1
|
Tong CY, Honda K, Derek CJC. Enhancing organic matter productivity in microalgal-bacterial biofilm using novel bio-coating. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167576. [PMID: 37804964 DOI: 10.1016/j.scitotenv.2023.167576] [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: 07/19/2023] [Revised: 09/20/2023] [Accepted: 10/01/2023] [Indexed: 10/09/2023]
Abstract
Research on renewable energy from microalgae has led to a growing interest in porous substrate photobioreactors, but their widespread adoption is currently limited to pure microalgal biofilm cultures. The behavior of microalgal-bacterial biofilms immobilized on microporous substrates remains as a research challenge, particularly in uncovering their mutualistic interactions in environment enriched with dissolved organic matter. Therefore, this study established a novel culture platform by introducing microalgal-derived bio-coating that preconditioned hydrophilic polyvinylidene fluoride membranes for the microalgal-bacterial biofilm growth of freshwater microalgae, Chlorella vulgaris ESP 31 and marine microalgae, Cylindrotheca fusiformis with bacteria, Escherichia coli. In the attached co-culture mode, the bio-coating we proposed demonstrated the ability to enhance microalgal growth for both studied species by a range of 2.5 % to 19 % starting from day 10 onwards. Additionally, when compared to co-culture on uncoated membranes, the bio-coating exhibited a significant bacterial growth promotion effect, increasing bacterial growth by at least 2.35 times for the C. vulgaris-E. coli co-culture after an initial adaptation phase. A significant increase of at least 72 % in intracellular biochemical compounds (including chlorophyll, polysaccharides, proteins, and lipids) was observed within just five days, primarily due to the high concentration of pre-coated organic matter, mainly sourced from the internal organic matter (IOM) of C. fusiformis. Higher accumulation of organic compounds in the bio-coating indirectly triggers a competition between microalgae and bacteria which potentially stimulate the production of additional intra-/extra-organic substances as a defensive response. In short, insight gained from this study may represent a paradigm shift in the ways that symbiotic interactions are promoted to increase the yield of specific bio-compounds with the presence of bio-coating.
Collapse
Affiliation(s)
- C Y Tong
- School of Chemical Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal, 14300 Penang, Malaysia
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - C J C Derek
- School of Chemical Engineering, Engineering Campus, Universiti Sains Malaysia, Nibong Tebal, 14300 Penang, Malaysia.
| |
Collapse
|
2
|
Adams JD, Sander KB, Criddle CS, Arkin AP, Clark DS. Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products. Microb Cell Fact 2023; 22:69. [PMID: 37046248 PMCID: PMC10091555 DOI: 10.1186/s12934-023-02064-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND Intracellular biomacromolecules, such as industrial enzymes and biopolymers, represent an important class of bio-derived products obtained from bacterial hosts. A common key step in the downstream separation of these biomolecules is lysis of the bacterial cell wall to effect release of cytoplasmic contents. Cell lysis is typically achieved either through mechanical disruption or reagent-based methods, which introduce issues of energy demand, material needs, high costs, and scaling problems. Osmolysis, a cell lysis method that relies on hypoosmotic downshock upon resuspension of cells in distilled water, has been applied for bioseparation of intracellular products from extreme halophiles and mammalian cells. However, most industrial bacterial strains are non-halotolerant and relatively resistant to hypoosmotic cell lysis. RESULTS To overcome this limitation, we developed two strategies to increase the susceptibility of non-halotolerant hosts to osmolysis using Cupriavidus necator, a strain often used in electromicrobial production, as a prototypical strain. In one strategy, C. necator was evolved to increase its halotolerance from 1.5% to 3.25% (w/v) NaCl through adaptive laboratory evolution, and genes potentially responsible for this phenotypic change were identified by whole genome sequencing. The evolved halotolerant strain experienced an osmolytic efficiency of 47% in distilled water following growth in 3% (w/v) NaCl. In a second strategy, the cells were made susceptible to osmolysis by knocking out the large-conductance mechanosensitive channel (mscL) gene in C. necator. When these strategies were combined by knocking out the mscL gene from the evolved halotolerant strain, greater than 90% osmolytic efficiency was observed upon osmotic downshock. A modified version of this strategy was applied to E. coli BL21 by deleting the mscL and mscS (small-conductance mechanosensitive channel) genes. When grown in medium with 4% NaCl and subsequently resuspended in distilled water, this engineered strain experienced 75% cell lysis, although decreases in cell growth rate due to higher salt concentrations were observed. CONCLUSIONS Our strategy is shown to be a simple and effective way to lyse cells for the purification of intracellular biomacromolecules and may be applicable in many bacteria used for bioproduction.
Collapse
Affiliation(s)
- Jeremy David Adams
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Kyle B Sander
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
| |
Collapse
|
3
|
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals. Metab Eng 2023; 76:179-192. [PMID: 36738854 DOI: 10.1016/j.ymben.2023.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/06/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance mechanisms are often unknown. To reveal tolerance mechanisms, an automated platform was utilized to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals (1,2-propanediol, 2,3-butanediol, glutarate, adipate, putrescine, hexamethylenediamine, butanol, isobutyrate, coumarate, octanoate, hexanoate), reaching tolerance at concentrations 60%-400% higher than initial toxic levels. Sequencing genomes of 223 isolates from 89 populations, reverse engineering, and cross-compound tolerance profiling were employed to uncover tolerance mechanisms. We show that: 1) cells are tolerized via frequent mutation of membrane transporters or cell wall-associated proteins (e.g., ProV, KgtP, SapB, NagA, NagC, MreB), transcription and translation machineries (e.g., RpoA, RpoB, RpoC, RpsA, RpsG, NusA, Rho), stress signaling proteins (e.g., RelA, SspA, SpoT, YobF), and for certain chemicals, regulators and enzymes in metabolism (e.g., MetJ, NadR, GudD, PurT); 2) osmotic stress plays a significant role in tolerance when chemical concentrations exceed a general threshold and mutated genes frequently overlap with those enabling chemical tolerance in membrane transporters and cell wall-associated proteins; 3) tolerization to a specific chemical generally improves tolerance to structurally similar compounds whereas a tradeoff can occur on dissimilar chemicals, and 4) using pre-tolerized starting isolates can hugely enhance the subsequent production of chemicals when a production pathway is inserted in many, but not all, evolved tolerized host strains, underpinning the need for evolving multiple parallel populations. Taken as a whole, this study provides a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 223 chemical tolerant isolates.
Collapse
|
4
|
Abel AJ, Hilzinger JM, Arkin AP, Clark DS. Systems-informed genome mining for electroautotrophic microbial production. Bioelectrochemistry 2022; 145:108054. [DOI: 10.1016/j.bioelechem.2022.108054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
|
5
|
Puspandari N, Sunarno S, Febrianti T, Febriyana D, Saraswati RD, Rooslamiati I, Amalia N, Nursofiah S, Hartoyo Y, Herna H, Mursinah M, Muna F, Aini N, Risniati Y, Dhewantara PW, Allamanda P, Wicaksana DN, Sukoco R, Efadeswarni, Nelwan EJ, Cahyarini, Haryanto B, Sihombing B, Soares Magalhães RJ, Kakkar M, Setiawaty V, Matheu J. Extended spectrum beta-lactamase-producing Escherichia coli surveillance in the human, food chain, and environment sectors: Tricycle project (pilot) in Indonesia. One Health 2021; 13:100331. [PMID: 34632041 PMCID: PMC8493575 DOI: 10.1016/j.onehlt.2021.100331] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/12/2021] [Accepted: 09/21/2021] [Indexed: 11/05/2022] Open
Abstract
The World Health Organization (WHO) has been implementing antimicrobial surveillance with a "One Health" approach, known as the Global Surveillance ESBL E. coli Tricycle Project. We describe the implementation of the Tricycle Project (pilot) in Indonesia, focusing on its results, challenges and recommendations. The samples were 116 patients with bloodstream infections caused by ESBL E. coli, 100 rectal swabs collected from pregnant women, 240 cecums of broiler, and 119 environmental samples, using the standardized method according to the guidelines. ESBL-producing E. coli was found in 40 (40%) of the 100 pregnant women, while the proportion of ESBL-producing E. coli was 57.7% among the total E. coli-induced bloodstream infections. ESBL-producing E. coli was isolated from 161 (67.1%) out of 240 broilers. On the other hand, the average concentration of E. coli in the water samples was 2.0 × 108 CFU/100 mL, and the ratio of ESBL-producing E. coli was 12.8% of total E. coli. Unfortunately, 56.7% of questionnaires for patients were incomplete. The Tricycle Project (pilot) identified that the proportion of ESBL-producing E. coli was very high in all types of samples, and several challenges and obstacles were encountered during the implementation of the study in Indonesia. The finding of this study have implication to health/the antimicrobial resistance (AMR) surveillance. We recommend continuing this project and extending this study to other provinces to determine the AMR burden as the baseline in planning AMR control strategies in Indonesia. We also recommend improving the protocol of this study to minimize obstacles in the field.
Collapse
Affiliation(s)
- Nelly Puspandari
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Sunarno Sunarno
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Tati Febrianti
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Dwi Febriyana
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Ratih Dian Saraswati
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Indri Rooslamiati
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Novi Amalia
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Sundari Nursofiah
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Yudi Hartoyo
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Herna Herna
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Mursinah Mursinah
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Fauzul Muna
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Nurul Aini
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Yenni Risniati
- Centre for Research and Development of Health Resources and Services, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Pandji Wibawa Dhewantara
- Centre for Research and Development of Public Health Efforts, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | | | | | - Rinto Sukoco
- Disease Investigation Center Subang, West Java, Indonesia
| | - Efadeswarni
- Research and Development for Environmental Quality and Laboratory Center, Banten, Indonesia
| | | | - Cahyarini
- Persahabatan Hospital, Jakarta, Indonesia
| | | | | | | | | | - Vivi Setiawaty
- Centre for Research and Development of Biomedical and Basic Health Technology, National Institute of Health Research and Development, Ministry of Health, Jakarta, Indonesia
| | - Jorge Matheu
- WHO Food Safety and Zoonoses Department, Geneva, Switzerland
| |
Collapse
|
6
|
Hou L, Jia L, Morrison HM, L-W Majumder E, Kumar D. Enhanced polyhydroxybutyrate production from acid whey through determination of process and metabolic limiting factors. BIORESOURCE TECHNOLOGY 2021; 342:125973. [PMID: 34563817 DOI: 10.1016/j.biortech.2021.125973] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
To sustainably produce biodegradable polyhydroxybutyrate (PHB), this study investigated effects of process and metabolic limiting factors during bioconversion of acid whey (AW) to PHB, offering economic and environmental advantages for dairy industry. Recombinant Escherichia coli LSBJ was used to achieve high PHB yields by utilizing both lactose and lactic acid as carbon source. Up to 85% PHB accumulation was achieved during growth on the synthetic AW. Growth on raw AW had the highest PHB yield of 4 g/L and a high substrate utilization efficiency (95%). Notably, ratios of lactate: lactose and C/N impacted metabolic flux and PHB yields. Maintaining the fermentation pH enhanced PHB production. Furthermore, additives of inorganic nitrogen sources, minerals and trace metals promoted PHB production from AW. The study improves the understanding of factors affecting utilization of AW and demonstrated the high PHB yields using recombinant E. coli that could be leveraged to design a sustainable process.
Collapse
Affiliation(s)
- Liyuan Hou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Linjing Jia
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Hailee M Morrison
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Erica L-W Majumder
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Deepak Kumar
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA.
| |
Collapse
|
7
|
Fidanza M, Panigrahi P, Kollmann TR. Lactiplantibacillus plantarum-Nomad and Ideal Probiotic. Front Microbiol 2021; 12:712236. [PMID: 34690957 PMCID: PMC8527090 DOI: 10.3389/fmicb.2021.712236] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
Probiotics are increasingly recognized as capable of positively modulating several aspects of human health. There are numerous attributes that make an ideal probiotic. Lactiplantibacillus plantarum (Lp) exhibits an ecological and metabolic flexibility that allows it to thrive in a variety of environments. The present review will highlight the genetic and functional characteristics of Lp that make it an ideal probiotic and summarizes the current knowledge about its potential application as a prophylactic or therapeutic intervention.
Collapse
Affiliation(s)
| | - Pinaki Panigrahi
- Georgetown University Medical Center, Department of Pediatrics, Washington, DC, United States
| | | |
Collapse
|
8
|
Lee HC, Metheny MM, Viliani S, Bennett DC, Hurley S, Kang I. Effects of subzero saline chilling on broiler chilling efficiency, meat quality, and microbial safety. Poult Sci 2020; 99:5158-5162. [PMID: 32988555 PMCID: PMC7598318 DOI: 10.1016/j.psj.2020.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 11/30/2022] Open
Abstract
The poultry industry has attempted to improve carcass chilling efficiency, meat quality, and product safety. The purpose of this research was to investigate the effects of subzero saline chilling on carcass chilling, breast fillet tenderness, and microbial safety. After evisceration, broiler carcasses were chilled using ice slurry control (0% NaCl/0.5°C) or subzero saline solutions (3% NaCl/-1.8°C and 4% NaCl/-2.41°C). Broiler carcasses in the subzero saline solutions were chilled efficiently and reduced the chilling time by 11% in 3% NaCl/-1.8°C and 37% in 4% NaCl/-2.41°C over the ice slurry chilling. The breast fillets of broiler carcasses in 4% NaCl/-2.41°C were significantly tenderized than those in water control (P < 0.05), with an intermediate value observed in 3% NaCl/-1.8°C. Before chilling, broiler carcasses possessed mesophilic aerobic bacteria, Escherichia coli, and total coliforms for 3.81, 0.78, and 1.86 log cfu/g, respectively, which were significantly reduced after chilling in 3% NaCl/-1.8°C or 4% NaCl/-2.41°C solution over the water control (P < 0.05), except the mesophilic aerobic bacteria. Based on these results, chilling of boiler carcass in 4% NaCl/-1.8°C solution appears to improve carcass chilling efficiency, meat tenderness, and bacterial reduction for E. coli and total coliforms.
Collapse
Affiliation(s)
- H C Lee
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - M M Metheny
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - S Viliani
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - D C Bennett
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - S Hurley
- Department of Agribusiness, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - I Kang
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
| |
Collapse
|
9
|
Cascaded valorization of seaweed using microbial cell factories. Curr Opin Biotechnol 2020; 65:102-113. [DOI: 10.1016/j.copbio.2020.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/17/2022]
|
10
|
Davis CR, Johnson CH, Robertson JB. A bioluminescent reporter for the halophilic archaeon Haloferax volcanii. Extremophiles 2020; 24:773-785. [PMID: 32749548 PMCID: PMC7462420 DOI: 10.1007/s00792-020-01193-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
Haloarchaea have evolved to thrive in hypersaline environments. Haloferax volcanii is of particular interest due to its genetic tractability; however, few in vivo reporters exist for halophiles. Haloarchaeal proteins evolved characteristics that promote proper folding and function at high salt concentrations, but many mesophilic reporter proteins lack these characteristics. Mesophilic proteins that acquire salt-stabilizing mutations, however, can lead to proper function in haloarchaea. Using laboratory-directed evolution, we developed and demonstrated an in vivo luciferase that functions in the hypersaline cytosol of H. volcanii.
Collapse
Affiliation(s)
- Chris R Davis
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Carl H Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - J Brian Robertson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA.
| |
Collapse
|
11
|
Wein T, Dagan T. The Effect of Population Bottleneck Size and Selective Regime on Genetic Diversity and Evolvability in Bacteria. Genome Biol Evol 2019; 11:3283-3290. [PMID: 31688900 PMCID: PMC7145630 DOI: 10.1093/gbe/evz243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2019] [Indexed: 12/20/2022] Open
Abstract
Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity, and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. In this study, we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, and large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size; hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.
Collapse
Affiliation(s)
- Tanita Wein
- Institute of Microbiology, Kiel University, Germany
| | - Tal Dagan
- Institute of Microbiology, Kiel University, Germany
| |
Collapse
|
12
|
Mandlaa, Sun Z, Wang R, Han X, Xu H, Yang W. Enhanced 2-keto-L-gulonic acid production by applying L-sorbose-tolerant helper strain in the co-culture system. AMB Express 2018; 8:30. [PMID: 29492704 PMCID: PMC5833332 DOI: 10.1186/s13568-018-0562-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/22/2018] [Indexed: 11/21/2022] Open
Abstract
2-Keto-L-gulonic acid (the precursor of vitamin C) is bio-converted from L-sorbose by mixed fermentation of Ketogulonicigenium vulgare and a helper strain. The helper strain promotes the conversion of 2-KLG by enhancing the growth of K. vulgare, but its growth is greatly inhibited by high concentration of L-sorbose, which consequently influence the 2-KLG production. The aim of this study is to obtain L-sorbose-tolerant helper strain (LHS) by experimental evolution for reduced L-sorbose-inhibition-effect and enhanced 2-KLG productivity in high concentration of L-sorbose. After three steps screening by using our devised screening strategy, three strains (i.e., Bc 21, Bc 47, Bc 50) with high resistance to high concentration of L-sorbose were obtained. The fermentation tests by co-culturing Bc 21 and K. vulgare 418 showed that the production of 2-KLG was increased by 17.9% in 11% L-sorbose medium than that in 8% after 55 h of fermentation and the conversion rate was 89.5%. The results suggested that Bc 21 could be an ideal helper strain for 2-KLG production under high concentration of L-sorbose and demonstrated the feasibility of using experimental evolution to breed LHS for vitamin C production.
Collapse
Affiliation(s)
- Mandlaa
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 010018 Hohhot, China
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 Wenhua Road, 110016 Shenyang, China
| | - Ziyu Sun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, 010018 Hohhot, China
| | - Ruigang Wang
- College of Life Science, Inner Mongolia Agricultural University, 010018 Hohhot, China
| | - Xiaodong Han
- College of Life Science, Inner Mongolia Agricultural University, 010018 Hohhot, China
| | - Hui Xu
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 Wenhua Road, 110016 Shenyang, China
| | - Weichao Yang
- Institute of Applied Ecology, Chinese Academy of Sciences, 72 Wenhua Road, 110016 Shenyang, China
| |
Collapse
|
13
|
Westphal LL, Lau J, Negro Z, Moreno IJ, Ismail Mohammed W, Lee H, Tang H, Finkel SE, Kram KE. Adaptation of Escherichia coli to long-term batch culture in various rich media. Res Microbiol 2018; 169:145-156. [PMID: 29454026 DOI: 10.1016/j.resmic.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/22/2017] [Accepted: 01/23/2018] [Indexed: 12/29/2022]
Abstract
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms. In contrast with other experimental evolution systems, because of cycling of nutrients and waste products, this is a heterogeneous environment, where selective pressures change over time, similar to natural environments. We determined that incubation in each environment leads to different adaptations by observing the growth advantage in stationary phase (GASP) phenotype. Re-sequencing whole genomes of populations identified both mutant alleles in a conserved set of genes and differences in evolutionary trajectories between environments. Reconstructing identified mutations in the parental strain background confirmed the adaptive advantage of some alleles, but also identified a surprising number of neutral or even deleterious mutations. This result indicates that complex epistatic interactions may be under positive selection within these heterogeneous environments.
Collapse
Affiliation(s)
- Lacey L Westphal
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, RRI 303, 1050 Child's Way, Los Angeles, CA, 90089-2910, USA.
| | - Jasmine Lau
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
| | - Zuly Negro
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
| | - Ivan J Moreno
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
| | - Wazim Ismail Mohammed
- School of Informatics and Computing, Indiana University, 150 S. Woodlawn Avenue, Bloomington, IN, 47405, USA.
| | - Heewook Lee
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, GHC 7719, 5000 Forbes Ave., Pittsburgh, PA, 15213, USA.
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, 150 S. Woodlawn Avenue, Bloomington, IN, 47405, USA.
| | - Steven E Finkel
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, RRI 303, 1050 Child's Way, Los Angeles, CA, 90089-2910, USA.
| | - Karin E Kram
- Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
| |
Collapse
|
14
|
Rawat D, Sharma RS, Karmakar S, Arora LS, Mishra V. Ecotoxic potential of a presumably non-toxic azo dye. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 148:528-537. [PMID: 29125956 DOI: 10.1016/j.ecoenv.2017.10.049] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 05/26/2023]
Abstract
Microbes have potential to convert non-toxic azo dyes into hazardous products in the environment. However, the role of microbes in biotransforming such presumably non-toxic dyes has not been given proper attention, thereby, questions the environmental safety of such compounds. The present study assessed salinity driven microbial degradation of an unregulated azo dye, Acid orange 7 (AO7), under moderately halophilic conditions of textile effluent. The halophilic microbial consortium from effluent decolorized ~97% AO7 (50-500mgL-1). The consortium efficiently decolorized the dye at different pH (5-8) and salinity (5-18% NaCl). The 16S rRNA sequence analyses confirmed the presence of Halomonas and Escherichia in the consortium. The FTIR and GC-MS analyses suggested microbial consortium degrade AO7 following symmetric and asymmetric cleavage and yield carcinogenic/mutagenic aromatic byproducts viz. aniline, 1-amino-2-naphthol, naphthalene, and phenyldiazene. In contrast to AO7, the biodegraded products caused molecular, cellular and organism level toxicity. The degraded products significantly reduced: radicle length in root elongation assay; shoot length/biomass in plant growth assays; and caused chromosomal abnormalities and reduced mitotic index in Allium cepa bioassay. We demonstrated that under saline conditions of textile effluent, halophilic microbes convert a presumably non-toxic azo dye into hazardous products. The study calls to review the current toxicity classification of azo dyes and develop environmentally sound regulatory policies by incorporating the role of environmental factors in governing dye toxicity, for environmental safety.
Collapse
Affiliation(s)
- Deepak Rawat
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Radhey Shyam Sharma
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Swagata Karmakar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Lakhbeer Singh Arora
- Department of Chemistry, Indian Institute of Technology, New Delhi 110016, India
| | - Vandana Mishra
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India.
| |
Collapse
|
15
|
Mohamed ET, Wang S, Lennen RM, Herrgård MJ, Simmons BA, Singer SW, Feist AM. Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution. Microb Cell Fact 2017; 16:204. [PMID: 29145855 PMCID: PMC5691611 DOI: 10.1186/s12934-017-0819-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/09/2017] [Indexed: 11/13/2022] Open
Abstract
Background There is a need to replace petroleum-derived with sustainable feedstocks for chemical production. Certain biomass feedstocks can meet this need as abundant, diverse, and renewable resources. Specific ionic liquids (ILs) can play a role in this process as promising candidates for chemical pretreatment and deconstruction of plant-based biomass feedstocks as they efficiently release carbohydrates which can be fermented. However, the most efficient pretreatment ILs are highly toxic to biological systems, such as microbial fermentations, and hinder subsequent bioprocessing of fermentative sugars obtained from IL-treated biomass. Methods To generate strains capable of tolerating residual ILs present in treated feedstocks, a tolerance adaptive laboratory evolution (TALE) approach was developed and utilized to improve growth of two different Escherichia coli strains, DH1 and K-12 MG1655, in the presence of two different ionic liquids, 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]) and 1-butyl-3-methylimidazolium chloride ([C4C1Im]Cl). For multiple parallel replicate populations of E. coli, cells were repeatedly passed to select for improved fitness over the course of approximately 40 days. Clonal isolates were screened and the best performing isolates were subjected to whole genome sequencing. Results The most prevalent mutations in tolerant clones occurred in transport processes related to the functions of mdtJI, a multidrug efflux pump, and yhdP, an uncharacterized transporter. Additional mutations were enriched in processes such as transcriptional regulation and nucleotide biosynthesis. Finally, the best-performing strains were compared to previously characterized tolerant strains and showed superior performance in tolerance of different IL and media combinations (i.e., cross tolerance) with robust growth at 8.5% (w/v) and detectable growth up to 11.9% (w/v) [C2C1Im][OAc]. Conclusion The generated strains thus represent the best performing platform strains available for bioproduction utilizing IL-treated renewable substrates, and the TALE method was highly successful in overcoming the general issue of substrate toxicity and has great promise for use in tolerance engineering. Electronic supplementary material The online version of this article (10.1186/s12934-017-0819-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elsayed T Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Shizeng Wang
- Joint Bioenergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Rebecca M Lennen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Blake A Simmons
- Joint Bioenergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint Bioenergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam M Feist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark. .,Department of Bioengineering, University of California, 9500 Gilman Drive La Jolla, San Diego, CA, 92093, USA.
| |
Collapse
|
16
|
Parimi NS, Durie IA, Wu X, Niyas AMM, Eiteman MA. Eliminating acetate formation improves citramalate production by metabolically engineered Escherichia coli. Microb Cell Fact 2017. [PMID: 28637476 PMCID: PMC5480221 DOI: 10.1186/s12934-017-0729-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Citramalate, a chemical precursor to the industrially important methacrylic acid (MAA), can be synthesized using Escherichia coli overexpressing citramalate synthase (cimA gene). Deletion of gltA encoding citrate synthase and leuC encoding 3-isopropylmalate dehydratase were critical to achieving high citramalate yields. Acetate is an undesirable by-product potentially formed from pyruvate and acetyl-CoA, the precursors of citramalate during aerobic growth of E. coli. This study investigated strategies to minimize acetate and maximize citramalate production in E. coli mutants expressing the cimA gene. RESULTS Key knockouts that minimized acetate formation included acetate kinase (ackA), phosphotransacetylase (pta), and in particular pyruvate oxidase (poxB). Deletion of glucose 6-phosphate dehydrogenase (zwf) and ATP synthase (atpFH) aimed at improving glycolytic flux negatively impacted cell growth and citramalate accumulation in shake flasks. In a repetitive fed-batch process, E. coli gltA leuC ackA-pta poxB overexpressing cimA generated 54.1 g/L citramalate with a yield of 0.64 g/g glucose (78% of theoretical maximum yield), and only 1.4 g/L acetate in 87 h. CONCLUSIONS This study identified the gene deletions critical to reducing acetate accumulation during aerobic growth and citramalate production in metabolically engineered E. coli strains. The citramalate yield and final titer relative to acetate at the end of the fed-batch process are the highest reported to date (a mass ratio of citramalate to acetate of nearly 40) without being detrimental to citramalate productivity, significantly improving a potential process for the production of this five-carbon chemical.
Collapse
Affiliation(s)
- Naga Sirisha Parimi
- School of Chemical, Materials and Biomedical Engineering, Driftmier Engineering Center, University of Georgia, Athens, GA, 30602, USA
| | - Ian A Durie
- School of Chemical, Materials and Biomedical Engineering, Driftmier Engineering Center, University of Georgia, Athens, GA, 30602, USA
| | - Xianghao Wu
- School of Chemical, Materials and Biomedical Engineering, Driftmier Engineering Center, University of Georgia, Athens, GA, 30602, USA
| | - Afaq M M Niyas
- School of Chemical, Materials and Biomedical Engineering, Driftmier Engineering Center, University of Georgia, Athens, GA, 30602, USA
| | - Mark A Eiteman
- School of Chemical, Materials and Biomedical Engineering, Driftmier Engineering Center, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
17
|
Hansen ASL, Lennen RM, Sonnenschein N, Herrgård MJ. Systems biology solutions for biochemical production challenges. Curr Opin Biotechnol 2017; 45:85-91. [PMID: 28319856 DOI: 10.1016/j.copbio.2016.11.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/20/2016] [Accepted: 11/23/2016] [Indexed: 11/28/2022]
Abstract
There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals.
Collapse
Affiliation(s)
- Anne Sofie Lærke Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Rebecca M Lennen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs., Lyngby, Denmark
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs., Lyngby, Denmark.
| |
Collapse
|
18
|
Efficient fermentative production of polymer-grade D-lactate by an engineered alkaliphilic Bacillus sp. strain under non-sterile conditions. Microb Cell Fact 2016; 15:3. [PMID: 26754255 PMCID: PMC4709905 DOI: 10.1186/s12934-015-0408-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/30/2015] [Indexed: 11/17/2022] Open
Abstract
Background Polylactic acid (PLA) is one important chemical building block that is well known as a biodegradable and a biocompatible plastic. The traditional lactate fermentation processes need CaCO3 as neutralizer to maintain the desired pH, which results in an amount of insoluble CaSO4 waste during the purification process. To overcome such environmental issue, alkaliphilic organisms have the great potential to be used as an organic acid producer under NaOH-neutralizing agent based fermentation. Additionally, high optical purity property in d-lactic acid is now attracting more attention from both scientific and industrial communities because it can improve mechanical properties of PLA by blending l- or d-polymer together. However, the use of low-price nitrogen source for d-lactate fermentation by alkaliphilic organisms combined with NaOH-neutralizing agent based process has not been studied. Therefore, our goal was the demonstrations of newly simplify high-optical-purity d-lactate production by using low-priced peanut meal combined with non-sterile NaOH-neutralizing agent based fermentation. Results In this study, we developed a process for high-optical-purity d-lactate production using an engineered alkaliphilic Bacillus strain. First, the native l-lactate dehydrogenase gene (ldh) was knocked out, and the d-lactate dehydrogenase gene from Lactobacillus delbrueckii was introduced to construct a d-lactate producer. The key gene responsible for exopolysaccharide biosynthesis (epsD) was subsequently disrupted to increase the yield and simplify the downstream process. Finally, a fed-batch fermentation under non-sterile conditions was conducted using low-priced peanut meal as a nitrogen source and NaOH as a green neutralizer. The d-lactate titer reached 143.99 g/l, with a yield of 96.09 %, an overall productivity of 1.674 g/l/h including with the highest productivity at 16 h of 3.04 g/l/h, which was even higher than that of a sterile fermentation. Moreover, high optical purities (approximately 99.85 %) of d-lactate were obtained under both conditions. Conclusions Given the use of a cheap nitrogen source and a non-sterile green fermentation process, this study provides a more valuable and favorable fermentation process for future polymer-grade d-lactate production.
Collapse
|
19
|
Eiteman MA, Ramalingam S. Microbial production of lactic acid. Biotechnol Lett 2015; 37:955-72. [PMID: 25604523 DOI: 10.1007/s10529-015-1769-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
Abstract
Lactic acid is an important commodity chemical having a wide range of applications. Microbial production effectively competes with chemical synthesis methods because biochemical synthesis permits the generation of either one of the two enantiomers with high optical purity at high yield and titer, a result which is particularly beneficial for the production of poly(lactic acid) polymers having specific properties. The commercial viability of microbial lactic acid production relies on utilization of inexpensive carbon substrates derived from agricultural or waste resources. Therefore, optimal lactic acid formation requires an understanding and engineering of both the competing pathways involved in carbohydrate metabolism, as well as pathways leading to potential by-products which both affect product yield. Recent research leverages those biochemical pathways, while researchers also continue to seek strains with improved tolerance and ability to perform under desirable industrial conditions, for example, of pH and temperature.
Collapse
Affiliation(s)
- Mark A Eiteman
- BioChemical Engineering Program, College of Engineering, University of Georgia, Athens, GA, 30602, USA,
| | | |
Collapse
|