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Drivers of soil biophysical processes along an elevational gradient at Pico de Orizaba volcano, Mexico


Elevational gradients are characterized by major shifts in environmental conditions, reflected through changes in climatic and soil variables. These shifts strongly impact the composition, community structure and specific functional traits of vegetation. Vegetation, in turn, influences soil properties through litter input, root growth and the release of root exudates, thereby influencing soil microbial and faunal communities. Here, we report and briefly describe data of soil and underlying bedrock physical and chemical properties, climatic variables, plant community composition and species abundance, soil microbial diversity and macro and mesofaunal abundance and diversity. Data are provided for 6 elevations (3400–4600 m) ranging from pine forest to alpine prairie. We focused on soil biophysical properties beneath several keystone or community-structuring plant species with different growth forms: (1) tree (Pinus hartwegii Lindl.); shrub (Oxylobus arbutifolius (Kunth) A. Gray and Chionolaena lavandulifolia (Kunth ex Kunth) Benth. & Hook.f. ex B.D.Jacks.); and (3) herb (Lupinus montanus Kunth and Senecio roseus Sch.Bip.). These data are useful for understanding how shifts in abiotic conditions and vegetation communities along an elevational gradient affect soil ecosystem services such as water infiltration, soil aggregation and carbon (C) storage, and modify soil biodiversity. The collected data also provide useful information to understand how alpine vegetation, soil macro- and meso-fauna, and soil bacterial communities may shift under a climate change scenario.


Elevational gradients and the associated biotic and abiotic changes provide useful frameworks to elucidate the drivers behind species distribution and their response to climate change (Cruz-Maldonado et al. 2021; Fukami and Wardle 2005; McCain and Grytnes 2010). Environmental factors such as temperature, radiation, and precipitation shift with altitude and strongly influence soil biophysical properties, including soil structure and moisture. Plant communities also change along altitudinal gradients, further modifying soil properties through litter and root carbon (C) inputs, thereby affecting soil biodiversity. Here, we collected belowground and aboveground data to elucidate the mechanisms through which altitude and the associated shifts in climate and vegetation affect soil properties and ecosystem processes, at different elevations.

The ecosystem services provided by (sub)alpine soils, e.g., C sequestration, nutrient cycling, and water retention, are threatened by a changing climate and land use conversion, as high mountains are particularly fragile ecosystems (Mountain Research Initiative 2015). These ecosystem services depend on soil physicochemical properties, its biodiversity, as well as on plant species composition and community structure. Therefore, our dataset includes data on soil porosity and aggregate stability at different soil depths and altitudinal levels and measurements of soil water infiltration and retention, which will allow a better understanding of the water flow dynamics along this Neotropical altitudinal gradient. We also collected data on soil macro- and meso-fauna diversity, as well as on microbial communities at the bulk soil and rhizosphere level, thus allowing researchers to explore the biotic and abiotic drivers behind soil biodiversity, which is key in mediating soil biophysical processes (Collins et al. 2020; Hernández-Cáceres et al. 2022). This dataset complements the already published data from our twin study in France (Stokes et al. 2021) and represents the largest freely available collection of data on plant traits, soil physicochemical variables and soil biodiversity along a 1200 m elevational gradient in a Neotropical climate. Methods for data collection and analysis are provided in the data files and supplementary materials (Table 1).

Table 1 Overview of data files/data sets. Pico de Oizaba, Mexico


Our objective was to determine how changes in environmental conditions with altitude affect edaphic properties, vegetation, and soil microbial and faunal communities, by collecting data along a 1200 m long gradient between 3400 and 4600 m.a.s.l. on the North-East flank of the highest mountain of Mexico, Pico de Orizaba volcano. A twin study with the same objective was carried out at Massif de Belledonne, in the French Alps.


Data file 1 shows an aerial map of the whole protected area named “Área Natural Protegida Pico de Orizaba (ANPPO)”, within which our study sites are located. Data file 1 also provides the names and numbers of each plot, with their respective coordinates and elevations. The studied elevational gradient lies on the North-East flank of Pico de Orizaba, the highest peak of Mexico. We hereby present data collected in 2017 and 2018, at six altitudes (elevational bands of 200 m each) along an elevational gradient ranging from 3400 to 4600 m.a.s.l. and from 3400 to 4400 m.a.s.l. for soil profile and soil moisture (Data files 2 and 4, respectively), at Pico de Orizaba volcano, Mexico. Climatic data (Data file 3) are also provided and were measured over 2 years (2018–2020).

The underlying bedrock is composed of intermediate to acid lavas and pyroclastic (volcaniclastic) material. Soil profiles were described for each altitudinal level (two soil profiles made per altitudinal band). Soil physico-chemical properties were analyzed from each identified soil horizon. The main soil units correspond to Endosilandic Andosols at Sleketic Regosol. The volumetric and tension soil moisture, as well as the soil surface temperature were monitored for one year, in six soil profiles distributed along the altitudinal gradient (Data file 4).

To obtain the floristic list of our study site, five 20 × 20 m plots were established at each altitude (every 200 m along our 1000 m long elevational gradient) up to 4000 m of elevation, to include keystone and community-structuring species with different growth forms: Pinus hartwegii (tree), Oxylobus arbutifolius and Chionolaena lavandulifolia (shrubs), and Lupinus montanus and Senecio roseus (herbs). From 4200 m.a.s.l. and above, the distance between our plots had to be reduced to 5 m for space availability reasons (mountain tapering). A botanical survey was performed inside each plot (Data file 5) and one adult individual of each structuring species was selected per plot. At the limit of the individual’s canopy on the downslope side, infiltration tests were performed to estimate water flow through soil and hydraulic conductivity of the quasi-steady phase was calculated (Data file 6). Aggregate stability measurements were made from soil blocks (10 × 10 × 15 cm depth) taken beside the monoliths (Data file 7). An earthworm survey was made on soil monoliths of 0.25 × 0. 25 × 0.15 m in the field to link the abundance of these ecosystem engineers with soil processes (Data file 8). To investigate the relationships between soil biophysical properties and vegetation, plant community composition was described in a 1 m2 subplot within each plot, which was established near each structuring species (Data file 10). Soil texture, bulk and real density, cationic exchange capacity, pH, electric conductivity, organic C, nitrogen (N) content, nitrate and ammonium concentrations, total and available phosphorus (P), and macronutrients (Ca, Mg, K, Na) concentrations were determined on pooled soil samples harvested within each monolith (Data file 9). A soil monolith (0.25 m × 0.25 m × 0.15 m depth) was excavated within each subplot (n = 83). Above the monolith, litter layer thickness and aboveground biomass per species were measured (Data file 10). Soil samples were collected from the monolith and from rhizospheric soil attached to fine roots of the three structuring plant species. DNA was extracted from these soil samples and 16S rDNA amplicon sequences were obtained to determine the changes in bacterial communities at the bulk soil and at the rhizosphere level along the elevational gradient (Data file 11). Soil mesofauna was collected beside each monolith from litter and soil with a cylinder (5 cm diameter and 10 cm high) and then extracted with a Berlese funnel in the laboratory. All the organisms were kept in 70% alcohol and identified at order taxonomical level, except for Collembola for which identification was made at the family level (Data file 12). Soil macroinvertebrates were hand-sorted from each monolith and fixed in 70% ethanol, except earthworms, which were fixed in 96% ethanol for the DNA barcoding. Macroinvertebrates were identified at the order level, except for earthworms for which morphological diagnoses were combined with DNA barcoding to obtain species level assignations. Invertebrates within each taxon were counted and weighed (Data file 13).


Although this dataset comprises a large number of field and laboratory data collected from 83 monoliths in 30 plots, it was not always possible to include all structuring species within the same plot. At higher altitudinal levels (4000–4400 m.a.s.l.), additional shrub and herbaceous species were sometimes included (S. roseus and C. lavandulifolia) to complement the data when L. montanus and O. arbutifolius were not present. Moreover, our focus on some keystone/structuring plant species does not allow generalization of rhizosphere processes under other species. Finally, our datasets do not provide information on plant functional traits nor on soil microbial functional diversity (i.e., enzymatic activities or microbial gene transcripts), the latter being a key factor to understand soil functioning as microorganisms are main contributors to soil biophysical processes.


Our data allow researchers to elucidate the changes in soil ecosystem services and their link with soil biodiversity along an altitudinal gradient in the Neotropical region, where high mountain ecosystems have been poorly studied. Under a climate change context, these data are particularly useful to improve our predictions of possible shifts in vegetation and soil organisms.

Availability of data and materials

The data described in this Data note can be freely and openly accessed on Please see Table 1 for details and links to the data.



Meters above sea level


  • Collins CG, Spasojevic MJ, Alados CL, Aronson EL, Benavides JC, Cannone N, Caviezel C, Grau O, Guo H, Kudo G, Kuhn NJ, Müllerová J, Phillips ML, Pombubpa N, Reverchon F, Shulman HB, Stajich JE, Stokes A, Weber SE, Diez JM. Belowground impacts of alpine woody encroachment are determined by plant traits, local climate and soil conditions. Glob Change Biol. 2020;26:7112–27.

    Article  Google Scholar 

  • Cruz-Maldonado N, Weemstra M, Jiménez L, Roumet C, Angeles G, Barois I, Santos Los de M, Morales-Martinez MA, Palestina RA, Rey H, Sieron K, Stokes A, Anthelme F. Aboveground-trait variations in 11 (sub)alpine plants along a 1000-m elevation gradient in tropical Mexico. Alpine Bot. 2021.

    Article  Google Scholar 

  • Fukami T, Wardle DA. Long-term ecological dynamics: reciprocal insights from natural and anthropogenic gradients. Proc Royal Soc b Biol Sci. 2005;272:2105–15.

    Article  Google Scholar 

  • Hernández-Cáceres D, Stokes A, Angeles-Alvarez G, Abadie J, Anthelme F, Bounous M, Freschet GT, Roumet C, Weemstra M, Merino-Martín L, Reverchon F. Vegetation creates microenvironments that influence soil microbial activity and functional diversity along an elevation gradient. Soil Biol Biochem. 2022;165:108485.

    Article  CAS  Google Scholar 

  • Mccain C, Grytnes JA. Elevational gradients in species richness. Encycl Life Sci. 2010.

    Article  Google Scholar 

  • Mountain Research Initiative EDW Working Group. Elevation-dependent warming in mountain regions of the world. Nature Clim Change. 2015;5:424–30.

    Article  Google Scholar 

  • Stokes A, Angeles G, Anthelme F, Aranda-Delgado E, Barois I, Bounous M, Cruz-Maldonado N, Decaëns T, Fourtier S, Freschet GT, Gabriac Q, Hernández-Cáceres D, Jiménez L, Ma J, Mao Z, Marín-Castro BE, Merino-Martín L, Mohamed A, Piedallu C, Pimentel-Reyes C, Reijnen H, Reverchon F, Rey H, Selli L, Siebe-Grabach CD, Sieron K, Weemstra M, Roumet C. Shifts in soil and plant functional diversity along aaltitudinal gradient in the French Alps. BMC Res Notes. 2021;14:54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Funding was provided by the French and Mexican governments (ECOPICS project, ANR–16-CE03-0009 and CONACYT–2 73659).

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Correspondence to Guillermo Angeles.

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Angeles, G., Álvarez-Jiménez, M., Anthelme, F. et al. Drivers of soil biophysical processes along an elevational gradient at Pico de Orizaba volcano, Mexico. CABI Agric Biosci 4, 4 (2023).

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