1
|
Hwang JH, Choi TR, Kim S, Lee Y, Shin Y, Choi S, Oh J, Kim SH, Park JH, Bhatia SK, Yang YH. Evaluation of simplified ester-linked fatty acid analysis (ELFA) for phospholipid fatty acid (PLFA) analysis of bacterial population. Anal Biochem 2024; 695:115638. [PMID: 39127328 DOI: 10.1016/j.ab.2024.115638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Phospholipid fatty acid (PLFA) analysis is used for characterizing microbial communities based on their lipid profiles. This method avoids biases from PCR or culture, allowing data collection in a natural state. However, PLFA is labor-intensive due to lipid fractionation. Simplified ester-linked fatty acid analysis (ELFA), which skips lipid fractionation, offers an alternative. It utilizes base-catalyzed methylation to derivatize only lipids, not free fatty acids, and found glycolipid and neutral lipid fractions are scarcely present in most bacteria, allowing lipid fractionation to be skipped. ELFA method showed a high correlation to PLFA data (r = 0.99) and higher sensitivity than the PLFA method by 1.5-2.57-fold, mainly due to the higher recovery of lipids, which was 1.5-1.9 times higher than with PLFA. The theoretical limit of detection (LOD) and limit of quantification (LOQ) for the ELFA method indicated that 1.54-fold less sample was needed for analysis than with the PLFA method. Our analysis of three bacterial cultures and a simulated consortium revealed the effectiveness of the ELFA method by its simple procedure and enhanced sensitivity for detecting strain-specific markers, which were not detected in PLFA analysis. Overall, this method could be easily used for the population analysis of synthetic consortia.
Collapse
Affiliation(s)
- Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Tae-Rim Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Suwon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yeda Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Yuni Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Suhye Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Jinok Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Sang-Hyoun Kim
- Department of Civil and Environmental Engineering, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jeong-Hoon Park
- Sustainable Technology and Wellness R&D Group, Korea Institute of Industrial Technology (KITECH), Jeju-si, 63243, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, 05029, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, 120, Neungdong-ro, Gwangjin-gu, Seoul, 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, 05029, Republic of Korea.
| |
Collapse
|
2
|
Lopes C, Barbosa J, Maciel E, da Costa E, Alves E, Ricardo F, Domingues P, Mendo S, Domingues MRM. Decoding the Fatty Acid Profile of Bacillus licheniformis I89 and Its Adaptation to Different Growth Conditions to Investigate Possible Biotechnological Applications. Lipids 2019; 54:245-253. [PMID: 30957876 DOI: 10.1002/lipd.12142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 03/01/2019] [Accepted: 03/01/2019] [Indexed: 01/08/2023]
Abstract
Bacillus licheniformis I89 is a Gram-positive bacterium, a producer of the lantibiotic lichenicidin. No information is available on its fatty acid (FA) composition. Bacillus species are rich in branched FA (BrFA), claimed to be beneficial to human health and to treat diseases. Herein, the FA profile of B. licheniformis I89 was evaluated under different growth conditions: at two growth temperatures (37 and 50 °C) and at different growth phases (lag, exponential, and stationary), using gas chromatography-mass spectrometry. The FA profile revealed predominant BrFA of the iso-series and anteiso-series (i-15:0, ai-15:0, i-16:0, i-17:0, and ai-17:0) and low amounts of saturated FA (14:0, 16:0, and 18:0). Comparing the FA profiles at different temperatures, in the lag phase, at 50 °C, there was a decrease of ai-17:0 and a decrease of i-15:0 in the exponential phase, in comparison with 37 °C. In all growth phases, there was a decrease of ai-15:0 and an increase of i-17:0. From the lag to the stationary phase, at 50 °C, there was a decrease of ai-17:0 and i-16:0, whereas i-15:0 increased, while at 37 °C, there was an increase of i-15:0 and i-16:0, and a decrease in ai-15:0 and ai-17:0. B. licheniformis I89 can adapt its FA profile, at moderate temperatures, by changing the iso-FA and anteiso-FA composition and the iso/anteiso ratio. This nonpathogenic bacterium species can be used as a source of BrFA with putative beneficial health effects for gut protection and with reported antitumor properties, foreseeing its use for producing compounds with biotechnological applications.
Collapse
Affiliation(s)
- Celestina Lopes
- Centro de Espectrometria de Massa, Departamento de Química & QOPNA, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Departamento de Química & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Joana Barbosa
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Elisabete Maciel
- Centro de Espectrometria de Massa, Departamento de Química & QOPNA, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Departamento de Química & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Elisabete da Costa
- Centro de Espectrometria de Massa, Departamento de Química & QOPNA, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Departamento de Química & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Eliana Alves
- Centro de Espectrometria de Massa, Departamento de Química & QOPNA, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Fernando Ricardo
- Departamento de Química & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Pedro Domingues
- Centro de Espectrometria de Massa, Departamento de Química & QOPNA, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Sónia Mendo
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - M Rosário M Domingues
- Centro de Espectrometria de Massa, Departamento de Química & QOPNA, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Departamento de Química & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| |
Collapse
|
3
|
Callac N, Posth NR, Rattray JE, Yamoah KKY, Wiech A, Ivarsson M, Hemmingsson C, Kilias SP, Argyraki A, Broman C, Skogby H, Smittenberg RH, Fru EC. Modes of carbon fixation in an arsenic and CO 2-rich shallow hydrothermal ecosystem. Sci Rep 2017; 7:14708. [PMID: 29089625 PMCID: PMC5665909 DOI: 10.1038/s41598-017-13910-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/29/2017] [Indexed: 01/01/2023] Open
Abstract
The seafloor sediments of Spathi Bay, Milos Island, Greece, are part of the largest arsenic-CO2-rich shallow submarine hydrothermal ecosystem on Earth. Here, white and brown deposits cap chemically distinct sediments with varying hydrothermal influence. All sediments contain abundant genes for autotrophic carbon fixation used in the Calvin-Benson-Bassham (CBB) and reverse tricaboxylic acid (rTCA) cycles. Both forms of RuBisCO, together with ATP citrate lyase genes in the rTCA cycle, increase with distance from the active hydrothermal centres and decrease with sediment depth. Clustering of RuBisCO Form II with a highly prevalent Zetaproteobacteria 16S rRNA gene density infers that iron-oxidizing bacteria contribute significantly to the sediment CBB cycle gene content. Three clusters form from different microbial guilds, each one encompassing one gene involved in CO2 fixation, aside from sulfate reduction. Our study suggests that the microbially mediated CBB cycle drives carbon fixation in the Spathi Bay sediments that are characterized by diffuse hydrothermal activity, high CO2, As emissions and chemically reduced fluids. This study highlights the breadth of conditions influencing the biogeochemistry in shallow CO2-rich hydrothermal systems and the importance of coupling highly specific process indicators to elucidate the complexity of carbon cycling in these ecosystems.
Collapse
Affiliation(s)
- Nolwenn Callac
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden.
| | - Nicole R Posth
- Nordcee, Department of Biology-University of Southern Denmark Campusvej 55, 5230, Odense M, Denmark.,Department of Geosciences and Natural Resource Management - IGN University of Copenhagen, Øster Voldgade, 10 1350, København K, Denmark
| | - Jayne E Rattray
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Kweku K Y Yamoah
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Alan Wiech
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Magnus Ivarsson
- Department of Palaeobiology and Nordic Center for Earth Evolution, Swedish Museum of Natural History, Stockholm, Sweden
| | - Christoffer Hemmingsson
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Stephanos P Kilias
- Department of Geology and Geoenvironment, Section of Economic Geology and Geochemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zographou, 157 84, Athens, Greece
| | - Ariadne Argyraki
- Department of Geology and Geoenvironment, Section of Economic Geology and Geochemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zographou, 157 84, Athens, Greece
| | - Curt Broman
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Henrik Skogby
- Department of Geosciences, Swedish Museum of Natural History, Stockholm, Sweden
| | - Rienk H Smittenberg
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden
| | - Ernest Chi Fru
- Stockholm University, Department of Geological Sciences and Bolin Centre for Climate Research, SE-106 91, Stockholm, Sweden. .,School of Earth and Ocean Sciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom.
| |
Collapse
|
4
|
Sathiyanarayanan G, Bhatia SK, Kim HJ, Kim JH, Jeon JM, Kim YG, Park SH, Lee SH, Lee YK, Yang YH. Metal removal and reduction potential of an exopolysaccharide produced by Arctic psychrotrophic bacterium Pseudomonas sp. PAMC 28620. RSC Adv 2016. [DOI: 10.1039/c6ra17450g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metal reducing potential of an exopolysaccharide (EPS) produced by Arctic glacier soil bacteriumPseudomonassp. PAMC 28620.
Collapse
|