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Ravin NV, Rudenko TS, Beletsky AV, Smolyakov DD, Mardanov AV, Grabovich MY, Muntyan MS. Phylogeny and Metabolic Potential of New Giant Sulfur Bacteria of the Family Beggiatoaceae from Coastal-Marine Sulfur Mats of the White Sea. Int J Mol Sci 2024; 25:6028. [PMID: 38892213 PMCID: PMC11172852 DOI: 10.3390/ijms25116028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The family Beggiatoaceae is currently represented by 25 genera in the Genome Taxonomy Database, of which only 6 have a definite taxonomic status. Two metagenome-assembled genomes (MAGs), WS_Bin1 and WS_Bin3, were assembled from metagenomes of the sulfur mats coating laminaria remnants in the White Sea. Using the obtained MAGs, we first applied phylogenetic analysis based on whole-genome sequences to address the systematics of Beggiatoaceae, which clarify the taxonomy of this family. According to the average nucleotide identity (ANI) and average amino acid identity (AAI) values, MAG WS_Bin3 was assigned to a new genus and a new species in the family Beggiatoaceae, namely, 'Candidatus Albibeggiatoa psychrophila' gen. nov., sp. nov., thus providing the revised taxonomic status of the candidate genus 'BB20'. Analysis of 16S rRNA gene homology allowed us to identify MAG WS_Bin1 as the only currently described species of the genus 'Candidatus Parabeggiatoa', namely, 'Candidatus Parabeggiatoa communis', and consequently assign the candidate genus 'UBA10656', including four new species, to the genus 'Ca. Parabeggiatoa'. Using comparative whole-genome analysis of the members of the genera 'Candidatus Albibeggiatoa' and 'Ca. Parabeggiatoa', we expanded information on the central pathways of carbon, sulfur and nitrogen metabolism in the family Beggiatoaceae.
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Affiliation(s)
- Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Tatyana S. Rudenko
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Dmitry D. Smolyakov
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prospect, 33-2, 119071 Moscow, Russia; (N.V.R.); (A.V.B.); (A.V.M.)
| | - Margarita Yu. Grabovich
- Department of Biochemistry and Cell Physiology, Voronezh State University, Universitetskaya pl., 1, 394018 Voronezh, Russia; (T.S.R.); (D.D.S.)
| | - Maria S. Muntyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
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Li J, Wu S, Zhang K, Sun X, Lin W, Wang C, Lin S. Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects. Microorganisms 2024; 12:118. [PMID: 38257946 PMCID: PMC10820777 DOI: 10.3390/microorganisms12010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.
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Affiliation(s)
- Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Shuaishuai Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou 570203, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Wenwen Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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Flores E, Mendoza U, Callbeck CM, Díaz R, Aguirre-Velarde A, Böttcher ME, Merma-Mora L, Moreira M, Saldarriaga MS, Silva-Filho EV, Albuquerque AL, Pizarro-Koch M, Graco M. Attenuation of wind intensities exacerbates anoxic conditions leading to sulfur plume development off the coast of Peru. PLoS One 2023; 18:e0287914. [PMID: 37647254 PMCID: PMC10468053 DOI: 10.1371/journal.pone.0287914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/15/2023] [Indexed: 09/01/2023] Open
Abstract
The release of vast quantities of sulfide from the sediment into the water column, known as a sulfidic event, has detrimental consequences on fish catches, including downstream effects on other linked element cycles. Despite being frequent occurrences in marine upwelling regions, our understanding of the factors that moderate sulfidic event formation and termination are still rudimentary. Here, we examined the biogeochemical and hydrodynamic conditions that underpinned the formation/termination of one of the largest sulfur plumes to be reported in the Peruvian upwelling zone. Consistent with previous research, we find that the sulfur-rich plume arose during the austral summer when anoxic conditions (i.e., oxygen and nitrate depletion) prevailed in waters overlying the upper shelf. Furthermore, the shelf sediments were organically charged and characterized by low iron-bound sulfur concentrations, further enabling the diffusion of benthic-generated sulfide into the water column. While these biogeochemical conditions provided a predicate to sulfidic event formation, we highlight that attenuations in local wind intensity served as an event trigger. Namely, interruptions in local wind speed constrained upwelling intensity, causing increased stratification over the upper shelf. Moreover, disturbances in local wind patterns likely placed additional constraints on wind-driven mesoscale eddy propagation, with feedback effects on coastal elemental sulfur plume (ESP) formation. We suggest ESP development occurs as a result of a complex interaction of biogeochemistry with regional hydrodynamics.
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Affiliation(s)
- Edgart Flores
- Programa de Maestría de Ciencias del Mar, Universidad Peruana Cayetano Heredia, Lima, Peru
- Millennium Institute of Oceanography, Universidad de Concepción, Concepción, Chile
- Department of Geological Sciences, Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, United States of America
| | - Ursula Mendoza
- Dirección General de Investigaciones en Oceanografía y Cambio Climático, Instituto del Mar del Perú, Callao, Peru
- Facultad de Ciencias Veterinarias y Biológicas, Escuela de Biología Marina, Universidad Científica del Sur, Lima, Peru
| | - Cameron M. Callbeck
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Rut Díaz
- Programa de Geoquímica, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Arturo Aguirre-Velarde
- Dirección General de Investigaciones en Acuicultura, Instituto del Mar del Perú, Callao, Peru
| | - Michael E. Böttcher
- Geochemistry & Isotope Biogeochemistry Group, Department of Marine Geology, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
- Marine Geochemistry, University of Greifswald, Greifswald, Germany
- Interdisciplinary Faculty, University of Rostock, Rostock, Germany
| | - Lander Merma-Mora
- Programa de Maestría de Ciencias del Mar, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Manuel Moreira
- Programa de Geoquímica, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Maritza S. Saldarriaga
- Dirección General de Investigaciones de Recursos Demersales y Litorales, Instituto del Mar del Perú, Callao, Peru
| | | | - Ana L. Albuquerque
- Departamento de Geologia e Geofísica, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Matias Pizarro-Koch
- Escuela de Ingeniería Civil Oceánica, Facultad de Ingeniería, Universidad de Valparaíso, Valparaíso, Chile
- Millennium Nucleus Understanding Past Coastal Upwelling Systems and Environmental Local and Lasting Impacts, Coquimbo, Chile
| | - Michelle Graco
- Programa de Maestría de Ciencias del Mar, Universidad Peruana Cayetano Heredia, Lima, Peru
- Dirección General de Investigaciones en Oceanografía y Cambio Climático, Instituto del Mar del Perú, Callao, Peru
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Fonseca A, Espinoza C, Nielsen LP, Marshall IPG, Gallardo VA. Bacterial community of sediments under the Eastern Boundary Current System shows high microdiversity and a latitudinal spatial pattern. Front Microbiol 2022; 13:1016418. [PMID: 36246233 PMCID: PMC9561620 DOI: 10.3389/fmicb.2022.1016418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
The sediments under the Oxygen Minimum Zone of the Eastern Boundary Current System (EBCS) along Central-South Peru and North-Central Chile, known as Humboldt Sulfuretum (HS), is an organic-matter-rich benthic habitat, where bacteria process a variety of sulfur compounds under low dissolved-oxygen concentrations, and high sulfide and nitrate levels. This study addressed the structure, diversity and spatial distribution patterns of the HS bacterial community along Northern and South-Central Chile using 16S rRNA gene amplicon sequencing. The results show that during the field study period, the community was dominated by sulfur-associated bacteria. Indeed, the most abundant phylum was Desulfobacterota, while Sva0081 sedimentary group, of the family Desulfosarcinaceae (the most abundant family), which includes sulfate-reducer and H2 scavenger bacteria, was the most abundant genus. Furthermore, a spatial pattern was unveiled along the study area to which the family Desulfobulbaceae contributed the most to the spatial variance, which encompasses 42 uncharacterized amplicon sequence variants (ASVs), three assigned to Ca. Electrothrix and two to Desulfobulbus. Moreover, a very high microdiversity was found, since only 3.7% of the ASVs were shared among localities, reflecting a highly diverse and mature community.
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Affiliation(s)
- Alexis Fonseca
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
- *Correspondence: Alexis Fonseca,
| | - Carola Espinoza
- Department of Oceanography, University of Concepción, Concepción, Chile
| | - Lars Peter Nielsen
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Ian P. G. Marshall
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Victor A. Gallardo
- Department of Oceanography, University of Concepción, Concepción, Chile
- Victor A. Gallardo,
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Díaz-Sánchez ÁG, Terrazas-López M, Aguirre-Reyes LG, Lobo-Galo N, Álvarez-Parrilla E, Martínez-Martínez A. Aspectos estructurales y funcionales de la N-Succinil-L, L-diaminopimelato desuccinilasa, una enzima clave para el crecimiento bacteriano y un blanco para el control antimicrobiano. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2019. [DOI: 10.22201/fesz.23958723e.2019.0.191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
La N-Succinil-L, L-diaminopimelato desuccinilasa (DapE) es una amidohidrolasa dependiente de iones de zinc, homodimérica estricta, que cataliza la descomposición del N-succinil-L, L-2,6-diaminopimelato (NSDAP), en succinato y diaminopimelato (DAP). Reacción que constituye la única fuente de meso-diaminopimelato (mDAP) y L-Lys en la mayoría de las bacterias. DapE es esencial para el crecimiento bacteriano y un blanco farmacológico antimicrobiano. El desarrollo de los inhibidores anti-DapE debe tener en cuenta las propiedades dinámicas de la enzima. Se buscan compuestos que interfieran con la formación del agujero del oxianión, en donde participan grupos de ambas subunidades del dímero, que se acomoda en posición catalítica mediante el cambio conformacional de la enzima de un estado abierto a uno cerrado, después de la unión del sustrato; estabilizando a los intermediarios de reacción y produciendo un descenso en la energía de activación. Con base en el análisis cristalográfico y el acoplamiento del sustrato en DapE que se presenta en este trabajo, se discute el papel de la flexibilidad conformacional de la enzima en la hidrólisis del sustrato. Se observa que tanto el grupo carbonilo del sustrato es susceptible al ataque como una molécula de agua ubicada en el sitio activo y se encuentran cercanos a la trayectoria de ataque, en el ángulo de Bürgi-Dunitz.
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