Seed associated microbial communities can strongly influence plant establishment, stress tolerance, and long-term resilience. While climate-adjusted provenancing focuses on matching plant genotypes to future climatic conditions, little attention has been paid to the microbial ‘provenance’ of seeds. Emerging evidence suggests that seed microbiomes vary across populations, and some may be locally adapted, raising concerns that moving genotypes could disrupt plant–microbe relationships. With the rise of centralised seed production, such microbial mismatches may become more common. To explore these issues, we used metabarcoding to characterise bacterial and fungal communities associated with seeds from native Australian plant species collected across a latitudinal gradient. We also isolated culturable microbes to test for plant growth-promoting (PGP) traits, examining how these traits varied across populations and environmental conditions. We found that geographically closer plant populations shared more similar PGP profiles, and that soil characteristics at the source site strongly influenced seed microbial composition and plant growth potential, whilst climatic conditions were of lesser importance. We identified a suite of core seed microbes present across the landscape, in addition to many rare taxa that were often associated with a single plant population. These findings suggest that sourcing seed from locations with similar soil conditions and geographic proximity to restoration sites may help retain functionally beneficial seed microbiomes. Incorporating seed microbiome considerations into provenance frameworks could enhance restoration outcomes by supporting resilient plant–microbe partnerships in a changing climate.

To address the Earth’s sixth extinction crisis, driven by human activities and climate change, evolutionary processes must be actively supported. We present three examples demonstrating how enhancing gene flow can significantly improve the health and adaptive capacity of populations, species, and ecosystems.
First, human-mediated gene flow can rescue isolated populations from lost fitness due to inbreeding. In the helmeted honeyeater, introducing genes from another subspecies increased reproduction and survival of the last remaining population, enabling population growth and the re-establishment of two additional populations.
Second, managing fragmented populations as metapopulations helps retain species’ standing genetic variation–fuel for adaptation–and reduce inbreeding. The endangered Macquarie perch, facing habitat loss, population fragmentation and catastrophic climate-driven habitat degradation, benefited from mixing two sources during population re-establishment through captive breeding and translocation. The resulting mixed offspring were fitter and more successful at colonizing nearby creeks. We recommend reconnecting isolated populations with augmented gene flow and establishing new ones in climate-resilient locations using multiple genetic sources.
Third, we propose ecosystem genetic management to maintain ecosystem function by enhancing adaptive potential of multiple keystone species. For Great Barrier Reef corals facing heat stress and environmental changes, we suggest augmenting populations of 60 species with individuals or genes from locations already surviving predicted climate conditions, unless experimental data for a species suggests that negative consequences will outweigh the benefits of gene flow.
Our case studies demonstrate that active genetic management can be a great cost-effective solution to promote population health and resilience, when implemented in combination with interventions mitigating original drivers of decline. Its successful implementation requires well-funded, multidisciplinary teams of scientists and practitioners. Mainstreaming genetic management through gene flow is vital to reversing global biodiversity declines and ensuring wildlife persistence under climate change.