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: Pest fish detection using environmental DNA – fact sheet

authors: Banks, Jonathan C.

abstract: Molecular tools using DNA sequencing can improve pest fish management by ensuring accurate identification of fish, especially larval fish, without the need for specialist taxonomic knowledge. DNA is made of four chemicals; guanine (G), adenine (A), thymine (T), or cytosine (C), joined together as a string (Figure 1). The order of the chemicals is unique to each species and can be used as a DNA "barcode" to identify organisms. It is relatively simple to obtain DNA sequences for a reference gene such as the widely accepted "barcode gene" cytochrome C oxidase subunit 1, and compare the sequence to a voucher specimen sequence in genetic databases such as GenBank and the Barcode of Life database BOLD.

text: Pest fish detection using environmental DNA – fact sheet Molecular tools using DNA sequencing can improve pest fish management by ensuring accurate identification of fish, especially larval fish, without the need for specialist taxonomic knowledge. DNA is made of four chemicals; guanine (G), adenine (A), thymine (T), or cytosine (C), joined together as a string (Figure 1). The order of the chemicals is unique to each species and can be used as a DNA "barcode" to identify organisms. It is relatively simple to obtain DNA sequences for a reference gene such as the widely accepted "barcode gene" cytochrome C oxidase subunit 1, and compare the sequence to a voucher specimen sequence in genetic databases such as GenBank and the Barcode of Life database BOLD.

year: 2015

title: Boat electrofishing survey of fish abundance in the Ohau Channel, Rotorua, in 2016

authors: Hicks, Brendan J.

abstract: The aim of the survey was to provide on-going monitoring of the fish communities and abundance by boat electrofishing in the Ohau Channel, especially fish species that are taonga to Maori (tuna, or eels, morihana, or goldfish, and kōura, or freshwater crayfish). In the current study, we present the findings from the tenth year of sampling (2016) and a summary of previous surveys.

text: Boat electrofishing survey of fish abundance in the Ohau Channel, Rotorua, in 2016 The aim of the survey was to provide on-going monitoring of the fish communities and abundance by boat electrofishing in the Ohau Channel, especially fish species that are taonga to Maori (tuna, or eels, morihana, or goldfish, and kōura, or freshwater crayfish). In the current study, we present the findings from the tenth year of sampling (2016) and a summary of previous surveys.

year: 2017