BackgroundMicrobial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function.FindingsBASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project’s data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the ‘Atlas of Living Australia’.ConclusionsDeveloped within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.

Summary Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome‐based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane‐associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the core microbiome that were influenced by YCS incidence. Our study revealed key hub microorganisms in the core microbiome networks of sugarcane leaves, stalks, roots and rhizosphere soil despite location and time‐associated shifts in the community assemblages. Elucidating their functional roles and identification of the keystone core microbiota that sustain plant health could provide a technological breakthrough for a sustainable increase in crop productivity.

The effects of short-term drought on soil microbial communities remain largely unexplored, particularly at large scales and under field conditions. We used seven experimental sites from two continents (North America and Australia) to evaluate the impacts of imposed extreme drought on the abundance, community composition, richness, and function of soil bacterial and fungal communities. The sites encompassed different grassland ecosystems spanning a wide range of climatic and soil properties. Drought significantly altered the community composition of soil bacteria and, to a lesser extent, fungi in grasslands from two continents. The magnitude of the fungal community change was directly proportional to the precipitation gradient. This greater fungal sensitivity to drought at more mesic sites contrasts with the generally observed pattern of greater drought sensitivity of plant communities in more arid grasslands, suggesting that plant and microbial communities may respond differently along precipitation gradients. Actinobateria, and Chloroflexi, bacterial phyla typically dominant in dry environments, increased their relative abundance in response to drought, whereas Glomeromycetes, a fungal class regarded as widely symbiotic, decreased in relative abundance. The response of Chlamydiae and Tenericutes, two phyla of mostly pathogenic species, decreased and increased along the precipitation gradient, respectively. Soil enzyme activity consistently increased under drought, a response that was attributed to drought-induced changes in microbial community structure rather than to changes in abundance and diversity. Our results provide evidence that drought has a widespread effect on the assembly of microbial communities, one of the major drivers of soil function in terrestrial ecosystems. Such responses may have important implications for the provision of key ecosystem services, including nutrient cycling, and may result in the weakening of plant-microbial interactions and a greater incidence of certain soil-borne diseases.

Summary Biodiversity is declining world‐wide with detrimental effects on ecosystems. However, we lack a quantitative understanding of the shape of the relationship between microbial biodiversity and ecosystem function (BEF). This limits our understanding of how microbial diversity depletion can impact key functions for human well‐being, including pollutant detoxification. Three independent microcosm experiments were conducted to evaluate the direction (i.e. positive, negative or null) and the shape of the relationships between bacterial diversity and both broad (i.e. microbial respiration) and specialized (i.e. toxin degradation) functions in five Australian and two UK freshwater ecosystems using next‐generation sequencing platforms. Reduced bacterial diversity, even after accounting for biomass, caused a decrease in broad (i.e. cumulative microbial respiration) and specialized (biodegradation of two important toxins) functions in all cases. Unlike the positive but decelerating BEF relationship observed most frequently in plants and animals, most evaluated functional measurements were related to bacterial diversity in a non‐redundant fashion (e.g. exponentially and/or linearly). Synthesis. Our results suggest that there is a lack of functional redundancy in the relationship between bacterial diversity and ecosystem functioning; thus, the consequences of declining microbial diversity on ecosystem functioning and human welfare have likely been considerably underestimated.

Despite the vital role of microorganisms for ecosystem functioning and human welfare, our understanding of their global diversity and biogeographical patterns lags significantly behind that of plants and animals. We conducted a meta‐analysis including ~600 soil samples from all continents to evaluate the biogeographical patterns and drivers of bacterial diversity in terrestrial ecosystems at the global scale. Similar to what has been found with plants and animals, the diversity of soil bacteria in the Southern Hemisphere decreased from the equator to Antarctica. However, soil bacteria showed similar levels of diversity across the Northern Hemisphere. The composition of bacterial communities followed dissimilar patterns between hemispheres, as the Southern and Northern Hemispheres were dominated by Actinobacteria and Acidobacteria, respectively. However, Proteobacteria was co‐dominant in both hemispheres. Moreover, we found a decrease in soil bacterial diversity with altitude. Climatic features (e.g., high diurnal temperature range and low temperature) were correlated with the lower diversity found at high elevations, but geographical gradients in soil total carbon and species turnover were important drivers of the observed latitudinal patterns. We thus found both parallels and differences in the biogeographical patterns of aboveground vs. soil bacterial diversity. Our findings support previous studies that highlighted soil pH, spatial influence, and organic matter as important drivers of bacterial diversity and composition. Furthermore, our results provide a novel integrative view of how climate and soil factors influence soil bacterial diversity at the global scale, which is critical to improve ecosystem and earth system simulation models and for formulating sustainable ecosystem management and conservation policies.

The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.

The legacy impacts of past climates on the current distribution of soil microbial communities are largely unknown. Here, we used data from >1000 sites from five separate global and regional datasets to identify the importance of paleoclimatic conditions (Last Glacial Maximum and Mid-Holocene) in shaping the current structure of soil bacterial communities in natural and agricultural soils. We show that paleoclimate explained a greater amount of the variation in the richness and composition of bacterial communities than current climate. Moreover, paleoclimate accounted for a unique fraction of this variation that could not be predicted by geographic location, current climate, soil properties, or plant diversity. Climatic legacies (temperature and precipitation anomalies from the present to ~20k years ago) likely shape soil bacterial communities both directly and indirectly via shifts in soil properties and plant communities. The ability of both paleo-and current climate to predict the distribution of soil bacteria declined dramatically in agricultural soils, highlighting the fact that anthropogenic activities have a strong influence on soil bacterial diversity. We illustrate how climatic legacies can help explain the current distribution of soil bacteria in natural ecosystems, and advocate that climate legacies should be considered when predicting microbial responses to climate change.

Summary We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres.