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Chen Y, Pan J, Yun Y, Zhi B, Li G, Li M, Ma T. Halomonas plays a central role in the syntrophic community of an alkaline oil reservoir with alkali-surfactant-polymer (ASP) flooding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141333. [PMID: 32795799 DOI: 10.1016/j.scitotenv.2020.141333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
Little is known about the microbial characteristics in oil reservoirs under alkali-surfactant-polymer (ASP)-flooding. In the present study, we collected two ASP-flooding samples and two nearby water-flooding samples from the Daqing oil field and performed 16S rRNA gene sequencing and metagenomic sequencing to fill this knowledge gap. The results indicated that the highly elevated pH resulted in a simple Euryarchaeotal community and a Halomonas &Nitrincola-dominated bacterial community in the production water of the alkaline oil reservoir. In addition, we hypothesized that multiple copies of genes encoding monovalent cation/proton antiporters in Halomonas and Nitrincola, and their facultative anaerobic and movable traits, were the adaptive mechanisms responsible for their competitive growth in the alkaline oil reservoir. We also revealed a unique syntrophic community in the alkaline oil reservoir and identified the central role of Halomonas within it. The present study revealed the microbial characteristics in an alkaline oil reservoir environment formed by ASP-flooding and indicated the application potential of Halomonas in AMP-flooding and microbial enhanced oil recovery (MEOR) technology to elevate the oil recovery rate from ASP-flooded oil reservoirs.
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Affiliation(s)
- Yu Chen
- College of Life Sciences, Nankai University, Tianjin, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yuan Yun
- College of Life Sciences, Nankai University, Tianjin, China
| | - Bo Zhi
- College of Life Sciences, Nankai University, Tianjin, China
| | - Guoqiang Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Ting Ma
- College of Life Sciences, Nankai University, Tianjin, China.
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Alvarado A, Behrens W, Josenhans C. Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility. Front Microbiol 2020; 10:3055. [PMID: 32010106 PMCID: PMC6978683 DOI: 10.3389/fmicb.2019.03055] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved complex sensing and signaling systems to react to their changing environments, most of which are present in all domains of life. Canonical bacterial sensing and signaling modules, such as membrane-bound ligand-binding receptors and kinases, are very well described. However, there are distinct sensing mechanisms in bacteria that are less studied. For instance, the sensing of internal or external cues can also be mediated by changes in protein conformation, which can either be implicated in enzymatic reactions, transport channel formation or other important cellular functions. These activities can then feed into pathways of characterized kinases, which translocate the information to the DNA or other response units. This type of bacterial sensory activity has previously been termed protein activity sensing. In this review, we highlight the recent findings about this non-canonical sensory mechanism, as well as its involvement in metabolic functions and bacterial motility. Additionally, we explore some of the specific proteins and protein-protein interactions that mediate protein activity sensing and their downstream effects. The complex sensory activities covered in this review are important for bacterial navigation and gene regulation in their dynamic environment, be it host-associated, in microbial communities or free-living.
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Affiliation(s)
- Alejandra Alvarado
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany
| | - Wiebke Behrens
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Christine Josenhans
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
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Feng H, Zhang N, Du W, Zhang H, Liu Y, Fu R, Shao J, Zhang G, Shen Q, Zhang R. Identification of Chemotaxis Compounds in Root Exudates and Their Sensing Chemoreceptors in Plant-Growth-Promoting Rhizobacteria Bacillus amyloliquefaciens SQR9. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:995-1005. [PMID: 29714096 DOI: 10.1094/mpmi-01-18-0003-r] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Chemotaxis-mediated response to root exudates, initiated by sensing-specific ligands through methyl-accepting chemotaxis proteins (MCP), is very important for root colonization and beneficial functions of plant-growth-promoting rhizobacteria (PGPR). Systematic identification of chemoattractants in complex root exudates and their sensing chemoreceptors in PGPR is helpful for enhancing their recruitment and colonization. In this study, 39 chemoattractants and 5 chemorepellents, including amino acids, organic acids, and sugars, were identified from 98 tested components of root exudates for the well-studied PGPR strain Bacillus amyloliquefaciens SQR9. Interestingly, mutant stain SQR9Δ8mcp, with all eight putative chemoreceptors completely deleted, lost the chemotactic responses to those 44 compounds. Gene complementation, chemotaxis assay, and isothermal titration calorimetry analysis revealed that McpA was mainly responsible for sensing organic acids and amino acids, while McpC was mostly for amino acids. These two chemoreceptors may play important roles in the rhizosphere chemotaxis of SQR9. In contrast, the B. amyloliquefaciens-unique chemoreceptor McpR was specifically responsible for arginine, and residues Tyr-78, Thr-131, and Asp-162 were critical for arginine binding. This study not only deepened our insights into PGPR-root interaction but also provided useful information to enhance the rhizosphere chemotaxis mobility and colonization of PGPR, which will promote their application in agricultural production.
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Affiliation(s)
- Haichao Feng
- 1 Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, P.R. China
- 2 Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; and
| | - Nan Zhang
- 1 Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Wenbin Du
- 3 State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huihui Zhang
- 1 Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Yunpeng Liu
- 2 Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; and
| | - Ruixin Fu
- 1 Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Jiahui Shao
- 1 Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Guishan Zhang
- 2 Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; and
| | - Qirong Shen
- 1 Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Ruifu Zhang
- 1 Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, P.R. China
- 2 Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China; and
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New motion analysis system for characterization of the chemosensory response kinetics of Rhodobacter sphaeroides under different growth conditions. Appl Environ Microbiol 2011; 77:4082-8. [PMID: 21515726 DOI: 10.1128/aem.00341-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We developed a new set of software tools that enable the speed and response kinetics of large numbers of tethered bacterial cells to be rapidly measured and analyzed. The software provides precision, accuracy, and a good signal-to-noise ratio combined with ease of data handling and processing. The software was tested on the single-cell chemosensory response kinetics of large numbers of Rhodobacter sphaeroides cells grown under either aerobic or photoheterotrophic conditions and either in chemostats or in batch cultures, allowing the effects of growth conditions on responses to be accurately measured. Aerobically and photoheterotrophically grown R. sphaeroides exhibited significantly different chemosensory response kinetics and cell-to-cell variability in their responses to 100 μM propionate. A greater proportion of the population of aerobically grown cells responded to a 100 μM step decrease in propionate; they adapted faster and showed less cell-to-cell variability than photosynthetic populations. Growth in chemostats did not significantly reduce the measured cell to cell variability but did change the adaptation kinetics for photoheterotrophically grown cells.
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Vlamakis HC, Kirby JR, Zusman DR. The Che4 pathway of Myxococcus xanthus regulates type IV pilus-mediated motility. Mol Microbiol 2005; 52:1799-811. [PMID: 15186426 DOI: 10.1111/j.1365-2958.2004.04098.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Myxococcus xanthus co-ordinates cell movement during its complex life cycle using multiple chemotaxis-like signal transduction pathways. These pathways regulate both type IV pilus-mediated social (S) motility and adventurous (A) motility. During a search for new chemoreceptors, we identified the che4 operon, which encodes homologues to a MCP (methyl-accepting chemotaxis protein), two CheWs, a hybrid CheA-CheY, a response regulator and a CheR. Deletion of the che4 operon did not cause swarming or developmental defects in either the wild-type (A(+)S(+)) strain or in a strain sustaining only A motility (A(+)S(-)). However, in a strain displaying only S motility (A(-)S(+)), deletion of the che4 operon or the gene encoding the response regulator, cheY4, caused enhanced vegetative swarming and prevented aggregation and sporulation. In contrast, deletion of mcp4 caused reduced vegetative swarming and enhanced development compared with the parent strain. Single-cell analysis of the motility of the A(-)S(+) parent strain revealed a previously unknown inverse correlation between velocity and reversal frequency. Thus, cells that moved at higher velocities showed a reduced reversal frequency. This co-ordination of reversal frequency and velocity was lost in the mcp4 and cheY4 mutants. The structural components of the S motility apparatus were unaffected in the che4 mutants, suggesting that the Che4 system affects reversal frequency of cells by modulating the function of the type IV pilus.
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Affiliation(s)
- Hera C Vlamakis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA
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Okubo Y, Futamata H, Hiraishi A. Distribution and Capacity for Utilization of Lower Fatty Acids of Phototrophic Purple Nonsulfur Bacteria in Wastewater Environments. Microbes Environ 2005. [DOI: 10.1264/jsme2.20.135] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yoko Okubo
- Department of Ecological Engineering, Toyohashi University of Technology
| | - Hiroyuki Futamata
- Department of Ecological Engineering, Toyohashi University of Technology
| | - Akira Hiraishi
- Department of Ecological Engineering, Toyohashi University of Technology
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Brehm-Stecher BF, Johnson EA. Single-cell microbiology: tools, technologies, and applications. Microbiol Mol Biol Rev 2004; 68:538-59, table of contents. [PMID: 15353569 PMCID: PMC515252 DOI: 10.1128/mmbr.68.3.538-559.2004] [Citation(s) in RCA: 297] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The field of microbiology has traditionally been concerned with and focused on studies at the population level. Information on how cells respond to their environment, interact with each other, or undergo complex processes such as cellular differentiation or gene expression has been obtained mostly by inference from population-level data. Individual microorganisms, even those in supposedly "clonal" populations, may differ widely from each other in terms of their genetic composition, physiology, biochemistry, or behavior. This genetic and phenotypic heterogeneity has important practical consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. New appreciation of the importance of cellular heterogeneity, coupled with recent advances in technology, has driven the development of new tools and techniques for the study of individual microbial cells. Because observations made at the single-cell level are not subject to the "averaging" effects characteristic of bulk-phase, population-level methods, they offer the unique capacity to observe discrete microbiological phenomena unavailable using traditional approaches. As a result, scientists have been able to characterize microorganisms, their activities, and their interactions at unprecedented levels of detail.
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Affiliation(s)
- Byron F Brehm-Stecher
- Department of Food Microbiology and Toxicology, University of Wisconsin-Madison Food Research Institute, 1925 Willow Drive, Madison, WI 53706, USA
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Romagnoli S, Packer HL, Armitage JP. Tactic responses to oxygen in the phototrophic bacterium Rhodobacter sphaeroides WS8N. J Bacteriol 2002; 184:5590-8. [PMID: 12270816 PMCID: PMC139605 DOI: 10.1128/jb.184.20.5590-5598.2002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The temporal and spatial behavior of a number of mutants of the photosynthetic, facultative anaerobe Rhodobacter sphaeroides to both step changes and to gradients of oxygen was analyzed. Wild-type cells, grown under a range of conditions, showed microaerophilic behavior, accumulating in a 1.3-mm band about 1.3 mm from the meniscus of capillaries. Evidence suggests this is the result of two signaling pathways. The strength of any response depended on the growth and incubation conditions. Deletion of either the complete chemosensory operons 1 and 2 plus the response regulator genes cheY(4) and cheY(5) or cheA(2) alone led to the loss of all aerotactic responses, although the cells still swam normally. The Prr system of R. sphaeroides responds to electron flow through the alternative high-affinity cytochrome oxidase, cbb(3), controlling expression of a wide range of metabolic pathways. Mutants with deletions of either the complete Prr operon or the histidine kinase, PrrB, accumulated up to the meniscus but still formed a thick band 1.3 mm from the aerobic interface. This indicates that the negative aerotactic response to high oxygen levels depends on PrrB, but the mutant cells still retain the positive response. Tethered PrrB(-) cells also showed no response to a step-down in oxygen concentration, although those with deletions of the whole operon showed some response. In gradients of oxygen where the concentration was reduced at 0.4 micro M/s, tethered wild-type cells showed two different phases of response, with an increase in stopping frequency when the oxygen concentration fell from 80 to 50% dissolved oxygen and a decrease in stopping at 50 to 20% dissolved oxygen, with cells returning to their normal stopping frequency in 0% oxygen. PrrB and CheA(2) mutants showed no response, while PrrCBA mutants still showed some response.
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Affiliation(s)
- Simona Romagnoli
- Microbiology Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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