Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil.

Andrea Manfredini,Stefano Mocali,Flavia Pinzari,Loredana Canfora,Eligio Malusà,Corrado Costa,Federico Pallottino

doi:10.3389/fmicb.2021.698491

Abstract

Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.

Highlights

Microbial-based products used to support plant nutrition and protection from abiotic and biotic stress have received considerable attention in the last decades by researchers, manufacturers and farmers, because they help to reduce the use of chemicals in agriculture (Adesemoye et al, 2009; Lacey et al, 2015; Bargaz et al, 2018; Harman and Uphoff, 2019; Singh and Prabha, 2019; Basu et al, 2021)
The Tracking and Monitoring Bioinoculants in Soil inoculation of the soil with beneficial microorganisms may affect its native microbial populations (Trabelsi and Mhamdi, 2013; Mawarda et al, 2020); with effects that depend on the soil chemical and physical characteristics and the environmental conditions
A method based on multiple culture conditions combined with the rapid identification of bacteria, named “culturomics,” which was developed for the identification of previously unculturable bacterial species of the human gut microbiome (Lagier et al, 2016, 2018) could be applied to isolate less abundant and unculturable microorganisms from the soil

Summary

Introduction

Microbial-based products ( named bioinoculants, biofertilisers, and biopesticides) used to support plant nutrition and protection from abiotic and biotic stress have received considerable attention in the last decades by researchers, manufacturers and farmers, because they help to reduce the use of chemicals in agriculture (Adesemoye et al, 2009; Lacey et al, 2015; Bargaz et al, 2018; Harman and Uphoff, 2019; Singh and Prabha, 2019; Basu et al, 2021). Mawarda et al (2020), by using a literature search-mapping approach, reported that 72% of studies addressing the impact of bioinocula on resident microbial communities used profiling methods including TRFLP, and 4% used quantitative PCR targeting particular taxonomic or functional groups.

Results

Conclusion