Macroalgae and microbial ecology in assessing nitrogen pollution of coastal regions

Overview

Tracking nitrogenous pollution sources, transport and sinks in dynamic coastal and estuarine waters presents a significant challenge, conventionally requiring significant water sample collection and understanding of complex flow patterns. Stable isotope ratios are an excellent tool to discern, or ascertain, biological, ecological and environmental processes. The modern nitrogen cycle has been heavily influenced by human activity. Waste products, such as sewage and fish farm effluent, are normally more enriched in 15N than seawater (Vizzini and Mazzola, 2004), whereas agricultural waste products are normally more depleted in 15N (Heaton, 1986). This has led to the application of using nitrogen isotope ratios of marine sediments, marine organisms and macroalgae to monitor nitrogen pollution/contamination (e.g., Savage 2005). Nitrogen isotope ratios can also be measured in dissolved inorganic nitrogen isotopes taken directly from the water (Deutsch et al. 2006; Korth et al. 2014). However, dissolved inorganic nitrogen isotopes is analytically more time-consuming and costly. To address this difficulty, nitrogen isotope ratios in macroalgal tissues have been utilized to discern sources of excess nutrients (Costanzo et al. 2001, 2005; Dailer et al. 2012). Groecke et al. (2017) indicate that the translocation of macroalgae with isotopically distinct signatures could be used as a rapid, cost-efficient method for nitrogen biomonitoring in estuarine environments.

Coastal and estuarine eutrophication is a widespread problem across the United Kingdom and often has multiple sources. The Environment Agency use macroalgae extent and biomass as an indicator of eutrophication; there are quite a number of UK estuaries that fail to meet Water Framework Directive standards due to excessive macroalgae growth. Macroalgae blooms have numerous deleterious effects on coastal environments; for example, smothering delicate intertidal seagrass habitats and saltmarsh environments causing bleaching and plant die back, which ultimately leads to coastal erosion. However, understanding the sources of nutrients contributing to the problem is extremely difficult and time consuming, especially when nutrient inputs are entering dynamic coastal ecosystems. Tracing the temporal flux of nutrients is further complicated by dynamic processing and repackaging by the microbiota associated with water, sediment and the indicator organism (macroalgae). To more fully understand the fate of nutrients within an ecosystem requires a detailed evaluation of the bridging role that the microbiota plays, linking environment to macroalgae. Ongoing work at Newcastle is showing dynamic (and strongly seasonal) exchanges between the microbiota associated with discharge water and the microbial communities living on and within macroalgae beds – particularly bacteria involved with nitrogen cycling. Coupling isotopic and microbial ecology of macroalgae allows for an innovative, cost-effective tool to determine the nutrient source and therefore direct efforts and put measures in place to reduce specific nutrient inputs, and environmental improvements.

This studentship will generate a modern database of nitrogen isotopes in macroalgae and the associated microbial communities from coastal marine environments around the north-east coast of England and Scotland. Specific estuaries and coastal regions will be assessed to determine seasonal variability. Laboratory studies will be employed to make isotopically-labelled macroalgae that will be subsequently employed in nitrogen-sensitive locations. These investigations will be used to pin-point nitrogen sources and develop local plans and procedures for remediating /reducing the nitrogen loading.

Methodology

The student will learn fieldwork and laboratory techniques associated with seawater and macroalgae analysis related to water quality and environmental analysis. Stable isotope analysis is fundamental to this project and will be completed in the Stable Isotope Biogeochemistry Laboratory (SIBL) at Durham University under the supervision of Dr Groecke. Macroalgae photophysiology will be monitored using imaging pulse amplitude modulated fluorometry. Microbial analysis is well established with Dr Caldwell’s lab, using the Illumina MiSeq platform with associated bioinformatics pipelines in Mothur and R (Robinson et al. 2016, 2018), including a novel microbial source tracking tool (FEAST: fast expectation-maximization for microbial source tracking; Shenhav et al. 2019). The student will ground truth the field data using isotope pulse-chase experiments, and will construct a nitrogen budget for the macroalgae and microbiota for various targeted locations around the north-east of England and Scotland.

Project Timeline

Year 1

Year 1: Fieldwork will be undertaken in the first 4 months of the studentship to generate a modern collection of macroalgae from around the north-east coast of England and Scotland during the winter months and as a means to train the student in the sampling and analytical techniques, and bioinformatics that will be the mainstay of Year 2. This will consist of multiple relatively short duration fieldtrips (e.g. 1–2 weeks). The macroalgae will be analysed in SIBL at Durham University, with photophysiology and biochemical data collected at Newcastle University.

Year 2

Year 2: Experimental studies will be conducted at Newcastle University and will involve the collection and incubation of macroalgae growing tips in different environmental conditions and seawater compositions. In addition, several locations will be selected to monitor nitrogen concentrations and isotopic and microbial composition of seawater and macroalgae to determine seasonal variability. During this year, sites of specific interest will be selected for environmental assessment using the translocation of isotopically-labelled macroalgae.

Year 3

Year 3: Selected sites will continue to be monitored using macroalgae present at the location and translocated macroalgae that is isotopically produced in the laboratory. Guided by Year 2 data, pulse-chase experiments paired with metabolomic analysis will be conducted to derive a complete time integrated nitrogen budget. These data will then be modelled for the north-east coast of England and Scotland. Publications, reports and presentations will be finalised during this year in order to complete the studentship by the end of year three.

Year 3.5

The student will develop the model into a policy document that can be used to guide industry investment decisions and can be used to inform environmental regulation. The student will be encouraged to actively engage with key decision makers in the sector.

Training
& Skills

Durham University will provide training in stable isotope mass spectrometry. Newcastle University will deliver training in microbial analyses, bioinformatics and ecological modelling as part of the Plant and Microbial Biosciences and the Ecological Modelling academic groups within the School of Natural and Environmental Sciences. The student will be trained in microbial sequencing through a long-established collaboration between Dr Caldwell’s group and the NU-OMICS facility at Northumbria University.

References & further reading

Costanzo, S.D., O’Donohue, M.J., Dennison, W.C., Loneragan, N.R., Thomas, M., 2001. Marine Pollution Bulletin 42:149-156.
Costanzo, S.D., Udy, J., Longstaff, B., Jones, A., 2005. Marine Pollution Bulletin 51:212-217.
Dailer, M.L., Smith, J.E., Smith, C.M., 2012. Harmful Algae 17:111-125.
Deutsch, B., Mewes, M., Liskow, I., Voss, M., 2006. Organic Geochemistry 37:1333-1342.
Groecke, D.R., Racionero Gómez, B., Marschalek, J.W., Greenwell, H.C. (2017). Chemosphere 184:1175-1185.
Heaton, T.H.E., 1986. Chemical Geology 59:87-102.
Korth, F., Deutsch, B., Frey, C., Moros, C., Voss, M., 2014. Biogeosciences 11:4913-4924.
Robinson, G., Caldwell, G.S., Wade, M.J., Free, A., Jones, C.L.W., Stead, S.M., 2016. Scientific Reports, 6:38850.
Robinson, G., MacTavish, T., Savage, C., Caldwell, G.S., Jones, C.L.W., Probyn, T., Eyre, B.D., Stead, S.M., 2018. Biogeosciences, 15:1863-78.
Savage, C., 2005. Ambio 34:145-150.
Shenhav, L., Thompson, M., Joseph, T.A., Briscoe, L., Furman, O., Bogumil, D., Mizrahi, I., Pe’er I., Halpern, E. 2019. Nature Methods 16:627-632.
Vizzini, S., Mazzola, A., 2004. Marine Pollution 49:61-70.

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