DOI: 10.5061/dryad.gb5mkkwws
title: Biogeochemical cycles in holm oak dehesas

description: In anthropic savannah ecosystems from the Iberian Peninsula (i.e.,
 dehesa), complex interactions between climate change, pathogen outbreaks
 and human land use are presumed to be behind the observed increase in holm
 oak decline. These environmental disturbances alter the plant-soil
 microbial continuum, which can destabilize the ecological balance that
 sustains tree health. Yet, little is known about the underlying
 mechanisms, particularly the directions and nature of the causal-effect
 relations between plants and soil microbial communities.  In this
 study, we aimed to determine the role of plant-soil feedbacks in
 climate-induced holm oak decline in the Iberian dehesa. Using a gradient
 of holm oak health, we reconstructed key soil biogeochemical cycles
 mediated by soil microbial communities. We used quantitative microbial
 element cycling (QMEC), a functional gene-array-based high-throughput
 technique to assess microbial functional potential in carbon (C),
 nitrogen (N), phosphorous (P), and sulfur (S) cycling.  The onset
 of holm oak decline was positively related with the increase in relative
 abundance of soil microbial functional genes associated with
 denitrification and phosphorous mineralization (i.e., nirS3, ppx and pqqC;
 parameter value: 0.21, 0.23 and 0.4; p&lt;0.05). The structural
 equation model (ꭓ2 = 32.26, p-value = 0.73), moreover, showed a negative
 association between these functional genes and soil nutrient availability
 (i.e., mainly mineral nitrogen and phosphate). Particularly, the holm oak
 crown health was mainly determined by the abundance of phosphate
 (parameter value=0.27; p-value&lt;0.05) and organic phosphorus
 (parameter value=-0.37; p-value&lt;0.5).  Hence, we propose a
 potential tree-soil feedback loop, in which the decline of holm oak
 promotes changes in the soil environment that trigger changes in key
 microbial-mediated metabolic pathways related to the net loss of soil N
 and P mineral forms. The shortage of essential nutrients, in turn, affects
 the ability of the trees to withstand the environmental stressors to which
 they are exposed. 
description: These data have been collected in holm oak dehesas. To account for the soil spatial heterogeneity,
 three different soil samples were collected below each of the 162 holm oak
 trees at a distance of 1 m from each trunk. The depth at which we
 collected the soil was determined by the depth where the shallowest holm
 oak fine root density peak was located. As we collected both the soil and
 the roots at the same depth, and this holm oak root depth was affected by
 the presence of the herbaceous root layer and historical land management
 practices, we excavated until we reached the soil layer predominantly
 containing holm oak roots. This typically occurred at an average depth of
 15 cm and generally did not exceed 30 cm. Then, the three soil subsamples
 were pooled in one single composite sample that was maintained at 4°C
 (12h) until processing in the laboratory. These soil samples were then
 used to do soil chemical analyses and to quantify soil microbial
 functional genes. Specifically, for the soil chemical analyses, the 162
 soil samples were dried at room temperature (~20ºC), sieved using a 2-mm
 mesh size and stored in darkness (cf. section 2.4.). Regarding the
 analysis of soil microbial functional genes, aliquots from the 162 soil
 samples were frozen at -20ºC just upon arrival at the laboratory every day
 after sampling and stored in darkness for approximately one month after
 sampling, until DNA extraction (cf. section 2.5.). 
description: # Biogeochemical cycles in holm oak dehesas
 [https://doi.org/10.5061/dryad.gb5mkkwws](https://doi.org/10.5061/dryad.gb5mkkwws) ## Description of the data and file structure This dataset contains data from 9 holm oak dehesas (n=162 trees) in which holm oak leaf biochemistry (photosynthetic performance index, chlorophylls, VAZ and total tocopherols), root functional parameters (fine root branching, fine root length and fine root diameter), soil functional genes (carbon, nitrogen, phosphorus and sulfur cycling) and soil chemistry (mineral nitrogen, phosphate, potassium, organic carbon, organic nitrogen, organic phosphorus and pH) are related. The dataset includes: **Aboveground leaf parameters:** * Photosynthetic performance index (PiAbs), as a proxy of the photosynthetic energy conservation. * Chlorophylls (Chl a + b, μmol m<sup>-2</sup>), as a proxy of light harvesting regulation and plant acclimation. * Violaxanthin cycle pigment pool (VAZ, violaxanthin + zeaxanthin + antheraxanthin, mmol mol Chl<sup>-1</sup>), as proxy photoprotective compounds through thermal dissipation. * Total tocopherols (mmol mol Chl<sup>-1</sup>), as a proxy of antioxidant compounds. * Defoliation (%), as a proxy of crown transparency. * Crown health. Is the linear combination of the variables mentioned above. **Belowground root parameters:** * Fine root branching. * Fine root leghth (cm). Mean length of the fine roots. * Fine root diameter (cm). Mean diameter of the fine roots. **Soil chemical analyses** * Total organic carbon content (org. C), total organic nitrogen content (org. N) and total organic phosphorus content (org. P). These analyses were expressed as mg of organic C, N or P per 100 mg of soil (%). * Mineral N (ammonium+nitrate+nitrite) was expresed as ppm, μg per g. * Phosphate was expresed as ppm, μg per g. * Potassium was expresed as ppm, μg per g. * pH **Soil microbial functional genes** * Carbon hydrolysis genes (i.e., genes involved in starch, hemicellulose, cellulose, chitin, pectin and lignin degradation). abfA, manB, Xyl, cex, pgu, glx, lig, mnp, apu, iso-plu, ammiA, sga, chiA * Carbon fixation genes. aclB,accA, mcrA, pccA, korA, smtA, frdA, rbcL, acsB, acsA, acsE. * Methane oxidation. pmoA, mmoX, mxaF, pqq-mdh * Nitrogen cycling (i.e., genes involved in N fixation, nitrification, denitrification, ammonification, anaerobic ammonium oxidation, assimilatory and dissimilatory N reduction and organic N mineralization. nifH, amoA1, amoA2, amoB, ureC, gdhA, hao, nxrA, nirS, nirK, nosZ, hzsB. * Phosphorus cycling genes (i.e., mineralization, solubilization, biosynthesis and hydrolysis of phosphorus). gcd, pqqC, phoD, phoX, phnK, ppx, ppk. * Sulfur cycling genes. soxY, yedZ, dsrA, dsrB, apsA. These genes were expresed as the abundance, gene copy number relative to 16S. The primer pairs and the encoded enzymes of the analyzed soil microbial functional genes may be found in the electronic supplementary material published in Table S2 of the manuscript.