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Duncan KE, Istock CA, Graham JB, Ferguson N. GENETIC EXCHANGE BETWEEN BACILLUS SUBTILIS AND BACILLUS LICHENIFORMIS: VARIABLE HYBRID STABILITY AND THE NATURE OF BACTERIAL SPECIES. Evolution 2017; 43:1585-1609. [PMID: 28564334 DOI: 10.1111/j.1558-5646.1989.tb02611.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/1988] [Accepted: 06/13/1989] [Indexed: 11/29/2022]
Abstract
Experiments employing both broth and soil cultures demonstrated the capacity for bidirectional genetic exchange between the eubacterial species Bacillus subtilis and Bacillus licheniformis. The process was studied using standard laboratory strains and wild isolates of these species. The genetic exchange in soil occurs spontaneously. The interspecific recombination involved markers for antibiotic resistance and for the use of specific carbon sources (API characters). Hybrids frequently had unstable phenotypes, i.e., lacked a consistent expression of foreign genes over repeated transfer and growth. This instability often involved a "correction" back toward the phenotype of one or the other of the parental species for many differentiating characters; the final phenotype was always that of the more probable or actually known recipient species. This "correction" process is reminiscent of phenomena associated with the instability of artificial fusion protoplasts or noncomplementing diploids of B. subtilis, as well as the merodiploids formed by intergeneric crosses with enteric bacteria. The hybrids observed here must also be diploid, in some manner, because they sequentially express traits of both parental species at rates well above the frequency of mutation. Among the unstable changes in hybrids of the wild strains there was a 3:1 bias in favor of "correction." The dynamics of the hybridization process in soil are described. It appears that the hybrids are formed most rapidly following outgrowth from spores and during the early growth of parental vegetative cell populations. Later on, the hybrids are much less frequent in the soil cultures, suggesting that they are competitively inferior to the parental species. It is argued that the capacity for recombination found between B. subtilis and B. licheniformis could locally erase their distinctness, even though they possess only about 15% DNA sequence homology. Yet they remain distinct in the wild. The methods and results of these experiments prepare the way for detailed studies of the nature of species and species boundaries throughout the genus Bacillus.
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Affiliation(s)
- Kathleen E Duncan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721
| | - Conrad A Istock
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721
| | - Julia Bell Graham
- Department of Biology and Biomedical Sciences, Western Michigan University, Kalamazoo, MI, 49008
| | - Nancy Ferguson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721
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Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus. Proc Natl Acad Sci U S A 2011; 108:E1236-43. [PMID: 22074846 DOI: 10.1073/pnas.1103630108] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many different systems of bacterial interactions have been described. However, relatively few studies have explored how interactions between different microorganisms might influence bacterial development. To explore such interspecies interactions, we focused on Bacillus subtilis, which characteristically develops into matrix-producing cannibals before entering sporulation. We investigated whether organisms from the natural environment of B. subtilis--the soil--were able to alter the development of B. subtilis. To test this possibility, we developed a coculture microcolony screen in which we used fluorescent reporters to identify soil bacteria able to induce matrix production in B. subtilis. Most of the bacteria that influence matrix production in B. subtilis are members of the genus Bacillus, suggesting that such interactions may be predominantly with close relatives. The interactions we observed were mediated via two different mechanisms. One resulted in increased expression of matrix genes via the activation of a sensor histidine kinase, KinD. The second was kinase independent and conceivably functions by altering the relative subpopulations of B. subtilis cell types by preferentially killing noncannibals. These two mechanisms were grouped according to the inducing strain's relatedness to B. subtilis. Our results suggest that bacteria preferentially alter their development in response to secreted molecules from closely related bacteria and do so using mechanisms that depend on the phylogenetic relatedness of the interacting bacteria.
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Christensen S, Griffiths BS, Ekelund F, Rønn R. Huge increase in bacterivores on freshly killed barley roots. FEMS Microbiol Ecol 2011. [DOI: 10.1111/j.1574-6941.1992.tb01765.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Muyzer G, de Bruyn AC, Schmedding DJ, Bos P, Westbroek P, Kuenen GJ. A Combined Immunofluorescence-DNA-Fluorescence Staining Technique for Enumeration of Thiobacillus ferrooxidans in a Population of Acidophilic Bacteria. Appl Environ Microbiol 2010; 53:660-4. [PMID: 16347315 PMCID: PMC203732 DOI: 10.1128/aem.53.4.660-664.1987] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An antiserum raised against whole cells of Thiobacillus ferrooxidans was allowed to react with a variety of acidophilic and nonacidophilic bacteria in an enzyme-linked immunosorbent assay and an indirect immunofluorescence assay. Both experiments demonstrated that the antiserum was specific at the species level. This preparation was used to evaluate the role of T. ferrooxidans in the microbial desulfurization process. Leaching experiments were performed, and the numbers of T. ferrooxidans cells and other bacteria were estimated by using a combined immunofluorescence-DNA-fluorescence staining technique that was adapted for this purpose. Nonsterile coal samples inoculated with T. ferrooxidans yielded high concentrations of soluble iron after 16 days. After this period, however, T. ferrooxidans cells could no longer be detected by the immunofluorescence assay, whereas the DNA-fluorescence staining procedure demonstrated a large number of microorganisms on the coal particles. These results indicate that T. ferrooxidans is removed by competition with different acidophilic microorganisms that were originally present on the coal.
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Affiliation(s)
- G Muyzer
- Department of Biochemistry, University of Leiden, 2333 AL Leiden, and Department of Microbiology and Enzymology, Delft University of Technology, 2628 BC Delft, The Netherlands
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Rivas LA, García-Villadangos M, Moreno-Paz M, Cruz-Gil P, Gómez-Elvira J, Parro V. A 200-antibody microarray biochip for environmental monitoring: searching for universal microbial biomarkers through immunoprofiling. Anal Chem 2008; 80:7970-9. [PMID: 18837515 DOI: 10.1021/ac8008093] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Environmental biomonitoring approaches require the measurement of either unequivocal biomarkers or specific biological profiles. Antibody microarrays constitute new tools for fast and reliable analysis of up to hundreds of biomarkers simultaneously. Herein we report 150 new polyclonal antibodies against microbial strains and environmental extracts, as well as the construction and validation of an antibody microarray (EMCHIP200, for "Environmental Monitoring Chip") containing 200 different antibodies. Each antibody was tested against its antigen for its specificity and cross-reactivity by a sandwich microarray immunoassay. The limit of detection was 0.2 ng mL (-1) for some proteins and 10 (4)-10 (5) cells mL (-1) for bacterial cells and spores. Partial biochemical characterization allowed identification of polymeric compounds (proteins and polysaccharides) as some of the targets recognized by the antibodies. We have successfully used the EMCHIP200 for the detection of biological polymers in samples from extreme environments around the world (e.g., a deep South African mine, Antarctica's dry valleys, Yellowstone National Park, Iceland, and Rio Tinto surface and subsurface). Clustering analysis permitted us to associate similar immunoprofiles or patterns to samples from apparently very different environments, indicating that they indeed share similar universal biomarkers. Our EMCHIP200 constitutes a new generation of immunosensors for biomarker detection and profiling, for either environmental, industrial, biotechnological, or astrobiological applications.
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Affiliation(s)
- Luis A Rivas
- Laboratories of Molecular Ecology, Centro de Astrobiología (INTA-CSIC), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
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Jones SM, Paton AM. The L-Phase ofErwinia carotovoravar.atrosepticaand its Possible Association with Plant Tissue. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1365-2672.1973.tb04158.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Christensen S, Griffiths B, Ekelund F, Rønn R. Huge increase in bacterivores on freshly killed barley roots. FEMS Microbiol Lett 2006. [DOI: 10.1111/j.1574-6968.1992.tb04822.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Fischer K, Hahn D, Hönerlage W, Sch nholzer F, Zeyer J. In situ Detection of Spores and Vegetative Cells of Bacillus megaterium in Soil by Whole Cell Hybridization. Syst Appl Microbiol 1995. [DOI: 10.1016/s0723-2020(11)80397-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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10 Methods for Studying the Microbial Ecology of Soil. METHODS IN MICROBIOLOGY 1990. [DOI: 10.1016/s0580-9517(08)70247-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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Immunofluorescent detection of the brown tide organism, Aureococcus anophagefferens. ACTA ACUST UNITED AC 1989. [DOI: 10.1029/ce035p0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Marshall KC. Microscopic methods for the study of bacterial behaviour at inert surfaces. J Microbiol Methods 1986. [DOI: 10.1016/0167-7012(86)90033-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Nickels JS, Bobbie RJ, Martz RF, Smith GA, White DC, Richards NL. Effect of Silicate Grain Shape, Structure, and Location on the Biomass and Community Structure of Colonizing Marine Microbiota. Appl Environ Microbiol 1981; 41:1262-8. [PMID: 16345778 PMCID: PMC243899 DOI: 10.1128/aem.41.5.1262-1268.1981] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbiota colonizing silica grains of the same size and water pore space, but with a different microtopography, showed differences in biomass and community structure after 8 weeks of exposure to running seawater. The absence of surface cracks and crevices resulted in a marked diminution of the total microbial biomass measured as lipid phosphate and total extractable palmitic acid. With increasing smoothness of the sand grain surface, examination of the community structure showed a marked decrease in procaryotes and algal microeucaryotes, with a relative increase in microeucaryotic grazers. A comparison of the colonizing sediment incubated in running seawater or at 32 m on the sea floor with a sediment core showed a decreased bacterial biomass with a different community structure and a decreased total microeucaryotic population of both grazers and algae. The quantitative differences in microbial biomass and community structure between the microcosms and the actual benthic population in the core were determined.
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Affiliation(s)
- J S Nickels
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
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Strayer RF, Tiedje JM. Application of the fluorescent-antibody technique to the study of a methanogenic bacterium in lake sediments. Appl Environ Microbiol 1978; 35:192-8. [PMID: 341807 PMCID: PMC242801 DOI: 10.1128/aem.35.1.192-198.1978] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fluorescent antibody (FA) was prepared for a methanogenic bacterium isolated from Wintergreen Lake pelagic sediment. The isolate resembles Methanobacterium formicicum. The FA did not cross-react with 9 other methanogens, including M. formicicum strains, or 24 heterotrophs, 18 of which had been isolated from Wintergreen Lake sediment. FA-reacting methanogens were detected in heat-fixed smears of several different lake sediments and anaerobic sewage sludge. Pretreatment of all samples with either rhodamine-conjugated geletin or bovine serum albumin adequately controlled nonspecific absorption of the FA. Autofluorescent particles were observed in the sediment samples but, with experience, they could easily be distinguished from FA-reacting bacteria. FA direct counts of the specific methanogen in Wintergreen Lake sediments were made on four different sampling dates and compared with five-tube most-probable-number estimates of the total methanogenic population that was present in the same samples. The FA counts ranged from 3.1 X 10(6) to 1.4 X 10(7)/g of dry sediment. The highest most-probable-number estimates were at least an order ofmagnitude lower.
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Greaves MP, Davies HA, Marsh JA, Winfield GI. Herbicides and soil microorganisms. CRC CRITICAL REVIEWS IN MICROBIOLOGY 1976; 5:1-38. [PMID: 11959 DOI: 10.3109/10408417609102308] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The production and usage of herbicides have increased dramatically in recent years. Consequently there is growing concern about the effects of these chemicals on the environment, particularly the possible long-term effects on soil fertility which may result from disturbance of the soil microflora. This review considers the recent developments in the study of the interactions between herbicides and microorganisms, and discusses the problems of evaluating the results of such studies with a view to determining or predicting possible short-term or long-term effects which may be of practical significance.
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Ibbotson R, Pugh GJF. Use of the fluorescent antibody technique for the evaluation of Arthroderma uncinatum in soil. Mycopathologia 1975. [DOI: 10.1007/bf00472583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bohlool BB, Brock TD. Immunofluorescence approach to the study of the ecology of Thermoplasma acidophilum in coal refuse material. Appl Microbiol 1974; 28:11-6. [PMID: 4602306 PMCID: PMC186572 DOI: 10.1128/am.28.1.11-16.1974] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Specific immunofluorescence staining was applied to the study of the localization, distribution, and growth of Thermoplasma acidophilum in its natural habitat, the coal refuse pile. Different antigenic groups of T. acidophilum could be isolated from the same refuse pile, and the same antigenic groups were isolated from piles from different geographical areas. No correlation could be established between the antigenic groups and the pH or temperature of the habitats. Brightly fluorescing cells of T. acidophilum were detected on microscope slides buried in contact with the coal refuse material or immersed in the water in the stream draining a refuse pile. T. acidophilum grew when inoculated into either coal refuse material and/or an aqueous extract of coal refuse when incubated at its optimal temperature of 55 C, but not when incubated at room temperature or 37 C. The coal refuse pile appears to be a primary habitat for T. acidophilum.
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Stotzky G. Activity, ecology, and population dynamics of microorganisms in soil. CRC CRITICAL REVIEWS IN MICROBIOLOGY 1972; 2:59-137. [PMID: 4567450 DOI: 10.3109/10408417209108383] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Henry RA, Johnson RC, Bohlool BB, Schmidt EL. Detection of Leptospira in soil and water by immunofluorescence staining. Appl Microbiol 1971; 21:953-6. [PMID: 4930040 PMCID: PMC377318 DOI: 10.1128/am.21.5.953-956.1971] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Specific immunofluorescence staining was used for the detection of leptospires in soil and water under laboratory and field conditions.
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Garcia MM, McKay KA. On the growth and survival of Clostridium septicum in soil. THE JOURNAL OF APPLIED BACTERIOLOGY 1969; 32:362-70. [PMID: 4904967 DOI: 10.1111/j.1365-2672.1969.tb00985.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Abstract
Application of fluorescent-antibody (FA) techniques to the study of rhizobia as free-living soil bacteria was explored. Antiserum to a particular strain of Rhizobium japonicum proved specific in both agglutination and FA tests. Within the R. japonicum group, 2 of 12 strains were stained by the conjugate and these fluoresced brightly; all others were entirely negative. FA tests were negative for 7 strains of R. meliloti, 9 strains of R. leguminosarum, 9 strains of R. trifolii, 6 strains of R. phaseoli, and 65 unidentified bacteria isolated from 12 soils. R. japonicum grew in autoclaved soil and was readily detectable by FA examination of contact slides. The FA technique also detected antibody-reacting bacteria in a field soil whose rhizobial content was unknown. Fluorescent cells were probably R. japonicum, since nodules developed on soybean plants grown in the same soil sample and FA preparations of the crushed nodules proved positive. Autofluorescence was not a problem, but nonspecific adsorption of conjugate restricted observations to microscopic fields free from soil particles. Nonspecific adsorption was substantial, irrespective of the soil used.
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Stotzky G. Relevance of soil microbiology to search for life on other planets. ADVANCES IN APPLIED MICROBIOLOGY 1968; 10:17-54. [PMID: 4882856 DOI: 10.1016/s0065-2164(08)70187-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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