Distinctive vegetation communities are associated with the long-lived coniferAgathis australis(New Zealand kauri, Araucariaceae) in New Zealand rainforests

Do Southeast Asia's paleo-Antarctic trees cool the planet?

Many tree genera in the Malesian uplands have Southern Hemisphere origins, often supported by austral fossil records. Weathering the vast bedrock exposures in the everwet Malesian tropics may have consumed sufficient atmospheric CO₂ to contribute significantly to global cooling over the past 15 Myr. However, there has been no discussion of how the distinctive regional tree assemblages may have enhanced weathering and contributed to this process. We postulate that Gondwanan-sourced tree lineages that can dominate higher-elevation forests played an overlooked role in the Neogene CO₂ drawdown that led to the Ice Ages and the current, now-precarious climate state. Moreover, several historically abundant conifers in Araucariaceae and Podocarpaceae are likely to have made an outsized contribution through soil acidification that increases weathering. If the widespread destruction of Malesian lowland forests continues to spread into the uplands, the losses will threaten unique austral plant assemblages and, if our hypothesis is correct, a carbon sequestration engine that could contribute to cooler planetary conditions far into the future. Immediate effects include the spread of heat islands, significant losses of biomass carbon and forest-dependent biodiversity, erosion of watershed values, and the destruction of tens of millions of years of evolutionary history.

Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families

Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.

Assessing the effectiveness of oxathiapiprolin toward Phytophthora agathidicida, the causal agent of kauri dieback disease

Phytophthora species cause disease and devastation of plants in ecological and horticultural settings worldwide. A recently identified species, Phytophthoraagathidicida, infects and ultimately kills the treasured kauri trees (Agathis australis) that are endemic to New Zealand. Currently, there are few options for managing kauri dieback disease. In this study, we sought to assess the efficacy of the oomycide oxathiapiprolin against several life cycle stages of two geographically distinct P. agathidicida isolates. The effective concentration to inhibit 50% of mycelial growth (EC50) was determined to be ∼0.1 ng/ml, indicating that P. agathidicida mycelia are more sensitive to oxathiapiprolin than those from most other Phytophthora species that have been studied. Oxathiapiprolin was also highly effective at inhibiting the germination of zoospores (EC50 = 2–9 ng/ml for the two isolates) and oospores (complete inhibition at 100 ng/ml). In addition, oxathiapiprolin delayed the onset of detached kauri leaf infection in a dose-dependent manner. Collectively, the results presented here highlight the significant potential of oxathiapiprolin as a tool to aid in the control of kauri dieback disease.

The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the "kauri killing" Phytophthora in New Zealand

Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0-304.4 years and 95% HPDs of 206.9-414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand.

Impact of Phytophthora agathidicida infection on canopy and forest floor plant nutrient concentrations and fluxes in a kauri-dominated forest

Kauri dieback, caused by Phytophthora agathidicida, is a biotic disturbance that poses a recent threat to the survival of kauri (Agathis australis) forests in New Zealand. Previous studies have shown that throughfall and stemflow play an important role in the kauri forests' internal nutrient cycle. However, the effects of P. agathidicida infection on canopy and forest floor nutrient fluxes in kauri forests remain unknown. Here, we measured throughfall, stemflow and forest floor water yield, nutrient (potassium, calcium, magnesium, manganese, silicon, sulfur, sodium, iron) concentrations and fluxes of ten kauri trees differing in soil P. agathidicida DNA concentration, and health status. We did not observe an effect of soil P. agathidicida DNA concentration on throughfall, stemflow, and forest floor water yield. Throughfall and forest floor nutrient concentrations and fluxes decreased (up to 50%) with increasing soil P. agathidicida DNA concentration. We found significant effects on potassium and manganese fluxes in throughfall; calcium and silicon fluxes in forest floor leachate. A decline in canopy and forest floor nutrient fluxes may result in soil nutrient imbalances, which in turn may negatively impact forest productivity and may increase the susceptibility of trees to future pathogen infection in these ecologically unique kauri forests. Given our findings and the increasing spread of Phytophthora species worldwide, research on the underlying physiological mechanisms linking dieback and plant-soil nutrient fluxes is critical.

Soil microbial diversity in adjacent forest systems - contrasting native, old growth kauri (Agathis australis) forest with exotic pine (Pinus radiata) plantation forest

Globally, the conversion of primary forests to plantations and agricultural landscapes is a common land use change. Kauri (Agathis australis) is one of the most heavily impacted indigenous tree species of New Zealand with <1% of primary forest remaining as fragments adjacent to pastoral farming and exotic forest plantations. By contrasting two forest systems, we investigated if the fragmentation of kauri forests and introduction of pine plantations (Pinus radiata) are significantly impacting the diversity and composition of soil microbial communities across Waipoua kauri forest, New Zealand. Using next generation based 16S rRNA and ITS gene region sequencing, we identified that fungal and bacterial community composition significantly differed between kauri and pine forest soils. However, fungal communities displayed the largest differences in diversity and composition. This research revealed significant shifts in the soil microbial communities surrounding remnant kauri fragments, including the loss of microbial taxa with functions in disease suppression and plant health. Kauri dieback disease, caused by Phytophthora agathidicida, currently threatens the kauri forest ecosystem. Results from this research highlight the need for further investigations into how changes to soil microbial diversity surrounding remnant kauri fragments impact tree health and disease expression.

Monitoring of Canopy Stress Symptoms in New Zealand Kauri Trees Analysed with AISA Hyperspectral Data

The endemic New Zealand kauri trees (Agathis australis) are under threat by the deadly kauri dieback disease (Phytophthora agathidicida (PA)). This study aimed to identify spectral index combinations for characterising visible stress symptoms in the kauri canopy. The analysis is based on an aerial AISA hyperspectral image mosaic and 1258 reference crowns in three study sites in the Waitakere Ranges west of Auckland. A field-based assessment scheme for canopy stress symptoms (classes 1–5) was further optimised for use with RGB aerial images. A combination of four indices with six bands in the spectral range 450–1205 nm resulted in a correlation of 0.93 (mean absolute error 0.27, RMSE 0.48) for all crown sizes. Comparable results were achieved with five indices in the 450–970 nm region. A Random Forest (RF) regression gave the most accurate predictions while a M5P regression tree performed nearly as well and a linear regression resulted in slightly lower correlations. Normalised Difference Vegetation Indices (NDVI) in the near-infrared / red spectral range were the most important index combinations, followed by indices with bands in the near-infrared spectral range from 800 to 1205 nm. A test on different crown sizes revealed that stress symptoms in smaller crowns with denser foliage are best described in combination with pigment-sensitive indices that include bands in the green and blue spectral range. A stratified approach with individual models for pre-segmented low and high forest stands improved the overall performance. The regression models were also tested in a pixel-based analysis. A manual interpretation of the resulting raster map with stress symptom patterns observed in aerial imagery indicated a good match. With bandwidths of 10 nm and a maximum number of six bands, the selected index combinations can be used for large-area monitoring on an airborne multispectral sensor. This study establishes the base for a cost-efficient, objective monitoring method for stress symptoms in kauri canopies, suitable to cover large forest areas with an airborne multispectral sensor.

Foundation Species, Non-trophic Interactions, and the Value of Being Common

Foundation species define ecosystems, control the biological diversity of associated species, modulate critical ecosystem processes, and often have important cultural values and resonance. This review summarizes current understanding of the characteristics and traits of foundation species and how to distinguish them from other “important” species in ecological systems (e.g., keystone, dominant, and core species); illustrates how analysis of the structure and function of ecological networks can be improved and enriched by explicit incorporation of foundation species and their non-trophic interactions; discusses the importance of pro-active identification and management of foundation species as a cost-effective and efficient method of sustaining valuable ecosystem processes and services and securing populations of associated rare, threatened, or endangered species; and suggests broader engagement of citizen-scientists and non-specialists in the identification and study of foundation species and their biological and cultural values.

High-Throughput Chemical Screening Identifies Compounds that Inhibit Different Stages of the Phytophthora agathidicida and Phytophthora cinnamomi Life Cycles

Oomycetes in the genus Phytophthora are among the most damaging plant pathogens worldwide. Two important species are Phytophthora cinnamomi, which causes root rot in thousands of native and agricultural plants, and Phytophthora agathidicida, which causes kauri dieback disease in New Zealand. As is the case for other Phytophthora species, management options for these two pathogens are limited. Here, we have screened over 100 compounds for their anti-oomycete activity, as a potential first step toward identifying new control strategies. Our screening identified eight compounds that showed activity against both Phytophthora species. These included five antibiotics, two copper compounds and a quaternary ammonium cation. These compounds were tested for their inhibitory action against three stages of the Phytophthora life cycle: mycelial growth, zoospore germination, and zoospore motility. The inhibitory effects of the compounds were broadly similar between the two Phytophthora species, but their effectiveness varied widely among life cycle stages. Mycelial growth was most successfully inhibited by the antibiotics chlortetracycline and paromomycin, and the quaternary ammonium salt benzethonium chloride. Copper chloride and copper sulfate were most effective at inhibiting zoospore germination and motility, whereas the five antibiotics showed relatively poor zoospore inhibition. Benzethonium chloride was identified as a promising antimicrobial, as it is effective across all three life cycle stages. While further testing is required to determine their efficacy and potential phytotoxicity in planta, we have provided new data on those agents that are, and those that are not, effective against P. agathidicida and P. cinnamomi. Additionally, we present here the first published protocol for producing zoospores from P. agathidicida, which will aid in the further study of this emerging pathogen.