Final Report Summary - PPEPSI (Precipitation pattern effects on plant-soil microbial interactions)
Objectives
The project objectives were:
1) to determine the effect of precipitation patterns on microbial community activity; and
2) to determine the effect of precipitation pattern on plant-microbial fluxes of carbon and nitrogen.
Both objectives relied on capacity building in several state-of-the-art molecular microbiology techniques, including quantitative polymerase chain reaction (qPCR), DNA and ribosomal RNA sequencing of soil bacteria and fungi (454 pyrosequencing), high-density microarrays (G3 PhyloChips).
Work performed and main results
Three main projects were set-up:
- the Avena experiment in the greenhouse,
- the Kearney experiments in the field and the greenhouse, and
- the Franz-Joseph project on available soil samples.
First, objectives 1 and 2 were addressed in the Avena experiment set-up in greenhouse conditions to subject Avena mesocosms of reconstituted natural grassland soil to precipitation treatments that contrasted in their frequency (water input every 3 - 4 days versus daily) but not in their total volume of water input, combined factorially with a fertilisation treatment. Isotopically labelled 15N root was grown and added as litter to the soil before the experiment started, to provide a tracer for plant-microbial competition for nitrogen. At the end of the experiment, the mesocosms were isotopically pulse-labelled with 13C-CO2, to trace C transfer from plants to soil and determine microorganism turnover. Microbial DNA and RNA were extracted from the soil and sequenced to assess community composition. The abundance of selected genes and transcripts was assessed using qPCR.
Increased frequency of water inputs increased the excess 13C in belowground plant biomass and soil microbial biomass, suggesting a tighter coupling between plants and soil. No evidence was found for effects of precipitation frequency on plant-microbial competition for nitrogen.
Second, the Kearney project expanded the scope of objective 1, by focusing on microbial activity during summer dry-down and first wet-up. This particular project was made possible through successful funding of a research grant by the Kearney Foundation of Soil Science, for which I was co-principal investigator. The first objective of the Kearney project followed soil microbial communities over summer dry-down and controlled rewetting to determine whether the observed patterns were consistent across three Californian grasslands with contrasting climate conditions. Bacterial and fungal DNA and RNA were extracted from the soil in three Californian grasslands over a dry-down period and subsequent controlled wet-up. Ribosomal RNA and DNA genes were sequenced, and the abundance of selected genes and transcritps was measured using qPCR, as well as soil CO2 efflux upon rewetting.
The rRNA-based bacterial community composition changed significantly as summer drought progressed, then returned to pre-drought composition within two hours of rewetting, highlighting the resilience of soil bacterial communities in California semiarid grassland soils. Moreover, despite both rRNA and ribosomal DNA gene-based bacterial community compositions being site-specific, all three sites shared a similar response pattern to dry-down and wet-up.
The second objective of the Kearney project was to determine whether soil dry-down patterns affected the subsequent wet-up response of the microbial community, which acts as catalytic controller of the rapid carbon mineralisation and associated large CO2 pulse that occurs upon rewetting a dry soil. Soil cores from one of the Californian grass-lands site was subjected to three different spring-summer dry-down treatments over four months, and the same measurements as mentioned above were performed.
The extent of drying changed the composition of the potentially active soil bacterial community. The soil dry-down pattern was reflected in the soil CO2 pulse upon rewetting, which was related to changes in the relative abundance of selected bacterial phyla and subphyla: the longer the drought, the larger the CO2 pulse emitted in the first two hours after rewetting, and the larger the changes in the composition of the potentially active bacterial community.
Third, the Franz-Josef chronosequence project was implemented to investigate the link between microbial community structure and function, over a well-defined 22 000 year chronosequence in a New Zealand water-input driven ecosystem. This project took advantage of available samples and of available technology, i.e. the high-density microarrays (G3 PhyloChips) developped at the Lawrence Berkeley National Laboratory. The G3 PhyloChips were run on bacterial and archaeal DNA extracted from available soil samples, and the abundance of several genes was assessed using qPCR. Our main findings are that soil age is a major driver of bacterial community structure, and that the pH gradient that established with soil development and aging was a major driver of nitrification and methane oxidation.
Conclusions and impact
This work shows the drought resistance of soil microbial communities that are adapted to alternating wet and dry conditions. Less frequent water inputs seem to decouple plant-soil C fluxes, but not to affect plant-microbial competition for N. Moreover, the present work highlights the extremely rapid (within hours) capacity of soil bacteria to return to pre-drought conditions, even after a prolonged period without water inputs. A major finding is the link found between the magnitude of the CO2 pulse upon wet-up to wet-up-related changes in the composition of the potentially active bacterial community. This is an important step towards predicting the carbon budget of Mediterranean grasslands under a future climate.%
The project objectives were:
1) to determine the effect of precipitation patterns on microbial community activity; and
2) to determine the effect of precipitation pattern on plant-microbial fluxes of carbon and nitrogen.
Both objectives relied on capacity building in several state-of-the-art molecular microbiology techniques, including quantitative polymerase chain reaction (qPCR), DNA and ribosomal RNA sequencing of soil bacteria and fungi (454 pyrosequencing), high-density microarrays (G3 PhyloChips).
Work performed and main results
Three main projects were set-up:
- the Avena experiment in the greenhouse,
- the Kearney experiments in the field and the greenhouse, and
- the Franz-Joseph project on available soil samples.
First, objectives 1 and 2 were addressed in the Avena experiment set-up in greenhouse conditions to subject Avena mesocosms of reconstituted natural grassland soil to precipitation treatments that contrasted in their frequency (water input every 3 - 4 days versus daily) but not in their total volume of water input, combined factorially with a fertilisation treatment. Isotopically labelled 15N root was grown and added as litter to the soil before the experiment started, to provide a tracer for plant-microbial competition for nitrogen. At the end of the experiment, the mesocosms were isotopically pulse-labelled with 13C-CO2, to trace C transfer from plants to soil and determine microorganism turnover. Microbial DNA and RNA were extracted from the soil and sequenced to assess community composition. The abundance of selected genes and transcripts was assessed using qPCR.
Increased frequency of water inputs increased the excess 13C in belowground plant biomass and soil microbial biomass, suggesting a tighter coupling between plants and soil. No evidence was found for effects of precipitation frequency on plant-microbial competition for nitrogen.
Second, the Kearney project expanded the scope of objective 1, by focusing on microbial activity during summer dry-down and first wet-up. This particular project was made possible through successful funding of a research grant by the Kearney Foundation of Soil Science, for which I was co-principal investigator. The first objective of the Kearney project followed soil microbial communities over summer dry-down and controlled rewetting to determine whether the observed patterns were consistent across three Californian grasslands with contrasting climate conditions. Bacterial and fungal DNA and RNA were extracted from the soil in three Californian grasslands over a dry-down period and subsequent controlled wet-up. Ribosomal RNA and DNA genes were sequenced, and the abundance of selected genes and transcritps was measured using qPCR, as well as soil CO2 efflux upon rewetting.
The rRNA-based bacterial community composition changed significantly as summer drought progressed, then returned to pre-drought composition within two hours of rewetting, highlighting the resilience of soil bacterial communities in California semiarid grassland soils. Moreover, despite both rRNA and ribosomal DNA gene-based bacterial community compositions being site-specific, all three sites shared a similar response pattern to dry-down and wet-up.
The second objective of the Kearney project was to determine whether soil dry-down patterns affected the subsequent wet-up response of the microbial community, which acts as catalytic controller of the rapid carbon mineralisation and associated large CO2 pulse that occurs upon rewetting a dry soil. Soil cores from one of the Californian grass-lands site was subjected to three different spring-summer dry-down treatments over four months, and the same measurements as mentioned above were performed.
The extent of drying changed the composition of the potentially active soil bacterial community. The soil dry-down pattern was reflected in the soil CO2 pulse upon rewetting, which was related to changes in the relative abundance of selected bacterial phyla and subphyla: the longer the drought, the larger the CO2 pulse emitted in the first two hours after rewetting, and the larger the changes in the composition of the potentially active bacterial community.
Third, the Franz-Josef chronosequence project was implemented to investigate the link between microbial community structure and function, over a well-defined 22 000 year chronosequence in a New Zealand water-input driven ecosystem. This project took advantage of available samples and of available technology, i.e. the high-density microarrays (G3 PhyloChips) developped at the Lawrence Berkeley National Laboratory. The G3 PhyloChips were run on bacterial and archaeal DNA extracted from available soil samples, and the abundance of several genes was assessed using qPCR. Our main findings are that soil age is a major driver of bacterial community structure, and that the pH gradient that established with soil development and aging was a major driver of nitrification and methane oxidation.
Conclusions and impact
This work shows the drought resistance of soil microbial communities that are adapted to alternating wet and dry conditions. Less frequent water inputs seem to decouple plant-soil C fluxes, but not to affect plant-microbial competition for N. Moreover, the present work highlights the extremely rapid (within hours) capacity of soil bacteria to return to pre-drought conditions, even after a prolonged period without water inputs. A major finding is the link found between the magnitude of the CO2 pulse upon wet-up to wet-up-related changes in the composition of the potentially active bacterial community. This is an important step towards predicting the carbon budget of Mediterranean grasslands under a future climate.%
