Changes to the Bacterial Microbiome in the Rhizosphere and Root Endosphere of Persea americana (Avocado) Treated With Organic Mulch and a Silicate-Based Mulch or Phosphite, and Infested With Phytophthora cinnamomi.

Plant growth and responses of the microbial profile of the rhizosphere soil and root endosphere were investigated for avocado plants infested or not infested with Phytophthora cinnamomi and the changes were compared in plants grown with various soil additives or by spraying plants with phosphite. Soil treatments were organic mulches or silica-based mineral mulch. Reduction of root growth and visible root damage was least in the infested plants treated with phosphite or mineral mulch applied to the soil. Rhizosphere soils and root endospheres were analyzed for bacterial communities using metabarcoding. Bacterial abundance and diversity were reduced in infested rhizospheres and root endospheres. The presence or absence of mineral mulch resulted in greater diversity and larger differences in rhizosphere community composition between infested and non-infested pots than any other treatment. Some rhizosphere bacterial groups, especially Actinobacteria and Proteobacteria, had significantly higher relative abundance in the presence of Phytophthora. The bacterial communities of root endospheres were lower in abundance than rhizosphere communities and not affected by soil treatments or phosphite but increased in abundance after infection with P. cinnamomi. These findings suggested that the addition of silicate-based mineral mulch protects against Phytophthora root rot, which may be partly mediated through changes in rhizosphere bacterial community composition. However, the changes to the microbiome induced by spraying plants with phosphite are different from those resulting from the application of mineral mulch to the soil.

Timing and abundance of sporangia production and zoospore release influences the recovery of different Phytophthora species by baiting.

Analysis of soil samples using High Throughput Sequencing (HTS) frequently detects more Phytophthora species compared with traditional soil baiting methods. This study investigated whether differences between species in the timing and abundance of sporangial production and zoospore release could be a reason for the lower number of species isolated by baiting. Stems of Eucalyptus marginata were inoculated with ten Phytophthora species (P. nicotianae, P. multivora, P. pseudocryptogea, P. cinnamomi, P. thermophila, P. arenaria, P. heveae, P. constricta, P. gondwanensis and P. versiformis), and lesioned sections for each species were baited separately in water. There were significant differences between species in timing of sporangia production and zoospore release. P. nicotianae, P. pseudocryptogea, P. multivora and P. thermophila released zoospores within 8-12 h and could be isolated from lesioned baits within 1-2 days. In contrast, P. constricta did not produce zoospores for over 48 h and was only isolated 5-7 days after baiting. P. heveae and P. versiformis did not produce zoospores and were not recovered from the baits. When species were paired in the same baiting tub, those that produced zoospores in the shortest time were isolated most frequently, while species slow to produce zoospores, or which produced them in lower numbers, were isolated from few baits or not at all. Thus, species differences in the timing of sporangia production and zoospore release may contribute to the ease of isolation of some Phytophthora species when they are present together with other Phytophthora species in an environmental sample.

Transitioning from phosphate mining to agriculture: Responses to urea and slow release fertilizers for Sorghum bicolor.

Globally, land-use transition from mining to agriculture is becoming increasingly attractive and necessary for many reasons. However, low levels of necessary plant nutrients, and high levels of heavy metals, can hamper plant growth, affecting yield, and potentially, food safety. In post-phosphate mining substrates, for example, nitrogen (N) is a key limiting nutrient, and, although legumes are planted prior to cereals, N supplementation is still necessary. We undertook two field trials on Christmas Island, Australia, to determine whether Sorghum bicolor could be grown successfully in a post-phosphate mining substrate. The first trial investigated N (urea) demand (amount of N required for adequate crop growth) for S. bicolor, and whether N addition could reduce the naturally occurring cadmium (Cd) concentrations in the crop. The second trial examined whether slow release nitrogen fertilizers (SRF) could replace urea to increase biomass and reduce Cd concentrations. Our first trial demonstrated that S. bicolor has a high N demand, with the highest biomass being recorded in the 160kg/ha urea treatment. However, plants treated with 80, 120 and 160kg/ha were not significantly different from one another. After 7weeks of growth, leaf Cd concentrations were significantly lower for all urea treatments compared with the control plants. However, after 23weeks, seed Cd concentrations did not differ across treatments. Our second trial demonstrated that the application of SRF (Macracote® and Sulsync®) and 160kg/ha urea significantly increased biomass above the control plants. There was, however, no treatment response in terms of Cd or N concentrations in the seed at final harvest. Thus, we have shown that N is currently critical for S. bicolor, even following legume cropping, and that high biomass and a significant reduction in Cd can be attained with appropriate levels of urea. Our work has important implications for cereal growth and food safety in post-mining agriculture.

Suppression of the auxin response pathway enhances susceptibility to Phytophthora cinnamomi while phosphite-mediated resistance stimulates the auxin signalling pathway.

BACKGROUND: Phytophthora cinnamomi is a devastating pathogen worldwide and phosphite (Phi), an analogue of phosphate (Pi) is highly effective in the control of this pathogen. Phi also interferes with Pi starvation responses (PSR), of which auxin signalling is an integral component. In the current study, the involvement of Pi and the auxin signalling pathways in host and Phi-mediated resistance to P. cinnamomi was investigated by screening the Arabidopsis thaliana ecotype Col-0 and several mutants defective in PSR and the auxin response pathway for their susceptibility to this pathogen. The response to Phi treatment was also studied by monitoring its effect on Pi- and the auxin response pathways. RESULTS: Here we demonstrate that phr1-1 (phosphate starvation response 1), a mutant defective in response to Pi starvation was highly susceptible to P. cinnamomi compared to the parental background Col-0. Furthermore, the analysis of the Arabidopsis tir1-1 (transport inhibitor response 1) mutant, deficient in the auxin-stimulated SCF (Skp1 - Cullin - F-Box) ubiquitination pathway was also highly susceptible to P. cinnamomi and the susceptibility of the mutants rpn10 and pbe1 further supported a role for the 26S proteasome in resistance to P. cinnamomi. The role of auxin was also supported by a significant (P < 0.001) increase in susceptibility of blue lupin (Lupinus angustifolius) to P. cinnamomi following treatment with the inhibitor of auxin transport, TIBA (2,3,5-triiodobenzoic acid). Given the apparent involvement of auxin and PSR signalling in the resistance to P. cinnamomi, the possible involvement of these pathways in Phi mediated resistance was also investigated. Phi (especially at high concentrations) attenuates the response of some Pi starvation inducible genes such as AT4, AtACP5 and AtPT2 in Pi starved plants. However, Phi enhanced the transcript levels of PHR1 and the auxin responsive genes (AUX1, AXR1and AXR2), suppressed the primary root elongation, and increased root hair formation in plants with sufficient Pi. CONCLUSIONS: The auxin response pathway, particularly auxin sensitivity and transport, plays an important role in resistance to P. cinnamomi in Arabidopsis, and phosphite-mediated resistance may in some part be through its effect on the stimulation of the PSR and auxin response pathways.

Transposable elements: powerful contributors to angiosperm evolution and diversity.

Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's "abominable mystery": the spectacular success of the angiosperms.

Survival of Phytophthora cinnamomi as oospores, stromata, and thick-walled chlamydospores in roots of symptomatic and asymptomatic annual and herbaceous perennial plant species.

Studies were conducted to determine how Phytophthora cinnamomi survives during hot and dry Mediterranean summers in areas with limited surviving susceptible hosts. Two Western Australian herbaceous perennials Chamaescilla corymbosa and Stylidium diuroides and one Western Australian annual Trachymene pilosa were collected weekly from a naturally infested site from the Eucalyptus marginata (jarrah) forest from winter to spring and less frequently during summer 2011/2012. Selfed oospores, thick-walled chlamydospores, and stromata of P. cinnamomi were observed in each species. Oospores and thick-walled chlamydospores germinated in planta confirming their viability. This is the first report of autogamy by P. cinnamomi in naturally infected plants. Stromata, reported for the first time for P. cinnamomi, were densely aggregated inside host cells, and germinated in planta with multiple germ tubes with hyphae capable of producing oospores and chlamydospores. Trachymene pilosa was completely asymptomatic, S. diuroides did not develop root lesions but some plants wilted, whilst C. corymbosa remained asymptomatic above ground but lesions developed on some tubers. The presence of haustoria suggests that P. cinnamomi grows biotrophically in some hosts. Asymptomatic, biotrophic growth of P. cinnamomi in some annual and herbaceous perennials and the production of a range of survival structures have implications for pathogen persistence over summer and its management.

Defining the phosphite-regulated transcriptome of the plant pathogen Phytophthora cinnamomi.

Phosphite, an analog of phosphate is used to control oomycete diseases on a wide range of horticultural crops and in native ecosystems. In this study, we investigated morphological and transcriptional changes induced in Phytophthora cinnamomi by phosphite. Cytological observations revealed that phosphite caused hyphal distortions and lysis of cell walls and had an adverse effect on hyphal growth. At the molecular level, the expression levels of 43 transcripts were changed. Many of these encoded proteins involved in cell wall synthesis, or cytoskeleton functioning. The results of both the microscopic and molecular investigations are consistent with phosphite inhibiting the function of the cytoskeleton and cell wall synthesis.

In planta selfing and oospore production of Phytophthora cinnamomi in the presence of Acacia pulchella.

This paper provides the first evidence of A2 type 1 and type 2 isolates of Phytophthora cinnamomi producing selfed oospores in planta in an Australian soil and in a potting mix. Oospores were observed in infected lupin (Lupinus angustifolius) roots incubated for 7d either in the substrate under potted Acacia pulchella plants, or in soils collected from under and near varieties of A. pulchella in jarrah (Eucalyptus marginata) forest. The A2 type isolates varied in their ability to produce selfed oospores and none were produced by A1 isolates. The gametangial association was amphigynous and spores were predominantly spherical with diameters from 13-40 microm. The oospores were viable but dormant. Two A2 type isolates produced small numbers of selfed oospores with amphigynous antheridia axenically in Ribeiro's liquid medium within 30 d, and one A2 type 2 isolate produced oospores after mating with an A1 strain. Evidence is presented that the presence of roots of Acacia pulchella, and particularly A. pulchella var. glaberrima and var. goadbyi, enhances the production of oospores.

Influence of Low Oxygen Levels in Aeroponics Chambers on Eucalypt Roots Infected with Phytophthora cinnamomi.

Aeroponics root chambers were designed to evaluate the influence of low oxygen on disease development in clones of Eucalyptus marginata susceptible or resistant to infection by Phytophthora cinnamomi. Actively growing 7-month-old clones of E. marginata were transferred into the aeroponics chambers, into which a nutrient solution was delivered in a fine spray, providing optimal conditions for root growth. Prior to inoculation by zoospores of P. cinnamomi under normal oxygen, the roots were exposed to four treatments: (i) normal oxygen, approximately 8 mg of O2 liter-1; (ii) 6 days of hypoxia, 2 mg of O2 liter-1; (iii) anoxic acclimatization 2 days at 2 mg of O2 liter-1, 2 days at 1 mg of O2 liter-1, 2 days at 0.5 mg of O2 liter-1, 2 days at 2 mg of O2 liter-1, and 6 h at <0.05 mg of O2 liter-1; and (iv) 6 h of anoxia, <0.05 mg of O2 liter-1. Root extension during hypoxia was greatly reduced. Lesion development was least for roots exposed to hypoxia and greatest for roots exposed to anoxia for 6 h, suggesting increased resistance of E. marginata to P. cinnamomi following hypoxia.