Ecosystem functions of microbial consortia in sustainable agriculture

Knowledge of the agricultural soil microbiota, of the microbial consortia that comprise it, and the promotion of agricultural practices that maintain and encourage them, is a promising way to improve soil quality for sustainable agriculture and to provide food security. Although numerous studies have demonstrated the positive effects of beneficial soil microorganisms on crop yields and quality, the use of microbial consortia in agriculture remains low. Microbial consortia have more properties than an individual microbial inoculum, due to the synergy of the microorganisms that make them up. This review describes the main characteristics, ecosystem functions, crop benefits and biotechnological applications of microbial consortia composed of arbuscular mycorrhizal fungi, plant growth promoting bacteria and actinobacteria, to promote the restoration of agricultural soils and, consequently, the quality and health of agricultural crops. The aim is to provide knowledge that will contribute to the development of sustainable and sufficiently productive agriculture, which will adapt in a good way to the pace of the growing human population and to climate change.

matter, regulation of pathogens, degradation of contaminants, reduction of greenhouse gases (GHG), which directly affect both crop productivity and the environmental quality [13][14][15].
In order to benefit from the enormous potential of the soil microbiome, it is necessary to know the distribution and composition of microbial communities in different territories and on different time scales, such as seasonal variations [16]. This information also allows predicting the changes that can be generated in a global climate change scenario. In addition, not knowing the effects of the loss of diversity in specific places and times, it can generate a great impact on ecosystem sustainability and therefore on human well-being [17][18][19]. The greater the diversity of microorganisms in the soil, the greater the functionality of that soil [20,21], which is turn means food with higher nutraceutical quality proportional to the soil nutrition and health.
Recently, increasing attention has been given to crops rich in nutrients, minerals, antioxidants, or other metabolites, as they represent higher food quality and reduce the risk of chronic diseases [22][23][24]. In this context, new crops practices have emerged that allow obtained high yields of biomass with high concentration of beneficial metabolites. The development of biofertilizers made up with beneficial microbial species has emerged [25], as well as the development of microbial consortia of different soil microorganisms [26].
Thus, it is necessary to understand the processes that determine the composition and abundance of soil microorganism communities in order to obtain their multiple benefits in the agricultural systems and indirectly in human health. This review aims at describing the main characteristics, ecosystem functions, crop benefits and biotechnological applications of microbial consortia composed of arbuscular mycorrhizal fungi, plant growth promoting bacteria and actinobacteria to promote sustainable agriculture and thus the quality and health of agricultural crops. microorganisms present in the soil, arbuscular mycorrhizal fungi (AMF) are fundamental to soil ecology and agriculture [28]. They form a symbiotic composite association with 93% of terrestrial plant families, including multiple agricultural crops. They are the oldest known and most prevalent associations in nature [29,30].
AMF belong to the subphylum Glomeromycotina containing Archaeosporales, Diversisporales, Glomerales, and Paraglomerales [31], and their symbiosis with plants consists of receiving carbohydrates and lipids from the plant and having specific structures such as arbuscula and vesicles that allow the exchange of nutrients with plants at the level of the root bark [32,33]. These have several functions and benefits for plants that are mainly related to increased nutrient uptake, promoting phosphorus, iron and zinc uptake by crops through direct plant root pathways [34,35], positively affecting crop growth, yield and reproductive success, thus reducing fertilizer needs in agricultural systems [36,37].
The establishment of mycorrhizae alters the biological and physicochemical properties of the rhizosphere, leading to the formation of the so-called mycorrhizosphere, where they improve the soil structure, the relationship of water in the soil [38], and have an important effect on the induction of systemic resistance to biotic stresses [39].
Conventional agriculture, with its intensive practices, generates a decrease in the diversity of arbuscular mycorrhizae, which means that fewer species of slow colonization potential and rapid sporulation prevail. This leads to a considerable decline in ecosystem functions of arbuscular mycorrhizae [40,41]. All the benefits that arbuscular mycorrhizae provide to crops can be used in sustainable agriculture to reduce environmental impact and obtain food of higher nutritional quality that benefits humans [42,43]. Within these alternatives, organic agriculture is the most widely reported [44][45][46][47][48].
AMF can be an excellent alternative as biofertilizer in agriculture, as shown by multiple laboratory and field studies [25,49]. In highly degraded soils, an external inoculum could be beneficial, taking into account some considerations such as the type of species and the characteristics of the agricultural system [50,51], considering that to overcome situations of biotic or abiotic stress a mixture of species is better than a single type of mycorrhiza [52], but in many agricultural systems native species communities could be promoted that are equally effective without including the ecological risks of an aggressive strain that could displace naturally beneficial species [53]. Burkholderia, Herbaspirillum and Rhodococcus [54]. The interactions between the plant and PGPR are synergistic leading to relevant benefits for both the plant crops and the plant microbiome.
On the one hand, the plant promotes PGPR establishment through the production of storage substances such as carbohydrates, organic acids and minerals, as well as the production of root exudates, which are used by PGPR for nutrition [55,56] or as a tool to establish symbiotic interactions such as the mycorrhizal or dinitrogen-fixing nodulation [10]. The establishment can be endophytic, leading to the colonization of the inner plant structures, including seeds, or to the colonization of the plant intercellular spaces; the establishment can involve also the free living bacterial cells in the rhizosphere [57,58]. Once established, PGPR show a benefit for plant growth (in terms of yields per hectare of land), crop quality traits, and plant health through direct or indirect mechanisms regulated for biotic and abiotic stress [54,58]. Direct mechanisms promote plant growth by releasing substances stimulating aerial biomass production, root development, and stem elongation. This is achieved through the release or solubilization of phosphates and other nutrients such as potassium (K), zinc (Zn) and silicon (Si), the uptake of biologically fixed di-nitrogen (N2), the chelation of iron (Fe) and other micronutrients such as Zn, B, Ca, Mg, Cu [54,59,60], and the increase of available lithospheric oxygen [61]. In addition, PGPR usually synthesize phytohormones such as gibberellins (gibberellic acid, GA3), auxins (indolacetic acid, AIA), cytokinins, ethylene, and abscisic acid (ABA) [54,60], which model plant growth and plant cell division. These substances can induce the production of the enzyme 1aminocyclopropane 1-carboxylate deaminase (ACC), which reduces the level of ethylene in the roots of the crops, thus improving the root length and density [62].
Indirect mechanisms of plant health induction involve modification of the rhizosphere environment and its ecology, inducing systemic resistance and stimulating the innate resilience of the plant (basal genetic resistance) [63]. Among them, PGPR release substances such as siderophores, antibiotics, pigments, organic acids (malic, acetic, citric, oxalic, lactic, formic, gluconic and 2-ketogluconic), water-soluble vitamins (niacin, thiamine and biotin molecules or antioxidants) and volatile organic compounds (monoterpene alcohols) [64]. These substances activate the protection mechanisms of plants against herbivores, insects and pathogenic microorganisms and promote the synthesis of physical and chemical barriers against abiotic stress. In turn, they allow PGPR to be more competitive in niche colonization since they can interfere with the quorum detection signal and inhibit the formation of biofilms by pathogenic bacteria [65].
PGPR also promote the synthesis of hydrolytic enzymes (such as glucanases and chitinases) that produce abnormal morphological changes in the fungal mycelium, such as the fracture and lysis of the spikes [66], preventing the development of pathogenic fungi. Pseudomonas frederiksbergensi, Bacillus spp. and Planomicrobium sp. have been shown to be effective in improving tolerance to cold and saline stress, which has been linked e.g. to the activity of antioxidant molecules [57,[67][68][69][70][71]; the production of volatile terpenoids by Pseudomonas spp. and Bacillus spp. have increased the protective barriers against soil-borne pathogens in Mentha piperita and V. vinifera plants [64,72].
The application of PGPR over time led to relevant benefits in agroforestry management. In this context, species of Azospirillum, Pseudomonas and Paenibacillus have been used for their beneficial effects on the growth and yield of different cereal crops, such as wheat and rice [56,73]. Specifically, Pseudomonas sp., and Paenibacillus sp. have shown a high capacity to make Fe 3+ available to plants [73].
Bacillus sp. and Pseudomonas sp. strains have proven to be excellent biofertilizer inoculants, having direct and indirect effects on insect pests associated with agricultural crops and also for the biological control of nematodes [74,75]; the bacterium Pseudomonas frederiksbergensis OS261 has been used as a biostimulant under water and salt stress conditions [70].
In plants after transplanting, which has been associated with better root development and consequently to an increase in the uptake of nutrients [60].
Another application for legume crops is the production of root nodules with high capacity to fix nitrogen in soybean (Glycine max L.  [82,84]. These pigments are not necessary for the growth of bacteria but have a significant contribution to improved survival.
In addition to morphological identification, the identification of actinobacteria has now been facilitated by the use of molecular tools. The genomic organization of actinobacteria has reported more than 20 sequenced species, which is still a small number. In general, they differ from other bacteria by having a large genome ranging from 1 to 12 Mb in size that is characterized by a high content of G + C, even higher than 70% and contain large plasmids [82]. Specifically, it is possible to use 16S rRNA sequence analysis and other preserved sequences to identify some actinobacterial genera [81,85,86]. Arthrobacter, Actinomyces, Corynebacterium and Frankia. These have been studied principally due to their great capacity to generate diverse bio-active molecules [84].
Actinobacteria have a wide economic and scientific interest, mainly focused on the study of their application in human health and agriculture [87]. On the one hand, these bacteria are able to synthesize a wide and diverse range of secondary metabolites (more than 10,000 compounds reported) with antimicrobial, antitumor and anti-inflammatory activity [84,88], and to promote plant growth under abiotic and biotic stress conditions, due to the synthesis of plant growth regulators (phytohormones) and organic acids [80]. In addition, Actinobacteria can fix atmospheric nitrogen, solubilize minerals such as phosphorus [89], produce siderophores [80] to overcome limited nitrogen, iron, and phosphorus conditions, respectively [79], and some species can produce antibiotics in situ contributing to maintain the plant health.
Actinobacteria also have the ability to synthesis volatile organic compounds that diffuse into the air and soil through the pores acting as chemical agents of communication between species, suppression of plant pathogens, formation of biofilms, indicators during differentiation, formation of mycelium and sporulation and modification of pH in the environment [90]. In addition, these can synthesize antimicrobial signaling peptides and quorum sensing regulators, which protect the organism from damage and facilitate interactions with the environment [87].
These bacteria play an important role in the decomposition of plant biomass, playing a vital role in ecologies and processes such as the carbon cycle [91]. Actinobacteria have a large reservoir of lytic enzymes such as proteases, exo-and endo-glucanases, amylases, lipases, pectinases and xylanases that degrade the components of the plant cell wall facilitating the entry of the cells into the root [79,80,87,92]. They also synthesize lytic enzymes such as chitinases, dextranases, cutinases, peroxidases, laccases, which degrade the cell wall of pathogens and are responsible for their inhibition and growth [93].
More importantly, these bacteria have the capacity to persist in the soil at high cell density with a high rate of viability, which has led to the study of different applications in agriculture. They act either by suppressing the growth of phytopathogens and promoting growth of important crop plants, i.e. corn, tomato and banana [94] or the ability to fix nitrogen in non-leguminous plants [80]. Nitrogen-fixing bacteria include members of the Frankia family, Corynebacterium sp., and Pseudonocardia dioxanivorans. Some of them are used as alternative nitrogen fertilizers [80]. Commercial products based on actinobacteria have been generated, mainly from species of the genus Streptomyces [95] that protect plants against foliar and soil-borne diseases. These organisms can be used as insecticides, herbicides, antifungals and biocontrol agents, as well as plant growth promoters [82]. 97]. Soil microfauna is fundamental to the functionality of the ecosystem and any changes in these key organisms can produce changes at the vegetational, biome and microbial level [20].
The most relevant groups of microorganisms in the soil are arbuscular mycorrhizal fungi and plant growth promoting bacteria. These microorganisms together increase nitrogen fixation and uptake, solubilize phosphorus, convert ammonium (which can be chemically bound to clay particles) into the soluble, easily assimilable nitrate, protect from other pathogenic microorganisms, and even remediate contaminated soils [98,99].
Arbuscular mycorrhizae, besides being related to plants, are also related to the PGPR in the rhizosphere and to the endobacteria, affecting their activity and generating a synergy in functionality [100,102]. The interactions between AM fungi and soil bacteria influence the expression of fungal genes. The interactions include the adhesion of bacteria to the surface of fungal spores, conidia and hyphae, the injection of molecules into the fungal spores, the degradation of the fungal cell wall and the production of volatile substances [102].
The consortia (fungi and bacteria) have multiple applications to sustainable agriculture that have been reported to allow greater nutrient uptake and biocontrol of pathogens, depending on agricultural practices that allow their maintenance [103]. Likewise, different communities of soil fungi have been detected to affect the soil formation or stabilization at the macro-and microaggregate scale through different mechanisms of physical, biochemical, and biological processes [104,105].
The biotechnological applications of consortia such as the application of biofertilizers or biostimulants is justified in agricultural soils of the Mediterranean climate that have a percentage of less than 3.5% of organic matter, where microorganisms can no longer perform their functions [106].
Considering that in these cases the soil microbiota must be restored with fundamental taxonomic groups or initiators such as arbuscular mycorrhizal fungi [107], the application of microbial consortia is the preferred approach. These inoculants will have less ecological impact on the ecosystem and therefore on the environment and health [7]. Although further studies at micro-and meso-cosm level, followed by field research, will allow to assess the ability of selected AMF and bacteria to interact with Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 October 2020 doi:10.20944/preprints202010.0592.v1 native microorganisms and maintain their beneficial activities [108], the agricultural use of microbial consortia containing bacteria, fungi and AMF is in its exponential phase [109], based on a range of evidences including wheat [110,111], Mediterranean vegetables [112], lettuce [113], vegetables [114] , basil [115], tomato [116], and maize [117].
Despite the demonstrated benefits produced by soil microorganisms, there is ample space for gaining further insight, especially on arbuscular mycorrhizal fungi, which are crucial for many ecosystem services, such as nutrient cycling and food production. An example is the case of Latin America [118]. In Latin America [119] and Africa there is a need to focus on soil health and biodiversity among farmers, major agribusinesses, and policy makers, complementing the current productivity paradigm with sustainability and conservation objectives. Therefore, it is vital to describe the development of rhizosphere microbiome in all relevant crops, as microbial communities are deeply affected by agricultural management [120,121]. The databases of association between higher plants and mycorrhizal fungi are critical for addressing biogeographic and evolutionary issues [17]. In addition, soil biota is a key factor for the application of appropriate microbial inoculants in the field, but the genotype/genotype interactions between the microbial strain(s) and the crop cultivar(s), e.g. maize, often requires prior screening to obtain the desired results [119]. And this is due to the lack of knowledge or neglect of the plant microbiome when selecting the germoplasm for higher productivity [1].
It has been observed that microbial communities are highly sensitive to changes in environmental properties, for example, the geographical location where the type of soil and its pH play a fundamental role in the distribution of species In the same way, the climatic conditions and the type of vegetation determine in a dynamic interrelationship the biodiversity of the microbial communities in the different ecosystems [123,124].
Likewise, the specific inoculants of a single group of commercially produced microorganisms represent a small genetic group of fungi and/or bacteria selected to be both generalists and aggressive colonizers [7]. These traits have the potential to affect local communities of microorganisms, which may not be resistant to the introduction of other exogenous species [125]. The role of potentially invasive species in soil ecosystems has received little attention, despite knowledge of the role of soil biodiversity in ecosystem processes.
Currently, the knowledge of the identity of the species that make up a microbial community can be achieved through metagenomics. In order to be able to associate the functionality of certain taxa with the characteristics of crop productivity and resilience it is necessary to carry on studies including the isolation and cultivation of the species [26]. In Latin America and Africa there are still many knowledge gaps, where microbial communities are not known or are unidentified taxa [39,119]. This represents a problem when predicting changes at the ecosystem level that may be generated in the future, which is relevant in decision making when designing public policies [17]. To protect the functionalities of terrestrial ecosystems in a productive eco-compatible modern agriculture, it is necessary to include soil microbiota and soil biota in environmental protection and impact assessment policies [16,20].
Climate change with its consequent events such as droughts, temperature increase and CO2 increase, generates environmental changes that affect the microbial community and therefore the whole ecosystem. In agriculture, this generates a great challenge since there is a great impact on the productivity and resilience of agricultural systems [6,7]. Currently, different strategies are being developed to abort this issue, one of them being the Climatic Smart Agriculture, which seeks to develop a sustainable food system, to increase crop productivity and quality, to reduce the impacts of climate change, through the adaptation and building of crop resilience, conserving and increasing carbon stocks in soils and reducing GHGs [21].
Some examples for smart agriculture are the reported associations of the bacteria Rahnella aquatilis which improves organic phosphorus solubilization when associated with the mycorrhizal fungus Rhizophagus irregularis. The rhizospheric yeast fungi Cryptococcus flavus or Candida railenensis and the arbuscular mycorrhizal fungus Rhizophagus irregularis whose association promotes root growth in corn plants [126]; the Brettanomyces naardensis yeast with fungi that reduce the incidence of the pathogen Macrophomina phaseolina in sunflower plants; in addition, this association significantly improves growth parameters such as plant height, dry weight and number of leaves [127]. It has also Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 28 October 2020 doi:10.20944/preprints202010.0592.v1 been reported that consortia between filamentous fungi and PGPR stimulate the growth and yield of substances produced by plants as essential oils [128].

Conclusions
The biotechnological application of microorganisms either through the selection and inoculation of specific microbial strains or just by promoting the activity of naturally occurring microbes, holds a great potential for sustainable agriculture, as these innovative agronomic practices have the capacity to replace conventional agricultural practices. Beneficial microbes are multifunctional, with effects ranging from protection from pathogens to reduction of drought, stimulation of nutrient uptake, and can reproduce and be self-sufficient. In addition, microbe management can promote systems that are resilient to climate change.
When thinking about the formulation of microbial consortia we should consider functional taxa of various species that are effective and compatible with other soil organisms where they will be applied according to their geographical and climatic conditions. It is expected that future research related to sustainable agriculture will focus on the importance of soil (micro)biota, focusing on both the morphology of cultivable microorganisms and the metagenomics of all species found in the soil, in order to formulate distribution maps that will allow us to make informed decisions on the effect of agricultural practices on (micro)biomes.