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.     

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.     

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.     

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.     

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.     

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.     

Early traces of life investigations in drilling Archean hydrothermal and sedimentary rocks of the Pilbara Craton,Western Australia and Barberton Greenstone Belt,South Africa

The Pilbara Craton of Western Australia and the Barberton Greenstone Belt of the Kaapvaal Craton, South Africa, contain some of the oldest and best preserved Archaean rocks and microfossils in the world. Two stratigraphic horizons in the Pilbara Craton were drilled as part of a collaborative effort between France and Australia (the Pilbara Drilling Project) during August 2004, including the 3481 Ma Dresser Formation (Warrawoona Group) and 2724 Ma Tumbiana Formation (Fortescue Group). A new diamond drill hole was cored in August 2008 through part of the ～3250 Ma Fig Tree Group in the Barberton Greenstone Belt as part of a joint project between France and South Africa. These pristine diamond drill cores present a unique opportunity to constrain the chemistry of the earliest ocean, the composition of the atmosphere, and the settings and types of microbial ecosystems spanning the Archean Eon. These drill core samples can also provide new clues on the earliest metabolic pathways.     

Recognizing intimate partner violence in primary care: Western Cape, South Africa

Introduction

Interpersonal violence in South Africa is the second highest contributor to the burden of disease after HIV/AIDS and 62% is estimated to be from intimate partner violence (IPV). This study aimed to evaluate how women experiencing IPV present in primary care, how often IPV is recognized by health care practitioners and what other diagnoses are made.

Methods

At two urban and three rural community health centres, health practitioners were trained to screen all women for IPV over a period of up to 8 weeks. Medical records of 114 thus identified women were then examined and their reasons for encounter (RFE) and diagnoses over the previous 2-years were coded using the International Classification of Primary Care. Three focus group interviews were held with the practitioners and interviews with the facility managers to explore their experience of screening.

Results

IPV was previously recognized in 11 women (9.6%). Women presented with a variety of RFE that should raise the index of suspicion for IPV– headache, request for psychiatric medication, sleep disturbance, tiredness, assault, feeling anxious and depressed. Depression was the commonest diagnosis. Interviews identified key issues that prevented health practitioners from screening.

Conclusion

This study demonstrated that recognition of women with IPV is very low in South African primary care and adds useful new information on how women present to ambulatory health services. These findings offer key cues that can be used to improve selective case finding for IPV in resource-poor settings. Universal screening was not supported by this study.     

Genetic variation of European grayling (Thymallus thymallus) populations in the Western Balkans

In order to elucidate genetic composition of European grayling (Thymallus thymallus) populations in the Western Balkans, the partial mitochondrial DNA (mtDNA) control region was sequenced and 12 microsatellite loci genotyped in 14 populations originating from tributaries of the Adriatic and Danube drainages. Eleven mtDNA haplotypes were found, one confined to the Adriatic clade, one to the Alpine group and the rest to the ‘Balkan’ grayling phylogenetic clade. Haplotypes from the Balkan clade were confined to the Danube drainage and constituted two groups: northern group with haplotypes found in the Slovenian part of the Danube drainage, and southern group, consisting from Bosnia–Herzegovina and Montenegro. Substantial genetic distance between northern and southern groups of haplotypes (0.75–1.8%) and well supported divisions within the northern group indicate very structured grayling population within the studied Danube basin that most probably did not evolve due to vicariance but rather as a consequence of multiple colonization waves that might have occurred during the Pleistocene. Furthermore, genetic distance of ~4% between Adriatic and Danube populations’ haplotypes, suggest that their separation occurred in mid-Pliocene. These findings imply a complex colonization pattern of the Western Balkans drainages. Microsatellite data also confirm high genetic diversity in Western Balkans populations of grayling (on average 7.5 alleles per microsatellite locus and H _exp 0.58). Limited stocking activities were detected based on microsatellites and mtDNA data. Regarding current knowledge of grayling phylogeography appropriate management strategies were proposed to preserve unique, autochthonous grayling populations in Western Balkan.