title: Carbon dynamics in restiad peatlands across different timescales

authors: Ratcliffe, Joshua Lee

subjects: bog

abstract: Peatlands contain one of the largest terrestrial carbon stores on the planet, and one which is known to interact with climate and global biogeochemical cycling of nutrients. Peatlands maintain their carbon primarily through a high and stable water table which restricts decomposition, and large amounts of carbon can be lost upon drying. However, peatlands are also characterised by non-linear responses to external forcing with a complex array of internal feedbacks which tend to dominate ecosystem response over long-timescales and may amplify or dampen external influences. This has made predicting the effects of environmental change, beyond a few years, highly challenging. Here we use CO₂ fluxes and down-core measurements of carbon accumulation to study the drivers of peatland carbon exchange across a wide range of timescales. First of all, we compare contemporary CO₂ fluxes at two raised bogs, one of which is extremely dry in an international context (Moanatuatua), with the summer water table drawdown approaching one metre, and another where the water table is high and stable (Kopuatai). We found that despite the low and fluctuating water table in the impacted bog the site remained a sink for CO₂ which is strong in an international context, but reduced compared to the wet bog. A key factor in the wet bog being able to maintain a net sink for CO₂ was the enhanced photosynthetic capacity compared to the wetter bog, especially in summer, which was able to partially compensate for enhanced ecosystem respiration. There was a clear difference in how the two sites responded to contemporaneous water table drawdown, which was consistent with differences seen across wet and dry bogs in the international literature. We found plant productivity to be restricted at the dry bog, at both wet and dry extremes, while at the wet bog water table lowering stimulated ecosystem respiration, with neither effect being consistent across both bogs.
To further investigate how the dry bog, Moanatuatua, has adapted to low water tables we re-analysed CO₂ flux data from 1999 and 2000, a period at least several years after the water table initially dropped, and we compared this flux to the present day (after a 16 year gap). Re-analysis of the older data showed that in 1999 and 2000 Moanatuatua was a moderate source for CO₂ with elevated ecosystem respiration and lower photosynthetic capacity compared to the present day. We attribute the change in photosynthetic capacity to the increased cover of the woody shrub Epacris Pauciflora, while a long term decline in ER would be consistent with changes in peat physical and chemical qualities as peat degrades making it further resistant to microbial decay.
In order to contextualise the CO₂ flux records and assess the drivers of carbon accumulation at the 50-100 year timescale we measured down-core C accumulation in unprecedented detail for a New Zealand bog, with supporting records available for fires, climate, eruptive events and plant species changes available from published and unpublished records at Moanatuatua. Contrary to our initial expectations, we found elevated C accumulation to be associated with at least three separate eruptive events, and possibly two others, with carbon accumulation rates increasing rapidly from a baseline typical of long-term accumulation rates, e.g. ~22 g C m⁻² yr⁻¹ to one which is more typical of contemporary uptake, 80-140 g C m⁻² yr⁻¹ . The complex eruptive history of the bog at this time makes it difficult to isolate any other effects, for instance climate.
Geochemical analysis of the peat suggests increased phosphorus inputs as a mechanism for rapid C accumulation, with the peat stoichiometry recording a shift towards phosphorus abundance relative to carbon and nitrogen. The eruptive events linked to elevated carbon accumulation rates are also known to contain phosphorus within the volcanic glass and the mineral apatite, both of which would be expected to weather and become biologically available due both to processes within the eruptive plume and within the bog post-deposition. As such we have found the restiad bogs studied to be highly resilient to water-table drawdown in the long-term but in contrast, the C sink is highly sensitive to phosphorus inputs.

text: Carbon dynamics in restiad peatlands across different timescales Peatlands contain one of the largest terrestrial carbon stores on the planet, and one which is known to interact with climate and global biogeochemical cycling of nutrients. Peatlands maintain their carbon primarily through a high and stable water table which restricts decomposition, and large amounts of carbon can be lost upon drying. However, peatlands are also characterised by non-linear responses to external forcing with a complex array of internal feedbacks which tend to dominate ecosystem response over long-timescales and may amplify or dampen external influences. This has made predicting the effects of environmental change, beyond a few years, highly challenging. Here we use CO₂ fluxes and down-core measurements of carbon accumulation to study the drivers of peatland carbon exchange across a wide range of timescales. First of all, we compare contemporary CO₂ fluxes at two raised bogs, one of which is extremely dry in an international context (Moanatuatua), with the summer water table drawdown approaching one metre, and another where the water table is high and stable (Kopuatai). We found that despite the low and fluctuating water table in the impacted bog the site remained a sink for CO₂ which is strong in an international context, but reduced compared to the wet bog. A key factor in the wet bog being able to maintain a net sink for CO₂ was the enhanced photosynthetic capacity compared to the wetter bog, especially in summer, which was able to partially compensate for enhanced ecosystem respiration. There was a clear difference in how the two sites responded to contemporaneous water table drawdown, which was consistent with differences seen across wet and dry bogs in the international literature. We found plant productivity to be restricted at the dry bog, at both wet and dry extremes, while at the wet bog water table lowering stimulated ecosystem respiration, with neither effect being consistent across both bogs.
To further investigate how the dry bog, Moanatuatua, has adapted to low water tables we re-analysed CO₂ flux data from 1999 and 2000, a period at least several years after the water table initially dropped, and we compared this flux to the present day (after a 16 year gap). Re-analysis of the older data showed that in 1999 and 2000 Moanatuatua was a moderate source for CO₂ with elevated ecosystem respiration and lower photosynthetic capacity compared to the present day. We attribute the change in photosynthetic capacity to the increased cover of the woody shrub Epacris Pauciflora, while a long term decline in ER would be consistent with changes in peat physical and chemical qualities as peat degrades making it further resistant to microbial decay.
In order to contextualise the CO₂ flux records and assess the drivers of carbon accumulation at the 50-100 year timescale we measured down-core C accumulation in unprecedented detail for a New Zealand bog, with supporting records available for fires, climate, eruptive events and plant species changes available from published and unpublished records at Moanatuatua. Contrary to our initial expectations, we found elevated C accumulation to be associated with at least three separate eruptive events, and possibly two others, with carbon accumulation rates increasing rapidly from a baseline typical of long-term accumulation rates, e.g. ~22 g C m⁻² yr⁻¹ to one which is more typical of contemporary uptake, 80-140 g C m⁻² yr⁻¹ . The complex eruptive history of the bog at this time makes it difficult to isolate any other effects, for instance climate.
Geochemical analysis of the peat suggests increased phosphorus inputs as a mechanism for rapid C accumulation, with the peat stoichiometry recording a shift towards phosphorus abundance relative to carbon and nitrogen. The eruptive events linked to elevated carbon accumulation rates are also known to contain phosphorus within the volcanic glass and the mineral apatite, both of which would be expected to weather and become biologically available due both to processes within the eruptive plume and within the bog post-deposition. As such we have found the restiad bogs studied to be highly resilient to water-table drawdown in the long-term but in contrast, the C sink is highly sensitive to phosphorus inputs.

year: 2020

title: New insights into the condensed nature and stratigraphic significance of the Late Neogene Ariki Formation, Taranaki Basin

authors: Hansen, Rochelle J.

subjects: Ariki Formation

abstract: The Ariki Formation is a distinctive Late Miocene – Early Pliocene marl facies rich in planktic foraminifera, reaching thicknesses in the range 70 - 109 m in most exploration holes drilled into the Western Platform northwest of Taranaki Peninsula. In Awatea-1 and Mangaa-1 in the Northern Graben, however, there are two marl units separated by the Mangaa “B” Sands. The lower unit has the same upper Tongaporutuan and Kapitean age as the lower part of the marl on the Western Platform, and the upper marl has an Upper Opoitian - Waipipian age, similar to the upper part of the Ariki Formation on the platform. In other holes located on the margins of the graben there can be one thin marly horizon, which usually correlates with the upper marl unit in Awatea-1 and Mangaa-1. 
The presence of two marly units in the Northern Graben, which are probably amalgamated on the western Platform, suggests two periods of late Neogene condensed sedimentation in northern Taranaki Basin arising from siliciclastic sediment starvation, separated by a period of submarine fan accumulation (Mangaa ‘B’ sands) following subsidence of the Northern Graben. We attribute the initial interval of marl accumulation mainly to a marked landward shift in the position of coastal onlap in central and southern Taranaki and in the region east of the Taranaki Fault Zone (southern King Country and northern Wanganui regions), which effectively shut-off the supply of siliciclastic sediment to northern Taranaki Basin, thereby enabling marl to accumulate. The start of accumulation of the upper part of the Ariki Formation and its marly correlatives in and around the Northern Graben, is attributed to a younger (upper Opoitian) landward shift in the position of coastal onlap, this time involving the formation of the Wanganui Basin depocentre and Toru Trough, which trapped the contemporary siliciclastic sediment being supplied from the south. A lower Opoitian phase of progradation between these two phases of retrogradation led to accumulation of the lower part of the Mangaa Formation (Mangaa ’B’ sands), which was limited in its extent to the Northern Graben because bounding normal faults had by then developed sea floor relief precluding mass-emplaced siliciclastic sediment from being deposited on the higher standing Western Platform. The accumulation of Ariki Formation marl in northern Taranaki Basin ended during the mid-Pliocene due to progradation of a thick continental margin wedge (Giant Foresets Formation) across the Northern Graben and Western Platform.

text: New insights into the condensed nature and stratigraphic significance of the Late Neogene Ariki Formation, Taranaki Basin The Ariki Formation is a distinctive Late Miocene – Early Pliocene marl facies rich in planktic foraminifera, reaching thicknesses in the range 70 - 109 m in most exploration holes drilled into the Western Platform northwest of Taranaki Peninsula. In Awatea-1 and Mangaa-1 in the Northern Graben, however, there are two marl units separated by the Mangaa “B” Sands. The lower unit has the same upper Tongaporutuan and Kapitean age as the lower part of the marl on the Western Platform, and the upper marl has an Upper Opoitian - Waipipian age, similar to the upper part of the Ariki Formation on the platform. In other holes located on the margins of the graben there can be one thin marly horizon, which usually correlates with the upper marl unit in Awatea-1 and Mangaa-1. 
The presence of two marly units in the Northern Graben, which are probably amalgamated on the western Platform, suggests two periods of late Neogene condensed sedimentation in northern Taranaki Basin arising from siliciclastic sediment starvation, separated by a period of submarine fan accumulation (Mangaa ‘B’ sands) following subsidence of the Northern Graben. We attribute the initial interval of marl accumulation mainly to a marked landward shift in the position of coastal onlap in central and southern Taranaki and in the region east of the Taranaki Fault Zone (southern King Country and northern Wanganui regions), which effectively shut-off the supply of siliciclastic sediment to northern Taranaki Basin, thereby enabling marl to accumulate. The start of accumulation of the upper part of the Ariki Formation and its marly correlatives in and around the Northern Graben, is attributed to a younger (upper Opoitian) landward shift in the position of coastal onlap, this time involving the formation of the Wanganui Basin depocentre and Toru Trough, which trapped the contemporary siliciclastic sediment being supplied from the south. A lower Opoitian phase of progradation between these two phases of retrogradation led to accumulation of the lower part of the Mangaa Formation (Mangaa ’B’ sands), which was limited in its extent to the Northern Graben because bounding normal faults had by then developed sea floor relief precluding mass-emplaced siliciclastic sediment from being deposited on the higher standing Western Platform. The accumulation of Ariki Formation marl in northern Taranaki Basin ended during the mid-Pliocene due to progradation of a thick continental margin wedge (Giant Foresets Formation) across the Northern Graben and Western Platform.

year: 2008

title: Studies on the health and bacterial symbionts of  toheroa (Paphies ventricosa)

authors: Bennion, Matthew Joseph

subjects: Shellfish health

abstract: Disease outbreaks in marine species can have devastating consequences for host populations, host-associated species assemblages, ecosystem functioning, and for human users of these marine resources. At present, the risk factors associated with disease outbreaks, such as warming and pollution, are increasing. Given the increasing risk of disease outbreaks and the role that parasites play in marine ecosystems, there is a vital need to gain knowledge of marine diseases for species conservation, and the monitoring, management, and forecasting of disease. The field of marine disease ecology is growing, but many facets of our understanding remain in their infancy. Faced with a lack of baseline health data, efforts to combat disease outbreak in the ocean are impeded, even though the future of food security hinges on an ability to source food from the ocean. With a shift towards aquaculture, in particular bivalve aquaculture, knowledge of ambient health of wild and farmed species will dictate both yield, and our ability to protect wild stocks. 
Disease outbreak poses added risk to species that are already in peril. The toheroa (Paphies ventricosa) is a threatened surf clam endemic to Aotearoa (New Zealand). Once bountiful, overharvesting and population collapse put an end to the large-scale fisheries of the early and mid-1900s. The protections enacted on toheroa populations should have ensured their recovery, but recovery has not occurred. Disease has been suggested as one possible explanation. However, without knowledge of disease dynamics in toheroa populations, restorative efforts risk failure, or worse, inflicting further damage. Intracellular microcolonies of bacteria (IMCs) have been linked to numerous shellfish mass mortality events (MMEs) in Aotearoa in recent years, and were first detected in toheroa in 2017. This discovery raised questions regarding the role IMCs might be playing in preventing the recovery of toheroa populations. 
To address this uncertainty, this thesis set out to investigate what pathogens and parasites are present in toheroa, and determine what effect they might be having on toheroa health. A histopathology survey was conducted to gather fundamental baseline health information on toheroa populations across their entire distribution. IMCs were found to be the only potential pathogens of note. Histology data coupled with Bayesian models indicated that the probability of higher IMC intensity was associated with decreased toheroa condition. Using PCR, DNA sequencing, and in situ hybridisation, IMCs were characterised as bacteria in the genus Endozoicomonas. In many marine organisms, Endozoicomonas spp. are cosmopolitan members of associated-bacterial communities, often fulfilling biogeochemical cycling functions in host tissues. In toheroa populations, Endozoicomonas spp. abundance was found to be seasonal, but site specificity indicated habitat characteristics (specifically, the presence of freshwater outflows) might be a significant driver of their abundance. The bacterial community of toheroa was subsequently investigated using 16S rRNA gene sequencing, and candidates common to other coastal bivalve molluscs were found to be dominant, including Spirochaetaceae, Mycoplasmataceae, and Endozoicomonadaceae (in order of relative dominance). Freshwater outflows appeared to be such a significant driver of microbiome taxonomic dissimilarity, that specimens collected from sites 1240 km apart hosted more similar bacterial communities than specimens from sites with and without streams on the same beach and within the same region. The key indicator taxa driving microbiome dissimilarity were found to be Endozoicomonas spp. and sulfate-reducing bacteria in the phylum Desulfobacterota. 
Gas bubbles were also observed on the shells of toheroa at the same time that IMCs were first detected. At that stage, temperature and total dissolved gaseous pressure was thought to contribute to their manifestation. To gain a better understanding of this phenomenon, a spatio-temporal survey was conducted which revealed an association of high gas bubble intensity with the austral-autumn/winter and freshwater outflows. A new hypothesis is therefore presented that links gas bubbles to sulfate-reducing bacteria and hydrogen sulfide (H₂S), a by-product of anaerobic digestion. Given the apparent influence of freshwater on toheroa intrinsic health, the capacity for streams to deliver pollutants to toheroa beds was assessed. Results gained from inductively coupled plasma-mass spectrometry (ICP-MS) suggest that despite the modified nature of adjacent land, streams do not deliver significant loads of bioavailable trace metals to toheroa beds in the intertidal zone. Instead, nutrition in the form of large phytoplankton blooms in autumn/winter is thought to be the primary source of bioavailable trace metals for toheroa.
No observations of significant pathogenesis, associated with Endozoicomonas species, were made throughout this research. Furthermore, during the timeframe of this research (apart from intermittent mortality events reported), there is no evidence of an ongoing disease epidemic in toheroa populations. While not providing evidence for the factor preventing the recovery of toheroa, this research does have implications for the ongoing conservation and management of toheroa. It seems reasonable to assume that infectious disease is not a major factor contributing to the limited recovery of toheroa throughout Aotearoa. Instead, associations made between freshwater outflows, nutrition, and detritus indicate that habitat requirements provided by freshwater streams are having significant effects on toheroa health, survival, and homeostasis. Furthermore, evidence presented suggests that the Endozoicomonas spp. present in toheroa and other Aotearoa shellfish are likely to be an important endosymbiont. In the future, studies on remaining toheroa populations should prioritise nutritional health. Namely, what role symbionts play in toheroa nutrition, and how niche requirements shape symbiont community composition and function in toheroa tissues. Answers to these questions could profoundly increase the success of toheroa restoration and conservation efforts.

text: Studies on the health and bacterial symbionts of  toheroa (Paphies ventricosa) Disease outbreaks in marine species can have devastating consequences for host populations, host-associated species assemblages, ecosystem functioning, and for human users of these marine resources. At present, the risk factors associated with disease outbreaks, such as warming and pollution, are increasing. Given the increasing risk of disease outbreaks and the role that parasites play in marine ecosystems, there is a vital need to gain knowledge of marine diseases for species conservation, and the monitoring, management, and forecasting of disease. The field of marine disease ecology is growing, but many facets of our understanding remain in their infancy. Faced with a lack of baseline health data, efforts to combat disease outbreak in the ocean are impeded, even though the future of food security hinges on an ability to source food from the ocean. With a shift towards aquaculture, in particular bivalve aquaculture, knowledge of ambient health of wild and farmed species will dictate both yield, and our ability to protect wild stocks. 
Disease outbreak poses added risk to species that are already in peril. The toheroa (Paphies ventricosa) is a threatened surf clam endemic to Aotearoa (New Zealand). Once bountiful, overharvesting and population collapse put an end to the large-scale fisheries of the early and mid-1900s. The protections enacted on toheroa populations should have ensured their recovery, but recovery has not occurred. Disease has been suggested as one possible explanation. However, without knowledge of disease dynamics in toheroa populations, restorative efforts risk failure, or worse, inflicting further damage. Intracellular microcolonies of bacteria (IMCs) have been linked to numerous shellfish mass mortality events (MMEs) in Aotearoa in recent years, and were first detected in toheroa in 2017. This discovery raised questions regarding the role IMCs might be playing in preventing the recovery of toheroa populations. 
To address this uncertainty, this thesis set out to investigate what pathogens and parasites are present in toheroa, and determine what effect they might be having on toheroa health. A histopathology survey was conducted to gather fundamental baseline health information on toheroa populations across their entire distribution. IMCs were found to be the only potential pathogens of note. Histology data coupled with Bayesian models indicated that the probability of higher IMC intensity was associated with decreased toheroa condition. Using PCR, DNA sequencing, and in situ hybridisation, IMCs were characterised as bacteria in the genus Endozoicomonas. In many marine organisms, Endozoicomonas spp. are cosmopolitan members of associated-bacterial communities, often fulfilling biogeochemical cycling functions in host tissues. In toheroa populations, Endozoicomonas spp. abundance was found to be seasonal, but site specificity indicated habitat characteristics (specifically, the presence of freshwater outflows) might be a significant driver of their abundance. The bacterial community of toheroa was subsequently investigated using 16S rRNA gene sequencing, and candidates common to other coastal bivalve molluscs were found to be dominant, including Spirochaetaceae, Mycoplasmataceae, and Endozoicomonadaceae (in order of relative dominance). Freshwater outflows appeared to be such a significant driver of microbiome taxonomic dissimilarity, that specimens collected from sites 1240 km apart hosted more similar bacterial communities than specimens from sites with and without streams on the same beach and within the same region. The key indicator taxa driving microbiome dissimilarity were found to be Endozoicomonas spp. and sulfate-reducing bacteria in the phylum Desulfobacterota. 
Gas bubbles were also observed on the shells of toheroa at the same time that IMCs were first detected. At that stage, temperature and total dissolved gaseous pressure was thought to contribute to their manifestation. To gain a better understanding of this phenomenon, a spatio-temporal survey was conducted which revealed an association of high gas bubble intensity with the austral-autumn/winter and freshwater outflows. A new hypothesis is therefore presented that links gas bubbles to sulfate-reducing bacteria and hydrogen sulfide (H₂S), a by-product of anaerobic digestion. Given the apparent influence of freshwater on toheroa intrinsic health, the capacity for streams to deliver pollutants to toheroa beds was assessed. Results gained from inductively coupled plasma-mass spectrometry (ICP-MS) suggest that despite the modified nature of adjacent land, streams do not deliver significant loads of bioavailable trace metals to toheroa beds in the intertidal zone. Instead, nutrition in the form of large phytoplankton blooms in autumn/winter is thought to be the primary source of bioavailable trace metals for toheroa.
No observations of significant pathogenesis, associated with Endozoicomonas species, were made throughout this research. Furthermore, during the timeframe of this research (apart from intermittent mortality events reported), there is no evidence of an ongoing disease epidemic in toheroa populations. While not providing evidence for the factor preventing the recovery of toheroa, this research does have implications for the ongoing conservation and management of toheroa. It seems reasonable to assume that infectious disease is not a major factor contributing to the limited recovery of toheroa throughout Aotearoa. Instead, associations made between freshwater outflows, nutrition, and detritus indicate that habitat requirements provided by freshwater streams are having significant effects on toheroa health, survival, and homeostasis. Furthermore, evidence presented suggests that the Endozoicomonas spp. present in toheroa and other Aotearoa shellfish are likely to be an important endosymbiont. In the future, studies on remaining toheroa populations should prioritise nutritional health. Namely, what role symbionts play in toheroa nutrition, and how niche requirements shape symbiont community composition and function in toheroa tissues. Answers to these questions could profoundly increase the success of toheroa restoration and conservation efforts.

year: 2021