The soil microbiome dynamics following microbial invasions

The risk where food demand will transcend crop production, propels the application of microbial technologies, including the provision of microbial inoculants to boost crop productivity. This approach is considered more sustainable and benign as it bypasses societal and environmental concerns from chemical inputs. However, there is a growing concern that these inoculants may become invasive. Thus, this thesis aims to investigate whether soil inoculation by microbes could alter the structure, composition, and metabolic potential of native soil microbiome. By making use the ecological concept of microbial invasion, we (i) explore the pattern and mechanism of Gram-positive spore-forming bacterial invasion, imposed by Bacillus spp; (ii) foster the understanding on microbial community-level consequences of soil microbial inoculation; (iii) examine the role of protists’ selective predation on the success of bacterial releases in soils; (iv) propose mechanistic framework, through resource competition and protist predation, on how microbial inoculants shift soil resident community structure and functioning

The Production of Corn Kernel Miso Based on Rice-koji Fermented by Aspergillus oryzae and Rhizopus oligosporus

The suitability of corn kernel as raw material to produce miso fermented by rice-koji containing Aspergillus oryzae and Rhizopus oligosporus has been investigated. The optimization was conducted on two important factors in miso production namely mold composition in rice-koji and salt concentration. The mold composition was prepared by inoculating the spores of 2% A. oryzae, 2% R. oligosporus, and 2% the mixture of both in a ratio of 1:1, 2:1, and 1:2 (v/v) into different rice media. The mold composition was optimized to produce rice-koji with high α-amylase and protease activity. Different NaCl concentrations of 10%, 15%, and 20% were subjected to optimization process and added to each mixture after five days of fermentation. The salt concentration was also optimized to produce corn kernel miso with high glucose and high dissolved protein concentration. The result showed that rice-koji containing A. oryzae and R. oligosporus in the ratio of 1:1 had the highest α-amylase and protease activity of 0.42 U/mL and 0.45 U/mL respectively. In addition, the presence of 10% NaCl in corn kernel miso fermented by A. oryzae and R. oligosporus in the ratio of 1:1 exhibited the highest glucose and dissolved protein concentration of 0.64 mg/mL and 8.80 mg/mL respectively. The optimized corn kernel miso by A. oryzae and R. oligosporus in the ratio of 1:1 with 10% NaCl was subjected to nutrient content analysis and compared to the result before the corn kernel was fermented. The nutrient content analysis showed nutrient enhancement after corn kernel was fermented and transformed into a miso. Glucose, dissolved protein, and fat content increased 6.74, 1.34, 7.63 times respectively. This study concludes corn kernel could be utilized to produce a novel corn kernel miso for dietary diversification and for improving nutritional and health status

Deliberate introduction of invisible invaders:A critical appraisal of the impact of microbial inoculants on soil microbial communities

Non-target effects of deliberately released organisms into a new environment are of great concern due to their potential impact on the biodiversity and functioning of ecosystems. Whereas these studies often focus on invasive species of macro-organisms, the use of microbial inoculants is often expected to have specific effects on particular functions but negligible overall effects on resident microbial communities. Here, we posit that such introductions often impact native microbial communities, which might influence ecosystem processes. Focusing on soil communities, we used a literature search to examine the impact of microbial inoculation (often the release of beneficial microorganisms in agricultural systems) on resident microbial communities. Of 108 studies analyzed, 86% showed that inoculants modify soil microbial communities in the short or long term. In addition, for studies analyzing the consequences of microbial inoculants in the longer term, 80% did not observe the resilience (return to the initial state) of the resident community following inoculation. Through the knowledge gathered from each study, we propose a synthetic and mechanistic framework explaining how inoculants may alter resident microbial communities. We also identify challenges as well as future approaches to shed more light on this unseen reality

Temporal dynamics of the soil bacterial community following <i>Bacillus</i> invasion

Microbial inoculants are constantly introduced into the soil as the deployment of sustainable agricultural practices increases. These introductions might induce soil native communities’ dynamics, influencing their assembly process. We followed the impact and successional trajectories of native soil communities of different diversity levels to the invasion by Bacillus mycoides M2E15 (BM) and B. pumilus ECOB02 (BP). Whereas the impact was more substantial when the invader survived (BM), the transient presence of BP also exerted tangible effects on soil bacterial diversity. Community assembly analyses revealed that deterministic processes primarily drove community turnover. This selection acted stronger in highly diverse communities invaded by BM than in those invaded by BP. We showed that resident bacterial communities exhibit patterns of secondary succession following invasions, even if the latter are unsuccessful. Furthermore, the intensification of biotic interactions in more diverse communities might strengthen the deterministic selection upon invasion in communities with higher diversity

The impact of protozoa addition on the survivability of <i>Bacillus</i> inoculants and soil microbiome dynamics

Protists’ selective predation of bacterial cells is an important regulator of soil microbiomes, which might influence the success of bacterial releases in soils. For instance, the survival and activity of introduced bacteria can be affected by selective grazing on resident communities or the inoculant, but this remains poorly understood. Here, we investigated the impact of the introduction in the soil of two protozoa species, Rosculus terrestris ECOP02 and/or Cerocomonas lenta ECOP01, on the survival of the inoculants Bacillus mycoides M2E15 (BM) or B. pumilus ECOB02 (BP). We also evaluated the impact of bacterial inoculation with or without protozoan addition on the abundance and diversity of native soil bacterial and protist communities. While the addition of both protozoa decreased the survival of BM, their presence contrarily increased the BP abundance. Protists’ selective predation governs the establishment of these bacterial inoculants via modifying the soil microbiome structure and the total bacterial abundance. In the BP experiment, the presence of the introduced protozoa altered the soil community structures and decreased soil bacterial abundance at the end of the experiment, favouring the invader survival. Meanwhile, the introduced protozoa did not modify the soil community structures in the BM experiment and reduced the BM + Protozoa inoculants’ effect on total soil bacterial abundance. Our study reinforces the view that, provided added protozoa do not feed preferentially on bacterial inoculants, their predatory behaviour can be used to steer the soil microbiome to improve the success of bacterial inoculations by reducing resource competition with the resident soil microbial communities

Interactions between bacterial inoculants and native soil bacterial community:The case of spore-forming <i>Bacillus</i> spp

Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities’ niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities’ niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity

Interactions between bacterial inoculants and native soil bacterial community: The case of spore-forming Bacillus spp

Microbial diversity can restrict the invasion and impact of alien microbes into soils via resource competition. However, this theory has not been tested on various microbial invaders with different ecological traits, particularly spore-forming bacteria. Here we investigated the survival capacity of two introduced spore-forming bacteria, Bacillus mycoides (BM) and B. pumillus (BP) and their impact on the soil microbiome niches with low and high diversity. We hypothesized that higher soil bacterial diversity would better restrict Bacillus survival via resource competition, and the invasion would alter the resident bacterial communities' niches only if inoculants do not escape competition with the soil community (e.g. through sporulation). Our findings showed that BP could not survive as viable propagules and transiently impacted the bacterial communities' niche structure. This may be linked to its poor resource usage and low growth rate. Having better resource use capacities, BM better survived in soil, though its survival was weakly related to the remaining resources left for them by the soil community. BM strongly affected the community niche structure, ultimately in less diverse communities. These findings show that the inverse diversity-invasibility relationship can be valid for some spore-forming bacteria, but only when they have sufficient resource use capacity