European Origin of Bradyrhizobium Populations Infecting Lupins and Serradella in Soils of Western Australia and South Africa

We applied a multilocus phylogenetic approach to elucidate the origin of serradella and lupin Bradyrhizobium strains that persist in soils of Western Australia and South Africa. The selected strains belonged to different randomly amplified polymorphic DNA (RAPD)-PCR clusters that were distinct from RAPD clusters of applied inoculant strains. Phylogenetic analyses were performed with nodulation genes (nodA, nodZ, nolL, noeI), housekeeping genes (dnaK, recA, glnII, atpD), and 16S-23S rRNA intergenic transcribed spacer sequences. Housekeeping gene phylogenies revealed that all serradella and Lupinus cosentinii isolates from Western Australia and three of five South African narrow-leaf lupin strains were intermingled with the strains of Bradyrhizobium canariense, forming a well supported branch on each of the trees. All nodA gene sequences of the lupin and serradella bradyrhizobia formed a single branch, referred to as clade II, together with the sequences of other lupin and serradella strains. Similar patterns were detected in nodZ and nolL trees. In contrast, nodA sequences of the strains isolated from native Australian legumes formed either a new branch called clade IV or belonged to clade I or III, whereas their nonsymbiotic genes grouped outside the B. canariense branch. These data suggest that the lupin and serradella strains, including the strains from uncultivated L.cosentinii plants, are descendants of strains that most likely were brought from Europe accidentally with lupin and serradella seeds. The observed dominance of B. canariense strains may be related to this species' adaptation to acid soils common in Western Australia and South Africa and, presumably, to their intrinsic ability to compete for nodulation of lupins and serradella.     

Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species

Bradyrhizobium are N₂-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.     

Effect of drought on Bradyrhizobium japonicum populations in Midwest soils

Background and aims

Bradyrhizobium japonicum and soybean (Glycine max (L.) Merr.) form a symbiotic association which allows for biological nitrogen fixation (BNF) to help meet the nitrogen (N) requirement of soybean plants. Rhizobial inoculants are not always used in soybean production in the Midwestern USA because of high naturalized soil populations, but drought conditions experienced in the region during the 2012 growing season may have led to a decline in numbers resulting in the need for inoculation the following growing season. Therefore, the effect of drought on B. japonicum population size was investigated in this study.

Methods

Drought conditions, 8 weeks long or 4 weeks long preceded (STOP) or followed (START) by 4 weeks of normal watering, were simulated in two contrasting soil types in a greenhouse setting with soybeans as host plants. Drought conditions were monitored by measuring water content. Population size of B. japonicum was quantified using quantitative real-time polymerase chain reaction (qPCR) and most probable number (MPN) methods and compared to population from non-drought treatment.

Results

Using both quantification methods, the response of B. japonicum to drought treatments was minimal.

Conclusions

Drought conditions 4 to 8 weeks long did not reduce B. japonicum population size to levels which would affect soybean growth and development.     

Bradyrhizobium canariense and Bradyrhizobium japonicum are the two dominant rhizobium species in root nodules of lupin and serradella plants growing in Europe

Forty three Bradyrhizobium strains isolated in Poland from root nodules of lupin species (Lupinus albus, L. angustifolius and L. luteus), and pink serradella (Ornithopus sativus) were examined based on phylogenetic analyses of three housekeeping (atpD, glnII and recA) and nodulation (nodA) gene sequences. Additionally, seven strains originating from root-nodules of yellow serradella (O. compressus) from Asinara Island (Italy) were included in this study. Phylogenetic trees revealed that 15 serradella strains, including all yellow serradella isolates, and six lupin strains grouped in Bradyrhizobium canariense (BC) clade, whereas eight strains from pink serradella and 15 lupin strains were assigned to Bradyrhizobium japonicum (BJ1). Apparently, these species are the two dominant groups in soils of central Europe, in the nodules of lupin and serradella plants. Only three strains belonged to other chromosomal lineages: one formed a cluster that was sister to B. canariense, one strain grouped outside the branch formed by B. japonicum super-group, and one strain occupied a distant position in the genus Bradyrhizobium, clustering with strains of the Rhodopseudomonas genus. All strains in nodulation nodA gene tree grouped in a cluster referred to as Clade II, which is in line with earlier data on this clade dominance among Bradyrhizobium strains in Europe. The nodA tree revealed four well-supported subgroups within Clade II (II.1-II.4). Interestingly, all B. canariense strains clustered in subgroup II.1 whereas B. japonicum strains dominated subgroups II.2-II.4.     

Molecular relationships between populations of South African citrus thrips (Scirtothrips aurantii Faure) in South Africa and Queensland, Australia

Abstract   In response to the recent establishment of a population of South African citrus thrips ( Scirtothrips aurantii Faure) in Australia, we used DNA sequence data to examine whether this population is distinct from populations in South Africa. Mitochondrial and internal transcribed spacer (ITS2) DNA from populations from different host plants in Australia and South Africa showed no clear separation between populations that was entirely congruent with host plant or country of origin. Analysis of the ITS2 data was confounded by the presence of multiple different copies of the spacer in some populations. Neither the presence or absence, nor the sequence of these copies was clearly diagnostic for any one population. These preliminary data suggest that the Australian population is not a distinct species or subspecies from the populations of S. aurantii on either citrus or Bryophyllum in South Africa.     

Mechanisms for enhancing nutrient uptake in plants,with particular reference to mediterranean South Africa and Western Australia

The major constraints to nutrient uptake by vascular plants in mediterranean South Africa and Western Australia are: very infertile soils, relatively low temperatures when water availability is high, and hot, dry summers. These constraints are partly overcome through increased efficiency of uptake, tapping novel sources of nutrients, and prolonging water uptake. Absorptive area per unit “cost” may be enlarged directly through increased fineness of the root system and proliferation of long root hairs. This reaches its greatest development in the root clusters of the Proteaceae (proteoid roots), Restionaceae (“capillaroid” roots) and Cyperaceae (dauciform roots). Absorptive area is increased indirectly through fungal hyphae which extend from hairless rootlets into the soil. Two major groups can be recognised: general (VA mycorrhizas) and host-specific (ericoid, orchid and sheathing mycorrhizas). Mycorrhizas are the most widespread specialised modes of nutrition and are probably universal in such major taxa here asPodocarpus, Acacia, Fabaceae, Poaceae, Asteraceae, Rutaceae, terrestrial orchids, Ericales and Myrtaceae. General mycorrhizas are the least drought-adapted of mechanisms for maximising absorptive area. All have been implicated in enhancing P uptake through increasing access to inorganic P, solubilisation and shortening the diffusion path. However, selective uptake of other nutrients, especially N, by host-specific mycorrhizas may be equally important. Included under novel sources of nutrients are free N₂ (utilised by N₂-fixing nodules), small-animal prey (carnivorous leaves) and persistent leaf bases (aerial roots ofKingia australis). Both legume and non-legume N₂-fixing species are well-represented in these two regions, with stands of individual species in southwestern Australia estimated to contribute 2–19 kg N/ha/yr to the ecosystem. Free nitrogen fixation requires additional nutrients, especially Mo and Co, but is enhanced following fires and by supplementary uptake mechanisms, especially VA mycorrhizas. Southwestern Australia is particularly rich in carnivorous species. Nitrogen, P, K and S are important nutrients absorbed, with digestion aided by enzymes provided by bacteria and the glands. Parasitic plants both tap novel sources of nutrients and capitalise on any efficient water and nutrient uptake mechanisms of the hosts. Root parasites are better represented than stem parasites in mediterranean South Africa and Western Australia. Phosphorus and K in particular are absorbed preferentially by the haustoria, but much remains to be known about their modes of operation. Maximum activity of all uptake mechanisms, except those attached to some deep-rooted plants, is restricted to winter-spring. Most new seasons’s rootlets and specialised roots are confined to the uppermost 15 cm of soil, especially in or near the decomposing litter zone. Nutrient uptake is further enhanced by the tendency for the rootlets to cluster, trapping water by capillary action and prolonging nutrient release. As an early product of decomposition, N tends to be available as NH₄ (rather than NO₃) and it is absorbed preferentially by almost all specialised modes of nutrition. Microorganisms are required in the formation and/or functioning of all these structures, except haustoria. Uptake mechanisms which are optional to the plant reach their peak contribution to the root system at soil nutrient levels well below those required for greatest plant growth, when they may be absent altogether. It is only over the narrow range of nutrient availability, where shoot content of a nutrient is greater in the presence of the mechanism than in its absence (other factors remaining constant), that specialised modes can be termed nutrient-uptake “strategies.” For all specialised modes of nutrition, the component genera are better represented in these two regions than in the surrounding more fertile, arid to subtropical regions of much greater area. Endemism of species with each mode exceeds that for the two floras overall (75%). This is taken as preliminary evidence that specialised modes of nutrition are best represented in nutrient-poor soils. While they serve to limit nutrient loss from the ecosystem, their proliferation is therefore not necessarily a response to increasing “leaks” in the system. A hierarchical scheme of the functional/structural relationships between the various mechanisms is presented, starting with the rootless, VA-mycorrhizal plant as the most primitive condition. Taxa with many of the specialised modes of nutrition at present in southwestern South Africa and Western Australia have been evident in the pollen record since the early Tertiary Period. The absence of ectomycorrhizal forests in mediterranean South Africa, in marked contrast to Western Australia, can be traced to differences in their paleohistory. In both regions, the combination of fluctuating, but essentially diminishing, nutrient and water availability that began with the first mediterranean climate < 5 million years ago resulted in decimation of the less-tolerant rainforest ancestors on the one hand, and remarkable rates of speciation of the pre-adapted sclerophyll nucleus on the other.     

Fire-stimulated flowering among resprouters and geophytes in Australia and South Africa

Data on 386 species with fire-stimulated flowering (fsf) in Australasia and South Africa/Madagascar were collated to show that they occur under a wide range of fire regimes, with 71% confined to the mediterranean-climate regions. About 40% only flower up to 2 years after fire (obligate), while the rest continue at a low rate until the next fire (facultative). Peak flowering occurs 5–18 months after fire in the mediterranean regions but at 1–7 months in savannas. Fsf is recorded in 34 families, headed by terrestrial orchids (45% of species), spread throughout the seed-plant phylogeny from cycads to daisies. Tuberous geophytes (essentially orchids) dominate (51%), but other resprouting growth forms include lignotuberous shrubs and forbs, rhizomatous and bunch grasses, leaf succulents, grasstrees, epicormic trees, and hemiparasites. Most have wind-dispersed diaspores (72%), store their diaspores in the soil (93%), and seeds that do not germinate until the next fire (72%). Fsf in association with resprouting takes advantage of optimal resources and minimal competition for growth and reproduction, conditions that favor wind dispersal and maximize the interval for seed accumulation before the next fire and build-up of fire-tolerant organs. Reduced herbivory has little role in accounting for its benefits. The proximal causes of fsf center around cueing factors (direct effects such as ethylene), resource factors (direct and indirect effects, e.g., extra nutrients), and predisposing factors (circumstantial effects, e.g., fire interval). The evolutionary history of fsf has been explored recently in orchids, proteas, blood roots, droseras, and mistletoes and shown to stretch back over a period of at least 50 million years, indicating that flowering in many groups has a long association with fire as an agent of natural selection.     

Bird pollination in South Western Australia: A checklist

At least 560 species of flowering plants distributed in 64 genera and 16 families native to Southern Western Australia are pollinated by birds. This represents 15% of the total flora, and indicates adaptation to bird pollination is a major evolutionary force in this region.     

Seed-borne alfalfa mosaic virus infecting annual medics (Medicago spp.) in Western Australia

Infection with alfalfa mosaic virus (AMV) was widespread in introduction, evaluation and seed increase plots of cultivars and numbered selections of annual medics (Medicago spp.) in Western Australia; the virus was detected in plots of seven species. When seed stocks from the West Australian annual medic collection harvested in 1984–1986 were sown and seedlings tested, seed-borne AMV was found in all 12 cultivars and in 44/50 numbered selections, belonging to 10 species. Seed transmission rates to seedlings ranged from 0.3–74% and exceeded 5% in 33 seed lots. By contrast, when seedlings of four species grown from seed harvested in 1971–1978 were tested, no AMV was detected; the oldest infected seed stock found was from 1980. In commercial seed stocks of two cultivars released in 1987, the levels of seedling infection with AMV found were 0–0.2% for M. polymorpha cv. Santiago and 526% for M. murex cv. Zodiac. In commercial 1986 seed of M. polymorpha cvs Serena and Circle Valley, AMV was detected in 3/13 and 6/9 stocks respectively; transmission rates to seedlings in infected stocks were 0.1–0.7%. In a survey of 47 annual medic pastures in medium and low rainfall zones of the Western Australian wheat belt in 1987, the virus was detected in leaf samples from only three sites. When inoculated mechanically, AMV systemically infected 11 cultivars and 12 selections belonging to 13 species, but did not infect one selection each of M. aculeata and M. orbicularis. Infected plants in ten species developed only faint mosaics or were symptomlessly infected, but M. littoralis, M. polymorpha and M. tornata developed distinct mottling, reduction in leaf size and, in some instances, leaf deformation and dwarfing. In pot tests, AMV infection decreased herbage and root production (dry wts) of M. polymorpha cvs Serena and Circle Valley by about 30% and 50–60% respectively, but did not decrease herbage production in M. murexcv. Zodiac. In spaced plants growing outside, AMV decreased herbage, root (dry wts) and seed production of M. polymorpha cvs Circle Valley and Santiago by about 60%.     

Founder populations and the current status of exotic parrots in South Africa

Parrots (families Psittacidae and Cacatuidae) are one of the most threatened taxa of birds, with a combination of threats to wild populations, including capture for the cage bird market, habitat modification and destruction, persecution, disease, and threats from introduced species. As a result of the group's popularity as a cage bird, and the transport of vast numbers of individuals across the globe (both legally and illegally), the establishment of populations beyond their natural ranges has likely been enhanced. This review reports on c. 30 parrot species that have been observed outside of their natural ranges in South Africa, most likely derived, and supplemented, from both intentional and unintentional releases. Of these, the Rose-ringed Parakeet Psittacula krameri and at least one Agapornis species have become established as breeding wild populations. Like other invasive species they may pose threats to local biodiversity; however, all are strongly associated with major urban centres where significant changes to natural biota have already occurred.     

Molecular characterisation of a haplosporidian parasite infecting rock oysters Saccostrea cuccullata in north Western Australia

A haplosporidian parasite was identified in rock oysters (Saccostrea cuccullata Born, 1778) from the Montebello Islands (latitude -20.4'S longitude 115.53'E) off the northern coast of Western Australia by histopathological examination, PCR amplification and DNA sequencing of a segment of the SSU region of the parasite's rRNA gene. An oligonucleotide probe was constructed from the parasite's SSU rRNA gene in order to confirm its presence by in situ hybridisation. The parasite was disseminated throughout the gonad follicles of the host and to a lesser extent in the gills. The only parasite life stages thus far observed in this study were a uninucleate naked cell assumed to be a precursor to multinucleate plasmodial stages and a binucleate plasmodial stage. Whilst no parasite spores were detected in affected rock oysters, a phylogenetic analysis of the SSU region of the parasite's rRNA gene indicates the parasite belongs to the genus Minchinia. A PCR and in situ hybridisation assay for the Minchinia sp. was used to identify haplosporidians described by Hine and Thorne [Hine, P.M.., Thorne, T., 2002. Haplosporidium sp. (Haplosporidia: Haplosporidiidae) associated with mortalities among rock oysters Saccostrea cuccullata in north Western Australia. Dis. Aquat. Organ. 51, 123-13], in archived rock oyster tissues from the same coastline.     

Comparing ecological restoration in South Africa and Western Australia: the benefits of a ‘travelling workshop’

Researchers and practitioners of ecological restoration from South Africa and Western Australia recently undertook a travelling workshop across several South African biomes to discuss and evaluate the various approaches currently being utilised in the field. Key findings from the workshop highlighted the contrasting nature of ecological restoration undertaken in these two ecologically similar, but socially and politically different regions.     

Using molecular methods to determine the origin of weed populations of Pereskia aculeata in South Africa and its relevance to biological control

New biological control agents are required in order to reach and sustain an adequate level of control of the declared environmental weed Pereskia aculeata Miller (Cactaceae) in South Africa. Identifying the origin of weed genotypes has been important in a number of biological control programmes and is likely to be of importance for the control of P. aculeata due to its disjunct native distribution and morphological polymorphisms between plants from different regions of the native and introduced distribution. DNA sequencing of the trnL chloroplastic intron and the phyC nuclear gene indicate that the South African weed population’s origin was in the southern region of native distribution. Inter-Simple Sequence Repeats (ISSRs) confirmed this result and added resolution to the analysis indicating that the native plants with the closest genetic distance to the South African weed population were found in Rio de Janeiro Province, Brazil. The relationship between the South African weed population and garden variety plants as well as the large genetic distance between the South African plants and the native plants suggests that the South African population may be the progeny of escaped garden variety plants that have been cultivated and possibly hybridized. The low levels of genetic variation within the South African population and the monophyly of the South African plants indicates that these plants are the progeny of a single introduction or multiple introductions from the same source. Rio de Janeiro Province in Brazil is the most appropriate region in which to survey for new biological control agents.     

Molecular characterisation of Cryptosporidium outbreaks in Western and South Australia

Molecular typing at the 18S rRNA and Gp60 loci was conducted on Cryptosporidium-positive stool samples from cases collected during 2007 Western Australian and South Australian outbreaks of cryptosporidiosis. Analysis of 48 Western Australian samples identified that all isolates were C. hominis and were from five different Gp60C. hominis subtype families. The IbA10G2 subtype was most common across all age groups (37/48). In South Australia, analysis of 24 outbreak samples, identified 21 C. hominis isolates, two C. parvum isolates and one sample with both C. hominis and C. parvum. All C. hominis isolates were identified as the IbA10G2 subtype.     

Investigation of keratinophilic fungi from soils in Western Australia a preliminary survey

In order to determine which species of geophilic dermatophytes were present in Western Australian soils 299 samples were investigated. These samples were collected from a range of locations, 208 from towns throughout the state and 91 samples from the Perth Metropolitan area.Most samples were collected from areas frequented by people and animals, such as home gardens, parks and animal yards.Of the total 299 soils, 271 (90.6 %) yielded keratinophilic fungi. A total of 181 dermatophytes were isolated, and there were 205 isolations of other keratinophilic fungi. Microsporum gypseum (30.7 %) was the most prevalent dermatophyte recovered from soil followed byMicrosporum cookei (21.7 %) and thenTrichophyton ajelloi (8.0 %). No other dermatophytes were recovered.Chrysosporium indicum was the most common of all the keratinophilic fungi and was isolated from 50.1 % of the samples. Mixed growth was obtained from 33.5 % of the soil samples.     

Analysis of 14 cystic fibrosis mutations in five South European populations

Summary We have analysed five Southern European populations (Albanian, Greek, Italian, Spanish and Yugoslavian) for 14 cystic fibrosis (CF) mutations. The most frequent mutations, apart from F508, were G542X (6.04%), R1162X (3.61%) and N1303K (3.24%). Each of the other analysed mutations were present at a frequency of less than 1% (R347P, R334W, S549RA, S549I, G551D, R553X and W1282X), and four mutations (D110H, I507, S549RT, and S1255X) were not found in this sample. The data presented here allows the use of mutation analysis in 69.5% of Spanish, 58% of Greek, and 56.5% of Italian CF cases.     

Genetic diversity of woolly apple aphid Eriosoma lanigerum (Hemiptera: Aphididae) populations in the Western Cape, South Africa

The woolly apple aphid Eriosoma lanigerum (Hausmann) is one of the most damaging apple pests in South Africa. Information on its genetic diversity is lacking and this study, in which the genetic structure of parthenogenetic E. lanigerum populations was characterized in the Western Cape Province of South Africa, represents the first local study of its kind. A total of 192 individuals from four different regions were collected and analysed using amplified fragment length polymorphism (AFLP). Using five selective AFLP primer pairs, 250 fragments were scored for analysis. Results indicated that a low level of genetic variation was apparent in E. lanigerum populations in the Western Cape (H = 0.0192). Furthermore, populations collected from geographically distant regions were very closely related, which can partly be explained by the fact that agricultural practices were responsible for dissemination of populations from a common ancestor to geographically distant areas. The low level of variation found indicated that the possibility of controlling E. lanigerum in the Western Cape using host plant resistance is favourable. This is the first report of AFLP being used to characterize the genetic structure of an aphid species. Results indicate that this marker may be useful for analysis of other aphid species.