon, Beletsky, Alexey V., Vlasova, Ksenia G., Novikov, Andrei A., Shcherbakova, Viktoria A., Mardanov, Andrey V., and Ravin, Nikolai V.

Subjects
ELECTRON donors, AEROBIC metabolism, POLYMER degradation, ELECTROPHILES, MALTODEXTRIN, XYLANS, MALTOSE
Abstract

The class Limnochordia harbors a single cultivated member, the mesophilic Limnochorda pilosa, which was isolated from a meromictic lake. Despite numerous molecular signatures reported in various ecosystems, the ecophysiological versatility of this deeply branched lineage of Firmicutes (Bacillota) remains poorly understood. The objective of this study was to use targeted cultivation, based on metagenome-assembled genomes from a deep terrestrial aquifer in Western Siberia, to isolate two new thermophilic members of the class. These isolates, described as Geochorda subterranea gen. nov. sp. nov. and Carboxydochorda subterranea gen. nov. sp. nov. within the Geochordaceae fam. nov., were capable of both anaerobic and aerobic respiration using fumarate and O2, respectively, with simple sugars as electron donors. The cultivated Geochordaceae have demonstrated fermentative growth and degradation of various polymers, including starch, maltose, maltodextrin, xylan, and chitin. The carboxydotrophic C. subterranea sp. nov. exhibited autotrophic growth via the Calvin–Benson–Bassham cycle, using CO, H2, and formate as electron donors and O2 as an electron acceptor, adding metabolic flexibility to the bacterium in the nutrient-depleted “deep biosphere” and supporting the possibility of aerobic metabolism in the deep subsurface. The broad physiological potential deciphered from physiological experiments and comparative genomic data explains the widespread distribution of uncultivated members of the class Limnochordia in various ecosystems, where they can oxidize complex organic substrates through both aerobic and anaerobic respiration, as well as pursue a chemolithotrophic lifestyle through the oxidation of H2 or CO. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Phenotypic and Genomic Characterization of a Sulfate-Reducing Bacterium Pseudodesulfovibrio methanolicus sp. nov. Isolated from a Petroleum Reservoir in Russia.

Author

Bidzhieva, Salimat K., Tourova, Tatyana P., Kadnikov, Vitaly V., Samigullina, Salima R., Sokolova, Diyana S., Poltaraus, Andrey B., Avtukh, Alexander N., Tereshina, Vera M., Beletsky, Alexey V., Mardanov, Andrey V., and Nazina, Tamara N.

Subjects
SULFATE-reducing bacteria, PETROLEUM reservoirs, OIL fields, GENOMICS, WATER temperature
Abstract

Simple Summary: Corrosion of steel equipment during oil production, transportation, and refining is a big global issue, leading to significant economic losses. The main agents of microbially influenced corrosion (MIC) of steel equipment are sulfate-reducing bacteria (SRB) and archaea (SRA), which reduce sulfate present in the reservoir water to form sulfide. Timely detection of sulfidogens in formations is necessary for the development of measures to suppress their growth. Existing 16S rRNA gene-based molecular methods for the detection of sulfidogens make it possible to identify them in their natural habitat, and the methods based on metagenomic analysis of components of the microbial community make it possible to predict their potential functional activity. However, selection of biocides or other methods for suppressing the growth of sulfidogens requires confirmation of their effectiveness on enrichment and/or pure cultures. In order to establish a collection of sulfidogens inhabiting the oil reservoirs of Tatarstan (Russia), a number of strains of sulfate-reducing bacteria were isolated. This study describes the 5S69T strain, which, based on the physiological and biochemical characteristics and genomic analysis, has been assigned to a new species, Pseudodesulfovibrio methanolicus sp. nov. The strain is able to grow at high salinity, at reservoir temperature, and on media with alcohols or H2/CO2 in the presence of acetate, which indicates its adaptation to environmental conditions and potential in sulfide production in the oil reservoir. The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0–4.0% (w/v) NaCl, at pH 6.5, and at 23–28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H2 and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H2/CO2/acetate for sulfate reduction. The genome size of the type strain 5S69T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69T ((VKM B-3653T = KCTC 25499T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential

Author

Kadnikov, Vitaly V., primary, Ravin, Nikolai V., additional, Sokolova, Diyana S., additional, Semenova, Ekaterina M., additional, Bidzhieva, Salimat K., additional, Beletsky, Alexey V., additional, Ershov, Alexey P., additional, Babich, Tamara L., additional, Khisametdinov, Marat R., additional, Mardanov, Andrey V., additional, and Nazina, Tamara N., additional

Published
2023
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10. The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams

Author

Karnachuk, Olga V., primary, Rusanov, Igor I., additional, Panova, Inna A., additional, Kadnikov, Vitaly V., additional, Avakyan, Marat R., additional, Ikkert, Olga P., additional, Lukina, Anastasia P., additional, Beletsky, Alexey V., additional, Mardanov, Andrey V., additional, Knyazev, Yuri V., additional, Volochaev, Mikhail N., additional, Pimenov, Nikolai V., additional, and Ravin, Nikolai V., additional

Published
2023
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13. Contributors

Author

Abdulla, Mohamed Hatha, Abramova, Anna, Akanmu, Akinlolu Olalekan, Ammini, Parvathi, Arockiaraj, Jesu, Arul Shiny, Mariadhason, Asha, Santhi, Ayangbenro, Ayansina Segun, Babalola, Olubukola Oluranti, Bacci, Giovanni, Bargiela, Rafael, Barik, Shubham, Becerra, Manuel, Bedse, Mandar, Bengtsson-Palme, Johan, Bhardwaj, Soumya, Bhavana, Karippadakam, Bombaywala, Sakina, Boulund, Fredrik, Casbarra, Lorenzo, Dafale, Nishant A., De, Rituparna, DeCastro, María-Eugenia, Deepthi, Mottakunja, Deo, Priya Nimish, Desgarennes, Damaris, Dhotre, Dhiraj Prakash, Escuder-Rodríguez, Juan-José, Fadiji, Ayomide Emmanuel, Ferrer, Manuel, Flores-Núñez, Víctor M., Fonseca-García, Citlali, González-Siso, María-Isabel, Gopinath, Devi, Grace, Tony, Guru, Ajay, Hassan, Saqib, Iyyadurai, Mariappan, Jairath, Gauri, Jonsson, Viktor, Jose, Mareena, Kadnikov, Vitaly V., Kamalakkannan, Ranganathan, Kannoth, Shalini, Karamveer, Karamveer, Karmarkar, Bhagyashree, Krishnaveni, Muthan, Kristiansson, Erik, Kumar, Anupam, Ma, Zhanshan (Sam), Mal, Gorakh, Malla, Muneer Ahmad, Mardanov, Andrey V., Martínez-Martínez, Mónica, Marunganathan, Vanitha, Meenatchi, Ramu, Méndez-García, Celia, Merlin Sobia, Poomani, Mohan, Suma, Nagarajan, Muniyandi, Nandi, Amartya, Nathan, Vinod Kumar, Partida-Martínez, Laila P., Pereira, Mariana Buongermino, Prabhu, Devachandana C., Prabhu, Vandana R., Prathiviraj, Ragothaman, Priya, P. Snega, Ramazzotti, Matteo, Rathika, Regurajan, Ravin, Nikolai V., Rialch, Ajayta, Rodríguez-Belmonte, Esther, Sadanandan, Shemmy, Sharma, Rinku, Singh, Birbal, Singh, Goldy, Singh, Kiran, Solanki, Jaykishan, Suravajhala, Prashanth, Suresh, Aparna, Tiwari, Arushi, Venkatesh, Subramanian, Vijayan, Jasna, and Yadav, Shweta

Published
2025
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14. Active Sulfate-Reducing Bacterial Community in the Camel Gut

Author

Karnachuk, Olga V., primary, Panova, Inna A., additional, Panov, Vasilii L., additional, Ikkert, Olga P., additional, Kadnikov, Vitaly V., additional, Rusanov, Igor I., additional, Avakyan, Marat R., additional, Glukhova, Lubov B., additional, Lukina, Anastasia P., additional, Rakitin, Anatolii V., additional, Begmatov, Shahjahon, additional, Beletsky, Alexey V., additional, Pimenov, Nikolai V., additional, and Ravin, Nikolai V., additional

Published
2023
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16. Contributors

Author

Asha, Santhi, primary, Bacci, Giovanni, additional, Bargiela, Rafael, additional, Becerra, Manuel, additional, Bengtsson-Palme, Johan, additional, Beraud, Mélanie, additional, Boulund, Fredrik, additional, Chan, Chia Sing, additional, Chan, Kok-Gan, additional, Citlali, Fonseca-García, additional, Dave, Bharti P., additional, DeCastro, María-Eugenia, additional, Desgarennes, Damaris, additional, Dieleman, Levinus A., additional, Escuder-Rodríguez, Juan-José, additional, Ferrer, Manuel, additional, Flores-Núñez, Víctor M., additional, Foster, James A., additional, Goh, Kian Mau, additional, González-Siso, María-Isabel, additional, Gosai, Haren B., additional, Griffin, Timothy J., additional, Halgamuge, Saman K., additional, Jagtap, Pratik D., additional, Jayasundara, Duleepa, additional, Jonsson, Viktor, additional, Joshi, Chaitanya G., additional, Jovel, Juan, additional, Kadnikov, Vitaly V., additional, Kamalakkannan, Ranganathan, additional, Kao, Dina, additional, Kimura, Nobutada, additional, Kothari, Ramesh K., additional, Krishnaveni, Muthan, additional, Kristiansson, Erik, additional, Liew, Kok Jun, additional, Lim, Chia Chiu, additional, Ma, Zhanshan (Sam), additional, Mardanov, Andrey V., additional, Martínez-Martínez, Mónica, additional, Mary Josephine Punitha, Stanislaus, additional, Mason, Andrew L., additional, Matallana-Surget, Sabine, additional, Méndez-García, Celia, additional, Mootapally, Chandrashekar, additional, Nagarajan, Muniyandi, additional, Nathani, Neelam M., additional, Partida-Martínez, Laila P., additional, Pereira, Mariana Buongermino, additional, Prabhu, Vandana R., additional, Ramazzotti, Matteo, additional, Rank, Jalpa K., additional, Ravin, Nikolai V., additional, Rodríguez-Belmonte, Esther, additional, Salleh, Madihah Md, additional, Sani, Rajesh Kumar, additional, Sharmin Vini, Stephen, additional, Tang, Sen-Lin, additional, Wattiez, Ruddy, additional, Wei, Kwek Yan, additional, Wine, Eytan, additional, and Zhbannikov, Ilya Y., additional

Published
2018
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19. Correction: Ravin et al. Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and ‘Candidatus Thiothrix sulfatifontis’ sp. nov. Microorganisms 2022, 10, 1300

Author

Ravin, Nikolai V., primary, Rossetti, Simona, additional, Beletsky, Alexey V., additional, Kadnikov, Vitaly V., additional, Rudenko, Tatyana S., additional, Smolyakov, Dmitry D., additional, Moskvitina, Marina I., additional, Gureeva, Maria V., additional, Mardanov, Andrey V., additional, and Grabovich, Margarita Yu., additional

Published
2022
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21. Desulfovibrio desulfuricans AY5 Isolated from a Patient with Autism Spectrum Disorder Binds Iron in Low-Soluble Greigite and Pyrite

Author

Karnachuk, Olga V., primary, Ikkert, Olga P., additional, Avakyan, Marat R., additional, Knyazev, Yurii V., additional, N.Volochaev, Mikhail, additional, Zyusman, Viacheslav S., additional, Panov, Vasily L., additional, Kadnikov, Vitaly V., additional, Mardanov, Andrey V., additional, and Ravin, Nikolai V., additional

Published
2021
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23. Sulfidogenic Microbial Communities of the Uzen High-Temperature Oil Field in Kazakhstan

Author

Sokolova, Diyana S., primary, Semenova, Ekaterina M., additional, Grouzdev, Denis S., additional, Bidzhieva, Salimat K., additional, Babich, Tamara L., additional, Loiko, Nataliya G., additional, Ershov, Alexey P., additional, Kadnikov, Vitaly V., additional, Beletsky, Alexey V., additional, Mardanov, Andrey V., additional, Zhaparov, Nurlan S., additional, and Nazina, Tamara N., additional

Published
2021
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24. A genomic catalog of Earth’s microbiomes

Author

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, IMG/M Data Consortium, Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, and IMG/M Data Consortium

Abstract

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.

Published
2021

27. Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix , Thiothrix winogradskyi sp. nov. and ' Candidatus Thiothrix sulfatifontis' sp. nov.

Author

Ravin, Nikolai V., Rossetti, Simona, Beletsky, Alexey V., Kadnikov, Vitaly V., Rudenko, Tatyana S., Smolyakov, Dmitry D., Moskvitina, Marina I., Gureeva, Maria V., Mardanov, Andrey V., and Grabovich, Margarita Yu.

Subjects
SULFUR bacteria, FILAMENTOUS bacteria, NUCLEIC acid hybridization, WHOLE genome sequencing, CANDIDATUS
Abstract

The metagenome of foulings from sulfidic spring "Serovodorodny" (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93–99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, 'Candidatus Thiothrix sulfatifontis' sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8–99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate. [ABSTRACT FROM AUTHOR]

Published
2022
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32. Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol’shie Khruslomeny at the White Sea Coast

Author

Savvichev, Alexander S., primary, Kadnikov, Vitaly V., additional, Rusanov, Igor I., additional, Beletsky, Alexey V., additional, Krasnova, Elena D., additional, Voronov, Dmitry A., additional, Kallistova, Anna Yu., additional, Veslopolova, Elena F., additional, Zakharova, Elena E., additional, Kokryatskaya, Nataliya M., additional, Losyuk, Galina N., additional, Demidenko, Nikolai A., additional, Belyaev, Nikolai A., additional, Sigalevich, Pavel A., additional, Mardanov, Andrey V., additional, Ravin, Nikolai V., additional, and Pimenov, Nikolay V., additional

Published
2020
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39. Targeted isolation based on metagenome‐assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere.

Author

Karnachuk, Olga V., Lukina, Anastasia P., Kadnikov, Vitaly V., Sherbakova, Viktoria A., Beletsky, Alexey V., Mardanov, Andrey V., and Ravin, Nikolai V.

Subjects
BIOSPHERE, BASE isolation system, SPIROCHETES, GENOMES, THERMOPHILIC bacteria, PHENOTYPES, MICROBIAL communities
Abstract

Most microorganisms from deep terrestrial subsurface remain yet uncultured. Recent achievements in recovery of metagenome‐assembled genomes (MAG) provide clues for improving cultivation via metabolic reconstructions and other genomic characteristics. Here we report the isolation in pure culture of a thermophilic spirochete with the use of MAGs binned from metagenomes of the deep (>2 km) aquifers broached by two artesian boreholes in Western Siberia. The organism constitutes a minor share in the aquifer microbial community and could not be cultivated by traditional techniques. The obtained two pure culture isolates along with three bacteria identified by MAGs represent a novel family‐level lineage in the order Brevinematales. Based on genomic and phenotypic characteristics the novel spirochete is proposed to be classified as Longinema margulisiae gen. nov., sp. nov. within a novel family, Longinemaceae fam. nov. Both cultivated strains, NST and N5R, are anaerobic hemoorganoheterotrophes growing by fermentation of starch and a few sugars. They can form recalcitrant round bodies under unfavourable growth conditions, which survive up to 15 min at 95°C and can revert to the original helical cells. We suggest that the round bodies may facilitate global distribution of this lineage, detected from molecular signaturesand colonization of subsurface environments. [ABSTRACT FROM AUTHOR]

Published
2021
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45. Genomic insights into a new acidophilic, copper-resistant Desulfosporosinus isolate from the oxidized tailings area of an abandoned gold mine

Author

Mardanov, Andrey V., Panova, Inna A., Beletsky, Alexey V., Avakyan, Marat R., Kadnikov, Vitaly V., Antsiferov, Dmitry V., Banks, David, Frank, Yulia A., Pimenov, Nikolay V., Ravin, Nikolai V., and Karnachuk, Olga V.

Subjects
TN, QR
Abstract

Microbial sulfate reduction in acid mine drainage is still considered to be confined to anoxic conditions, although several reports have shown that sulfate-reducing bacteria (SRB) occur under microaerophilic or aerobic conditions. We have measured sulfate reduction rates of up to 60 nmol S cm−3day−1 in oxidized layers of gold mine tailings in Kuzbass (SW Siberia). A novel, acidophilic, copper-tolerant Desulfosporosinus sp. I2 was isolated from the same sample and its genome was sequenced. The genomic analysis and physiological data indicate the involvement of transporters and additional mechanisms to tolerate metals, such as sequestration by polyphosphates. Desulfosporinus sp. I2 encodes systems for a metabolically versatile life style. The genome possessed a complete Embden-Meyerhof pathway for glycolysis and gluconeogenesis. Complete oxidation of organic substrates could be enabled by the complete TCA cycle. Genomic analysis found all major components of the electron transfer chain necessary for energy generation via oxidative phosphorylation. Autotrophic CO2 fixation could be performed through the Wood-Ljungdahl pathway. Multiple oxygen detoxification systems were identified in the genome. Taking into account the metabolic activity and genomic analysis, the traits of the novel isolate broaden our understanding of active sulfate reduction and associated metabolism beyond strictly anaerobic niches.

Published
2016

50. Sugar metabolism of the first thermophilic Planctomycete Thermogutta terrifontis:comparative genomic and transcriptomic approaches

Author

Elcheninov, Alexander G., Menzel, Peter, Gudbergsdottir, Soley R., Slesarev, Alexei I., Kadnikov, Vitaly V., Krogh, Anders, Bonch-Osmolovskaya, Elizaveta A., Peng, Xu, Kublanov, Ilya V., Elcheninov, Alexander G., Menzel, Peter, Gudbergsdottir, Soley R., Slesarev, Alexei I., Kadnikov, Vitaly V., Krogh, Anders, Bonch-Osmolovskaya, Elizaveta A., Peng, Xu, and Kublanov, Ilya V.

Published
2017

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