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Spoerke JM, Wilkinson HH, Parker MA. NONRANDOM GENOTYPIC ASSOCIATIONS IN A LEGUME—
BRADYRHIZOBIUM
MUTUALISM. Evolution 2017; 50:146-154. [PMID: 28568881 DOI: 10.1111/j.1558-5646.1996.tb04481.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/1994] [Accepted: 09/21/1994] [Indexed: 11/27/2022]
Affiliation(s)
- Jill M. Spoerke
- Department of Biological Sciences State University of New York Binghamton New York 13902‐6000
| | - Heather H. Wilkinson
- Department of Biological Sciences State University of New York Binghamton New York 13902‐6000
| | - Matthew A. Parker
- Department of Biological Sciences State University of New York Binghamton New York 13902‐6000
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Rodríguez-Echeverría S, Le Roux JJ, Crisóstomo JA, Ndlovu J. Jack-of-all-trades and master of many? How does associated rhizobial diversity influence the colonization success of Australian Acacia species? DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00787.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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The International Workshop on Establishment of Microbial Inocula in Soils: Cooperative Research Project on Biological Resource Management of the Organization for Economic Cooperation and Development (OECD). ACTA ACUST UNITED AC 2009. [DOI: 10.1017/s0889189300006160] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Low-input agriculture is likely to be the focal point for future cropping systems. Worldwide there is increasing concern that we must decrease the use of chemicals in agriculture. A leading reason for this concern has been the effects of pesticides on food quality, consumer health, and the environment. There also is concern regarding fertilizers and energy inputs because of environmental pollution from excessive application rates and poor timing of fertilization and because of the depletion of nonrenewable energy resources. Overuse of these materials not only is an economic waste but also may require environmental cleanup. Legislation may mandate the development of alternative methods of pest control. For example, the Dutch Government has demanded a 35% decrease in the use of farm pesticides in 1995 and a 50% reduction by the year 2000. Other governments may impose similar limitations.
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LAW R, LEWIS DH. Biotic environments and the maintenance of sex-some evidence from mutualistic symbioses. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1983.tb01876.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schwieger F, Tebbe CC. Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and a non-target plant (Chenopodium album)-linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. Appl Environ Microbiol 2000; 66:3556-65. [PMID: 10919821 PMCID: PMC92185 DOI: 10.1128/aem.66.8.3556-3565.2000] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fourteen weeks after field release of luciferase gene-tagged Sinorhizobium meliloti L33 in field plots seeded with Medicago sativa, we found that the inoculant also occurred in bulk soil from noninoculated control plots. In rhizospheres of M. sativa plants, S. meliloti L33 could be detected in noninoculated plots 12 weeks after inoculation, indicating that growth in the rhizosphere preceded spread into bulk soil. To determine whether inoculation affected bacterial diversity, 1,119 bacteria were isolated from the rhizospheres of M. sativa and Chenopodium album, which was the dominant weed in the field plots. Amplified ribosomal DNA restriction analysis (ARDRA) revealed plant-specific fragment size frequencies. Dominant ARDRA groups were identified by 16S rRNA gene nucleotide sequencing. Database comparisons indicated that the rhizospheres contained members of the Proteobacteria (alpha, beta, and gamma subgroups), members of the Cytophaga-Flavobacterium group, and gram-positive bacteria with high G+C DNA contents. The levels of many groups were affected by the plant species and, in the case of M. sativa, by inoculation. The most abundant isolates were related to Variovorax sp., Arthrobacter ramosus, and Acinetobacter calcoaceticus. In the rhizosphere of M. sativa, inoculation reduced the numbers of cells of A. calcoaceticus and members of the genus Pseudomonas and increased the number of rhizobia. Cultivation-independent PCR-single-strand conformation polymorphism (SSCP) profiles of a 16S rRNA gene region confirmed the existence of plant-specific rhizosphere communities and the effect of the inoculant. All dominant ARDRA groups except Variovorax species could be detected. On the other hand, the SSCP profiles revealed products which could not be assigned to the dominant cultured isolates, indicating that the bacterial diversity was greater than the diversity suggested by cultivation.
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Affiliation(s)
- F Schwieger
- Institut für Agrarökologie, Bundesforschungsanstalt für Landwirtschaft (FAL), Braunschweig, Germany
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Palmer KM, Young JP. Higher diversity of Rhizobium leguminosarum biovar viciae populations in arable soils than in grass soils. Appl Environ Microbiol 2000; 66:2445-50. [PMID: 10831423 PMCID: PMC110555 DOI: 10.1128/aem.66.6.2445-2450.2000] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/1999] [Accepted: 04/10/2000] [Indexed: 11/20/2022] Open
Abstract
The bacterial genetic diversity after long-term arable cultivation was compared with that under permanent grassland using replicated paired contrasts. Pea-nodulating Rhizobium leguminosarum populations were sampled from pairs of arable and grass sites at four locations in Yorkshire, United Kingdom. Isolates were characterized using both chromosomal (16S-23S ribosomal DNA internal transcribed spacer PCR-restriction fragment length polymorphism) and plasmid (group-specific repC PCR amplification) markers. The diversities of chromosomal types, repC profiles, and combined genotypes were calculated using richness in types (adjusted to equal sample sizes by rarefaction), Shannon-Wiener index, and Simpson's index. The relative differences in diversity within each pair of sites were similar for all three diversity measures. Chromosomal types, repC profiles, and combined genotypes were each more diverse in arable soils than in grass soils at two of the four locations. The other comparisons showed no significant differences. We conclude that rhizobial diversity can be affected by differences between these two management regimens. Multiple regression analyses indicated that lower diversity was associated with high potential nitrogen and phosphate levels or with acidity.
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Affiliation(s)
- K M Palmer
- Department of Biology, University of York, York, United Kingdom
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Uhde C, Schmidt R, Jording D, Selbitschka W, Pühler A. Stationary-phase mutants of Sinorhizobium meliloti are impaired in stationary-phase survival or in recovery to logarithmic growth. J Bacteriol 1997; 179:6432-40. [PMID: 9335293 PMCID: PMC179560 DOI: 10.1128/jb.179.20.6432-6440.1997] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A screening method was used to identify Sinorhizobium meliloti mutants which are affected in stationary-phase survival. Of 20,000 individual colonies mutagenized with transposon Tn5-B20, 10 mutant strains which showed poor or no survival in the stationary phase were identified. Analyses of expression patterns of the promoterless lacZ genes in the mutant strains revealed individual induction patterns. Most strains were induced in stationary phase as well as under carbon limitation and in pure H2O, but none of the mutants was induced under heat, alkali stress conditions, or low oxygen tension. Plant inoculation tests revealed that the symbiotic proficiency of the mutants was not affected. Two mutants, however, showed gene induction not only in the stationary phase under free-living conditions but also in the bacteroid state. A long-term starvation test was carried out to examine the ability of the 10 mutants to survive prolonged stationary-phase conditions. All mutants showed a clear decrease in the colony-forming ability under the chosen experimental conditions. Staining with green and red fluorescent nucleic acid stain showed that the mutants fell into two different classes. Seven mutants died during stationary phase; the three other mutants remained viable but did not resume growth after prolonged starvation. Five of the ten Tn5-B20 insertions were cloned from the genomes of the mutant strains. Nucleotide sequence analyses established that the transposon had inserted in five distinctive genes. Database searches revealed that four of the tagged loci corresponded to already characterized genes whose gene products are involved in important cellular processes such as amino acid metabolism or aerobic respiration.
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Affiliation(s)
- C Uhde
- Lehrstuhl für Genetik, Universität Bielefeld, Germany
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11
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Wernegreen JJ, Harding EE, Riley MA. Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum. Proc Natl Acad Sci U S A 1997; 94:5483-8. [PMID: 9144264 PMCID: PMC24705 DOI: 10.1073/pnas.94.10.5483] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Lateral transfer of bacterial plasmids is thought to play an important role in microbial evolution and population dynamics. However, this assumption is based primarily on investigations of medically or agriculturally important bacterial species. To explore the role of lateral transfer in the evolution of bacterial systems not under intensive, human-mediated selection, we examined the association of genotypes at plasmid-encoded and chromosomal loci of native Rhizobium, the nitrogen-fixing symbiont of legumes. To this end, Rhizobium leguminosarum strains nodulating sympatric species of native Trifolium were characterized genetically at plasmid-encoded symbiotic (sym) regions (nodulation AB and nodulation CIJT loci) and a repeated chromosomal locus not involved in the symbiosis with legumes. Restriction fragment length polymorphism analysis was used to distinguish genetic groups at plasmid and chromosomal loci. The correlation between major sym and chromosomal genotypes and the distribution of genotypes across host plant species and sampling location were determined using chi2 analysis. In contrast to findings of previous studies, a strict association existed between major sym plasmid and chromosomal genetic groups, suggesting a lack of successful sym plasmid transfer between major Rhizobium chromosomal types. These data indicate that previous observations of sym plasmid transfer in agricultural settings may seriously overestimate the rates of successful conjugation in systems not impacted by human activities. In addition, a nonrandom distribution of Rhizobium genotypes across host plant species and sampling site demonstrates the importance of both factors in shaping Rhizobium population dynamics.
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Affiliation(s)
- J J Wernegreen
- Department of Biology, Yale University, New Haven, CT 06511, USA.
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12
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Esiobu N. Indigenous bradyrhizobia populations in tropical farm-lands. Lett Appl Microbiol 1994. [DOI: 10.1111/j.1472-765x.1994.tb00983.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Streit W, Kipe-Nolt J, Werner D. Competitive growth ofRhizobium leguminosarum bv.phaseoli strains under oligotrophic conditions. Curr Microbiol 1991. [DOI: 10.1007/bf02091976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ladha JK, Garcia M, Miyan S, Padre AT, Watanabe I. Survival of
Azorhizobium caulinodans
in the Soil and Rhizosphere of Wetland Rice under
Sesbania rostrata
-Rice Rotation. Appl Environ Microbiol 1989; 55:454-60. [PMID: 16347853 PMCID: PMC184130 DOI: 10.1128/aem.55.2.454-460.1989] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The survival of indigenous and introduced strains of
Azorhizobium caulinodans
in flooded soil and in the rice rhizosphere, where in situ
Sesbania rostrata
was incorporated before the rice crop, is reported. The azorhizobia studied were both root and stem nodulating. In a pot experiment, two crop cycles each of inoculated and noninoculated
Sesbania
-rice were compared with two crop cycles of flooded fallow-rice. In a field experiment, the effect of repeated incorporation of in situ
S. rostrata
in the
Sesbania
-rice sequence was studied. Soils in which inoculated
S. rostrata
was incorporated contained about 3,000 times more azorhizobia than did soils in the flooded fallow treatment and about 50 times more azorhizobia than did soils in the noninoculated
Sesbania
treatment. Azorhizobial numbers in the inoculated
Sesbania
treatment declined toward rice harvest but remained much higher than in the flooded fallow-rice treatment. Repeated incorporation of
S. rostrata
increased the population density of indigenous soil azorhizobia, whereas the population of inoculated strain ORS571 (Str
r
Spc
r
) declined to an undetectable level; this finding suggested low competitiveness by the introduced strain. In the incorporated
Sesbania
treatment, the rice rhizosphere harbored significantly more
A. caulinodans
and supported higher nitrogenase activity per plant than did the rhizosphere of the flooded fallow-rice treatment. Sterile rice seedlings inoculated with
A. caulinodans
showed nitrogenase activity comparable to that of seedlings inoculated with
Azospirillum lipoferum
34H, a rice root isolate. Rhizobia from
Sesbania aculeata, Sesbania sesban
, a
Trifolium
sp., and
Vigna unguiculata
did not support appreciable nitrogenase activity.
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Affiliation(s)
- J K Ladha
- The International Rice Research Institute, P. O. Box 933, Manila, Philippines
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Bleakley BH, Gaskins MH, Hubbell DH, Zam SG. Floc Formation by
Azospirillum lipoferum
Grown on Poly-β-Hydroxybutyrate. Appl Environ Microbiol 1988; 54:2986-95. [PMID: 16347792 PMCID: PMC204416 DOI: 10.1128/aem.54.12.2986-2995.1988] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Azospirillum lipoferum
RG6xx was grown under conditions similar to those resulting in encystment of
Azotobacter
spp.
A. lipoferum
produced cells of uniform shape when grown on nitrogen-free β-hydroxybutyrate agar. Cells accumulated poly-β-hydroxybutyrate and often grew as chains or filaments that eventually lost motility and formed capsules. Within 1 week, vegetative
A. lipoferum
inocula were converted into microflocs arising from filaments or chains. Cells within microflocs were pleomorphic, contained much poly-β-hydroxybutyrate, and were encapsulated. Some cells had a cystlike morphology. Up to 57% of the dry weight of encapsulated flocs was poly-β-hydroxybutyrate, whereas vegetative cells grown in broth with combined nitrogen had only 3% of their dry weight as poly-β-hydroxybutyrate. Neither encapsulated cells in flocs nor nonencapsulated vegetative cells were significantly desiccation resistant. Under starvation conditions (9 days) only 25% of encapsulated cells remained viable, whereas vegetative cells multiplied severalfold. In short-term germination experiments with encapsulated flocs, nitrate, ammonium, and soil extract promoted formation of motile vegetative cells. Most cells in treatments lacking combined nitrogen eventually depleted their visible poly-β-hydroxybutyrate reserves without germinating. The remaining cells retained the reserve polymer and underwent size reduction.
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Affiliation(s)
- B H Bleakley
- Department of Agronomy, Department of Soil Science, and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
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Brunel B, Cleyet-Marel JC, Normand P, Bardin R. Stability of
Bradyrhizobium japonicum
Inoculants after Introduction into Soil. Appl Environ Microbiol 1988; 54:2636-42. [PMID: 16347768 PMCID: PMC204348 DOI: 10.1128/aem.54.11.2636-2642.1988] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bradyrhizobium japonicum
USDA 125-Sp, USDA 138, and USDA 138-Sm had been used as inoculants for soybean (
Glycine max
(L.) Merr.) in soils previously free of
B. japonicum.
At 8 to 13 years after their release, these strains were reisolated from soil samples. A total of 115 isolates were obtained through nodules, and seven colonies were obtained directly by a serological method. The stability of the inoculants was confirmed by comparing the reisolated cultures with their respective parental strains which had been preserved by being lyophilized or stored on a yeast extract-mannitol agar slant at 4°C. Comparisons were made on morphological and serological characters, carbon compound utilization (8 tested), intrinsic antibiotic resistance (9 tested), and enzymatic activity (19 tested). Mucous and nonmucous isolates of serogroup 125 were analyzed for symbiotic effectiveness and restriction fragment hybridization with a DNA probe. Our data suggest that the
B. japonicum
inoculants have survived for up to 13 years in the soils without significant mutation except for two reisolates with a slightly increased kanamycin resistance level.
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Affiliation(s)
- B Brunel
- Laboratoire d'Ecologie Microbienne CNRS U.A. 697, Université Lyon I, 43 Bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France; Laboratoire de Recherche sur les Symbiotes des Racines INRA, 34060 Montpellier Cedex, France ; and Centre de Recherche en Biologie Forestière, Université Laval, Québec GIK 7P4, Canada
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Germida JJ. Growth of Indigenous
Rhizobium leguminosarum
and
Rhizobium meliloti
in Soils Amended with Organic Nutrients. Appl Environ Microbiol 1988; 54:257-263. [PMID: 16347530 PMCID: PMC202430 DOI: 10.1128/aem.54.1.257-263.1988] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability of indigenous
Rhizobium leguminosarum
and
Rhizobium meliloti
to use organic nutrients as growth substrates in soil was assessed by indirect bacteriophage analysis. A total of 17 organic compounds, including 9 carbohydrates, 3 organic acids, and 5 amino acids, were tested (1,000 μg g
−1
) in three soils with different cropping histories. Four additional soils were screened with a glucose amendment. Nutrient amendments stimulated growth of indigenous rhizobia, allowing subsequent replication of indigenous bacteriophages. Phage populations were enumerated by plating soil extracts on 19
R. leguminosarum
and 9
R. meliloti
indicator strains, including root nodule isolates from the soils assayed. On the basis of indirect phage analysis, all soils contained native rhizobia similar to one or more of the indicator strains, although not all indicator strains were detected in soil. All organic compounds stimulated growth of indigenous rhizobia, but the growth response varied for each rhizobial strain depending on the nutrient, the nutrient concentration, and the soil. Indigenous rhizobia readily utilized most organic compounds except phenylalanine, glycine, and aspartic acid. The ability of indigenous rhizobia to utilize a wide range of organic compounds as growth substrates in situ indicates their ability to successfully compete with other soil bacteria for nutrients in these soils.
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Affiliation(s)
- James J Germida
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W0
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18
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Kamicker BJ, Brill WJ. Identification of
Bradyrhizobium japonicum
Nodule Isolates from Wisconsin Soybean Farms. Appl Environ Microbiol 1986; 51:487-92. [PMID: 16347009 PMCID: PMC238906 DOI: 10.1128/aem.51.3.487-492.1986] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis was a more discriminating method than serotyping for identifying strains of
Bradyrhizobium japonicum.
Analysis of 543 nodule isolates from southeastern Wisconsin soybean farms revealed that none of the isolates were formed by any of the inoculant strains supplied by either of two inoculant companies. Twenty-nine indigenous strains and six inoculant strains were identified. Strain 61A76, the most competitive indigenous strain, formed 21% of the nodules. Indigenous strains 3030, 3058, 0336, and 3052 formed 15, 11, 9, and 9% of the nodules, respectively. These predominant strains were not associated with a particular soybean cultivar, soil type, or farm location.
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Affiliation(s)
- B J Kamicker
- Department of Bacteriology and Center for Studies of Nitrogen Fixation, University of Wisconsin, Madison, Wisconsin 53706
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Habte M. Selective Medium for Recovering Specific Populations of Rhizobia Introduced into Tropical Soils. Appl Environ Microbiol 1985; 50:1553-5. [PMID: 16346957 PMCID: PMC238800 DOI: 10.1128/aem.50.6.1553-1555.1985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Experiments were designed to evaluate the usefulness of antifungal agents and streptomycin for recovering low densities of rhizobia inoculated into tropical soils. The results showed that yeast-mannitol agar (pH 6.0) containing 500 μg of streptomycin, 400 μg of cycloheximide and 50 μg of benomyl or chlorothalonil per ml was the best selective medium.
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Affiliation(s)
- M Habte
- Department of Agronomy and Soil Science, University of Hawaii, Honolulu, Hawaii 96822
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