Periodic Reporting for period 1 - Microbial-light (Illuminating black boxes in the nitrogen cycle)
Période du rapport: 2019-04-01 au 2021-03-31
Currently, climate change predictions describe outcomes of biological ecosystems. However, they avoid noting the changes at the microbial level and their effect on e.g. crop production.
Why is it important for society? The predictions of the effects of climate change on crop production concur that they won’t be distributed equally around the world. Most northern countries will see an increase in crop production, however, the rest will suffer from decreases in crop production. A decrease in crop production under an increasing human world population is a recipe for disaster, hence resistance and resilient measures are sought to counteract the impact of climate change.
As a consequence, the resistance and resilience of microorganisms involved in the nitrogen cycle affected by physicochemical soil disturbances have to be discovered. The microbial-based function nitrification, which in turn has a direct effect on crop production, need to be part of the current models on climate change. Understanding the resistance and plasticity of soil microbial functions, will enable greater precision in predicting crop production under climate change pressures.
Resistant and resilient microbial communities to climate change effects may palliate crop production decrease via the introduction of biofertilizers. Biofertilizers are crop amendments which contain plant growth promoting microorganisms (PGPM). However, these are usually used individually. The use of an individual strain as a biofertilizer increases the chances of its function being less efficient due to the vast completion it faces when inoculated into a natural soil with diverse microbial community.
Single PGPMs are studied and used globally as biofertilizers to enhance crop production and increase health by controlling pests, as well as maintaining nutrient cycling. Yet, we believe that the incorporation of these biological units in the fertilizers into complex and diverse soil ecosystems will prevail longer when composed of social multi-species microorganisms.
Recently, microbial communities have been observed to function best when the microorganisms have positive or neutral social behaviours. The use of a web based tool called BSocial (http://m4m.ugr.es/BSocial.html) describes the net social behaviour of individual strains, from combinatorial growths of these individuals.
Hence, the main objective was to study the impact of disturbances, such as humidity and temperature on soil microorganisms, and observe how their social interactions changed, as well as how the function of nitrification changed before and after the disturbances.
Furthermore, enhancement of the BSocial tool would increase further projects using social microorganisms for the creation of multi-species biofertilizers.
Physicochemical disturbances affect soil geochemical functions driven by microorganisms, thus further studies should highlight the factors that do not allow for microbial functions to recovery in short time spans in order to predict its effect on crop production.
Overall global warming increases stress disturbance frequencies, and these affect soil functions directly, and their macro/microorganisms. Although nitrifying microorganisms are resilient to dry spells, the nitrification process is severely affected with both dry (rel. humidity 5%) and intense temperatures (50°C). However, flooding can also alter the nitrification process in the soil, hence destabilizing the fluctuations of the processes within the nitrogen cycle. Since microbial functions work best with positive or neutral social species, a BSocial R package will be available soon for deciphering social interactions.
Why is it important for society? The predictions of the effects of climate change on crop production concur that they won’t be distributed equally around the world. Most northern countries will see an increase in crop production, however, the rest will suffer from decreases in crop production. A decrease in crop production under an increasing human world population is a recipe for disaster, hence resistance and resilient measures are sought to counteract the impact of climate change.
As a consequence, the resistance and resilience of microorganisms involved in the nitrogen cycle affected by physicochemical soil disturbances have to be discovered. The microbial-based function nitrification, which in turn has a direct effect on crop production, need to be part of the current models on climate change. Understanding the resistance and plasticity of soil microbial functions, will enable greater precision in predicting crop production under climate change pressures.
Resistant and resilient microbial communities to climate change effects may palliate crop production decrease via the introduction of biofertilizers. Biofertilizers are crop amendments which contain plant growth promoting microorganisms (PGPM). However, these are usually used individually. The use of an individual strain as a biofertilizer increases the chances of its function being less efficient due to the vast completion it faces when inoculated into a natural soil with diverse microbial community.
Single PGPMs are studied and used globally as biofertilizers to enhance crop production and increase health by controlling pests, as well as maintaining nutrient cycling. Yet, we believe that the incorporation of these biological units in the fertilizers into complex and diverse soil ecosystems will prevail longer when composed of social multi-species microorganisms.
Recently, microbial communities have been observed to function best when the microorganisms have positive or neutral social behaviours. The use of a web based tool called BSocial (http://m4m.ugr.es/BSocial.html) describes the net social behaviour of individual strains, from combinatorial growths of these individuals.
Hence, the main objective was to study the impact of disturbances, such as humidity and temperature on soil microorganisms, and observe how their social interactions changed, as well as how the function of nitrification changed before and after the disturbances.
Furthermore, enhancement of the BSocial tool would increase further projects using social microorganisms for the creation of multi-species biofertilizers.
Physicochemical disturbances affect soil geochemical functions driven by microorganisms, thus further studies should highlight the factors that do not allow for microbial functions to recovery in short time spans in order to predict its effect on crop production.
Overall global warming increases stress disturbance frequencies, and these affect soil functions directly, and their macro/microorganisms. Although nitrifying microorganisms are resilient to dry spells, the nitrification process is severely affected with both dry (rel. humidity 5%) and intense temperatures (50°C). However, flooding can also alter the nitrification process in the soil, hence destabilizing the fluctuations of the processes within the nitrogen cycle. Since microbial functions work best with positive or neutral social species, a BSocial R package will be available soon for deciphering social interactions.
Microcosms in glass pots with filled with agricultural soil, and the experimental set-up included an acclimation, a stress and a recovery phase. Press disturbances for two weeks included a full combinatorial of temperature (50°C, 20°C, 4°C), pH (8) and relative humidity (50%, 25%, 1%), i.e. 9 different press disturbances. Soil sampling occurred during different time points before and after stress. At sampling times, physicochemical conditions of the soils and nitrification rates were determined. DNA and RNA extractions were also performed. Illumina sequencing of the DNA samples, and quantification of nitrification genes were performed on RNA and DNA samples.
The project has been successful in determining the disturbances which negatively affect soil nitrification the most (2 weeks at 50°C, at rel. humidity of 5% - T50H5), and which other disturbances the soil can recover from in a short space of time (T50H25, T20H5, T4H5). Publication of these results will include the microbial/gene response to the disturbances, where overview of the response to microorganisms in the nitrogen cycle and PGPMs will be highlighted.
The online BSocial analysis is a great tool to decipher social microbial behaviour among species with a common function, however there were limitations to its use, hence it enhancement in the form of an R package, which can be used more freely by other scientists. Tool enhancement included: uncapping the limit of individual strains; Calculation of growth rate and number of generations from spectrophotometric raw data using different growth models; include an analysis “Hill climbing” to determine sequence of species addition for maximum growth; remove dependency on the lab server; and maintain a graphic interphase in the R package.
The BSocial tool will be published additionally as an R package, where R is a free software environment, to include raw data input, stability analyses and extra ecological analyses not seen in the BSocial web-tool.
Overall, with the results that have been obtained so far, and the microbial diversity analysis, we can uncover not only nitrifying microorganisms that can withstand environmental stress, but also others, such as PGPMs that can be directly used and commercialized as biofertilizers. Dissemination of the results will include 2 publications in high impact journals, and will be featured in two YouTube videos. The latter will be featured in the following website: https://jessicapurswani.wordpress.com/2020/10/06/intro-to-microbial-light/
Currently two videos are available to see the overall objectives of the Microbial Light project (https://youtu.be/2FsOTvEQ4Ak) and another on the use of BSocial (https://youtu.be/l_0MR45T7jk).
The project has been successful in determining the disturbances which negatively affect soil nitrification the most (2 weeks at 50°C, at rel. humidity of 5% - T50H5), and which other disturbances the soil can recover from in a short space of time (T50H25, T20H5, T4H5). Publication of these results will include the microbial/gene response to the disturbances, where overview of the response to microorganisms in the nitrogen cycle and PGPMs will be highlighted.
The online BSocial analysis is a great tool to decipher social microbial behaviour among species with a common function, however there were limitations to its use, hence it enhancement in the form of an R package, which can be used more freely by other scientists. Tool enhancement included: uncapping the limit of individual strains; Calculation of growth rate and number of generations from spectrophotometric raw data using different growth models; include an analysis “Hill climbing” to determine sequence of species addition for maximum growth; remove dependency on the lab server; and maintain a graphic interphase in the R package.
The BSocial tool will be published additionally as an R package, where R is a free software environment, to include raw data input, stability analyses and extra ecological analyses not seen in the BSocial web-tool.
Overall, with the results that have been obtained so far, and the microbial diversity analysis, we can uncover not only nitrifying microorganisms that can withstand environmental stress, but also others, such as PGPMs that can be directly used and commercialized as biofertilizers. Dissemination of the results will include 2 publications in high impact journals, and will be featured in two YouTube videos. The latter will be featured in the following website: https://jessicapurswani.wordpress.com/2020/10/06/intro-to-microbial-light/
Currently two videos are available to see the overall objectives of the Microbial Light project (https://youtu.be/2FsOTvEQ4Ak) and another on the use of BSocial (https://youtu.be/l_0MR45T7jk).
The expected results include the identification of autochthonous social microorganisms that can resist extreme microbial conditions.
The socio economic impact is the foreseeable exploitation of the projects results via the link of resistant and social microorganisms which benefit crop production, and use equivalent species to build multi-species social and resistant units which can be used as a more stable and effective biofertilizers.
Furthermore, the availability of BSocial will increase other research studies which will include micro-/organism social behaviour as an important factor for mixed population experimentation. These may include studies of beneficial biofilms in the form of probiotics, or detrimental biofilms such as those affecting human health. Other areas which could also benefit on the knowledge of multi-species units tackling singular functions are biotechnologies for: degradation of xenobiotic compounds; production of fermented foods; or generation of bio-based energy (gas, electricity, sugars).
The socio economic impact is the foreseeable exploitation of the projects results via the link of resistant and social microorganisms which benefit crop production, and use equivalent species to build multi-species social and resistant units which can be used as a more stable and effective biofertilizers.
Furthermore, the availability of BSocial will increase other research studies which will include micro-/organism social behaviour as an important factor for mixed population experimentation. These may include studies of beneficial biofilms in the form of probiotics, or detrimental biofilms such as those affecting human health. Other areas which could also benefit on the knowledge of multi-species units tackling singular functions are biotechnologies for: degradation of xenobiotic compounds; production of fermented foods; or generation of bio-based energy (gas, electricity, sugars).