Ecology
rbudhathoki1
atmosphericnitrogenpollution.pdf
RESEARCH ARTICLE
Mapping Portuguese Natura 2000 sites in risk
of biodiversity change caused by atmospheric
nitrogen pollution
Pedro Pinho 1,2☯*, Teresa Dias1☯, Cláudia M. d. S. Cordovil3, Ulrike Dragosits4, Nancy
B. Dise 4 , Mark A. Sutton
4 , Cristina Branquinho
1
1 cE3c, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 2 CERENA, Centro de Recursos Naturais e Ambiente, Instituto Superior Técnico,
Universidade de Lisboa, Portugal, 3 LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada
da Ajuda, Lisboa, Portugal, 4 NERC Centre for Ecology & Hydrology (CEH), Edinburgh Research Station,
Bush Estate, Penicuik, Midlothian, United Kingdom
Abstract
In this paper, we assess and map the risk that atmospheric nitrogen (atN) pollution poses to
biodiversity in Natura 2000 sites in mainland Portugal. We first review the ecological impacts
of atN pollution on terrestrial ecosystems, focusing on the biodiversity of Natura 2000 sites.
These nature protection sites, especially those located within the Mediterranean Basin, are
under-characterized regarding the risk posed by atN pollution. We focus on ammonia (NH3)
because this N form is mostly associated with agriculture, which co-occurs at or in the imme-
diate vicinity of most areas of conservation interest in Portugal. We produce a risk map inte-
grating NH3 emissions and the susceptibility of Natura 2000 sites to atN pollution, ranking
habitat sensitivity to atN pollution using expert knowledge from a panel of Portuguese eco-
logical and habitat experts. Peats, mires, bogs, and similar acidic and oligotrophic habitats
within Natura 2000 sites (most located in the northern mountains) were assessed to have
the highest relative risk of biodiversity change due to atN pollution, whereas Natura 2000
sites in the Atlantic and Mediterranean climate zone (coastal, tidal, and scrubland habitats)
were deemed the least sensitive. Overall, results allowed us to rank all Natura 2000 sites in
mainland Portugal in order of evaluated risk posed by atN pollution. The approach is of great
relevance for stakeholders in different countries to help prioritize site protection and to define
research priorities. This is especially relevant in countries with a lack of expertise to assess
the impacts of nitrogen on biodiversity and can represent an important step up from current
knowledge in such countries.
Introduction
Atmospheric N pollution
Nitrogen (N) pollution is a major environmental challenge [1, 2]. Without the use of N-con-
taining fertilizers, the human population would have been approximately half of its current
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 1 / 19
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OPEN ACCESS
Citation: Pinho P, Dias T, Cordovil CMd.S,
Dragosits U, Dise NB, Sutton MA, et al. (2018)
Mapping Portuguese Natura 2000 sites in risk of
biodiversity change caused by atmospheric
nitrogen pollution. PLoS ONE 13(6): e0198955.
https://doi.org/10.1371/journal.pone.0198955
Editor: Julian Aherne, Trent University, CANADA
Received: November 25, 2017
Accepted: May 28, 2018
Published: June 21, 2018
Copyright: © 2018 Pinho et al. This is an open access article distributed under the terms of the
Creative Commons Attribution License, which
permits unrestricted use, distribution, and
reproduction in any medium, provided the original
author and source are credited.
Data Availability Statement: All relevant data are
within the paper and its Supporting Information
files.
Funding: We are grateful for the funding through
the project ‘NitroPortugal: Strengthening
Portuguese research and innovation capacities in
the field of excess reactive nitrogen’, funded by EU
H2020-TWINN-2015 692331 and Fundação para a Ciência e Tecnologia (FCT) through the Post- Doctoral grants SFRH/BPD/75425/2010 to Pedro
Pinho and SFRH/BPD/85419/2012 to Teresa Dias,
size [1], but 50–75% of the N applied in agriculture is not taken up by crops. This excess is lost
to the environment, affecting human health, air, water, soil, climate, and ecosystems’ stability
and biodiversity. In Europe alone, this represents an estimated societal cost of 70–320 billion
Euros per year [3]. Humankind’s intervention in the N cycle is considered to have already
crossed the Earth’s ecological safety boundary, thus threatening our own security [2]. How-
ever, the demand for more food and energy due to increasing population and changing con-
sumption patterns hampers the efforts of reducing N emissions [1].
Most of the observed increase in deposited N take two main forms: reduced N (NHy: NH3
and NH4 + ), primarily from volatilized agricultural emissions, and oxidized N (NOx: nitric
acid, particulate nitrate, etc.), primarily from fossil fuel combustion. These different N forms
can be deposited by both dry and wet deposition, in proportions that depend on their relative
concentrations, precipitation patterns, and environmental drivers of biosphere-atmosphere
exchange [4, 5]. Although an approximately 50% decrease in European NOx deposition has
been achieved since the 1980s, progress in reducing NHy deposition has been much slower.
This is especially true for the Iberian Peninsula, which has become a significant meat-export-
ing region [6, 7], an activity that releases high levels of reduced nitrogen through excrement
and fertilizer used to produce animal feed. The ongoing revision of the EU National Emissions
Ceilings Directive [8] proposes a 69% reduction in NOx emissions and 27% reduction in NH3
emissions by 2030 compared with a 2005 baseline. In the case of Portugal, a 71% reduction in
NOx emissions is proposed, but only a 16% reduction in NH3 [8]. Thus, NH3 is expected to
make a proportionately larger contribution to Portuguese N deposition in the future. In a
global perspective, increased food demands and more fertilizer use may further increase agri-
cultural N use [9] and NH3 emissions, while a combination of increased agricultural produc-
tion and climate warming may lead to a doubling of global NH3 emissions by 2100 [10].
Nitrogen pollution and biodiversity
Impacts of atN pollution on ecosystems and their biodiversity. Most natural terrestrial
ecosystems have evolved under a specific and often low N availability, and thus can be changed
by excessive N (i.e. atN pollution), through both direct and indirect mechanisms [11]. High
levels of gaseous or aerosol-borne N (usually NH3) can be directly toxic to higher plants [12,
13] and to organisms that adsorb elements directly from the environment, such as algae,
lichens, or bryophytes [14, 15]. Existing atN pollution also acts indirectly on organisms
through factors such as nutrient enrichment, soil or water acidification, altered nutrient ratios,
or by intensifying the impact of other stressors such as pathogens, herbivory or climate change
[11]. Under atN pollution, species composition changes over time and diversity often declines,
as characteristic species of oligotrophic, mesotrophic or circumneutral habitats (including spe-
cies of conservation interest) are out-competed by faster-growing, more nitrophytic or acid-
resistant plants, many of which are ruderals or invasive [11, 16]. In general, forbs, bryophytes,
lichens and oligotrophic shrubs are the main functional types negatively affected by atN pollu-
tion, while grasses, adapted to higher nutrient levels, are the main functional type to benefit.
The impacts of atN pollution on biodiversity [15, 17–19] and on species’ physiology [20,
21] are a particular problem immediately downwind of sources such as intensive livestock pro-
duction. Direct foliar damage is usually due to high local concentrations of NH3[11] while
broader ecosystem-scale changes in soil and vegetation often result from chronically-elevated
local and regional N deposition, including a combination of wet and dry deposition of NHy
and NOx compounds [19, 22]. Within the soil, atN pollution can reduce the allocation of car-
bon from the vegetation to mycorrhizal fungi [23, 24] and other free-living microorganisms
(e.g. other fungi, N-fixing bacteria, phosphorus solubilizers) thus impacting soil microbial
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 2 / 19
and Investigador FCT contract to Cristina
Branquinho.
Competing interests: The authors have declared
that no competing interests exist.
communities and the ecosystem functions and services they provide (e.g. decomposition, bio-
logical N fixation). The atN pollution also impacts soil fauna [25]. N-driven changes in soil
fauna and microbial communities influence the physical properties of soil, such as soil aggre-
gation, water infiltration and organic matter turnover [26]. The impacts of atN pollution on a
species or ecosystem depend on several factors [27], including the duration of exposure, total
amount and form of N, species sensitivity, intrinsic ecosystem properties (e.g. fertility and acid
neutralizing capacity) and climate [11].
Overall, atN pollution threatens biodiversity globally [11, 28], but a global analysis identi-
fied northern temperate, boreal, arctic, alpine, grassland, savannah and Mediterranean biomes
as being particularly sensitive to atN pollution [28]. Biodiversity loss is of special concern in
biodiversity hotspots such as Mediterranean type ecosystems [29, 30], which are thought to be
experiencing the greatest proportional biodiversity change [28]. Of the five global Mediterra-
nean regions (California, central Chile, Mediterranean Basin, southern Cape region and south-
western and southern Australia), California and the Mediterranean are considered those most
threatened by atN pollution [31]. In contrast to Californian ecosystems, however, those in the
Mediterranean Basin are still relatively poorly studied regarding the impacts of atN pollution
[11, 31, 32].
Impacts of atN pollution on European habitats, including the Natura 2000 network. In
this work, we focused on Natura 2000 areas because they host a significant portion of Europe’s
biodiversity, including most of its sensitive and unique species. atN pollution constitutes a seri-
ous challenge for the conservation of such habitats and species under the Habitats Directive
(92/43/EEC). The Habitats Directive, a cornerstone of Europe’s nature conservation policy, pro-
motes the maintenance of biodiversity and requires the Member States to take measures to
maintain or restore natural habitats at a favourable conservation status. The Directive estab-
lished the Natura 2000 network with the aim of assuring the long-term survival of Europe’s
most valuable and threatened species and habitats. These sites are afforded the highest degree of
protection under European legislation: the provisions of the Directive require strict site protec-
tion measures, any avoidance of deterioration and a precautionary approach to permitting
“plans or projects” which are likely to have a significant effect on a site. However, the Habitats
Directive does not directly address air pollution impacts, of which N deposition and ozone are
currently the most important, and until now, there has been no common European approach
for determining the impacts of air pollution on individual sites or their conservation status [33].
To protect ecosystems from atN pollution, thresholds for N have been set as critical levels
(atmospheric concentration) and critical loads (deposition in ecosystems) [34]. Exceedance of crit-
ical loads for N deposition is often associated with a reduction in plant species richness in a broad
range of ecosystems. Critical loads of 5–10 kg N ha -1
yr -1
have been defined for sensitive ecosys-
tems [24, 35], although there is evidence that individual sensitive species may decline at levels
below the critical load [36], and effects may occur over the longer-term at lower loads [11]. Com-
bining global modelled N deposition with the spatial distribution of protected areas under the UN
Convention on Biological Diversity showed that 40% of all protected areas (or 11% of all ecosys-
tems, by area) are projected to receive N deposition higher than 10 kg N ha -1
yr -1
by 2030 [37].
The Portuguese case. The Natura 2000 network together with the national network of
protected areas covers approximately 22% of the mainland Portuguese terrestrial territory.
Portuguese nature conservation areas are created and managed by the national authority for
nature conservation ICNF (www.icnf.pt).
Emissions of NH3 are distributed unevenly throughout Portugal due to the patchy location
of intensive livestock farming and agriculture, which comprise 85% of the total NH3 emissions.
Some municipalities have relatively high emission densities due to the presence of point source
emissions associated with industrial activities such as intensive pig and poultry rearing (6%).
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 3 / 19
Overall, there has been a downward trend in NH3 emissions since 1990 (-22.7%), mainly due
to decreasing numbers of cattle and energy production from renewable sources [38].
Only a few studies deal with the impact of atN pollution on Portuguese ecosystems. In a
Mediterranean Basin matorral habitat (http://eunis.eea.europa.eu/habitats/1699), the form and
dose of available N are being manipulated in an ongoing field experiment running since 2007.
The study site, located south of Lisbon (Natura 2000 site PTCON0010 Arrábida/Espichel), has
low ambient N deposition (<4 kg N ha -1
yr -1
) and low soil N content (0.1%). N availability is
increased in three N-treatments through additions of 40 kg N ha -1
yr -1
as a 1:1 NH4Cl to
(NH4)2SO4 mixture, and 40 and 80 kg N ha -1
yr -1
as NH4NO3. The impacts on plant composi-
tion and diversity (richness and evenness) [16, 39] and ecosystem characteristics (soil extractable
N and organic matter, aboveground biomass and % of bare soil) [16, 40] and functions (decom-
position, nitrification, biological N fixation) [41] are assessed. In contrast to most similar studies,
plant species richness increased with enhanced N input and was more related to ammonium
than to nitrate. Data suggest that enhanced NH4 +
availability affects the structure of the matorral,
which may promote soil erosion and N leakage, whereas enhanced NOx availability leads to bio-
mass accumulation, which may increase fire risk [16]. Based on this experiment, the first empiri-
cal critical load of N for this European habitat was set at between 20–30 kg N ha -1
yr -1
[35].
Sclerophyllous grazed forests (dehesas in Spain and montados in Portugal - http://eunis.eea. europa.eu/habitats/10129) have been characterized regarding their NH3 critical levels and N
critical loads [19], including for situations in which other pollution sources co-occur with N
[22]. This was done using the changes in functional diversity of one of the most sensitive com-
ponents of the ecosystem, epiphytic lichens [15]. Under atN pollution, the total plant species
richness of these ecosystems did not change, but their functional diversity has undergone a
complete shift from a community dominated by oligotrophic species to one dominated by
nitrophytic ones [42]. This led to the establishment of a critical level for ammonia at 0.6 μgm−3
and a critical load for N at 26 kg ha −1
yr −1
[19], which is within the upper range established for
other semi-natural ecosystems [19].
Aim. Taking into consideration the risk posed by N to biodiversity [43, 44], and the
knowledge gaps identified for Portugal, the main objective of this work was to map the risk
that atN pollution poses to changing biodiversity at Natura 2000 sites located in mainland Por-
tugal. Because most areas with a conservation interest in Portugal occur within or in the imme-
diate vicinity of agriculture fields, which emit mostly NHx, we have focused on NH3 emissions
and used it as a proxy for overall atN pollution. We used the most recent spatially distributed
NH3 emission inventory available for Portugal at the municipality level together with the loca-
tion of the Natura 2000 sites. Then we ranked the sensitivity of the habitats within the Habitats
Directive (92) to atN pollution using expert knowledge and produced a risk map integrating
both NH3 emissions and Natura 2000 sites’ susceptibility to atN pollution. The risk map
enables prioritisation of conservation strategies within the Natura 2000 network and identifi-
cation of research gaps in evaluating the impacts of atN pollution on habitat conservation. In
the following section, we review the ecological impacts of N deposition within the context of
the EU Natura 2000 network and in relation to Portuguese conditions. Afterwards, we describe
the assessment and mapping methodologies applied, and then present and discuss the results.
Material and methods
We considered all Portuguese Natura 2000 sites where habitat information is publicly available
(http://www.icnf.pt), resulting in a selection of 60 sites in mainland Portugal. Within these
Natura 2000 sites, all habitats listed in Annex 1 of the Habitats Directive were considered for
further analysis (88 habitats).
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 4 / 19
Only two of the habitats occurring in mainland Portugal have been studied regarding their
sensitivity to atN pollution (see section 2.3). Therefore, the assessment of the sensitivity to atN
pollution of the habitat types of Annex I of the Habitats Directive occurring in mainland Por-
tugal was done by expert judgment. Seven experts were selected from professionals working in
environmental companies and researchers working in biogeography, vegetation science, con-
servation and ecology with considerable experience of Portuguese habitats and an understand-
ing of nitrogen pollution impacts. A higher number of experts was not possible since we
required them to classify most of the habitats present in mainland Portugal, and only a
restricted number of people have enough knowledge of such high number of habitats. More-
over, the impacts of nitrogen on biodiversity remain understudied in Portugal, making the
choice of experts even narrower. Nevertheless, we are confident in the knowledge of the
expert’s selected for this work. We are also confident that the results obtained are a major step
up in current knowledge.
Each of the habitats in Table 1 was assessed by these experts regarding sensitivity to atN pol-
lution on a score of 1 (least sensitive) to 10 (most sensitive). The N sensitivity of a given habitat
Table 1. Sensitivity of habitats designated under the Habitats Directive (92 - http://ec.europa.eu/environment/nature/legislation/habitatsdirective) to atN pollution
and occurring in mainland Portugal.
Habitat N
sensitivity
Coastal and halophytic
habitats
Open sea and tidal areas 1110 Sandbanks which are slightly covered by sea water all the time 2.6 0.44
1130 Estuaries 2.8 0.30
1140 Mudflats and sandflats not covered by seawater at low tide 2.6 0.44
1150 � Coastal lagoons 3.8 0.51
1160 Large shallow inlets and bays 3.6 0.32
1170 Reefs 4.0 0.64
Sea cliffs and shingle or stony beaches 1210 Annual vegetation of drift lines 3.0 0.51
1230 Vegetated sea cliffs of the Atlantic and Baltic coasts 3.5 0.47
1240 Vegetated sea cliffs of the Mediterranean coasts with endemic Limonium spp.
4.0 0.35
Atlantic and continental salt marshes
and salt meadows
1310 Salicornia and other annuals colonizing mud and sand 4.0 0.32 1320 Spartina swards (Spartinion maritimae) 3.8 0.42 1330 Atlantic salt meadows (Glauco-Puccinellietalia maritimae) 4.0 0.42
Mediterranean and thermo-Atlantic
saltmarshes and salt meadows
1410 Mediterranean salt meadows (Juncetalia maritimi) 4.0 0.42 1420 Mediterranean and thermo-Atlantic halophilous scrubs (Sarcocornetea fruticosi)
4.2 0.35
1430 Halo-nitrophilous scrubs (Pegano-Salsoletea) 4.2 0.49 Salt and gypsum inland steppes 1510 � Mediterranean salt steppes (Limonietalia) 3.2 0.46 Sea dunes of the Atlantic, North Sea
and Baltic coasts
2110 Embryonic shifting dunes 4.8 0.48
2120 Shifting dunes along the shoreline with Ammophila arenaria (white dunes) 4.6 0.49 2130 � Fixed coastal dunes with herbaceous vegetation (grey dunes) 5.5 0.41
2150 � Atlantic decalcified fixed dunes (Calluno-Ulicetea) 6.0 0.35 2170 Dunes with Salix repens ssp. argentea (Salicion arenariea) 5.8 0.33 2180 Wooded dunes of the Atlantic, Continental and Boreal region 5.5 0.38
2190 Humid dune slacks 6.3 0.36
Sea dunes of the Mediterranean coast 2230 Malcolmietalia dune grasslands 3.7 0.48 2250 � Coastal dunes with Juniperus spp. 4.1 0.47 2260 Cisto-Lavenduletalia dune sclerophyllous scrubs 4.6 0.42 2270 � Wooded dunes with Pinus pinea and/or Pinus pinaster 4.4 0.41
Inland dunes, old and decalcified 2330 Inland dunes with open Corynephorus and Agrostis grasslands 4.7 0.32
(Continued)
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 5 / 19
Table 1. (Continued )
Habitat N
sensitivity
Freshwater Habitats Standing water 3110 Oligotrophic waters containing very few minerals of sandy plains
(Littorelletalia uniflorae) 8.1 0.17
3120 Oligotrophic waters containing very few minerals generally on sandy soils of
the West Mediterranean with Isoetes spp. 8.1 0.17
3130 Oligotrophic to mesotrophic standing waters with vegetation of the
Littorelletea uniflorae and/or Isoeto-Nanojuncetea 8.0 0.18
3140 Hard oligo-mesotrophic waters with benthic vegetation of Chara spp. 7.8 0.20 3150 Natural eutrophic lakes with Magnopotamion or Hydrocharition—type vegetation
5.1 0.52
3160 Natural dystrophic lakes and ponds 5.6 0.55
3170 � Mediterranean temporary ponds 7.1 0.28
Running water 3250 Constantly flowing Mediterranean rivers with Glaucium flavum 4.8 0.53 3260 Water courses of plain to montane levels with the Ranunculion fluitantis and Callitricho-Batrachion vegetation
5.8 0.39
3270 Rivers with muddy banks with Chenopodion rubri p.p. and Bidention p.p vegetation
4.3 0.23
3280 Constantly flowing Mediterranean rivers with Paspalo-Agrostidion species and hanging curtains of Salix and Populus alba
4.8 0.53
3290 Intermittently flowing Mediterranean rivers of the Paspalo-Agrostidion 4.8 0.53 Temperate heath and scrub 4010 Northern Atlantic wet heaths with Erica tetralix 7.6 0.23
4020 � Temperate Atlantic wet heaths with Erica ciliaris and Erica tetralix 7.7 0.23 4030 European dry heaths 6.1 0.26
4060 Alpine and boreal heaths 6.5 0.29
4090 Endemic oro-Mediterranean heaths with gorse 5.8 0.43
Sclerophyllous scrub
(matorral)
Sub-Mediterranean and temperate
scrub
5110 Stable xerothermophilous formations with Buxus sempervirens on rock slopes (Berberidion p.p.)
5.7 0.24
5120 Mountain Cytisus purgans formations 5.6 0.27 5140 � Cistus palhinhae formations on maritime wet heaths 5.9 0.33
Mediterranean arborescent matorral 5210 Arborescent matorral with Juniperus spp. 5.5 0.15 5230 � Arborescent matorral with Laurus nobilis 5.7 0.14
Thermo-Mediterranean and pre-
steppe brush
5320 Low formations of Euphorbia close to cliffs 5.1 0.36 5330 Thermo-Mediterranean and pre-desert scrub 5.0 0.35
Phrygana 5410 West Mediterranean clifftop phryganas (Astragalo-Plantaginetum subulatae) 5.8 0.40 Natural and semi-natural
grassland formations
Natural grasslands 6110 � Rupicolous calcareous or basophilic grasslands of the Alysso-Sedion albi 4.2 0.38 6160 Oro-Iberian Festuca indigesta grasslands 4.3 0.45
Semi-natural dry grasslands and
scrubland facies
6210 Semi-natural dry grasslands and scrubland facies on calcareous substrates
(Festuco-Brometalia) (� important orchid sites) 6.3 0.18
6220 � Pseudo-steppe with grasses and annuals of the Thero-Brachypodietea 5.2 0.36 6230 � Species-rich Nardus grasslands, on siliceous substrates in mountain areas
(and submountain areas, in Continental Europe)
6.2 0.22
Sclerophillous grazed forests
(dehesas)
6310 Dehesas with evergreen Quercus spp. 5.3 0.26
Semi-natural tall-herb humid
meadows
6410 Molinia meadows on calcareous, peaty or clayey-silt-laden soils (Molinion caeruleae)
6.8 0.22
6420 Mediterranean tall humid herb grasslands of the Molinio-Holoschoenion 5.8 0.14 6430 Hydrophilous tall herb fringe communities of plains and of the montane to
alpine levels
5.8 0.17
Mesophile grasslands 6510 Lowland hay meadows (Alopecurus pratensis, Sanguisorba officinalis) 6.5 0.37 Raised bogs and mires and
fens
Sphagnum acid bogs 7140 Transition mires and quaking bogs 8.2 0.22 7150 Depressions on peat substrates of the Rhynchosporion 8.2 0.22
(Continued)
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 6 / 19
was taken as the likelihood of biodiversity changes in response to atN pollution due to the
proximity of an agricultural area. The average classification given by all experts (n = 7) was
assumed as the habitat’s sensitivity to atN pollution, and the habitats were ranked accordingly.
The relative standard deviations of the experts’ estimates are also shown (averaged per habitat),
providing as a measure of uncertainty in the classification.
We considered as the habitat’s susceptibility the potential adverse effects caused by atN pol-
lution to the organisms living in each Natura 2000 Portuguese sites. Then, all Natura2000 sites
were classified according to their susceptibility to atN pollution, considering the average of
their habitats’ sensitivity to atN pollution.
The NH3 emissions reported by the Portuguese authorities (http://www.apambiente.pt/)
were used as a proxy for atN pollution (including atmospheric concentrations and dry deposi-
tion of ammonia). This is feasible because NH3 is generally deposited close to its emission
sources [45–47]. The most recent NH3 emission data available at the municipality level (year
Table 1. (Continued )
Habitat N
sensitivity
Rocky habitats and caves Scree 8130 Western Mediterranean and thermophilous scree 4.5 0.29
Rocky slopes with chasmophytic
vegetation
8210 Calcareous rocky slopes with chasmophytic vegetation 5.0 0.35
8220 Siliceous rocky slopes with chasmophytic vegetation 5.4 0.36
8230 Siliceous rock with pioneer vegetation of the Sedo-Scleranthion or of the Sedo albi-Veronicion dillenii
5.4 0.36
8240 � Limestone pavements 5.0 0.35
Other rocky habitats 8310 Caves not open to the public 2.3 0.65
8330 Submerged or partially submerged sea caves 3.3 0.96
Forests Forests of temperate Europe 9160 Sub-Atlantic and medio-European oak or oak-hornbeam forests of the
Carpinion betuli 6.2 0.24
91B0 Thermophilous Fraxinus angustifolia woods 5.4 0.32 91E0 � Alluvial forests with Alnus glutinosa and Fraxinus excelsior (Alno-Padion, Alnion incanae, Salicion albae)
6.5 0.23
91F0 Riparian mixed forests of Quercus robur, Ulmus laevis and Ulmus minor, Fraxinus excelsior or Fraxinus angustifolia, along the great rivers (Ulmenion minoris)
5.8 0.25
Mediterranean deciduous forests 9230 Galicio-Portuguese oak woods with Quercus robur and Quercus pyrenaica 6.3 0.29 9240 Quercus faginea and Quercus canariensis Iberian woods 6.3 0.33 9260 Castanea sativa woods 6.6 0.30 92A0 Salixalba and Populus alba galleries 6.5 0.32 92B0 Riparian formations on intermittent Mediterranean water courses with
Rhododendron ponticum, Salix and others 7.0 0.30
92D0 Southern riparian galleries and thickets (Nerio-Tamaricetea and Securinegion tinctoriae)
5.9 0.39
Mediterranean sclerophyllous forests 9320 Olea and Ceratonia forests 6.0 0.26 9330 Quercus suber forests 6.3 0.33 9340 Quercus ilex and Quercus rotundifolia forests 6.2 0.31 9380 Forests of Ilex aquifolium 7.2 0.18
Mediterranean and Macaronesian
mountainous coniferous forests
9560 � Endemic forests with Juniperus spp. 6.5 0.27 9580 � Mediterranean Taxus baccata woods 6.7 0.26
Sensitivity to atN pollution was assessed by expert judgement (average and relative standard deviation; n = 7 experts) ranging from 1 to 10, with 10 corresponding to the
most N sensitive habitat and 1 to the least N sensitive habitat.
� indicates priority habitat types according to the European Union Habitats Directive.
https://doi.org/10.1371/journal.pone.0198955.t001
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 7 / 19
2009) were spatially disaggregated to the area occupied by each Natura 2000 site. Then the
average NH3 emissions were calculated for each Natura 2000 site.
Finally, we considered environmental risk as "the combination of the probability, or fre-
quency, of occurrence of a defined hazard and the magnitude of the consequences of the
occurrence" [48]. Combining each site’s susceptibility to atN pollution with the estimated local
NH3 emissions enabled assessment of the relative risk of biodiversity change occurring for
each Natura 2000 site, due to atN pollution. The maximum risk was defined as the combina-
tion of highest NH3 emissions and highest susceptibility to atN pollution; in total, nine classes
of risk were defined.
Results & discussion
Of the 88 habitat types defined for Natura 2000 sites across mainland Portugal (Fig 1), 37
occur in the Atlantic region, 81 in the Mediterranean region and 36 in both (see S1 File). Fur-
thermore, from the 121 plant species of Community Importance, 117 occur in the Mediterra-
nean region, and 27 in the Atlantic region, thus making the Mediterranean region biologically
‘richer’ than the Atlantic one for conservation purposes. Table 1 shows all habitats classified
according to their sensitivity to atN pollution, with average expert ranking ranging from 2.3 to
8.2 (higher values representing the most sensitive habitats). Ranking the habitats’ sensitivity to
atN pollution (Fig 1) gave that the most sensitive habitats as:
i) ‘Raised bogs and mires and fens–Sphagnum acid bogs’, particularly habitat 7140—Transi- tion mires and quaking bogs and habitat 7150—Depressions on peat substrates of the
Rhynchosporion;
ii) ‘Freshwater Habitats—Standing water’, particularly habitat 3130—Oligotrophic to meso-
trophic standing waters with Littorelletea uniflorae and/or Isoete Nanojuncetea, habitat 3110—Oligotrophic waters containing very few minerals of sandy plains (Littorelletalia uniflorae) and habitat 3120—Oligotrophic waters containing very few minerals generally on sandy soils of the West Mediterranean with Isoetes spp.
The least sensitive habitats were:
i) ‘Rocky habitats and caves–Other rocky habitats’, particularly habitat 8310—Caves not open
to the public;
ii) ‘Coastal and halophytic habitats—Open sea and tidal areas’, particularly habitat 1110—
Sandbanks which are slightly covered by sea water all the time, habitat 1140—Mudflats and
sandflats not covered by seawater at low tide and habitat 1130—Estuaries.
The most sensitive habitats were acidic and oligotrophic while the least sensitive were
coastal open sea, tidal habitats and caves, which often house large bat colonies that emit large
amounts of NH3 through the accumulation of guano in the caves.
Distributing the 88 habitats along the 60 Natura 2000 sites in which they occur enabled
mapping the susceptibility to atN pollution for each site (Fig 2). The sites’ susceptibility to atN
pollution ranged from 6.6 at the most susceptible site to 3.9 at the least susceptible site. Sites
located inland in the northern mountains were considered to be more susceptible to atN pollu-
tion than the sites located along the coast. Sites located inland in the Mediterranean region of
mainland Portugal showed intermediate scores of susceptibility to atN pollution. Examples of
the Natura 2000 sites most susceptible to atN pollution included PTCON0039 (Serra de Arga),
PTCON0040 (Côrno do Bico) and PTCON0025 (Montemuro), while examples of the least
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
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Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
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susceptible to atN pollution included PTCON0006 (Arquipélago da Berlenga), PTCON0058
(Ria de Alvor) and PTCON0013 (Ria Formosa/Castro Marim).
Given that the Natura 2000 network and protected areas occupy ca. 22% of the area of
mainland Portugal, and that the distribution of the Portuguese population and anthropogenic
activities is not uniform across the territory, several Natura 2000 sites are in close proximity to
important sources of NH3 pollution. Such sites near intensive agricultural areas were within
Fig 1. Ranking of the habitats (Habitats Directive) occurring in mainland Portugal according to their sensitivity to
atmospheric Nitrogen pollution (higher values in red indicate higher sensitivity). The bars represent the average relative
standard deviation (the same as in Table 1). See full habitat names in Table 1.
https://doi.org/10.1371/journal.pone.0198955.g001
Fig 2. Map and plot of Natura 2000 sites in mainland Portugal, classified according to their susceptibility to atmospheric Nitrogen pollution. Higher
values indicate higher susceptibility, on a scale from 1 to 10.
https://doi.org/10.1371/journal.pone.0198955.g002
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 10 / 19
grid squares with the highest NH3 emissions (and so were assumed to have high NH3 concen-
trations), in contrast to more remote sites (Fig 3). PTCON0006 (Arquipélago da Berlenga),
PTCON0017 (Litoral Norte), PTCON0056 (Peniche/Santa Cruz) and PTCON0046 (Azabuxo-
Leiria) had NH3 emissions > 1 ton km -2
yr -1
while PTCON0051 (Complexo do Açor) and
PTCON0060 (Serra da Lousã) had NH3 emissions one order of magnitude smaller (< 0.1 ton km
-2 yr
-1 ).
The combined analysis of the Natura 2000 sites’ susceptibility to atN pollution and NH3
emissions was used to calculate the relative risk of habitat change caused by atN pollution
(Figs 4 and 5 and S1 File). No Natura 2000 site was found to fall into the maximum risk cate-
gory (9), i.e. a combination of the highest susceptibility to atN pollution and highest NH3 emis-
sions (Fig 4). Four sites were considered to be in the second-highest risk category (8): Paúl de
Arzila, Côrno do Bico, Cambarinho and Serra d’Arga. The sites with the lowest risk (category
1) were Rio Minho, Arade/Odelouca, Arrábida/Espichel, Ria de Alvor, Ria Formosa/ Castro
Marim and Samil. In general, the Natura 2000 sites with the lower relative risk of biodiversity
Fig 3. Map and plot of Natura 2000 sites in mainland Portugal, classified according to the average atmospheric ammonia emissions
(2009, tonne km -2
year -1
).
https://doi.org/10.1371/journal.pone.0198955.g003
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 11 / 19
change due to atN pollution were either coastal or dominated by Mediterranean evergreen
species (Matorral and semi-natural grassland formations). Most coastal sites have saltmarshes,
which are thought to cope relatively well with atN pollution because their naturally low aerobic
conditions make ammonia the predominant N form [49]. Sites dominated by evergreen
Mediterranean oaks, which dominate most of the southern part of mainland Portugal, are
already adapted to some degree of disturbance, i.e. mainly low-intensity agriculture and
grazing [50]. These ecosystems were shaped over millennia, and their current species pool–
including those of conservation interest–reflect that long-term process, by showing a lower
susceptibility to atN pollution and thus an overall lower relative risk of biodiversity change due
to atN pollution.
Fig 4. Plot of Natura 2000 sites’ susceptibility to atmospheric nitrogen (atN) pollution vs. average ammonia emissions, showing the relative
risk of biodiversity change due to atN pollution. It is notable that there are no Natura 2000 sites in the highest risk category (9) of highest
susceptibility to atN pollution and highest ammonia emissions, which may reflect some degree of spatial separation between agricultural activities
and natural habitats.
https://doi.org/10.1371/journal.pone.0198955.g004
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 12 / 19
The Natura 2000 sites located further north are dominated by deciduous Mediterranean
oaks and showed higher risk of biodiversity change due to atN pollution than the southern
sites. This is likely associated with granitic soil in these areas, and the presence of the most N
sensitive habitat types, i.e. peatland, mires and bogs. These habitats were not shaped by low-
level agricultural activities and their soil (more acidic) offer less buffering capacity to atN pol-
lution. Although studies have shown that the species richness of bogs is less sensitive to N
deposition than other oligotrophic habitats such as acid grassland or heathland [51, 52] (which
Fig 5. Map and plot of Natura 2000 sites classified according to the relative risk of biodiversity change caused by atmospheric Nitrogen (atN) pollution. Higher
values indicate higher risk, which is caused by a combination of site’s high susceptibility to atN pollution and high emission of ammonia.
https://doi.org/10.1371/journal.pone.0198955.g005
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 13 / 19
are not represented in the Natura 2000 sites), this is because bog vegetation, particularly Sphag- num, can shift from pollution-sensitive species to less sensitive ones as pollution increases [52, 53], resulting in comparatively little change in species richness but a significant change in com-
munity composition.
In this study, we only mapped the Natura 2000 sites at higher relative risk of biodiversity
change due to atN pollution taking NH3 as a proxy for overall atN pollution. Other forms of N
could be considered, namely NOx. However, NOx is only relevant for a few sites located near
large urban or industrial areas and in general, reduced N (ammonia/ammonium) has been
shown to cause more negative impacts than similar doses of oxidized N [16, 54, 55]. Alto-
gether, NH3 emission can be regarded as a surrogate of overall atN pollution on each site,
because it is the prevailing N form emitted in the airsheds of Portuguese Natura 2000 sites. In
our study, all habitats were treated as being of the same conservation value. Further studies
could investigate ranking habitat value within the Ecosystem Services framework [56], by
including which services would be lost or gained if a given habitat disappeared due to atN pol-
lution. In this work we focused in atmospheric nitrogen. However, for habitats greatly influ-
enced by running water, the main threats may come from surface runoff of nitrogen rich
water. Thus, those habitats risk of change would have increased if we could consider such
nitrogen source. However, that information is not available, and thus this work represents the
best approach possible to those habitats susceptibility to nitrogen pollution.
This study relied on the relative classification of all Natura 2000 in mainland Portugal using
expert knowledge. Thus, we stress that we obtained the relative position of sites, not an abso-
lute valuing of their sensitivity. Moreover, this study is limited by the use of expert knowledge.
However, this is currently the only approach available to define research and action priorities
regarding atN pollution. The alternative option would be to establish the empirical critical
loads for N of the habitats present in all Natura 2000 sites, and if those critical loads are being
exceeded. However, this type of knowledge is not available for the vast majority of the Portu-
guese mainland ecosystem (but see [40] [41]). Thus, the use of expert knowledge is currently
the only option available for this study. Although seven experts may seem a small number of
replicates, we could only consider those experts with knowledge on most habitats and on N
issues, and that combination of skills is not frequent. One way to take into account the uncer-
tainty of the responses of experts is to consider the habitat classification deviation (see standard
deviation values in Table 1). This deviation was not very high (average relative standard devia-
tion average = 0.35) reflecting that experts coincided in general in their appraisal. However,
some habitats presented rather conflicting evaluations, with a relative standard deviation of
0.55 or higher, namely 3160 (Natural dystrophic lakes and ponds), 1170 (Reefs), 8310 (Caves
not open to the public) and 8330 (Submerged or partially submerged sea caves). Among the
other habitats with high deviation, we found mostly marine and aquatic habitats, which proba-
bly reflect the poorer knowledge available for those habitat types.
Conclusions
In this study, we combined mainland Portuguese NH3 emission estimates with an expert-based
classification of Natura 2000 habitats’ sensitivity to atN pollution. This allowed us to calculate and
map the relative risk of biodiversity change in Natura 2000 sites due to atN pollution. Results iden-
tified mountain habitats with mires, fens and bogs as the most sensitive to atN pollution, while
coastal salt marshes were considered the least sensitive. By combining habitat sensitivity with local
NH3 emissions, we identified the Natura 2000 sites in mainland Portugal that are at higher relative
risk of biodiversity change due to atN pollution: these are mostly located in the northern moun-
tains, close to areas with agricultural activities of moderate intensity.
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 14 / 19
This ranking approach can be used to prioritize conservation efforts to those sites most at
risk. The most sensitive Portuguese habitats (bogs, mires) are relatively widespread in temper-
ate northern Europe, and the impacts of atN pollution on these types of ecosystems have been
previously evaluated [11, 35, 51]. It remains an open question to what extent the sensitivity of
these habitats in the warm Atlantic context of Portugal is different from Northern Europe.
More importantly, very little is still known about the impacts of long-term elevated atN pollu-
tion on Mediterranean habitats that, in Europe, only occur in the south, and constitute major
biodiversity hotspots which are considered a global conservation priority [29, 30]. Therefore,
and despite their lower current estimated susceptibility to atN pollution, we consider that
these Mediterranean habitats’ uniqueness and a large contribution to Europe’s biodiversity
and natural capital make them a priority in terms of improving future understanding the
impacts of atN pollution. Understanding the role of heterogeneity, patchiness and disturbance
over millennia on the resilience of these habitats [57] may also be a key to better management
[58] and to building resilience in the most sensitive habitats.
Supporting information
S1 File. Final map as kml (google earth). Map showing all Natura 2000 sites in mainland Por-
tugal classified according to the relative risk from nitrogen pollution. Blue represent the lowest
potential risk, red represents the highest risk.
(7Z)
Acknowledgments
We are grateful for the funding through the project ‘NitroPortugal: Strengthening Portuguese
research and innovation capacities in the field of excess reactive nitrogen’, funded by EU
H2020-TWINN-2015 692331 and Fundação para a Ciência e Tecnologia (FCT) through the Post-Doctoral grants SFRH/BPD/75425/2010 to Pedro Pinho and SFRH/BPD/85419/2012 to
Teresa Dias. We also acknowledge INMS—Towards the Establishment of an International
Nitrogen Management System. Finally, we are grateful to the team of Portuguese experts for
their expert judgment.
Author Contributions
Conceptualization: Pedro Pinho, Teresa Dias, Ulrike Dragosits, Mark A. Sutton, Cristina
Branquinho.
Data curation: Pedro Pinho, Teresa Dias.
Formal analysis: Pedro Pinho, Teresa Dias, Cristina Branquinho.
Funding acquisition: Cláudia M. d. S. Cordovil, Ulrike Dragosits, Cristina Branquinho.
Investigation: Pedro Pinho, Teresa Dias, Cristina Branquinho.
Methodology: Pedro Pinho, Teresa Dias, Cristina Branquinho.
Project administration: Cláudia M. d. S. Cordovil, Ulrike Dragosits, Cristina Branquinho.
Supervision: Ulrike Dragosits, Mark A. Sutton, Cristina Branquinho.
Validation: Mark A. Sutton, Cristina Branquinho.
Writing – original draft: Pedro Pinho, Teresa Dias.
Mapping Portuguese Natura 2000 sites in risk of biodiversity change caused by atmospheric nitrogen pollution
PLOS ONE | https://doi.org/10.1371/journal.pone.0198955 June 21, 2018 15 / 19
Writing – review & editing: Pedro Pinho, Teresa Dias, Cláudia M. d. S. Cordovil, Ulrike Dra-
gosits, Nancy B. Dise, Mark A. Sutton, Cristina Branquinho.
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