Papers by Francina Phalane
South African Journal of Botany, Mar 1, 2018
opposite was observed at higher concentrations (at 10% and 20%). The reduction in germination per... more opposite was observed at higher concentrations (at 10% and 20%). The reduction in germination percentage, morphology and biomass was also correlated to the water potential of PEG solutions. Shoot and root length and biomass were significantly reduced with increased osmotic stress at 10% and 20% (± 57% and ± 60%). Photosynthetic pigments in chia leaves were significantly decreased with increased levels of osmotic stress. These findings presented in this study suggest that chia can resist moderate levels of osmotic stress but sensitive at higher levels. Thus further investigations of this "superfood" includes looking at proteomic profiles across all treatments and possibly obtaining protein biomarkers that are responsible for drought tolerance in this crop, which can also be implemented in other staple food crops.
Frontiers in Microbiology, Jun 4, 2019
Vachellia karroo (formerly Acacia karroo) is a widespread legume species indigenous to southern A... more Vachellia karroo (formerly Acacia karroo) is a widespread legume species indigenous to southern Africa. Little is known regarding the identity or diversity of rhizobia that associate with this plant in its native range in South Africa. The aims of this study were therefore: (i) to gather a collection of rhizobia associated with V. karroo from a wide range of geographic locations and biomes; (ii) to identify the isolates and infer their evolutionary relationships with known rhizobia; (iii) to confirm their nodulation abilities by using them in inoculation assays to induce nodules under glasshouse conditions. To achieve these aims, soil samples were collected from 28 locations in seven biomes throughout South Africa, which were then used to grow V. karroo seedlings under nitrogen-free conditions. The resulting 88 bacterial isolates were identified to genus-level using 16S rRNA sequence analysis and to putative species-level using recA-based phylogenetic analyses. Our results showed that the rhizobial isolates represented members of several genera of Alphaproteobacteria (Bradyrhizobium, Ensifer, Mesorhizobium, and Rhizobium), as well as Paraburkholderia from the Betaproteobacteria. Our study therefore greatly increases the known number of Paraburkholderia isolates which can associate with this southern African mimosoid host. We also show for the first time that members of this genus can associate with legumes, not only in the Fynbos biome, but also in the Albany Thicket and Succulent Karoo biomes. Twenty-six putative species were delineated among the 88 isolates, many of which appeared to be new to Science with other likely being conspecific or closely related to E. alkalisoli, M. abyssinicae, M. shonense, and P. tropica. We encountered only a single isolate of Bradyrhizobium, which is in contrast to the dominant association of this genus with Australian Acacia. V. karroo also associates with diverse genera in the Grassland biome where it is quite invasive and involved in bush encroachment. Our findings therefore suggest that V. karroo is a promiscuous host capable of forming effective nodules with both alphaand beta-rhizobia, which could be a driving force behind the ecological success of this tree species.
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, May 3, 2019
Twelve nodulating Paraburkholderia strains isolated from indigenous South African fynbos legume H... more Twelve nodulating Paraburkholderia strains isolated from indigenous South African fynbos legume Hypocalyptus sophoroides were investigated to determine their taxonomic status. Genealogical concordance analysis, based on six loci (16S rRNA, atpD, recA, rpoB, lepA and gltB), revealed that they separate into two consistent and exclusive groups. Average nucleotide identity and DNA-DNA hybridisation comparisons indicated that they were sufficiently divergent from their closest known phylogenetic relatives (Paraburkholderia caledonica and Paraburkholderia terrae, respectively) to be regarded as novel species. This was also supported by the results of fatty acid analysis and metabolic characterisation. For these two isolate groups, we accordingly propose the new species Paraburkholderia strydomiana sp. nov. with WK1.1f T (= LMG 28731 T = SARCC1213 T) as its type strain and Paraburkholderia steynii sp. nov. with HC1.1ba T (= LMG 28730 T = SARCC696 T) as its type strain. Our data thus showed that H. sophoroides may be considered a promiscuous symbiotic partner due to its ability to associate with multiple species of Paraburkholderia. Keywords Beta-rhizobia Á Burkholderia Á Genealogical concordance Á Hypocalyptus Á Paraburkholderia Á South Africa The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA sequences of type strains WK1.1f T and HC1.1ba T are HF674688 and HF674712, the atpD gene sequences are LN555593 and LN555601, the rpoB accession numbers are LN555614 and LN555624 and the recA accession numbers are HF544384 and HF544408. Lastly the accession numbers for the lepA gene sequences of WK1.1f T and HC1.1ba T are LT708273 and LT708274, while the gltB accessions are LT708294 and LT708295. The NCBI genome accession numbers for the type strains are MWMK00000000 and MWML00000000.
Antonie van Leeuwenhoek, 2019
Twelve nodulating Paraburkholderia strains isolated from indigenous South African fynbos legume H... more Twelve nodulating Paraburkholderia strains isolated from indigenous South African fynbos legume Hypocalyptus sophoroides were investigated to determine their taxonomic status. Genealogical concordance analysis, based on six loci (16S rRNA, atpD, recA, rpoB, lepA and gltB), revealed that they separate into two consistent and exclusive groups. Average nucleotide identity and DNA-DNA hybridisation comparisons indicated that they were sufficiently divergent from their closest known phylogenetic relatives (Paraburkholderia caledonica and Paraburkholderia terrae, respectively) to be regarded as novel species. This was also supported by the results of fatty acid analysis and metabolic characterisation. For these two isolate groups, we accordingly propose the new species Paraburkholderia strydomiana sp. nov. with WK1.1f T (= LMG 28731 T = SARCC1213 T) as its type strain and Paraburkholderia steynii sp. nov. with HC1.1ba T (= LMG 28730 T = SARCC696 T) as its type strain. Our data thus showed that H. sophoroides may be considered a promiscuous symbiotic partner due to its ability to associate with multiple species of Paraburkholderia. Keywords Beta-rhizobia Á Burkholderia Á Genealogical concordance Á Hypocalyptus Á Paraburkholderia Á South Africa The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA sequences of type strains WK1.1f T and HC1.1ba T are HF674688 and HF674712, the atpD gene sequences are LN555593 and LN555601, the rpoB accession numbers are LN555614 and LN555624 and the recA accession numbers are HF544384 and HF544408. Lastly the accession numbers for the lepA gene sequences of WK1.1f T and HC1.1ba T are LT708273 and LT708274, while the gltB accessions are LT708294 and LT708295. The NCBI genome accession numbers for the type strains are MWMK00000000 and MWML00000000.
South African Journal of Botany, 2018
opposite was observed at higher concentrations (at 10% and 20%). The reduction in germination per... more opposite was observed at higher concentrations (at 10% and 20%). The reduction in germination percentage, morphology and biomass was also correlated to the water potential of PEG solutions. Shoot and root length and biomass were significantly reduced with increased osmotic stress at 10% and 20% (± 57% and ± 60%). Photosynthetic pigments in chia leaves were significantly decreased with increased levels of osmotic stress. These findings presented in this study suggest that chia can resist moderate levels of osmotic stress but sensitive at higher levels. Thus further investigations of this "superfood" includes looking at proteomic profiles across all treatments and possibly obtaining protein biomarkers that are responsible for drought tolerance in this crop, which can also be implemented in other staple food crops.
Frontiers in Microbiology, 2019
Vachellia karroo (formerly Acacia karroo) is a widespread legume species indigenous to southern A... more Vachellia karroo (formerly Acacia karroo) is a widespread legume species indigenous to southern Africa. Little is known regarding the identity or diversity of rhizobia that associate with this plant in its native range in South Africa. The aims of this study were therefore: (i) to gather a collection of rhizobia associated with V. karroo from a wide range of geographic locations and biomes; (ii) to identify the isolates and infer their evolutionary relationships with known rhizobia; (iii) to confirm their nodulation abilities by using them in inoculation assays to induce nodules under glasshouse conditions. To achieve these aims, soil samples were collected from 28 locations in seven biomes throughout South Africa, which were then used to grow V. karroo seedlings under nitrogen-free conditions. The resulting 88 bacterial isolates were identified to genus-level using 16S rRNA sequence analysis and to putative species-level using recA-based phylogenetic analyses. Our results showed that the rhizobial isolates represented members of several genera of Alphaproteobacteria (Bradyrhizobium, Ensifer, Mesorhizobium, and Rhizobium), as well as Paraburkholderia from the Betaproteobacteria. Our study therefore greatly increases the known number of Paraburkholderia isolates which can associate with this southern African mimosoid host. We also show for the first time that members of this genus can associate with legumes, not only in the Fynbos biome, but also in the Albany Thicket and Succulent Karoo biomes. Twenty-six putative species were delineated among the 88 isolates, many of which appeared to be new to Science with other likely being conspecific or closely related to E. alkalisoli, M. abyssinicae, M. shonense, and P. tropica. We encountered only a single isolate of Bradyrhizobium, which is in contrast to the dominant association of this genus with Australian Acacia. V. karroo also associates with diverse genera in the Grassland biome where it is quite invasive and involved in bush encroachment. Our findings therefore suggest that V. karroo is a promiscuous host capable of forming effective nodules with both alphaand beta-rhizobia, which could be a driving force behind the ecological success of this tree species.
Molecular phylogenetics and evolution, Jul 1, 2016
The genus Bradyrhizobium contains predominantly nitrogen-fixing legume symbionts. Phylogenetic an... more The genus Bradyrhizobium contains predominantly nitrogen-fixing legume symbionts. Phylogenetic analysis of the genes responsible for their symbiotic abilities (i.e., those encoded on the nodulation [nod] and nitrogen-fixation [nif] loci) has facilitated the development of an extensive phylogeographic framework for the genus. This framework however contains only a few nodulating isolates from Africa. Here we focused on nodulating Bradyrhizobium isolates associated with native southern African legumes in the tribes Genisteae and Crotalarieae found along the Great Escarpment in the Mpumalanga Province of South Africa. The aims of this study were to: (1) obtain rhizobial isolates from legumes in the Genisteae and Crotalarieae; (2) verify their nodulation ability; (3) characterize them to species level based on phylogenetic analyses of several protein coding gene regions (atpD, dnaK, glnII, recA, rpoB and gyrB) and (4) determine their placement in the phylogeographic framework inferred f...
Systematic and Applied Microbiology, 2015
Despite the diversity of Burkholderia species known to nodulate legumes in introduced and native ... more Despite the diversity of Burkholderia species known to nodulate legumes in introduced and native regions, relatively few taxa have been formally described. For example, the Cape Floristic Region of South Africa is thought to represent one of the major centres of diversity for the rhizobial members of Burkholderia, yet only five species have been described from legumes occurring in this region and numerous are still awaiting taxonomic treatment. Here, we investigated the taxonomic status of 12 South African root-nodulating Burkholderia isolates from native papilionoid legumes (Hypocalyptus coluteoides, H. oxalidifolius, H. sophoroides and Virgilia oroboides). Analysis of four gene regions (16S rRNA, recA, atpD and rpoB) revealed that the isolates represent a genealogically unique and exclusive assemblage within the genus. Its distinctness was supported by all other aspects of the polyphasic approach utilized, including the genome-based criteria DNA-DNA hybridization (70.9%) and average nucleotide identities (96%). We accordingly propose the name B. kirstenboschensis sp. nov. for this taxon with isolate Kb15 T (=LMG 28727 T ; =SARC 695 T) as its type strain. Our data showed that intraspecific genome size differences (0.81 Mb) and the occurrence of large DNA regions that are apparently unique to single individuals (16-23% of an isolate's genome) can significantly limit the value of data obtained from DNA-DNA hybridization experiments. Substitution of DNA-DNA hybridization with whole genome sequencing as a prerequisite for the description of Burkholderia species will undoubtedly speed up the pace at which their diversity are documented, especially in hyperdiverse regions such as the Cape Floristic Region.
South African Journal of Botany, 2015
infestation, and 48 h later. For both susceptible and resistant cultivars, Alexin™ treatment at a... more infestation, and 48 h later. For both susceptible and resistant cultivars, Alexin™ treatment at a concentration of 0.25% did not induce any significant increase in activity compared to control. Infestation of Alexin™ treated (0.375% and 0.5%) susceptible plants induced almost similar responses in both enzyme activities, which were significantly higher than those of control; a concentration of 0.375% caused a 2.5-fold increase in β-1,3-glucanase and a 2.3-fold increase in peroxidase activity. In the resistant plants, RWA infestation of Alexin™-treated (0.375%) plants activated specific changes in enzyme activities; a significant increase was noted only in peroxidase activity of Elands but not PAN 3379. Furthermore, Alexin™ treatment and infestation did not induce any significant increase in β-1,3-glucanase activity of either Elands or PAN 3379. These results suggest that Alexin™ has a specific priming effect that is sensitive to concentration and depends on plant genotype. Future studies should indicate if Alexin™ treatment is also biotype specific in the protection of wheat against the RWA.
Current Plant Science and Biotechnology in Agriculture
Isolation of rhizobia from Lebeckia species indigenous to South Africa and their nodulation prope... more Isolation of rhizobia from Lebeckia species indigenous to South Africa and their nodulation properties on Lebeckia and the promiscuous legumes cowpea and siratro CHAPTER 3 DNA fingerprinting and 16S rRNA gene analysis of rhizobia associated with Lebeckia species in South Africa
South African Journal of Botany, 2009
to (1) assess the useful-plant diversity, (2) determine the origin of the species (alien or indig... more to (1) assess the useful-plant diversity, (2) determine the origin of the species (alien or indigenous), (3) examine the different use categories, and (4) document the positions of plants in indigenous gardening systems. We conducted a survey of 40 muzis selected from eight locations along an urbanisation gradient in northeastern KwaZulu-Natal. A total of 149 useful plant species belonging to 72 plant families were recorded, comprising 91 medicinal, 32 food and 26 spiritual plants. Most of these species (68%) are indigenous (semi-wild domesticates), while the rest (32%) are aliens (naturalized and cultivated exotics). The ten most dominant plant species (50-65% frequency) were the fruit trees Hyphaene coriacea, Mangifera indica, Persea americana, Psidium guajava and Vangueria infausta, the crops Cucurbita pepo, Ipomoea batatas and Zea mays, and medicinals Bidens pilosa and Catharanthus roseus. A comparison between rural and peri-urban gardens revealed that rural gardens have a higher mean species richness (26 compared to 17), and 35% of the taxa are alien in contrast to the 44% of peri-urban gardens. Nearly 78% of the plants from the peri-urban homesteads were cultivated, whereas 46% of the species from the rural gardens occur naturally (54% cultivated). For instance, the third most dominant species in rural gardens is Sclerocarya birrea (marula), an indigenous fruit tree (80% of gardens). No significant difference was evident with regard to different use categories. Homegarden floras are collectively planted and positioned according to cultural practices passed down generations. This results in a common layout plan which is repeated in the gardens of rural areas, but is absent from the peri-urban areas.
PLoS ONE, 2013
The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied... more The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied, even though recent reports suggest the occurrence of nodulating Burkholderia species unique to the region. In this study, we considered the diversity and evolution of nodulating Burkholderia associated with the endemic papilionoid tribes Hypocalypteae and Podalyrieae. We identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16S rRNA and recA housekeeping gene regions. In order to gain insight into the evolution of the nodulation and diazotrophy of these rhizobia we analysed the genes encoding NifH and NodA. The majority of these 69 isolates appeared to be unique, potentially representing novel species. Evidence of horizontal gene transfer determining the symbiotic ability of these Cape Floristic Region isolates indicate evolutionary origins distinct from those of nodulating Burkholderia from elsewhere in the world. Overall, our findings suggest that Burkholderia species associated with fynbos legumes are highly diverse and their symbiotic abilities have unique ancestries. It is therefore possible that the evolution of these bacteria is closely linked to the diversification and establishment of legumes characteristic of the Cape Floristic Region.
Biology and Fertility of Soils, 2006
Strain CB756 is usually an effective competitor against indigenous bradyrhizobia for nodulation o... more Strain CB756 is usually an effective competitor against indigenous bradyrhizobia for nodulation of peanut in South Africa. Recently, inoculation of peanut and cowpea with CB756 in loamy sand soils of Botswana or a sandy clay loam in South Africa proved unsuccessful, achieving <2% nodule occupancy. A survey of 'cowpea' bradyrhizobia from five soils in Botswana and one in South Africa showed that many were effective in ability to fix N 2 on peanut and cowpea. However, 15 isolates from Good Hope, Botswana were all effective on cowpea but ineffective on peanut, three failing to nodulate the latter. Selected cowpea isolates were significantly more competitive than CB756 for nodulation of cowpea in Leonard jars, but four were unsuccessful when inoculated at Roodeplaat, South Africa. When strain CB756 and two isolates were inoculated in pots containing Roodeplaat soil, at a 4:1 inoculant to soil bradyrhizobia ratio, their average nodule occupancy was 8% on cowpea compared to 40% on peanut. Significant differences in strain nodule occupancy were not detected on either cowpea or peanut. In contrast, nodule occupancy in loamy sand from Good Hope, Botswana, inoculated at a 40:1 inoculant to soil bradyrhizobia ratio, was 22.4% on cowpea and only 6.8% on peanut. In Good Hope soil, strain CB756 was the weakest competitor on cowpea but strain differences were insignificant on peanut. Whereas the Good Hope soil population was effective on cowpea, it was ineffective on peanut. DNA fingerprinting showed that isolates from Gaborone, Francistown and Roodeplaat contained several different genotypes, whereas those from Good Hope, Rasesa and Maun were more homogeneous. The dominance at Good Hope of genotypes effective on cowpea but ineffective on peanut emphasises the value of assessing the symbiotic capabilities and structures of indigenous populations.
PLoS ONE, 2013
The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied... more The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied, even though recent reports suggest the occurrence of nodulating Burkholderia species unique to the region. In this study, we considered the diversity and evolution of nodulating Burkholderia associated with the endemic papilionoid tribes Hypocalypteae and Podalyrieae. We identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16S rRNA and recA housekeeping gene regions. In order to gain insight into the evolution of the nodulation and diazotrophy of these rhizobia we analysed the genes encoding NifH and NodA. The majority of these 69 isolates appeared to be unique, potentially representing novel species. Evidence of horizontal gene transfer determining the symbiotic ability of these Cape Floristic Region isolates indicate evolutionary origins distinct from those of nodulating Burkholderia from elsewhere in the world. Overall, our findings suggest that Burkholderia species associated with fynbos legumes are highly diverse and their symbiotic abilities have unique ancestries. It is therefore possible that the evolution of these bacteria is closely linked to the diversification and establishment of legumes characteristic of the Cape Floristic Region.
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Papers by Francina Phalane