Ecological and toxicological effects of inorganic nitrogen pollution in aquatic ecosystems: A global assessment.

In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in
the world’s lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only
2.3% of the Earth’s surface, these ecosystems host at least 9.5% of the Earth’s described animal species. Furthermore,
using the World Wide Fund for Nature’s Living Planet Index, freshwater population declines (83% between 1970 and
2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought
multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats
to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii)
e-commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging
contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation;
(xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes,
plants, turtles and waterbirds, with potential for ecosystem-level changes through bottom-up and top-down processes.
In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However,
we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows,
environmental DNA) and specific conservation-oriented actions (e.g. dam removal, habitat protection policies,managed
relocation of species) that have been met with varying levels of success.Moving forward, we advocate hybrid approaches
that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and
ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap
between the aspirations of conservation biologists and the accelerating rate of species endangerment.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/brv.12480

Emerging threats and persistent conservation challenges for freshwater biodiversity

Running waters are perhaps the most impacted ecosystem on the planet as they have been the focus for human settlement and are heavily exploited for water supplies, irrigation, electricity generation, and waste disposal. Lotic systems also have an intimate contact with their catchments and so land-use alterations affect them directly. Here long-term trends in the factors that currently impact running waters are reviewed with the aim of predicting what the main threats to rivers will be in the year 2025. The main ultimate factors forcing change in running waters (ecosystem destruction, physical habitat and water chemistry alteration, and the direct addition or removal of species) stem from proximate influences from urbanization, industry, land-use change and water-course alterations. Any one river is likely to be subjected to several types of impact, and the management of impacts on lotic systems is complicated by numerous links between different forms of anthropogenic effect. Long-term trends for different impacts vary. Concentrations of chemical pollutants such as toxins and nutrients have increased in rivers in developed countries over the past century, with recent reductions for some pollutants (e.g. metals, organic toxicants, acidification), and continued increases in others (e.g. nutrients); there are no long-term chemical data for developing countries. Dam construction increased rapidly during the twentieth century, peaking in the 1970s, and the number of reservoirs has stabilized since this time, whereas the transfer of exotic species between lotic systems continues to increase. Hence, there have been some success stories in the attempts to reduce the impacts from anthropogenic impacts in developed nations. Improvements in the pH status of running waters should continue with lower sulphurous emissions, although emissions of nitrous oxides are set to continue under current legislation and will continue to contribute to acidification and nutrient loadings. Climate change also will impact running waters through alterations in hydrology and thermal regimes, although precise predictions are problematic; effects are likely to vary between regions and to operate alongside rather than override those from other impacts. Effects from climate change may be more extreme over longer time scales (>50 years). The overriding pressure on running water ecosystems up to 2025 will stem from the predicted increase in the human population, with concomitant increases in urban development, industry, agricultural activities and water abstraction, diversion and damming. Future degradation could be substantial and rapid (c. 10 years) and will be concentrated in those areas of the world where resources for conservation are most limited and knowledge of lotic ecosystems most incomplete; damage will centre on lowland rivers, which are also relatively poorly studied. Changes in management practices and public awareness do appear to be benefiting running water ecosystems in developed countries, and could underpin conservation strategies in developing countries if they were implemented in a relevant way.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0376892902000097

Threats to the running water ecosystems of the world

https://www.jstor.org/stable/10.1641/0006-3568(2001)051%5B0180:ADITNU%5D2.0.CO;2

Acidic Deposition in the Northeastern United States: Sources and Inputs, Ecosystem Effects, and Management Strategies

The transport sector as a source of air pollution

Rates of acidic deposition from the atmosphere (‘acid rain’) have decreased throughout the 1980s and 1990s across large portions of North America and Europe1,2. Many recent studies have attributed observed reversals in surface-water acidification at national3 and regional4 scales to the declining deposition. To test whether emissions regulations have led to widespread recovery in surface-water chemistry, we analysed regional trends between 1980 and 1995 in indicators of acidification (sulphate, nitrate and base-cation concentrations, and measured (Gran) alkalinity) for 205 lakes and streams in eight regions of North America and Europe. Dramatic differences in trend direction and strength for the two decades are apparent. In concordance with general temporal trends in acidic deposition, lake and stream sulphate concentrations decreased in all regions with the exception of Great Britain; all but one of these regions exhibited stronger downward trends in the 1990s than in the 1980s. In contrast, regional declines in lake and stream nitrate concentrations were rare and, when detected, were very small. Recovery in alkalinity, expected wherever strong regional declines in sulphate concentrations have occurred, was observed in all regions of Europe, especially in the 1990s, but in only one region (of five) in North America. We attribute the lack of recovery in three regions (south/central Ontario, the Adirondack/Catskill mountains and midwestern North America) to strong regional declines in base-cation concentrations that exceed the decreases in sulphate concentrations.

Regional trends in aquatic recovery from acidification in North America and Europe

BACKROUND TO RESEARCH: This project (WFD60) forms part of the UK Strategy for the implementation of the EC Water Framework
Directive (WFD: European Union, 2000). Within its broad remit the WFD requires the development of
ecological classification tools for the purpose of determining ecological status with reference to specific
environmental pressures. The WFD requires that these tools should assign lakes to one of five categories
(High, Good, Moderate, Poor, Bad) to indicate conditions relative to what is considered “high status”.
This report focuses on the further development of a tool with which to determine the extent of the
pressure of acidification on lake macroinvertebrate communities. OBJECTIVES OF RESEARCH: The primary objective is the development of a method and tool with which to assess the pressure of
acidification (a major threat to the ecology of acid-sensitive freshwaters, particularly in the UK uplands)
on the benthic macroinvertebrate assemblage of lakes. This phase of the WFD60 project focuses on the
development of a new, improved version of the original WFD60 classification tool made possible by a
programme of new data collection. KEY FINDINGS AND RECOMMENDATION: Development of the new WFD60 tool was based closely on the observations from and the results of the
first phase of the WFD60 project (Monteith and Simpson 2007). Briefly, knowledge on lake acidification
status was combined into a simple measure of acidification damage based upon acid neutralising capacity
(ANC) and lake water Calcium concentration (Ca^{2+}), and a simple classification scheme known as the
“damage matrix” was produced. This damage matrix represents our current understanding of ecosystem
damage resulting from acidification, and is used to provide an assessment of the true acidification status
of lakes in the WFD60 data set.
We then employed Random Forests, a sophisticated statistical data mining methodology to build an
ensemble (collection) of classification trees that contained decision rules that attempt to predict the a prior
assigned damage matrix classification using only the macro species data. We supplement the raw
macroinvertebrate data with “meta taxa”; aggregations of subsets of the species data that reflect aspects of
the community such as total species richness or richness of important acid tolerant or acid intolerant
indicator groups.
We show that the random forest approach can produce a classification tool that is able to correctly predict
the damage matrix class for 99% of the samples in the WFD60 data set, incorrectly assigning the wrong
class to a single observation. This represents the apparent performance of the tool and will over-estimate
the expected performance when the tool is applied to new samples that have not taken part in the model
building. Cross-validated performance estimates suggest that the correct class is assigned 50% of the
time. Whilst this figure appears low, it is twice as good as randomly guessing the class and is comparable
to other WFD tools developed for acidification status (LAMM and CPET). However, due to uneven sampling of the four status classes predicted by the new tool we believe this performance estimate to be
an under-estimate due to problems performing the bootstrap sampling in cases where some classes
contain relatively few samples. We believe the true performance of the tool lies somewhere between the
apparent and cross-validated error and as such the new tool performs favourably compared to LAMM and
much better than CPET for the subset of samples to which the three tools have been applied.
A major addition to the new tool is the calculation of sample EQRs from the output form the random
forest. The four classes predicted by the new tool are assigned a base score. The final EQR for an
individual sample or site is computed as a weighted average of these base scores, with weights for each
base score given by the probability that the sample belong to that status class. We show that this EQR
performs favourably compared to WFD normative definitions and measures of acidification damage.
Furthermore, we show that the EQR contains an element of uncertainty in the assigned classification; a
site that could just as likely be assigned Good status or Moderate status should have a lower EQR than a
site that is clearly in Good status, even if both sites are ultimately assigned to Good status on the basis of
majority votes from the random forest.
A further development of the new tool has allowed sample-specific estimates of prediction uncertainty or
confidence of class to be determined. The confidence of class is taken as the proportion of votes for the
assigned class out of the total votes for all classes for individual samples. This measure is computed for
all four classes. As such, to simplify the confidence of class information, we use Shannon's entropy
measure to combine the four confidence of class measures. A low value (close to 0) of Shannon's entropy
indicates high confidence of class and a high value (close to 1) indicates low confidence of class.
Several assessments of the new tool have been performed as part of this phase of WFD60. The first
assessment looked at performance of the tool against temporal data from the lake sites of the UK Acid
Waters Monitoring Network (UK AWMN). The second assessment compared the results from AWIST
with data from palaeoecological studies at two acidified sites and one minimally impacted site. Despite
complications arising from the nature of the individual data (large temporal variability in the
macroinvertebrate time series data, and incomplete preservation of the macroinvertebrate community in
the palaeoecological data), the results from applying AWIST to the test sites show that the new tool can
track recovery in the macroinvertebrate community through time in several UK AWMN sites and that the
tool predicts acidification status that reflects the acidification history of the two acidified test lakes as
demonstrated by diatom and macrofossil remains.
In conclusion, the new tool developed as part of the second phase of WFD60 is capable of providing
relevant information for WFD purposes and that AWIST is able to capture and reflect known acidification
status and track temporal recovery in macroinvertebrate assemblages where this is occuring in UK
AWMN sites.
Additional work should be performed to investigate whether and how LAMM, CPET and AWIST
predictions can be combined to provide an ensemble classification tool that draws upon the best features
of each of the tools. This will require further collaborative work between the tool developers and the
relevant agencies to conduct relevant comparisons and testing. This additional work may allow time to
tweak the underlying AWIST random forest to improve the cross-validation performance statistics by
performing stratified bootstrap resampling within with random forest algorithm.

S. Patrick

Papers

Regional trends in aquatic recovery from acidification in North America and Europe

Acid Waters macroInvertebrate Status Tool