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1. A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

Author

Timmis, Kenneth N. [0000-0002-0066-4670], Hallsworth, John E. [0000-0001-6797-9362], McGenity, Terry J. [0000-0002-1497-8822], Armstrong, Rachel [0000-0002-3516-6815], Colom, María Francisca [0000-0002-8672-5429], Karahan, Z. Ceren [0000-0001-7727-3363], Chavarría, Max [0000-0001-5901-3576], Bernal, Patricia [0000-0002-6228-0496], Boyd, Eric S. [0000-0003-4436-5856], Ramos, Juan L. [0000-0002-8731-7435], Kaltenpoth, Martin [0000-0001-9450-0345], Pruzzo, Carla [0000-0002-1280-4677], Clarke, Gerard [0000-0001-9771-3979], López-García, Purificación [0000-0002-0927-0651], Yakimov, Michail M. [0000-0003-1418-363X], Perlmutter, Jessamyn [0000-0002-9789-4674], Greening, Chris [0000-0001-7616-0594], Eloe-Fadrosh, Emiley [0000-0002-8162-1276], Verstraete, Willy [0000-0002-3140-3713], Nunes, Olga [0000-0003-4742-2537], Kotsyurbenko, Oleg R. [0000-0002-4748-3017], Nikel, Pablo I. [0000-0002-9313-7481], Scavone, Paola [0000-0002-8840-3757], Häggblom, Max M. [0000-0001-6307-7863], Lavigne, Rob [0000-0001-7377-1314], Le Roux, Frédérique [0000-0002-9112-6199], Timmis, James Kenneth [0000-0002-7773-0859], Parro, Victor [0000-0003-3738-0724], Michán, Carmen [0000-0003-2921-0987], García, José Luis [0000-0002-9238-2485], Casadevall, A. [0000-0002-9402-9167], Payne, Shelley M. [0000-0003-3112-4340], Frey, Joachim [0000-0001-9133-0280], Koren, Omry [0000-0002-7738-1337], Prosser, James I. [0000-0003-1757-5102], Lal, Rup [0000-0001-8364-8547], Anand, S. [0000-0001-7852-3512], Sood, U [0000-0002-0886-0107], Offre, Pierre [0000-0002-3660-2164], Bryce, Casey C. [0000-0002-1132-5201], Mswaka, Allen Y. [0000-0003-4868-1530], Jores, Jörg [0000-0003-3790-5746], Kaçar, Betül [0000-0002-0482-2357], Blank, Lars M. [0000-0003-0961-4976], Pope, Phillip B. [0000-0002-2067-4059], Banciu, Horia L. [0000-0002-6563-3226], Armitage, Judith [0000-0003-4983-9731], Lee, Sang Yup [0000-0003-0599-3091], Wang, Feng-Ping [0000-0002-0376-6947], Makhalanyane, Thulani P. [0000-0002-8173-1678], Gilbert, Jack A. [0000-0001-7920-7001], Wood, Thomas K. [0000-0002-6258-529X], Vasiljevic, Branka [0000-0002-2315-3590], Soberón, Mario [0000-0002-1593-9227], Udaondo, Zulema [0000-0003-3445-6842], Rojo, Fernando [0000-0003-1848-7745], Giraud, Tatiana [0000-0002-2685-6478], Ropars, Jeanne [0000-0002-3740-9673], Ezeji, T. C. [0000-0002-8384-895X], Müller, Volker [0000-0001-7955-5508], Averhoff, Beate [0000-0003-1460-3649], Sessitsch, Angela [0000-0003-0137-930X], Partida-Martinez, Laila Pamela [0000-0001-8037-2856], Huang, Wei [0000-0003-1302-6528], Molin, Søren [0000-0002-7973-2639], Junier, Pilar [0000-0002-8618-3340], Amils, Ricardo [0000-0002-7560-1033], Wu, Xiao-Lei [0000-0002-9897-6903], Ron, Eliora [0000-0003-2615-8685], Erten, Hüseyin [0000-0003-1537-2416], De Martinis, E.C.P. [0000-0002-6089-6238], Rapoport, Alexander [0000-0002-6185-0039], Öpik, Maarja [0000-0001-8025-7460], Pokatong, W. Donald R. [0009-0009-6692-9879], Stairs, Courtney W. [0000-0001-6650-0970], Amoozegar, Mohammad Ali [0000-0002-9638-0532], Gil-Serna, Jessica [0000-0002-2113-1830], Timmis, Kenneth N., Hallsworth, John E., McGenity, Terry J., Armstrong, Rachel, Colom, María Francisca, Karahan, Z. Ceren, Chavarría, Max, Bernal, Patricia, Boyd, Eric S., Ramos, Juan L., Kaltenpoth, Martin, Pruzzo, Carla, Clarke, Gerard, López-García, Purificación, Yakimov, Michail M., Perlmutter, Jessamyn, Greening, Chris, Eloe-Fadrosh, Emiley, Verstraete, Willy, Nunes, Olga, Kotsyurbenko, Oleg R., Nikel, Pablo I., Scavone, Paola, Häggblom, Max M., Lavigne, Rob, Le Roux, Frédérique, Timmis, James Kenneth, Parro, Victor, Michán, Carmen, García, José Luis, Casadevall, A., Payne, Shelley M., Frey, Joachim, Koren, Omry, Prosser, James I., Lal, Rup, Anand, S., Sood, U, Offre, Pierre, Bryce, Casey C., Mswaka, Allen Y., Jores, Jörg, Kaçar, Betül, Blank, Lars M., Pope, Phillip B., Banciu, Horia L., Armitage, Judith, Lee, Sang Yup, Wang, Feng-Ping, Makhalanyane, Thulani P., Gilbert, Jack A., Wood, Thomas K., Vasiljevic, Branka, Soberón, Mario, Udaondo, Zulema, Rojo, Fernando, Giraud, Tatiana, Ropars, Jeanne, Ezeji, T. C., Müller, Volker, Averhoff, Beate, Sessitsch, Angela, Huang, Wei, Molin, Søren, Junier, Pilar, Amils, Ricardo, Wu, Xiao-Lei, Ron, Eliora, Erten, Hüseyin, De Martinis, E.C.P., Rapoport, Alexander, Öpik, Maarja, Pokatong, W. Donald R., Stairs, Courtney W., Amoozegar, Mohammad Ali, Gil-Serna, Jessica, Timmis, Kenneth N. [0000-0002-0066-4670], Hallsworth, John E. [0000-0001-6797-9362], McGenity, Terry J. [0000-0002-1497-8822], Armstrong, Rachel [0000-0002-3516-6815], Colom, María Francisca [0000-0002-8672-5429], Karahan, Z. Ceren [0000-0001-7727-3363], Chavarría, Max [0000-0001-5901-3576], Bernal, Patricia [0000-0002-6228-0496], Boyd, Eric S. [0000-0003-4436-5856], Ramos, Juan L. [0000-0002-8731-7435], Kaltenpoth, Martin [0000-0001-9450-0345], Pruzzo, Carla [0000-0002-1280-4677], Clarke, Gerard [0000-0001-9771-3979], López-García, Purificación [0000-0002-0927-0651], Yakimov, Michail M. [0000-0003-1418-363X], Perlmutter, Jessamyn [0000-0002-9789-4674], Greening, Chris [0000-0001-7616-0594], Eloe-Fadrosh, Emiley [0000-0002-8162-1276], Verstraete, Willy [0000-0002-3140-3713], Nunes, Olga [0000-0003-4742-2537], Kotsyurbenko, Oleg R. [0000-0002-4748-3017], Nikel, Pablo I. [0000-0002-9313-7481], Scavone, Paola [0000-0002-8840-3757], Häggblom, Max M. [0000-0001-6307-7863], Lavigne, Rob [0000-0001-7377-1314], Le Roux, Frédérique [0000-0002-9112-6199], Timmis, James Kenneth [0000-0002-7773-0859], Parro, Victor [0000-0003-3738-0724], Michán, Carmen [0000-0003-2921-0987], García, José Luis [0000-0002-9238-2485], Casadevall, A. [0000-0002-9402-9167], Payne, Shelley M. [0000-0003-3112-4340], Frey, Joachim [0000-0001-9133-0280], Koren, Omry [0000-0002-7738-1337], Prosser, James I. [0000-0003-1757-5102], Lal, Rup [0000-0001-8364-8547], Anand, S. [0000-0001-7852-3512], Sood, U [0000-0002-0886-0107], Offre, Pierre [0000-0002-3660-2164], Bryce, Casey C. [0000-0002-1132-5201], Mswaka, Allen Y. [0000-0003-4868-1530], Jores, Jörg [0000-0003-3790-5746], Kaçar, Betül [0000-0002-0482-2357], Blank, Lars M. [0000-0003-0961-4976], Pope, Phillip B. [0000-0002-2067-4059], Banciu, Horia L. [0000-0002-6563-3226], Armitage, Judith [0000-0003-4983-9731], Lee, Sang Yup [0000-0003-0599-3091], Wang, Feng-Ping [0000-0002-0376-6947], Makhalanyane, Thulani P. [0000-0002-8173-1678], Gilbert, Jack A. [0000-0001-7920-7001], Wood, Thomas K. [0000-0002-6258-529X], Vasiljevic, Branka [0000-0002-2315-3590], Soberón, Mario [0000-0002-1593-9227], Udaondo, Zulema [0000-0003-3445-6842], Rojo, Fernando [0000-0003-1848-7745], Giraud, Tatiana [0000-0002-2685-6478], Ropars, Jeanne [0000-0002-3740-9673], Ezeji, T. C. [0000-0002-8384-895X], Müller, Volker [0000-0001-7955-5508], Averhoff, Beate [0000-0003-1460-3649], Sessitsch, Angela [0000-0003-0137-930X], Partida-Martinez, Laila Pamela [0000-0001-8037-2856], Huang, Wei [0000-0003-1302-6528], Molin, Søren [0000-0002-7973-2639], Junier, Pilar [0000-0002-8618-3340], Amils, Ricardo [0000-0002-7560-1033], Wu, Xiao-Lei [0000-0002-9897-6903], Ron, Eliora [0000-0003-2615-8685], Erten, Hüseyin [0000-0003-1537-2416], De Martinis, E.C.P. [0000-0002-6089-6238], Rapoport, Alexander [0000-0002-6185-0039], Öpik, Maarja [0000-0001-8025-7460], Pokatong, W. Donald R. [0009-0009-6692-9879], Stairs, Courtney W. [0000-0001-6650-0970], Amoozegar, Mohammad Ali [0000-0002-9638-0532], Gil-Serna, Jessica [0000-0002-2113-1830], Timmis, Kenneth N., Hallsworth, John E., McGenity, Terry J., Armstrong, Rachel, Colom, María Francisca, Karahan, Z. Ceren, Chavarría, Max, Bernal, Patricia, Boyd, Eric S., Ramos, Juan L., Kaltenpoth, Martin, Pruzzo, Carla, Clarke, Gerard, López-García, Purificación, Yakimov, Michail M., Perlmutter, Jessamyn, Greening, Chris, Eloe-Fadrosh, Emiley, Verstraete, Willy, Nunes, Olga, Kotsyurbenko, Oleg R., Nikel, Pablo I., Scavone, Paola, Häggblom, Max M., Lavigne, Rob, Le Roux, Frédérique, Timmis, James Kenneth, Parro, Victor, Michán, Carmen, García, José Luis, Casadevall, A., Payne, Shelley M., Frey, Joachim, Koren, Omry, Prosser, James I., Lal, Rup, Anand, S., Sood, U, Offre, Pierre, Bryce, Casey C., Mswaka, Allen Y., Jores, Jörg, Kaçar, Betül, Blank, Lars M., Pope, Phillip B., Banciu, Horia L., Armitage, Judith, Lee, Sang Yup, Wang, Feng-Ping, Makhalanyane, Thulani P., Gilbert, Jack A., Wood, Thomas K., Vasiljevic, Branka, Soberón, Mario, Udaondo, Zulema, Rojo, Fernando, Giraud, Tatiana, Ropars, Jeanne, Ezeji, T. C., Müller, Volker, Averhoff, Beate, Sessitsch, Angela, Huang, Wei, Molin, Søren, Junier, Pilar, Amils, Ricardo, Wu, Xiao-Lei, Ron, Eliora, Erten, Hüseyin, De Martinis, E.C.P., Rapoport, Alexander, Öpik, Maarja, Pokatong, W. Donald R., Stairs, Courtney W., Amoozegar, Mohammad Ali, and Gil-Serna, Jessica

Abstract

The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us–individuals/communities/nations/the human world–and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI.

Published
2024

2. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.

Author

Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos-Caparros, Esteban, Sanchez-Martinez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Gridan, Ionuț Mădălin, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., Rossello-Mora, Ramon, Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos-Caparros, Esteban, Sanchez-Martinez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Gridan, Ionuț Mădălin, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., and Rossello-Mora, Ramon

Abstract

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.

Published
2023

3. Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

Author

Universidad de Alicante. Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Buda, Doriana Mădălina, Szekeres, Edina, Tudoran, Lucian Barbu, Esclapez, Julia, Banciu, Horia L., Universidad de Alicante. Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Buda, Doriana Mădălina, Szekeres, Edina, Tudoran, Lucian Barbu, Esclapez, Julia, and Banciu, Horia L.

Abstract

Background The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance. Results The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM–EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data. Conclusions Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.

Published
2023

4. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov

Author

Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, National Science Foundation (US), Ministry of Research, Innovation and Digitization (Romania), Consejo Federal de Ciencia y Tecnología (Argentina), Ministerio de Universidades (España), Govern de les Illes Balears, Viver, Tomeu [0000-0001-8868-], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L, Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Commission, National Science Foundation (US), Ministry of Research, Innovation and Digitization (Romania), Consejo Federal de Ciencia y Tecnología (Argentina), Ministerio de Universidades (España), Govern de les Illes Balears, Viver, Tomeu [0000-0001-8868-], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L, Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., and Rosselló-Mora, Ramón

Abstract

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.

Published
2023

5. Description of four new Salinibacter species, two cultivated and named following the rules of the bacteriological code: Salinibacter pepae sp. nov., Salinibacter grassmerensis sp. nov.; and two uncultivated and named following the rules of the SeqCode: Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. [Dataset]

Author

Viver, Tomeu [0000-0001-8868-9292], Urdiain, Mercedes [0000-0001-6834-0237], Viver, Tomeu [tviver@imedea.uib-csic.es], Rosselló-Mora, Ramón [ramon@imedea.uib-csic.es], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., Rosselló-Mora, Ramón, Viver, Tomeu [0000-0001-8868-9292], Urdiain, Mercedes [0000-0001-6834-0237], Viver, Tomeu [tviver@imedea.uib-csic.es], Rosselló-Mora, Ramón [ramon@imedea.uib-csic.es], Viver, Tomeu, Conrad, Roth E., Lucio, Marianna, Harir, Mourad, Urdiain, Mercedes, Gago, Juan F., Suárez-Suárez, Ana, Bustos, Esteban, Sánchez-Martínez, Rodrigo, Mayol, Eva, Fassetta, Federico, Pang, Jinfeng, Mădălin Gridan, Ionuț, Venter, Stephanus, Santos, Fernando, Baxter, Bonnie, Llames, María E., Cristea, Adorján, Banciu, Horia L., Hedlund, Brian P., Stott, Matthew B., Kämpfer, Peter, Amann, Rudolf, Schmitt-Kopplin, Philippe, Konstantinidis, Konstantinos T., and Rosselló-Mora, Ramón

Abstract

Figure S1. Geographical distribution of the six locations studied here and their inter-location distances (given in the table). The distances given in each location refer to Mallorca. The hypersaline here are: Mallorca (Es Trenc and S’Avall and separated by 3.5 km) and Santa Pola in Spain, Fără Fund in Romania, Great Salt Lake (USA), Pampa (Laguna Colorada Chica and Laguna Colorada Grande, separated by 23 Km), and Lake Grassmere (New Zealand). Table S1. Statistics of Salinibacter MAGs recovered using different bioinformatic tools. MAGs selected for further analysis and taxonomic classification are marked in red. Text S1: In addition to the taxonomic study, here we assessed the different tools SPADES and MegaHIT assemblers, and MetaBAT binning tools selecting contigs with length > 2,000 pbs or > 5,000 pbs to retrieve the best quality MAG (Sup. Table S1). We observed that different tools and combinations rendered different qualities of the MAGs. The selection of contigs with length > 5,000 pbs binning rendered MAGs with a lower genome size, lower completeness and similar contamination. From the FF metagenome (Romania), the highest quality MAG was retrieved using the assembler SPADES and MetaBAT binning tool using a minimum contig length of 2,000 pbs. From CCH and CG metagenomes (Argentina), the highest quality MAGs were retrieved using the assembler MegaHIT and MetaBAT binning tool using a minimum contig length of 2,000 pbs (Sup. Table S1). Figure S2. Genomic clustering based on Average Amino-acid Identity (AAI) of genomes included in the study. Figure S3. Pangenome hierarchical clustering based on the presence (grey) or absence (black) of orthologous genes. Table S2. Pangenome statistics between genomes belonging to the same species. Table S3: CRISPR-Cas systems found in the Salinibacter pepae and Salinibacter grassmerensis genomes. Table S4. Cell morphologies of the new isolates. All cells have been cultivated onto MA agar. for 10 days at 12ºC. The morphology was ob

Published
2023

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