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Quantifying and predicting benthic enrichment : lessons learnt from southern temperate aquaculture systems


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Keeley, NB 2013 , 'Quantifying and predicting benthic enrichment : lessons learnt from southern temperate aquaculture systems', PhD thesis, University of Tasmania.

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The increasing demand for aquaculture products globally is leading to greater demand
for coastal marine farm space, intensification within existing aquaculture areas, and
conversion of production to high value species, especially finfish. Among the many
environmental interactions that arise with finfish aquaculture development, one of the most
dramatic impacts is local-scale organic enrichment of the benthic ecosystem due to deposition
of fish faeces and uneaten feed. A benthic impact is typically evident as severe organic
enrichment beneath finfish cages (e.g. species-poor, near-azoic conditions), with a gradient of
decreasing enrichment extending to background conditions across scales of tens to hundreds
of metres distant from cages.
The overall hypothesis of this thesis was that seabed organic enrichment (degradation
and recovery) can be accurately and quantitatively determined using biological and physicochemical
variables that can be applied across geographic regions and contrasting
environments. This was accompanied by an objective to refine knowledge of processes
underpinning benthic enrichment, and to develop or refine tools for the prediction, monitoring
and management of enrichment effects associated with fish aquaculture. The thesis comprises
six sequential, related chapters that address: site- and region-specific ecological
characterisation of benthic communities and the development on a new environmental
indicator variable; comparisons of existing biological indicators and indices in different
hydrodynamic regimes; application and validation of a depositional model for predicting
effects under very different environmental conditions; and a detailed analysis of long-term
and medium-term recovery from highly enriched states, and consideration of re-impact rates
and implications for farm management strategies. The analyses are based on both targeted
recent studies as well as longer-term monitoring undertaken at six salmon farms situated in
the Marlborough Sounds, New Zealand; four of which are situated in low flow environments,
and two are situated in high flow (dispersive) environments. Characterising the differences
associated with the sites’ dispersive properties is a theme that runs throughout this study.
Chapter 2 used best professional judgement methods to develop a quantitative benthic
enrichment index termed ‘enrichment stage’, which unifies information from biological and physico-chemical variables. The resulting seven stage bounded continuous variable was used
to assign enrichment tolerance groups to benthic taxa using quantile regression splines. A
number of key indicator taxa were discriminated along the enrichment gradient, including
several that were responsive to low-level changes in enrichment stage (ES), but not necessarily
organic matter (%OM), and 10 taxa for which ecological understanding was previously limited.
In Chapter 3, the gradient was also used to evaluate the performance of five benthic indicators
and ten biotic indices for defining organic enrichment under different flow regimes. A subset
of variables was recommended comprising: two biotic indices, total abundance, and a
geochemical variable. A subsequent but related study in Chapter 4 revealed pronounced flowrelated
differences in the magnitude and spatial extent of benthic enrichment. Total
macrofaunal abundances at high-flow sites were nearly an order of magnitude greater than at
comparable low flow sites, representing a significant benthic biomass, and occurred in
conjunction with moderate-to-high species richness and the absence of appreciable organic
accumulation. The atypical ecological conditions associated with high-flow sites were
attributed to i) minimal accumulation of fine sediments, ii) maintenance of aerobic conditions
in near-surface sediments, and iii) an abundant food supply.
Chapter 5 explored the relationship between predicted depositional flux (using
DEPOMOD) and enrichment stage, calculated using the methods developed in the previous
chapters (1 to 3). Observed impacts at farms with contrasting flow regimes were examined to
evaluate the role of modelled resuspension dynamics in determining impacts. When
resuspension was included in the model, net particle export was predicted at the most
dispersive sites. However, significant seabed effects were observed, suggesting that although
the model outputs were theoretically plausible they were inconsistent with the observational
data. When the model was run without resuspension the results were consistent with the
field survey data. This retrospective validation suggested that approximately twice the flux
was needed to induce an effect level at the dispersive sites equivalent to that at the nondispersive
sites. Flux estimates are provided for detectable enrichment and highly enriched
states. This study shows that the association between current flow, sediment resuspension
and ecological impacts is more complex than presently encapsulated within DEPOMOD and
emphasises the need for validation of such models, particularly at dispersive sites.
The final two data chapters (Chapters 6 and 7) examine the spatial and temporal
recovery processes that take place following a highly enriched state. Chapter 6 provides a comprehensive analysis of a long-term (8 year) dataset in relation to a variety of proposed
recovery and remediation definitions. Many challenges associated with quantifying the
endpoint of ‘recovery’ were identified. The concept of dynamic and spatial equilibria proved
to be valid in this situation, and alternate state theories may apply. In combination with
visualisation of plotted data, statistical tests for parallelism in temporal trajectories of cage and
reference sites proved to be an effective method for characterising recovery, but the method
was highly sensitive to window time-length. Simple, univariate indicators of enrichment
tended to be less sensitive, and indicate recovery earlier, than more complex multivariate
indicators. Recovery was assessed to be complete after approximately five years, but there
was some evidence of on-going instability in the composition of the macrofauna, which was
partly attributed to spatial and temporal processes and patterning in the macrobenthos. The
last data chapter (Chapter 7) examined shorter-term recovery and re-impact patterns and
revealed some interesting successional patterns in time and space, especially between %OM,
TFS and abundances of opportunistic taxa. The discussion brings together findings from the
targeted and long-term studies to reveal alternate oscillations between sediment chemistry
and biological response, which have temporally distinct signals. It is proposed that the large
oscillations that occur in the early stages of recovery represent the extreme end of the
environmental instability that occurs as a result of a severe perturbation (in this case,
cessation of extreme enrichment) that abates through time as recovery ensues.
This integrated study has a number of important implications for the management of
organic enrichment in general but is especially pertinent for fish farming. In particular,
recommendations are made regarding the i) adequacy of chemical and biological benthic
indicators and their performance in typical non-dispersive and atypical dispersive sites; ii) use
and applicability of depositional models in the same environments with emphasis on the role
of resuspension, and iii) timing and approach for reintroduction of impacts, with respect to
monitoring and management of rotational fallowing strategies to ensure on-going

Item Type: Thesis - PhD
Authors/Creators:Keeley, NB
Keywords: benthic ecology, organic enrichment, salmon farm, seabed, recovery, deposition
Copyright Information:

Copyright 2013 the Author

Additional Information:

Chapter 2 appears to be the equivalent of a post-print version of an article published as: Keeley, N.B., MacLeod, C.K., Forrest, B.M. 2012. Combining best professional judgement and quantile regression splines to improve characterisation of macrofaunal responses to enrichment. Ecological indicators, 12(1), 154-166.

Chapter 3 appears to be the equivalent of a post-print version of an article published as: Keeley N.B., Forrest, B.M., Crawford, C., Macleod, C.K. 2012. Exploiting salmon farm benthic enrichment gradients to evaluate the regional performance of biotic indices and environmental indicators. Ecological indicators 23, 453-466.

Chapter 4 appears to be the equivalent of a post-print version of an article published as: Keeley, N.B., Forrest, B.M., MacLeod, C.K. 2013. Novel observations of benthic enrichment in contrasting flow regimes with implications for marine farm monitoring and management. Marine pollution bulletin, 66(1-2), 105-116

Chapter 5 appears to be the equivalent of a post-print version of an article published as: Keeley, N.B., Cromey, C.J., Goodwin, E.O., Gibbs, M.T., Macleod, C.M. 2013. Predictive depositional modelling (DEPOMOD) of the interactive effect of current flow and resuspension on ecological impacts beneath salmon farms. Aquaculture environment interactions 3(3), 275-291. The article was published under a Creative Commons Attribution 3.0 Unported (CC BY 3.0) license.

Chapter 6 appears to be the equivalent of a pre or post-print version of an article published as: Keeley, N.B., MacLeod, C.K., Hopkins, G.A., Forrest, B.M. 2014. Spatial and temporal dynamics in macrobenthos during recovery from salmon farm induced organic enrichment: when is recovery complete? Marine pollution bulletin, 80(1-2), 250-262.

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