Assessing soil health by measuring fauna

This chapter provides examples of the impact of soil fauna on soil health within different ecosystems and how the soil habitat changes in relation to this biodiversity. It focuses specifically on mesofauna in agriculture, grasslands, woodlands and as bioindicators, before concluding with an overview of how the development of mesofauna as bioindicators is important in establishing a healthy soil.

Three-Year Investigation of Tillage Management on the Soil Physical Environment, Earthworm Populations and Crop Yields in Croatia

The aim of this study was to determine the environmental suitability of conservation tillage systems. A 3-year experiment was conducted in Croatia, to study the effects of different tillage treatments on soil properties, with the following: deep (DC), shallow tine cultivation (SC) and ploughing (P). Soil penetration resistance (SPR) was significantly greater in P compared to DC in all three years. In 2016, it was found at 30–40 and 40–50 cm; in 2017 at 10–20 cm; in 2018 at 0–10 and 10–20 cm. However, SC was significantly greater at 20–30, 30–40 and 40–50 cm compared to P and DC in 2017. The greater surface coverage in DC and SC (>30%) as compared to P (<1%) provided significantly higher soil moisture content (SMC) in maize (2016) and soybean (2018). In 2017, SMC in SC was significantly lower than in P and DC. Regarding all the 3 years, the agronomic structure in DC and SC had significantly greater crumb ratio compared to P, whereas P had significantly higher dust ratio than DC and SC. Throughout the 15 measurements, DC provided the most favorable soil habitat (11 occasions out of 15). In 2017, the earthworm abundance was significantly higher in DC compared to SC. In all the three years, DC resulted the highest yield, however the difference was not significant. Higher surface coverage and SMC positively impacted the ratio of agronomic structure (decreased dust and increased crumb ratio) and earthworm abundance. It can be concluded that DC and SC provided greater soil coverage which positively affected SPR, SMC, agronomic structure and earthworm abundance as compared to P.

The Soil Habitat and Considerations for Synthetic Biology

Microorganisms serve as agents for synthetic biology. It certain instances, the technology is reliant on survival of the genetically-altered microorganism in the natural environment. This chapter offers insight into the soil system to improve the performance of genetically-altered microorganisms in the natural environment. This chapter covers the soil system, the fitness of genetically altered organisms, and considerations for their survival and proliferation in nature. This chapter does not discuss the ecological consequences of survival in the natural environment or the regulatory considerations to distribute a genetically-altered organism in the environment. In addition to regulatory approval, both considerations should be critically reviewed before a genetically-altered organism is distributed in the environment.

Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community

The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.

Draft Genome Sequence of Mercury-Resistant Serratia sp. Strain SRS-8-S-2018

A mercury (Hg)-resistant Serratia sp. strain, SRS-8-S-2018, was isolated, followed by generation of its draft genome sequence, which indicated a genomic size of 5,323,630 bp composed of 5,261 coding sequences. A suite of genomic functions in strain SRS-8-S-2018 was identified, and these likely facilitate survival in a metalliferous soil habitat.

Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China

The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.