Responses of Soil Microbes to Hydrological Perturbations in Tropical Forest Soils

<p>Model projections predict that climate change impacts on the tropics will include an increased frequency of drought and precipitation cycles. Such environmental fluctuations at the soil pore-scale play an important role in shaping microbial adaptive capacity, and trait composition of a community, which feeds back on to the breakdown and formation of soil organic matter (SOM). Understanding the factors controlling the carbon balance of humid tropical forest soils remains a social imperative. Microbial feedback to SOM pools is critical. Herein, we examine the microbial response to drought perturbations across  3 different, but complementary scales. At the largest scale, we explored the impacts of drought across a 1 m precipitation gradient spanning four sites from the Caribbean coast to the interior of Panama. At each site 4, throughfall exclusion plots (10 x 10 m) were established to reduce precipitation by 50 %. In addition, 4 corresponding control plots were also constructed. At the meso-scale, we incubated intact soil cores from one of these sites (P12) under 3 different hydrological treatments (control, drought, rewetting-drying cycles) for over a 5-month period. For the field and meso-scale experiments, we evaluated changes imparted by hydrological perturbations using multi-omic approaches, and physico-chemical measurements.   In order to identify the traits involved in response to drought at the field and meso-scale, we isolated a range of bacteria to subject to stress at the scale of the single-cell and simple communities.  Cell extracts were subjected to osmotic or matric stress and the short-term physiological responses determined using non-destructive synchrotron radiation-based Fourier Transform-Infrared spectromicroscopy. Through this approach, we identified changes in metabolic allocation within different cells, in particular to the secondary metabolome of the different bacteria. Our contribution will discuss the outcomes of these multi-scale experiments.  Specifically focusing on how shifts in the microbial community and physiological changes may influence tropical soil carbon stability under future scenarios of altered drought and precipitation cycles.</p>

The ¹⁵N gas-flux method to determine N₂ flux: a comparison of different tracer addition approaches

The 15N gas-flux method allows for the quantification of N2 flux and tracing soil N transformations. An important requirement for this method is a homogeneous distribution of the 15N tracer added to soil. This is usually achieved through soil homogenization and admixture of the 15N tracer solution or multipoint injection of tracer solution to intact soil. Both methods may create artefacts. We aimed at comparing the N2 flux determined by the gas-flux method using both tracer distribution approaches. Soil incubation experiments with silt loam soil using (i) intact soil cores injected with 15N label solution, (ii) homogenized soil with injected label solution, and (iii) homogenized soil with admixture of label solution were performed. Intact soil cores with injected 15N tracer solution show a larger variability of the results. Homogenized soil shows better agreement between repetitions, but significant differences in 15N enrichment measured in soil nitrate and in emitted gases were observed. For intact soil, the larger variability of measured values results rather from natural diversity of non-homogenized soil cores than from inhomogeneous label distribution. Generally, comparison of the results of intact cores and homogenized soil did not reveal statistically significant differences in N2 flux determination. In both cases, a pronounced dominance of N2 flux over N2O flux was noted. It can be concluded that both methods showed close agreement, and homogenized soil is not necessarily characterized by more homogenous 15N label distribution.

Three-year dynamics of N2O fluxes from soil, stem and canopy in a hemiboreal forest: Impacts of floods and droughts

<p>Forests are important regulators of carbon dioxide fluxes, whereas overall greenhouse gas (GHG) budgets, in particular, nitrous oxide (N<sub>2</sub>O), are still largely unknown. No studies on ecosystem-level N<sub>2</sub>O budgets (soil and tree stem fluxes with eddy covariance (EC) measurements above the canopy) are found. Only a few examples are available on N<sub>2</sub>O emissions from tree stems. Nevertheless, estimation of the N<sub>2</sub>O and the full GHG balance in different forest ecosystems under various environmental conditions is essential to understand their impact on climate.</p><p>During the period of August 2017 to December 2019, we measured the N<sub>2</sub>O budget of a 40-yr old hemiboreal grey alder (Alnus incana) forest stand on former agricultural land in Estonia considering fluxes from the soil, tree stems and whole ecosystem. Grey alder (Alnus incana) is a fast-growing tree species typically found in riparian zones, with great potential for short-rotation forestry. Their symbiotic dinitrogen (N<sub>2</sub>) fixation ability makes alders important for the regulation of nitrogen (N) cycle in forested areas.</p><p>We measured the N<sub>2</sub>O budget considering fluxes from the soil surface (12 automated chambers; Picarro 2508), tree stems (60 manual sampling campaigns from 12 model trees with chambers at 0.1, 0.8 and 1.7 m; gas chromatographic analysis in lab) and whole ecosystem (EC technique: Aerodyne TILDAS). Simultaneously, soil water level, temperature and moisture were measured automatically, and composite soil samples were taken for physico-chemical analysis. Potential N<sub>2</sub> flux in intact soil cores was measured in the lab using the He-O incubation method.</p><p>Average N<sub>2</sub>O fluxes from the soil and tree stems varied from 1.2 to 3.0 and 0.01 to 0.03 kg N<sub>2</sub>O-N ha<sup>–1</sup> yr<sup>–1</sup>, respectively, being the highest during the wet periods, peaking during the freezing-thawing, and being the lowest in dry periods. The average annual potential N<sub>2</sub> flux in the soil was 140 kg N<sub>2</sub> ha<sup>–1</sup> yr<sup>–1</sup> which made the average N<sub>2</sub>:N<sub>2</sub>O-N ratio in the soil about 60. According to the EC measurements, the forest was a net annual source of N<sub>2</sub>O (3.4 kg N<sub>2</sub>O ha<sup>–1</sup>). Thus, the main gaseous nitrogen flux in this forest was N<sub>2</sub> emission. Our carbon (C) budget showed that the forest was a significant net annual C sink.</p><p>Results of our long-term study underline the high N and C buffering capacity of riparian alder forests. For better understanding of C and nutrient budgets of riparian forests, we need long-term, high-frequency measurements of N<sub>2</sub>O fluxes from the soil and tree stems in combination with ecosystem-level EC measurements. The identification of microorganisms and biogeochemical pathways associated with N<sub>2</sub>O production and consumption is another future challenge.</p>

Denitrification Rate and Its Potential to Predict Biogenic N2O Field Emissions in a Mediterranean Maize-Cropped Soil in Southern Italy

The denitrification rate in C2H2-amended intact soil cores and soil N2O fluxes in closed static chambers were monitored in a Mediterranean irrigated maize-cropped field. The measurements were carried out during: (i) a standard fertilization management (SFM) activity and (ii) a manipulation experimental (ME) test on the effects of increased and reduced application rates of urea at the late fertilization. In the course of the SFM, the irrigations following early and late nitrogen fertilization led to pulses of denitrification rates (up to 1300 μg N2O-N m−2 h−1) and N2O fluxes (up to 320 μg N2O-N m−2 h−1), thanks to the combined action of high soil temperatures and not limiting nitrates and water filled pore space (WFPS). During the ME, high soil nitrates were noted in all the treatments in the first one month after the late fertilization, which promoted marked N-losses by microbial denitrification (from 500 to 1800 μg N2O-N m−2 h−1) every time the soil WFPS was not limiting. At similar maize yield responses to fertilizer treatments, this result suggested no competition for N between plant roots and soil microbial community and indicated a probable surplus of nitrogen fertilizer input at the investigated farm. Correlation and regression analyses (CRA) on the whole set of data showed significant relations between both the denitrification rates and the N2O fluxes with three soil physical-chemical parameters: nitrate concentration, WFPS and temperature. Specifically, the response functions of denitrification rate to soil nitrates, WFPS and temperature could be satisfactorily modelled according to simple Michaelis-Menten kinetic, exponential and linear functions, respectively. Furthermore, the CRA demonstrated a significant exponential relationship between N2O fluxes and denitrification and simple empirical functions to predict N2O emissions from the denitrification rate appeared more fitting (higher concordance correlation coefficient) than the predictive empirical algorithm based on soil nitrates, WFPS and temperature. In this regard, the empirically established relationships between the denitrification rate on intact soil cores under field conditions and the soil variables provided local-specific threshold values and coefficients which may effectively work to calibrate and adapt existing N2O process-based simulation models to the local pedo-climatic conditions.

Advantages of multi-region kriging over bi-region techniques for computed tomography-scan segmentation

Quantifying the structure of soil is essential for developing effective soil management for farming and environmental conservation efforts. One approach to quantify soil structure is to scan intact soil cores by X-ray computed tomography (CT), which allows using computer vision algorithms to identify internal components within the soil. One commonly used approach is the colour-based segmentation of CT-scan soil images into two regions – matter and void – for the purpose of determining the soil porosity. A key problem with this approach is that soil CT images tend to be rather complicated, and thus this type of bi-region segmentation is a non-trivial problem, with algorithms following this type of bi-region approach typically performing unreliability across a variety of image sets. In this work, a technique is proposed that identifies an optimal number of regions present in the soil, rather than just two. It is claimed that this more sophisticated representation of soil structure leads to a more accurate representation than traditional bi-region segmentation; however, it is reducible to a bi-region segmentation yielding the required estimation of porosity with more accuracy and robustness than traditional methods. It is also proposed that segmentation is performed using a multi-region kriging algorithm, which establishes relationships between distance and regions that allows the segmentation to overcome many of the artefacts and noise issues associated with CT scanning. Our experiments focused on layer-by-layer segmentation and results demonstrated that the proposed approach produced segmentations consistent across a variety of scanned cores and were visually more correct than current state-of-the-art bi-region techniques.