Joanne Ellis

Mangrove growth in New Zealand estuaries: the role of nutrient enrichment at sites with contrasting rates of sedimentation

Mangrove forest coverage is increasing in the estuaries of the North Island of New Zealand, causing changes in estuarine ecosystem structure and function. Sedimentation and associated nutrient enrichment have been proposed to be factors leading to increases in mangrove cover, but the relative importance of each of these factors is unknown. We conducted a fertilization study in estuaries with different sedimentation histories in order to determine the role of nutrient enrichment in stimulating mangrove growth and forest development. We expected that if mangroves were nutrient-limited, nutrient enrichment would lead to increases in mangrove growth and forest structure and that nutrient enrichment of trees in our site with low sedimentation would give rise to trees and sediments that converged in terms of functional characteristics on control sites in our high sedimentation site. The effects of fertilizing with nitrogen (N) varied among sites and across the intertidal zone, with enhancements in growth, photosynthetic carbon gain, N resorption prior to leaf senescence and the leaf area index of canopies being significantly greater at the high sedimentation sites than at the low sedimentation sites, and in landward dwarf trees compared to seaward fringing trees. Sediment respiration (CO2 efflux) was higher at the high sedimentation site than at the low one sedimentation site, but it was not significantly affected by fertilization, suggesting that the high sedimentation site supported greater bacterial mineralization of sediment carbon. Nutrient enrichment of the coastal zone has a role in facilitating the expansion of mangroves in estuaries of the North Island of New Zealand, but this effect is secondary to that of sedimentation, which increases habitat area and stimulates growth. In estuaries with high sediment loads, enrichment with N will cause greater mangrove growth and further changes in ecosystem function.

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.

First evaluation of foraminiferal metabarcoding for monitoring environmental impact from an offshore oil drilling site

At present, environmental impacts from offshore oil and gas activities are partly determined by measuring changes in macrofauna diversity. Morphological identification of macrofauna is time-consuming, expensive and dependent on taxonomic expertise. In this study, we evaluated the applicability of using foraminiferal-specific metabarcoding for routine monitoring. Sediment samples were collected along distance gradients from two oil platforms off Taranaki (New Zealand) and their physico-chemical properties, foraminiferal environmental DNA/RNA, and macrofaunal composition analyzed. Macrofaunal and foraminiferal assemblages showed similar shifts along impact gradients, but responded differently to environmental perturbations. Macrofauna were affected by hypoxia, whereas sediment grain size appeared to drive shifts in foraminifera. We identified eight foraminiferal molecular operational taxonomic units that have potential to be used as bioindicator taxa. Our results show that metabarcoding represents an effective tool for assessing foraminiferal communities near offshore oil and gas platforms, and that it can be used to complement current monitoring techniques.

Science and Societal Partnerships to Address Cumulative Impacts

Funding and priorities for ocean research are not separate from the underlying sociological, economic, and political landscapes that determine values attributed to ecological systems. Here we present a variation on science prioritisation exercises, focussing on inter-disciplinary research questions with the objective of shifting broad scale management practices to better address cumulative impacts and multiple users. Marine scientists in New Zealand from a broad range of scientific and social-scientific backgrounds ranked 48 statements of research priorities. At a follow up workshop, participants discussed five over-arching themes based on survey results. These themes were used to develop mechanisms to increase the relevance and efficiency of scientific research while acknowledging socio-economic and political drivers of research agendas in New Zealand’s ocean ecosystems. Overarching messages included the need to: 1) determine the conditions under which ‘surprises’ (sudden and substantive undesirable changes) are likely to occur and the socio-ecological implications of such changes; 2) develop methodologies to reveal the complex and cumulative effects of change in marine systems, and their implications for resource use, stewardship, and restoration; 3) assess potential solutions to management issues that balance long-term and short-term benefits and encompass societal engagement in decision-making; 4) establish effective and appropriately resourced institutional networks to foster collaborative, solution-focused marine science; and 5) establish cross-disciplinary dialogues to translate diverse scientific and social-scientific knowledge into innovative regulatory, social and economic practice. In the face of multiple uses and cumulative stressors, ocean management frameworks must be adapted to build a collaborative framework across science, governance and society that can help stakeholders navigate uncertainties and socio-ecological surprises.

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence

The semi-enclosed nature of the Red Sea (20.2°N–38.5°N) makes it a natural laboratory to study the influence of environmental gradients on microbial communities. This study investigates the composition and structure of microbial prokaryotes and eukaryotes using molecular methods, targeting ribosomal RNA genes across different regions and seasons. The interaction between spatial and temporal scales results in different scenarios of turbulence and nutrient conditions allowing for testing of ecological theory that categorizes the response of the plankton community to these variations. The prokaryotic reads are mainly comprised of Cyanobacteria and Proteobacteria (Alpha and Gamma), with eukaryotic reads dominated by Dinophyceae and Syndiniophyceae. Periodic increases in the proportion of Mamiellophyceae and Bacillariophyceae reads were associated with alterations in the physical oceanography leading to nutrient increases either through the influx of Gulf of Aden Intermediate Water (south in the fall) or through water column mixing processes (north in the spring). We observed that in general dissimilarity amongst microbial communities increased when nutrient concentrations were higher, whereas richness (observed OTUs) was higher in scenarios of higher turbulence. Maximum abundance models showed the differential responses of dominant taxa to temperature giving an indication how taxa will respond as waters become warmer and more oligotrophic.

A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations

Standardized ecosystem-based monitoring surveys are critical for providing information on marine ecosystem health. Environmental DNA/RNA (eDNA/eRNA) metabarcoding may facilitate such surveys by quickly and effectively characterizing multi-trophic levels. In this study, we assessed the suitability of eDNA/eRNA metabarcoding to evaluate changes in benthic assemblages of bacteria, Foraminifera and other eukaryotes along transects at three offshore oil and gas (O&G) drilling and production sites, and compared these to morphologically characterized macro-faunal assemblages. Bacterial communities were the most responsive to O&G activities, followed by Foraminifera, and macro-fauna (the latter assessed by morphology). The molecular approach enabled detection of hydrocarbon degrading taxa such as the bacteria Alcanivorax and Microbulbifer at petroleum impacted stations. Most identified indicator taxa, notably among macro-fauna, were highly specific to site conditions. Based on our results we suggest that eDNA/eRNA metabarcoding can be used as a stand-alone method for biodiversity assessment or as a complement to morphology-based monitoring approaches.

Mechanisms and risk of cumulative impacts to coastal ecosystem services: An expert elicitation approach

Coastal environments are some of the most populated on Earth, with greater pressures projected in the future. Managing coastal systems requires the consideration of multiple uses, which both benefit from and threaten multiple ecosystem services. Thus understanding the cumulative impacts of human activities on coastal ecosystem services would seem fundamental to management, yet there is no widely accepted approach for assessing these. This study trials an approach for understanding the cumulative impacts of anthropogenic change, focusing on Tasman and Golden Bays, New Zealand. Using an expert elicitation procedure, we collected information on three aspects of cumulative impacts: the importance and magnitude of impacts by various activities and stressors on ecosystem services, and the causal processes of impact on ecosystem services. We assessed impacts to four ecosystem service benefits - fisheries, shellfish aquaculture, marine recreation and existence value of biodiversity-addressing three main research questions: (1) how severe are cumulative impacts on ecosystem services (correspondingly, what potential is there for restoration)?; (2) are threats evenly distributed across activities and stressors, or do a few threats dominate?; (3) do prominent activities mainly operate through direct stressors, or do they often exacerbate other impacts? We found (1) that despite high uncertainty in the threat posed by individual stressors and impacts, total cumulative impact is consistently severe for all four ecosystem services. (2) A subset of drivers and stressors pose important threats across the ecosystem services explored, including climate change, commercial fishing, sedimentation and pollution. (3) Climate change and commercial fishing contribute to prominent indirect impacts across ecosystem services by exacerbating regional impacts, namely sedimentation and pollution. The prevalence and magnitude of these indirect, networked impacts highlights the need for approaches like this to understand mechanisms of impact, in order to develop strategies to manage them.

Cross shelf benthic biodiversity patterns in the Southern Red Sea

The diversity of coral reef and soft sediment ecosystems in the Red Sea has to date received limited scientific attention. This study investigates changes in the community composition of both reef and macrobenthic communities along a cross shelf gradient. Coral reef assemblages differed significantly in species composition and structure with location and depth. Inner shelf reefs harbored less abundant and less diverse coral assemblages with higher percentage macroalgae cover. Nutrient availability and distance from the shoreline were significantly related to changes in coral composition and structure. This study also observed a clear inshore offshore pattern for soft sediment communities. In contrast to the coral reef patterns the highest diversity and abundance of soft sediment communities were recorded at the inshore sites, which were characterized by a higher number of opportunistic polychaete species and bivalves indicative of mild disturbance. Sediment grain size and nutrient enrichment were important variables explaining the variability. This study aims to contribute to our understanding of ecosystem processes and biodiversity in the Red Sea region in an area that also has the potential to provide insight into pressing topics, such as the capacity of reef systems and benthic macrofaunal organisms to adapt to global climate change.

Multiple stressor effects on marine infauna: responses of estuarine taxa and functional traits to sedimentation, nutrient and metal loading

Sedimentation, nutrients and metal loading to coastal environments are increasing, associated with urbanization and global warming, hence there is a growing need to predict ecological responses to such change. Using a regression technique we predicted how maximum abundance of 20 macrobenthic taxa and 22 functional traits separately and interactively responded to these key stressors. The abundance of most taxa declined in response to sedimentation and metal loading while a unimodal response was often associated with nutrient loading. Optimum abundances for both taxa and traits occurred at relatively low stressor levels, highlighting the vulnerability of estuaries to increasing stressor loads. Individual taxa were more susceptible to stress than traits, suggesting that functional traits may be less sensitive for detecting changes in ecosystem health. Multiplicative effects were more common than additive interactions. The observed sensitivity of most taxa to increasing sedimentation and metal loading and the documented interaction effects between multiple stressors have important implications for understanding and managing the ecological consequences of eutrophication, sedimentation and contaminants on coastal ecosystems.

Group elicitations yield more consistent, yet more uncertain experts in understanding risks to ecosystem services in New Zealand bays

The elicitation of expert judgment is an important tool for assessment of risks and impacts in environmental management contexts, and especially important as decision-makers face novel challenges where prior empirical research is lacking or insufficient. Evidence-driven elicitation approaches typically involve techniques to derive more accurate probability distributions under fairly specific contexts. Experts are, however, prone to overconfidence in their judgements. Group elicitations with diverse experts can reduce expert overconfidence by allowing cross-examination and reassessment of prior judgements, but groups are also prone to uncritical “groupthink” errors. When the problem context is underspecified the probability that experts commit groupthink errors may increase. This study addresses how structured workshops affect expert variability among and certainty within responses in a New Zealand case study. We find that experts’ risk estimates before and after a workshop differ, and that group elicitations provided greater consistency of estimates, yet also greater uncertainty among experts, when addressing prominent impacts to four different ecosystem services in coastal New Zealand. After group workshops, experts provided more consistent ranking of risks and more consistent best estimates of impact through increased clarity in terminology and dampening of extreme positions, yet probability distributions for impacts widened. The results from this case study suggest that group elicitations have favorable consequences for the quality and uncertainty of risk judgments within and across experts, making group elicitation techniques invaluable tools in contexts of limited data.