1
|
Egas RA, Sahonero-Canavesi DX, Bale NJ, Koenen M, Yildiz Ç, Villanueva L, Sousa DZ, Sánchez-Andrea I. Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans. Environ Microbiol 2024; 26:e16565. [PMID: 38356112 DOI: 10.1111/1462-2920.16565] [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: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 02/16/2024]
Abstract
Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.
Collapse
Affiliation(s)
- Reinier A Egas
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana X Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
| | - Çağlar Yildiz
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Texel, Den Burg, The Netherlands
- Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Environmental Sciences and Sustainability Department, Science & Technology School, IE University, Segovia, Spain
| |
Collapse
|
2
|
Li M, Chu Y, Dong X, Ji H. General mechanisms of weak acid-tolerance and current strategies for the development of tolerant yeasts. World J Microbiol Biotechnol 2023; 40:49. [PMID: 38133718 DOI: 10.1007/s11274-023-03875-y] [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: 11/01/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
Yeast cells are often subjected to various types of weak acid stress in the process of industrial production, food processing, and preservation, resulting in growth inhibition and reduced fermentation performance. Under acidic conditions, weak acids enter the near-neutral yeast cytoplasm and dissociate into protons and anions, leading to cytoplasmic acidification and cell damage. Although some yeast strains have developed the ability to survive weak acids, the complexity and diversity of stresses during industrial production still require the application of appropriate strategies for phenotypes improvement. In this review, we summarized current knowledge concerning weak acid stress response and resistance, which may suggest important targets for further construction of more robust strains. We also highlight current feasible strategies for improving the weak acid resistance of yeasts, such as adaptive laboratory evolution, transcription factors engineering, and cell membrane/wall engineering. Moreover, the challenges and perspectives associated with improving the competitiveness of industrial strains are also discussed. This review provides effective strategies for improving the industrial phenotypes of yeast from multiple dimensions in future studies.
Collapse
Affiliation(s)
- Mengmeng Li
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Yunfei Chu
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Xiameng Dong
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, 325006, PR China.
| | - Hao Ji
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
| |
Collapse
|
3
|
Yu Y, Zhang J, Zhu F, Fan M, Zheng J, Cai M, Zheng L, Huang F, Yu Z, Zhang J. Enhanced protein degradation by black soldier fly larvae ( Hermetia illucens L.) and its gut microbes. Front Microbiol 2023; 13:1095025. [PMID: 36704554 PMCID: PMC9871565 DOI: 10.3389/fmicb.2022.1095025] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Black soldier fly larvae (BSFL) can convert a variety of organic wastes into biomass, and its gut microbiota are involved in this process. However, the role of gut microbes in the nutrient metabolism of BSFL is unclear. In this study, germ-free BSFL (GF) and gnotobiotic BSFL (GB) were evaluated in a high-protein artificial diet model. We used 16S rDNA sequencing, ITS1 sequencing, and network analysis to study gut microbiota in BSFL that degrade proteins. The protein reduction rate of the GB BSFL group was significantly higher (increased by 73.44%) than that of the GF BSFL group. The activity of gut proteinases, such as trypsin and peptidase, in the GB group was significantly higher than the GF group. The abundances of different gut microbes, including Pseudomonas spp., Orbus spp. and Campylobacter spp., were strongly correlated with amino acid metabolic pathways. Dysgonomonas spp. were strongly correlated with protein digestion and absorption. Issatchenkia spp. had a strong correlation with pepsin activity. Campylobacter spp., Pediococcus spp. and Lactobacillus spp. were strongly correlated with trypsin activity. Lactobacillus spp. and Bacillus spp. were strongly correlated with peptidase activity. Gut microbes such as Issatchenkia spp. may promote the gut proteolytic enzyme activity of BSFL and improve the degradation rate of proteins. BSFL protein digestion and absorption involves gut microbiota that have a variety of functions. In BSFL the core gut microbiota help complete protein degradation. These results demonstrate that core gut microbes in BSFL are important in protein degradation.
Collapse
Affiliation(s)
- Yongqiang Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China
| | - Jia Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China
| | - Fengling Zhu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China
| | - Mingxia Fan
- Renmin Hospital of Wuhan University, Wuhan, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China
| | - Feng Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, China,*Correspondence: Jibin Zhang, ✉
| |
Collapse
|
4
|
Wang Y, Li X, Li K, Huang Y, Yang H, Zhu P, Chi Z, Xu Y, Li Q. Signature of dissolved organic matter and microbial communities based on different oxygen levels response during distillers dried grains with solubles plus sugarcane pith co-fermentations. BIORESOURCE TECHNOLOGY 2022; 349:126868. [PMID: 35183724 DOI: 10.1016/j.biortech.2022.126868] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The objective of this study was to investigate the relationship between dissolved organic matter (DOM) and microbial communities during the co-fermentation of distillers dried grains with solubles (DDGS) and sugarcane pith at different oxygen levels. In aerobic fermentation (AF), the content of DOM decreased from 32.61 mg/g to 14.14 mg/g, and decreased from 32.61 mg/g to 30.83 mg/g in anaerobic fermentation (ANF). Phenols and alcohols were consumed first in AF, while lipids and proteins were consumed first in ANF. Degradation rates of cellulose, hemicellulose and lignin in AF (6.67%, 39.93%, 36.50%) were higher than those in ANF (0.69%, 18.36%, 9.12%). Firmicutes, Actinobacteriota and Ascomycota were the main phyla in community. Distance-based redundancy analysis showed that pH, organic matter (OM) and DOM were the main driving factors of microbial community succession.
Collapse
Affiliation(s)
- Yiwu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Xiaolan Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Kecheng Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yite Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hongxiang Yang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Pengfei Zhu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Zhanyou Chi
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yongping Xu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Qunliang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
| |
Collapse
|
5
|
Tian S, Zeng W, Zhou J, Du G. Correlation between the microbial community and ethyl carbamate generated during Huzhou rice wine fermentation. Food Res Int 2022; 154:111001. [DOI: 10.1016/j.foodres.2022.111001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 11/04/2022]
|
6
|
Metabolic changes of Issatchenkia orientalis under acetic acid stress by transcriptome profile using RNA-sequencing. Int Microbiol 2021; 25:417-426. [PMID: 34811604 DOI: 10.1007/s10123-021-00217-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022]
Abstract
Issatchenkia orientalis (I. orientalis) is tolerant to various environmental stresses especially acetic acid stress in wine making. However, limited literature is available on the transcriptome profile of I. orientalis under acetic acid stress. RNA-sequence was used to investigate the metabolic changes due to underlying I. orientalis 166 (Io 166) tolerant to acetic acid. Transcriptomic analyses showed that genes involved in ergosterol biosynthesis are differentially expressed under acetic acid stress. Genes associated with ribosome function were downregulated, while energy metabolism-related genes were upregulated. Moreover, Hsp70/Hsp90 and related molecular chaperones were upregulated to recognize and degrade misfolded proteins. Compared to Saccharomyces cerevisiae, transcriptomic changes of Io 166 showed many similarities under acetic acid stress. There were significant upregulation of genes in ergosterol biosynthesis and for the application of wine production.
Collapse
|
7
|
Proteomic analysis of serial isolates of Trichosporon asahii identifies host-specific adaptations using the TMT/MRM approach. J Proteomics 2021; 245:104309. [PMID: 34153541 DOI: 10.1016/j.jprot.2021.104309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022]
Abstract
The opportunistic fungal pathogen Trichosporon asahii (T. asahii) is an important causal agent of mortality in immunocompromised patients and associated with frequent relapses, even with sufficient antifungal treatment. Investigating the proteomes of initial and recurrent isolates may help to identify within-host adaptive changes. In this study, using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) technology, we analyzed the proteomes of two T. asahii strains that were isolated 15 years apart from the same patient who suffered initial and recurrent episodes of systemic disseminated trichosporonosis. A total of 597 differentially expressed proteins were identified. Functional analysis showed that the increased proteins were primarily concentrated on peptide/protein/energy/drug metabolism and translation. Most of the results were determined to be consistent with the findings of phenotypic assays, such as tests for drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays. Moreover, we performed multiple reaction monitoring (MRM) mass spectrometry to verify 27 candidate proteins, and the results of this experiment were also highly consistent with the results of the TMT analysis. Therefore, to the best of our knowledge, these data provide the first molecular evidence of how the T. asahii proteome changes related to host-specific adaptation during human infection. SIGNIFICANCE: Systemic infection with Trichosporon asahii (T. asahii) has recently been recognized as an important causal agent of mortality in immunocompromised patients. Although triazole treatment usually works efficiently in the early phase of infection, many patients relapse. Hence, comparative analyses of the proteomics of initial and recurrent isolates may reveal evidence of adaptive changes within the host. Our study demonstrates that the recurrent strain has undergone proteomic changes using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Moreover, the results of phenotypic assays, including drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays, were highly consistent with the proteomic changes, and multiple reaction monitoring (MRM) verification also showed similar trends to the TMT results. In summary, our study is the first to investigate the adaptation of T. asahii under pressure from antifungal chemotherapy and host immune responses.
Collapse
|