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Doose C, Hubas C. The metabolites of light: Untargeted metabolomic approaches bring new clues to understand light-driven acclimation of intertidal mudflat biofilm. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168692. [PMID: 38008320 DOI: 10.1016/j.scitotenv.2023.168692] [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: 08/17/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
The microphytobenthos (MPB), a microbial community of primary producers, play a key role in coastal ecosystem functioning, particularly in intertidal mudflats. These mudflats experience challenging variations of irradiance, forcing the micro-organisms to develop photoprotective mechanisms to survive and thrive in this dynamic environment. Two major adaptations to light are well described in literature: the excess of light energy dissipation through non-photochemical quenching (NPQ), and the vertical migration in the sediment. These mechanisms trigger considerable scientific interest, but the biological processes and metabolic mechanisms involved in light-driven vertical migration remain largely unknown. To our knowledge, this study investigates for the first time metabolomic responses of a migrational mudflat biofilm exposed for 30 min to a light gradient of photosynthetically active radiation (PAR) from 50 to 1000 μmol photons m-2 s-1. The untargeted metabolomic analysis allowed to identify metabolites involved in two types of responses to light irradiance levels. On the one hand, the production of SFAs and MUFAs, primarily derived from bacteria, indicates a healthy photosynthetic state of MPB under low light (LL; 50 and 100 PAR) and medium light (ML; 250 PAR) conditions. Conversely, when exposed to high light (HL; 500, 750 and 1000 PAR), the MPB experienced light-induced stress, triggering the production of alka(e)nes and fatty alcohols. The physiological and ecological roles of these compounds are poorly described in literature. This study sheds new light on the topic, as it suggests that these compounds may play a crucial and previously unexplored role in light-induced stress acclimation of migrational MPB biofilms. Since alka(e)nes are produced from FAs decarboxylation, these results thus emphasize for the first time the importance of FAs pathways in microphytobenthic biofilms acclimation to light.
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Affiliation(s)
- Caroline Doose
- Muséum National d'Histoire Naturelle, UMR BOREA, MNHN-CNRS-UCN-UPMC-IRD-UA, Station Marine de Concarneau, Concarneau, France.
| | - Cédric Hubas
- Muséum National d'Histoire Naturelle, UMR BOREA, MNHN-CNRS-UCN-UPMC-IRD-UA, Station Marine de Concarneau, Concarneau, France.
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Zhila NO, Kiselev EG, Volkov VV, Mezenova OY, Sapozhnikova KY, Shishatskaya EI, Volova TG. Properties of Degradable Polyhydroxyalkanoates Synthesized from New Waste Fish Oils (WFOs). Int J Mol Sci 2023; 24:14919. [PMID: 37834364 PMCID: PMC10573456 DOI: 10.3390/ijms241914919] [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: 08/14/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/15/2023] Open
Abstract
The synthesis of PHA was first investigated using WFOs obtained from smoked-sprat heads, substandard fresh sprats, and fresh mackerel heads and backbones. All the WFOs ensured the growth of the wild-type strain Cupriavidus necator B-10646 and the synthesis of PHA, regardless of the degree of lipid saturation (from 0.52 to 0.65) and the set and ratio of fatty acids (FA), which was represented by acids with chain lengths from C14 to C24. The bacterial biomass concentration and PHA synthesis were comparable (4.1-4.6 g/L and about 70%) when using WFO obtained from smoked-sprat heads and fresh mackerel, and it was twice as high as the bacterial biomass concentration from the fresh sprat waste. This depended on the type of WFO, the bacteria synthesized P(3HB) homopolymer or P(3HB-co-3HV-co-3HHx) copolymer, which had a lower degree of crystallinity (Cx 71%) and a lower molecular weight (Mn 134 kDa) compared to the P(3HB) (Mn 175-209 kDa and Cx 74-78%) at comparable temperatures (Tmelt and Tdegr of 158-168 °C and 261-284 °C, respectively). The new types of WFO, studied for the first time, are suitable as a carbon substrates for PHA synthesis. The WFOs obtained in the production of canned Baltic sprat and Baltic mackerel can be considered a promising and renewable substrate for PHA biosynthesis.
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Affiliation(s)
- Natalia O. Zhila
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (E.G.K.); (K.Y.S.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Evgeniy G. Kiselev
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (E.G.K.); (K.Y.S.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Vladimir V. Volkov
- Centre for Advanced Protein Use Technologies, Kaliningrad State Technical University, Sovetsky Avenue, 1, Kaliningrad 236022, Russia; (V.V.V.); (O.Y.M.)
| | - Olga Ya. Mezenova
- Centre for Advanced Protein Use Technologies, Kaliningrad State Technical University, Sovetsky Avenue, 1, Kaliningrad 236022, Russia; (V.V.V.); (O.Y.M.)
| | - Kristina Yu. Sapozhnikova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (E.G.K.); (K.Y.S.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Ekaterina I. Shishatskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (E.G.K.); (K.Y.S.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
| | - Tatiana G. Volova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia; (E.G.K.); (K.Y.S.); (E.I.S.); (T.G.V.)
- Basic Department of Biotechnology, School of Fundamental Biology and Biotechnology, Siberian Federal University, 79 Svobodnyi Av., Krasnoyarsk 660041, Russia
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Zhang D, Zhou Y, Bugge TV, Mayanti B, Yang A, Poh LS, Gao X, Majid MBA, Ng WJ. Soluble microbial products (SMPs) in a sequencing batch reactor with novel cake filtration system. CHEMOSPHERE 2017; 184:1286-1297. [PMID: 28672727 DOI: 10.1016/j.chemosphere.2017.06.110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/18/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The formation, composition and characteristics of soluble microbial products (SMPs) were investigated in a novel system which coupled a sequencing batch reactor with a cake filtration system. Both suspended solids (SS) and turbidity were significantly removed, resulting in effluent SS of 0.12 mg L-1 and turbidity of 0.72 NTU after cake filtration. The average concentrations of proteins and carbohydrates decreased respectively from 4.0 ± 0.4 and 7.1 ± 0.6 mg/L in the sequencing batch reactor (SBR) mixed liquor, to 0.85 ± 0.21 and 1.39 ± 0.29 mg/L in the cake filtration effluent. Analysis of the molecular weight (MW) distribution of SMPs revealed a substantial reduction in the intensity of high-MW peaks (503 and 22.71 kDa) after cake filtration, which implied the sludge cake layer and the underlying gel layer may play a role in the effectiveness of cake filtration beyond the physical phenomenon. Three-dimensional excitation emission matrix fluorescence spectroscopy indicated that polycarboxylate- and polyaromatic humic acids were the dominant compounds and a noticeable decrease in the fraction of these compounds was observed in the cake filtration effluent. Analysis with GC-MS set for detecting low-MW SMPs identified aromatics, alcohols, alkanes and esters as the dominant compounds. SMPs exhibited both biodegradable and recalcitrant characteristics. More SMPs (total number of 91) were accumulated during the SBR start-up stage. A noticeable increase in the aromatic fractions was seen in the SBR effluent accoutring for 39% of total compounds, compared to the SBR mixed liquor (28%). Fewer compounds (total number of 66) were identified in cake filtration effluent compared to the SBR effluent (total number of 75).
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Affiliation(s)
- Dongqing Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, #06-10, Singapore, 637141, Singapore.
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, #06-10, Singapore, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, N1-01a-29, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | | | - Bening Mayanti
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, #06-10, Singapore, 637141, Singapore
| | - Adrian Yang
- Grundfos (Singapore) Pte. Ltd., 25 Jalan Tukang, Singapore, 619264, Singapore
| | - Leong Soon Poh
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, #06-10, Singapore, 637141, Singapore
| | - Xin Gao
- Grundfos (Singapore) Pte. Ltd., 25 Jalan Tukang, Singapore, 619264, Singapore
| | - Maszenan Bin Abdul Majid
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, #06-10, Singapore, 637141, Singapore
| | - Wun Jern Ng
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, #06-10, Singapore, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, N1-01a-29, 50 Nanyang Avenue, Singapore, 639798, Singapore.
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Lerch TZ, Dignac MF, Barriuso E, Mariotti A. Effect of glucose on the fatty acid composition of Cupriavidus necator JMP134 during 2,4-dichlorophenoxyacetic acid degradation: implications for lipid-based stable isotope probing methods. Appl Environ Microbiol 2011; 77:7296-306. [PMID: 21856833 PMCID: PMC3194869 DOI: 10.1128/aem.06438-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 08/10/2011] [Indexed: 11/20/2022] Open
Abstract
Combining lipid biomarker profiling with stable isotope probing (SIP) is a powerful technique for studying specific microbial populations responsible for the degradation of organic pollutants in various natural environments. However, the presence of other easily degradable substrates may induce significant physiological changes by altering both the rate of incorporation of the target compound into the biomass and the microbial lipid profiles. In order to test this hypothesis, Cupriavidus necator JMP134, a 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium, was incubated with [(13)C]2,4-D, [(13)C]glucose, or mixtures of both substrates alternatively labeled with (13)C. C. necator JMP134 exhibited a preferential use of 2,4-D over glucose. The isotopic analysis showed that glucose had only a small effect on the incorporation of the acetic chain of 2,4-D into the biomass (at days 2 and 3) and no effect on that of the benzenic ring. The addition of glucose did change the fatty acid methyl ester (FAME) composition. However, the overall FAME isotopic signature reflected that of the entire biomass. Compound-specific individual isotopic analyses of FAME composition showed that the (13)C-enriched FAME profiles were slightly or not affected when tracing the 2,4-D acetic chain or 2,4-D benzenic ring, respectively. This batch study is a necessary step for validating the use of lipid-based SIP methods in complex environments.
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Affiliation(s)
- Thomas Z Lerch
- UMR Biogeochimie et Ecologie des Milieux Continentaux, CNRS-UMPC-ENS-AgroParisTech-IRD-UPEC, Campus INRA, 78850 Thiverval-Grignon, France.
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Zabeti N, Bonin P, Volkman JK, Jameson ID, Guasco S, Rontani JF. Potential alteration of U37K' paleothermometer due to selective degradation of alkenones by marine bacteria isolated from the haptophyte Emiliania huxleyi. FEMS Microbiol Ecol 2010; 73:83-94. [PMID: 20491919 DOI: 10.1111/j.1574-6941.2010.00885.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The unsaturation ratio of C(37) alkenones (U(37)(K')) produced by haptophyte microalgae such as Emiliania huxleyi is often used as proxy for past sea surface temperature. In this study, 29 bacterial strains were isolated from cultures of the strain E. huxleyi TWP1. Among alkenone-degrading isolates, the strain Dietzia maris sp. S1 appeared to be able to selectively degrade alkenones leading to increases in the palaeoenvironmental proxy U(37)(K') by +0.05 to +0.10 units, which is equivalent to the change seen when the growth temperature is increased by 1.5-3.0 degrees C. This degradation was shown to involve initial epoxidation of the alkenone double bonds presumably by a monooxygenase, which showed a preference for oxidation of the omega29 double bond. Inconsistencies observed in previous studies of the aerobic microbial degradation of alkenones may simply reflect which species of bacteria were present. Our results confirm that intense aerobic bacterial degradative processes can introduce a bias in palaeotemperature reconstructions especially when there is evidence of substantial aerobic bacterial degradation of the deposited organic matter. The widespread occurrence of epoxyalkenones in the marine environment strongly suggests that selective aerobic bacterial degradation could be major source of uncertainty for palaeotemperature estimation.
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Affiliation(s)
- Nathalie Zabeti
- Laboratoire de Microbiologie de Géochimie et d'Ecologie Marines (UMR 6117), Centre d'Océanologie de Marseille, Marseille, France
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Proteomic analysis of Marinobacter hydrocarbonoclasticus SP17 biofilm formation at the alkane-water interface reveals novel proteins and cellular processes involved in hexadecane assimilation. Res Microbiol 2009; 160:829-37. [PMID: 19786096 DOI: 10.1016/j.resmic.2009.09.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 09/14/2009] [Accepted: 09/16/2009] [Indexed: 11/21/2022]
Abstract
Many hydrocarbon-degrading bacteria form biofilms at the hydrocarbon-water interface to overcome the weak accessibility of these poorly water-soluble substrates. In order to gain insight into the cellular functions involved, we undertook a proteomic analysis of Marinobacter hydrocarbonoclasticus SP17 biofilm developing at the hexadecane-water interface. Biofilm formation on hexadecane led to a global change in cell physiology involving modulation of the expression of 576 out of 1144 detected proteins when compared with planktonic cells growing on acetate. Biofilm cells overproduced a protein encoded by MARHY0478 that contains a conserved domain belonging to the family of the outer membrane transporters of hydrophobic compounds. Homologs of MARHY0478 were exclusively found in marine bacteria degrading alkanes or possessing alkane degradation genes, and hence presumably constitute a family of alkane transporters specific to marine bacteria. Interestingly, we also found that sessile cells growing on hexadecane overexpressed type VI secretion system components. This secretion system has been identified as a key factor in virulence and in symbiotic interaction with host organisms. This observation is the first experimental evidence of the contribution of a type VI secretion system to environmental adaptation, and raises the intriguing question about the role of this secretion machine in alkane assimilation.
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Klein B, Grossi V, Bouriat P, Goulas P, Grimaud R. Cytoplasmic wax ester accumulation during biofilm-driven substrate assimilation at the alkane–water interface by Marinobacter hydrocarbonoclasticus SP17. Res Microbiol 2008; 159:137-44. [DOI: 10.1016/j.resmic.2007.11.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 11/12/2007] [Accepted: 11/13/2007] [Indexed: 11/24/2022]
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Soltani M, Metzger P, Largeau C. Fatty acid and hydroxy acid adaptation in three gram-negative hydrocarbon-degrading bacteria in relation to carbon source. Lipids 2006; 40:1263-72. [PMID: 16477811 DOI: 10.1007/s11745-005-1494-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The lipids of three gram-negative bacteria, Acinetobacter calcoaceticus, Marinobacter aquaeolei, and Pseudomonas oleovorans grown on mineral media supplemented with ammonium acetate or hydrocarbons, were isolated, purified, and their structures determined. Three pools of lipids were isolated according to a sequential procedure: unbound lipids extracted with organic solvents, comprising metabolic lipids and the main part of membrane lipids, OH--labile lipids (mainly ester-bound in the lipopolysaccharides, LPS) and H+-labile lipids (mainly amide-bound in the LPS). Unsaturated FA composition gave evidence for an aerobic desaturation pathway for the synthesis of these acids in A. calcoaceticus and M. aquaeolei, a nonclassic route in gram-negative bacteria. Surprisingly, both aerobic and anaerobic pathways are operating in the studied strain of P. oleovorans. The increase of the proportion of saturated FA observed for the strain of P. oleovorans grown on light hydrocarbons would increase the temperature transition of the lipids for maintaining the inner membrane fluidity. An opposite phenomenon occurs in A. calcoaceticus and M. aquaeolei grown on solid or highly viscous C19 hydrocarbons. The increases of FA < C18 when the bacteria were grown on n-nonadecane, or of iso-FA in cultures on isononadecane would decrease the transition temperature of the lipids, to maintain the fluidity of the inner membranes. Moreover, P. oleovorans grown on hydrocarbons greatly decreases the proportion of P-hydroxy acids of LPS, thus likely maintaining the physical properties of the outer membrane. By contrast, no dramatic change in hydroxy acid composition occurred in the other two bacteria.
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Affiliation(s)
- Mohamed Soltani
- Centre National de la Recherche Scientifique UMR 7618, Ecole Nationale Supérieure de Chimie de Paris, 75231 Paris, France
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