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.
•New primers were designed to study bacterial phoC gene abundance in soil.•Higher abundances of phoC genes compared to phoD across all sites.•Higher phosphatase activity (pH 6.5) in rhizosphere ...soil.•Soil labile P was negatively correlated with phosphatase activity and phoC and phoD gene abundance.•No relationship between pre-seeding soil test P and plant P uptake or yield.
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.
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.
•Alkaline phosphatase activity was highest in organic soils regardless of P treatment.•Alkaline phosphatase responded to increasing rates of manure P, but not mineral P.•The phoD gene abundance was significantly correlated to ALP activity.•The highest number of unique phoD OTUs was in the organic soil.•Soils from the conventional system had the highest number of transcribed phoD OTUs.
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.
Background and aims Microbially driven mineralization of organic phosphorus forms is of particular importance in the soil environment, where it becomes available to plants as inorganic ...orthophosphates. In acidic soils, microbes produce non-specific acid phosphatases (NSAPs; E.C. 3.1.3.2) which act on the most common forms of organic P in the soil. Our understanding of phosphorus turnover in soils would greatly benefit from an improvement in research tools targeting these genes. Methods Thus, in this study we developed two novel oligonucleotide PCR primer sets, that will enable researchers to target the present and active communities of bacteria with the genetic potential of acid phosphatase production. A total of three primer sets were validated to target the three classes of NSAPs. Utilizing Illumina MiSeq, amplicons from grassland pasture soils were sequenced. Results The resulting target specificity was high for all three groups; CAAP (97.2%), CBAP (99.5%), and CCAP (94.8%). Quantification of target genes by qPCR indicated measurable differences between classes, ranging from 5 log to 7.5 log for CAAP, 6 log to 8 log for CBAP, and 4 log to 5 log for CCAP. Conclusions The validated primer sets were specific to the target genes and identified potential quantitative differences between the NSAP classes.
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.
Extracellular soil enzymes play a key role in soil organic matter decomposition and nutrient cycling. However, it is not fully understood how these enzymes respond to different land use. Long-term ...research studies were used to evaluate how diversified management practices affect extracellular enzymes driving C cycling phenol oxidases (PO), peroxidases (PP), α-glucosidase (AG), β-glucosidase (BG), cellobiohydrolase (CB), β-1,-4-Nacetylglucosaminidase (NAG), N cycling leucine aminopeptidase (LAP), and P cycling phosphomonoesterase (PME). The soil pH, contents of total organic C, total N, mehlich-3 P, soil respiration and soil nitrogen supply capacity were also measured. Different land use included tillage frequency, tillage regimes, mineral N fertilization, crop rotations and liquid dairy manure. Compared to medium or high tillage frequency, low tillage frequency increased total organic C and total N and soil respiration as well as NAG and PME activities, whereas it decreased soil nitrogen supply, mehlich-3 P, and soil pH, as well as PO, PP, AG, BG, CB, and LAP activities. Non till was associated with lower PP and PO activities than moldboard plow. Nitrogen fertilization decreased soil pH and PO activity but increased PME activity. Barley (
Hordeum vulgare
) in rotation with forage increased total organic C, total N, soil nitrogen supply and soil respiration by 31, 21, 44, and 33%, respectively, in comparison with barley in monoculture. The application of liquid dairy manure increased soil pH, total N and soil nitrogen supply and soil enzyme activities (AG, BG, NAG) in comparison to the mineral N fertilizer. When principal component analysis was performed, soil pH, PO, PP, CB, LAP, and PME were grouped in the first component, which explained the highest variance. This is the core group controlling the C, N, and P cycling. The activities of C, N, and P acquiring enzymes, soil nitrogen supply and soil respiration were related to changes in soil total C and N, and extractable P contents across a broad range of management practices. Increased PO and PP activities reflect total C decline.
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