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Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis. mSystems 2023; 8:e0057422. [PMID: 36537799 PMCID: PMC9948732 DOI: 10.1128/msystems.00574-22] [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] [Indexed: 12/24/2022] Open
Abstract
Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.
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Lui LM, Majumder ELW, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol 2021; 12:642422. [PMID: 33841364 PMCID: PMC8024649 DOI: 10.3389/fmicb.2021.642422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.
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Affiliation(s)
- Lauren M. Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Heidi J. Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Hans K. Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Matthew W. Fields
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology & Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Paul D. Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P. Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
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Sensitive Detection of E. coli in Artificial Seawater by Aptamer-Coated Magnetic Beads and Direct PCR. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9245392] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ‘One Health’ approach recommended by WHO recognizes the inseparable link between human, animal and environmental health [...]
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Zhang J, Oueslati R, Cheng C, Zhao L, Chen J, Almeida R, Wu J. Rapid, highly sensitive detection of Gram-negative bacteria with lipopolysaccharide based disposable aptasensor. Biosens Bioelectron 2018; 112:48-53. [PMID: 29698808 DOI: 10.1016/j.bios.2018.04.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/14/2018] [Accepted: 04/16/2018] [Indexed: 01/08/2023]
Abstract
Gram-negative bacteria are one of the most common microorganisms in the environment. Their differential detection and recognition from Gram-positive bacteria has been attracting much attention over the years. Using Escherichia coli (E. coli) as a model, we demonstrated on-site detection of Gram-negative bacteria by an AC electrokinetics-based capacitive sensing method using commercial microelectrodes functionalized with an aptamer specific to lipopolysaccharides. Dielectrophoresis effect was utilized to enrich viable bacteria to the microelectrodes rapidly, achieving a detection limit of 102 cells/mL within a 30 s' response time. The sensor showed a negligible response to Staphylococcus aureus (S. aureus), a Gram-positive species. The developed sensor showed significant advantages in sensitivity, selectivity, cost, operation simplicity, and response time. Therefore, this sensing method has shown great application potential for environmental monitoring, food safety, and real-time diagnosis.
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Affiliation(s)
- Jian Zhang
- School of Electronic Science and Applied Physics, Hefei University of Technology, Hefei 230009, China; Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Rania Oueslati
- Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Cheng Cheng
- Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Ling Zhao
- Department of Nutrition, The University of Tennessee, Knoxville, TN 37996, USA
| | - Jiangang Chen
- Department of Public Health, The University of Tennessee, Knoxville, TN 37996, USA
| | - Raul Almeida
- Department of Animal Science, The University of Tennessee, Knoxville, TN 37996, USA
| | - Jayne Wu
- Department of Electrical Engineering and Computer Science, The University of Tennessee, Knoxville, TN 37996, USA.
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Liu X, Cheng C, Wu J, Eda S, Guo Y. A low cost and palm-size analyzer for rapid and sensitive protein detection by AC electrokinetics capacitive sensing. Biosens Bioelectron 2017; 90:83-90. [DOI: 10.1016/j.bios.2016.10.098] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/28/2016] [Accepted: 10/31/2016] [Indexed: 12/11/2022]
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Cheng C, Cui H, Wu J, Eda S. A PCR-free point-of-care capacitive immunoassay for influenza A virus. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2140-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Capacitive Biosensors and Molecularly Imprinted Electrodes. SENSORS 2017; 17:s17020390. [PMID: 28218689 PMCID: PMC5336051 DOI: 10.3390/s17020390] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/16/2017] [Accepted: 02/08/2017] [Indexed: 01/05/2023]
Abstract
Capacitive biosensors belong to the group of affinity biosensors that operate by registering direct binding between the sensor surface and the target molecule. This type of biosensors measures the changes in dielectric properties and/or thickness of the dielectric layer at the electrolyte/electrode interface. Capacitive biosensors have so far been successfully used for detection of proteins, nucleotides, heavy metals, saccharides, small organic molecules and microbial cells. In recent years, the microcontact imprinting method has been used to create very sensitive and selective biorecognition cavities on surfaces of capacitive electrodes. This chapter summarizes the principle and different applications of capacitive biosensors with an emphasis on microcontact imprinting method with its recent capacitive biosensor applications.
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Lin X, Cheng C, Terry P, Chen J, Cui H, Wu J. Rapid and sensitive detection of bisphenol a from serum matrix. Biosens Bioelectron 2016; 91:104-109. [PMID: 28006678 DOI: 10.1016/j.bios.2016.12.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 12/28/2022]
Abstract
Bisphenol A (BPA) is an endocrine disrupting compound that may have adverse developmental, reproductive, neurological, and immune system effects. Low-level exposure to BPA is ubiquitous in human populations due to its widespread use in consumer products. Therefore, highly sensitive methods are needed to quantify BPA in various matrices including water, serum, and food products. In this study, we developed a simple, rapid, highly sensitive and specific sensor based on an aptamer probe and AC electrokinetics capacitive sensing method that successfully detected BPA at femto molar (fM) levels, which is an improvement over prior work by a factor of 10. We were able to detect BPA spiked in human serum as well as in maternal and cord blood within 30s. The sensor is responsive to BPA down to femto molar levels, but not to structurally similar compounds including bisphenol F (BPF) or bisphenol S (BPS) even at much higher concentration. Further development of this platform may prove useful in monitoring exposure to BPA and other small molecules in various matrices.
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Affiliation(s)
- Xiaogang Lin
- Key Laboratory of Optoelectronic Technology and System of the Education Ministry of China, Chongqing University, Chongqing 400044, China; Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA
| | - Cheng Cheng
- Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA
| | - Paul Terry
- Department of Medicine, Graduate School of Medicine, the University of Tennessee Medical Center, USA
| | - Jiangang Chen
- Department of Public Health, the University of Tennessee, Knoxville, TN 37996, USA.
| | - Haochen Cui
- Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA
| | - Jayne Wu
- Department of Electrical Engineering and Computer Science, the University of Tennessee, Knoxville, TN 37996, USA.
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Mirzajani H, Cheng C, Wu J, Chen J, Eda S, Najafi Aghdam E, Badri Ghavifekr H. A highly sensitive and specific capacitive aptasensor for rapid and label-free trace analysis of Bisphenol A (BPA) in canned foods. Biosens Bioelectron 2016; 89:1059-1067. [PMID: 27825518 DOI: 10.1016/j.bios.2016.09.109] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/24/2016] [Accepted: 09/30/2016] [Indexed: 12/13/2022]
Abstract
A rapid, highly sensitive, specific and low-cost capacitive affinity biosensor is presented here for label-free and single step detection of Bisphenol A (BPA). The sensor design allows rapid prototyping at low-cost using printed circuit board material by benchtop equipment. High sensitivity detection is achieved through the use of a BPA-specific aptamer as probe molecule and large electrodes to enhance AC-electroelectrothermal effect for long-range transport of BPA molecules toward electrode surface. Capacitive sensing technique is used to determine the bounded BPA level by measuring the sample/electrode interfacial capacitance of the sensor. The developed biosensor can detect BPA level in 20s and exhibits a large linear range from 1 fM to 10 pM, with a limit of detection (LOD) of 152.93 aM. This biosensor was applied to test BPA in canned food samples and could successfully recover the levels of spiked BPA. This sensor technology is demonstrated to be highly promising and reliable for rapid, sensitive and on-site monitoring of BPA in food samples.
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Affiliation(s)
- Hadi Mirzajani
- The University of Tennessee, Knoxville, Department of Electrical Engineering and Computer Science, 1520 Middle Drive, Knoxville, TN 37966, USA; Sahand University of Technology, Department of Electrical Engineering, Microelectronics Research Lab., Tabriz, Iran
| | - Cheng Cheng
- The University of Tennessee, Knoxville, Department of Electrical Engineering and Computer Science, 1520 Middle Drive, Knoxville, TN 37966, USA
| | - Jayne Wu
- The University of Tennessee, Knoxville, Department of Electrical Engineering and Computer Science, 1520 Middle Drive, Knoxville, TN 37966, USA.
| | - Jiangang Chen
- The University of Tennessee, Department of Public Health, 1914 Andy Holt Avenue, Knoxville, TN 37996, USA
| | - Shigotoshi Eda
- University of Tennessee Institute of Agriculture, Department of Forestry, Wildlife and Fisheries, 2431 Joe Johnson Drive, Knoxville, TN 37996, USA
| | - Esmaeil Najafi Aghdam
- Sahand University of Technology, Department of Electrical Engineering, Microelectronics Research Lab., Tabriz, Iran
| | - Habib Badri Ghavifekr
- Sahand University of Technology, Department of Electrical Engineering, Microelectronics Research Lab., Tabriz, Iran
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