Introduction
Crop quality is of increasing concern with the expanded demands from consumers. Recently,
increasing attention has been paid on the crops rich in mineral nutrients, antioxidants,
or other metabolites, as they represent high quality and reduce the risk of chronic
diseases (Li and Eunice, 2015; Timmusk et al., 2017). Such high-quality crops are
more profitable for farmers compared with conventional crops. However, the methods
to improve crop quality are limited to breeding, fertilizing regimes, and farming
practices.
Soil microbiome significantly contributes to the fitness improvement of plants, in
facing abiotic/biotic stress and nutritional deficiency (Bakker et al., 2018; Oyserman
et al., 2018). Crop quality can be potentially modified by the soil microbiome. However,
conventional farming practices, e.g., tillage, over use of chemical fertilizers, pesticide
and fungicide, and monoculture, disturb the soil microbiome. The overuse of agro-chemicals
is especially detrimental to agricultural ecosystems, threatening soil quality and
human health (Hartman et al., 2018). Crop quality may subsequently decline with the
degradation of the soil microbiome. Hence, it is urgent to search for alternative
methods to produce high-quality crops in an efficient, safe and environment-friendly
manner.
Beneficial soil microbes, such as plant growth promoting bacteria (PGPB), actinomycetes,
and arbuscular mycorrhizal fungi (AMF), can interact with plants and induce the accumulation
of plants' metabolites which benefit people's health (Gianinazzi et al., 2010; Glick,
2012). Hence, using microbial biostimulants may be useful for producing high-quality
crops sustainably (Bhardwaj et al., 2014). However, it is not easy to replace the
agro-chemicals by biostimulants to produce nutritional crop safely. Natural rhizosphere
communities are complex and diverse, comprising an entire food web (Bender et al.,
2016). Commercially available biostimulants, however, are generally limited to one,
or few, microbial taxa. While these products have yet to be thoroughly tested, it
is unlikely that they will sufficiently compensate for reduced microbial diversity
in farmlands due to human activity (Hart et al., 2018).
Borrowing from the ideas of synthetic biology, synthetic microbial consortia (SMC)
could potentially replace and/or reshape the structure and function of plant microbiome.
It is possible to construct SMC consisting of a microbial guild (rather than limited
microbial taxa in the existing biofertilizers) with multiple functions to promote
crop growth and quality (Wallenstein, 2017). In this regard, using SMC could potentially
solve the drawbacks of traditional biofertilizers (Qin et al., 2016), such as ineffectiveness
in competing with indigenous microbes, incompatibility with host plants and inadaptation
to the local conditions (Hart et al., 2018). Here, we summarize how SMC may be used
to produce high-quality crops, focusing on: (1) constructing the desired SMC; (2)
assessing the efficacy of SMC; (3) assessing ecological impacts of SMC.
How to construct the desired SMC?
Previously, developing SMC was largely based on combining specific microbial genotypes
with desirable traits (Whipps, 2001; Dodd and Ruiz-Lozano, 2012; Thijs et al., 2014).
Currently, the typical SMC often include PGPB and AMF, targeting to enhance the metabolites
contents (e.g., essential oil, zein, glucosinolate, sugar, ascorbic and folic acid,
volatile compounds, vitamin, and anthocyanin) and nutrients (N, Ca, P, Mg, K, Na,
Fe, Mn, Cu, Zn, and B), which represent higher nutraceutical values in crops (Hart
and Forsythe, 2012; Berta et al., 2014; Cosme et al., 2014; Bona et al., 2015, 2017;
Hart et al., 2015; Weisany et al., 2015; Battini et al., 2016; Torres et al., 2016;
Avio et al., 2017). However, previous studies dealing with SMC have reported a range
of plant responses and contradictory results (Lucas García et al., 2004; Estévez et
al., 2009; Rosier et al., 2016), suggesting that different microbes may not have additive
effects. Importantly, the compatibility within microbes and with new environment is
an essential consideration for constructing SMC. Given the variability among microbes
and soil heterogeneity, this is no small task. Clearly, the way forward must capitalize
on existing co-adapted SMC.
Firstly, the origin of microbes is critical to construct SMC. Indigenous microbes
were reported to be more efficient in augmenting plant stress tolerance (Estrada et
al., 2013; Armada et al., 2014; Ortiz et al., 2015). The environmental adaptation
of autochthonous microbes might underlie their ability to improve plant fitness. Thus
it is expected that the soil microbiome from high-quality crops is an ideal origin
for SMC to confer the same plants better growth and quality. Further, the rhizosphere
is a hotspot for selecting members for SMC, due to their intensive interactions with
plants. Moreover, the endophytes beneficial to plants can also be used to devise SMC
(Huang et al., 2018), since they are more likely to persist in environments (Kong
and Glick, 2017).
Secondly, how can we obtain the core microorganisms? Now, next generation sequencing
(NGS) allows us to perceive the whole microbial community of crops using meta-genomics,
which was previously impossible (Figure 1). However, it is unnecessary to inoculate
the whole soil microbiome to target fields. The functional redundancy in microbial
communities indicates that only the core microbes are needed to fulfill their ecological
services to plants (Qin et al., 2016). Microbial network analysis is a powerful tool
for identifying the “hubs” (also termed keystone operational taxonomic units), which
are highly associated in a microbiome (Banerjee et al., 2018). When basic information
about the topology of a microbial network is obtained using the package “igraph” (Csardi
and Nepusz, 2006) in R software, the properties of the network structure can be evaluated.
Microbial networks can be compartmentalized into several “network modules,” within
which microbial species are highly connected with each other. Based on network topological
properties, the “hub” species, which coexist with most other species in each module,
can be further identified (Toju et al., 2018). These hub species of modules are the
candidates of core microorganisms. The information on hub species provides us the
very first step in core microorganisms screening.
Figure 1
The diagram of technical flow of artificial construction of synthetic microbial consortia
(SMC) targeting to augment crop quality. The crops with good quality can be a good
origin of SMC. The core microbes can be isolated from the rhizospheric soils or the
plant roots of crops with good quality, and their composition can be predicted by
next generation sequencing and network analysis. The network analysis will provide
the core microbial taxa and hubs which are needed to fulfill ecological services to
plants. The web-based platform KOMODO (Known Media Database) can be used to predict
the proper medium for the core microbes. The synergism among the microbial members
in SMC will be analyzed based on the crop quality (metabolites and nutrients). Plant
growth promotion activities and population dynamic changes of the core microbiome
are tested to provide reference for constructing the SMC. After the assessment of
efficacy and ecological impacts of SMC, they can be utilized in field.
The next step is to culture these core microbes. As is known, about 99% of the soil
microbes cannot be artificially cultured, it is challenging to reproduce all the pure
cultures included in SMC. Finding the proper culture media is the key to get the microbial
inoculant. Web-based platforms, such as KOMODO (Known Media Database) can be used
to predict the media components for culturing the core microbiome (Oberhardt et al.,
2015).
Thirdly, the optimization of microbial interactions would be crucial for constructing
stable, efficient, and controllable SMC. Cooperation among the SMC members is crucial
to exert additive effect in promoting crop quality. Utilizing the positive interactions
between fungi (Trichoderma reesei) and bacteria, Hu et al. (2017) devised a synergistic
SMC with higher lignocellulolytic enzyme activity. The SMC composed of Enterococcus
and Clostridium species degrade wheat straw into hydrogen and butanol in a two-step
reaction (Valdez-Vazquez et al., 2015). Constructed SMC using multiple Escherichia
coli strains successfully assemble 34 proteins in a single culturing, lysis, and purification
procedure (Villarreal et al., 2018). The crop quality (metabolites, nutrients) should
be integrated as a standard to test the synergistic effect of SMC. The SMC with larger
effect than the sum effect of individual microbial taxa, can be regarded as a synergistic
SMC. Besides, plant growth promotion activities (ACC deaminase, IAA, siderophores,
phosphate solubilization, and etc.), dynamic changes of the core microbes provide
reference for constructing a synergistic SMC. Under environmental stresses (such as
salinity, drought, or acidity, commonly found worldwide), tolerance traits of the
SMC should also be taken into consideration.
Assessing the efficacy of SMC
The challenges for utilizing SMC in field are the adaptation to new environments.
As the SMC are usually isolated from one crop species, they can be expected to positively
interact with the same plants in the original soils. A common assumption for field
applications is that the microbial inoculants are effective and they have to adapt
to a given soil or crop (Rodriguez and Sanders, 2015). Indeed, the variations of soil
conditions, such as soil type, moisture, nutrients content, and pH, may affect the
functioning and proliferation of SMC. Thus, the efficacy evaluation of SMC mainly
focusing on the magnitude in improving crop quality should be conducted in the target
field. The strategy from Hart et al. (2018), but also previously used by other authors,
as Bona et al. (2016), can be referred to direct the evaluation. The evaluation should
start from pot culture in greenhouse involving the factors e.g., soil properties,
climatic factors and crop traits (including physiological and phenological traits).
Meanwhile, the growth, mineral nutrients and metabolites of crops should be integrated
to determine the efficacy of SMC (Figure 1). Following the greenhouse study, plots
experiments are subsequently carried out to check the efficacy of the SMC in field.
Moreover, the relative longer period (2–3 years) is needed to determine the consistency
of the effect of SMC in practice. Based on the above observations, the efficacy of
SMC can be obtained.
Assessing ecological impacts of SMC
In recent years, scientists have developed a much better understanding of how various
beneficial soil microbes contribute to plant growth and health. For sustainable development
of agricultural ecosystems, it is not only necessary to improve crop yield and quality,
but also to ensure a good bioactivity and stability of the soil microbiome in farmland.
In this regard, the ecological risks, including invasiveness and the interactions
between SMC and indigenous soil microbes should be considered (Hart et al., 2017,
2018). Firstly, the invasiveness should be estimated before releasing SMC in farmland.
It should be ascertained how the inoculated strains survive or colonize the rhizosphere
of host crops, how the SMC interacts with the indigenous soil microbiome and function,
and how the indigenous soil microbiome structurally and functionally responds to the
exotic SMC. It is important to clarify all of these issues before implementing SMC
on a larger scale in fields. For example, if the introduced soil microbes can inhibit
the pathogen populations, the antagonistic interactions would enhance the beneficial
effects of SMC to promote the crop health. On the other hand, if the antagonistic
interactions occurred between SMC and indigenous beneficial microbes (like AMF and
rhizobia), cautions must be taken for using this SMC. Extensive metagenomics and population
genomics studies can help assess the environmental impacts of SMC (Rodriguez and Sanders,
2015). With this knowledge in hand, site assessment, potentially ecological risks
and regulatory acceptability would all be simplified.
Concluding remarks
Using SMC is a promising way to improve crop quality in sustainable agriculture. Though
abundant studies had shown the positive effects of beneficial soil microbes on the
crop yield and quality, the employment of SMC in practices is still infant in developing
countries. SMC possesses more merits than individual microbial inoculant. Here, we
propose a technical flow of utilizing SMC to promote crop quality. The technical flow
starts from how to construct the SMC. The microbes from one crop species with good
quality potentially render the same plants higher quality. The core microbes can be
isolated from the rhizospheric soils or the plant roots, predicted by next generation
sequencing and network analysis. KOMODO can be used to predict the media components
for culturing the core microbes. The members of core microbes should be tested for
synergy, plant growth promoting activities, and population dynamic changes. The improved
crop quality is a main principle for constructing SMC. Further, the efficacy of SMC
is needed to test in consideration of the environmental impacts. Finally, the ecological
risks evaluation of SMC is essential to maintain the environmental sustainability.
The technical flow would be helpful for biostimulant manufacturers and farmers to
enhance crop nutritional quality.
Author contributions
ZK and HL conceived the idea. ZK, HL, and MH prepared the manuscript.
Conflict of interest statement
The authors declare that the research was conducted in the absence of any commercial
or financial relationships that could be construed as a potential conflict of interest.
The handling editor declared a past co-authorship with one of the authors ZK.