title: Thermophilic methanotrophy in the Taupō volcanic zone

authors: Houghton, Karen M.

subjects: Microbiology

abstract: Methanotrophs are widely distributed in the environment and play an important role in the global methane cycle by oxidising the majority of methane produced each year. Geological sources of methane contribute substantial volumes of this greenhouse gas to the atmosphere, but research on methanotrophs to date has focused on low temperature environments. This study aimed to investigate thermophilic methanotrophy in geothermal environments within the Taupō Volcanic Zone.
A comprehensive survey of methane oxidation in geothermal soils and sediments was carried out, in conjunction with DNA sequencing of 16S rRNA genes from each sample. Methane oxidation is prevalent within the geothermal samples. This is the first survey of methane oxidation of multiple geothermal samples, and emphasises the importance of these ecosystems to the biogeochemical methane cycle. Geothermal samples encompassed highly diverse microbial communities with few ubiquitous genera, and communities were significantly different between methane oxidizing and non-oxidising microcosms. Some methane-oxidising communities did not include 16S rRNA gene sequences from known methanotrophs, suggesting the presence in geothermal ecosystems of taxa currently not recognised as capable of methane oxidation.
Enrichment microcosms were created using the methane-oxidising geothermal samples, and evaluated in terms of methane oxidation and transcriptional activity. Methanotrophy was observed at temperatures between 37 and 75 °C, which complemented the detection of mRNA transcripts for the complete oxidation of methane. Stress response genes were also highly expressed in the microcosms, identifying a variety of mechanisms within the communities to adapt to environmental change. 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.
Methane-oxidising bacteria were obtained in axenic culture from five enrichment microcosms, confirming the hypothesis that thermophilic methanotrophs could be enriched and isolated from geothermal environments. Many methanotrophs are poorly described in terms of their physiology and ecology, and to address these knowledge gaps, the strains isolated in this study were subjected to thorough phylogenetic and phenotypic characterisation. This research will also facilitate future cultivation, cryostorage and revival of methane oxidisers.
Several described methanotrophs are capable of oxidising hydrogen in addition to methane, but the association between hydrogen oxidation and cell growth is poorly understood. This research aimed to investigate if mixotrophic hydrogen oxidation was used to optimise growth, and if this could be linked to survival at elevated temperatures. [NiFe]- hydrogenases were identified in four of the methanotrophs isolated in this study but hydrogen oxidation was observed in only three of the isolates, which highlights the importance of culture-based investigations to confirm phenotypes predicted by metagenomics. One isolate showed increasing hydrogen oxidation with increasing temperature, but this did not appear to be linked to survival at elevated temperatures.
This study used a combination of culture-independent and cultivation studies to demonstrate that methanotrophs are both abundant and highly active within geothermal environments. Methanotrophs from these ecosystems have also been successfully isolated and characterised, adding to our knowledge both of their physiology and ecological role in methane cycling.

text: Thermophilic methanotrophy in the Taupō volcanic zone Methanotrophs are widely distributed in the environment and play an important role in the global methane cycle by oxidising the majority of methane produced each year. Geological sources of methane contribute substantial volumes of this greenhouse gas to the atmosphere, but research on methanotrophs to date has focused on low temperature environments. This study aimed to investigate thermophilic methanotrophy in geothermal environments within the Taupō Volcanic Zone.
A comprehensive survey of methane oxidation in geothermal soils and sediments was carried out, in conjunction with DNA sequencing of 16S rRNA genes from each sample. Methane oxidation is prevalent within the geothermal samples. This is the first survey of methane oxidation of multiple geothermal samples, and emphasises the importance of these ecosystems to the biogeochemical methane cycle. Geothermal samples encompassed highly diverse microbial communities with few ubiquitous genera, and communities were significantly different between methane oxidizing and non-oxidising microcosms. Some methane-oxidising communities did not include 16S rRNA gene sequences from known methanotrophs, suggesting the presence in geothermal ecosystems of taxa currently not recognised as capable of methane oxidation.
Enrichment microcosms were created using the methane-oxidising geothermal samples, and evaluated in terms of methane oxidation and transcriptional activity. Methanotrophy was observed at temperatures between 37 and 75 °C, which complemented the detection of mRNA transcripts for the complete oxidation of methane. Stress response genes were also highly expressed in the microcosms, identifying a variety of mechanisms within the communities to adapt to environmental change. 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.
Methane-oxidising bacteria were obtained in axenic culture from five enrichment microcosms, confirming the hypothesis that thermophilic methanotrophs could be enriched and isolated from geothermal environments. Many methanotrophs are poorly described in terms of their physiology and ecology, and to address these knowledge gaps, the strains isolated in this study were subjected to thorough phylogenetic and phenotypic characterisation. This research will also facilitate future cultivation, cryostorage and revival of methane oxidisers.
Several described methanotrophs are capable of oxidising hydrogen in addition to methane, but the association between hydrogen oxidation and cell growth is poorly understood. This research aimed to investigate if mixotrophic hydrogen oxidation was used to optimise growth, and if this could be linked to survival at elevated temperatures. [NiFe]- hydrogenases were identified in four of the methanotrophs isolated in this study but hydrogen oxidation was observed in only three of the isolates, which highlights the importance of culture-based investigations to confirm phenotypes predicted by metagenomics. One isolate showed increasing hydrogen oxidation with increasing temperature, but this did not appear to be linked to survival at elevated temperatures.
This study used a combination of culture-independent and cultivation studies to demonstrate that methanotrophs are both abundant and highly active within geothermal environments. Methanotrophs from these ecosystems have also been successfully isolated and characterised, adding to our knowledge both of their physiology and ecological role in methane cycling.

year: 2018

title: Combination of Mean Shift of Colour Signature and Optical Flow for Tracking During Foreground and Background Occlusion

authors: Hedayati, Mohammad

subjects: Object Tracking

abstract: This paper proposes a multiple hypothesis tracking for multiple object tracking with moving camera. The proposed model makes use of the stability of sparse optical flow along with the invariant colour property under size and pose variation, by merging the colour property of objects into optical flow tracking. To evaluate the algorithm five different videos are selected from broadcast horse races where each video represents different challenges that present in object tracking literature. A comparison study of the proposed method, with a colour based mean shift tracking proves the significant improvement in accuracy and stability of object tracking.

text: Combination of Mean Shift of Colour Signature and Optical Flow for Tracking During Foreground and Background Occlusion This paper proposes a multiple hypothesis tracking for multiple object tracking with moving camera. The proposed model makes use of the stability of sparse optical flow along with the invariant colour property under size and pose variation, by merging the colour property of objects into optical flow tracking. To evaluate the algorithm five different videos are selected from broadcast horse races where each video represents different challenges that present in object tracking literature. A comparison study of the proposed method, with a colour based mean shift tracking proves the significant improvement in accuracy and stability of object tracking.

year: 2015

title: 2016 Subtidal Ecological Survey of Tauranga Harbour and development of benthic health models

authors: Clark, Dana

abstract: This report summarises the results of biological and physical data collected from a broad-scale subtidal survey of Tauranga Harbour conducted between March and May 2016. The survey was designed to understand more fully the role of various anthropogenic stressors on ecosystem health and feed into management of the harbour. Community-based models of ecosystem health called Benthic Health Models (BHMs) were developed to assess ecosystem health in response to mud and metal loading. This is the first comprehensive quantitative survey of Tauranga Harbour’s subtidal environment since 1990/91. 
The research was conducted as part of the Oranga Taiao Oranga Tangata (OTOT) programme. The wider research project aims to provide knowledge and toolsets to support co-management of estuaries. The three phases of this programme include 1) gathering Mātauranga Māori (a body of knowledge of Māori experience in the area) from local iwi/hapū, 2) consolidating the ecological knowledge of the Tauranga Harbour and providing modelling and indicators of estuarine ecosystem health, resilience and functioning, and 3) creating an Integrative Spatial Planning Tool (ISPT) that can help inform decision making in the harbour. The subtidal survey fits into the latter two research objectives, as the information collected will be used to develop indicators of ecosystem health, which will be used as components of the ISPT. 
Water, sediment and benthic macrofauna samples were collected from 45 subtidal sites across the harbour. Subtidal sediments were predominantly sandy with low levels of nutrients and metal loading. Upper reaches of channels tended to have higher mud, organic content and nutrient concentrations than sites closer to the main channels. Maximum subtidal sediment metal concentrations were well below guideline values and all metals, except lead, were less than median national values for intertidal estuarine sites. Highest metal concentrations were in the urbanised southern harbour or in areas of high mud deposition. 
Many of the numerically dominant macrofaunal taxa were present in both the 1990/91 and 2016 subtidal surveys, with pipi the most abundant bivalve in both surveys. Although the 2016 survey was not designed to quantitatively measure large bivalves, compared with the 1990/91 survey, fewer scallops and horse mussels were observed. The apparent decline in these species is concerning as large bivalves stabilise the sediment and provide complex physical structure to soft sediment habitats, providing predation refuges and settlement substrate for epifauna. The invasive Asian date mussel, on the other hand, has also become common in the harbour. 
Mud and metals were identified as key variables affecting the ecology of the harbour. To determine how environmental gradients in these variables affected ecosystem health, two Benthic Health Models (BHMs) were developed based on variability in community structure, one for each environmental gradient. The BHM approach is a useful management tool that can be used to determine the relative health of benthic communities at a single point in time, or track sites over time to assess whether communities are moving towards a more healthy or unhealthy state. It has been found to be more sensitive to changing ecosystem health than simple univariate community measures because it preserves more information about the community. 
Most sites were ranked in the lower BHM groups, suggesting Tauranga Harbour had fairly healthy subtidal communities with regard to mud and metal impacts. This was supported by values from other biotic indices, which indicated that all subtidal sites in Tauranga would be classified as having ‘good’ ecological status. Sites identified as most impacted by elevated mud and metals were generally located in the upper reaches of estuaries or near the urbanised southern portion of the harbour. In terms of mud, this to some extent reflects the natural progression of an estuary from land to sea; however, the rates of accumulation of sediments have been accelerated because of anthropogenic land-based activities. Although currents and mud were highly coupled in Tauranga’s subtidal environment, the Mud BHM could draw out community responses that were only associated with mud.

text: 2016 Subtidal Ecological Survey of Tauranga Harbour and development of benthic health models This report summarises the results of biological and physical data collected from a broad-scale subtidal survey of Tauranga Harbour conducted between March and May 2016. The survey was designed to understand more fully the role of various anthropogenic stressors on ecosystem health and feed into management of the harbour. Community-based models of ecosystem health called Benthic Health Models (BHMs) were developed to assess ecosystem health in response to mud and metal loading. This is the first comprehensive quantitative survey of Tauranga Harbour’s subtidal environment since 1990/91. 
The research was conducted as part of the Oranga Taiao Oranga Tangata (OTOT) programme. The wider research project aims to provide knowledge and toolsets to support co-management of estuaries. The three phases of this programme include 1) gathering Mātauranga Māori (a body of knowledge of Māori experience in the area) from local iwi/hapū, 2) consolidating the ecological knowledge of the Tauranga Harbour and providing modelling and indicators of estuarine ecosystem health, resilience and functioning, and 3) creating an Integrative Spatial Planning Tool (ISPT) that can help inform decision making in the harbour. The subtidal survey fits into the latter two research objectives, as the information collected will be used to develop indicators of ecosystem health, which will be used as components of the ISPT. 
Water, sediment and benthic macrofauna samples were collected from 45 subtidal sites across the harbour. Subtidal sediments were predominantly sandy with low levels of nutrients and metal loading. Upper reaches of channels tended to have higher mud, organic content and nutrient concentrations than sites closer to the main channels. Maximum subtidal sediment metal concentrations were well below guideline values and all metals, except lead, were less than median national values for intertidal estuarine sites. Highest metal concentrations were in the urbanised southern harbour or in areas of high mud deposition. 
Many of the numerically dominant macrofaunal taxa were present in both the 1990/91 and 2016 subtidal surveys, with pipi the most abundant bivalve in both surveys. Although the 2016 survey was not designed to quantitatively measure large bivalves, compared with the 1990/91 survey, fewer scallops and horse mussels were observed. The apparent decline in these species is concerning as large bivalves stabilise the sediment and provide complex physical structure to soft sediment habitats, providing predation refuges and settlement substrate for epifauna. The invasive Asian date mussel, on the other hand, has also become common in the harbour. 
Mud and metals were identified as key variables affecting the ecology of the harbour. To determine how environmental gradients in these variables affected ecosystem health, two Benthic Health Models (BHMs) were developed based on variability in community structure, one for each environmental gradient. The BHM approach is a useful management tool that can be used to determine the relative health of benthic communities at a single point in time, or track sites over time to assess whether communities are moving towards a more healthy or unhealthy state. It has been found to be more sensitive to changing ecosystem health than simple univariate community measures because it preserves more information about the community. 
Most sites were ranked in the lower BHM groups, suggesting Tauranga Harbour had fairly healthy subtidal communities with regard to mud and metal impacts. This was supported by values from other biotic indices, which indicated that all subtidal sites in Tauranga would be classified as having ‘good’ ecological status. Sites identified as most impacted by elevated mud and metals were generally located in the upper reaches of estuaries or near the urbanised southern portion of the harbour. In terms of mud, this to some extent reflects the natural progression of an estuary from land to sea; however, the rates of accumulation of sediments have been accelerated because of anthropogenic land-based activities. Although currents and mud were highly coupled in Tauranga’s subtidal environment, the Mud BHM could draw out community responses that were only associated with mud.

year: 2018