The ecology of heterogeneity: soil bacterial communities and C dynamics

International audienc

Isothermal microcalorimetry provides new insight into terrestrial carbon cycling

Energy is continuously transformed in environmental systems through the metabolic activities of living organisms, but little is known about the relationship between the two. In this study, we tested the hypothesis that microbial energetics are controlled by microbial community composition in terrestrial ecosystems. We determined the functional diversity profiles of the soil biota (i.e., multiple substrate-induced respiration and microbial energetics) in soils from an arable ecosystem with contrasting long-term management regimes (54 years). These two functional profiling methods were then related to the soils' microbial community composition. Using isothermal microcalorimetry, we show that direct measures of energetics provide a functional link between energy flows and the composition of below-ground microbial communities at a high taxonomic level (Mantel R = 0.4602, P = 0.006). In contrast, this link was not apparent when carbon dioxide (CO2) was used as an aggregate measure of microbial metabolism (Mantel R = 0.2291, P = 0.11). Our work advocates that the microbial energetics approach provides complementary information to soil respiration for investigating the involvement of microbial communities in below-ground carbon dynamics. Empirical data of our proposed microbial energetics approach can feed into carbon-climate based ecosystem feedback modeling with the suggested conceptual ecological model as a base

Habitat constraints on the functional significance of soil microbial communities

Habitat constraints on the functional significance of soil microbial communities. EGU 2017, European Geophysical Union General Assembly 201

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with otherdrivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Grampositive/ Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change

Long-term ley and manure managements have consistent effects on microbial functional profiles and organic C groups across soils from a latitudinal gradient

Soil organic matter (SOM) is important in maintaining soil fertility and other ecosystem functions. Yet, land management in intensive agriculture has caused SOM level to decrease, with knock-on effects for soil fertility and quality. Therefore, land management options that ensure that SOM is not depleted and that soil functions are better sustained are of increasing interest. However, there is limited knowledge on how different land managements affect the composition of SOM and associated microbial functional profiles. Twelve long-term field experiments, covering a wide range of climatic zones and soil types, were selected in Sweden. They focused on the role of combining ley in crop rotations with the manure application (livestock farm), as opposed to the management without ley and receiving only inorganic fertilizer (arable farm). In ten out of the 12 study sites, livestock farm management tended to have higher proportions of aliphatic and double bonded C groups, as estimated by mid-infrared spectroscopy. This was further confirmed by C-13 NMR analysis, which found greater proportions of O-alkyl and di-O-alkyl groups and less aromatic C in livestock farm than arable farm management in five of the eight sites analyzed. The changes in SOM composition were reflected in microbial functional profiles across many sites: soils from livestock farm management utilized more carbohydrates and amino acids, while polymer and aromatic compounds were associated with arable farm management. Overall, shifts in both microbial functional profiles and SOM composition showed great consistency across geographical and climatic zones. Livestock farm management maintained higher levels of microbial functional diversity and were associated with higher proportions of "reactive" C functional groups. Our investigation demonstrates that livestock farm management could maintain soil fertility over the long-term via the changes in SOM composition and the regulation of microbial functional profiles

Potential energetic return on investment positively correlated with overall soil microbial activity

Microbial communities are a critical component of the soil carbon (C) cycle as they are responsible for the decomposition of both organic inputs from plants and of soil organic C. However, there is still no consensus about how to explicitly represent their role in terrestrial C cycling. The objective of the study was to determine how the molecular and energetic properties of readily available organic matter affect the metabolic activity of the resident microbial communities in soils. This was achieved by cross-amending six soils, taken from woodland and grassland sites along an urban pressure gradient, with organic matter extracted from the same six soils and measuring heat dissipated due to the increase in microbial metabolic activity. The energetic properties of the organic matter were used to estimate a potential energetic return on investment (ROI) that microbial communities could obtain from the transformation of the organic matter. Specifically, the ROI was calculated as the ratio between the total net energy available (ΔE) and the weighted average standard state Gibbs energies of oxidation half reactions of organic C (ΔG°Cox). ΔE was measured as the heat of combustion using bomb calorimetry. ΔG°Cox was estimated using the average nominal oxidation state of C (NOSC) of the molecular species in the organic matter. The overall metabolic activity of microbial communities was positively related to the potential energetic return on investment but no significant relationship was found with the molecular diversity of organic matter. The temporal differences in metabolism across soils indicate that bacterial communities do not exploit the potential energetic return on investment in the same way: the suburban grassland communities responded more rapidly and the suburban woodland communities more slowly to the organic matter additions than the other communities. The urban gradient did not affect the properties of the molecular or energetic properties of the organic matter nor the response of the microbial communities to the organic matter additions. However, the organic matter from the grassland soils caused soils to dissipate 36.4% more heat than organic matter from the woodland soils. The metabolic response was also more rapid after the addition of grassland organic matter: the time taken for half the heat to be dissipated was 6.4 h after the addition of grassland organic matter and 6.1 h after the addition of woodland organic matter. Overall, our results suggest that microbial communities preferentially use organic matter with a high potential energetic return on investment, i.e. organic molecules that do not require high cost associated with catalysis whilst yielding a high net energetic benefit

Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate

Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion Lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it

Emergent properties of microbial activity in heterogeneous soil microenvironments:Different research approaches are slowly converging, yet major challenges remain

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gases. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale). For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. In terms of microbial aspects, whereas a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because relevant experimental data are extremely scarce. For the overall research to move forward, it will be crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead