Identifying potential threats to soil biodiversity

A decline in soil biodiversity is generally considered to be the reduction of forms of life living in soils, both in terms of quantity and variety. Where soil biodiversity decline occurs, it can significantly affect the soils’ ability to function, respond to perturbations and recover from a disturbance. Several soil threats have been identified as having negative effects on soil biodiversity, including human intensive exploitation, land-use change and soil organic matter decline. In this review we consider what we mean by soil biodiversity, and why it is important to monitor. After a thorough review of the literature identified on a Web of Science search concerning threats to soil biodiversity (topic search: threat* “soil biodiversity”), we compiled a table of biodiversity threats considered in each paper including climate change, land use change, intensive human exploitation, decline in soil health or plastic; followed by detailed listings of threats studied. This we compared to a previously published expert assessment of threats to soil biodiversity. In addition, we identified emerging threats, particularly microplastics, in the 10 years following these knowledge based rankings. We found that many soil biodiversity studies do not focus on biodiversity sensu stricto, rather these studies examined either changes in abundance and/or diversity of individual groups of soil biota, instead of soil biodiversity as a whole, encompassing all levels of the soil food web. This highlights the complexity of soil biodiversity which is often impractical to assess in all but the largest studies. Published global scientific activity was only partially related to the threats identified by the expert panel assessment. The number of threats and the priority given to the threats (by number of publications) were quite different, indicating a disparity between research actions versus perceived threats. The lack of research effort in key areas of high priority in the threats to soil biodiversity are a concerning finding and requires some consideration and debate in the research community

Identification of extracellular glycerophosphodiesterases in Pseudomonas and their role in soil organic phosphorus remineralisation

In soils, phosphorus (P) exists in numerous organic and inorganic forms. However, plants can only acquire inorganic orthophosphate (Pi), meaning global crop production is frequently limited by P availability. To overcome this problem, rock phosphate fertilisers are heavily applied, often with negative environmental and socio-economic consequences. The organic P fraction of soil contains phospholipids that are rapidly degraded resulting in the release of bioavailable Pi. However, the mechanisms behind this process remain unknown. We identified and experimentally confirmed the function of two secreted glycerolphosphodiesterases, GlpQI and GlpQII, found in Pseudomonas stutzeri DSM4166 and Pseudomonas fluorescens SBW25, respectively. A series of co-cultivation experiments revealed that in these Pseudomonas strains, cleavage of glycerolphosphorylcholine and its breakdown product G3P occurs extracellularly allowing other bacteria to benefit from this metabolism. Analyses of metagenomic and metatranscriptomic datasets revealed that this trait is widespread among soil bacteria with Actinobacteria and Proteobacteria, specifically Betaproteobacteria and Gammaproteobacteria, the likely major players

Soil Biodiversity Integrates Solutions for a Sustainable Future

Soils are home to more than 25% of the earth’s total biodiversity and supports life on land and water, nutrient cycling and retention, food production, pollution remediation, and climate regulation. Accumulating evidence demonstrates that multiple sustainability goals can be simultaneously addressed when soil biota are put at the center of land management assessments; this is because the activity and interactions of soil organisms are intimately tied to multiple processes that ecosystems and society rely on. With soil biodiversity at the center of multiple globally relevant sustainability programs, we will be able to more efficiently and holistically achieve the Sustainable Development Goals and Aichi Biodiversity Targets. Here we review scenarios where soil biota can clearly support global sustainability targets, global changes and pressures that threaten soil biodiversity, and actions to conserve soil biodiversity and advance sustainability goals. This synthesis shows how the latest empirical evidence from soil biological research can shape tangible actions around the world for a sustainable future

Quantification of bacterial non-specific acid (phoC) and alkaline (phoD) phosphatase genes in bulk and rhizosphere soil from organically managed soybean fields

Phosphorus (P) is a limiting nutrient in many environments but plants and microbes have evolved with mechanisms for acquiring soil P, including the excretion of phosphatase enzymes. Molecular analysis of bacterial phosphatase genes can provide insight into biological P transformations and the contribution to soil P availability and plant uptake. To assess these relationships, soil and plant samples were collected from 12 organically-managed soybean fields varying in pH, labile P concentration, and potential phosphatase activity (pH 6.5) across Prince Edward Island, Canada. Real-time PCR was used to quantify bacterial phosphatase genes (phoC and phoD) in bulk and rhizosphere soil. Primers targeting class A (phoC) of the bacterial non-specific acid phosphatases (NSAPs) were designed and confirmed as effectively targeting phoC genes through sequencing, and phylogenetic comparison with acid phosphatase genes from Genbank. Across all sites, we found that labile P in bulk soil was negatively correlated with phoC and phoD gene abundance and phosphatase activity. In addition, phosphatase activity was consistently higher in rhizosphere compared to bulk soil and was significantly correlated with phoC (bulk soil only) and phoD (rhizosphere soil only) gene abundance. A positive relationship was observed between phosphatase activity, nodule weight, and plant P uptake. Quantification of bacterial genes involved in organic P transformations has been limited, with this study providing the first attempt at quantifying phoC genes in field soils

Stimulation of distinct rhizosphere bacteria drives phosphorus and nitrogen mineralization in oilseed rape under field conditions

Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the “active” plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health

Soil bacterial phoD gene abundance and expression in response to applied phosphorus and long-term management

Bacterial transformation of phosphorus (P) compounds in soil is largely dependent on soil microbial community function, and is therefore sensitive to anthropogenic disturbances such as fertilization or cropping systems. However, the effect of soil management on the transcription of bacterial genes that encode phosphatases, such as phoD, is largely unknown. This greenhouse study examined the effect of long-term management and P amendment on potential alkaline phosphatase (ALP) activity and phoD gene (DNA) and transcript (RNA) abundance. Soil samples (0–15 cm) were collected from the Glenlea Long-term Rotation near Winnipeg, Manitoba, to compare organic, conventional and prairie management systems. In the greenhouse, pots of soil from each management system were amended with P as either soluble mineral fertilizer or cattle manure and then planted with Italian ryegrass (Lolium multiforum). Soils from each pot were sampled for analysis immediately and after 30 and 106 days. Significant differences among the soil/P treatments were detected for inorganic P, but not the organic P in NaHCO3-extracts. At day 0, ALP activity was similar among the soil/P treatments, but was higher after 30 days for all P amendments in soil from organically managed plots. In contrast, ALP activity in soils under conventional and prairie management responded to increasing rates of manure only, with significant effects from medium and high manure application rates at 30 and 106 days. Differences in ALP activity at 30 days corresponded to the abundance of bacterial phoD genes, which were also significantly higher in soils under organic management. However, this correlation was not significant for transcript abundance. Next-generation sequencing allowed the identification of 199 unique phoD operational taxonomic units (OTUs) from the metagenome (soil DNA) and 35 unique OTUs from the metatranscriptome (soil RNA), indicating that a subset of phoD genes was being transcribed in all soils

Global soil biodiversity atlas

2015 was the United Nations International Year of Soils and, for the first time, soils and the life within them were in the spotlight globally. An international group of experts and scientists from the European Commission’s Joint Research Centre (JRC), in close collaboration with colleagues from the Commission’s Directorate-General for the Environment and the Global Soil Biodiversity Initiative, have produced the first ever Global Soil Biodiversity Atlas. Soils are vital for human survival and underpin many sectors of our economy. It is estimated that 99% of the world’s food comes from the terrestrial environment. But soils are also home to over a quarter of global biodiversity. Millions of soil-dwelling organisms promote essential ecosystem services – from plant growth to food production. They support biodiversity, benefit human health, promote the regulation of nutrient cycles that in turn influence climate, and represent an unexplored capital of natural sources. Our knowledge of soil life is growing continuously, thanks to recent technological advances and awareness of its value. However, it is estimated that only 1% of soil microorganism species have been identified. Therefore, understanding the highly complex and dynamic life below ground remains one of the most fascinating challenges facing scientists today. A clearer picture of our soils will allow us to better understand environmental and global climate change processes whilst also exploring possible adaptation strategies. Pressures on soil organisms are well known. An ever increasing global population, and increased demand for food and fibre lead to intensified agriculture, greater use of fertilisers and pesticides as well as monocultures. Unsustainable agricultural practices, climate change, soil erosion and loss of aboveground diversity all negatively affect organisms that live in soil. To develop actions that will preserve soil life, we need to better understand the consequences of the loss of soil biodiversity. The Global Soil Biodiversity Atlas raises awareness of the role of soil organisms in sustaining life on our planet, and presents the latest research on soil biodiversity. It is also a major contribution to the EU target of halting the loss of biodiversity and ecosystem services in the EU by 2020, and the goals of the 2030 Agenda for Sustainable Development on sustainable food production and fighting land degradation. This publication marks a crucial step towards a global coordinated effort to assess life below ground, and highlights the need to improve soil conservation and the diversity of life within it