A systematic review of the treatment of phosphorus in biogeochemical and ecological models

Aquatic biogeochemical and ecological models have become increasingly detailed, both in resolution and in the number of processes and components represented. It is timely to pause and take stock of these models. Do these models accurately reflect our current understanding of the biogeochemistry of aquatic systems? Is their predictive performance improving? Are they improving in the range of system properties and behaviours that can be predicted? Where there is variety in approaches or algorithms, can we demonstrate that one method is better than another and should be preferred? This review begins this process, focusing on how phosphorus cycles are represented in models of aquatic systems. A systematic review of 71 distinct published biogeochemical and ecological models of aquatic systems in 167 applications finds: Lake models and marine models are very similar, while river and catchment models differ. This appears largely to be due to different traditions within modelling communities rather than real differences in biogeochemical processes. River models tend to have simpler representations of phosphorus than lake or marine models. The performance of river models is usually quantitatively assessed using standard metrics (77% of publications include some performance metrics), while this is usually not the case for lake models (35% include some quantitative metric) or marine models (only 29%). Across all three domains, models are becoming more complex over time (Figure 1), but there is no clear evidence that this is improving the predictive performance of models. The appropriate degree of model complexity depends on a number of factors, including the resources and data available to support the model and the purpose for which the model is being developed. Simpler models can be more rigorously calibrated and evaluated and may have just as much predictive capacity, while physiologically-based models, which are usually more complex, may be more generalisable and better able to anticipate unexpected responses and emergent properties of the system. A range of phosphorus papers not included in current models is discussed, including the biogeochemistry of organic phosphorus, the biogeochemical implications of flow through sediments, and sediment drying and re-wetting. In some aquatic environments, these processes are likely to be important. It is concluded that a broader community toolkit of model algorithms is required

How integrative modelling can break down disciplinary silos

This paper has been published in a peer-reviewed journal as: Kragt, M.E., Robson, B.J. & Macleod, C.J.A. (2013) Modellers’ roles in structuring integrative research projects. Environmental Modelling & Software, 39(1): 322-330. DOI: 10.1016/j.envsoft.2012.06.015Environmental modelling, Interdisciplinary research, Transdisciplinarity, Integration, Research Methods/ Statistical Methods, Q57, Y80, Z19,

Incorporating a generalised additive model of river nutrient concentrations into a mechanistic receiving water model

eReefs is a large, collaborative project that is building catchment and marine models for Australia's Great Barrier Reef Lagoon (GBRL), a world-heritage environmental asset. The eReefs package includes three-dimensional mechanistic biogeochemical, sediment and hydrodynamic models for the entire GBRL on 4 km and 1 km grid scales, along with a relocatable coastal and estuary model (RECOM) that can be nested within the larger-scale models. Source Catchment models developed by the Government of Queensland for each GBRL catchment will be used to run scenarios to predict the effects of management and land use changes on nitrogen, phosphorus and sediment loads reaching each river. For day-to-day near-real-time and forecast-mode running of the marine models, however, another approach is needed to provide the river loads of sediments, dissolved and particulate loads required as boundary conditions. Generalised Additive Models (GAMs) have been shown (e. g. Kuhnert et al., 2012) to be powerful tools for the prediction of suspended sediment and particulate nutrient loads in tropical rivers. Here, we extend previous work to build GAMs that are able to predict concentrations of suspended sediments, dissolved and particulate nutrients in the Fitzroy River (Queensland) on a daily time-step. In developing the GAMs, we tested a number of routinely and frequently measured meteorological and hydrological variables for potential predictive power. The new terms considered included water temperature (which may alter biogeochemical processing rates), air temperature (a more reliably measured proxy for water temperature), electrical conductivity (which may reflect the influence of particular subcatchment sources), barometric pressure (an indicator of local storm activity), wind stress (which may affect resuspension and mixing in the river and its weirs) and flow from river tributaries (a direct measure of the influence of particular subcatchments). The models generated were tested with regard to the validity of key statistical assumptions, and were then validated against a subset of observational data that had been held back from the original calibration. The strongest models included flow in the Fitzroy River, flow in one or more tributaries, and a discounted flow term that reflected flow in the preceding days and weeks. Models that did not include tributary flow were able to predict concentrations of particulate, but not dissolved materials. Neither meteorological terms nor electrical conductivity proved to be useful predictors, while water temperature was of marginal value. The final GAM provide more accurate predictions on a daily time-step than previously available methods, for both dissolved and particulate materials, and is being used to provide time-series input (e. g. Figure 1) to mechanistic marine models

Fish and Fishing Communities: Understanding Ancient and Modern Fisheries through Archaeological Fish Remains

The papers in this special issue of the International Journal of Osteoarchaeology (IJO) were presented at the 19th biennial meeting of the Fish Remains Working Group (FRWG) of the International Council of Archaeozoology (ICAZ), which was held in Alghero and Stintino, Sardinia, Italy, from October 1–7, 2017. Entitled Fish and Fishing Communities: Understanding Ancient and Modern Fisheries through Archaeological Fish Remains, this conference brought together a diverse group of 120 scholars from 29 countries with specializations in archaeology, zoology, history, and anthropology. These fish specialists ranged from undergraduate students to emeritus professors

eReefs modelling suggests Trichodesmium may be a major nitrogen source in the Great Barrier Reef

Trichodesmium can fix nitrogen that is later released into the water column. This process may be a major source of ‘new’ nitrogen in the Great Barrier Reef (GBR), but to date this contribution is poorly resolved. We have estimated the seasonal, spatial and annual contributions of Trichodesmium to the annual nitrogen budget of the GBR using the eReefs marine models. Models were run for the interval December 2010 to November 2012. During this period La Niña conditions produced record rainfalls and widespread flooding of GBR catchments. Model outputs suggest nitrogen fixation by Trichodesmium in the GBR (which covers about 348,000 km2) contributes approximately 0.5 MT/yr, exceeding the total average annual riverine nitrogen loads (0.05–0.08 MT/yr). Nitrogen fixation loads are exceeded by riverine loads only if the comparison is restricted to inshore waters and during the wet season. The river pollution is likely to have impacts in freshwater wetlands, mangroves, seagrasses and in-shore coral reefs; while Trichodesmium blooms are likely to be less intense but more widespread and affect offshore coral reefs and other oceanic ecosystems. Phosphorus and iron are suggested to be potential drivers of Trichodesmium growth and nitrogen fixation. This result is provisional but reinforces the need for more detailed assessment and reliable quantification of the annual nitrogen contribution from nitrogen fixation in the GBR and other coastal waters. Such advances will improve understandings of the role of terrestrial nitrogen loads in the GBR and of terrestrial phosphorus and iron loads which can modulate Trichodesmium abundance. These findings will help to broaden the focus of water quality management programmes and support management to improve GBR water quality

Becaplermin gel in the treatment of pressure ulcers: a phase II randomized, double-blind, placebo-controlled study

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72172/1/j.1524-475X.1999.00141.x.pd

Model for deriving benthic irradiance in the Great Barrier Reef from MODIS satellite imagery

We demonstrate a simple, spectrally resolved ocean color remote sensing model to estimate benthic photosynthetically active radiation (bPAR) for the waters of the Great Barrier Reef (GBR), Australia. For coastal marine environments and coral reefs, the underwater light field is critical to ecosystem health, but data on bPAR rarely exist at ecologically relevant spatio-temporal scales. The bPAR model presented here is based on Lambert-Beer’s Law and uses: (i) sea surface values of the downwelling solar irradiance, Es(λ); (ii) high-resolution seafloor bathymetry data; and (iii) spectral estimates of the diffuse attenuation coefficient, Kd(λ), calculated from GBR-specific spectral inherent optical properties (IOPs). We first derive estimates of instantaneous bPAR. Assuming clear skies, these instantaneous values were then used to obtain daily integrated benthic PAR values. Matchup comparisons between concurrent satellite-derived bPAR and in situ values recorded at four optically varying test sites indicated strong agreement, small bias, and low mean absolute error. Overall, the matchup results suggest that our benthic irradiance model was robust to spatial variation in optical properties, typical of complex shallow coastal waters such as the GBR. We demonstrated the bPAR model for a small test region in the central GBR, with the results revealing strong patterns of temporal variability. The model will provide baseline datasets to assess changes in bPAR and its external drivers and may form the basis for a future GBR water-quality index. This model may also be applicable to other coastal waters for which spectral IOP and high-resolution bathymetry data exist

Developing an effective marine eDNA monitoring: eDNA detection at pre-outbreak densities of corallivorous seastar (Acanthaster cf. solaris)

Outbreaks of the corallivorous Crown-of-Thorns Seastar (CoTS) Acanthaster cf. solaris contribute significantly to coral reef loss. Control of outbreaks is hampered because standard monitoring techniques do not detect outbreaks at early (low density) stages, thus preventing early intervention. We previously demonstrated that eDNA monitoring can detect CoTS at intermediate densities. Here, we test whether detection probability can be improved by (i) targeted site selection or collection at specific times and (ii) moving from an average eDNA copy number approach (based on the limit of quantification) to a presence/absence approach (based on the limit of detection). Using a dataset collected over three years and multiple reef sites, we demonstrated that adding water residence age, sea surface level and temperature into generalized linear models explained low amounts of variance of eDNA copy numbers. Site specific CoTS density, by contrast, was a significant predictor for eDNA copy numbers. Bayesian multi-scale occupancy modelling of the presence/absence data demonstrated that the probability of sample capture (theta) on most reefs with intermediate or high CoTS densities was >0.8. Thus, confirming CoTS presence on these reefs would only require 2-3 samples. Sample capture decreased with decreasing CoTS density. Collecting ten filters was sufficient to reliably (based on the lower 95 % Credibility Interval) detect CoTS below nominal outbreak levels (3 Ind. ha-1). Copy number-based estimates may be more relevant to quantify CoTS at higher densities. Although water residence age did contribute little to our models, sites with higher residence times may serve as sentinel sites accumulating eDNA. The approach based on presence or absence of eDNA facilitates eDNA monitoring to detect CoTS densities below outbreak thresholds and we continue to further develop this method for quantification

Aquatic food web structure and the flow of carbon

Carbon cycling is a cornerstone concept of ecosystem ecology, which has implications for climate change, ecosystem health, and human activities.  This review investigates pathways of carbon within freshwater ecosystems, the role of terrestrial carbon in food webs, and the effects of food web structure on C emissions.  Carbon may co-limit primary production even in waters super-saturated with CO2.  Allochthonous carbon-subsidies make most lakes and rivers net heterotrophic; however, the use of carbon-subsidies by the food web (FW) may be limited by low nutritional quality of terrestrial C-compounds and the inability of bacteria to synthesise polyunsaturated fatty acids (PUFA), which are essential for metazoan growth.  Bacterivorous nanoflagellates which can synthesise PUFA are likely to create a channel connecting allochthonous C with metazoan production in some water bodies.  Published studies suggest that FW structure may affect: carbon fluxes in and out of lake ecosystems; carbon accumulation and distribution within food webs; burial of carbon and carbon sequestration.  Food web structure and nutrients can affect the carbon-emission/sequestration ratio and shift the state of the aquatic ecosystem between being a source or a sink for atmospheric carbon.  Small lakes, such as farm ponds, are the dominant type of world fresh waters with highest carbon burial rates.  Their productivity and FW structure are often modified by humans through nutrient fertilisation and fisheries management.  We hypothesise that the planned management of these activities targeting a desirable emission/sequestration ratio, can be used as a tool for the reduction of carbon emissions to the atmosphere