Bacterial rhizosphere microbiome diversity has been strongly associated with beneficial effects on plant growth in both natural and agricultural environments (Mendes et al., 2013; Yu et al., 2019). Such beneficial diversity effects are often associated with increased functional diversity and community multifunctionality (Saleem et al., 2019; Raza et al., 2020; Hu et al., 2021; Raza et al., 2021; Lindsay et al., 2021), where different taxa play complementary roles in plant growth promotion, specializing in nutrient solubilization, plant immune priming or for example by interacting with beneficial or pathogenic rhizosphere microbes (Hayat et al., 2010; Lugtenberg and Kamilova, 2009). Moreover, high microbial diversity can have other benefits such as providing functional redundancy in the case of species extinctions (Allison and Martiny, 2008), community stability (Hu et al., 2016), or provide emergent consortia-level properties that cannot be predicted based on the sum of individual species (Netzker et al., 2018; Abrudan et al., 2015; Tilman, 1982; Tilman, 2004). While several studies have tried to harness positive effects of bacterial diversity for crop production (Weidner et al., 2015; Hu et al., 2017; Wu et al., 2018), diverse inoculants often fail to produce the desired benefits in field conditions. This discrepancy could rise due to constraints set by external factors, such as resource availability (De-la-Peña et al., 2010; Gransee and Wittenmayer, 2000; Chaparro et al., 2013), that constrains the expression of plant growth promotion traits, or the presence of competitors, parasites, and predators that reduce the survival of the inoculated bacteria in the rhizosphere (Hibbing et al., 2010; Gao et al., 2019). Also intrinsic factors, such as interactions between inoculant consortia members, could constrain their survival in the rhizosphere (Wang et al., 2021; Jousset et al., 2011; Gu et al., 2020). It has thus been suggested that microbial inoculant design should aim to minimize negative interactions within the inoculated consortia without compromising consortia competitive ability, which is important for consortia establishment in the diverse rhizosphere microbiome, especially when being initially rare (Gu et al., 2020; Li et al., 2019; Wei et al., 2015).

Diversity-ecosystem functioning experiments are widely used to study if communities perform better due to inherent benefits of diversity or because certain communities contain specific species that are important for the community functioning (i.e., species identity effects due to presence of certain microbial keystone species) (Banerjee et al., 2018; Jousset et al., 2014). In microbial context, such experiments have been mostly conducted by using taxonomically diverse communities, where associations between community diversity and functioning have been found to range from positive to neutral and negative (Jousset et al., 2011; Wei et al., 2015; Maynard et al., 2017). One reason for such variety of outcomes might be that increasing community diversity often also introduces competition between the community members, which might overshadow and constrain the benefits of inoculant diversity. For example, antimicrobial activity of pathogen-suppressing volatile organic compounds has been shown to peak at intermediate levels of bacterial community diversity (Raza et al., 2020), and a similar hump-shaped pattern has also been found between toxin production and bacterial community richness (Jousset et al., 2011). Likely explanation for these findings is that the same compounds that are responsible for pathogens suppression also affect the competition between other consortia members (Gu et al., 2020). One way to reduce this negative effect would be to quantify species interactions in advance to assemble multifunctional bioinoculants with weak within-consortia competitive interactions (Li et al., 2019; Wei et al., 2015). Such optimization could be achieved by using highly related bioinoculant strains because genetic relatedness is predicted to favor cooperation instead of conflict due to kin selection (Simonet and McNally, 2021; Crespi, 2001; Kolter and Greenberg, 2006; Raymond et al., 2012). For example, if bioinoculant species produce antimicrobials, it is likely that related strains share the same antibiotic biosynthesis and resistance genes, and hence, unlikely antagonize each other (Xia et al., 2022). Increasing intra-species diversity could further lead to increased bioinoculant consortia multifunctionality, which has been shown to play an important role in the functioning of microbial ecosystems (Van Rossum et al., 2020; Fields et al., 2021; Raffard et al., 2019; Nicastro et al., 2020; Blake et al., 2021; Dragoš et al., 2018). Multifunctionality could be optimized based on ecological complementarity by assembling consortia from strains that use different niches or specialize in different functions within the same niche (Dragoš et al., 2018; Martin et al., 2016). This might allow more efficient expression or production of different compounds at the consortia level and help to overcome any antagonistic pleiotropic effects experienced at the individual strain level (i.e., trade-offs between plant growth promotion traits). Moreover, interactions between near clonal specialist genotypes could allow division of labor, where shared workload by two specialists leads to higher productivity relative to one generalist as has been demonstrated with Bacillus subtilis bacterium during biofilm matrix production (Dragoš et al., 2018). Such overperformance (or overyielding) could also be driven by other mechanisms such as resource partitioning, abiotic facilitation, or biotic feedbacks (Barry et al., 2019), leading to higher consortia functioning than predicted based on the sum of its individual members.

Here, we used a combination of genetics, molecular biology, and biodiversity-ecosystem functioning theory (Saleem et al., 2019; Hu et al., 2016) to test if increasing phenotypic diversity of a single plant growth-promoting Bacillus amyloliquefaciens T-5 bacterium offers a viable strategy to improve bioinoculant consortia multifunctionality. We chose B. amyloliquefaciens T-5 strain as our model species because it originates from the tomato rhizosphere (Tan et al., 2013) and has previously been shown to protect plants from various diseases, including bacterial wilt caused by phytopathogenic Ralstonia solanacearum bacterium (Jiang et al., 2017). To increase functional diversity within a single species, we first created a B. amyloliquefaciens mutant library using TnYLB-1 transposon mutagenesis (Le Breton et al., 2006), resulting in 1999 unique insertion mutants. A representative subset of 479 mutants were chosen for high-throughput phenotyping in vitro in the lab regarding four important plant growth promotion traits: biomass production, biofilm formation, swarming motility, and pathogen suppression (Lugtenberg and Kamilova, 2009; Turnbull et al., 2001; Raaijmakers et al., 2002). After phenotyping, a subset of 47 mutants that performed better or equally well as the wild-type strain were taken forward to plant experiments to determine if in vitro phenotyping could predict mutant success in terms of tomato root colonization and plant protection from R. solanacearum in vivo. Finally, we tested if plant growth promotion could be improved by combining phenotypically distinct mutants into multi-strain consortia. We predicted that increasing mutant consortia richness would lead to improved root colonization and plant protection if mutants are phenotypically dissimilar, which could result in positive diversity-ecosystem relationships or trait multifunctionality. These two hypotheses were tested by comparing the performance between phenotypically dissimilar and randomly assembled mutant consortia. Our results demonstrate that transposon insertion mutagenesis is an effective way to improve and identify genes underlying plant growth promotion traits in B. amyloliquefaciens. Importantly, we show that in vitro phenotyping can be used to optimize inoculant consortia functioning in vivo and that diverse mutant consortia are better at colonizing and protecting tomato plants when they are assembled based on phenotypic dissimilarity.

In this work, we tested if increasing intra-species diversity of B. amyloliquefaciens T-5 bacterium via mutagenesis could offer a viable strategy for improving mutant consortia multifunctionality and plant health (Figure 3G–H). Our results show that mutations that improved bacterial performance regarding one trait often led to specialism and reduced performance regarding other traits. Such trait trade-offs experienced at the individual genotype level could be overcome by assembling consortia of phenotypically distinct mutants, that showed increase in average trait performance. Crucially, the consortia richness and average trait performance correlated positively with increased root colonization and plant protection, indicative of increased consortia multifunctionality and improved plant health. Especially, diverse 8-mutant consortium that consisted of phenotypically distinct mutants performed better compared to randomly assembled 8-mutant consortia consisting of phenotypically similar mutants. Together, these findings suggest that increasing intra-species functional diversity could offer an easy solution for improving the performance of bacterial consortia.

We specifically focused on four B. amyloliquefaciens traits that have previously been linked to plant growth promotion: swarming motility, biomass production, biofilm formation, and direct pathogen suppression via antibiosis (Chen et al., 2013; Huang et al., 2020; Fira et al., 2018; Moreno-Velandia et al., 2019). While most transposon insertions reduced the strains’ performance, some of them improved at least one measured trait. However, all trait improvements were costly and reduced mutants’ performance regarding other traits, indicative of trade-offs and antagonistic pleiotropy (Eyre-Walker and Keightley, 2007). Such costs of adaptation are common with microbes and have previously been linked to a wide range of functions, including metabolism, antibiotic production, motility, and stress resistance (Yang et al., 2019; Ferenci, 2016). Overall, transposon insertions were identified in several genes associated with broad range of functions (Figure 1—figure supplement 3, Supplementary file 1c). With eight phenotypically distinct mutants that were used for consortia assembly experiment, increased swarming motility was associated with insertions in parE (DNA topoisomerase IV subunit B) and DeoR (DNA-binding transcriptional repressor) genes, which has previously been linked to antibiotic resistance and bacterial deoxyribonucleoside and deoxyribose utilization (Saxild et al., 1996), respectively. While it remains unclear how these genes were linked with swarming motility, their disruption also affected other traits as evidenced by reduced biofilm formation. Increased biomass production was linked to disruption of comQ (competence protein) and hutI (imidazolonepropionase) genes and trade-offs with the other three measured traits. ComQ gene controls the production of ComX pheromone (Bacon Schneider et al., 2002) and has recently been linked to antimicrobial activity (Esmaeilishirazifard et al., 2018), which could explain reduction in the pathogen suppression by this mutant. Insertion in histidine utilization (hut) system gene, hutI, could have potentially impaired catabolite and amino acid repression, resulting in improved biomass production with one of the mutants (Eda et al., 1999; Bender, 2012). Interestingly, increased biofilm formation was also linked to insertion in hut system (hutU) with one mutant, while the other mutant had insertion in YsnB gene, which encodes for a putative metallophosphoesterase. While both insertions were linked to trade-offs with swarming motility and biomass production, they are not commonly associated with biofilm formation in Bacillus (Dragoš et al., 2018; Prágai et al., 2001). Finally, moderate improvement in pathogen suppression was observed with two mutants that had insertions in nhaC (sodium-proton antiporter) and dfnG (difficidin polyketide synthesis) genes. The nhaC gene is known to act as repressor for Pho regulon in Bacillus (Prágai et al., 2001), while mutations in Pho regulon have been linked to increased antibiotics production with several Streptomyces species (Santos-Beneit, 2015). Moreover, the dfnG gene controls the production of difficidin antibiotic, which has previously been linked to biocontrol activity against fire blight and Xanthomonas oryzae rice pathogen (Wu et al., 2015) and could have also suppressed the growth of R. solanacearum. Similar to the other phenotypically distinct mutants, insertions associated with increased pathogen suppression led to trade-offs with other measured traits. While more work is required to unequivocally link these mutations with associated traits at the molecular level, our findings show that all above trait improvements achieved via mutagenesis resulted in trade-offs with other traits and that this technique could be used to identify genes underlying plant growth promotion and pathogen suppression.

To overcome trait trade-offs experienced at the individual mutant level, we tested if we could improve the plant growth promotion by combining phenotypically distinct mutants into multifunctional consortia. We found that mutant performance measured in monocultures was a poor predictor of B. amyloliquefaciens performance in consortia in vitro, except for the pathogen suppression. This suggest that while the selected mutants did not show direct antagonism toward each other, they likely interacted in other ways leading to unpredictable trait expression when growing together (e.g. via certain emergent effects; Goldford et al., 2018). Despite this, we found clear diversity effects, where consortia richness and average performance were positively associated with both plant root colonization and plant protection from R. solanacearum pathogen infection. While important mutant identity effects were also observed, omission of these strains did not change the significance of underlying diversity effects, highlighting the importance of interactions between the consortia members in determining the positive effects on the plant health. Together, these results suggest that consortia that performed well regarding all measured traits on average had improved ability to colonize rhizosphere and suppress the pathogen. To test if these effects were driven by diversity per se or underlying trait variation between consortia members, we compared the optimized 8-mutant consortium with eight randomly assembled 8-mutant consortia that were phenotypically more similar. We found that randomly assembled consortia performed less well on average, while consortia functioning improved along with consortia relative performance, suggesting that diverse consortia performed better only when they had been assembled from phenotypically dissimilar mutants. While similar positive diversity-ecosystem functioning relationships have previously been found in more complex Pseudomonas (Hu et al., 2021; Hu et al., 2016; Hu et al., 2017), leaf bacterial (Laforest-Lapointe et al., 2017) and grass-land soil microbiomes (Wagg et al., 2019), we here show that this pattern also holds along with intra-species diversity gradient. While the measured phenotypic traits are considered to be robust to inoculum densities, it will be important to evaluate in the future if the absolute abundances of each mutant play a role in the consortia functioning.

Positive diversity effects have previously been explained by facilitation, ecological complementarity, and division of labor, which can reduce competition between the consortia members within or between niches (Dragoš et al., 2018; Martin et al., 2016; Bulleri et al., 2016). Moreover, high diversity could provide stability for consortia functioning via insurance effects by increasing the likelihood of certain consortia members surviving in the soil after the inoculation (Yachi and Loreau, 1999; Boles et al., 2004). While our experiments were not designed to disentangle the relative importance of these potential mechanisms, we analyzed which mutant traits could significantly explain the dynamics of root colonization and plant protection at seedling, vegetative, and flowering stages of the tomato growth by focusing on 47 mutants. While the effect of Bacillus biomass production was consistently non-significant, both motility and biofilm formation were positively associated with the root colonization. However, motility was significant only at the seedling stage, while biofilm became significant during vegetative and flowering stages. In line with ecological succession often taking place in the rhizosphere (Chen et al., 2013), high motility might have allowed faster colonization of relatively ‘sterile’ young roots by Bacillus, while biofilm formation could have promoted stress tolerance and resource competition in more diverse and mature microbial communities during the later stages of tomato growth (Bais et al., 2004; Xu et al., 2013). Interestingly, increase in pathogen suppression, biofilm formation, and motility were positively associated with improved plant protection at the flowering stage, which suggests that all these traits were positively associated with the ecosystem functioning in terms of plant health. It is thus possible that consortia were together able to overcome the trait trade-offs experienced at the individual mutant level, leading to improved and more stable ecosystem functioning for the whole duration of tomato growth cycle. In addition, it is possible that some of the measured plant growth promotion traits might act as public goods (Lee et al., 2010; Driscoll et al., 2011), which could have been shared between different mutants, leading to overall improvement in the mutant population fitness. Such micro-scale mechanisms could be potentially validated in the future using transcriptomics and barcoded Tn-seq mutants, which would allow estimating activity and changes in mutant frequencies during bioinoculation.

In conclusion, we here demonstrate that the beneficial effects provided by a single B. amyloliquefaciens bacterium can be improved by increasing consortia functional diversity using transposon mutagenesis. Our approach highlights the importance of intra-species genetic diversity for the ecosystem functioning and provides a trait-based approach for designing microbial communities for biotechnological applications. Our approach does not require a priori knowledge on specific genes or molecular mechanisms, but instead relies on generation of trait variation which is screened and selected by the experimenter. Our method can also help to identify novel functional roles of previously characterized and uncharacterized genes. While the benefit of this method was here demonstrated in the context of agriculture, it could be applied in other biotechnological contexts, such as biofermentation, waste degradation, and food manufacturing. Future work focusing on the population dynamics, metabolism, and gene expression of different mutants will help to understand the relative importance of ecological complementarity, division of labor, insurance effects, population asynchrony (Blüthgen et al., 2016), and facilitation for the consortia ecosystem functioning.

All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided in Source data 1.

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Author details

1. Jingxuan Li

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Formal analysis, Investigation, Visualization, Writing – original draft

   Contributed equally with

   Chunlan Yang

   Competing interests

   No competing interests declared

2. Chunlan Yang

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Formal analysis, Investigation, Visualization, Writing – original draft

   Contributed equally with

   Jingxuan Li

   Competing interests

   No competing interests declared

3. Alexandre Jousset

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Conceptualization, Writing – review and editing

   Competing interests

   No competing interests declared

4. Keming Yang

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Formal analysis, Investigation, Visualization

   Competing interests

   No competing interests declared

5. Xiaofang Wang

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Formal analysis, Investigation

   Competing interests

   No competing interests declared

6. Zhihui Xu

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Writing – review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-3987-8836

7. Tianjie Yang

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Formal analysis, Investigation

   Competing interests

   No competing interests declared

8. Xinlan Mei

   Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

   Contribution

   Investigation

   Competing interests

   No competing interests declared

9. Zengtao Zhong

   College of Life Science, Nanjing Agricultural University, Nanjing, China

   Contribution

   Resources, Methodology, Writing – review and editing

   Competing interests

   No competing interests declared

10. Yangchun Xu

    Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

    Contribution

    Conceptualization, Supervision, Project administration

    Competing interests

    No competing interests declared

11. Qirong Shen

    Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

    Contribution

    Supervision, Project administration

    Competing interests

    No competing interests declared

12. Ville-Petri Friman

    1. Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
    2. Department of Microbiology, University of Helsinki, Helsinki, Finland

    Contribution

    Conceptualization, Formal analysis, Visualization, Writing – review and editing

    For correspondence

    ville-petri.friman@helsinki.fi

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-1592-157X

13. Zhong Wei

    Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China

    Contribution

    Conceptualization, Data curation, Supervision, Funding acquisition, Project administration

    For correspondence

    weizhong@njau.edu.cn

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-7967-4897

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