Plasmids are extra-chromosomal DNA molecules capable of autonomous replication, stable inheritance in a bacterial population, and horizontal transfer to other bacteria. Plasmids can harbour auxiliary genetic material that contributes to host bacterial fitness, the most prominent example being antimicrobial resistance (AMR) determinants, which remain the greatest threat to modern medicine. Since their discovery in the early 1950s, plasmids have been extensively studied due to their diversity, their capacity to spread between bacterial hosts, and their ability to carry and disseminate multiple AMR genes simultaneously. Recent advances in sequencing technology have transformed plasmid research, with transposon–insertion sequencing (TIS) enabling simultaneous analysis of millions of mutants and providing unprecedented scale, speed and resolution for studying plasmid biology. Here, we briefly outline a recommended methodology for generating plasmid transposon mutant libraries, which can be combined with TIS to investigate plasmid replication, maintenance and conjugation. We further summarise data from nine comprehensive plasmid TIS studies to date on five distinct plasmids, discuss alternative uses for plasmid libraries, challenges and future perspectives.
Building climate resilience into ecosystem restoration is an adaptation priority for sustainable land management. A well-established approach to achieve this is climate-adjusted seed provenancing – sourcing a mix of local and non-local seeds from populations across a climatic gradient likely to be encountered in the future. However, this strategy has limits as terrestrial ecosystems comprise far more than their vegetation alone. Here, we propose climate-adjusted soil microbiome provenancing – the sourcing and deployment of soil microbiomes from provenances that confer climate resilience to ecosystem being repaired under future conditions – as a complementary, nature-based solution for enhancing the climate resilience of restoration projects. The soil microbiome – the community of bacteria, fungi and other microbes (and its theatre of activity) that drive plant health, nutrient cycling and drought tolerance – remains largely overlooked in restoration science, policy and practice. Extending the climate-adjusted provenancing concept to the microbial domain requires theoretical, laboratory and field development. This approach offers potential to strengthen ecosystem climate resilience by restoring the adaptive capacity of soils – the living foundations of terrestrial ecosystems.
Antimicrobial resistance (AMR) is a complex ecological problem that has expanded beyond people to include animals (domesticated and wildlife) and the environment. The connectivity between people and other animals within shared environments and the transmission of antimicrobial-resistant pathogens across these three dimensions demonstrates the necessity for One Health systems approaches to manage and mitigate AMR. The ecological AMR system now encompasses climate change which can impact microbial factors, host factors, and environmental factors, presenting more complex problems for AMR mitigation. Wildlife species are now well integrated in AMR ecology with detections of diverse antibiotic resistance genes and resistant microbes in many species of birds, reptiles, marsupials and placental mammals. Importantly, many wildlife hosts have also never received antimicrobials. Whole genome sequencing of antimicrobial resistant bacteria isolated from wildlife indicates that wildlife acquire antimicrobial-resistant microbes via anthropogenic contaminated environments. Climate change is already a significant threat to wildlife globally, with mounting evidence that climate hazards are also driving increased prevalence and diversity of antimicrobial resistance in wildlife. Importantly, to avoid masking the complex nature of environmental AMR pollution and climate change for wildlife health, communication of primary AMR drivers should not continue to focus on, and be limited to, use and misuse of antimicrobials in people and agriculture. Recognising the importance of climate change for AMR ecology is vital for advancing One Heath strategies for AMR mitigation and wildlife protection.
Host–microbe symbioses are central to organismal health, yet these complex partnerships are often strongly shaped by the environment. Climate change is increasingly altering environmental conditions, disrupting the balance of host–microbe interactions and pushing them along a continuum from mutualism (both partners benefit) toward parasitism (one partner gains at the other’s expense). Reef-building corals provide a clear example of this vulnerability, as the coral holobiont, an ecological unit comprising diverse photosynthetic algal symbionts (Symbiodiniaceae) and other microbial partners, depends largely on these mutualistic interactions for nutrition, immunity, and stress tolerance. Increasingly, evidence suggests that under heat stress, the algal symbionts retain more photosynthetic products and proliferate, shifting the relationship more toward parasitism as the net benefits to the host decrease. Similarly, heat stress also restructures coral-associated bacterial communities, allowing opportunistic or pathogenic taxa to increase. These changing interactions highlight that symbiosis is not a fixed state and should instead be viewed as a dynamic continuum that will be highly influenced by climate change. This has important conservation implications – including the intentional integration of heat-evolved algal symbionts and beneficial bacteria in the form of probiotics to enhance coral stress tolerance. Understanding when and how host–microbe interactions can vary along the mutualism–parasitism continuum is essential for designing conservation strategies that enhance resilience under climate change.
Microbial communities dominate terrestrial ecosystems in Antarctica and underpin key biogeochemical processes, yet their responses to environmental change remain poorly understood. Ice-free areas comprise only ~0.3% of the continent but function as critical refugia for soil biodiversity and are projected to expand under future warming, particularly in rapidly changing regions. While soil microbial biodiversity of the Antarctic Peninsula has been relatively well studied, continental regions within the Australian Antarctic Territory remain under-sampled, limiting baseline understanding and long-term change detection. Recent work has identified microbial diversity hotspots, harbouring previously poorly uncharacterised taxa, including members of the Vulcanimicrobiota (formerly Candidatus Eremiobacterota) and class Dormibacteria, which possess rare metabolisms – specifically the genetic capacity to ‘live on thin air’. Spatio-temporal analyses of polar soils after a decade of change indicate that increasing soil moisture favours photosynthetic primary producers at the expense of dry-adapted, trace gas chemosynthetic taxa. Despite their ecological importance, microbial communities are largely absent from Antarctic conservation frameworks and long-term monitoring programs, which remain biased toward charismatic megafauna. Continued, coordinated microbial monitoring is therefore essential to resolve ecosystem trajectories, assess the resilience of novel taxa, and inform conservation and policy decisions in a rapidly changing Antarctic terrestrial environment.
Drylands cover approximately 30% of the Earth’s surface, forming the largest terrestrial biome, yet they are among the most threatened ecosystems globally. These systems are strongly constrained by water availability and characterised by high climatic variability, making them particularly vulnerable to climate change. Dryland functioning is fundamentally driven by soil microbial communities, which regulate key biogeochemical processes including nutrient cycling, soil stability, and water retention. Australian drylands provide a globally important case study, covering approximately 70% of the continent and experiencing extreme climatic variability. In the absence of recent volcanic activity, ecosystem functioning in these landscapes is heavily dependent on biological inputs, with soil microbial communities playing a central role in maintaining soil fertility. Strong coevolutionary relationships between dryland plants, soil microbes, and animals further structure these systems, with nutrient inputs from animal excrement and soil disturbance by digging fauna enhancing microbial activity and resource redistribution. This tight coupling between above- and belowground biodiversity makes Australian drylands uniquely valuable for examining how changes in soil microbial communities influence ecosystem resilience and for evaluating trophic rewilding as a restoration tool under a changing climate.
Harmful algal blooms (HAB) are increasing worldwide, including across Australia’s Great Southern Reef, causing mass mortalities of marine life and economic loss. This mini-review examines the phytoplankton species associated with the SA2025 bloom, particularly dinoflagellates, and explores the potential roles of associated bacteria and viruses in shaping bloom dynamics. Karenia cristata was identified during the bloom, with toxin analyses revealing the presence of brevetoxin analogues not previously reported in Australian HABs. Beyond algal toxicity, interactions with bacteria may influence bloom development through nutrient exchange, growth promotion, or algicidal activity. Similarly, diverse marine viruses can infect phytoplankton and may regulate bloom progression or termination through host lysis. Despite growing recognition of these microbial interactions, the bacterial and viral communities associated with the SA2025 bloom remain largely unexplored. Understanding the tripartite interactions between dinoflagellates, bacteria, and viruses alongside oceanography is critical for investigating bloom initiation, persistence, and collapse.
Aquatic microbiomes deliver critical ecosystem services, spanning primary production, nutrient cycling, degradation of contaminants and climate regulation. However, a small fraction of the microbial assemblages inhabiting marine and freshwater ecosystems can also have detrimental impacts on human populations that use these aquatic environments for recreation and food provision. Some naturally occurring aquatic microorganisms, including diverse species of pathogenic bacteria and toxic microalgae can cause a wide range of often severe human health effects. Furthermore, anthropogenic pollution leads to the introduction of allochthonous microbiological hazards, including diverse enteric viral, bacterial and protozoan pathogens present in urban runoff. Notably, the threats posed by many harmful aquatic microorganisms are increasing due to climate change. Chronic and acute increases in water temperature enhance the growth and virulence of pathogenic and toxic microbes, often triggering bloom events that can threaten human health. Furthermore, increasingly frequent intense precipitation events escalate intrusions of allochthonous pathogens within coastal pollution and runoff. These often-overlooked microbiological implications of climate change have the potential to profoundly impact the health and economies of human populations that increasingly rely on marine and freshwater ecosystems.
Climate change is reshaping the environmental foundations of agriculture, altering soil temperature, moisture, and salinity regimes that govern plant–microbe interactions. Soil and root-associated microbiomes underpin nutrient cycling, water regulation, and disease suppression, yet their activity and composition are highly sensitive to these shifting conditions. Here, I apply a process-based ecological framework to illustrate how climate change affects crop microbiomes through three core pathways: (1) phenological shifts that decouple microbial activity from crop growth; (2) range and distribution changes that favour stress-tolerant but functionally narrow taxa; and (3) community reorganisation that alters cooperation, competition, and network stability. Together, these processes can disrupt nutrient cycling efficiency and microbial resilience to environmental change, with consequences for crop health and productivity. Addressing knowledge gaps in temporal dynamics, multi-stressor interactions, and microbial network stability will be key to predicting and sustaining the biological foundations of agricultural productivity in a warming world.
Microbial diversity underpins the health and function of all ecosystems on our planet, yet considerations of microbes in ecosystem conservation efforts do not generally exist. International efforts are now underway to incorporate microbial diversity into more general frameworks and platforms for biodiversity and species conservation (i.e. the International Union for Conservation of Nature). Here, we discuss three broad areas (host-associated microbial communities, soil microbiomes, and Antarctic ecosystems) where microbial diversity is critical for function and which warrant attempts for conservation. We highlight how environmental change causes vulnerability for microbial function and propose ways how conservation of microbial diversity can be achieved. Future efforts will need national and international commitments and collaborations to financially resource conservation projects, develop best-practice protocols and support shared data and sample access.
Carotenoids are a diverse group of bioactive pigments produced by plants, microbes and some animals, with significant roles in human health and environmental sustainability. This paper highlights the biological importance of microbial carotenoids, focusing on their health benefits and their role in preventing chronic diseases. Carotenoids also influence the gut microbiota, promoting beneficial microbes and enhancing host immunity. While dietary carotenoids remain the primary source, emerging evidence suggests that carotenoid-producing microbes may provide localised and sustained benefits within the gut. Microbial production offers advantages over conventional sources, including higher yields and lower environmental impact. The use of agro-industrial waste as feedstock presents a sustainable approach aligned with circular bioeconomy principles. Advances in metabolic engineering and fermentation technologies further enhance production efficiency. Overall, microbial carotenoids represent a promising avenue for developing sustainable, health-promoting nutraceuticals and functional bioproducts.
The application of probiotics in both human and animal continues to expand rapidly. Over the past decade, there has been a significant increase in the use of probiotics as feed supplements in livestock production. The use of probiotics in young animals has been recognised since 1990s, particularly in dairy cattle. More recently, advanced analytical techniques have enabled deeper investigation into the benefits of probiotic supplementation, especially in milk replacers for neonatal animals. Lactic acid bacteria (LAB) especially Lactobacillus spp., Bacillus spp. and Saccharomyces spp., which can enhance immune function of gastrointestinal and respiratory systems, are among the most widely used probiotics in young livestock. This minireview focuses on probiotic applications in cattle, sheep and pigs, highlighting recent studies and various probiotic combinations used to improve animal health and productivity.
The paternal pre-conception environment has been demonstrated in preclinical models to alter the sperm epigenome and offspring phenotypes. Recent studies have reported that modulating the paternal gut microbiota through non-absorbable antibiotics altered offspring body weight, survival, brain transcriptomics and behaviour. Other paternal environmental factors including diet composition, stress and pollutant exposure have also been shown to alter the paternal gut microbiome. This review discusses current evidence on the role of the paternal gut microbiome in epigenetic inheritance and explores its potential as a target to prevent alterations in the sperm epigenome and subsequent detrimental effects on offspring outcomes. This nascent research field (at the nexus of microbiology, epigenetics and neuroscience) will facilitate the prevention and treatment of the growing challenge of ‘intergenerational epigenopathy’ in a rapidly changing world.
Saccharomyces boulardii (S. cerevisiae var. boulardii) is a non-pathogenic yeast recognised as a eukaryotic probiotic. This probiotic is considered safe for use in both adults and children and functions as a biotherapeutic agent due to its antioxidant, anti-inflammatory and immune-modulatory properties. Saccharomyces boulardii has proven to be beneficial for promoting human health, particularly in the prevention and treatment of various acute and chronic gastrointestinal disorders, including multiple forms of diarrhoea. This review highlights the unique physiological traits of S. boulardii, its mechanisms of probiotic action, health benefits, clinical applications and emerging applications in the food industry.
