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Effect of land use induced shifts in soil microbial diversity and function on carbon cycling in soil

Periodic Reporting for period 1 - Terra-Micro-Carbo (Effect of land use induced shifts in soil microbial diversity and function on carbon cycling in soil)

Reporting period: 2015-07-14 to 2017-07-13

Rationale: The need for food and energy for the growing human population has led to an immense pressure on the planet’s soil resources. Intensive land use practices have been applied to improve food production. Many studies suggest that such practices lead to loss of soil organic carbon (C) – a relatively large C pool with a fast response time. Thus, there is a need to manage soils sustainably in order to mitigate atmospheric CO2 levels while maintaining agricultural productivity. Soil microorganisms act as gatekeepers for soil-atmosphere C exchange by regulating the storage and release of organic C in soil through decomposition of soil and plant derived resources. However, there is a lack of understanding on how land use induced shifts in soil microbial diversity and functionality affects these soil C cycling processes, necessitating more detailed research on the microbial mechanisms driving soil C gains and losses in response to land use.

Overall objective of the project was to discern the effects of land use on soil microbial diversity and function, specifically addressing whether differences in communities lead to differences in soil C storage. The novelty of this research project was that it aimed to provide direct evidence to prove diversity-function linkages and gain mechanistic understanding of the physiological responses of soil microbial communities to land use change. The question we addressed were:
Q1: What is the effect of land use on soil microbial taxonomic and functional diversity in differing soil types? What factors are driving this shift?
Q2: Does this shift have implications for soil carbon cycling? Do certain microbial functional groups have a greater capacity for soil carbon storage?
We used existing metagenomics data from eight geographically distributed soils at opposing ends of a landscape soil pH gradient and evaluated its functional differences. The large differences in soil bacterial taxonomic richness at opposite ends of a pH gradient were not strongly reflected in functional richness. However, consistent changes in the abundance of related functional genes were observed, characteristic of differential ecological and nutrient acquisition strategies between high pH and anaerobic low pH soils (figure 1). Our assessment at opposing ends of a landscape soil gradient encapsulates the limits of soil functional diversity in temperate climates, and identifies key pathways which may serve as indicators for soil element cycling and C storage processes in other soil systems. These results have been published in an open access journal ‘mBio’.

Soils collected from across Britain were used for a landscape scale assessment of microbial functional traits that were then linked to soil C. A subset of 3 sites with a land use contrast in each was used in a small-scale experiment aimed at examining the temporal trends of microbial functional traits. Results from these experiments are quite novel and will be published in a highly-reputed journal very soon. We discern two distinct pH-related mechanisms of soil carbon storage and highlight that the response of these mechanistic indicators is shaped by the environmental context. Land use intensification in low pH soils that increases soil pH above a threshold value (~ 6.2) leads to loss of carbon due to increased microbial degradation as a result of lower acid retardation of plant organic matter decomposition. On the contrary, the loss of carbon through intensification in high pH soils was linked to decreased microbial biomass and reduced microbial growth efficiency. This was in turn linked to tradeoffs with stress alleviation and resource acquisition. We conclude that more extensive land management practices at higher soil pH have greater potential for soil carbon storage through increased microbial metabolic efficiency, whereas in organic acidic soils abiotic factors exert a greater influence.
From the landscape scale metagenomics data, we link taxonomy to function and highlight the bacterial physiological adaptations to life in contrasting soil habitats. We’ve made this data as well as the raw sequences freely available, which given the geographic scale of our sampling may be of value in future studies assessing the novel genetic diversity of a wide range of soil functional attributes. From the land use study, we present landscape scale empirical links of microbial ecophysiological traits with soil C suggesting a key microbial role in belowground carbon cycling. We also provide a novel mechanistic understanding of the microbial physiological trade-offs that determine the proportion of organic C biomass investment, which has consequences to soil C storage. This knowledge will not only help scientist and climate modellers understand soil microbial processes better and improve predictions to environmental change, but will also help relevant stakeholders in designing and implementing effective land management strategies to maximise plant productivity while mitigating the effects of climate change.
Varying ecological and nutrient acquisition strategies of microbes in high and low pH soils