title: Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields

authors: Houghton, Karen M.

abstract: Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5–8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g−1 d−1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d−1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.

text: Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5–8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g−1 d−1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d−1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.

year: 2023-01-01

title: The Creation of Sustainable Development: What it means to CFOs in New Zealand

authors: Dimitrov, Dara

subjects: sustainability

abstract: Abstract currently unavailable

text: The Creation of Sustainable Development: What it means to CFOs in New Zealand Abstract currently unavailable

year: 2009

title: The modification of toheroa habitat by streams on Ripiro Beach

authors: Cope, Jane

abstract: Habitat modification and loss are key factors driving the global extinction and displacement of species. The scale and consequences of habitat loss are relatively well understood in terrestrial environments, but in marine ecosystems, and particularly soft sediment ecosystems, this is not the case. The characteristics which determine the suitability of soft sediment habitats are often subtle, due to the apparent homogeneity of sandy environments. This can make it difficult to detect habitat change in the first place let alone understand ecological consequences. Subtle differences in habitat quality are even harder to detect on dynamic surf beaches which are controlled by the interactions between the wave climate and the beach sands, and experience frequent and large changes. The exposed surf beaches of northern New Zealand, are home to toheroa (Paphies ventricosa), an endemic surf clam and New Zealand‘s most protected shell fish species. Over the course of the 20th century, toheroa were harvested to the point of collapse resulting in the closure of an important cultural, recreational and commercial fishery. Despite more than 40 years of protection, toheroa populations have failed to recover with populations in most locations continuing to decline. 

In northern New Zealand toheroa distribution is strongly associated with the small streams which flow across the toheroa beaches. A reduction in the flow of fresh water to the beach via these streams has been suggested as one possible factor which may be preventing the recovery of toheroa. However, little is known about the characteristics of the habitat, and the mechanism driving this toheroa-stream relationship has not received specific attention. The objective of this research was to better understand the effect of streams on beach habitat in the hope of determining the drivers of toheroa distribution. Specifically, I investigated how sediment type, topography, water table depth and sediment temperatures varied across exposed intertidal sediments adjacent to and away from streams. Sampling took place at four sites along Ripiro Beach during the summer, the season when toheroa are most susceptible to thermal stress and streams are thought to provide some protection from dissipation and heat stress. Grainsize distributions from the sampled sediment cores were processed using a Malvern Mastersizer 3000 laser diffractometer (Malvern, UK). The surface elevation and sediment temperature profiles of the subaerial beach was measured using a theodolite CDN pro accurate waterproof thermometers (Model DTW450L). Temperatures were measured at five sediment depths (2cm, 4cm, 7.5cm, 10.5cm, 20.5cm) throughout the sampling period. 

The effect of the streams on the grain size distribution of intertidal sediments appeared to be limited to the high tide, where the proportion of fine sediments was highest in stream adjacent sediments. Greater variations in grain size occurred along the beach, but the greatest difference in sediment sizes occurred when contrasting current day beach grain size distributions with sediment data collected in 1974. Beach sediments from 2017 contained 26661% time more medium sediment indicating the beach is now much coaster than it was 44 years ago. However, as no time series is available for sediment composition at Ripiro it is uncertain whether this change in beach make up is indicative of year-to-year variation or a long term trend. Beach topography varied consistently in the vicinity of streams. The elevation and slope of the beach face was lowest in the path of streams. Along the upper beach, low elevation in the path of the stream lead to the formation of deep bowl like features. As a result of this topography, adjacent to the stream, the water table remained close to the sediment surface throughout the sampling period (< 20 cm), in contrast to point‘s away from the stream where the water table was below the sampling depth. 

The hypothesis that streams would provide a thermal refuge for toheroa was one of the key questions of this thesis. What I found was that stream driven difference in sediment temperatures were only apparent in the upper intestinal, the area occupied by juvenile toheroa when they first recruit to the beach. Temperatures away from streams were significantly higher (> 3.5 °C) than stream adjacent sediments. However, in the middle intestinal, the area occupied by adult toheroa, the seep face exerted a greater influence on sediment temperatures than the stream and temperatures were no different regardless of stream proximity. The findings of this study suggest that the toheroa-stream relationship is not a direct response to the presence of freshwater, but rather is driven by the modification of the intertidal sediments by the streams. The increased erosion in these areas reduces the distance between the sediment surface and the water table, increasing the moisture content of the sediments. Additionally, the formation of the basin like depressions in the upper intertidal may act to aggregate spat and juvenile toheroa through the effect of this topography on the beach swash regime. At mid-tide areas adjacent to streams, the depth of the water table was such that adult toheroa are likely to be either fully or partially immersed throughout the low tide. Away from streams, the water table is beyond the burrowing depth of toheroa. For both juveniles and adults, stream associated areas may provide important protection against desiccation, through increasing moisture content of the sediments and for juveniles through reduced sediment temperatures. 

Evidently, streams do modify beach habitat in a way that makes it inhabitable for toheroa. Just not in the way that was anticipated. This study has increased our knowledge of beach characteristics that provide good toheroa habitat. Further research is required to test these hypotheses and better understand the effects of climate and terrestrial land use on beach state and therefore the suitability of the beach for toheroa.

text: The modification of toheroa habitat by streams on Ripiro Beach Habitat modification and loss are key factors driving the global extinction and displacement of species. The scale and consequences of habitat loss are relatively well understood in terrestrial environments, but in marine ecosystems, and particularly soft sediment ecosystems, this is not the case. The characteristics which determine the suitability of soft sediment habitats are often subtle, due to the apparent homogeneity of sandy environments. This can make it difficult to detect habitat change in the first place let alone understand ecological consequences. Subtle differences in habitat quality are even harder to detect on dynamic surf beaches which are controlled by the interactions between the wave climate and the beach sands, and experience frequent and large changes. The exposed surf beaches of northern New Zealand, are home to toheroa (Paphies ventricosa), an endemic surf clam and New Zealand‘s most protected shell fish species. Over the course of the 20th century, toheroa were harvested to the point of collapse resulting in the closure of an important cultural, recreational and commercial fishery. Despite more than 40 years of protection, toheroa populations have failed to recover with populations in most locations continuing to decline. 

In northern New Zealand toheroa distribution is strongly associated with the small streams which flow across the toheroa beaches. A reduction in the flow of fresh water to the beach via these streams has been suggested as one possible factor which may be preventing the recovery of toheroa. However, little is known about the characteristics of the habitat, and the mechanism driving this toheroa-stream relationship has not received specific attention. The objective of this research was to better understand the effect of streams on beach habitat in the hope of determining the drivers of toheroa distribution. Specifically, I investigated how sediment type, topography, water table depth and sediment temperatures varied across exposed intertidal sediments adjacent to and away from streams. Sampling took place at four sites along Ripiro Beach during the summer, the season when toheroa are most susceptible to thermal stress and streams are thought to provide some protection from dissipation and heat stress. Grainsize distributions from the sampled sediment cores were processed using a Malvern Mastersizer 3000 laser diffractometer (Malvern, UK). The surface elevation and sediment temperature profiles of the subaerial beach was measured using a theodolite CDN pro accurate waterproof thermometers (Model DTW450L). Temperatures were measured at five sediment depths (2cm, 4cm, 7.5cm, 10.5cm, 20.5cm) throughout the sampling period. 

The effect of the streams on the grain size distribution of intertidal sediments appeared to be limited to the high tide, where the proportion of fine sediments was highest in stream adjacent sediments. Greater variations in grain size occurred along the beach, but the greatest difference in sediment sizes occurred when contrasting current day beach grain size distributions with sediment data collected in 1974. Beach sediments from 2017 contained 26661% time more medium sediment indicating the beach is now much coaster than it was 44 years ago. However, as no time series is available for sediment composition at Ripiro it is uncertain whether this change in beach make up is indicative of year-to-year variation or a long term trend. Beach topography varied consistently in the vicinity of streams. The elevation and slope of the beach face was lowest in the path of streams. Along the upper beach, low elevation in the path of the stream lead to the formation of deep bowl like features. As a result of this topography, adjacent to the stream, the water table remained close to the sediment surface throughout the sampling period (< 20 cm), in contrast to point‘s away from the stream where the water table was below the sampling depth. 

The hypothesis that streams would provide a thermal refuge for toheroa was one of the key questions of this thesis. What I found was that stream driven difference in sediment temperatures were only apparent in the upper intestinal, the area occupied by juvenile toheroa when they first recruit to the beach. Temperatures away from streams were significantly higher (> 3.5 °C) than stream adjacent sediments. However, in the middle intestinal, the area occupied by adult toheroa, the seep face exerted a greater influence on sediment temperatures than the stream and temperatures were no different regardless of stream proximity. The findings of this study suggest that the toheroa-stream relationship is not a direct response to the presence of freshwater, but rather is driven by the modification of the intertidal sediments by the streams. The increased erosion in these areas reduces the distance between the sediment surface and the water table, increasing the moisture content of the sediments. Additionally, the formation of the basin like depressions in the upper intertidal may act to aggregate spat and juvenile toheroa through the effect of this topography on the beach swash regime. At mid-tide areas adjacent to streams, the depth of the water table was such that adult toheroa are likely to be either fully or partially immersed throughout the low tide. Away from streams, the water table is beyond the burrowing depth of toheroa. For both juveniles and adults, stream associated areas may provide important protection against desiccation, through increasing moisture content of the sediments and for juveniles through reduced sediment temperatures. 

Evidently, streams do modify beach habitat in a way that makes it inhabitable for toheroa. Just not in the way that was anticipated. This study has increased our knowledge of beach characteristics that provide good toheroa habitat. Further research is required to test these hypotheses and better understand the effects of climate and terrestrial land use on beach state and therefore the suitability of the beach for toheroa.

year: 2018