Role of Microbes in Agriculture and Food (2nd Edition)

1. Introduction

The use of microorganisms in agriculture and food is a very broad issue that faces many challenges. The scientific literature on sustainable agriculture is characterised by four main trends: (1) the role of microorganisms in the transformation, degradation, and recycling of organic matter [1]; (2) the use of microbes as biostimulants and biopesticides, as an alternative to chemical agents [2,3,4]; (3) understanding the soil microbiome and microorganisms interrelationships using modern imaging techniques and algorithms, and the use of microbial consortia for specific applications [1,3]; and (4) plant–microbiome interactions that ensure plant health [5]. Microbiological preparations or vaccines for use in agriculture may contain monocultures or consortia of living microorganisms that are well understood and safe, and which can contribute to the growth, health, and development of the host plant [2]. The use of such beneficial microorganisms is not only an important tool for supporting crop health and productivity, but an effective alternative to the use of agrochemicals [6]. In essence, microbiological products for agriculture are based on the same active substances (living microorganisms) that are produced in similar industrial processes (fermentation, formulation), are managed and used in a similar way, and are intended to have a beneficial effect on a given crop/host. Research on soil biodiversity has seen rapid development, including that on new biostimulants and pools of specific genes, thanks to new omics tools, including genome sequencing (NGS) and metabolomics techniques, which have a direct impact on the dynamics of the agricultural sector [7].

Key topics concerning the role of microorganisms in food include (1) further development of fermentation processes, including the genetic improvement of strains; (2) the improvement of techniques for identifying microorganisms and their metabolites; and (3) the detection of pathogens in production processes [8,9]. Microbial fermentation, a practice more than 7000 years old, is a basic method of producing a variety of food products. During fermentation, microorganisms such as bacteria, yeasts, and moulds are used to convert carbohydrates into various metabolites. In various, often perishable, food products, fermentation contributes to preservation and the improvement of sensory characteristics, nutritional quality, and safety [10,11]. Existing and changing consumer preferences are driving new ideas and development opportunities for the fermented food and beverage sector. Consumers are looking for products that they perceive as natural and wholesome, free from artificial ingredients, handmade, and environmentally friendly [12]. Among such foods, functional products containing health-promoting additives, including probiotic microorganisms, paraprobiotics, postbiotics, and minimally processed products, stand out [13,14,15,16,17]. Fermented foods can be consumed as a non-invasive method of managing various disorders and diseases (including hypertension, diabetes, and hyperlipidaemia, among others) due to the release of bioactive compounds, enzymatic transformations, and probiotic activity [14,18]. Among key innovations in the field of food fermentation are advances in fermentation technologies aimed at increasing efficiency, product range expansions, and the promotion of sustainable development [10].

2. An Overview of Published Articles

The Special Issue contains both research articles and reviews presenting current areas of interest. Among contributions on the role of microorganisms in agriculture, the majority focus on the impact of bacterial consortia or monocultures on crop growth. Researchers used isolates of nitrogen-fixing bacteria from the Bacillaceae family as bioinoculants to promote the growth of Lactuca sativa and observed a synergistic effect when the bacteria acted on the rhizosphere and phyllosphere, highlighting plant–microbe interactions. Bacillus thuringensis also had a beneficial effect on the development of blackberry shoots and roots and their mass, confirming the importance of Bacillus bacteria for plants. Another bacterium with potential as a biofertiliser and factor in soil bioremediation is Pseudomonas fluorescens, capable of decomposing isofetamid in the soil. In turn, studies on the dependence of soil microbiota diversity on horse bean cultivation technology have shown that the cultivation type affects the microbiota composition. Using NGS technology, key species associated with soil fertility and yields, such as Gemmatimonas aurantiaca and Aeromicrobium ponti, were identified, whose abundance increased in simplified cultivation technologies, suggesting their importance for sustainable and even regenerative agriculture [19].

Microorganism use in food primarily concerns fermentation processes involving lactic and acetic acid bacteria and yeasts, including the use of probiotic strains and the potential of paraprobiotics for the production of functional foods. An important topic in this research is the technological usefulness of new strains of Gluconobacter oxydans belonging to acetic acid bacteria for the preservation of raw-matured meat products with increased antioxidant properties [20]. Several articles herein focus on yeast, either on the isolation and selection of potentially probiotic yeast or on the use of non-Saccharomyces yeast isolates to modify the properties of sauerkraut, and the application of probiotic yeast S. cerevisiae var. boulardii to obtain fermented fruit juices. In their review article, Sionek and Gantner [21] present noteworthy aspects of paraprobiotics, i.e., non-viable bioactive food components, emphasising their health-promoting effects. Though their effects are similar to those of probiotics (including anti-inflammatory, immunomodulatory, antiproliferative, antioxidant, and antibacterial), their better safety profile favours their use in sensitive individuals. At the same time, the authors pointed out the lack of separate regulations concerning this group of non-living components, which currently prevents their implementation in the production of functional foods [21]. Moreover, another noteworthy article expands on the adaptation of fungi to low temperatures, as well as the role of these psychrophilic organisms, their enzymes, and their secondary metabolites in widespread use in biotechnology, food technology, agriculture, pharmacy, and other applications in cold environments.

3. Conclusions

The articles presented in this Special Issue largely reflect current research topics concerning increasingly accurate studies of soil microorganism biodiversity, their isolation, and their use as biostimulants or biopesticides, in line with the current trend towards sustainable and organic farming. It is worth highlighting the use of new genome sequencing techniques in agricultural research, allowing for a comprehensive assessment of soil biodiversity and its susceptibility to cultivation methods. Research into new strains with the potential for use as biostimulants or biological protective agents is of great importance. Many analogies can be found between microorganisms that have a beneficial effect on plant health, i.e., plant probiotics, and probiotics for humans, which are still eagerly researched, isolated, and used in fermentation processes to produce innovative food products with functional potential while protecting against food pathogens. Of particular note are the in-depth studies on paraprobiotics and postbiotics, which may inform the reader that new application perspectives remain to be discovered in the field of microorganisms beneficial to humans.