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.

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.

Microbes are the most dominant and diverse lifeform on Earth, yet the vast majority remain uncultivated.Despite advances in isolation methods, less than 0.5% of bacteria and archaea, and under 2% of fungal species, have been successfully cultured. [1][2]2][3] In extreme environments like terrestrial Antarctica, the gap is even wider, as metagenomic surveys continue to uncover diverse, underexplored microbial communities. [4][5]5][6] Most microbial life continues to exist as this microbial dark matter, recalcitrant to laboratory cultivation efforts.Given the role of microbes in climate change, geochemical cycling and their biomining potential, our focus needs to shift back to the isolation of the yet-to-be cultured majority.The advent of single-cell sequencing technologies, metagenomics and sophisticated differential coverage binning approaches now allow for the reconstruction of metagenome assembled genomes (MAGs) from diverse ecosystems. [5][6]6][7][8] The significant increase in genome data has led to ever changing views of the tree of life, and the development of new hypotheses around what metabolic capacities and ecological roles uncultivated taxa perform. 4,6While metagenomics has revolutionised our understanding of microbial diversity and functioning, it cannot replace experimental validation to confirm predictions on the cell biology, metabolism and physiological traits of microbial dark matter through the cultivation of pure cultures, co-cultures or stable enrichments.In the early 2000s, novel cultivation approaches began to close this gap, by simply mimicking the natural environment, extending incubation times and using dilute media, the ubiquitous SAR11 clade that had evaded cultivation for decades were recovered. 9,10e began to understand that not all microbes grow as macrocolonies, instead slow growing oligophiles or k-strategists which prefer nutrient poor-stable environments, and grow as microcolonies only -invisible to the naked eye. 11,12Once isolated, domestication allows microbes to adapt to an r-strategist lifestyle and become a faster growing species.Additionally, new understanding of metabolic cooperation and the requirements for signalling molecules have emerged, such as syntrophic relationships thus 'pure' cultures may not be possible, 13 and in 2018, a reverse-genomics cultivation method was developed that combined the design of antibodies to predicted surface proteins with cell sorting. 8These innovations led to the targeted isolation of the first members of the Saccharibacteria (formerly TM7), an epiparasite requiring an Actinobacterial host. 8,13ut the isolation of such rare, recalcitrant taxa requires patience, thinking outside the box, and in some cases a lot of luck.A new resurgence in targeted and innovative cultivation efforts is needed, and is timely, as genomes have been retrieved from a myriad of extreme environments with metabolic reconstructions of a taxa's functional potential invaluable for informing isolation efforts.For example, we discovered bacteria from novel phyla (formerly AD3 and WPS-2) in Antarctic soils support primary production via the genomic capacity to 'live on air' -using high affinity enzymes to oxidise atmospheric levels of molecular hydrogen and carbon monoxide to provide energy requirements to not only sustain dormancy, but support growth via CO 2 fixation (Fig. 1). 6However, difficulty in laboratory isolation of a trace gas chemotroph means this hypothesis has not been confirmed experimentally.Can we select for, and enrich for these air-eating bacteria through the addition of these gasses in enrichment cultures?A pioneering study by Nobs et al., supports this approach. 14 In this work, culture conditions informed by MAG reconstructions led to the enrichment of an Asgard archaeon alongside a sulfate-reducing bacterium.These enrichment cultures were derived from incubating anoxic layers of modern microbial mats from Hamelin Pool, Shark Bay, and incubation under anerobic and hypersaline conditions, thereby mimicking their natural environment.The successful enrichment and subsequent analysis of these critical putative syntrophic partners have major implications for the origin of eukaryogenesis.

Klebsiella pneumoniae (Kp) is a Gram-negative bacterium and priority antimicrobial resistant (AMR) pathogen, ranked #1 in the World Health Organization's AMR pathogen list. 1 Kp is a major cause of opportunistic healthcare-associated infections globally, and among the top three causes of neonatal sepsis in low resource countries. 2Strains with resistance to the 3rd generation cephalosporins and the carbapenems are increasing in frequency worldwide and cause infections that are extremely difficult to treat.Therefore, there is an urgent need for novel control strategies, and growing interest in the development of vaccines, monoclonal antibody and phage therapies.The capsule (K) and outer-lipopolysaccharide (O) are the two major Kp surface polysaccharides.Both are pathogenicity factors and major targets for vaccines and monoclonal antibody therapies; however, there is some debate over the potential efficacy of anti-O strategies due to the possibility that the capsule will block anti-O antibodies. 3he capsule also serves as a major binding receptor for anti-Klebsiella bacteriophage, wherein most can bind only one or a subset of capsule types. 4ighty-two K phenotypes are recognised by serological typing techniques, 5 but more than 160 have been predicted from genome data based on distinct gene content within the capsule synthesis (K) locus. 6,7Similarly, nine O phenotypes were recognised by traditional typing approaches, but genomics data indicate >20 distinct O polysaccharides can be produced through combinations of distinct O loci and genes elsewhere in the genome that are known to play a role in O polysaccharide modification. 8Given that protein-polysaccharide conjugate vaccines and monoclonal antibody therapies have limited valency (up to 20-25 antigens in a single vaccine 3 ), and phage cocktails generally cannot exceed 5-10 phage, there is a clear need to understand the epidemiology of K and O types in order to prioritise them as targets.K and O loci can be rapidly identified from Kp whole-genome sequences using the bioinformatics tool, Kaptive, 6,7 which is available as a stand-alone command line tool, and integrated into the Kp-specific genomic typing tool, Kleborate. 9For broader accessibility, Kaptive was also made available as the graphical web tool, Kaptive Web (kaptiveweb.erc.monash.edu)and has been integrated into the Pathogenwatch genomic surveillance platform (pathogen.watch).Kaptive can identify K and O loci from draft genome assemblies with very high accuracy (98%), 7 and a recent comparison of >700 matched genomes with serological K typing data indicated high concordance (85%), but highlighted that there remain gaps in the knowledge-base about the K genotype-phenotype relationship. 5enomic evolutionary analyses have revealed that K and O diversity differs among common Kp sub-lineages, or 'clones' (referenced here by the dominant 7-gene multi-locus sequence type, ST).Specifically, clones associated with so-called 'hypervirulent' communityacquired Kp infections have carried KL1 (encoding K1, found in ST23) or KL2 (encoding K2, ST86, ST65) throughout their evolutionary histories. 10In contrast, the common globally distributed multidrug resistant (MDR) healthcare-associated clones display diverse K and O loci, with acquisition of novel loci driven through chromosomal recombination. 10However, despite this diversity, each of the major MDR clones is dominated by just one or two K loci e.g.KL107 among ST258, 9,10 KL51 and KL64 among ST231. 11 While it is well documented that hypervirulent infections are dominated by K1 and K2-producing Kp, healthcare-associated infections have been associated with a diverse array of K types.In a 12-month study at the Alfred Health Network (Melbourne, Vic, Australia), 91 distinct K loci were represented among 294 unique Kp infections, reflecting the high diversity of clones capable of causing disease (n = 179 STs detected). 12The top 16 K loci accounted for just 50% of all infections.In contrast, only 12 predicted O types were detected, and the top four accounted for >50% of infections, reflecting a comparatively lower level of diversity among O antigens that is replicated across broad geographies. 9,11,13,

The microbial diversity of palm tree ecosystems is fundamental to the health and productivity of these ecosystems. Palm trees, which are essential in tropical and subtropical regions, interact with a variety of microorganisms, including bacteria, fungi, archaea and viruses. These microorganisms engage in crucial processes such as nutrient cycling, soil health maintenance and plant defence mechanisms. For instance, nitrogen-fixing bacteria like Rhizobium and Azospirillum enhance soil fertility, while mycorrhizal fungi facilitate nutrient uptake by palm tree roots. Pathogenic bacteria and fungi, however, pose significant risks, causing diseases like Fusarium wilt and basal stem rot, which can affect palm tree health and productivity. Environmental factors such as soil type, moisture and temperature play a pivotal role in shaping microbial communities. Additionally, microbial interactions are highly dynamic, with beneficial microorganisms often forming mutualistic relationships with palm trees, promoting growth and resilience. Understanding the complexities of microbial communities in palm tree ecosystems is essential to the development of sustainable agricultural practices, especially in industries like palm oil production. Continued research into these microbial interactions is critical to developing strategies that protect palm trees from pathogens and enhance ecosystem services, ensuring the sustainability of these vital ecosystems.

The authors advise of errors in Tables 2 and3 of the paper.In Table 2, the correct propagation host for phage 4 should be Nocardia asteroides (ACM 2963).In both Tables 2 and3, the correct code for DSMZ cultures should be DSM.The corrected Tables are provided below.