Summary
Soil is a non-renewable resource that requires constant monitoring to prevent its degradation and promote its sustainable management. The ‘Land Use/Cover Area frame statistical Survey Soil’ (LUCAS Soil) is an extensive and regular topsoil survey that is carried out across the European Union to derive policy-relevant statistics on the effect of land management on soil characteristics. Approximately 45 000 soil samples have been collected from two time-periods, 2009–2012 and 2015. A new sampling series will be undertaken in 2018, with new measurements included. The organization for the 2018 sampling campaign represents an opportunity to summarize past LUCAS Soil achievements and present its future objectives. In 2009–2012 and 2015, LUCAS Soil surveys targeted physicochemical properties, including pH, organic carbon, nutrient concentrations and cation exchange capacity. Data from 2009–2012 (ca. 22 000 points) and derived output (more than 20 maps) are available freely from the European Soil Data Centre website. Analyses of samples collected during 2015 are ongoing and data will be available at the end of 2017. In the 2018 LUCAS Soil sampling campaign, additional properties, including bulk density, soil biodiversity, specific measurements for organic-rich soil and soil erosion will be measured. Here we present the current dataset (LUCAS Soil 2009–2012 and 2015), its potential for reuse and future development plans (LUCAS Soil 2018 and over). LUCAS Soil represents the largest harmonized open-access dataset of topsoil properties available for the European Union at the global scale. It was developed as an expandable resource, with the possibility to add new properties and sampling locations during successive sampling campaigns. Data are available to the scientific community and decision makers, thus contributing to both research and the development of the land-focused policy agenda.

Highlights
LUCAS Soil consists of soil physicochemical and biological properties data from Europe.
Harmonized and open-access dataset allowing inclusion of soil in large-scale inter-disciplinary assessments.
LUCAS Soil has a broad pool of users from scientists to policy makers, and applications from map validation to modelling.
LUCAS Soil confirms the need for open-access and a large-scale dataset for soil properties.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/ejss.12499

LUCAS Soil, the largest expandable soil dataset for Europe: a review

Cultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities. Given that phototroph abundance varies across these Antarctic soils, an enduring question is what supports life in those communities with low photosynthetic capacity. Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation. Soil microcosms aerobically scavenged atmospheric H2 and CO at rates sufficient to sustain their theoretical maintenance energy and mediated substantial levels of chemosynthetic but not photosynthetic CO2 fixation. We propose that atmospheric H2, CO2 and CO provide dependable sources of energy and carbon to support these communities, which suggests that atmospheric energy sources can provide an alternative basis for ecosystem function to solar or geological energy sources. Although more extensive sampling is required to verify whether this process is widespread in terrestrial Antarctica and other oligotrophic habitats, our results provide new understanding of the minimal nutritional requirements for life and open the possibility that atmospheric gases support life on other planets.

/pdf/atmospheric-trace-gases-support-primary-production-in-1aer92tffc.pdf

Atmospheric trace gases support primary production in Antarctic desert surface soil

Culture-independent molecular surveys of plant root microbiomes indicate that soil type generally has a stronger influence on microbial communities than host phylogeny. However, these studies have mostly focussed on model plants and crops. Here, we examine the root microbiomes of multiple plant phyla including lycopods, ferns, gymnosperms, and angiosperms across a soil chronosequence using 16S rRNA gene amplicon profiling. We confirm that soil type is the primary determinant of root-associated bacterial community composition, but also observe a significant correlation with plant phylogeny. A total of 47 bacterial genera are associated with roots relative to bulk soil microbial communities, including well-recognized plant-associated genera such as Bradyrhizobium, Rhizobium, and Burkholderia, and major uncharacterized lineages such as WPS-2, Ellin329, and FW68. We suggest that these taxa collectively constitute an evolutionarily conserved core root microbiome at this site. This lends support to the inference that a core root microbiome has evolved with terrestrial plants over their 400 million year history. Yeoh et al. study root microbiomes of different plant phyla across a tropical soil chronosequence. They confirm that soil type is the primary determinant of root-associated bacterial communities, but also observe a clear correlation with plant phylogeny and define a core root microbiome at this site.

/pdf/evolutionary-conservation-of-a-core-root-microbiome-across-15bv1vs3kv.pdf

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence.

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.

https://espace.library.uq.edu.au/view/UQ:716294/UQ716294_postprint_OA.pdf

Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere.

Coral reefs are facing unprecedented pressure on local and global scales. Sensitive and rapid markers for ecosystem stress are urgently needed to underpin effective management and restoration strategies. Although the fundamental contribution of microbes to the stability and functioning of coral reefs is widely recognised, it remains unclear how different reef microbiomes respond to environmental perturbations and whether microbiomes are sensitive enough to predict environmental anomalies that can lead to ecosystem stress. However, the lack of coral reef microbial baselines hinders our ability to study the link between shifts in microbiomes and ecosystem stress. In this study, we established a comprehensive microbial reference database for selected Great Barrier Reef sites to assess the diagnostic value of multiple free-living and host-associated reef microbiomes to infer the environmental state of coral reef ecosystems. A comprehensive microbial reference database, originating from multiple coral reef microbiomes (i.e. seawater, sediment, corals, sponges and macroalgae), was generated by 16S rRNA gene sequencing for 381 samples collected over the course of 16 months. By coupling this database to environmental parameters, we showed that the seawater microbiome has the greatest diagnostic value to infer shifts in the surrounding reef environment. In fact, 56% of the observed compositional variation in the microbiome was explained by environmental parameters, and temporal successions in the seawater microbiome were characterised by uniform community assembly patterns. Host-associated microbiomes, in contrast, were five-times less responsive to the environment and their community assembly patterns were generally less uniform. By applying a suite of indicator value and machine learning approaches, we further showed that seawater microbial community data provide an accurate prediction of temperature and eutrophication state (i.e. chlorophyll concentration and turbidity). Our results reveal that free-living microbial communities have a high potential to infer environmental parameters due to their environmental sensitivity and predictability. This highlights the diagnostic value of microorganisms and illustrates how long-term coral reef monitoring initiatives could be enhanced by incorporating assessments of microbial communities in seawater. We therefore recommend timely integration of microbial sampling into current coral reef monitoring initiatives.

/pdf/microbial-indicators-of-environmental-perturbations-in-coral-1zr0rw3tfa.pdf

Microbial indicators of environmental perturbations in coral reef ecosystems

Microbial 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. BASE 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’. Developed 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.

/pdf/introducing-base-the-biomes-of-australian-soil-environments-2u77sxr92h.pdf

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

In the article 'Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database GigaScience 2016 5:21' [1] the authorship list should have included Leon Court, who was responsible for sample collection and preparation, sampling design and sequencing method design. The authors regret this omission.

Matt Tinning

Papers

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

Erratum to: Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.