Soil is essential for life, providing ecosystem services such as food, water filtration, and carbon sequestration. Unfortunately, human activities like excessive cultivation, urban sprawl, chemical runoff, and erosion are degrading this vital resource. Improving soil management and increasing carbon content can stabilise global carbon emissions, combat climate change, and enhance agricultural productivity. Neglecting soil health puts both our food security and our sustainable future at risk.

This year's World Soil Day theme, "Caring for Soils: Measure, Monitor, Manage" invites us to reflect on the importance of accurate soil data and information in understanding soil characteristics. This knowledge is essential for making informed decisions about sustainable soil management and food security. To support this theme, we showcase research published across the BMC Series.

BMC Ecology and Evolution - Land use and soil characteristics affect soil organisms differently from above-ground assemblages

Soil is a living ecosystem that houses nearly a quarter of all known species, including mammals, invertebrates, bacteria and fungi, which interact in complex and intricate ways to support life on earth. However, current soil quality assessments, which often focus only on surface-level indicators like birds and butterflies, fail to consider the rich biodiversity beneath our feet.

A study published in BMC Ecology and Evolution, led by Victoria Burton, a post-doctoral researcher at the Natural History Museum in London, explores how land-use practices affect soil biodiversity. By modeling data from the PREDICTS project, the research compares the responses of below-ground and above-ground organisms to changes in land use and soil properties. The PREDICTS project is a global biodiversity database that examines how terrestrial biodiversity is influenced by human actions, including changes and intensification in land use.

The researchers found that soil organisms are less abundant in intensively used habitats like cropland and plantations compared to less-altered areas such as pasture. Notably, the study also found that soil biodiversity recovers more slowly than above-ground biodiversity after human impacts cease. This highlights the need for further research to understand the complexities of soil biodiversity and its relationship with above-ground communities. For instance, while plantation forests can offset carbon emissions, the potential loss of soil biodiversity, essential for ecosystem health, should be considered.

BMC Methods - Microfluidic platform for microbial spore germination studies in multiple growth conditions

Concerns about the environmental impact of chemical pesticides and fertilizers are growing, driving interest in eco-friendly alternatives like soil-dwelling microbes. These microbes, such as bacteria and fungi, form resilient spores that endure harsh conditions and germinate when conditions improve. This process supports soil health by recycling nutrients, promoting plant growth, and protecting against disease. For instance, farmers use Trichoderma fungi to protect crops from a broad spectrum of soil-borne pathogens. Understanding spore germination is crucial to leveraging these microbes for sustainable agriculture and reducing agrochemical use.

In BMC Methods, researchers from Imperial College London describe a new microfluidic platform that allows for the parallel study of microbial spore germination under four different environmental conditions within a single device. Microfluidic platforms are tools that enable the handling of fluids at the microscale. By making things smaller, these platforms require low volumes of fluids to achieve multiplexing, automation and high throughput screening. They are especially useful for studying individual cells. By keeping single cells in a thin layer, researchers can closely observe their behaviour over space and time, uncovering details often missed when looking at a large population.

The study focuses on soil microbes, such as  Bacillus subtilis, Ammoniphilus oxalaticus, and Trichoderma rossicum, which are already being used or have the potential to be used as biocontrol agents to control soil-borne plant diseases. Using the microfluidic platform, the group analysed the effects of four growth conditions in parallel. 

This versatile tool enables researchers to probe the interplay between microbial spores and environmental factors at the single-cell level, paving the way for promising research in several fields, including biotechnological applications such as biocontrol agent formulations. 

BMC Plant Biology - The impact of root systems and their exudates in different tree species on soil properties and microorganisms in a temperate forest ecosystem

Trees affect the soil in many ways. Their roots and fallen leaves feed the soil with nutrients, while their root exudates (organic substances released from roots) serve as food for soil microorganisms like bacteria and fungi. These microorganisms are essential for soil health, playing important roles in nutrient cycling, organic matter decomposition, and carbon storage. We need healthy forests to combat climate change and slow biodiversity loss. Therefore, a better understanding of how different tree species impact the soil could help identify species that improve soil health and support resilient forest ecosystems.

Research in BMC Plant Biology investigates how tree root systems influence soil properties and microbial biodiversity. The researchers examined six tree species commonly found in temperate forests: Scots pine, European larch, English oak, European beech, European hornbeam, and English ash to understand the relationship between these trees' roots, soil conditions, and the communities of microorganisms in the soil.

Soil properties were closely linked to root structure, with root exudates improving pH, calcium levels, and nutrient cycling. Among the tree species studied, ash trees stood out for their positive impact, supporting diverse bacterial and fungal communities. In contrast, coniferous species like pine and larch were associated with lower microbial diversity, highlighting the ecological value of ash trees and their rooting systems for soil quality and biodiversity. Unfortunately, ash is severely threatened by ash dieback, a fungal disease projected to cause a 70% mortality rate across European ash populations. Therefore, efforts to combat ash dieback are needed.

BMC Microbiology - The role of New World vultures as carriers of environmental antimicrobial resistance

Soil ecosystems naturally harbor diverse microbial communities, including bacteria that carry antimicrobial resistance genes (ARGs). However, human activities, such as waste mismanagement and excessive antibiotic use, amplify the presence and spread of these genes. Landfill soils, in particular, become hotspots where resistant bacteria can thrive. 

A study published in BMC Microbiology analysed soil samples from three types of locations in East-Central Mississippi, USA: three vulture roosting sites, a recreational area, and two landfills. The research aimed to investigate how landfills may contribute to the ability of New World vultures to spread environmental AMR. Enterococci, Escherichia coli , and Salmonella bacteria were isolated from the samples and tested to see how resistant they were to antibiotics, and specific genes that make them resistant were identified. 

This study confirmed that wildlife can carry antibiotic-resistant bacteria in their faeces, which can persist in the environment, such as the soil. New World vultures may serve as indicators for monitoring antibiotic-resistant and multi-drug-resistant bacteria. Additionally, human-altered habitats, such as landfills, could act as reservoirs for the occurrence and spread of resistant strains of E. coli, enterococci, and Salmonella. However,  “natural” sites can also pose a similar risk of AMR/MDR as landfills. While managing anthropogenic waste to prevent wildlife access is important, the findings suggest that reducing pollution may not prevent AMR transmission to wildlife. More research is needed to compare resistance levels in natural versus urban environments. The study highlights the interconnectedness of soil health with global challenges like AMR. 

BMC Genomics - Evolutionary history of arbuscular mycorrhizal fungi and genomic signatures of obligate symbiosis

Arbuscular mycorrhizal (AM) fungi have co-evolved alongside plants for 400 million years, forming symbioses with about 72% of land plants. In these symbiotic relationships, plants supply photosynthetically captured carbon—such as lipids and sugars—in return for essential minerals, particularly phosphorus and nitrogen. These fungi play important toles in plant nutrition, soil biology and soil chemistry.  

In BMC Genomics, researchers from Upsalla University, Sweden assemble a large genomic dataset to infer the evolutionary relationships between three phyla of fungi: Glomeromycota, Mucoromycota, and Morteriellomycota. The group used phylogenetic analysis to better understand how these groups are related and how their ability to live symbiotically with plants evolved.

The results indicate that Mucoromycota and Mortierellomycota form a monophyletic grouping, with Glomeromycota as their sister group.  AM fungi within Glomeromycota and fine root endophytes, specifically Endogonales in Mucoromycota, developed mutualistic relationships with plants independently. The low number of genes for plant cell wall degradation enzymes (PCWDEs) found in AM fungi and Endogonales does not represent an adaptation to plant symbiosis; rather, it reflects an ancestral genomic trait. Gene families such as PCWDEs were already absent in the common ancestor of these three fungal lineages. Additionally, several genes previously considered unique "missing genes" in AM fungi, like fatty acid synthesis genes, are either missing in all three lineages or found only in specific AM fungal genomes. This finding challenges previous assumptions about the genetic features that are specific to AM fungi. The absence of fatty acid synthesis genes in AM fungi further underscores their dependence on host plants for energy and carbon.

These findings further our understanding of fungal evolution, especially the genomic adaptations linked to mutualistic relationships with plants, and question some long-held assumptions about the genetic basis of symbiosis.

BMC Bioinformatics - Improving crop production using an agro-deep learning framework in precision agriculture

Precision agriculture is a general term to describe technology tools, such as drones and sensors, along with new data collection and interpretation methods to make farming more efficient and allow farmers to produce more with less resources. 

In BMC Bioinformatics, researchers describe the Agro Deep Learning Framework (ADLF), which leverages artificial intelligence to process complex datasets like soil moisture, temperature, and humidity. It uses this information to optimize resource use, detect crop issues early, and forecast crop productivity. By integrating deep learning into precision agriculture, the ADLF exemplifies how technology can address the challenges of modern farming. With continued innovation and collaboration, such frameworks can support farmers in preserving soil health, improving productivity, and advancing global food security sustainably.

Call for papers!

If you're interested in learning more about soil science, explore the following BMC Series article collections that are currently open for submissions:

BMC Agriculture: Soil-plant-microbiota interactions in global food systems

BMC Plant Biology: Climate-smart soils to enhance sustainable crop yield