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Normand P, Pujic P, Abrouk D, Vemulapally S, Guerra T, Carlos-Shanley C, Hahn D. Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions. J Genomics 2022; 10:61-68. [PMID: 35979511 PMCID: PMC9379372 DOI: 10.7150/jgen.75779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/08/2022] [Indexed: 11/08/2022] Open
Abstract
The genomes of two nitrogen-fixing Frankia strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of Alnus glutinosa, but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species. Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.7 Mb smaller than or similar to those of other cultivated Alnus-infective cluster 1 strains. Genes essential for nitrogen-fixation, clusters of orthologous genes, secondary metabolite clusters and transcriptional regulators analyzed by comparative genomic analyses were typical of those from Alnus-infective cluster 1 cultivated strains in both genomes. Compared to other cultivated Alnus-infective strains with large genomes, those of AgB32 and AgKG'84/4 had lost 380 or 409 genes, among which one hup cluster, one shc gene and the gvp cluster, which indicates genome erosion is taking place in these two strains.
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Affiliation(s)
- Philippe Normand
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Petar Pujic
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Danis Abrouk
- Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, Cedex 69622, France
| | - Spandana Vemulapally
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Camila Carlos-Shanley
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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Alnus glutinosa seedlings grown following co-inoculation with Frankia torreyi strain CpI1 and Frankia asymbiotica strain NRRL B-16386. Symbiosis 2022. [DOI: 10.1007/s13199-022-00845-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Comparison of the Antagonistic Potential of the Entomopathogenic Bacterium Serratia nematodiphila GCSR38 with other Effective Microorganisms for the Control of Rice Bacterial Leaf Blight. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The efficacy of antagonistic microorganisms and secondary metabolites of entomopathogenic bacteria was evaluated in vitro and in vivo against Xanthomonas oryzae pv. oryzae (Xoo), a causal agent of rice bacterial leaf blight. The effect of the culture filtrates of the microorganisms was tested against Xoo, using the agar well diffusion assay. Trichoderma sp. UB05/3 was the most effective against Xoo. However, the results were not statistically different from those of the entomopathogenic bacterium Serratia nematodiphila GCSR38 with a 22.97 mm and 19.15 mm zone of inhibition, respectively. The effect of the secondary metabolite crude extracts of antagonistic microorganisms (2,000 µg/ml) on Xoo inhibition was tested by the paper disc diffusion method. Only S. nematodiphila GCSR38 was able to control Xoo, with an inhibition zone of 17.60 mm. Minimum inhibitory concentration (MIC) was determined using a 96-well microtiter plate. The MIC of secondary metabolites crude extracts of S. nematodiphila GCSR38 was 1,000 µg/ml and the minimum bactericidal concentration (MBC) was 1,000 µg/ml. The efficacy of the secondary metabolite crude extract of S. nematodiphila GCSR38 against Xoo was tested using the detached leaf technique; the secondary metabolite crude extracts controlled the disease, with 24.45% and 15.56% disease severity when used before and after inoculation with Xoo, respectively. Inoculation with Xoo alone resulted in a disease severity of 44.45%. The secondary metabolite crude extracts of S. nematodiphila GCSR38 can reduce disease severity of bacterial leaf blight in rice by 28.89%, whereas zinc thiazole causes a disease severity of 22.22% and Xoo alone causes a disease severity of 66.67%.
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Vemulapally S, Guerra T, Hahn D. Effect of different Alnus taxa on abundance and diversity of introduced and indigenous Frankia in soils and root nodules. FEMS Microbiol Ecol 2022; 98:6529231. [PMID: 35170731 DOI: 10.1093/femsec/fiac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The effect of host plants on the abundance and distribution of introduced and indigenous Frankia populations was assessed in soils and root nodules of four alder species, Alnus glutinosa, Alnus cordata, Alnus rubra and Alnus viridis. Plants were grown in microcosms with either a sandy soil without detectable frankiae, with or without inoculation of a mixture of Frankia isolates, or with a silty clay loam soil with indigenous Frankia. The presence of frankiae in soils increased plant height and root nodule formation, with significant increases in the presence of indigenous frankiae. Abundance in soils increased significantly for both introduced and indigenous Frankia populations independent of alder species, with generally largest increases in cluster 1b frankiae. Root nodules formed by introduced frankiae did not reflect the diversity of strains inoculated, with nodules generally only formed by strain ArI3 representing cluster 1a/d. All indigenous Frankia populations detected in soil were also found in A. glutinosa nodules, while A. cordata or A. rubra nodules contained different subsets of frankiae with unique abundances dependent on plant species. These results demonstrate the intrageneric differences of host plants in the selection of specific Frankia populations in soils for root nodule formation.
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Affiliation(s)
- Spandana Vemulapally
- Texas State University, Department of Biology, 601 University Dr., San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Dr., San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Dr., San Marcos, TX 78666, USA
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Carlos-Shanley C, Guerra T, Hahn D. Draft genomes of non-nitrogen-fixing Frankia strains. J Genomics 2021; 9:68-75. [PMID: 34703504 PMCID: PMC8542509 DOI: 10.7150/jgen.65429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/14/2021] [Indexed: 12/04/2022] Open
Abstract
In this study, we describe the genomes of two novel candidate species of non-nitrogen fixing Frankia that were isolated from the root nodules of Coriaria nepalensis and Alnus glutinosa, genospecies CN and Ag, respectively. Comparative genomic analyses revealed that both genospecies lack genes essential for nitrogen-fixation and possess genes involved in the degradation of plant cell walls. Additionally, we found distinct biosynthetic gene clusters in each genospecies. The availability of these genomes will contribute to the study of the taxonomy and evolution of actinorhizal symbioses.
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Affiliation(s)
- Camila Carlos-Shanley
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Trina Guerra
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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Balkan MA, Stewart NU, Kauffman ES, Wolfe ER, Ballhorn DJ. Genotypic Diversity and Host-Specificity of Frankia Bacteria Associated with Sympatric Populations of Alnus rubra and Alnus rhombifolia in Oregon. NORTHWEST SCIENCE 2020. [DOI: 10.3955/046.093.0307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mehmet A. Balkan
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Nathan U. Stewart
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Emily S. Kauffman
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
| | - Emily R. Wolfe
- Portland State University, 1719 SW 10th Avenue, Portland, Oregon 97201
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In Planta Sporulation of Frankia spp. as a Determinant of Alder-Symbiont Interactions. Appl Environ Microbiol 2018; 84:AEM.01737-18. [PMID: 30217853 DOI: 10.1128/aem.01737-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/12/2018] [Indexed: 02/07/2023] Open
Abstract
The Alnus genus forms symbiosis with the actinobacteria Frankia spp. and ectomycorrhizal fungi. Two types of Frankia lineages can be distinguished based on their ability to sporulate in planta Spore-positive (Sp+) strains are predominant on Alnus incana and Alnus viridis in highlands, while spore-negative (Sp-) strains are mainly associated with Alnus glutinosa in lowlands. Here, we investigated whether the Sp+ predominance in nodules is due to host selection of certain Frankia genotypes from soil communities or the result of the ecological history of the alder stand soil, as well as the effect of the sporulation genotype on the ectomycorrhizal (ECM) communities. Trapping experiments were conducted using A. glutinosa, A. incana, and A. viridis plantlets on 6 soils, differing in the alder species and the frequency of Sp+ nodules in the field. Higher diversity of Frankia spp. and variation in Sp+ frequencies were observed in the trapping than in the fields. Both indigenous and trapping species shape Frankia community structure in trapped nodules. Nodulation impediments were observed under several trapping conditions in Sp+ soils, supporting a narrower host range of Sp+ Frankia species. A. incana and A. viridis were able to associate equally with compatible Sp+ and Sp- strains in the greenhouse. Additionally, no host shift was observed for Alnus-specific ECM, and the sporulation genotype of Frankia spp. defined the ECM communities on the host roots. The symbiotic association is likely determined by the host range, the soil history, and the type of in planta Frankia species. These results provide an insight into the biogeographical drivers of alder symbionts in the Holarctic region.IMPORTANCE Most Frankia-actinorhiza plant symbioses are capable of high rates of nitrogen fixation comparable to those found on legumes. Yet, our understanding of the ecology and distribution of Frankia spp. is still very limited. Several studies have focused on the distribution patterns of Frankia spp., demonstrating a combination of host and pedoclimatic parameters in their biogeography. However, very few have considered the in planta sporulation form of the strain, although it is a unique feature among all symbiotic plant-associated microbes. Compared with Sp- Frankia strains, Sp+ strains would be obligate symbionts that are highly dependent on the presence of a compatible host species and with lower efficiency in nitrogen fixation. Understanding the biogeographical drivers of Sp+ Frankia strains might help elucidate the ecological role of in planta sporulation and the extent to which this trait mediates host-partner interactions in the alder-Frankia-ECM fungal symbiosis.
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Zhang J, Wang P, Tian H, Jiang H, Wang Y, Yan C. Identification of interior salt-tolerant bacteria from ice plant Mesembryanthemum crystallinum and evaluation of their promoting effects. Symbiosis 2018. [DOI: 10.1007/s13199-018-0551-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Frankia Diversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity of Frankia Populations in Corresponding Rhizosphere Soils. Appl Environ Microbiol 2018; 84:AEM.02248-17. [PMID: 29247058 DOI: 10.1128/aem.02248-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/09/2017] [Indexed: 12/17/2022] Open
Abstract
Actinorhizal plants form nitrogen-fixing root nodules in symbiosis with soil-dwelling actinobacteria within the genus Frankia, and specific Frankia taxonomic clusters nodulate plants in corresponding host infection groups. In same-soil microcosms, we observed that some host species were nodulated (Alnus glutinosa, Alnus cordata, Shepherdia argentea, Casuarina equisetifolia) while others were not (Alnus viridis, Hippophaë rhamnoides). Nodule populations were represented by eight different sequences of nifH gene fragments. Two of these sequences characterized frankiae in S. argentea nodules, and three others characterized frankiae in A. glutinosa nodules. Frankiae in A. cordata nodules were represented by five sequences, one of which was also found in nodules from A. glutinosa and C. equisetifolia, while another was detected in nodules from A. glutinosa Quantitative PCR assays showed that vegetation generally increased the abundance of frankiae in soil, independently of the target gene (i.e., nifH or the 23S rRNA gene). Targeted Illumina sequencing of Frankia-specific nifH gene fragments detected 24 unique sequences from rhizosphere soils, 4 of which were also found in nodules, while the remaining 4 sequences in nodules were not found in soils. Seven of the 24 sequences from soils represented >90% of the reads obtained in most samples; the 2 most abundant sequences from soils were not found in root nodules, and only 2 of the sequences from soils were detected in nodules. These results demonstrate large differences between detectable Frankia populations in soil and those in root nodules, suggesting that root nodule formation is not a function of the abundance or relative diversity of specific Frankia populations in soils.IMPORTANCE The nitrogen-fixing actinobacterium Frankia forms root nodules on actinorhizal plants, with members of specific Frankia taxonomic clusters nodulating plants in corresponding host infection groups. We assessed Frankia diversity in root nodules of different host plant species, and we related specific populations to the abundance and relative distribution of indigenous frankiae in rhizosphere soils. Large differences were observed between detectable Frankia populations in soil and those in root nodules, suggesting that root nodule formation is not a function of the abundance or relative diversity of specific Frankia populations in soils but rather results from plants potentially selecting frankiae from the soil for root nodule formation. These data also highlight the necessity of using a combination of different assessment tools so as to adequately address methodological constraints that could produce contradictory data sets.
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Yasmin S, Hafeez FY, Mirza MS, Rasul M, Arshad HMI, Zubair M, Iqbal M. Biocontrol of Bacterial Leaf Blight of Rice and Profiling of Secondary Metabolites Produced by Rhizospheric Pseudomonas aeruginosa BRp3. Front Microbiol 2017; 8:1895. [PMID: 29018437 PMCID: PMC5622989 DOI: 10.3389/fmicb.2017.01895] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/15/2017] [Indexed: 01/28/2023] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is widely prevalent and causes Bacterial Leaf Blight (BLB) in Basmati rice grown in different areas of Pakistan. There is a need to use environmentally safe approaches to overcome the loss of grain yield in rice due to this disease. The present study aimed to develop inocula, based on native antagonistic bacteria for biocontrol of BLB and to increase the yield of Super Basmati rice variety. Out of 512 bacteria isolated from the rice rhizosphere and screened for plant growth promoting determinants, the isolate BRp3 was found to be the best as it solubilized 97 μg/ mL phosphorus, produced 30 μg/mL phytohormone indole acetic acid and 15 mg/ L siderophores in vitro. The isolate BRp3 was found to be a Pseudomonas aeruginosa based on 16S rRNA gene sequencing (accession no. HQ840693). This bacterium showed antagonism in vitro against different phytopathogens including Xoo and Fusarium spp. Strain BRp3 showed consistent pathogen suppression of different strains of BLB pathogen in rice. Mass spectrometric analysis detected the production of siderophores (1-hydroxy-phenazine, pyocyanin, and pyochellin), rhamnolipids and a series of already characterized 4-hydroxy-2-alkylquinolines (HAQs) as well as novel 2,3,4-trihydroxy-2-alkylquinolines and 1,2,3,4-tetrahydroxy-2-alkylquinolines in crude extract of BRp3. These secondary metabolites might be responsible for the profound antibacterial activity of BRp3 against Xoo pathogen. Another contributing factor toward the suppression of the pathogen was the induction of defense related enzymes in the rice plant by the inoculated strain BRp3. When used as an inoculant in a field trial, this strain enhanced the grain and straw yields by 51 and 55%, respectively, over non-inoculated control. Confocal Laser Scanning Microscopy (CLSM) used in combination with immunofluorescence marker confirmed P. aeruginosa BRp3 in the rice rhizosphere under sterilized as well as field conditions. The results provide evidence that novel secondary metabolites produced by BRp3 may contribute to its activity as a biological control agent against Xoo and its potential to promote the growth and yield of Super Basmati rice.
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Affiliation(s)
- Sumera Yasmin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Fauzia Y Hafeez
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Muhammad S Mirza
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Maria Rasul
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Hafiz M I Arshad
- Plant Protection Division, Nuclear Institute of Agriculture and Biology, Faisalabad, Pakistan
| | - Muhammad Zubair
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Mazhar Iqbal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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Ben Tekaya S, Ganesan AS, Guerra T, Dawson JO, Forstner MRJ, Hahn D. Sybr Green- and TaqMan-Based Quantitative PCR Approaches Allow Assessment of the Abundance and Relative Distribution of Frankia Clusters in Soils. Appl Environ Microbiol 2017; 83:e02833-16. [PMID: 27986724 PMCID: PMC5311412 DOI: 10.1128/aem.02833-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/09/2016] [Indexed: 11/20/2022] Open
Abstract
The nodule-forming actinobacterial genus Frankia can generally be divided into 4 taxonomic clusters, with clusters 1, 2, and 3 representing nitrogen-fixing strains of different host infection groups and cluster 4 representing atypical, generally non-nitrogen-fixing strains. Recently, quantitative PCR (qPCR)-based quantification methods have been developed for frankiae of clusters 1 and 3; however, similar approaches for clusters 2 and 4 were missing. We amended a database of partial 23S rRNA gene sequences of Frankia strains belonging to clusters 1 and 3 with sequences of frankiae representing clusters 2 and 4. The alignment allowed us to design primers and probes for the specific detection and quantification of these Frankia clusters by either Sybr Green- or TaqMan-based qPCR. Analyses of frankiae in different soils, all obtained from the same region in Illinois, USA, provided similar results, independent of the qPCR method applied, with abundance estimates of 10 × 105 to 15 × 105 cells (g soil)-1 depending on the soil. Diversity was higher in prairie soils (native, restored, and cultivated), with frankiae of all 4 clusters detected and those of cluster 4 dominating, while diversity in soils under Alnus glutinosa, a host plant for cluster 1 frankiae, or Betula nigra, a related nonhost plant, was restricted to cluster 1 and 3 frankiae and generally members of subgroup 1b were dominating. These results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.IMPORTANCE Root nodule formation by the actinobacterium Frankia is host plant specific and largely, but not exclusively, correlates with assignments of strains to specific clusters within the genus. Due to the lack of adequate detection and quantification tools, studies on Frankia have been limited to clusters 1 and 3 and generally excluded clusters 2 and 4. We have developed tools for the detection and quantification of clusters 2 and 4, which can now be used in combination with those developed for clusters 1 and 3 to retrieve information on the ecology of all clusters delineated within the genus Frankia Our initial results indicate that vegetation affects the basic composition of frankiae in soils, with higher diversity in prairie soils compared to much more restricted diversity under some host and nonhost trees.
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Affiliation(s)
| | | | - Trina Guerra
- Texas State University, Department of Biology, San Marcos, Texas, USA
| | - Jeffrey O Dawson
- University of Illinois at Urbana-Champaign, Department of Natural Resources and Environmental Sciences, Urbana, Illinois, USA
| | | | - Dittmar Hahn
- Texas State University, Department of Biology, San Marcos, Texas, USA
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Rodriguez D, Guerra TM, Forstner MR, Hahn D. Diversity of Frankia in soil assessed by Illumina sequencing of nifH gene fragments. Syst Appl Microbiol 2016; 39:391-7. [DOI: 10.1016/j.syapm.2016.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 02/02/2023]
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Põlme S, Bahram M, Kõljalg U, Tedersoo L. Global biogeography of Alnus-associated Frankia actinobacteria. THE NEW PHYTOLOGIST 2014; 204:979-988. [PMID: 25124146 DOI: 10.1111/nph.12962] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/03/2014] [Indexed: 06/03/2023]
Abstract
Macroecological patterns of microbes have received relatively little attention until recently. This study aimed to disentangle the determinants of the global biogeographic community of Alnus-associated actinobacteria belonging to the Frankia alni complex. By determining a global sequence similarity threshold for the nitrogenase reductase (nifH) gene, we separated Frankia into operational taxonomic units (OTUs) and tested the relative effects of Alnus phylogeny, geographic relatedness, and climatic and edaphic variables on community composition at the global scale. Based on the optimal nifH gene sequence similarity threshold of 99.3%, we distinguished 43 Frankia OTUs from root systems of 22 Alnus species on four continents. Host phylogeny was the main determinant of Frankia OTU-based community composition, but there was no effect on the phylogenetic structure of Frankia. Biogeographic analyses revealed the strongest cross-continental links over the Beringian land bridge. Despite the facultative symbiotic nature of Frankia, phylogenetic relations among Alnus species play a prominent role in structuring root-associated Frankia communities and their biogeographic patterns. Our results suggest that Alnus species exert strong phylogenetically determined selection pressure on compatible Actinobacteria.
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Affiliation(s)
- Sergei Põlme
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., 51005, Tartu, Estonia; Natural History Museum of Tartu University, 46 Vanemuise Street, 51014, Tartu, Estonia
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Bouizgarne B, Ait Ben Aouamar A. Diversity of Plant Associated Actinobacteria. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2014. [DOI: 10.1007/978-3-319-05936-5_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Samant S, Amann RI, Hahn D. Evaluation of the 23S rRNA gene as target for qPCR based quantification of Frankia in soils. Syst Appl Microbiol 2013; 37:229-34. [PMID: 24315016 DOI: 10.1016/j.syapm.2013.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/08/2013] [Indexed: 12/30/2022]
Abstract
The 23S rRNA gene was evaluated as target for the development of Sybr Green-based quantitative PCR (qPCR) for the analysis of nitrogen-fixing members of the genus Frankia or subgroups of these in soil. A qPCR with a primer combination targeting all nitrogen-fixing frankiae (clusters 1, 2 and 3) resulted in numbers similar to those obtained with a previously developed qPCR using nifH gene sequences, both with respect to introduced and indigenous Frankia populations. Primer combinations more specifically targeting three subgroups of the Alnus host infection group (cluster 1) or members of the Elaeagnus host infection group (cluster 3) were specific for introduced strains of the target group, with numbers corresponding to those obtained by quantification of nitrogen-fixing frankiae with both the 23S rRNA and nifH genes as target. Method verification on indigenous Frankia populations in soils, i.e. in depth profiles from four sites at an Alnus glutinosa stand, revealed declining numbers in the depth profiles, with similar abundance of all nitrogen-fixing frankiae independent of 23S rRNA or nifH gene targets, and corresponding numbers of one group of frankiae of the Alnus host infection only, with no detections of frankiae representing the Elaeagnus, Casuarina, or a second subgroup of the Alnus host infection groups.
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Affiliation(s)
- Suvidha Samant
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA.
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Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest. Appl Environ Microbiol 2013; 80:281-8. [PMID: 24162570 DOI: 10.1128/aem.02362-13] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth.
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Diversity of Frankia Strains, Actinobacterial Symbionts of Actinorhizal Plants. SOIL BIOLOGY 2013. [DOI: 10.1007/978-3-642-39317-4_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mirza BS, Rodrigues JLM. Development of a direct isolation procedure for free-living diazotrophs under controlled hypoxic conditions. Appl Environ Microbiol 2012; 78:5542-9. [PMID: 22660701 PMCID: PMC3406155 DOI: 10.1128/aem.00714-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 05/22/2012] [Indexed: 11/20/2022] Open
Abstract
Free-living diazotrophs are diverse and ubiquitous in soil, contributing the nitrogen pool in natural ecosystems. The isolation of nitrogen-fixing microorganisms has relied on semisolid nitrogen-free medium enrichment, followed by multiple subculturing steps. These procedures limit the diversity of recovered isolates. In the current study, we investigated three different isolation strategies for free-living diazotrophs using a soil sample from the Amazon forest. The methods were (i) direct plating on solid nitrogen-free medium under a 2% O(2) concentration, (ii) enrichment in semisolid nitrogen-free medium before plating on solid nitrogen-free medium under 2% O(2), and (iii) enrichment followed by subculturing in the semisolid nitrogen-free medium before plating on nitrogen containing medium under a 21% O(2) concentration. A total of 794 isolates were differentiated by their genomic fingerprinting patterns, and strains with unique profiles were identified on the basis of sequencing of their 16S rRNA gene. Isolates belonged to four bacterial phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodetes. The novel strategy of combining a solid N-free medium and hypoxic conditions showed an increase of 62.6% in the diversity of diazotrophs in comparison to that obtained by the conventional semisolid medium-based methods. All isolates grew on the nitrogen-free medium under a 2% O(2) concentration, 78% of them showed the presence of the nifH gene, and 39% tested positive for acetylene reduction activity. Our results suggest that direct plating of soil dilutions on nitrogen-free solid medium under a 2% O(2) concentration is a useful strategy for the isolation of the diverse diazotrophic communities.
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Affiliation(s)
- Babur S Mirza
- Department of Biology, University of Texas, Arlington, Texas, USA
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19
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Gaby JC, Buckley DH. A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PLoS One 2012; 7:e42149. [PMID: 22848735 PMCID: PMC3405036 DOI: 10.1371/journal.pone.0042149] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 07/02/2012] [Indexed: 11/30/2022] Open
Abstract
The nifH gene is the most widely sequenced marker gene used to identify nitrogen-fixing Bacteria and Archaea. Numerous PCR primers have been designed to amplify nifH, but a comprehensive evaluation of nifH PCR primers has not been performed. We performed an in silico analysis of the specificity and coverage of 51 universal and 35 group-specific nifH primers by using an aligned database of 23,847 nifH sequences. We found that there are 15 universal nifH primers that target 90% or more of nitrogen fixers, but that there are also 23 nifH primers that target less than 50% of nifH sequences. The nifH primers we evaluated vary in their phylogenetic bias and their ability to recover sequences from commonly sampled environments. In addition, many of these primers will amplify genes that do not mediate nitrogen fixation, and thus it would be advisable for researchers to screen their sequencing results for the presence of non-target genes before analysis. Universal primers that performed well in silico were tested empirically with soil samples and with genomic DNA from a phylogenetically diverse set of nitrogen-fixing strains. This analysis will be of great utility to those engaged in molecular analysis of nifH genes from isolates and environmental samples.
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Affiliation(s)
- John Christian Gaby
- Department of Crop and Soil Sciences, Cornell University, Ithaca, New York, United States of America
| | - Daniel H. Buckley
- Department of Crop and Soil Sciences, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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20
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Samant S, Sha Q, Iyer A, Dhabekar P, Hahn D. Quantification of Frankia in soils using SYBR Green based qPCR. Syst Appl Microbiol 2012; 35:191-7. [PMID: 22326815 DOI: 10.1016/j.syapm.2011.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/11/2011] [Accepted: 12/12/2011] [Indexed: 10/14/2022]
Abstract
A SYBR Green based qPCR method was developed for the quantification of clusters 1 and 3 of the actinomycete Frankia in soils. Primer nifHr158 was designed to be used as reverse primer in combination with forward primer nifHf1 specifically amplifying a 191-bp fragment of the nifH gene of these Frankia. The primer combination was tested for specificity on selected pure cultures, and by comparative sequence analyses of randomly selected clones of a clone library generated with these primers from soil DNA extracts. After adjustments of DNA extraction conditions, and the determination of extraction efficiencies used for sample normalization, copy numbers of nifH genes representing Frankia of clusters 1 and 3 were quantified in different mineral soils, resulting in cell density estimates for these Frankia of up to 10(6) cells [g soil {dry weight}](-1) depending on the soil. Despite indications that the nifH gene is not a perfect target for the quantification of Frankia, the qPCR method described here provides a new tool for the quantification and thus a more complete examination of the ecology of Frankia in soils.
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Affiliation(s)
- Suvidha Samant
- Texas State University, Department of Biology, San Marcos, TX 78666, USA
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21
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Hahn D, Mirza B, Benagli C, Vogel G, Tonolla M. Typing of nitrogen-fixing Frankia strains by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry. Syst Appl Microbiol 2011; 34:63-8. [PMID: 21242047 DOI: 10.1016/j.syapm.2010.11.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/27/2010] [Accepted: 11/16/2010] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) was evaluated as a technique to characterize strains of the nitrogen-fixing actinomycete Frankia. MALDI-TOF MS reliably distinguished 37 isolates within the genus Frankia and assigned them to their respective host infection groups, i.e., the Alnus/Casuarina and the Elaeagnus host infection groups. The assignment of individual strains to sub-groups within the respective host infection groups was consistent with classification based on comparative sequence analysis of nifH gene fragments, confirming the usefulness of MALDI-TOF MS as a rapid and reliable tool for the characterization of Frankia strains.
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Affiliation(s)
- Dittmar Hahn
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
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22
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Pokharel A, Mirza BS, Dawson JO, Hahn D. Frankia populations in soil and root nodules of sympatrically grown Alnus taxa. MICROBIAL ECOLOGY 2011; 61:92-100. [PMID: 20838787 DOI: 10.1007/s00248-010-9726-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 07/13/2010] [Indexed: 05/29/2023]
Abstract
The genetic diversity of Frankia populations in soil and in root nodules of sympatrically grown Alnus taxa was evaluated by rep-polymerase chain reaction (PCR) and nifH gene sequence analyses. Rep-PCR analyses of uncultured Frankia populations in root nodules of 12 Alnus taxa (n=10 nodules each) growing sympatrically in the Morton Arboretum near Chicago revealed identical patterns for nodules from each Alnus taxon, including replicate trees of the same host taxon, and low diversity overall with only three profiles retrieved. One profile was retrieved from all nodules of nine taxa (Alnus incana subsp. incana, Alnus japonica, Alnus glutinosa, Alnus incana subsp. tenuifolia, Alnus incana subsp. rugosa, Alnus rhombifolia, Alnus mandshurica, Alnus maritima, and Alnus serrulata), the second was found in all nodules of two plant taxa (A. incana subsp. hirsuta and A. glutinosa var. pyramidalis), and the third was unique for all Frankia populations in nodules of A. incana subsp. rugosa var. americana. Comparative sequence analyses of nifH gene fragments in nodules representing these three profiles assigned these frankiae to different subgroups within the Alnus host infection group. None of these sequences, however, represented frankiae detectable in soil as determined by sequence analysis of 73 clones from a Frankia-specific nifH gene clone library. Additional analyses of nodule populations from selected alders growing on different soils demonstrated the presence of different Frankia populations in nodules for each soil, with populations showing identical sequences in nodules from the same soil, but differences between plant taxa. These results suggest that soil environmental conditions and host plant genotype both have a role in the selection of Frankia strains by a host plant for root nodule formation, and that this selection is not merely a function of the abundance of a Frankia strain in soil.
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Affiliation(s)
- Anita Pokharel
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
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23
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Kennedy PG, Schouboe JL, Rogers RH, Weber MG, Nadkarni NM. Frankia and Alnus rubra canopy roots: an assessment of genetic diversity, propagule availability, and effects on soil nitrogen. MICROBIAL ECOLOGY 2010; 59:214-220. [PMID: 19787390 DOI: 10.1007/s00248-009-9587-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 08/15/2009] [Accepted: 08/22/2009] [Indexed: 05/28/2023]
Abstract
The ecological importance of microbial symbioses in terrestrial soils is widely recognized, but their role in soils that accumulate in forest canopies is almost entirely unknown. To address this gap, this study investigated the Frankia-Alnus rubra symbiosis in canopy and forest floor roots at Olympic National Park, WA, USA. Sixteen mature A. rubra trees were surveyed and Frankia genetic diversity in canopy and forest floor nodules was assessed with sequence-based nifH analyses. A seedling bioassay experiment was conducted to determine Frankia propagule availability in canopy and forest floor soils. Total soil nitrogen from both environments was also quantified. Nodules were present in the canopies of nine of the 16 trees sampled. Across the study area, Frankia canopy and forest floor assemblages were similar, with both habitats containing the same two genotypes. The composition of forest floor and canopy genotypes on the same tree was not always identical, however, suggesting that dispersal was not a strictly local phenomenon. Frankia seedling colonization was similar in canopy soils regardless of the presence of nodules as well as in forest floor soils, indicating that dispersal was not likely to be a major limiting factor. The total soil nitrogen of canopy soils was higher than that of forest floor soils, but the presence of Frankia nodules in canopy soils did not significantly alter soil nitrogen levels. Overall, this study indicates that the Frankia-A. rubra symbiosis is similar in canopy and forest floor environments. Because canopy roots are exposed to different environmental conditions within very small spatial areas and because those areas can be easily manipulated (e.g., fertilizer or watering treatments), they present microbial ecologists with a unique arena to examine root-microbe interactions.
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Affiliation(s)
- Peter G Kennedy
- Department of Biology, Lewis and Clark College, Portland, OR 97219, USA.
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Welsh AK, Dawson JO, Gottfried GJ, Hahn D. Diversity of Frankia populations in root nodules of geographically isolated Arizona alder trees in central Arizona (United States). Appl Environ Microbiol 2009; 75:6913-8. [PMID: 19734342 PMCID: PMC2772444 DOI: 10.1128/aem.01103-09] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 08/26/2009] [Indexed: 11/20/2022] Open
Abstract
The diversity of uncultured Frankia populations in root nodules of Alnus oblongifolia trees geographically isolated on mountaintops of central Arizona was analyzed by comparative sequence analyses of nifH gene fragments. Sequences were retrieved from Frankia populations in nodules of four trees from each of three mountaintops (n = 162) and their levels of diversity compared using spatial genetic clustering methods and single-nucleotide or 1, 3, or 5% sequence divergence thresholds. With the single-nucleotide threshold level, 45 different sequences with significant differences between the mountaintops were retrieved, with the southern site partitioning in a separate population from the two other sites. Some of these sequences were identical in nodules from different mountaintops and to those of strains isolated from around the world. A high level of diversity that resulted in the assignment of 14 clusters of sequences was also found on the 1% divergence level. Single-nucleotide and 1% divergence levels thus demonstrate microdiversity of frankiae in root nodules of A. oblongifolia trees and suggest a partitioning of diversity by site. At the 3 and 5% divergence levels, however, diversity was reduced to three clusters or one cluster, respectively, with no differentiation by mountaintop. Only at the 5% threshold level do all Frankia strains previously assigned to one genomic group cluster together.
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Affiliation(s)
- Allana K. Welsh
- Texas State University, Department of Biology, 601 University Drive, San Marcos, Texas 78666, University of Illinois at Urbana-Champaign, Department of Natural Resources and Environmental Sciences, 1201 South Dorner Drive, Urbana, Illinois 61801, USDA Forest Service, Rocky Mountain Research Station, Tonto National Forest, 2324 E. McDowell Road, Phoenix, Arizona 85006
| | - Jeffrey O. Dawson
- Texas State University, Department of Biology, 601 University Drive, San Marcos, Texas 78666, University of Illinois at Urbana-Champaign, Department of Natural Resources and Environmental Sciences, 1201 South Dorner Drive, Urbana, Illinois 61801, USDA Forest Service, Rocky Mountain Research Station, Tonto National Forest, 2324 E. McDowell Road, Phoenix, Arizona 85006
| | - Gerald J. Gottfried
- Texas State University, Department of Biology, 601 University Drive, San Marcos, Texas 78666, University of Illinois at Urbana-Champaign, Department of Natural Resources and Environmental Sciences, 1201 South Dorner Drive, Urbana, Illinois 61801, USDA Forest Service, Rocky Mountain Research Station, Tonto National Forest, 2324 E. McDowell Road, Phoenix, Arizona 85006
| | - Dittmar Hahn
- Texas State University, Department of Biology, 601 University Drive, San Marcos, Texas 78666, University of Illinois at Urbana-Champaign, Department of Natural Resources and Environmental Sciences, 1201 South Dorner Drive, Urbana, Illinois 61801, USDA Forest Service, Rocky Mountain Research Station, Tonto National Forest, 2324 E. McDowell Road, Phoenix, Arizona 85006
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Mirza BS, Welsh A, Rieder JP, Paschke MW, Hahn D. Diversity of frankiae in soils from five continents. Syst Appl Microbiol 2009; 32:558-70. [PMID: 19692194 DOI: 10.1016/j.syapm.2009.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 07/26/2009] [Accepted: 07/27/2009] [Indexed: 11/17/2022]
Abstract
Clone libraries of nifH gene fragments specific for the nitrogen-fixing actinomycete Frankia were generated from six soils obtained from five continents using a nested PCR. Comparative sequence analyses of all libraries (n=247 clones) using 96 to 97% similarity thresholds revealed the presence of three and four clusters of frankiae representing the Elaeagnus and the Alnus host infection groups, respectively. Diversity of frankiae was represented by fewer clusters (i.e., up to four in total) within individual libraries, with one cluster generally harboring the vast majority of sequences. Meta-analysis including sequences previously published for cultures (n=48) and for uncultured frankiae in root nodules of Morella pensylvanica formed in bioassays with the respective soils (n=121) revealed a higher overall diversity with four and six clusters of frankiae representing the Elaeagnus and the Alnus host infection groups, respectively, and displayed large differences in cluster assignments between sequences retrieved from clone libraries and those obtained from nodules, with assignments to the same cluster only rarely encountered for individual soils. These results demonstrate large differences between detectable Frankia populations in soil and those in root nodules indicating the inadequacy of bioassays for the analysis of frankiae in soil and the role of plants in the selection of frankiae from soil for root nodule formation.
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Affiliation(s)
- Babur S Mirza
- Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA
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Mirza BS, Welsh A, Hahn D. Growth of Frankia strains in leaf litter-amended soil and the rhizosphere of a nonactinorhizal plant. FEMS Microbiol Ecol 2009; 70:132-41. [PMID: 19678845 DOI: 10.1111/j.1574-6941.2009.00746.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The ability of Frankia strains to grow in the rhizosphere of a nonactinorhizal plant, Betula pendula, in surrounding bulk soil and in soil amended with leaf litter was analyzed 6 weeks after inoculation of pure cultures by in situ hybridization. Growth responses were related to taxonomic position as determined by comparative sequence analysis of nifH gene fragments and of an actinomycetes-specific insertion in Domain III of the 23S rRNA gene. Phylogenetic analyses confirmed the basic classification of Frankia strains by host infection groups, and allowed a further differentiation of Frankia clusters within the Alnus host infection group. Except for Casuarina-infective Frankia strains, all other strains of the Alnus and the Elaeagnus host infection groups displayed growth in the rhizosphere of B. pendula, and none of them grew in the surrounding bulk soil that was characterized by a very low organic matter content. Only a small number of strains that all belonged to a distinct phylogenetic cluster within the Alnus host infection group grew in soil amended with ground leaf litter from B. pendula. These results demonstrate that saprotrophic growth of frankiae is a common trait for most members of the genus, and the supporting factors for growth (i.e. carbon utilization capabilities) varied with the host infection group and the phylogenetic affiliation of the strains.
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Affiliation(s)
- Babur S Mirza
- Department of Biology, Texas State University, San Marcos, TX 78666, USA
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