Marlien van der Merwe

Grasslands are one of the most threatened ecological communities globally and are under increased risk from extreme compound events, such as those experienced during heatwaves. Arbuscular mycorrhizal (AM) fungi can facilitate plants during environmental stress and may help grasses mitigate climate stressors. When stressors occur simultaneously, it is particularly stressful for plants, and the role of AM fungi in ameliorating this stress in grassland species is poorly understood. This study investigated the role of AM fungi in facilitating growth and fitness responses of temperate grassland species to heat stress, water stress and their combination. Additionally, this study explores the influence of C ₃ /C ₄ photosynthetic pathways and seasonal factors in influencing grass responses. AM fungi had variable effects on plant performance under ecologically relevant heat and water stress events. While the influence of AM fungi showed some positive influence on plant performance under stress, overall biomass was reduced in the presence of AM fungi. C ₃ species had increased fitness when grown with AM fungi in warmer seasons but were sensitive to heat and water stress in winter, suggesting seasonal acclimation of C ₃ grasses. No such trends were shown for C ₄ grasses, which were resilient across all stressors and unaffected by the presence of AM fungi. Colonisation levels of AM fungi were variable, with no patterns associated with photosynthetic pathway, and colonisation tending to be lower with higher stress. The results highlight the risk of community scale shifts in temperate grassland communities, informing restoration and management of grasslands under the global increase of extreme compound events.

Microbial diversity is a key driver of ecosystem function, yet it remains poorly integrated into ecological restoration frameworks. While seeds are the primary dispersal unit of plants and the foundation of most restoration programs, the microbial communities they carry are rarely considered. Here, we assess whether sites that have undergone restoration have altered seed-associated microbial communities. We do this by comparing bacterial and fungal seed microbiomes across natural and restored landscapes. Using a landscape-scale sampling design, seeds were collected from multiple plant host species and populations across 41 sites spanning a broad latitudinal gradient. High-throughput sequencing of the 16S rRNA gene and ITS2 region was used to characterise bacterial and fungal communities, respectively, and differences in diversity, composition, and network structure were assessed using multivariate and network-based approaches. Seed microbiomes differed between natural and restored sites, but the magnitude and nature of these changes varied among host species. Restored sites were associated with shifts in microbial diversity, community composition, and network structure, including changes in the retention of putative keystone taxa. In some species, restoration was linked to pronounced restructuring of seed-associated microbial communities, whereas in others, microbiomes remained comparatively stable. Together, these results demonstrate that restoration can alter seed microbial communities in ways that are not consistently predicted by soil-focused restoration outcomes and that host identity mediates these responses. Incorporating seed microbiome data into restoration monitoring may therefore provide a complementary and previously overlooked indicator of restoration success, with implications for improving plant germination and health.

Establishing genetically diverse ex situ collections, particularly seed production areas (SPAs), is essential not only for safeguarding biodiversity but also for generating high‐quality and high‐quantity germplasm material. However, practical tools for sourcing genetically representative material remain limited, especially for widespread, common species. Here, we present a flexible, data‐driven workflow that integrates genomic data, future climate projections and real‐world constraints to guide the design of representative SPAs. Using the widespread rainforest tree Neolitsea dealbata as a case study, we identified genetic neighbourhoods (GNs) across its range and used a climate‐matching tool to pinpoint an external GN with a future climate analogous to a target restoration area (the Big Scrub). We evaluated how common allelic diversity is captured under three practitioner‐defined decisions: (1) whether to minimise individuals or sites sampled, (2) whether to apply sampling constraints and (3) whether to sample randomly or optimally. To support the third decision, we developed a novel optimisation method that identifies combinations of individuals or sites using a down‐projected site frequency spectrum ( psfs ), aiming to maximise allele representation in the final collection. These decisions were then implemented across three provenancing strategies: local, predictive and climate‐adjusted. Our results show that multiple sampling approaches can capture over 90% of common alleles (a predefined threshold) for the local GN , even under various logistical and practical constraints. The same is feasible when including future climate‐matched sources from an external GN , which nearly doubled allelic representation of the species in the SPA. This workflow is adaptable to practical limitations, such as site inaccessibility or reliance on existing collections. By balancing genetic resolution with practitioner flexibility, our approach supports scalable, evidence‐based design of ex situ collections, such as SPAs, to maximise genetic representation under environmental change.

Accurate kinship estimation between close relatives is crucial in conservation and restoration but remains challenging in wild populations due to structure and inbreeding. The efficacy of kinship inference using reduced‐representation sequencing data (e.g., DArTseq, RADseq) is also uncertain. We evaluated the sensitivity and precision of six kinship methods (Goudet's beta dosage, KING Homo, KING Robust, PC‐Relate, PLINK, RelateAdmix) at detecting parent–offspring and sibling relationships. Analyses were conducted on 3395 individuals and 363 families from six non‐model Australian plant species: Acacia terminalis , Acacia suaveolens , Banksia serrata , Banksia aemula , Hakea sericea and Hakea teretifolia . Method performance varied across species and filtering parameters. Goudet's beta dosage and RelateAdmix performed well in low‐structure, noninbred species but were less reliable in structured or inbred contexts. PLINK offered a balance of sensitivity and precision but was sensitive to filtering and often underestimated relatedness. KING Robust was highly precise but missed many true relatives. PC‐Relate showed high false positives and is not recommended for similar applications. We recommend PLINK for general use, Goudet's beta dosage and RelateAdmix for low‐structure species, and KING Robust for high‐precision needs. Comparing multiple methods is advisable, as each has different assumptions and complementary strengths. Further theoretical development is needed for species with high inbreeding.

Seed microbes play crucial roles in plant health, but studying their diversity is challenging due to host DNA contamination. This study aimed to optimise methodologies for investigating seed microbiomes across diverse plant species, focusing on the efficacy of peptide nucleic acid (PNA) clamps to reduce host DNA amplification. We tested PNA clamps on three plant species: Melaleuca quinquenervia (tree), Microlaena stipoides, and Themeda triandra (grasses). The effectiveness of PNA clamps was assessed through in silico analysis, axenic tissue culture, and metabarcoding techniques. In silico analysis confirmed the specificity of PNA clamps to the 16S rRNA gene V4 region of chloroplasts in the grass species. Axenic tissue culture experiments showed that applying PNA clamps at both 1 µM and 0.25 µM concentrations significantly reduced plant DNA amplification. Metabarcoding analyses further confirmed that PNA clamps effectively suppressed host DNA, enhancing microbial diversity estimates across all three species while preserving core microbial taxa. The efficacy of the clamps varied among host species, with T. triandra exhibiting the highest blocking efficacy, and chloroplast clamps outperforming mitochondrial ones. This study demonstrates that PNA clamps are a useful for improving seed endophyte metabarcoding datasets, although they require optimisation for some plant species. This knowledge will contribute to enhancing our understanding of seed microbiome diversity and its ecological implications.

Over the past two decades, our understanding of Lauraceae, a large family of woody plants, has undergone significant advances in phylogeny, taxonomy, and biogeography. Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages, leading to the recognition of nine tribes: Hypodaphnideae, Cryptocaryeae, Cassytheae, Neocinnamomeae, Caryodaphnopsideae, Mezilaureae, Perseeae, Laureae, and Cinnamomeae, with Mezilaureae validated here. Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity. Taxonomic studies have focused mainly on the most diverse regions, e.g., tropical Asia, tropical America, and Africa (Madagascar), with six new genera described and five reinstated since the last major overview of the family. The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic. Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages, with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events. Phylogeographic studies, predominantly from East Asia, have shown patterns of in situ survival and demographic stability or expansion during the Quaternary. Nevertheless, many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae. A multifaceted approach integrating genomic studies, field work, morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.

The relationship between intra-specific and inter-specific patterns and processes over evolutionary time is key to ecological investigations. We examine this relationship taking an approach of focussing on the association between vegetation and floristic classifications, summaries of inter-specific processes, and intra-specific genetic structuring. Applying an innovative, multispecies, and standardised population genomic approach, we test the relationship between vegetation mapping schemes and structuring of genetic variation across a large, environmentally heterogenous region in eastern Australia. We show that intra-specific genetic variation shows limited correspondence to vegetation and floristic classifications and is better explained by distance between sampled populations and the location of biogeographical features which limit gene flow. Mapping schemes with contiguous mapping classes, particularly larger ones, were more predictive of genetic lineages, whether based on environmental factors or not, than geographically non-contiguous schemes. We conclude that vegetation and floristic classifications are not closely correlated with intra-specific genetic patterns, showing that intra-specific processes are not recapitulated by inter-specific floristic assembly processes. This study showcases the need to implement landscape level evolutionary patterns, based on species specific datasets, in restoration and conservation activities.

Myrtaceae are a large family of woody plants, including hundreds that are currently under threat from the global spread of a fungal pathogen, Austropuccinia psidii (G.Winter) Beenken, which causes myrtle rust. A reference genome for the Australian native rainforest tree Rhodamnia argentea Benth. (malletwood) was assembled from Oxford Nanopore Technologies (ONT) long-reads, 10x Genomics Chromium linked-reads, and Hi-C data (N50 = 32.3 Mbp and BUSCO completeness 98.0%) with 99.0% of the 347 Mbp assembly anchored to 11 chromosomes (2n = 22). The R. argentea genome will inform conservation efforts for Myrtaceae species threatened by myrtle rust, against which it shows variable resistance. We observed contamination in the sequencing data and further investigation revealed an arthropod source. This study emphasises the importance of checking sequencing data for contamination, especially when working with non-model organisms. It also enhances our understanding of a tree that faces conservation challenges, contributing to broader biodiversity initiatives.

Premise: Obligate fire ephemerals are annual plants that have germination and reproduction cued by fire occurrence, persisting between fire events in a long‐lived soil seed bank. Within these species, gene flow is restricted not only geographically but also temporally because individuals are limited to reproducing with others affected by the same fire event. The patchwork‐like distribution of fires may therefore promote population isolation. In contrast to past fires, the Australian fires of 2019–2020 were of unprecedented extent, providing an opportunity to investigate the landscape genetics of a fire ephemeral, Actinotus forsythii, across multiple populations and to compare it to a common congener, Actinotus helianthi.Methods: For both species, we used single nucleotide polymorphisms to infer patterns of population structure and calculate measures of genetic diversity. We also estimated a phylogeny of Actinotus forsythii to understand the differentiation of a geographically isolated population.Results: For A. forsythii, the within‐population diversity (allelic richness = 1.56) was greater, and the among‐population differentiation (F_ST = 0.30) was lower than that observed for A. helianthi (allelic richness = 1.33, F_ST = 0.57). Actinotus forsythii had distinct geographic groupings, and a geographically isolated population of this species was genetically highly differentiated.Conclusions: Despite the fire‐dependent, asynchronous gene flow, predicted between site disconnect, and possible within‐site homogeneity, our results suggest that burn mosaic could be influencing gene flow patterns and fire‐triggered mass flowering may promote genetic diversity within Actinotus forsythii.

SUMMARY: Seed banks are a vital resource for preserving plant species diversity globally. However, seedling establishment and survival rates from banked seeds can be poor. Despite a growing appreciation for the role of seed microbiota in supporting seed quality and plant health, our understanding of the effects of conventional seed banking processes on seed microbiomes remains limited. We investigated the composition and functional potential of the epiphytic seed microbiome of a native plant species using both 16S rRNA gene sequencing and culture-based approaches. Comparing the bacterial community composition of freshly collected seeds and those sourced from seed banking organisations, we found stored seeds hosted significantly less diverse bacterial populations, with substantial reductions in both low-abundance taxa and some core community members identified in unstored seeds. Bacteria with key plant growth promoting traits including IAA production, ACC deaminase activity, phosphate solubilisation, siderophore activity, and nitrogen fixation were identified in seed epiphytic communities, but these beneficial traits were less prevalent in stored seed compared to fresh seeds. Overall, these results suggest that epiphytic seed microbiomes may undergo significant changes during the storage process, selecting for bacteria tolerant to storage conditions, and potentially reducing the population of plant-growth promoting bacteria on seeds.