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Gao L, Zhao Y, Wang Z, Zhang Y, Ming J, Sun X, Ni SQ. Seasonal and distance-decay patterns of surface sediments microbial nitrogen and sulfur cycling linkage in the eastern coast of China. MARINE POLLUTION BULLETIN 2024; 201:116169. [PMID: 38428046 DOI: 10.1016/j.marpolbul.2024.116169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 03/03/2024]
Abstract
The surface sediments as a repository of pelagic environment changes and microbial community structural succession tend to have a profound effect on global and local nitrogen and sulfur cycling. In this study, analysis of sediment samples collected from the Bohai Sea, Yellow Sea, and north of the East China Seas (BYnECS) revealed longitude, latitude, depth, and chlorophyll had the strongest influence on microbial community structure (p-values < 0.005). A clear distance-decay pattern was exhibited in BYnECS. The result of co-occurrence network modularization implied that the more active pathway in winter was thiosulfate reduction and nitrate reduction, while in summer it was nitrification. The potential functional genes were predicted in microbial communities, and the most dominant genes were assigned to assimilatory sulfur reduction, denitrification, and dissimilatory nitrate reduction. This study innovatively explored the potential relationships between nitrogen and sulfur cycling genes of these three sea regions in the China Sea.
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Affiliation(s)
- Linjie Gao
- Shenzhen Research Institute of Shandong University, School of Environmental Science and Engineering, Shandong University, China
| | - Yiyi Zhao
- School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, China
| | - Zhibin Wang
- School of Life Sciences, Shandong University, China
| | - Yong Zhang
- Shenzhen Xinbaoying Technology Co., Ltd, Guangdong, China
| | - Jie Ming
- Shenzhen Research Institute of Shandong University, School of Environmental Science and Engineering, Shandong University, China
| | - Xiaojie Sun
- Shenzhen Research Institute of Shandong University, School of Environmental Science and Engineering, Shandong University, China
| | - Shou-Qing Ni
- Shenzhen Research Institute of Shandong University, School of Environmental Science and Engineering, Shandong University, China.
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Frolov EN, Elcheninov AG, Gololobova AV, Toshchakov SV, Novikov AA, Lebedinsky AV, Kublanov IV. Obligate autotrophy at the thermodynamic limit of life in a new acetogenic bacterium. Front Microbiol 2023; 14:1185739. [PMID: 37250036 PMCID: PMC10213532 DOI: 10.3389/fmicb.2023.1185739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
One of the important current issues of bioenergetics is the establishment of the thermodynamic limits of life. There is still no final understanding of what is the minimum value of the energy yield of a reaction that is sufficient to be used by an organism (the so-called "biological quantum of energy"). A reasonable model for determination of the minimal energy yield would be microorganisms capable of living on low-energy substrates, such as acetogenic prokaryotes. The most prominent metabolic feature of acetogens is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates, which is hardly competitive in environments. Most probably, that is why only facultative autotrophic acetogens have been known so far. Here, we describe the first obligately autotrophic acetogenic bacterium Aceticella autotrophica gen. nov., sp. nov., strain 3443-3AcT. Phylogenetically, the new genus falls into a monophyletic group of heterotrophic bacteria of the genera Thermoanaerobacterium, Thermoanaerobacter, and Caldanaerobacter (hereinafter referred to as TTC group), where the sole acetogenic representative has so far been the facultatively autotrophic Thermoanaerobacter kivui. A. autotrophica and T. kivui both are acetogens employing energy-converting hydrogenase (Ech-acetogens) that are likely to have inherited the acetogenesis capacity vertically from common ancestor. However, their acetogenic machineries have undergone different adjustments by gene replacements due to horizontal gene transfers from different donors. Obligate autotrophy of A. autotrophica is associated with the lack of many sugar transport systems and carbohydrate catabolism enzymes that are present in other TTC group representatives, including T. kivui.
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Affiliation(s)
- Evgenii N. Frolov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander G. Elcheninov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra V. Gololobova
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Stepan V. Toshchakov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Andrei A. Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, Moscow, Russia
| | - Alexander V. Lebedinsky
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kublanov
- Federal Research Center of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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Parada-Pinilla MP, Díaz-Cárdenas C, López G, Díaz-Riaño JI, Gonzalez LN, Restrepo S, Trujillo ME, Baena S. Salifodinibacter halophilus gen. nov., sp. nov., a halophilic gammaproteobacterium in the family Salinisphaeraceae isolated from a salt mine in the Colombian Andes. Int J Syst Evol Microbiol 2020; 70:5888-5898. [PMID: 33034549 DOI: 10.1099/ijsem.0.004490] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two morphologically similar halophilic strains, named USBA 874 and USBA 960T, were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. Both isolates had non-spore-forming, Gram-stain-negative and motile cells that grew aerobically. The strains grew optimally at 30 °C, pH 7.0 and with 25 % NaCl (w/v). The isolates showed almost identical 16S rRNA gene sequences (99.0 % similarity). The predominant quinones of USBA-960T were Q-8, Q-7 and Q-9. The major cellular fatty acids were C19 : 0 cyclo ω8c, C18 : 0 and C16 : 0. According to 16S rRNA gene sequencing, the closest phylogenetic relatives are Salinisphaera species (similarity between 93.6 and 92.3 %), Abyssibacter profundi OUC007T (88.6 %) and Oceanococcus atlanticus 22II-S10r2T (88.7 %). In addition, the result of genome blast distance phylogeny analysis between strains USBA 874 and USBA 960T, Salinisphaera halophila (YIM 95161T), Salinisphaera shabanensis (E1L3AT), Salinisphaera orenii (MK-B5T) and Salinisphaera japonica (YTM-1T) was 18.5 %. Other in silico species delineation analyses also showed low identity such as ANIb and ANIm values (<69.0 and <84.0 % respectively), TETRA (<0.81) and AAI values (<0.67). Genome sequencing of USBA 960T revealed a genome size of 2.47 Mbp and a G+C content of 59.71 mol%. Phylogenetic analysis of strains USBA 874 and USBA 960T indicated that they formed a different lineage within the family Salinisphaeraceae. Based on phenotypic and chemotaxonomic characteristics, phylogenetic analysis and DNA-DNA relatedness values, along with identity at whole genome level, it can be concluded that strains USBA 960T and USBA 874 represent a novel genus of the family Salinisphaeraceae and the name Salifodinibacter halophilus gen. nov., sp. nov. is proposed. The type strain is USBA 960T (CMPUJ U095T=CECT 30006T).
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Affiliation(s)
- María Paula Parada-Pinilla
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá DC, Colombia
| | - Carolina Díaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá DC, Colombia
| | - Gina López
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá DC, Colombia
| | - Jorge Iván Díaz-Riaño
- Vicepresidency of Research and Creation, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá DC, Colombia
| | - Laura N Gonzalez
- Vicepresidency of Research and Creation, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá DC, Colombia
| | - Silvia Restrepo
- Chemical Engineering Department, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá DC, Colombia
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca 37007, Spain
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental (USBA), Departamento de Biología, Pontificia Universidad Javeriana, POB 56710, Bogotá DC, Colombia
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Rubiano-Labrador C, Díaz-Cárdenas C, López G, Gómez J, Baena S. Colombian Andean thermal springs: reservoir of thermophilic anaerobic bacteria producing hydrolytic enzymes. Extremophiles 2019; 23:793-808. [PMID: 31555903 DOI: 10.1007/s00792-019-01132-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 09/13/2019] [Indexed: 11/25/2022]
Abstract
Anaerobic cultivable microbial communities in thermal springs producing hydrolytic enzymes were studied. Thermal water samples from seven thermal springs located in the Andean volcanic belt, in the eastern and central mountain ranges of the Colombian Andes were used as inocula for the growth and isolation of thermophilic microorganisms using substrates such as starch, gelatin, xylan, cellulose, Tween 80, olive oil, peptone and casamino acids. These springs differed in temperature (50-70 °C) and pH (6.5-7.5). The predominant ion in eastern mountain range thermal springs was sulphate, whereas that in central mountain range springs was bicarbonate. A total of 40 anaerobic thermophilic bacterial strains that belonged to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium were isolated. To investigate the metabolic potential of these isolates, selected strains were analysed for enzymatic activities to identify strains than can produce hydrolytic enzymes. We demonstrated that these thermal springs contained diverse microbial populations of anaerobic thermophilic comprising different metabolic groups of bacteria including strains belonging to the genera Thermoanaerobacter, Caloramator, Anoxybacillus, Caloranaerobacter, Desulfomicrobium, Geotoga, Hydrogenophilus, Desulfacinum and Thermoanaerobacterium with amylases, proteases, lipases, esterases, xylanases and pectinases; therefore, the strains represent a promising source of enzymes with biotechnological potential.
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Affiliation(s)
- Carolina Rubiano-Labrador
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
- Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, Cartagena de Indias D.T. y C., Colombia
| | - Carolina Díaz-Cárdenas
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia.
| | - Gina López
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
| | - Javier Gómez
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
| | - Sandra Baena
- Unidad de Saneamiento y Biotecnología Ambiental, Departamento de Biología, Pontificia Universidad Javeriana, 56710, Bogotá DC, Colombia
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2019; 69:1247-1250. [PMID: 31066659 DOI: 10.1099/ijsem.0.003357] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Aharon Oren
- 1The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- 2Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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