Importance of microorganisms in the soil

The microbial activity of the soil, and its benefits on it, is strongly impacted by unsustainable intensive agricultural practices and climatic conditions, through modifications of soil characteristics at the physical, chemical and biological level; for example, temperature, humidity, salinity, aeration, oxide-reduction state, content and composition of gases in the porous space, bioavailability of nutrients, pH (^{Ibarra-Villarreal et al., 2021}). In this way, the imbalance in soil microbial communities triggers processes of biological degradation, reducing crop yield/quality by increasing vulnerability to various types of stress and limiting the ability to carry out their main ecosystem services, such as: plant biomass production, nutrient storage and recycling, water storage and filtering, climate and flood regulation, climate change mitigation and habitat for biological activity (^{Díaz-Rodríguez et al., 2021}).

The bioprospecting of microorganisms that live in the soil represents a promising tool for the development of sustainable agricultural practices focused on meeting the demand for food associated with the global population increase [which is projected to reach 10 billion inhabitants by 2050 and consequently it will require an increase in food production between 70 and 100% (^{FAO, 2017}; ^{De los Santos-Villalobos et al., 2018})].

Microbial communities in soils conduct between 80 and 90% of the biological processes developed in the soil (^{Bajsa et al., 2013}), due to its multiple ecological niches, among which the next stand out, the mitigation of exogenous alterations, promotion of plant growth, biocontrol activity, nutrient cycling, production of plant biomass, soil structure and fertility, the degradation of toxic compounds, among others (^{Delgado-Baquerizo et al., 2016}).

Among this microbiota, there is a particular set called plant growth promoting microorganisms (MPCV), which directly or indirectly favor vegetative growth, generate tolerance to abiotic and biotic stress in the plant, facilitate the nutrition of the plant and antagonize phytopathogens in host plants. Among the most studied microbial genera of this group the next stand out, Pseudomonas, Enterobacter, Bacillus, Variovorax, Klebsiella, Burkholderia, Azospirillum, Serratia, Azotobacter and Trichoderma (teleomorph Hypocrea) (^{Dohrmann et al., 2013}).

The production of peptide antibiotics and metabolites that protect plants from possible attacks by pathogenic organisms are among the metabolic capabilities of MPCV strains; they also stimulate the immune system of the plant to protect them against infections by bacteria, fungi, or pathogenic nematodes (^{Valenzuela-Ruiz et al., 2020}). On the other hand, various strains of MPCV have the ability to synthesize phytohormones, both to regulate plant growth and development and to increase the bioavailability of nutrients in the soil, thus allowing better nutrition of the plant (^{Orozco-Mosqueda and Santoyo, 2020}).

As well, MPCVs have the ability to fix atmospheric nitrogen and solubilize phosphorus (mechanisms that provide nutrients to plants, mitigating environmental pollution events caused by the application of synthetic fertilizers), as well as iron sequestration by siderophores that prevents the development of phytopathogens, when their growth depends on this element (^{Valenzuela-Aragón et al., 2019}; ^{Rojas-Padilla et al., 2020}).

In this way, beneficial soil microorganisms with application in agriculture can be divided into 1) phytostimulants, which enhance seed germination, rootedness, and plant growth through the production of growth regulators, vitamins and other substances; 2) improvers, which favor the structure of the soil and its physicochemical properties due to the formation of aggregates, which increases its fertility; 3) bioremedials, these are associated with the elimination of recalcitrant synthetic and highly harmful agricultural inputs to the environment and human health, such as pesticides, herbicides, among others; and 4) biofertilizers, which have the ability to provide bioavailable nutrients and bioactive molecules for the growth and increased development of plants, including the control of phytopathogens (^{Joshi et al., 2019}).

Biofertilizers, prior to their use, must be analyzed based on the problem to be addressed, their capacity for colonization of the soil and the plant, the synthesis of bioactive compounds of interest and the native microbial communities (^{Chávez-Díaz et al., 2020}), since its activity of promoting plant growth can be focused on different levels of action, i.e. metabolic activities for the solubilization or mineralization of nutrients, the biosynthesis of widely studied or undiscovered beneficial metabolites, the production of antagonistic compounds of phytopathogens (^{Díaz-Rodríguez et al., 2021}).

The importance of soil microorganisms and their close relationship with sustainable agriculture depends on the use of the metabolic and functional diversity of MPCVs (Figure 1). For this, it is crucial to focus efforts and financing for the bioprospecting of beneficial microbial communities and determine their role in the complex network of physical, chemical and biological interactions occurring in the soil, which will lead to the design of sustainable strategies to improve soil fertility and health, the production and quality of agricultural crops and mitigate the negative economic, environmental and health impact of the use of unsustainable intensive agricultural practices.

Figure 1 Biological processes regulated by microorganisms involved in soil fertility and plant productivity. 

Microorganisms in sustainable agriculture

Sustainable agriculture seeks to maintain in balance the microbial communities (bacteria, fungi, protozoa, and viruses) associated with agricultural crops, this is the phytomicrobiome, since the diversity, stability and resilience of the phytomicrobiome are the main determinants of the productivity and plant health of an agroecosystem (^{Basu and Kumar, 2020}). MPCVs, through different types of symbiotic relationships they establish with plants, carry out direct and indirect beneficial mechanisms to promote plant growth.

Based on the mode of action presented by MPCVs, these can be used for the development of bioproducts, such as biofertilizers, phytostimulants, biofungicides or biopesticides (Mamani and Filippone, 2018). Generally, these microbial inoculants contain one or more strains that have different mechanisms of action, so they can be used at different stages of the culture crop; however, it is necessary to develop the appropriate formulation, production and management systems to ensure the survival and effective establishment of MPCVs in the plant, as well as to monitor the effect they have on the previous microbial community and the stability of the new generated community (^{Richardson and Simpson, 2011}).

In this sense, biotechnological and molecular techniques can help to better understand the mode of action of MPCVs to establish successful plant-microorganism interactions and a favorable application of MPCVs (^{Khalid et al., 2009}), to consider the phytomicrobiome as an integral part of plant breeding programs in the near future (^{Córdova-Albores et al., 2021}).

Development of an ecological approach to the choice of microbial inoculants in Mexico

As for the origin of the organisms used as biofertilizers, there are data that show the importance of the identity of the symbionts to increase the efficiency of the association and the benefits for the plant; for instance, light (^{Villegas et al., 2017}) and low temperatures cause changes in the colonization of different species of arbuscular mycorrhizal fungi (HMA) (^{Latef and Chaoxing, 2011}).

For their part, ^{Gavito and Azcón-Aguilar (2012)} found that organisms from cold zones tolerate low temperatures better than those from temperate zones, since they present genetic variations and plasticity, which allows them to adapt to these extreme environmental conditions. In broad beans grown in alkaline soils, inoculation of nitrogen-fixing bacteria and HMA increases plant growth measured as total dry biomass (^{Abd-Alla et al., 2014}). It is extremely important to consider that, unlike agrochemicals, microbiological formulation products for their proper functioning depend on the ecological interactions between the strains of the formulation, the microbial communities present in the soil and the plant, in addition to the abiotic and climatic factors of the agroecosystem (^{Sruthilaxmi and Babu, 2017}).

Most of the success in the operation of a microbiological product depends on the degree of ecological knowledge of the agroecosystem where the product will be applied and the characteristics of the strains to be used (^{Compant et al., 2019}). It is a fact that not all microorganisms contained in these products work in the same way for all crops, this is because microorganisms have coevolved with plants in particular habitats, establishing specific interactions regulated by the agroclimatic factors of each region over time (^{Pérez-Jaramillo et al., 2018}).

These soil properties and functions are the result of a complex network of microbial interactions, which are modulated by specific factors such as: 1) the microbiota present in each region; 2) the specific agroclimatic conditions of the site where the agroecosystem is established; 3) the genotype of the crop or crops established in the agroecosystem; and finally, 4) anthropocentric management and influence on the agroecosystem (^{Compant et al., 2019}; ^{Saad et al., 2020}).

Until now, the formulators of biological products available in the Mexican market have focused on some specific qualities of certain microorganisms (Table 1), which has made genera such as Bacillus, Trichoderma, Rhizophagus or Bauberia attractive to the producer. However, the microorganisms with which the biological products are formulated are obtained from diverse environments and have not coevolved with the environment in which they are released, so they must adapt to the conditions of the environment and to the autochthonous populations of the agroecosystem (^{Basu et al., 2021}).

Considering that the use of microorganisms in agriculture follows ecological principles in which the proper functioning and balance of the agroecosystem is sought, it is necessary to correctly choose an input formulated with microorganisms for the field. However, it is still largely unknown what happens when microorganisms are released into agroecosystems, as well as the ecological implications that could arise with the applications of these repeatedly and constantly over time (Hart et al., 2017).

Therefore, when using a product of microbiological formulation, it must be taken into account: 1) the strains used do not represent a risk to human, animal or plant health, so it is recommended that they have a high expression of virulence factors; 2) the strains are native to the agroecosystem in which they are intended to be applied, in such a way that their activity is easily associated with the environment in which they will be released; and 3) have microbiological studies that allow adequate decision-making regarding the use and management of strains (^{Basu et al., 2021}).

Advances in government policy regarding the use of microbial inoculants in Mexico

There are specific issues that would allow generating important advances in the use of these microorganisms in the development of a sustainable agriculture in Mexico, the topics are concentrated in four general aspects: i) update in the technological development of microbial products by specialists in the field; ii) promotion of the link between science and private industry; iii) implementation of programs to promote and support research into microbial developments; and iv) establishment of national legislation on the proper use of these products (^{Salgado-Sánchez, 2015}).

Mexico has a wide network of institutions committed to the development of microbial products and highly trained human resources in the area, so various research programs on microorganisms have been consolidated in many academic entities throughout the country and today there is a growing supply of specialists in this area, many of these institutions already provide services to the industry and it is increasingly common to develop joint research and technology transfer (^{Chávez-Díaz et al., 2020}).

In addition, some scientists have begun to generate interest in the spin-offs, companies that derive from technological developments carried out in universities or research centers, with a license to use this technology, since they offer the industry very specialized products and services that could be of great help to the sustainable development of our country (^{Hernández et al., 2017}). The still limited number of laws, rules and regulations regulating the development of technologies based on microorganisms and their use in sustainable agriculture implies a lag in the growth of the country's agriculture (^{Sabourin et al., 2017}).

In Mexico, there are efforts in regulatory matter such as the Official Mexican Standard NOM-077-FITO-2000. Studies of biological effectiveness in plant nutrition inputs for agricultural use and their ‘technical opinion’, official standard in which the requirements and specifications for the realization of studies of biological effectiveness of plant nutrition inputs are established; however, the generation or updating of standards for those technologies based on microorganisms is decisive, since it focuses mainly on chemical nutrition rather than biological and copyright protection has not yet been addressed in a diligent manner.

Therefore, continuing to develop strategies to solve the challenges and considerations to promote sustainable development using microorganisms will strengthen both the primary sector and various existing productive sectors, generating a supply of greater added value to agricultural products. As well, it can contribute to solving many social needs that are identified in Mexico and worldwide, such as: food supply, care of natural resources, care of the environment and improve the quality of life, to name a few.

Perspectives for the dissemination of the use of microbial inoculants in Mexico

In Mexico, the use of microorganisms in agriculture has advanced through the last decades; ensuring that these advances permeate producers through dissemination is the best way for science to be increasingly seen as a necessary tool in the sustainable development of our country.

In this sense, in the National Institute of Forestry, Agriculture and Livestock Research (INIFAP), various efforts have been developed and consolidated in terms of dissemination of the use of microorganisms in agriculture in Mexico, such as the AgroEvento 2020 ‘biological products, a tool to potentiate the Mexican countryside’ (^{AgroEvento, 2020}), organized by the National Center for Genetic Resources (CNGR) of INIFAP and the Technological Institute of Sonora, this event aimed to bring together academics, scientists, students, technicians, advisors, trainers, marketers, producers of agricultural inputs and farmers to share their experiences, knowledge and perspectives regarding the use of biological products, or other agrobiotechnologies for sustainable innovation as an alternative to conventional agricultural production in Mexico.

This type of events allows Mexican researchers involved in the development and implementation of technologies based on microorganisms that favor the conservation and use of national biodiversity, with this type of actions, producers and people in the agricultural sector are informed about the advances in isolation, identification, and characterization of beneficial microorganisms for crops, design, application, management and formulation of biological formulation products for the countryside. Efforts such as this should be promoted to ensure that producers have access to information and can decide how to take advantage of advances in the use of microorganisms in agriculture with the support of scientific research.