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Yakovleva E, Danilova I, Maximova I, Shabaev A, Dmitrieva A, Belov A, Klyukina A, Perfilieva K, Bonch-Osmolovskaya E, Markov A. Salt concentration in substrate modulates the composition of bacterial and yeast microbiomes of Drosophila melanogaster. MICROBIOME RESEARCH REPORTS 2024; 3:19. [PMID: 38846022 PMCID: PMC11153085 DOI: 10.20517/mrr.2023.56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 06/09/2024]
Abstract
Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter, potentially beneficial to D. melanogaster, decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.
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Affiliation(s)
- Ekaterina Yakovleva
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina Danilova
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina Maximova
- Faculty of Soil Science, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Shabaev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia Dmitrieva
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Andrey Belov
- Faculty of Soil Science, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexandra Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Ksenia Perfilieva
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Elizaveta Bonch-Osmolovskaya
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Alexander Markov
- Biological Faculty, Lomonosov Moscow State University, Moscow 119991, Russia
- Borisyak Paleontological Institute, Russian Academy of Sciences, Moscow 117997, Russia
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Dmitrieva AS, Maksimova IA, Kachalkin AV, Markov AV. Age-Related Changes in the Yeast Component of the Drosophila melanogaster Microbiome. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Maksimova IA, Kachalkin AV, Yakovleva EY, Krivosheina MG, Markov AV. Yeast Communities Associated with Diptera of the White Sea Littoral. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720020071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Dmitrieva AS, Ivnitsky SB, Maksimova IA, Panchenko PL, Kachalkin AV, Markov AV. Yeasts affect tolerance of Drosophila melanogaster to food substrate with high NaCl concentration. PLoS One 2019; 14:e0224811. [PMID: 31693706 PMCID: PMC6834263 DOI: 10.1371/journal.pone.0224811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/22/2019] [Indexed: 11/21/2022] Open
Abstract
The ability of model animal species, such as Drosophila melanogaster, to adapt quickly to various adverse conditions has been shown in many experimental evolution studies. It is usually assumed by default that such adaptation is due to changes in the gene pool of the studied population of macroorganisms. At the same time, it is known that microbiome can influence biological processes in macroorganisms. In order to assess the possible impact of microbiome on adaptation, we performed an evolutionary experiment in which some D. melanogaster lines were reared on a food substrate with high NaCl concentration while the others were reared on the standard (favourable) substrate. We evaluated the reproductive efficiency of experimental lines on the high salt substrate three years after the experiment started. Our tests confirmed that the lines reared on the salty substrate became more tolerant to high NaCl concentration. Moreover, we found that pre-inoculation of the high salt medium with homogenized salt-tolerant flies tended to improve reproductive efficiency of naïve flies on this medium (compared to pre-inoculation with homogenized control flies). The analysis of yeast microbiome in fly homogenates revealed significant differences in number and species richness of yeasts between salt-tolerant and control lines. We also found that some individual yeast lines extracted from the salt-tolerant flies improved reproductive efficiency of naïve flies on salty substrate (compared to baker's yeast and no yeast controls), whereas the effect of the yeast lines extracted from the control flies tended to be smaller. The yeast Starmerella bacillaris extracted from the salt-tolerant flies showed the strongest positive effect. This yeast is abundant in all salt-tolerant lines, and very rare or absent in all control lines. The results are consistent with the hypothesis that some components of the yeast microbiome of D. melanogaster contribute to to flies' tolerance to food substrate with high NaCl concentration.
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Affiliation(s)
- A. S. Dmitrieva
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - S. B. Ivnitsky
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - I. A. Maksimova
- Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia
| | - P. L. Panchenko
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - A. V. Kachalkin
- Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Russia
| | - A. V. Markov
- Department of Biological Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow, Russia
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Elgart M, Soen Y. Microbiome-Germline Interactions and Their Transgenerational Implications. Bioessays 2017; 40:e1700018. [DOI: 10.1002/bies.201700018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 10/30/2017] [Indexed: 01/16/2023]
Affiliation(s)
| | - Yoav Soen
- Biomolecular Sciences; Rehovot Israel
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