The role of lateral exchange in modulating the seaward flux of C, N, P.

Lead Research Organisation: Queen Mary, University of London
Department Name: Sch of Biological and Chemical Sciences


All living organisms that make up life on Earth are made from a profusion of elements in the periodic table, including trace metals. However, in addition to oxygen (O) and hydrogen (H), the constituents of water, the three most important are Carbon (C), Nitrogen (N) and Phosphorus (P). These have become known as the Macro-Nutrients. These macronutrients are in constant circulation between living organisms (microbes, plants, animals, us) and the environment (atmosphere, land, rivers, oceans). Until human intervention (circa post industrial revolution and even more so since WWII) these 'cycles' were largely in balance: plants took up CO2 and produced O2 and, in order to do so, took up limited amounts of N and P from the environment (soils, rivers) and, on death, this "sequestered" C,N,P was returned back to the Earth. The problem is that human or anthropogenic activity has put these key macro-nutrient cycles out of balance. For example, vast quantities of once fossilised carbon, taken out of the atmosphere before the age of the dinosaurs, are being burnt in our power stations and this has increased atmospheric CO2 by about 30 % in recent times. More alarmingly, perhaps, is that man's industrial efforts have more than doubled the amount of N available to fertilize plants, and vast amounts of P are also released through fertilizer applications and via sewage. As the population continues to grow, and the developing world catches up, and most likely overtakes, the western world, these imbalances in the macro-nutrient cycles are set to be exacerbated. Indeed, such is the impact of man's activity on Earth that some are calling this the 'Anthropocene': Geology's new age. The environmental and social problems associated with these imbalances are diverse and complex; most people would be familiar with the ideas behind global warming and CO2 but fewer may appreciate the links to methane and nitrous oxide or the potential health impacts of excess nitrate in our drinking water. These imbalances are not being ignored and indeed a great deal of science, policy and management has been expended to mitigate the impacts of these imbalances. However, despite our progress in the science underpinning this understanding over the last 30-40 years or so, too much of this science has been focused on the individual macro-nutrients e.g. N, and in isolated parts of the landscape e.g. rivers. To compound this even further, such knowledge and understanding has often been garnered using disparate, or sometimes even antiquated, techniques. Anthropogenic activity has spread this macro-nutrient pollution all over the landscape. Some of it is taken up by life, some is stored, but a good deal of it works its way through the landscape towards our already threatened seas. We need to understand what happens to the macronutrients as they move, or flux, through different parts of the landscape and such understanding can only come about by a truly integrated science programme which examines the fate of the macronutrients simultaneously in different parts of the landscape. Here we will for the first time make parallel measurements, using truly state-of-the-art technologies, of the cycling and flux of all three macronutrients on the land and in the rivers that that land drains and, most importantly, the movement of water that transports the macro-nutrients from the land to the rivers e.g. the hydrology. Moreover, we will compare these parallel measurements across land to river in different types of landscapes: clay, sandstone and chalk, subjected to different agricultural usage in order to understand how the cycling on the land is connected, via the movement of water, to that in the rivers.

Planned Impact

Who will benefit? This blue skies research will quantify the flux and dynamics of the lateral exchange of organic C through the Avon catchment & how this in turn modulates the scale of flux, & nature of N & P transformations, towards the coast. There are several end-users & beneficiaries in both private & public sectors e.g. Defra, Environment Agency (EA), CEFAS, Wessex Water, wastewater companies, Local Authorities, agricultural & farming sectors. Learning how catchment changes directly influence C,N,P cycles will enable these organisations to save resources by targeting their actions on those aspects of the nutrient cycles that have the greatest benefit. The project also benefits academics & the public.
How will they benefit? The project enhances quality of life, health & environment as follows:
1. Data on N & P transformations under perturbed C cycles will inform Defra's policies on the impact of nutrient pollution on the environment (e.g. Nitrates Directive, Water Framework Directive, National Emissions Ceilings Directive).
2. Data on the spatial & temporal scales of P, NH4+, NO3- transformations, the timescales for nutrient transport through the catchment & whether interactions with P increase DN will inform Defra's strategy on N2O emissions & the interactions between N2O & other forms of N (& P) enabling improved mitigation strategies to be developed for reducing both pollution & greenhouse gas emissions (Low C Transition Plan, Climate Change Act)
3. Data on air to soil exchange of CO2 (& CH4) under increased temperatures & perturbed C cycle in the catchment will inform Defra's policy on mitigating climate change by reducing CH4 emissions and improve environmental air quality.
4. Data on the lateral exchange of organic C through the catchment will also determe the potential cycles & sinks for C in other water bodies. For e.g., there is significant policy interest in Defra on C fluxes within water column to benthic sediments (e.g. Cefas) via the Marine Strategy Framework which manages sustainable marine resources.
5. Data on how elevated temperatures effects microbial diversity will inform how climate change impacts on microbial biodiversity.
6. Data on fecal indicator organisms (FIO) will inform FIO mitigation by improved agricultural management.
The project increases the effectiveness of public services & policy as follows:
1. Data generated will test & parameterise a model, which can be used by Defra's UKCIP to more accurately predict potential cycles & sinks for C under future climate scenarios, helping Local Authorities (e.g. Hampshire County Council) adapt to climate change.
2. The project gives added value to Defra's Demonstration Test Catchments (DTC) monitoring program with additional nutrient data from sites within the catchment not currently monitored by Defra and will give important information on how different agricultural management practices influence scale of flux of C,N, P cycling in the catchment.
3. Data on C, N & P flux through river food webs will inform Defra's policy on biodiversity & information on how diffuse pollution & N impacts biodiversity decline.
4. Data obtained will inform EA policy of Urban Wastewater Treatment Directive, Habitats Directive & Marine Environment.
5.Data will inform policy on C sequestration & UK C inventories & help to meet the Government's goals for protecting & sustaining natural resources.
Production of trained staff: The project will produce 4 trained PhD students & 9 PDRAs with molecular, analytical, hydrology, ecology and modelling skills who can enter private/public sector marketplace.
Economic benefits: IP resulting from the project will foster industrial collaborators and enhance economic competitiveness of UK.
Timescales for benefits to be realized: The SAG set up in month 1 with representatives from stakeholders, regulators & policymakers (see pathways to impact) will inform the project throughout to ensure policy aims are realised.


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publication icon
Guignard M (2017) Impacts of Nitrogen and Phosphorus: From Genomes to Natural Ecosystems and Agriculture in Frontiers in Ecology and Evolution

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Leitch AR (2014) Impact of genomic diversity in river ecosystems. in Trends in plant science

Description Our project has studied this imbalance of
macronutrients in the context of a lowland
agricultural environment in the UK: the Hampshire
Avon. We have made measurements to
understand the different pathways by which
macronutrients are travelling from grassland fields
through the river system and out to the coast in
different parts of the landscape - including on clay,
sand and chalk geologies. We have also focused
on the extent to which these macronutrients are
being transformed in rivers along their route to the
sea and, in particular, whether they are altered
to form harmless chemical species or potent
greenhouse gases. And we have measured the
bacteria and environmental factors that control
these transformations and alter the magnitude,
rate and timing of the transport and transformation
processes throughout the year.

Our results show that the chalk and clay soils
respond quite differently to fertiliser addition. Chalk
soil produced the most N2O when ammonium
nitrate was added, but the clay soil continued to
release N2O for several days after its application.
On its own, phosphate didn't have a big effect on
N2O but when combined with ammonium nitrate,
the greensand soils also gave a large initial release
of N2O. Warming the plots by just 2-3 °C, during
the dry summer of 2015, caused the grass to die
back, photosynthesis (uptake of CO2) to stop, and
increased the overall release of CO2. The chalk
soils didn't suffer from this problem as much as
the other sites, suggesting they were already
better at coping with dry conditions, which might
give grassland on chalk better chance of survival
or continued healthy growth under future climate
change scenarios for the UK.

The production of greenhouse gases in soils is
caused by soil micro-organisms such as bacteria
using carbon and nitrogen as an energy source.
As part of the process, these micro-organisms
transform these macronutrients from one chemical
form to another. Our challenge was to determine
how the bacteria in soils overlying clay, greensand
and chalk varied in diversity, abundance and activity
over a yearly cycle. It is important to measurethese properties of the soil micro-organisms in
order to fully understand how the production
of greenhouse gases might vary in response to
climate change. Diversity is a measure of the
different types of microorganisms, abundance is
the number of the microorganisms and the activity
measures how active the microorganisms are
in their environment. In order to measure these
properties we collected soils from the same sites
as described above, and extracted the genetic
material from the bacteria present in the soil.
We found an abundance of bacteria in our soils.
There are approximately 1-10 billion bacteria
per gram of soil and the bacterial numbers were
generally similar across geologies. In our soils the
removal of nitrate by denitrification is controlled
by soil temperature and water content - both
environmental factors that are likely to vary in the
future due to the effects of climate change. We
also found the formation of the two greenhouse
gases, nitrous oxide and methane, only occurred
at significant levels in the clay soils. Methane can
be removed from soils by oxidation processes
which turn the methane into carbon dioxide, a less
potent greenhouse gas. The rate of removal of
methane by this process increased as temperature
increased. Thus under climate change scenarios,
clay soils are more likely to be better sinks for
methane. However, we found that when fertilisers
(such as nitrogen and phosphorus) were added to
clay soils methane removal decreased. Therefore,
the management of agricultural practices in clay
soils is crucial, for future levels of greenhouse
gases that will be released to the atmosphere.

Rivers are strongly linked to the landscape that
they flow through. River water was originally rain
that has travelled from the surrounding land via
soil and underlying rocks to the river channel. As
the water moves through the soil it carries with it
chemicals that it has encountered along its route,
such as the macronutrients (nitrogen, phosphorus
and carbon) which are the focus of our study.
The Hampshire Avon is underlain by various
different geologies, with chalk, greensand and
clay being of particular interest to us because
they have differing permeabilities (a measure of
how easy it is for water to move through the soil
or rock). Chalk has the greatest permeability and
clay has the smallest. Thus water travels through
landscapes made of these different geologies via
different routes. In a landscape underlain by chalk
much of the rain will travel through the soil to the
underlying chalk aquifer and may take decades to
reach the river channel. In a landscape dominated
by clay the rainfall can make its way to the river
rapidly by flowing over the soil surface or through
man-made drainage channels that have been
created to make farming possible on these low
permeability, and often waterlogged, soils. We
were interested in the consequences of these
different pathways for the concentrations and
quantity of macronutrients (carbon, nitrogen
and phosphorus) reaching the river channel.
We also wanted to understand how changes in
the pathways by which water travels to the river
channel during different seasons affects the
transport of the nutrients.
To do this we installed probes at each of our sites
to measure water quality along with automatic
water samplers to take water samples at preprogrammed
time intervals. We also measured
water height in the river to calculate river discharge
and we installed pipes (called piezometers) in the
river to measure the direction that water flowed
into and out of the river during different times of
the year. These pipes also allowed us to measure
water quality in the riverbed itself.
We found that the link between groundwater and
the river varied across our six sites. At some sites
our rivers received groundwater throughout the
year, whilst others were continuously losing river
water to the ground. Two of our sites switched
between the river losing water and river gaining
water depending on the time of year.
We found that the concentration of nitrate in
our rivers increased as the permeability of the
landscape increased. This may be a legacy issue,
due to a history of intensive farming practices in
the UK. It takes decades for rainwater to move
from fields to the groundwater, and to the rivers in
these catchments.

One fundamental parameter of rivers to be
assessed is the stream metabolism. This consists
of the primary production by photosynthetic
organisms, such as algae and aquatic plants,
and the respiration (the action of breathing
which produces CO2) by fauna and microbial
communities in the stream. Primary production is
the creation of organic compounds, for example
the growth of plant material in a river, primarily
arising from photosynthesis (which uses light as
a source of energy). These processes are highly
dependent on the local environment and may
differ substantially among rivers.
To assess conditions in the Avon river catchment
we used the state-of-the-art methods to quantify
and characterize stream metabolism at the
streambed and in the water column. The activity in
the streambed is quantified with a novel technique
called eddy covariance, which enables activity
measurements over a large area (tens of m2)
of the streambed, without altering the stream's
4. Metabolism in rivers
Measuring stream metabolism in the Hampshire Avon.
Lorenzo Rovelli and Ronnie Glud (Southern Denmark University)
Eddy covariance system measuring river metabolism in the River Ebble.
natural flow temperature or light regimes. The
technique represents a substantial improvement
over traditionally more invasive approaches.
The investigations covered four seasons and
revealed that each stream was characterized by
highly varying rates of metabolism in the river
water itself. This contrasted with the common
conception that metabolism in river water is low
because suspended algae and microbial densities
are very low in comparison to the abundance
of organisms (such as bacteria) in or on the
streambed. We also observed a clear shift from
net production of organic material during spring
to periods of net degradation of organic material
during autumn and winter. This would be related
to processes such as the growth and die-back
of aquatic plants in these rivers. Clear trends in
stream metabolism were observed in the streams
from clay river reaches, compared to river reaches
underlain by greensand and chalk geology.

We measured production of both carbon dioxide
(CO2) and methane (CH4) in the riverbeds, in both
light and dark conditions. At the same time we
measured the flux of these gases from the river
to the atmosphere (out-gassing). All riverbeds
produced both CO2 and CH4, due to microbial
activity in the sediment. However, the amount of
CO2 out-gassed to the atmosphere was much
higher than could be explained by production
in the riverbed; whilst for CH4 the opposite was
true, with much less being out-gassed than was
produced in the riverbed.

This shows that the microbial production of these
gases is not the most important factor in the flux
to the atmosphere from the river. Instead, for CO2
at least, atmospheric flux was more dependent on
river conditions: during periods of high water flow
after rain, much more CO2 was out-gassed than
under low flow conditions. This may be because
CO2-rich waters from the surrounding catchment
get flushed into the rivers by the rain, and the CO2
is then released to the atmosphere. At the same
time, the production in the riverbeds is responsible
for modulating the amount of flux between the day
and night time. These findings should lead to a
greater understanding of how these important
greenhouse gases are transported between
terrestrial and riverine ecosystems.

Not only did we consider carbon in rivers, but
we also wanted to understand what happens to
nitrogen once it enters a river. There is a global
problem with excess nitrogen in surface waters,
and the UK is no exception to this. It is important
of us to understand the processes by which
nitrogen, in its different forms, is transported
to our rivers and the processes by which these
different forms of nitrogen are transformed in
our rivers. In particular, we want to understand
whether excess nitrogen is simply converted
from one form to another with no overall removal
or are there processes which remove excess
nitrogen permanently by making harmless N2 gas
which is emitted to the atmosphere? All of these
macronutrient processes are driven by microorganisms
(such as bacteria and archaea) which
use carbon and nitrogen species as their food or
energy source.
The most exciting discovery in this research
was that two process that remove nitrogen were
occurring in rivers - denitrification and anaerobic
ammonium oxidation (anammox). Denitrification
is a much-studied pathway of nitrogen removal
whereby micro-organisms convert nitrate to
harmless N2 gas. Anammox is also a microbial
process but involves ammonium and nitrate reacting to form N2 gas that previously was only
thought to occur in estuaries, marine environments
and wastewater treatment plants. As well as
measuring nitrogen removal rates, we also studied
the micro-organisms responsible for carrying out
the anammox process. Many micro-organisms
have preferences as to where they live or particular
needs- for example in the case of bacteria that
carry out anammox, it is widely thought that they
prefer environments that are free from oxygen.
In our rivers we found the presence of anammox
bacteria with particularly high abundance
of a particular gene called hzo (hydrazine
oxidoreductase). This gene was associated with
high rates of the anammox process. Our results
were surprising to us because bacteria that carry
out the anammox process are typically associated
with environments that contain no oxygen unlike
the oxygen-rich environments of chalk streams.
The contribution of anammox to total nitrate
removal from rivers seems to vary across our
different landscape settings; chalk, greensand and
clay. We find anammox is most important in chalk
rivers with a gravel substrate where land-river
connectivity is low. Anammox is least important in
clays were land-river connectivity is high (~30%
and 5% of N2 production, respectively). Finding
that anammox is an active nitrogen removal
process in rivers is important because compared
to denitrification, anammox uses less energy to
remove to nitrogen and does not produce N2O
(a potent greenhouse gas) as a by-product. We
hope to keep researching anammox in river
sediments in the future to better understand what
environmental factors favour this nitrogen removal
We have also shown that microbial communities in
clay and greensand river catchments have higher
rates of respiration than photosynthesis, whereas
chalk rivers have higher rates photosynthesis
than respiration. Ultimately, this leads to different
nutrient-processing functions, helping us understand
that rivers may not all behave the same
after nutrient addition.
Another major task of this research project was
to establish the extent to which C, N and P limit
the growth and reproduction of invertebrates
and fish in these streams. To achieve this, the
biological components (invertebrates, algae,
detritus and fish) at each site were sampled every
two months for one full year. We measured the
abundance and biomass (numbers and mass
per m2) of each species, and have used this
information to determine their production (growth
and reproduction of that species). We also looked
at the C, N and P content of all food items, so that
we can estimate the stocks of these elements in
each system.
The next step was to establish what everything
was eating. We did this in two ways:
a) by looking at the stomach contents of a sample
of the fish (by pumping their stomachs) and
invertebrates (by dissection), and
b) by using stable isotopes, naturally occurring
tracers of carbon and nitrogen that are conserved
between predators and prey.Hence, we constructed a food web for each
stream, where we knew how much of each food
type was eaten by each species. As we knew the
C, N and P content of the food, we could then work
out how much C, N and P they were consuming,
and relate this to their growth and reproduction.
Our results suggest:
1. The invertebrates and fish use a wider variety
of food items in the chalk streams, where
groundwater is an important source. In the
clay streams, where food and nutrients enter
the river from the land by surface and shallow
subsurface flows, there is less variety of food
and everything is competing for the same food.
2. Because there are a wider variety of things
to eat, more species can co-exist in the chalk
streams and hence the numbers and growth
of fish is higher than in the clay rivers.
We have shown that the way the water flows bring
nutrients from the landscape to the river influences
the species and food webs of rivers.
Exploitation Route This consortium project generated a large amount of output with a diverse array of applications which we presented to our stakeholders in June 2016.
Sectors Agriculture, Food and Drink,Communities and Social Services/Policy,Environment

Title Riverine nitrogen gas production by anaerobic ammonium oxidation across contrasting geologies 
Description This dataset contains anaerobic ammonium oxidation (anammox) and denitrification activity of riverine sediments in the Hampshire Avon catchment (UK). Nine rivers within sub-catchments of contrasting geology (clay, sand, chalk) were investigated. Data were obtained via laboratory incubations (potential data) and direct, field-based measurements (in situ data) in summer 2013. Also included are chemical parameters determined in porewaters prior to in situ rate measurements. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact NA