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Skinner J, Delgado AG, Hyman M, Chu MYJ. Implementation of in situ aerobic cometabolism for groundwater treatment: State of the knowledge and important factors for field operation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171667. [PMID: 38485017 DOI: 10.1016/j.scitotenv.2024.171667] [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: 09/27/2023] [Revised: 03/04/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
In situ aerobic cometabolism of groundwater contaminants has been demonstrated to be a valuable bioremediation technology to treat many legacy and emerging contaminants in dilute plumes. Several well-designed and documented field studies have shown that this technology can concurrently treat multiple contaminants and reach very low cleanup goals. Fundamentally different from metabolism-based biodegradation of contaminants, microorganisms that cometabolically degrade contaminants do not obtain sufficient carbon and energy from the degradation process to support their growth and require an exogenous growth supporting primary substrate. Successful applications of aerobic cometabolic treatment therefore require special considerations beyond conventional in situ bioremediation, such as competitive inhibition between growth-supporting primary substrate(s) and contaminant non-growth substrates, toxic effects resulting from contaminant degradation, and differences in microbial population dynamics exhibited by biostimulated indigenous consortia versus bioaugmentation cultures. This article first provides a general review of microbiological factors that are likely to affect the rate of aerobic cometabolic biodegradation. We subsequently review fourteen well documented field-scale aerobic cometabolic bioremediation studies and summarize the underlying microbiological factors that may affect the performance observed in these field studies. The combination of microbiological and engineering principles gained from field testing leads to insights and recommendations on planning, design, and operation of an in situ aerobic cometabolic treatment system. With a vision of more aerobic cometabolic treatments being considered to tackle large, dilute plumes, we present several novel topics and future research directions that can potentially enhance technology development and foster success in implementing this technology for environmental restoration.
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Affiliation(s)
- Justin Skinner
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ 85281, USA; Engineering Research Center for Bio-mediated and Bio-inspired Geotechnics (CBBG), Arizona State University, 650 E Tyler Mall, Tempe, AZ 85281, USA; Andrews Engineering, Inc., 3300 Ginger Creek Drive, Springfield, IL 62711, USA
| | - Anca G Delgado
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85281, USA; School of Sustainable Engineering and the Built Environment, Arizona State University, 660 S College Ave, Tempe, AZ 85281, USA; Engineering Research Center for Bio-mediated and Bio-inspired Geotechnics (CBBG), Arizona State University, 650 E Tyler Mall, Tempe, AZ 85281, USA
| | - Michael Hyman
- Department of Plant and Microbial Biology, North Carolina State University, Thomas Hall 4545, 112 Derieux Place, Raleigh, NC 27607, USA
| | - Min-Ying Jacob Chu
- Haley & Aldrich Inc., 400 E Van Buren St, Ste 545, Phoenix, AZ 85004, USA.
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2
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Akbar WA, Rahim HU, Rutigliano FA. Microbial- and seaweed-based biopolymers: Sources, extractions and implications for soil quality improvement and environmental sustainability - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120964. [PMID: 38692027 DOI: 10.1016/j.jenvman.2024.120964] [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: 11/27/2023] [Revised: 03/10/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
Improving soil quality without creating any environmental problems is an unescapable goal of sustainable agroecosystem management, according to the United Nations 2030 Agenda for Sustainable Development. Therefore, sustainable solutions are in high demand. One of these is the use of biopolymers derived from microbes and seaweed. This paper aims to provide an overview of the sources of extraction and use of microbial (bacteria and cyanobacteria) and seaweed-based biopolymers as soil conditioners, the characteristics of biopolymer-treated soils, and their environmental concerns. A preliminary search was also carried out on the entire Scopus database on biopolymers to find out how much attention has been paid to biopolymers as biofertilizers compared to other applications of these molecules until now. Several soil quality indicators were evaluated, including soil moisture, color, structure, porosity, bulk density, temperature, aggregate stability, nutrient availability, organic matter, and microbial activity. The mechanisms involved in improving soil quality were also discussed.
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Affiliation(s)
- Waqas Ali Akbar
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, via Vivaldi, n. 43, 81100, Caserta, Italy.
| | - Hafeez Ur Rahim
- Department of Chemical, Pharmaceutical and Agricultural Sciences (DOCPAS), University of Ferrara, Italy
| | - Flora Angela Rutigliano
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, via Vivaldi, n. 43, 81100, Caserta, Italy
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3
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Tienda S, Gutiérrez-Barranquero JA, Padilla-Roji I, Arrebola E, de Vicente A, Cazorla FM. Polyhydroxyalkanoate production by the plant beneficial rhizobacterium Pseudomonas chlororaphis PCL1606 influences survival and rhizospheric performance. Microbiol Res 2024; 278:127527. [PMID: 37863020 DOI: 10.1016/j.micres.2023.127527] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Pseudomonas chlororaphis PCL1606 (PcPCL1606) is a model rhizobacterium used to study beneficial bacterial interactions with the plant rhizosphere. Many of its beneficial phenotypes depend on the production of the antifungal compound 2-hexyl, 5-propyl resorcinol (HPR). Transcriptomic analysis of PcPCL1606 and the deletional mutant in HPR production ΔdarB strain, assigned an additional regulatory role to HPR, and allowed the detection of differentially expressed genes during the bacterial interaction with the avocado rhizosphere. Interestingly, the putative genes phaG (PCL1606_46820) and phaI (PCL1606_56560), with a predicted role in polyhydroxyalkanoate biosynthesis, were detected to be under HPR control. Both putative genes were expressed in the HPR-producing wild-type strain, but strongly repressed in the derivative mutant ΔdarB, impaired in HPR production. Thus, a derivative mutant impaired in the phaG gene was constructed, characterized and compared with the wild-type strain PcPCL1606 and with the derivative mutant ΔdarB. The phaG mutant had strongly reduced PHA production by PcPCL1606, and displayed altered phenotypes involved in bacterial survival on the plant roots, such as tolerance to high temperature and hydrogen peroxide, and decreased root survival, in a similar way that the ΔdarB mutant. On the other hand, the phaG mutant does not have altered resistance to desiccation, motility, biofilm formation or adhesion phenotypes, as displayed by the HPR-defective ΔdarB mutant have. Interestingly, the mutant defective in PHA production also lacked a biocontrol phenotype against the soilborne pathogenic fungus Rosellinia necatrix, even when the derivative mutant still produced the antifungal HPR compound, demonstrating that the final biocontrol phenotype of PcPCL1606 first requires bacterial survival and adaptation traits to the soil and rhizosphere environment.
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Affiliation(s)
- Sandra Tienda
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - José Antonio Gutiérrez-Barranquero
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Isabel Padilla-Roji
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Eva Arrebola
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos, Avda. Louis Pasteur 31, 29071 Málaga, Spain; Grupo de Biología y Control de Enfermedades de Plantas, Área de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", IHSM-UMA-CSIC, Avda. Louis Pasteur 49, 29010 Málaga, Spain.
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Butler OM, Manzoni S, Warren CR. Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients. THE ISME JOURNAL 2023; 17:2259-2269. [PMID: 37853184 PMCID: PMC10689824 DOI: 10.1038/s41396-023-01527-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023]
Abstract
Many microorganisms synthesise carbon (C)-rich compounds under resource deprivation. Such compounds likely serve as intracellular C-storage pools that sustain the activities of microorganisms growing on stoichiometrically imbalanced substrates, making them potentially vital to the function of ecosystems on infertile soils. We examined the dynamics and drivers of three putative C-storage compounds (neutral lipid fatty acids [NLFAs], polyhydroxybutyrate [PHB], and trehalose) across a natural gradient of soil fertility in eastern Australia. Together, NLFAs, PHB, and trehalose corresponded to 8.5-40% of microbial C and 0.06-0.6% of soil organic C. When scaled to "structural" microbial biomass (indexed by polar lipid fatty acids; PLFAs), NLFA and PHB allocation was 2-3-times greater in infertile soils derived from ironstone and sandstone than in comparatively fertile basalt- and shale-derived soils. PHB allocation was positively correlated with belowground biological phosphorus (P)-demand, while NLFA allocation was positively correlated with fungal PLFA : bacterial PLFA ratios. A complementary incubation revealed positive responses of respiration, storage, and fungal PLFAs to glucose, while bacterial PLFAs responded positively to PO43-. By comparing these results to a model of microbial C-allocation, we reason that NLFA primarily served the "reserve" storage mode for C-limited taxa (i.e., fungi), while the variable portion of PHB likely served as "surplus" C-storage for P-limited bacteria. Thus, our findings reveal a convergence of community-level processes (i.e., changes in taxonomic composition that underpin reserve-mode storage dynamics) and intracellular mechanisms (e.g., physiological plasticity of surplus-mode storage) that drives strong, predictable community-level microbial C-storage dynamics across gradients of soil fertility and substrate stoichiometry.
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Affiliation(s)
- Orpheus M Butler
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
| | - Stefano Manzoni
- Stockholm University and Bolin Centre for Climate Research, Stockholm, Sweden
| | - Charles R Warren
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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5
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Wang C, Kuzyakov Y. Energy use efficiency of soil microorganisms: Driven by carbon recycling and reduction. GLOBAL CHANGE BIOLOGY 2023; 29:6170-6187. [PMID: 37646316 DOI: 10.1111/gcb.16925] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023]
Abstract
Carbon use efficiency (CUE) is being intensively applied to quantify carbon (C) cycling processes from microbial cell to global scales. Energy use efficiency (EUE) is at least as important as the CUE because (i) microorganisms use organic C mainly as an energy source and not as elemental C per se, and (ii) microbial growth and maintenance are limited by energy, but not by C as a structural element. We conceptualize and review the importance of EUE by soil microorganisms and focus on (i) the energy content in organic compounds depending on the nominal oxidation state of carbon (NOSC), (ii) approaches to assess EUE, (iii) similarities and differences between CUE and EUE, and (iv) discuss mechanisms responsible for lower EUE compared to CUE. The energy content per C atom (enthalpy of combustion, the total energy stored in a compound) in organic compounds is very closely (R2 = 0.98) positively related to NOSC and increases by 108 kJ mol-1 C per one NOSC unit. For the first time we assessed the NOSC of microbial biomass in soil (-0.52) and calculated the corresponding energy content of -510 kJ mol-1 C. We linked CUE and EUE considering the NOSC of microbial biomass and element compositions of substrates utilized by microorganisms. The mean microbial EUE (0.32-0.35) is 18% lower than CUE (0.41) using glucose as a substrate. This definitely indicates that microbial growth is limited by energy relative to C. Based on the comparison of a broad range of processes of C and energy utilization for cell growth and maintenance, as well as database of experimental CUE from various compounds, we clearly explained five mechanisms and main factors why EUE is lower than CUE. The two main mechanisms behind lower EUE versus CUE are: (i) microbial recycling: C can be microbially recycled, whereas energy is always utilized only once, and (ii) chemical reduction of organic and inorganic compounds: Energy is used for reduction, which is ongoing without C utilization.
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Affiliation(s)
- Chaoqun Wang
- Biogeochemistry of Agroecosystems, University of Goettingen, Goettingen, Germany
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Goettingen, Germany
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6
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Zhao Y, Liu Z, Zhang B, Cai J, Yao X, Zhang M, Deng Y, Hu B. Inter-bacterial mutualism promoted by public goods in a system characterized by deterministic temperature variation. Nat Commun 2023; 14:5394. [PMID: 37669961 PMCID: PMC10480208 DOI: 10.1038/s41467-023-41224-7] [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: 01/30/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Mutualism is commonly observed in nature but not often reported for bacterial communities. Although abiotic stress is thought to promote microbial mutualism, there is a paucity of research in this area. Here, we monitor microbial communities in a quasi-natural composting system, where temperature variation (20 °C-70 °C) is the main abiotic stress. Genomic analyses and culturing experiments provide evidence that temperature selects for slow-growing and stress-tolerant strains (i.e., Thermobifida fusca and Saccharomonospora viridis), and mutualistic interactions emerge between them and the remaining strains through the sharing of cobalamin. Comparison of 3000 bacterial pairings reveals that mutualism is common (~39.1%) and competition is rare (~13.9%) in pairs involving T. fusca and S. viridis. Overall, our work provides insights into how high temperature can favour mutualism and reduce competition at both the community and species levels.
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Affiliation(s)
- Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Baofeng Zhang
- Hangzhou Ecological and Environmental Monitoring Center, Hangzhou, China
| | - Jingjie Cai
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Meng Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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7
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Martínez MDLÁM, Urzúa LS, Carrillo YA, Ramírez MB, Morales LJM. Polyhydroxybutyrate Metabolism in Azospirillum brasilense and Its Applications, a Review. Polymers (Basel) 2023; 15:3027. [PMID: 37514417 PMCID: PMC10383645 DOI: 10.3390/polym15143027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Gram-negative Azospirillum brasilense accumulates approximately 80% of polyhydroxybutyrate (PHB) as dry cell weight. For this reason, this bacterium has been characterized as one of the main microorganisms that produce PHB. PHB is synthesized inside bacteria by the polymerization of 3-hydroxybutyrate monomers. In this review, we are focusing on the analysis of the PHB production by A. brasilense in order to understand the metabolism during PHB accumulation. First, the carbon and nitrogen sources used to improve PHB accumulation are discussed. A. brasilense accumulates more PHB when it is grown on a minimal medium containing a high C/N ratio, mainly from malate and ammonia chloride, respectively. The metabolic pathways to accumulate and mobilize PHB in A. brasilense are mentioned and compared with those of other microorganisms. Next, we summarize the available information to understand the role of the genes involved in the regulation of PHB metabolism as well as the role of PHB in the physiology of Azospirillum. Finally, we made a comparison between the properties of PHB and polypropylene, and we discussed some applications of PHB in biomedical and commercial areas.
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Affiliation(s)
- María de Los Ángeles Martínez Martínez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Lucía Soto Urzúa
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Yovani Aguilar Carrillo
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Mirian Becerril Ramírez
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
| | - Luis Javier Martínez Morales
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio y Av. 24 Sur, Col. San Manuel Ciudad Universitaria, Puebla 72570, Mexico
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Pooja N, Chakraborty I, Rahman MH, Mazumder N. An insight on sources and biodegradation of bioplastics: a review. 3 Biotech 2023; 13:220. [PMID: 37265543 PMCID: PMC10230146 DOI: 10.1007/s13205-023-03638-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/15/2023] [Indexed: 06/03/2023] Open
Abstract
Durability and affordability are two main reasons for the widespread consumption of plastic in the world. However, the inability of these materials to undergo degradation has become a significant threat to the environment and human health To address this issue, bioplastics have emerged as a promising alternative. Bioplastics are obtained from renewable and sustainable biomass and have a lower carbon footprint and emit fewer greenhouse gases than petroleum-based plastics. The use of these bioplastics sourced from renewable biomass can also reduce the dependency on fossil fuels, which are limited in availability. This review provides an elaborate comparison of biodegradation rates of potential bioplastics in soil from various sources such as biomass, microorganisms, and monomers. These bioplastics show great potential as a replacement for conventional plastics due to their biodegradable and diverse properties.
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Affiliation(s)
- Nag Pooja
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Ishita Chakraborty
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Md. Hafizur Rahman
- Department of Quality Control and Safety Management, Faculty of Food Sciences and Safety, Khulna Agricultural University, Khulna, Bangladesh
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
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Zhao C, Sun J, Shen Y, Xia Z, Hu M, Wu T, Zhuang M, Li Y, Tong Y, Yang J, Zhang J, He P. Removable carbon and storage carbon of golden tides. MARINE POLLUTION BULLETIN 2023; 191:114974. [PMID: 37116250 DOI: 10.1016/j.marpolbul.2023.114974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/13/2023]
Abstract
Due to ever-increasing global warming, ocean acidification, and inshore eutrophication, the outbreak of golden tides with Sargassum horneri has increased in the Yellow sea, where the biomass carbon enters three main carbon pathways: a. Removal of carbon from seawater by salvage, known as removable carbon; b. Biomass carbon is deposited to the seafloor through POC and RDOC through Biological Carbon Pump and Microbial Carbon Pump; c. Re-entering the carbon cycle through the food chain or re-entering the atmosphere through the action of microbes. Estimating carbon fixation (removable carbon) and storage (particulate organic carbon (POC) and refractory dissolved organic carbon (RDOC)) is vital in studying the global carbon cycle. In this research, it was observed that the C content of S. horneri was high, and the utilization rate of dissolved organic carbon (DOC), RDOC, and POC was also high in the eutrophication environment, where only 2.71 % of algal biomass carbon was converted to RDOC, and only 0.20 % converted to POC. The C + N + P combination has a restart effect on the seasonal accumulation of RDOC in relevant sea areas. It is suggested that the salvage and resource utilization should be strengthened to effectively control the golden tide and reduce the substantial economic losses to realize the win-win situation of carbon sink and environmental restoration.
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Affiliation(s)
- Chunyan Zhao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jingyi Sun
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Yifei Shen
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Zhangyi Xia
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Meijuan Hu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Tingjian Wu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Minmin Zhuang
- State Key Lab of Estuarine & Coastal Research, East China Normal University, Shanghai 200062, China
| | - Yaru Li
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Yupei Tong
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jia Yang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jianheng Zhang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
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10
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Pittaway P, Scobie M, Schmidt E. Evaporative loss and environmental impact of covers on water storages: A review. JOURNAL OF ENVIRONMENTAL QUALITY 2023; 52:241-257. [PMID: 36715076 DOI: 10.1002/jeq2.20454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Commercial products to reduce evaporation from water storages have been developed since the 1960s. Categorised as suspended and floating continuous covers, floating modular covers, and monomolecular (monolayer) and multimolecular chemical films, product adoption by agricultural water managers is low. The role of evaporation reduction in improving water use efficiency is well established, but information on the suitability of product categories for farm water storages is lacking. We reviewed the environmental and operational performance of commercial evaporation reduction products using published and supplier information on design, mode of action, installation, operation, maintenance, the evaporation reduction achieved, and the impact on water quality, to analyze the suitability of the five product classes for water storages ranging in size from ≤2 to 100 ha. Span loading, cable tensioning and anchorage limit continuous covers to storages ≤2 ha. The cover fabric must reduce light transmittance by 80%, to reduce evaporation by 71%. Ballasting, tethering, and removal during dry times limit the use of continuous floating covers to storages ≤2 ha, managed close to full capacity. Floating modules must cover 88% of the surface to reduce evaporation by 70%, limiting their use to storages of ≤5 ha. Monolayer application is more flexible, but smart product selection and automated application strategies are required to improve performance. The number of application sites required to achieve full surface coverage limits monolayer use to storages ≤100 ha. Higher rates of application and poor self-spreading may limit multimolecular films to storages ≤10 ha.
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Affiliation(s)
- Pamela Pittaway
- Centre for Agricultural Engineering, University of Southern Queensland, Toowoomba, Australia
| | - Michael Scobie
- Centre for Agricultural Engineering, University of Southern Queensland, Toowoomba, Australia
| | - Erik Schmidt
- Centre for Agricultural Engineering, University of Southern Queensland, Toowoomba, Australia
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Slaninova E, Obruca S, Kocherbitov V, Sedlacek P. On the bioprotective effects of 3-hydroxybutyrate: Thermodynamic study of binary 3HB-water systems. Biophys J 2023; 122:460-469. [PMID: 36617191 PMCID: PMC9941717 DOI: 10.1016/j.bpj.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/22/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Microorganisms must face various inconvenient conditions; therefore, they developed several approaches for protection. Such a strategy also involves the accumulation of compatible solutes, also called osmolytes. It has been proved that the monomer unit 3-hydroxybutyrate (3HB), which is present in sufficient concentration in poly(3-hydroxybutyrate) (PHB)-accumulating cells, serves as a chemical chaperone protecting enzymes against heat and oxidative stress and as a cryoprotectant for enzymes, bacterial cells, and yeast. The stress robustness of the cells is also strongly dependent on the behavior and state of intracellular water, especially during stress exposure. For a better understanding of the protective mechanism and effect of strongly hydrophilic 3HB in solutions at a wide range of temperatures, a binary phase diagram of system sodium 3HB (Na3HB)-water in equilibrium and the state diagrams showing the glass transitions in the system were constructed. To investigate the activity of water in various compositions of the Na3HB/water system, three experimental techniques have been used (dynamic water sorption analysis, water activity measurements, and sorption calorimetry). First, Na3HB proved its hydrophilic nature, which is very comparable with known compatible solutes (trehalose). Results of differential scanning calorimetry demonstrated that Na3HB is also highly effective in depressing the freezing point and generating a large amount of nonfrozen water (1.35 g of water per gram of Na3HB). Therefore, Na3HB represents a very effective cryoprotectant that can be widely used for numerous applications.
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Affiliation(s)
- Eva Slaninova
- Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Stanislav Obruca
- Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Vitaly Kocherbitov
- Biomedical Science, Faculty of Health & Society, Malmö University, Malmö, Sweden.
| | - Petr Sedlacek
- Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic.
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12
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Flow cytometry: a tool for understanding the behaviour of polyhydroxyalkanoate accumulators. Appl Microbiol Biotechnol 2023; 107:581-590. [PMID: 36525042 DOI: 10.1007/s00253-022-12318-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/23/2022]
Abstract
The use of mixed microbial cultures (MMCs) is seen as an attractive strategy for polyhydroxyalkanoate (PHA) production. In order to optimize the MMC-PHA production process, tools are required to improve our understanding of the physiological state of the PHA-storing microorganisms within the MMC. In the present study, we explored the use of flow cytometry to analyse the metabolic state and polyhydroxybutyrate (PHB) content of the microorganisms from an MMC-PHA production process. A sequencing batch reactor under a feast and famine regime was used to enrich an MMC with PHB-storing microorganisms. Interestingly, once the PHB-storing microorganisms are selected, the level of PHB accumulation depends largely on the metabolic state of these microorganisms and not exclusively on the consortium composition. These results demonstrate that flow cytometry is a powerful tool to help to understand the PHA storage response of an MMC-PHA production process. KEY POINTS: • Flow cytometry allows to measure PHB content and metabolic activity over time. • Microorganisms showing high PHB content also have high metabolic activity. • PHB producers with low metabolic activity show low PHB content.
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13
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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14
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From Organic Wastes and Hydrocarbons Pollutants to Polyhydroxyalkanoates: Bioconversion by Terrestrial and Marine Bacteria. SUSTAINABILITY 2022. [DOI: 10.3390/su14148241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The use of fossil-based plastics has become unsustainable because of the polluting production processes, difficulties for waste management sectors, and high environmental impact. Polyhydroxyalkanoates (PHA) are bio-based biodegradable polymers derived from renewable resources and synthesized by bacteria as intracellular energy and carbon storage materials under nutrients or oxygen limitation and through the optimization of cultivation conditions with both pure and mixed culture systems. The PHA properties are affected by the same principles of oil-derived polyolefins, with a broad range of compositions, due to the incorporation of different monomers into the polymer matrix. As a consequence, the properties of such materials are represented by a broad range depending on tunable PHA composition. Producing waste-derived PHA is technically feasible with mixed microbial cultures (MMC), since no sterilization is required; this technology may represent a solution for waste treatment and valorization, and it has recently been developed at the pilot scale level with different process configurations where aerobic microorganisms are usually subjected to a dynamic feeding regime for their selection and to a high organic load for the intracellular accumulation of PHA. In this review, we report on studies on terrestrial and marine bacteria PHA-producers. The available knowledge on PHA production from the use of different kinds of organic wastes, and otherwise, petroleum-polluted natural matrices coupling bioremediation treatment has been explored. The advancements in these areas have been significant; they generally concern the terrestrial environment, where pilot and industrial processes are already established. Recently, marine bacteria have also offered interesting perspectives due to their advantageous effects on production practices, which they can relieve several constraints. Studies on the use of hydrocarbons as carbon sources offer evidence for the feasibility of the bioconversion of fossil-derived plastics into bioplastics.
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15
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Müllerová L, Marková K, Obruča S, Mravec F. Use of Flavin-Related Cellular Autofluorescence to Monitor Processes in Microbial Biotechnology. Microorganisms 2022; 10:microorganisms10061179. [PMID: 35744697 PMCID: PMC9231254 DOI: 10.3390/microorganisms10061179] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Cellular autofluorescence is usually considered to be a negative phenomenon because it can affect the sensitivity of fluorescence microscopic or flow cytometric assays by interfering with the signal of various fluorescent probes. Nevertheless, in our work, we adopted a different approach, and green autofluorescence induced by flavins was used as a tool to monitor fermentation employing the bacterium Cupriavidus necator. The autofluorescence was used to distinguish microbial cells from abiotic particles in flow cytometry assays, and it was also used for the determination of viability or metabolic characteristics of the microbial cells. The analyses using two complementary techniques, namely fluorescence microscopy and flow cytometry, are simple and do not require labor sample preparation. Flavins and their autofluorescence can also be used in a combination with other fluorophores when the need for multi-parametrical analyses arises, but it is wise to use dyes that do not emit a green light in order to not interfere with flavins' emission band (500-550 nm).
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16
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Maheshwari N, Thakur IS, Srivastava S. Role of carbon-dioxide sequestering bacteria for clean air environment and prospective production of biomaterials: a sustainable approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:38950-38971. [PMID: 35304714 DOI: 10.1007/s11356-022-19393-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
The increase in demand of fossil fuel uses for developmental activity and manufacturing of goods have resulted a huge emission of global warming gases (GWGs) in the atmosphere. Among all GWGs, CO2 is the major contributor that inevitably causes global warming and climate change. Mitigation strategies like biological CO2 capture through sequestration and their storage into biological organic form are used to minimize the concentration of atmospheric CO2 with the goal to control climate change. Since increasing atmospheric CO2 level supports microbial growth and productivity thus microbial-based CO2 sequestration has remarkable advantages as compared to plant-based sequestration. This review focuses on CO2 sequestration mechanism in bacteria through different carbon fixation pathways, involved enzymes, their role in calcite, and other environmentally friendly biomaterials such as biofuel, bioplastic, and biosurfactant.
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Affiliation(s)
- Neha Maheshwari
- Amity School of Earth and Environmental Science, Amity University, Gurugram, Haryana, India
| | - Indu Shekhar Thakur
- Amity School of Earth and Environmental Science, Amity University, Gurugram, Haryana, India
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Shaili Srivastava
- Amity School of Earth and Environmental Science, Amity University, Gurugram, Haryana, India.
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17
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Digestibility Kinetics of Polyhydroxyalkanoate and Poly(butylene succinate-co-adipate) after In Vitro Fermentation in Rumen Fluid. Polymers (Basel) 2022; 14:polym14102103. [PMID: 35631985 PMCID: PMC9146987 DOI: 10.3390/polym14102103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Using polyhydroxyalkanoate (PHA) materials for ruminal boluses could allow for longer sustained release of drugs and hormones that would reduce administration time and unneeded animal discomfort caused by continuous administration. The objective of this study was to determine ruminal degradability and kinetics of biodegradable polymers and blends. A proprietary PHA-based polymer, poly(butylene succinate-co-adipate) (PBSA), PBSA:PHA melt blends, and forage controls were incubated in rumen fluid for up to 240 h. Mass loss was measured after each incubation time, and digestion kinetic parameters were estimated. Thermogravimetric, differential scanning calorimetry, and intrinsic viscosity analyses were conducted on incubated samples. Generally, across treatments, mass loss was significant by 96 h with a minimum increase of 0.25% compared to 0 h but did not change thereafter. Degradation kinetics demonstrated that polymer treatments were still in the exponential degradation phase at 240 h with a maximum disappearance rate of 0.0031 %/h. Melting temperature increased, onset thermal degradation temperature decreased, and intrinsic viscosity decreased with incubation time, indicating structural changes to the polymers. Based on these preliminary findings, the first stage of degradation occurs within 24 h and PHA degrades slowly. However, further ruminal degradation studies of biodegradable polymers are warranted to elucidate maximum degradation and its characteristics.
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18
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The role of polyhydroxyalkanoates in adaptation of Cupriavidus necator to osmotic pressure and high concentration of copper ions. Int J Biol Macromol 2022; 206:977-989. [PMID: 35314264 DOI: 10.1016/j.ijbiomac.2022.03.102] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/24/2022] [Accepted: 03/16/2022] [Indexed: 01/14/2023]
Abstract
Polyhydroxyalkanoates (PHA) are abundant microbial polyesters accumulated in the form of intracellular granules by numerous prokaryotes primarily as storage of carbon and energy. Apart from their storage function, the presence of PHA also enhances the robustness of the microbial cells against various stressors. In this work, we investigated the role of PHA in Cupriavidus necator, a model organism concerning PHA metabolism, for adaptation to osmotic pressure and copper ions. In long-term laboratory evolution experiments, the bacterial culture was cultivated in presence of elevated doses of sodium chloride or copper ions (incubations lasted 78 passages for Cu2+ and 68 passages for NaCl) and the evolved strains were compared with the wild-type strain in terms of growth and PHA production capacity, cell morphology (investigated by various electron microscopy techniques), activities of selected enzymes involved in PHA metabolism and other crucial metabolic pathways, the chemical composition of bacterial biomass (determined by infrared and Raman spectroscopy) and also considering robustness against various stressors. The results confirmed the important role of PHA metabolism for adaptation to both tested stressors.
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19
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Chin JHC, Samian MR, Normi YM. Characterization of polyhydroxyalkanoate production capacity, composition and weight synthesized by Burkholderia cepacia JC-1 from various carbon sources. Heliyon 2022; 8:e09174. [PMID: 35368536 PMCID: PMC8971576 DOI: 10.1016/j.heliyon.2022.e09174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/27/2021] [Accepted: 03/17/2022] [Indexed: 12/17/2022] Open
Abstract
Polyhydroxyalkanoates (PHA) are microbial polymers that have received widespread attention in recent decades as potential alternatives to some petrochemical-based plastics. However, widespread use of PHA is often impeded by its cost of production. Therefore, the search for and systematic investigation of versatile microbial PHA producers capable of using various carbon sources, even in the form of animal fats, for PHA biosynthesis is desirable. This study highlights the PHA production capacity, monomer composition and molecular weight synthesized by Burkholderia cepacia JC-1, a locally isolated strain from soil, from various carbon sources. In the category of simple sugars and plant oils, the use of glucose and palm oil at C:N ratio of 40 resulted in the highest accumulation of 52 wt% and 36 wt% poly(3-hydroxybutyrate) [P(3HB)] homopolymer and dry cell weight of 2.56 g/L and 3.17 g/L, respectively. Interestingly, B. cepacia JC-1 was able to directly utilize animal-derived lipid in the form of crude and extracted chicken fat, resulting in appreciable dry cell weight and PHA contents of up to 3.19 g/L and 47 wt% respectively, surpassing even that of palm oil in the group of triglycerides as substrates. The presence of antibiotics (streptomycin) in cultivation medium did not significantly affect cell growth and polymer production. The supply of sodium pentanoate as a co-substrate resulted in the incorporation of 3-hydroxyvalerate (3HV) monomer at fractions up to 37 mol%. The molecular weight of polymers produced from glucose, palm oil and chicken fat were in the range of 991–2118 kDa, higher than some reported studies involving native strains. The results from this study form an important basis for possible improvements in using B. cepacia JC-1 and crude chicken fats in solid form for PHA production in the future.
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Affiliation(s)
- Julian Hock-Chye Chin
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Mohd Razip Samian
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Bimolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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20
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Samadhiya K, Sangtani R, Nogueira R, Bala K. Insightful Advancement and Opportunities for Microbial Bioplastic Production. Front Microbiol 2022; 12:674864. [PMID: 35058887 PMCID: PMC8763809 DOI: 10.3389/fmicb.2021.674864] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 11/11/2021] [Indexed: 12/28/2022] Open
Abstract
Impetuous urbanization and population growth are driving increased demand for plastics to formulate impeccable industrial and biomedical commodities. The everlasting nature and excruciating waste management of petroleum-based plastics have catered to numerous challenges for the environment. However, just implementing various end-of-life management techniques for assimilation and recycling plastics is not a comprehensive remedy; instead, the extensive reliance on finite resources needs to be reduced for sustainable production and plastic product utilization. Microorganisms, such as bacteria and algae, are explored substantially for their bioplastic production repertoire, thus replacing fossil-based plastics sooner or later. Nevertheless, the utilization of pure microbial cultures has led to various operational and economical complications, opening the ventures for the usage of mixed microbial cultures (MMCs) consisting of bacteria and algae for sustainable production of bioplastic. The current review is primarily focuses on elaborating the bioplastic production capabilities of different bacterial and algal strains, followed by discussing the quintessence of MMCs. The present state-of-the-art of bioplastic, different types of bacterial bioplastic, microalgal biocomposites, operational factors influencing the quality and quantity of bioplastic precursors, embracing the potential of bacteria-algae consortia, and the current global status quo of bioplastic production has been summarized extensively.
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Affiliation(s)
- Kanchan Samadhiya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Rimjhim Sangtani
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Regina Nogueira
- Institute for Sanitary Engineering and Waste Management, Leibniz Universitaet Hannover, Hanover, Germany
| | - Kiran Bala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
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21
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Haloarchaea as emerging big players in future polyhydroxyalkanoate bioproduction: Review of trends and perspectives. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Manzoni S, Ding Y, Warren C, Banfield CC, Dippold MA, Mason-Jones K. Intracellular Storage Reduces Stoichiometric Imbalances in Soil Microbial Biomass – A Theoretical Exploration. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.714134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Microbial intracellular storage is key to defining microbial resource use strategies and could contribute to carbon (C) and nutrient cycling. However, little attention has been devoted to the role of intracellular storage in soil processes, in particular from a theoretical perspective. Here we fill this gap by integrating intracellular storage dynamics into a microbially explicit soil C and nutrient cycling model. Two ecologically relevant modes of storage are considered: reserve storage, in which elements are routed to a storage compartment in proportion to their uptake rate, and surplus storage, in which elements in excess of microbial stoichiometric requirements are stored and limiting elements are remobilized from storage to fuel growth and microbial maintenance. Our aim is to explore with this model how these different storage modes affect the retention of C and nutrients in active microbial biomass under idealized conditions mimicking a substrate pulse experiment. As a case study, we describe C and phosphorus (P) dynamics using literature data to estimate model parameters. Both storage modes enhance the retention of elements in microbial biomass, but the surplus storage mode is more effective to selectively store or remobilize C and nutrients according to microbial needs. Enhancement of microbial growth by both storage modes is largest when the substrate C:nutrient ratio is high (causing nutrient limitation after substrate addition) and the amount of added substrate is large. Moreover, storage increases biomass nutrient retention and growth more effectively when resources are supplied in a few large pulses compared to several smaller pulses (mimicking a nearly constant supply), which suggests storage to be particularly relevant in highly dynamic soil microhabitats. Overall, our results indicate that storage dynamics are most important under conditions of strong stoichiometric imbalance and may be of high ecological relevance in soil environments experiencing large variations in C and nutrient supply.
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23
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Mieszkin S, Pouder E, Uroz S, Simon-Colin C, Alain K. Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate. Microorganisms 2021; 9:microorganisms9102053. [PMID: 34683374 PMCID: PMC8537097 DOI: 10.3390/microorganisms9102053] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 12/02/2022] Open
Abstract
Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).
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Affiliation(s)
- Sophie Mieszkin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
- Correspondence:
| | - Eva Pouder
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Stéphane Uroz
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
| | - Christelle Simon-Colin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
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24
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Paredes GF, Viehboeck T, Lee R, Palatinszky M, Mausz MA, Reipert S, Schintlmeister A, Maier A, Volland JM, Hirschfeld C, Wagner M, Berry D, Markert S, Bulgheresi S, König L. Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces. mSystems 2021; 6:e0118620. [PMID: 34058098 PMCID: PMC8269255 DOI: 10.1128/msystems.01186-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.
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Affiliation(s)
- Gabriela F. Paredes
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Tobias Viehboeck
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Raymond Lee
- Washington State University, School of Biological Sciences, Pullman, Washington, USA
| | - Marton Palatinszky
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Michaela A. Mausz
- University of Warwick, School of Life Sciences, Coventry, United Kingdom
| | - Siegfried Reipert
- University of Vienna, Core Facility Cell Imaging and Ultrastructure Research, Vienna, Austria
| | - Arno Schintlmeister
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- University of Vienna, Center for Microbiology and Environmental Systems Science, Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Vienna, Austria
| | - Andreas Maier
- University of Vienna, Faculty of Geosciences, Geography, and Astronomy, Department of Geography and Regional Research, Geoecology, Vienna, Austria
| | - Jean-Marie Volland
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Claudia Hirschfeld
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Michael Wagner
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Aalborg University, Department of Chemistry and Bioscience, Aalborg, Denmark
| | - David Berry
- University of Vienna, Center for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Stephanie Markert
- University of Greifswald, Institute of Pharmacy, Department of Pharmaceutical Biotechnology, Greifswald, Germany
| | - Silvia Bulgheresi
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
| | - Lena König
- University of Vienna, Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, Vienna, Austria
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25
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Microbial cell factories for the production of polyhydroxyalkanoates. Essays Biochem 2021; 65:337-353. [PMID: 34132340 DOI: 10.1042/ebc20200142] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/14/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022]
Abstract
Pollution caused by persistent petro-plastics is the most pressing problem currently, with 8 million tons of plastic waste dumped annually in the oceans. Plastic waste management is not systematized in many countries, because it is laborious and expensive with secondary pollution hazards. Bioplastics, synthesized by microorganisms, are viable alternatives to petrochemical-based thermoplastics due to their biodegradable nature. Polyhydroxyalkanoates (PHAs) are a structurally and functionally diverse group of storage polymers synthesized by many microorganisms, including bacteria and Archaea. Some of the most important PHA accumulating bacteria include Cupriavidus necator, Burkholderia sacchari, Pseudomonas sp., Bacillus sp., recombinant Escherichia coli, and certain halophilic extremophiles. PHAs are synthesized by specialized PHA polymerases with assorted monomers derived from the cellular metabolite pool. In the natural cycle of cellular growth, PHAs are depolymerized by the native host for carbon and energy. The presence of these microbial PHA depolymerases in natural niches is responsible for the degradation of bioplastics. Polyhydroxybutyrate (PHB) is the most common PHA with desirable thermoplastic-like properties. PHAs have widespread applications in various industries including biomedicine, fine chemicals production, drug delivery, packaging, and agriculture. This review provides the updated knowledge on the metabolic pathways for PHAs synthesis in bacteria, and the major microbial hosts for PHAs production. Yeasts are presented as a potential candidate for industrial PHAs production, with their high amenability to genetic engineering and the availability of industrial-scale technology. The major bottlenecks in the commercialization of PHAs as an alternative for plastics and future perspectives are also critically discussed.
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Grillo-Puertas M, Villegas JM, Pankievicz VCS, Tadra-Sfeir MZ, Teles Mota FJ, Hebert EM, Brusamarello-Santos L, Pedraza RO, Pedrosa FO, Rapisarda VA, Souza EM. Transcriptional Responses of Herbaspirillum seropedicae to Environmental Phosphate Concentration. Front Microbiol 2021; 12:666277. [PMID: 34177845 PMCID: PMC8222739 DOI: 10.3389/fmicb.2021.666277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/29/2021] [Indexed: 12/02/2022] Open
Abstract
Herbaspirillum seropedicae is a nitrogen-fixing endophytic bacterium associated with important cereal crops, which promotes plant growth, increasing their productivity. The understanding of the physiological responses of this bacterium to different concentrations of prevailing nutrients as phosphate (Pi) is scarce. In some bacteria, culture media Pi concentration modulates the levels of intracellular polyphosphate (polyP), modifying their cellular fitness. Here, global changes of H. seropedicae SmR1 were evaluated in response to environmental Pi concentrations, based on differential intracellular polyP levels. Cells grown in high-Pi medium (50 mM) maintained high polyP levels in stationary phase, while those grown in sufficient Pi medium (5 mM) degraded it. Through a RNA-seq approach, comparison of transcriptional profiles of H. seropedicae cultures revealed that 670 genes were differentially expressed between both Pi growth conditions, with 57% repressed and 43% induced in the high Pi condition. Molecular and physiological analyses revealed that aspects related to Pi metabolism, biosynthesis of flagella and chemotaxis, energy production, and polyhydroxybutyrate metabolism were induced in the high-Pi condition, while those involved in adhesion and stress response were repressed. The present study demonstrated that variations in environmental Pi concentration affect H. seropedicae traits related to survival and other important physiological characteristics. Since environmental conditions can influence the effectiveness of the plant growth-promoting bacteria, enhancement of bacterial robustness to withstand different stressful situations is an interesting challenge. The obtained data could serve not only to understand the bacterial behavior in respect to changes in rhizospheric Pi gradients but also as a base to design strategies to improve different bacterial features focusing on biotechnological and/or agricultural purposes.
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Affiliation(s)
- Mariana Grillo-Puertas
- Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT) and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Josefina M. Villegas
- Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT) and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Vânia C. S. Pankievicz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Michelle Z. Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Francisco J. Teles Mota
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Elvira M. Hebert
- Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | | | - Raul O. Pedraza
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán (UNT), San Miguel de Tucumán, Argentina
| | - Fabio O. Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Viviana A. Rapisarda
- Instituto de Química Biológica, “Dr. Bernabé Bloj”, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán (UNT) and Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Emanuel M. Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
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Ghergab A, Mohanan N, Saliga G, Brassinga AKC, Levin D, de Kievit T. The effect of polyhydroxyalkanoates in Pseudomonas chlororaphis PA23 biofilm formation, stress endurance, and interaction with the protozoan predator Acanthamoeba castellanii. Can J Microbiol 2021; 67:476-490. [PMID: 34057367 DOI: 10.1139/cjm-2020-0497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pseudomonas chlororaphis PA23 is a biocontrol agent capable of protecting canola against the fungal pathogen Sclerotinia sclerotiorum. In addition to producing antifungal compounds, this bacterium synthesizes and accumulates polyhydroxyalkanoate (PHA) polymers as carbon and energy storage compounds. Because the role of PHA in PA23 physiology is currently unknown, we investigated the impact of this polymer on stress resistance, adherence to surfaces, and interaction with the protozoan predator Acanthamoeba castellanii. Three PHA biosynthesis mutants were created, PA23phaC1, PA23phaC1ZC2, and PA23phaC1ZC2D, which accumulated reduced PHA. Our phenotypic assays revealed that PA23phaC1ZC2D produced less phenazine (PHZ) compared with the wild type (WT) and the phaC1 and phaC1ZC2 mutants. All three mutants exhibited enhanced sensitivity to UV irradiation, starvation, heat stress, cold stress, and hydrogen peroxide. Moreover, motility, exopolysaccharide production, biofilm formation, and root attachment were increased in strains with reduced PHA levels. Interaction studies with the amoeba A. castellanii revealed that the WT and the phaC1 and phaC1ZC2 mutants were consumed less than the phaC1ZC2D mutant, likely due to decreased PHZ production by the latter. Collectively these findings indicate that PHA accumulation enhances PA23 resistance to a number of stresses in vitro, which could improve the environmental fitness of this bacterium in hostile environments.
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Affiliation(s)
- Akrm Ghergab
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Grace Saliga
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - David Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Teresa de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Clavero-León C, Ruiz D, Cillero J, Orlando J, González B. The multi metal-resistant bacterium Cupriavidus metallidurans CH34 affects growth and metal mobilization in Arabidopsis thaliana plants exposed to copper. PeerJ 2021; 9:e11373. [PMID: 34040892 PMCID: PMC8127957 DOI: 10.7717/peerj.11373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 04/07/2021] [Indexed: 11/20/2022] Open
Abstract
Copper (Cu) is important for plant growth, but high concentrations can lead to detrimental effects such as primary root length inhibition, vegetative tissue chlorosis, and even plant death. The interaction between plant-soil microbiota and roots can potentially affect metal mobility and availability, and, therefore, overall plant metal concentration. Cupriavidus metallidurans CH34 is a multi metal-resistant bacterial model that alters metal mobility and bioavailability through ion pumping, metal complexation, and reduction processes. The interactions between strain CH34 and plants may affect the growth, metal uptake, and translocation of Arabidopsis thaliana plants that are exposed to or not exposed to Cu. In this study, we looked also at the specific gene expression changes in C. metallidurans when co-cultured with Cu-exposed A. thaliana. We found that A. thaliana’s rosette area, primary and secondary root growth, and dry weight were affected by strain CH34, and that beneficial or detrimental effects depended on Cu concentration. An increase in some plant growth parameters was observed at copper concentrations lower than 50 µM and significant detrimental effects were found at concentrations higher than 50 µM Cu. We also observed up to a 90% increase and 60% decrease in metal accumulation and mobilization in inoculated A. thaliana. In turn, copper-stressed A. thaliana altered C. metallidurans colonization, and cop genes that encoded copper resistance in strain CH34 were induced by the combination of A. thaliana and Cu. These results reveal the complexity of the plant-bacteria-metal triad and will contribute to our understanding of their applications in plant growth promotion, protection, and phytoremediation strategies.
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Affiliation(s)
- Claudia Clavero-León
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Daniela Ruiz
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Javier Cillero
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,(CAPES), Center of Applied Ecology and Sustainability, Santiago, Chile
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29
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Raturi G, Shree S, Sharma A, Panesar PS, Goswami S. Recent approaches for enhanced production of microbial polyhydroxybutyrate: Preparation of biocomposites and applications. Int J Biol Macromol 2021; 182:1650-1669. [PMID: 33992649 DOI: 10.1016/j.ijbiomac.2021.05.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022]
Abstract
In modern decades, an increase in environmental awareness has attracted the keen interest of researchers to investigate eco-sustainable, recyclable materials to minimize reliance on petroleum-based polymeric compounds. Poly (3-hydroxybutyrate) is amorphous, linear, and biodegradable bacterial polyesters that belong to the polyhydroxyalkanoates family with enormous applications in many fields. The present review provides comprehensive information on polyhydroxybutyrate production from different biomass feedstock. Various studies on PHB production by genetically engineered bacterial cells and optimization of parameters have been discussed. Recent technological innovation in processing polyhydroxybutyrate-based biocomposite through the different process has also been examined. Besides this, the potential applications of the derived competent biocomposites in the other fields have been depicted.
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Affiliation(s)
- Gaurav Raturi
- Department of Agri-Biotechnology, National Agri-food Biotechnology Institute, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Shweta Shree
- Department of Biotechnology, Texas A&M University, USA
| | - Amita Sharma
- Department of Chemical Engineering, Centre of Innovative and Applied Bioprocessing, Knowledge City, Sector-81, Mohali, Punjab 140306, India
| | - Parmjit S Panesar
- Department of Food Engineering and Technology, Sant Longowal Institute of Engineering and Technology, Longowal 148106, Punjab, India
| | - Saswata Goswami
- Department of Chemical Engineering, Centre of Innovative and Applied Bioprocessing, Knowledge City, Sector-81, Mohali, Punjab 140306, India.
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30
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Tugarova AV, Dyatlova YA, Kenzhegulov OA, Kamnev AA. Poly-3-hydroxybutyrate synthesis by different Azospirillum brasilense strains under varying nitrogen deficiency: A comparative in-situ FTIR spectroscopic analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 252:119458. [PMID: 33601223 DOI: 10.1016/j.saa.2021.119458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/23/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Monitoring of poly-3-hydroxybutyrate accumulation and changes in its relative contents in biomass of the plant-growth-promoting bacteria Azospirillum brasilense (strains Sp7, Cd and Sp245) was performed during aerobic cultivation for 1 to 8 days at various initial concentrations of bound nitrogen (0.1 to 0.5 g∙L-1 NH4Cl) in the culture medium using in-situ transmission FTIR spectroscopy. A methodology has been proposed based on calculating band areas in FTIR spectra (instead of band intensities commonly used earlier) for determining relative contents of PHB in dry bacterial biomass, using the ester ν(C=O) band as a PHB marker (in the region 1750-1720 cm-1) and amide II band of cellular proteins (at ca. 1540 cm-1). Differences in PHB accumulation levels and their changes in the course of cultivation under various trophic stress for the three strains are discussed in relation to their different ecological niches which they occupy in the rhizosphere.
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Affiliation(s)
- Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Yulia A Dyatlova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Odissey A Kenzhegulov
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia
| | - Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prosp. Entuziastov, 410049 Saratov, Russia.
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31
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Di Caprio F. A fattening factor to quantify the accumulation ability of microorganisms under N-starvation. N Biotechnol 2021; 66:70-78. [PMID: 33862285 DOI: 10.1016/j.nbt.2021.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 04/06/2021] [Accepted: 04/10/2021] [Indexed: 01/04/2023]
Abstract
Many microorganisms can accumulate biomass in the form of lipids and polysaccharides, which can be used for biofuels, bioplastics, food and feed. Some innovative bioprocesses exploit the competitive advantage provided by such accumulation ability, mainly under N-starvation, to select high-accumulating strains against biological contaminants, by using uncoupled nutrient feeding. However, there is no general and easily comparable parameter available to compare biomass accumulation ability among different microbial strains, which could measure the competitive advantage. Here, a parameter termed "fattening factor" (ηx) is described to quantify such strain-specific biomass accumulation ability in bacteria, yeasts and microalgae. This parameter measures how many fold a microbial population can increase its biomass just as the result of accumulation. It is derived from considerations about the main metabolic aspects of cells' response to N-starvation, which induces variations in cell cycle, biomass production and biochemical composition. The fattening factor described here should be easily estimatable in N-starvation for every culturable microbial strain, by measuring the amount of accumulated biomass.
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Affiliation(s)
- Fabrizio Di Caprio
- Department of Chemistry, University Sapienza of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
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Di Caprio F. Cultivation processes to select microorganisms with high accumulation ability. Biotechnol Adv 2021; 49:107740. [PMID: 33838283 DOI: 10.1016/j.biotechadv.2021.107740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/26/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
The microbial ability to accumulate biomolecules is fundamental for different biotechnological applications aiming at the production of biofuels, food and bioplastics. However, high accumulation is a selective advantage only under certain stressful conditions, such as nutrient depletion, characterized by lower growth rate. Conventional bioprocesses maintain an optimal and stable environment for large part of the cultivation, that doesn't reward cells for their accumulation ability, raising the risk of selection of contaminant strains with higher growth rate, but lower accumulation of products. Here in this work the physiological responses of different microorganisms (microalgae, bacteria, yeasts) under N-starvation and energy starvation are reviewed, with the aim to furnish relevant insights exploitable to develop tailored bioprocesses to select specific strains for their higher accumulation ability. Microorganism responses to starvation are reviewed focusing on cell cycle, biomass production and variations in biochemical composition. Then, the work describes different innovative bioprocess configurations exploiting uncoupled nutrient feeding strategies (feast-famine), tailored to maintain a selective pressure to reward the strains with higher accumulation ability in mixed microbial populations. Finally, the main models developed in recent studies to describe and predict microbial growth and intracellular accumulation upon N-starvation and feast-famine conditions have been reviewed.
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Affiliation(s)
- Fabrizio Di Caprio
- Department of Chemistry, University Sapienza of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
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Optimization of the culture conditions for production of Polyhydroxyalkanoate and its characterization from a new Bacillus cereus sp. BNPI-92 strain, isolated from plastic waste dumping yard. Int J Biol Macromol 2020; 156:1064-1080. [DOI: 10.1016/j.ijbiomac.2019.11.138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 11/20/2022]
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34
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Rogala MM, Gawor J, Gromadka R, Kowalczyk M, Grzesiak J. Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods. Genes (Basel) 2020; 11:genes11080873. [PMID: 32752049 PMCID: PMC7464897 DOI: 10.3390/genes11080873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 01/31/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red–PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the Comamonadaceae family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, Microbacteriaceae and Micrococcaceae also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.
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Affiliation(s)
- Małgorzata Marta Rogala
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5A, 02-106 Warszawa, Poland;
| | - Jan Gawor
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland; (J.G.); (R.G.)
| | - Magdalena Kowalczyk
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5A, 02-106 Warszawa, Poland;
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5A, 02-106 Warszawa, Poland;
- Correspondence:
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35
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Mohanan N, Gislason A, Sharma PK, Ghergab A, Plouffe J, Levin DB, de Kievit T. Quorum sensing and the anaerobic regulator (ANR) control polyhydroxyalkanoate (PHA) production in Pseudomonas chlororaphis PA23. FEMS Microbiol Lett 2020; 366:5613363. [PMID: 31688920 DOI: 10.1093/femsle/fnz223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/31/2019] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas chlororaphis PA23 is a biocontrol agent that, in addition to producing antifungal compounds, synthesizes polyhydroxyalkanoate (PHA) polymers as a carbon and energy sink. Quorum sensing (QS) and the anaerobic regulator (ANR) are required for PA23-mediated fungal suppression; however, the role of these regulators in PHA production is unknown. Strains lacking either QS or ANR accumulated less PHA polymers when propagated on Ramsay's minimal medium (RMM) with glucose or octanoate as the carbon source. In the acyl-homoserine lactone (AHL)-deficient background, all six of the genes in the pha locus (phaC1, phaC2, phaZ, phaD, phaF, phaI) showed reduced expression in RMM glucose, and all except phaC2 were repressed in RMM octanoate. Although changes in gene activity were observed in the anr mutant, they were less pronounced. Analysis of the promoter regions for QS- and ANR-binding consensus sequences revealed putative phzboxes upstream of phaZ and phaI, but no anr boxes were identified. Our findings indicate that altered pha gene expression likely contributes to the lower PHA accumulation in the QS- and ANR-deficient strains, which may be in part indirectly mediated. This study is the first to show that mcl-PHA production is under QS and ANR control.
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Affiliation(s)
- Nisha Mohanan
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - April Gislason
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Parveen K Sharma
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Akrm Ghergab
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Jocelyn Plouffe
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
| | - Teresa de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 5V6, Canada
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36
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Novel unexpected functions of PHA granules. Appl Microbiol Biotechnol 2020; 104:4795-4810. [PMID: 32303817 DOI: 10.1007/s00253-020-10568-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/10/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
Polyhydroxyalkanoates (PHA), polyesters accumulated by numerous prokaryotes in the form of intracellular granules, have been for decades considered being predominantly storage molecules. However, numerous recent discoveries revealed and emphasized their complex biological role for microbial cells. Most of all, it was repeatedly reported and confirmed that the presence of PHA granules in prokaryotic cells enhances stress resistance and robustness of microbes against various environmental stress factors such as high or low temperature, freezing, oxidative, and osmotic pressure. It seems that protective mechanisms of PHA granules are associated with their extraordinary architecture and biophysical properties as well as with the complex and deeply interconnected nature of PHA metabolism. Therefore, this review aims at describing novel and unexpected properties of PHA granules with respect to their contribution to stress tolerance of various prokaryotes including common mesophilic heterotrophic bacteria, but also extremophiles or photo-autotrophic cyanobacteria. KEY POINTS: • PHA granules present in bacterial cells reveal unique properties and functions. • PHA enhances stress robustness of bacterial cells.
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37
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Wang X, Tang D, Wang W. Adaptation strategies of
Pseudomonas protegens
SN15‐2 to hyperosmotic growth environment. J Appl Microbiol 2020; 128:1720-1734. [DOI: 10.1111/jam.14582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/02/2020] [Accepted: 01/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- X. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - D. Tang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
| | - W. Wang
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology Shanghai China
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Kumar V, Kumar S, Singh D. Microbial polyhydroxyalkanoates from extreme niches: Bioprospection status, opportunities and challenges. Int J Biol Macromol 2019; 147:1255-1267. [PMID: 31739043 DOI: 10.1016/j.ijbiomac.2019.09.253] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/23/2019] [Accepted: 09/30/2019] [Indexed: 01/20/2023]
Abstract
Extreme niches are offered with unusual physiochemical conditions that impose stress to the life-forms including microbial communities. Microbes have evolved unique physiology and genetics to interact dynamically with extreme environments for their adaptation and survival. Amongst the several adaptive features of microbes in stressed conditions, polyhydroxyalkanoates synthesis is a crucial strategy of many bacteria and archaea to reserve carbon and energy inside the cell. Apart from the relevance of PHA to microbial world, these intracellular polyesters are seen as essential biological macromolecules for the bio-material industry owing to their plastic-like properties, biodegradable and eco-friendly nature. Recently, much attention has been attracted by the microbes of extreme habitats for a new source of industrially suited PHA producers and novel PHA with unique properties. Therefore, the current review is focused on the critical evaluation of microbes from extreme niches for PHA production and opportunities for the development of commercially feasible PHA bioprocess.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176 061, India.
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Production of Polyhydroxyalkanoates and Extracellular Products Using Pseudomonas Corrugata and P. Mediterranea: A Review. Bioengineering (Basel) 2019; 6:bioengineering6040105. [PMID: 31739507 PMCID: PMC6955742 DOI: 10.3390/bioengineering6040105] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 11/16/2022] Open
Abstract
Some strains of Pseudomonas corrugata (Pco) and P. mediterranea (Pme) efficiently synthesize medium-chain-length polyhydroxyalkanoates elastomers (mcl-PHA) and extracellular products on related and unrelated carbon sources. Yield and composition are dependent on the strain, carbon source, fermentation process, and any additives. Selected Pco strains produce amorphous and sticky mcl-PHA, whereas strains of Pme produce, on high grade and partially refined biodiesel glycerol, a distinctive filmable PHA, very different from the conventional microbial mcl-PHA, suitable for making blends with polylactide acid. However, the yields still need to be improved and production costs lowered. An integrated process has been developed to recover intracellular mcl-PHA and extracellular bioactive molecules. Transcriptional regulation studies during PHA production contribute to understanding the metabolic potential of Pco and Pme strains. Data available suggest that pha biosynthesis genes and their regulations will be helpful to develop new, integrated strategies for cost-effective production.
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40
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Wang J, Hua M, Li Y, Ma F, Zheng P, Hu B. Achieving high nitrogen removal efficiency by optimizing nitrite-dependent anaerobic methane oxidation process with growth factors. WATER RESEARCH 2019; 161:35-42. [PMID: 31176104 DOI: 10.1016/j.watres.2019.05.101] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/05/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a newly discovered bioprocess which uses methane as electron donor to reduce nitrite into dinitrogen. It is a promising clean bioprocess for denitrification in wastewater treatment. However, the low reaction rate and slow growth rate of N-DAMO bacteria within NC10 phylum limit the application of the process. In this study, we chose vitamin, heme, nucleobase and betaine to investigate their short- and long-term effects on N-DAMO bacteria. The concentrations of the growth factors of medium were improved according to the short-term experiments. The results were subsequently verified via long-term inoculations and were applied in a magnetically stirred gas lift reactor (MSGLR). The results indicated that nucleobase and betaine (5.0 and 200 μg L-1, respectively) significantly stimulated the N-DAMO activity, whereas vitamin and heme had no significant effects in the tested concentration ranges. During the long-term incubation, N-DAMO bacteria continuously increased and finally achieved a relative abundance of 14.4% on day 300. Notably, larger aggregates of N-DAMO bacteria were observed at the end of the long-term incubation. And the nitrogen removal rate of the MSGLR increased to 70 mg N L-1 day-1, with the total nitrogen removal efficiency over 99.0%. However, the addition of betaine introduced methyl into the reactors and this made methylotrophs account a considerable part of the bacterial community, which limited the enrichment degree of N-DAMO bacteria. This work will contribute to the engineering application and enrichment of N-DAMO bacteria.
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Affiliation(s)
- Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Miaolian Hua
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Yufen Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, 310058, China.
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Mason-Jones K, Banfield CC, Dippold MA. Compound-specific 13 C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:795-802. [PMID: 30719792 DOI: 10.1002/rcm.8407] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/27/2019] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Many bacteria synthesize carbon (C) and energy storage compounds, including water-insoluble polyester lipids composed mainly or entirely of poly(3-hydroxybutyrate) (PHB). Despite the potential significance of C and energy storage for microbial life and C cycling, few measurements of PHB in soil have been reported. METHODS A new protocol was implemented, based on an earlier sediment extraction and derivatization procedure, with quantification by gas chromatography/mass spectrometry (GC/MS) and 13 C-isotopic analysis by GC/combustion/isotope ratio mass spectrometry (GC/C/IRMS). RESULTS The PHB content was 4.3 μg C g-1 in an agricultural soil and 1.2 μg C g-1 in a forest topsoil. This was an order of magnitude more PHB than obtained by the existing extraction method, suggesting that native PHB in soil has been previously underestimated. Addition of glucose increased the PHB content by 135% and 1,215% over 5 days, with the largest increase in the relatively nutrient-poor forest soil. In the agricultural soil, 68% of the increase was derived from added 13 C-labeled glucose, confirming synthesis of PHB from glucose for the first time in soil. CONCLUSIONS The presence and responsiveness of PHB in both these contrasting soils show that PHB could provide a useful indicator of bacterial nutritional status and unbalanced growth. Microbial storage could be important to C and nutrient cycling and be a widespread strategy in the life of soil bacteria. The presented method offers new insight into the significance of this compound in soil.
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Affiliation(s)
- Kyle Mason-Jones
- Agricultural Soil Science, University of Goettingen, Büsgenweg 2, 37077, Goettingen, Germany
| | - Callum C Banfield
- Biogeochemistry of Agroecosystems, University of Goettingen, Büsgenweg 2, 37077, Goettingen, Germany
| | - Michaela A Dippold
- Biogeochemistry of Agroecosystems, University of Goettingen, Büsgenweg 2, 37077, Goettingen, Germany
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42
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Bradley JA, Amend JP, LaRowe DE. Survival of the fewest: Microbial dormancy and maintenance in marine sediments through deep time. GEOBIOLOGY 2019; 17:43-59. [PMID: 30248245 PMCID: PMC6585783 DOI: 10.1111/gbi.12313] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/17/2018] [Accepted: 08/21/2018] [Indexed: 06/01/2023]
Abstract
Microorganisms buried in marine sediments are known to endure starvation over geologic timescales. However, the mechanisms of how these microorganisms cope with prolonged energy limitation is unknown and therefore yet to be captured in a quantitative framework. Here, we present a novel mathematical model that considers (a) the physiological transitions between the active and dormant states of microorganisms, (b) the varying requirement for maintenance power between these phases, and (c) flexibility in the provenance (i.e., source) of energy from exogenous and endogenous catabolism. The model is applied to sediments underlying the oligotrophic South Pacific Gyre where microorganisms endure ultra-low fluxes of energy for tens of millions of years. Good fits between model simulations and measurements of cellular carbon and organic carbon concentrations are obtained and are interpreted as follows: (a) the unfavourable microbial habitat in South Pacific Gyre sediments triggers rapid mortality and a transition to dormancy; (b) there is minimal biomass growth, and organic carbon consumption is dominated by catabolism to support maintenance activities rather than new biomass synthesis; (c) the amount of organic carbon that microorganisms consume for maintenance activities is equivalent to approximately 2% of their carbon biomass per year; and (d) microorganisms must rely solely on exogenous rather than endogenous catabolism to persist in South Pacific Gyre sediments over long timescales. This leads us to the conclusion that under oligotrophic conditions, the fitness of an organism is determined by its ability to simply stay alive, rather than to grow. This modelling framework is designed to be flexible for application to other sites and habitats, and thus serves as a new quantitative tool for determining the habitability of and an ultimate limit for life in any environment.
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Affiliation(s)
- James A. Bradley
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Jan P. Amend
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
- Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Douglas E. LaRowe
- Department of Earth SciencesUniversity of Southern CaliforniaLos AngelesCalifornia
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Muller KE, Denison RF. Resource acquisition and allocation traits in symbiotic rhizobia with implications for life-history outside of legume hosts. ROYAL SOCIETY OPEN SCIENCE 2018; 5:181124. [PMID: 30662731 PMCID: PMC6304121 DOI: 10.1098/rsos.181124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/13/2018] [Indexed: 05/07/2023]
Abstract
Resources that microbial symbionts obtain from hosts may enhance fitness during free-living stages when resources are comparatively scarce. For rhizobia in legume root nodules, diverting resources from nitrogen fixation to polyhydroxybutyrate (PHB) has been discussed as a source of host-symbiont conflict. Yet, little is known about natural variation in PHB storage and its implications for rhizobial evolution. We therefore measured phenotypic variation in natural rhizobia populations and investigated how PHB might contribute to fitness in the free-living stage. We found that natural populations of rhizobia from Glycine max and Chamaecrista fasciculata had substantial, heritable variation in PHB acquisition during symbiosis. A model simulating temperature-dependent metabolic activity showed that the observed range of stored PHB per cell could support survival for a few days, for active cells, or over a century for sufficiently dormant cells. Experiments with field-isolated Bradyrhizobium in starvation culture suggest PHB is partitioned asymmetrically in dividing cells, consistent with individual-level bet-hedging previously demonstrated in E. meliloti. High-PHB isolates used more PHB over the first month, yet still retained more PHB for potential long-term survival in a dormant state. These results suggest that stored resources like PHB may support both short-term and long-term functions that contribute to fitness in the free-living stage.
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Affiliation(s)
- Katherine E. Muller
- Graduate Program in Plant and Microbial Biology, University of Minnesota, St Paul, MN 55108, USA
| | - R. Ford Denison
- Department of Ecology Evolution and Behavior, University of Minnesota, St Paul, MN, USA
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44
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Kuang S, Fan X, Peng R. Quantitative proteomic analysis ofRhodococcus ruberresponsive to organic solvents. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1533432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sufang Kuang
- Department of Bioengineering, College of Life Science, Jiangxi Normal University, Nanchang, PR China
| | - Xin Fan
- Department of Bioengineering, College of Life Science, Jiangxi Normal University, Nanchang, PR China
| | - Ren Peng
- Department of Bioengineering, College of Life Science, Jiangxi Normal University, Nanchang, PR China
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45
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Martínez-Gutiérrez CA, Latisnere-Barragán H, García-Maldonado JQ, López-Cortés A. Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. PeerJ 2018; 6:e4780. [PMID: 29761063 PMCID: PMC5944434 DOI: 10.7717/peerj.4780] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/23/2018] [Indexed: 11/20/2022] Open
Abstract
Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.
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Affiliation(s)
- Carolina A Martínez-Gutiérrez
- Laboratorio de Geomicrobiología y Biotecnología, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - Hever Latisnere-Barragán
- Laboratorio de Geomicrobiología y Biotecnología, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Alejandro López-Cortés
- Laboratorio de Geomicrobiología y Biotecnología, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
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Involvement of polyhydroxyalkanoates in stress resistance of microbial cells: Biotechnological consequences and applications. Biotechnol Adv 2018; 36:856-870. [DOI: 10.1016/j.biotechadv.2017.12.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/24/2017] [Accepted: 12/12/2017] [Indexed: 01/30/2023]
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47
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Al Rowaihi IS, Paillier A, Rasul S, Karan R, Grötzinger SW, Takanabe K, Eppinger J. Poly(3-hydroxybutyrate) production in an integrated electromicrobial setup: Investigation under stress-inducing conditions. PLoS One 2018; 13:e0196079. [PMID: 29698424 PMCID: PMC5919402 DOI: 10.1371/journal.pone.0196079] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/05/2018] [Indexed: 11/19/2022] Open
Abstract
Poly(3-hydroxybutyrate) (PHB), a biodegradable polymer, can be produced by different microorganisms. The PHB belongs to the family of polyhydroxyalkanoate (PHA) that mostly accumulates as a granule in the cytoplasm of microorganisms to store carbon and energy. In this study, we established an integrated one-pot electromicrobial setup in which carbon dioxide is reduced to formate electrochemically, followed by sequential microbial conversion into PHB, using the two model strains, Methylobacterium extorquens AM1 and Cupriavidus necator H16. This setup allows to investigate the influence of different stress conditions, such as coexisting electrolysis, relatively high salinity, nutrient limitation, and starvation, on the production of PHB. The overall PHB production efficiency was analyzed in reasonably short reaction cycles typically as short as 8 h. As a result, the PHB formation was detected with C. necator H16 as a biocatalyst only when the electrolysis was operated in the same solution. The specificity of the source of PHB production is discussed, such as salinity, electricity, concurrent hydrogen production, and the possible involvement of reactive oxygen species (ROS).
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Affiliation(s)
- Israa Salem Al Rowaihi
- King Abdullah University of Science and Technology, KAUST Catalysis Center, Physical Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Alexis Paillier
- King Abdullah University of Science and Technology, KAUST Catalysis Center, Physical Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Shahid Rasul
- King Abdullah University of Science and Technology, KAUST Catalysis Center, Physical Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Ram Karan
- King Abdullah University of Science and Technology, KAUST Catalysis Center, Physical Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Stefan Wolfgang Grötzinger
- Technical University of Munich, Department of Mechanical Engineering, Institute of Biochemical Engineering, Garching, Germany
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Kazuhiro Takanabe
- King Abdullah University of Science and Technology, KAUST Catalysis Center, Physical Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
| | - Jörg Eppinger
- King Abdullah University of Science and Technology, KAUST Catalysis Center, Physical Sciences and Engineering Division, Thuwal, Kingdom of Saudi Arabia
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48
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Kamnev AA, Tugarova AV, Dyatlova YA, Tarantilis PA, Grigoryeva OP, Fainleib AM, De Luca S. Methodological effects in Fourier transform infrared (FTIR) spectroscopy: Implications for structural analyses of biomacromolecular samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 193:558-564. [PMID: 29310090 DOI: 10.1016/j.saa.2017.12.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/10/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Alexander A Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia.
| | - Anna V Tugarova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia
| | - Yulia A Dyatlova
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia
| | - Petros A Tarantilis
- Laboratory of Chemistry, Department of Food Science and Human Nutrition, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens 11855, Greece
| | - Olga P Grigoryeva
- Department of Chemistry of Heterochain Polymers and Interpenetrating Polymer Networks, Institute of Macromolecular Chemistry, National Academy of Sciences of Ukraine, Kyiv 02160, Ukraine
| | - Alexander M Fainleib
- Department of Chemistry of Heterochain Polymers and Interpenetrating Polymer Networks, Institute of Macromolecular Chemistry, National Academy of Sciences of Ukraine, Kyiv 02160, Ukraine
| | - Stefania De Luca
- Institute of Biostructures and Bioimaging, National Research Council, 80134 Naples, Italy
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49
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Agaras BC, Iriarte A, Valverde CF. Genomic insights into the broad antifungal activity, plant-probiotic properties, and their regulation, in Pseudomonas donghuensis strain SVBP6. PLoS One 2018. [PMID: 29538430 PMCID: PMC5851621 DOI: 10.1371/journal.pone.0194088] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Plant-growth promotion has been linked to the Pseudomonas genus since the beginning of this research field. In this work, we mined the genome of an Argentinean isolate of the recently described species P. donghuensis. Strain SVBP6, isolated from bulk soil of an agricultural plot, showed a broad antifungal activity and several other plant-probiotic activities. As this species has been recently described, and it seems like some plant-growth promoting (PGP) traits do not belong to the classical pseudomonads toolbox, we decide to explore the SVBP6 genome via an bioinformatic approach. Genome inspection confirmed our previous in vitro results about genes involved in several probiotic activities. Other genetic traits possibly involved in survival of SVBP6 in highly competitive environments, such as rhizospheres, were found. Tn5 mutagenesis revealed that the antifungal activity against the soil pathogen Macrophomina phaseolina was dependent on a functional gacS gene, from the regulatory cascade Gac-Rsm, but it was not due to volatile compounds. Altogether, our genomic analyses and in vitro tests allowed the phylogenetic assignment and provided the first insights into probiotic properties of the first P. donghuensis isolate from the Americas.
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Affiliation(s)
- Betina Cecilia Agaras
- Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Claudio Fabián Valverde
- Laboratorio de Bioquímica, Microbiología e Interacciones Biológicas en el Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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50
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Marshall AC, Bond CS, Bruning JB. Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Andrew C. Marshall
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Charles S. Bond
- School
of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - John B. Bruning
- Institute
for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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