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\begin{document}

\title{Ecosystem function associated with soil organic carbon declines with
tropical dry forest degradation}



\author[1]{Laura L. de Sosa}%
\author[2]{Inmaculada Carmona}%
\author[3]{M. Panettieri}%
\author[2]{Daniel M. Griffith}%
\author[2]{Carlos I. Espinosa}%
\author[2]{Andrea Jara-Guerrero}%
\author[3]{Cesar Plaza}%
\author[1]{Engracia Madejón}%
\affil[1]{Instituto de Recursos Naturales y Agrobiologia de Sevilla}%
\affil[2]{Universidad Tecnica Particular de Loja}%
\affil[3]{Instituto de Ciencias Agrarias}%


\vspace{-1em}



  
  \date{May 26, 2024}


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\selectlanguage{english}
\begin{abstract}
Forest degradation is increasingly recognized as a major threat to
global biodiversity and ecosystems' capacity to provide ecosystem
services. This study examined the impacts of forest degradation on soil
quality and function in a seasonally dry tropical forest (SDTF) of
Ecuador. We compared soil physical-chemical properties, enzymatic
activity, particulate organic carbon (POC) and mineral-associated
organic carbon (MAOC) along a gradient of SDTF degradation in the dry
and rainy season. Our findings showed a consistent and steady reduction
in soil quality (total C and N) and function (dehydrogenase and
\selectlanguage{greek}β-\selectlanguage{english}glucosidase activity) that paralleled the loss of vegetative structure
and diversity along the degradation gradient. Soil physical-chemical
properties were less variable and enzymatic activity was generally
higher in the dry season compared to the rainy season. We also showed
for the first time a significant and uniform decrease in POC and MAOC
with ecosystem degradation in a SDTF. The relative proportion of these
two components was constant along the gradient except for the most
degraded state (arid land), where POC was higher in proportion to MAOC,
suggesting that a functional tipping point may be crossed with extreme
forest degradation. These findings address an important knowledge gap
for SDTFs by showing a consistent loss of soil quality and functionality
with degradation and suggest that extreme degradation can result in an
alternate state with compromised resilience.%
\end{abstract}%



\sloppy


\textbf{Ecosystem function associated with soil organic carbon declines
with tropical dry forest degradation}

Laura L. de Sosa\textsuperscript{1}@, Inmaculada
Carmona\textsuperscript{2} Marco Panettieri\textsuperscript{3}, Daniel
M. Griffith\textsuperscript{2}, Carlos I. Espinosa\textsuperscript{2},
Andrea Jara-Guerrero\textsuperscript{2}, C\selectlanguage{ngerman}ésar Plaza\textsuperscript{3},
Engracia Madejón\textsuperscript{1}

\begin{enumerate}
\tightlist
\item
  \emph{Instituto de Recursos Naturales y Agrobiología de Sevilla
  (IRNAS-CSIC) Av. Reina Mercedes 10 41012 Sevilla}
\item
  \emph{Laboratorio de Ecología Tropical y Servicios Ecosistémicos
  (EcoSs-Lab), Departamento de Ciencias Biológicas y Agropecuarias,
  Universidad Técnica Particular de Loja, Loja, Ecuador}
\item
  \emph{Instituto de Ciencias Agrarias (ICA-CSIC), c/Serrano 115-dpdo,
  28006, Madrid, (Spain)}
\end{enumerate}

\textbf{@corresponding author: lauralozano@csic.es}

\textbf{Abstract.} Forest degradation is increasingly recognized as a
major threat to global biodiversity and ecosystems' capacity to provide
ecosystem services. This study examined the impacts of forest
degradation on soil quality and function in a seasonally dry tropical
forest (SDTF) of Ecuador. We compared soil physical-chemical properties,
enzymatic activity, particulate organic carbon (POC) and
mineral-associated organic carbon (MAOC) along a gradient of SDTF
degradation in the dry and rainy season. Our findings showed a
consistent and steady reduction in soil quality (total C and N) and
function (dehydrogenase and \selectlanguage{greek}β-\selectlanguage{english}glucosidase activity) that paralleled the
loss of vegetative structure and diversity along the degradation
gradient. Soil physical-chemical properties were less variable and
enzymatic activity was generally higher in the dry season compared to
the rainy season. We also showed for the first time a significant and
uniform decrease in POC and MAOC with ecosystem degradation in a SDTF.
The relative proportion of these two components was constant along the
gradient except for the most degraded state (arid land), where POC was
higher in proportion to MAOC, suggesting that a functional tipping point
may be crossed with extreme forest degradation. These findings address
an important knowledge gap for SDTFs by showing a consistent loss of
soil quality and functionality with degradation and suggest that extreme
degradation can result in an alternate state with compromised
resilience.

\textbf{Keywords (max 6):} forest degradation; seasonally dry tropical
forest; soil function; enzyme activity; POC; MAOC

\textbf{Introduction}

Forest degradation resulting from chronic anthropogenic modification of
ecosystem structure, composition or function is gaining increasing
attention as a major issue affecting human societies and biodiversity
(Ghazoul and Chazdon, 2017; Grantham et al., 2020). Degradation
compromises many of the benefits that forests provide (IPBES, 2018), and
evidence suggests that the environmental consequences of degradation are
potentially as significant as those from deforestation (Walker et al.,
2020). The effect of forest degradation on soil dynamics and function is
of particular concern given the fundamental role soils play in the
provision of multiple ecosystem services (Smith et al., 2015). Given the
scale and impacts of forest degradation resulting from chronic
disturbance, it is urgent to understand its effects on soil
functionality and the implications for ecosystem resilience.

A critical global ecosystem that has experienced widespread degradation
is seasonally dry tropical forest (SDTF) (Miles et al., 2006).
Representing 42\% of tropical ecosystems worldwide and recognized for
their high levels of endemicity, species richness, and functional
diversity (Dirzo, 2011; Banda-Rodr\selectlanguage{ngerman}íguez et al., 2016), SDTFs are
considered to be one of the most threatened ecosystems globally due to
centuries of land use conversion and chronic disturbance (Dimson and
Gillespie, 2020; Portillo-Quintero and Sánchez-Azofeifa, 2010). As in
tropical rain forests, the study of degradation has experienced a recent
upsurge in SDTFs due to a growing recognition of its widespread impacts
on biodiversity and ecosystem function (Ribeiro-Neto et al., 2016; Sfair
et al., 2018; Souza et al., 2019). The focus of most studies of
degradation in SDTFs has been on its effects on taxonomic and functional
plant diversity (Arnan et al., 2022; Jara-Guerrero et al., 2021; Ribeiro
et al., 2019; Sagar et al., 2003). However, how degradation of SDTFs
affects the conditions and ecosystem functions underpinning this
diversity, particularly those related to the soil, remains poorly
understood (Mora et al., 2018; Schulz et al. 2016).

Two important indicators of soil quality and function are soil organic
matter (SOM) content and enzyme activity. As with deforestation and land
use conversion, forest degradation drives SOM loss (Jiang et al., 2023,
Jiménez et al., 2011), which has major repercussions for the capacity of
forests to store C, cycle nutrients, and self-regenerate (Zhou et al.,
2018). However, persistent knowledge gaps exist pertaining to the
accrual, decomposition and transformation pathways of SOM (Angst et al.,
2021; Sokol et al., 2022). These knowledge gaps can be partially
addressed by comparing the different components of SOM. Recent
approaches distinguish particulate organic matter (POM) from
mineral-associated organic matter (MAOM) as two operational physical
fractions of SOM with different origins and rates of turnover (Lavallee
et al., 2020; Wiesmeier et al., 2019; Yu et al., 2022). Considered to be
primarily plant derived, POM contains many structural C compounds with
low N content and is preserved in soil via biochemical recalcitrance,
physical protection in micro aggregates, and microbial inhibition. MAOM
originates largely from soil microbes, contains higher N, and has a
longer residence time due to chemical bonding with minerals and physical
protection in small aggregates (Cotrufo et al., 2019). It is generally
assumed that POM is more accessible but its quality for decomposers
varies, whereas MAOM provides labile C and nutrients to microbiota and
plants only following destabilization. Thus, POM is considered to be
less persistent and more sensitive to disturbance than MAOM (Cambardella
and Elliott, 1992; Cotrufo et al., 2019; Poeplau et al., 2018). These
functional differences underscore the utility of quantifying POM and
MAOM separately in order to better understand the effect of forest
degradation on SOM (Lavallee et al., 2020).

Soil enzyme activity is related to SOM fluxes and can provide a useful
indicator of soil function in response to disturbance (Barbosa et al.,
2023). Among the myriad biotic (e.g., microbial community structure and
abundance, plant inputs) and abiotic (e.g., organo-mineral interactions,
soil and climatic conditions, chemical quality of C inputs) factors
influencing SOM dynamics, soil enzyme activity plays a prominent role
(Panettieri et al., 2022). For example, Bernard et al. (2022)
demonstrated that turnover rates of SOM integrated by different pools
depend on its biochemical composition and accessibility to enzymes.
Kandeler et al. (1999, 2019) identified higher rates of enzyme activity
in the MAOM fraction due to a greater contribution of microbial
compounds. Decomposition of compounds in POM depends on processes of
microbial and enzymatic inhibition, while MAOM is more subject to
spatial constraints such as mineral association (Lavallee et al., 2020).
While studies have demonstrated that enzyme activity decreases with the
conversion of STDF to agriculture (e.g., Medeiros et al., 2015; Oliveira
Silva et al., 2019), few have addressed how this crucial aspect of soil
function is affected by SDTF degradation.

In this study, we examined soil quality and function along a gradient of
ecosystem degradation in the STDF of Ecuador in the dry and rainy
season. Our objectives were to: (1) compare soil physical-chemical
properties under different levels of forest degradation between seasons;
(2) evaluate the response of dehydrogenase, \selectlanguage{greek}β-\selectlanguage{english}glucosidase and urease to
degradation to understand how enzyme activity affects soil carbon (C)
and nitrogen (N) across the degradation gradient in each season; and (3)
compare particulate organic carbon (POC) and mineral-associated organic
carbon (MAOC) along the degradation gradient to gain insights into the
underlying mechanisms of accrual, transformation and persistence of
these components of SOM. We discuss the results in the context of the
impact of forest degradation on soil functionality in SDTFs, the
relationship between this functionality and vegetative structure and
diversity, and how extreme degradation could lead to loss of ecosystem
resilience.

\textbf{2. Materials and methods}

\emph{2.1. Study area}

The study was carried out in the SDTF of southwestern Ecuador located in
Zapotillo canton within the province of Loja (Fig. 1). This ecosystem
lies within the Tumbesian biogeographic region, which extends from the
central coast of Ecuador to north-western Peru and forms part of the
Tumbes-Choco-Magdalena biodiversity hotspot (Mittermeier et al., 2011).
As a consequence of chronic anthropogenic disturbance over decades (if
not centuries), most of the original SDTF of the Tumbesian region has
been degraded or lost (Mittermeier et al., 2005; Tapia-Armijos et al.,
2015). This process of degradation has been more a consequence of
low-intensity, chronic use and disturbance of SDTF over time than
outright forest conversion to anthropogenic land uses (Jara-Guerrero et
al. 2019). The resulting landscape is a mosaic of relatively undisturbed
forest fragments, forest fragments with different levels of degradation
caused by livestock grazing, selective logging, and firewood extraction,
and highly degraded areas nearly devoid of woody vegetation
(Tapia-Armijos et al., 2015).

Annual precipitation in the study area ranges from 300-700 mm and mean
annual temperature varies between 20-26 \selectlanguage{ngerman}°C, with daily temperatures
reaching as high as 35 °C during the rainy season (Leal-Pinedo and
Linares-Palomino, 2005). The climate is highly seasonal, with a rainy
season occurring from January to April and a dry season lasting from May
to December (Espinosa et al., 2018). The period from September to
November is particularly dry with precipitation generally dropping to
below 10 mm per month (Maass and Burgos, 2011). The region is affected
by El Nin\selectlanguage{english}o/Southern Oscillation (ENSO) every 3-7 years, which brings a
dramatic rise in ocean surface temperatures and high levels of
precipitation (Trenberth, 2019).

According to the geopedological map of Ecuador, soils of the area are
primarily Inceptisols, Alfisols and Entisols and are considered eroded
and poorly evolved with low to moderate depth, low stoniness, and
textures ranging from sandy clay loam to loamy sand with some classfied
as loam or sand (Espinosa et al. 2016; MAG, 2019). Elevation of the
study sites ranges from 200 to 500 m above sea level.

\emph{2.2 Forest states}

To define the gradient of ecosystem degradation in the region, we used
the state-transition model developed by Jara-Guerrero et al. (2019).
Based on expert scientific and local knowledge, this model identifies
five states of the SDTF of Ecuador, which can be differentiated
according to vegetation structure, species diversity, and the drivers
leading to each state. These states are:

\begin{itemize}
\tightlist
\item
  \textbf{Natural forest} : High richness of woody plants and high
  canopy cover with three clear strata (arboreal, shrub and herbaceous)
  and abundant natural regeneration. Resource extraction is low and
  limited to small areas.
\item
  \textbf{Semi-natural forest} : Lower woody species richness, tree
  density and natural regeneration compared to natural forest, as well
  as higher density of herbaceous and shrub species. Persistent
  livestock grazing (primarily by goats) and/or selective logging drive
  the transition from natural to semi-natural forest over time.
\item
  \textbf{Shrub-dominated forest} : Significantly reduced woody species
  richness, tree density and regeneration. Trees are isolated or absent
  and the shrub and herbaceous strata dominate. Common species tend to
  have high wood density that likely enables them to resist browsing by
  livestock. Intensification of grazing pressure and logging trigger the
  transition from semi-natural forest to this state over time.
\item
  \textbf{Simplified forest:} Dominance of the tree layer by one or a
  few species (e.g., \emph{Handroanthus chrysanthus} or \emph{Bursera
  graveolens} ), moderate canopy cover, and regeneration of few species
  compared to natural forest. This state results from a history of land
  use favouring few species followed by a transition from
  shrub-dominated forest when livestock have been removed.
\item
  \textbf{Arid land}: Nearly complete absence of woody species except
  for isolated trees and shrubs. Herbaceous species comprise the only
  stratum and are highly seasonal, proliferating in the rainy season.
  Regeneration is low to absent and the soil is highly exposed and
  eroded. This state results from a transition from shrub-dominated
  forest when extensive livestock grazing and logging are practiced
  continually over time.
\end{itemize}

\emph{2.3. Soil sampling and chemical and enzyme analysis}

Soil samples were collected from 25 sites representing the five forest
states (Fig. 1). Sampling sites were located at least 500 m from one
another and are considered independent. Soils were sampled from each
site once in the middle of the dry season in October 2021 and once
towards the end of the rainy season in May 2022. Four samples were
extracted from the topsoil (0-10 cm) at each site and combined to
produce a composite sample. After sieving at 2 mm, samples were split
into two subsamples: the first was stored at 4 \selectlanguage{ngerman}°C prior to biochemical
analysis and the second was air dried, crushed and sieved (\textless{}60
\selectlanguage{greek}μ\selectlanguage{english}m) for chemical analysis.

Soil pH was measured in a 1 M KCl extract (1:2.5, m/v) after shaking for
one hour (Hesse, 1971) using a pH meter (CRISON micro pH 2002).
Electrical conductivity (EC) was determined in water extract (1:5, m/v)
after shaking for one hour using a Conductivity Meter (CRISON micro CM
2201). Sample dry weights were used to calculate soil water content
(SWC) by the gravimetric method. Water-soluble carbon (WSC) content was
determined using a TOC-VE Shimadzu analyser after extraction with water
using a sample-to-extractant ratio of 1:10. Dehydrogenase activity (DHA)
was determined according to Trevors (1984) after soil incubation with
p-Iodonitrotetrazolium chloride
(2-(4-Iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride,
INT) and measurement of the Iodonitrotetrazolium formazan
(1-(4-Iodophenyl)-5-(4-nitrophenyl)-3-phenylformazan, INTF) absorbance
at 490 nm. Glucosidase activity (\selectlanguage{greek}β-\selectlanguage{english}Glu) was measured according to Eivazi
and Tabatabai (1988) following soil incubation with
p-Nitrophenyl-\selectlanguage{greek}β-\selectlanguage{english}D-glucopyranoside and measurement of the p-Nitrophenol
absorbance at 400 nm. Urease activity was determined according the
method proposed by Kandeler and Gerber (1988) and modified by Kandeler
et al. (1999).

\emph{2.4 Physical fractionation of soil organic matter}

Total organic carbon (TOC) and total nitrogen (TN) were determined using
a ThermoFlash 2000 NC Soil Analyzer. For organic C analysis, carbonates
were removed from soil samples by acid fumigation with HCl prior to
analysis (Harris et al., 2001).

Soils were fractionated by size after aggregate dispersion following the
method described by Cambardella and Elliott (1992) and Sokol and
Bradford (2019). A 10.5-g portion of each sample, sieved at 2 mm, was
shaken for 18 hr in 5 g L\textsuperscript{-1} sodium hexametaphosphate,
Na\textsubscript{6}{[}(PO\textsubscript{3})\textsubscript{6}{]}. After
dispersion, samples were sieved again at 53 \selectlanguage{greek}μ\selectlanguage{english}m using a vibratory sieve
shaker (AS 200, Retsch). Soil POM and MAOM represented the fraction
remaining on the sieve (\textgreater{}53 \selectlanguage{greek}μ\selectlanguage{english}m) and that which passed
through the sieve (\textless{}53 \selectlanguage{greek}μ\selectlanguage{english}m), respectively. All fractions were
oven-dried at 60\selectlanguage{ngerman}°C, weighed, and ground with a zirconium ball mill (MM
400, Retsch) for analyses. Carbon and nitrogen contents of POM and MAOM
fractions were analysed as described for TOC and TN. Hereafter,
particulate organic and mineral-associated organic C contents are
referred to as POC and MAOC, respectively.

\emph{2.5 Statistical analysis}

To characterize the physical-chemical differences among the five forest
states and reduce these parameters to a limited number of factors, we
applied principal components analysis (PCA). Differences between states
were examined using biplots displaying the first two PCA factor scores.
To analyse the effects of ecosystem degradation and seasonality on soil
physical-chemical properties and enzymatic activity, generalized linear
models (GLMs) followed by Tukey's post hoc test were applied. The five
forest states and dry/rainy season were established as the independent
variables and soil physical-chemical variables, enzymatic activity, and
POC and MAOC fractions were the dependent variables. Given that the
interaction between forest state and season was not significant for any
of the variables, only their principal effects were interpreted.
Levene's test was applied in the GLMs to ensure that the assumption of
homogeneity of variance was met. All data are represented as means ±
standard error of the mean (SEM).

Pearson correlations were used to assess relationships between
variables. For all statistical tests, p \textless{} 0.05 was selected as
the level of significance. Statistical analyses were performed with R
version 4.2.3 (R Core Team 2023) and SPSS v25 for Windows (IBM Corp.,
Armonk, NY, USA).

\textbf{3. Results}

\emph{3.1 Soil physical-chemical properties}

PCA of the soil physical-chemical variables among the five forest states
(n\selectlanguage{english} =\selectlanguage{english} 25) identified two principal components (PC) which together
explained 87.8\% and 69.2\% of the total variance in the dry and rainy
season, respectively (Fig.~2). Represented by cluster centroids (i.e.,
the average score on both PC1 and PC2 with standard errors), the forest
states were aligned in the two-dimensional PC space along a gradient of
ecosystem degradation from natural, semi-natural, simplified and
shrub-dominated forests to arid land. In both seasons, natural and
semi-natural forest were associated with high levels of C/N, TOC, TN and
WSC as opposed to simplified forest, shrub-dominated forest and arid
land, which were associated with low levels of these parameters. In
general, these variables declined with ecosystem degradation. For
example, TOC on average showed a significant reduction of 15, 37, 54,
and 68\% and TN decreased significantly by 11, 32, 47 and 55\% from
natural forest to semi-natural, simplified, shrub-dominated forests, and
arid land, respectively (Table 1). Likewise, WSC decreased significantly
by 3, 19, 29 and 42\% along the same gradient. In contrast, SWC, pH, EC
and C/N did not decrease significantly along the gradient although arid
land was consistently and, in some cases, significantly lower than
natural and/or semi-natural forest for these variables.

In terms of seasonal differences, in the rainy season, natural,
semi-natural and simplified forest were clustered with overlapping
standard errors while shrub-dominated forest and arid land were
separated from this cluster (Fig 2). Variation in the PC1 and PC2 scores
of each forest state, as measured by the size of the centroids, was
generally greater in natural, semi-natural and simplified forest than
shrub-dominated forest and arid land and during the rainy season
compared to the dry season. The only soil properties that differed
significantly between seasons were SWC and WSC, which, on average,
increased by 42.2\% +- 5.1 and decreased by 58.7\% +- 1.4 across all
forest states from the dry to the rainy season, respectively.

\emph{3.2 Enzymatic activity}

Enzymatic activity generally declined with ecosystem degradation
although differences among forest states were more exacerbated during
the dry season (Fig. 3). Dehydrogenase and \selectlanguage{greek}β-\selectlanguage{english}glucosidase in both seasons
declined significantly and at a near constant rate with increasing
degradation from natural forest to arid land. Relative to natural
forest, dehydrogenase activity decreased by 33, 64 and 70\% on average
in simplified forest, shrub-dominated forest and arid land, respectively
for the dry season whereas for the rainy season this enzyme activity was
reduced by 11, 22, 28 and 62\% from the natural forest compared to
semi-natural, simplified, shrub-dominated forests and arid land
respectively (Fig. 3a). \selectlanguage{greek}β-\selectlanguage{english}glucosidase activity declined by 12, 41, 62
and 72\% on average for both seasons among the natural forest and the
gradient of forest degradation (Fig. 3b). In each case, the difference
between natural and semi-natural forest was not significant. Urease
activity followed the same trend, although the only significant
difference was in arid land, where the activity was approximately 63 and
72\% less on average compared to the other states for the dry and the
rainy seasons respectively (Fig. 3c).

Overall, the rainy season entailed both a reduction in soil enzymatic
activity and a weakening of the association between enzymatic activity
and most soil properties compared to the dry season. Dehydrogenase and
urease activity declined significantly by 63\% and 33\% in the rainy
season relative to the dry season across all forest states, respectively
(Fig. 3). \selectlanguage{greek}β-\selectlanguage{english}glucosidase activity also decreased in the rainy season but
this difference (12\%) was not significant. During the dry season, the
activity of the three enzymes was significantly and positively
correlated with all soil properties except the POC/MAOC ratio, which
showed a significant negative correlation, and pH, which was not
significantly correlated with urease activity (Fig. S1a). During the
rainy season, the correlation between both dehydrogenase and
\selectlanguage{greek}β-\selectlanguage{english}glucosidase activity and SWC, pH, EC and POC/MAOC was no longer
significant, while the correlation between urease activity and most
properties remained significant but less so (Fig. S1b).

\emph{3.3 Organic carbon allocation in soil organic matter fractions}

Both POC and MAOC declined along the gradient of ecosystem degradation,
whereas the POC/MAOC ratio was nearly constant across all forest states
and seasons except in arid land, where it was significantly higher (Fig.
4). POC content was significantly higher in natural and semi-natural
forest compared to other forest states by ca. 45\% on average (Fig. 4a).
MAOC content followed the same pattern, with a reduction during the dry
season of 8, 33, 56 and 54\% from natural forest to semi-natural forest,
simplified forest, shrub-dominated forest and arid land, respectively,
and a similar reduction of 21-55\% during the rainy season.

Regarding changes in SOM fractions between seasons within the same
forest state, the greatest POC losses were detected in semi-natural
forest and simplified forest (\textasciitilde{}30\%) followed by natural
forest (17\%), shrub-dominated forest (14\%) and arid land (12\%).
Losses of MAOC between seasons were less intense and no significant,
showing a decrease of 7\% for natural forest and 4\% for shrub-dominated
forest and arid land, while reaching 26\% for semi-natural and
simplified forest. POC/MAOC ratios remained constant across forest
states and seasons, with the exception of a slight but non-significant
decline of ca. 17\% from the dry to rainy season in shrub-dominated
forest and a significant increase in arid land in both seasons.

\textbf{4. Discussion}

Our results showed a consistent and steady reduction in soil quality and
function along the gradient of ecosystem degradation in SDTF. While
previous studies have shown loss of soil organic carbon (SOC) (Andrade
et al., 2020; Maestre et al., 2022; Menezes et al., 2021) and total
nitrogen (Andrade et al., 2020) resulting from the conversion of SDTF to
different land uses, few studies have focused explicitly on the soil
effects of SDTF degradation (Schulz et al., 2016). We show for the first
time a significant and uniform decrease in POC and MAOC along a broad
gradient of ecosystem degradation in SDTF. The relative proportion of
these two components of SOC was constant along the gradient except for
the most degraded state (arid land), where POC was higher in proportion
to MAOC, suggesting that a functional tipping point may be crossed in
the transition from shrub-dominated forest to arid land (Ghazoul and
Chazdon, 2017). The patterns of soil C were corroborated by a reduction
in the activity of dehydrogenase and \selectlanguage{greek}β-\selectlanguage{english}glucosidase, while those of N led
to a decrease in urease activity. These findings address an important
knowledge gap for SDTFs by showing a consistent loss of SOM and soil
functionality with degradation and suggest that extreme degradation can
result in an alternate state with compromised resilience (Oliver et al.,
2015).

\emph{4.1 Soil quality declines with ecosystem degradation}

The alignment of forest states in the PCA biplots indicates a clear
gradient of declining soil quality that parallels the decline in
vegetation biomass, complexity, and diversity from natural forest to
arid land (Jara-Guerrero et al., 2021; Ribeiro et al., 2019). Similar to
other studies that have found differences in total C and N between
undisturbed and disturbed SDTF (Andrade et al. 2020; Menezes et al.
2021; Schulz et al., 2016), these two important constituents of SOM
decreased steadily with degradation. SDTFs tend to have a larger
proportion of biomass belowground compared to wet tropical forests
(Murphy and Lugo, 1986), with high biomass of roots in the upper soil
layers, especially that of fine roots (Castellanos et al. 1991). Thus,
belowground biomass associated with the abundant woody vegetation found
in natural, semi-natural and, to a lesser degree, simplified forest, can
partly explain why these states have high C, N and WSC content as well
as a high C/N ratio relative to shrub-dominated forest and arid land.
Higher C and N stocks may also be attributed to the different quality
and quantity of the litter input in less degraded forests (Machado et
al., 2019). Furthermore, variation in the PC scores was higher in these
three states than shrub-dominated forest and arid land, likely due to
greater heterogeneity in species composition and functional diversity
between sampling sites (Ribeiro et al., 2019; Sagar et al., 2003). The
scarcity of woody vegetation in shrub-dominated forest and arid land
likely increased water stress and had a homogenizing effect on
environmental conditions (Andrade et al. 2020; Jara-Guerrero et al.,
2019; Menezes et al. 2021), which was reflected as reduced variation in
physical-chemical properties.

Plant growth flourishes in all SDTF states during the rainy season,
which probably explains the apparent mitigation of the effects provoked
by of the degradation gradient relative to the dry season. Most plants
in SDTFs shed their leaves during the dry season, contributing a high
flux of nutrients (Anaya et al. 2007) that likely exacerbated
physical-chemical differences between natural and semi-natural forest
and the other states in this season. WSC was especially high in these
two states in the dry season, accumulating in substantial quantities due
to limited leaching and decomposition in the absence of significant
rainfall. In the rainy season, such differences abated because growth in
all vegetative strata and functional types attenuated differences in
biomass and fresh organic matter among states. This was especially
evident for simplified forest, which overlapped with semi-natural forest
in the rainy season. Increased variation in PC scores in the rainy
season was also probably due to plant growth in all states, revealing
heterogeneity among sites within each state (Waring et al., 2021).
Despite these seasonal differences, the consistency in the order of
forest states in both seasons reinforces the notion that soil quality
declined along the gradient of SDTF degradation.

\emph{4.2 Enzymatic activity declines with ecosystem degradation}

The likely driver of differences in soil quality among forest states was
enzymatic activity, which decreased at a steady rate along the gradient
of SDTF degradation. In a global meta-analysis, enzyme activity was also
found to decrease due to less substrate availability in intensive
management practices (Sinsabaugh et al., 2008). The decline in enzymatic
activity found in this study paralleled that of soil C and N, which
again can be attributed to differences in vegetation biomass and
diversity among forest states. The largest declines were in
dehydrogenase and \selectlanguage{greek}β-\selectlanguage{english}glucosidase activity, indicating their usefulness as
indicators of soil quality, whereas urease activity also decreased but
not significantly, except in arid land. Likewise, Oliveria Silva et al.
(2019) found that \selectlanguage{greek}β-\selectlanguage{english}glucosidase activity was the best indicator of dry
forest conversion to agriculture in the Brazilian Caatinga. However,
Sandoval-P\selectlanguage{ngerman}érez et al. (2009) found that urease and dehydrogenase were
not good indicators of land-use effects on soil fertility in a Mexican
dry forest. Thus, while enzymatic activity can provide a useful
indicator of soil function in response to anthropic disturbance, these
studies underscore the need for further research to generalize results
for SDTFs.

The activity of all three enzymes was similar between natural and
semi-natural forest, indicating minimal loss of soil function with
moderate degradation of SDTF. In contrast, activity of dehydrogenase and
\selectlanguage{greek}β-\selectlanguage{english}glucosidase was significantly reduced in shrub-dominated forest and
arid land, and urease activity was significantly lower in arid land.
Loss of canopy cover and woody species richness in shrub-dominated
forest and arid land likely caused this severe reduction in soil
function (Singh et al., 2018). This may result from the direct effects
of plant species loss or indirect effects like increased soil erosion
and water stress due to removal of the canopy (Jara-Guerrero et al.,
2021; Singh et al., 2018). However, the results also showed that the
transition to simplified forest that occurs when livestock are excluded
from shrub-dominated forest and natural regeneration is allowed to
proceed (Jara-Guerrero et al., 2019) facilitated the recovery of
moderate levels of dehydrogenase and \selectlanguage{greek}β-\selectlanguage{english}glucosidase activity. Given that
simplified forest is species poor relative to natural and semi-natural
forest, these results suggest that a threshold of canopy cover and tree
density is more important than species diversity to recover the
functionality associated with these enzymes (Singh et al., 2018).

Higher enzymatic activity in the dry season than the rainy season was
counterintuitive, but could be explained by the exact moment soils were
sampled in each season. For the rainy season, samples were collected
near the end of the season in May when the leaf litter and SOM had
largely been decomposed and leaf fall had not yet occurred (Anaya et
al., 2007). The low quantity of substrate may explain why enzymatic
activity was significantly reduced in the rainy season. For the dry
season, soils were sampled in October following the peak of leaf fall
and after several months of accumulation of plant litter and exudates
(Anaya et al., 2007), which increase the OM content of the soil and in
the process mitigate the conditions to which soil microbes are exposed,
particularly soil moisture. Both urease and \selectlanguage{greek}β-\selectlanguage{english}glucosidase are
extracellular enzymes, meaning they can continue to function as long as
some moisture remains, even after the cells that synthesized them are
gone (Barbosa et al. 2023). Strong correlations between most soil
properties and the three enzymes indicated the importance of these
parameters for enzyme function in the dry season, whereas total N and
WSC were highly correlated with enzyme function in the rainy season,
which were likely related to OM flush events caused by rainfall (Murphy
and Lugo, 1986; Oliveria Silva et al., 2019).

\emph{4.3 Drivers of soil organic matter fractions}

The uniform decline in POC and MAOC in the same relative proportion
among forest states except arid land indicated similar effects of
degradation on both fractions. POM and MAOM are assumed to have
different C turnover rates and degrees of physical-chemical protection
owing to distinct origins (Lavallee et al., 2020; Nicol\selectlanguage{ngerman}ás et al., 2012).
Comparing these fractions between different ecosystems, Yu et al. (2022)
found that 90\% of grassland/shrubland soils stored more SOC as MAOM
than POM, whereas 40\% of forest soils exhibited a higher POM fraction,
which was attributed to the contribution of woody vegetation. Similarly,
POC was shown to be highly sensitive to soil changes resulting from the
conversion of dry forest to crops in the semiarid Chaco (Villarino et
al., 2017). Focusing on the C component in POM and MAOM, we thus
expected a proportionally larger fraction of POC in less degraded SDTF
states given its origin primarily from plants (Baldock and Skjemstad,
2000). Contrary to our expectations, however, the POC/MAOC ratio was
constant across natural, semi-natural, simplified and shrub-dominated
forests in both seasons, despite large differences in vegetative biomass
and structure among these states. This suggests that POC and MAOC were
equally susceptible to forest degradation and, in general, degradation
resulted in SOC loss despite mineral protection in soil aggregates. In
contrast, studies from other ecosystems show a decoupling of POC and
MAOC. For example, soils with high SOC tend to store more C as POC given
that MAOC reaches saturation (Cotrufo et al., 2019). In disturbed soils,
MAOC is more stable and less sensitive to disturbance (Sokol and
Bradford, 2019). However, our results support the hypothesis that the
two fractions are coupled, suggesting that microbial and plant residues
contribute to both components to a similar extent and with the same
dynamics (Angst et al., 2021; Córdova et al., 2018; Yu et al., 2022). It
is also possible that soil texture, SOC content, and precipitation play
important roles in the distribution of organic C within physically and
chemically defined pools (Haddix et al., 2020; Yu et al., 2022). Despite
significant progress toward understanding the intrinsic mechanisms of
POC and MAOC distribution and functions in soils, further research is
needed to identify the primacy of biotic versus abiotic controls on
their dynamics in SDTFs subjected to different degrees of disturbance.

The higher POC/MAOC ratio in arid land compared to the other forest
states implies a functional tipping point with extreme degradation
(Ghazoul and Chazdon, 2017). This anomaly in arid land is likely the
outcome of several related factors. First, the microbial C pump
conceptualized by Liang (2020) that transforms plant residues to POC and
finally to MAOC through microbial anabolism was probably disrupted by
the harsh biotic and abiotic conditions of this state. Functioning of
this mechanism occurs via microbial transformation of POC through
microbial biomass and ultimately conversion into MAOC. Low inputs of
leaf litter and root exudates as well as water stress inhibit microbial
activity and biomass and constrain the C pump (Liang 2020), which could
lead to changes in the proportions of POC and MAOC. Likewise, low
vegetative cover means that arid land is prone to erosion, which leads
to nutrient leaching and depletion of SOC stocks (Villarino et al.,
2017). Second, lower quality litter tends to favour the formation of POC
over MAOC (Cotrufo et al., 2013). Therefore, low litter quantity and
quality combined with water stress in arid land likely contributed low
decomposition rates (Machado et al., 2019) which, in turn, inhibited the
conversion of POC into MAOC. Third, sandier soils in arid land could
inhibit the formation of MAOC given that it tends to associate with fine
silt and clay particles (Lavallee et al., 2020; Machado et al. 2019;
Schulz et al. 2016). Any or all of these factors could result in a lower
proportion of MAOC compared to less degraded states, altering the
delicate balance between these two fractions and disrupting an important
function of SOC storage and turnover. Given the implications of this
tipping point for the resilience of the STDF ecosystem, we urgently need
to better understand the mechanism underlying this result.

\textbf{5. Conclusions}

Forest degradation is increasingly recognized as a major threat to
global biodiversity and ecosystems' capacity to provide ecosystem
services. This study contributes to our understanding of the impacts of
forest degradation on soil quality and function in SDTFs. Whereas
previous studies of this ecosystem have focused on the effects of
land-use conversion on soils, particularly agriculture, our study is
among the first to examine soil impacts of forest degradation resulting
from chronic disturbance. The effects of forest degradation might not be
as obvious as those from deforestation, but understanding them is as
important for ensuring ecosystem integrity and resilience as fathoming
the impacts of land-use change.

Our findings showed a consistent and steady reduction in soil quality
and function that paralleled the loss of vegetative structure and
diversity along a gradient of SDTF degradation. Above and belowground
conditions were clearly linked in the different forest states and
between seasons. This implies that while degradation can drive the loss
of soil C, N and enzymatic activity through the depletion of vegetation
biomass and richness, well-designed restoration strategies can help
reverse those losses.

The case of arid land, however, suggests that extreme forest degradation
could lead to an alternate state in which critical biochemical pathways
cease to function. Diminished soil quality, low enzymatic activity, and
a high POC/MAOC ratio suggested that this state lies beyond a critical
threshold of ecosystem resilience and requires serious intervention to
recover soil functionality. The question as to whether continued
disturbance to this state would lead to desertification requires urgent
attention.

\textbf{Acknowledgments}

This project was funded by LINCGLOBAL 2021 under the title Circular
economy and hydro sustainability for agriculture in vulnerable
ecosystems of Andean and Mediterranean regions (LINCGLO0013). de Sosa
thanks the Junta Andalucía and European Union for the research grant
awarded in the area of the Andalusian Research Development and
Innovation (PAIDI 2020). We are grateful to our students and technicians
(Dario Nole, Pamela Zhumi, Diego González, Carlos Avila, Christian
Mendoza, Sandro Reyes and Freddy Gutierrez) of EcoSs-Lab, Universidad
Técnica Particular de Loja who greatly assisted with soil sampling in
the field and the technicians (Noelia Gonzalez, Cristina García de
Arboleya, Patricia Puente and Carmen Navarro) of the ICA-IRNAS, CSIC
team for their help in laboratory analysis. Funding for this study was
provided in part by the Concurso Ecuatoriano de Proyectos CEPRA research
grant XV-2021-017.

\textbf{Declarations}

\textbf{Conflict of interest} The authors declare that there is no
conflict of interest

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