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Kelliher JM, Johnson LYD, Robinson AJ, Longley R, Hanson BT, Cailleau G, Bindschedler S, Junier P, Chain PSG. Fabricated devices for performing bacterial-fungal interaction experiments across scales. Front Microbiol 2024; 15:1380199. [PMID: 39171270 PMCID: PMC11335632 DOI: 10.3389/fmicb.2024.1380199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.
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Affiliation(s)
- Julia M. Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Leah Y. D. Johnson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aaron J. Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Reid Longley
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Buck T. Hanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
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Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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Jin Y, Yuan Y, Liu Z, Gai S, Cheng K, Yang F. Effect of humic substances on nitrogen cycling in soil-plant ecosystems: Advances, issues, and future perspectives. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 351:119738. [PMID: 38061102 DOI: 10.1016/j.jenvman.2023.119738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/18/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Nitrogen (N) cycle is one of the most significant biogeochemical cycles driven by soil microorganisms on the earth. Exogenous humic substances (HS), which include composted-HS and artificial-HS, as a new soil additive, can improve the water retention capacity, cation exchange capacity and soil nutrient utilization, compensating for the decrease of soil HS content caused by soil overutilization. This paper systematically reviewed the contribution of three different sources of HS in the soil-plant system and explained the mechanisms of N transformation through physiological and biochemical pathways. HS convert the living space and living environment of microorganisms by changing the structure and condition of soil. Generally, HS can fix atmospheric and soil N through biotic and abiotic mechanisms, which improved the availability of N. Besides, HS transform the root structure of plants through physiological and biochemical pathways to promote the absorption of inorganic N by plants. The redox properties of HS participate in soil N transformation by altering the electron gain and loss of microorganisms. Moreover, to alleviate the energy crisis and environmental problems caused by N pollution, we also illustrated the mechanisms reducing soil N2O emissions by HS and the application prospects of artificial-HS. Eventually, a combination of indoor simulation and field test, molecular biology and stable isotope techniques are needed to systematically analyze the potential mechanisms of soil N transformation, representing an important step forward for understanding the relevance between remediation of environmental pollution and improvement of the N utilization in soil-plant system.
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Affiliation(s)
- Yongxu Jin
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Yue Yuan
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Zhuqing Liu
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Shuang Gai
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China
| | - Kui Cheng
- International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China; College of Engineering, Northeast Agricultural University, Harbin, 150030, China.
| | - Fan Yang
- School of Water Conservancy and Civil Engineering, Northeast Agricultural University, Harbin, 150030, China; International Cooperation Joint Laboratory of Health in Cold Region Black Soil Habitat of the Ministry of Education, China.
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Kim J, Lu LC, Gao X, Hofmockel KS, Masiello CA, Silberg JJ. Using Methyl Bromide for Interspecies Cell-Cell Signaling and As a Reporter in a Model Soil Consortium. ACS Synth Biol 2023; 12:3743-3753. [PMID: 37991716 DOI: 10.1021/acssynbio.3c00559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Soil microbial communities with reduced complexity are emerging as model systems for studying consortia-scale phenotypes. To establish synthetic biology tools for studying these communities in hard-to-image environmental materials, we evaluated whether a single member of a model soil consortium (MSC) can be programmed to report on gene expression without requiring matrix disruption. For these studies, we targeted a five-membered MSC that includes Dyadobacter fermentans, Ensifer adhaerens, Rhodococcus sp003130705, Streptomyces sp001905665, and Variovorax beijingensis. By coupling the expression of a methyl halide transferase to a constitutive promoter, we show that V. beijingensis can be programmed to synthesize methyl halides that accumulate in the soil headspace at levels that are ≥24-fold higher than all other MSC members across a range of environmentally relevant hydration conditions. We find that methyl halide production can report on an MSC promoter that is activated by changes in water potential, and we demonstrate that a synthetic gas signal can be read out directly using gas chromatography and indirectly using a soil-derived Methylorubrum that is programmed to produce a visual output in response to methyl halides. These tools will be useful for future studies that investigate how MSC responds to dynamic hydration conditions, such as drought and flood events induced by climate change, which can alter soil water potential and induce the release of stored carbon.
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Affiliation(s)
- Jiwoo Kim
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Li Chieh Lu
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
| | - Xiaodong Gao
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Caroline A Masiello
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, 6100 Main St, MS-126, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Jonathan J Silberg
- Department of Biosciences, Rice University, 6100 Main Street, MS-140, Houston, Texas 77005, United States
- Department of Bioengineering, Rice University, 6100 Main Street, MS-142, Houston, Texas 77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, Texas 77005, United States
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Jansson JK, McClure R, Egbert RG. Soil microbiome engineering for sustainability in a changing environment. Nat Biotechnol 2023; 41:1716-1728. [PMID: 37903921 DOI: 10.1038/s41587-023-01932-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/01/2023] [Indexed: 11/01/2023]
Abstract
Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.
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Affiliation(s)
- Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Ryan McClure
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robert G Egbert
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
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Lozano-Andrade CN, Nogueira CG, Henriksen NNSE, Wibowo M, Jarmusch SA, Kovács ÁT. Establishment of a transparent soil system to study Bacillus subtilis chemical ecology. ISME COMMUNICATIONS 2023; 3:110. [PMID: 37838789 PMCID: PMC10576751 DOI: 10.1038/s43705-023-00318-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS, and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.
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Affiliation(s)
| | - Carla G Nogueira
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | | | - Mario Wibowo
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Scott A Jarmusch
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Ákos T Kovács
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark.
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
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