title: The Taxonomy of Demospongiae (Porifera) from the Bay of Plenty, New Zealand - Connecting Linnaean and Phylogenetic Classification

authors: Mc Cormack, Samuel Patrick

abstract: The ability to accurately identify species is prerequisite for assessing levels of biological diversity and a fundamental requirement for ecological research. In recent times, there has been a shortfall in biologists who practice traditional alpha taxonomy, leading to difficulties in assessment of biodiversity in some taxonomic groups. The use of a molecular DNA barcoding approach has been suggested as a tool that can be used to complement and accelerate traditional alpha taxonomy, without supplanting or invalidating existing taxonomic practices.
Two different techniques were used to identify organisms, molecular and alpha taxonomy. This thesis addressees several questions relating to sponge systematics. Research was focused on three areas; (1) record sponge biodiversity from the Bay of Plenty region, (2) undertake a systematic revision of the fauna correlating ‘historical’ taxonomy with a modern phylogenetic assessment (3) determine whether identifications based on genetic barcoding are congruent with those produced via traditional morphological methods (alpha taxonomy), and to assess the use of molecular techniques for Demospongiae species identifications.
This was the first focused research on sponge diversity in the Bay of Plenty region. Fifty five species are described in this research. Of these, there are up to three new families, three new genera and thirty four species which are un-described and deemed new to science. However, a more conservative estimate with grouped specimens suggests that there is a minimum of at least one new family, one new genus, and eighteen new species that are un-described and deemed new to science. In summary, we conclude that for New Zealand Demospongiae, sequence variation present in the barcoding region of the COI gene is sufficient to allow for the identification individuals to their nominate species. The use of mtDNA barcoding can without doubt complement classical morphological taxonomy and accelerate the identification process and may in fact revive an interest classical morphological taxonomy.

text: The Taxonomy of Demospongiae (Porifera) from the Bay of Plenty, New Zealand - Connecting Linnaean and Phylogenetic Classification The ability to accurately identify species is prerequisite for assessing levels of biological diversity and a fundamental requirement for ecological research. In recent times, there has been a shortfall in biologists who practice traditional alpha taxonomy, leading to difficulties in assessment of biodiversity in some taxonomic groups. The use of a molecular DNA barcoding approach has been suggested as a tool that can be used to complement and accelerate traditional alpha taxonomy, without supplanting or invalidating existing taxonomic practices.
Two different techniques were used to identify organisms, molecular and alpha taxonomy. This thesis addressees several questions relating to sponge systematics. Research was focused on three areas; (1) record sponge biodiversity from the Bay of Plenty region, (2) undertake a systematic revision of the fauna correlating ‘historical’ taxonomy with a modern phylogenetic assessment (3) determine whether identifications based on genetic barcoding are congruent with those produced via traditional morphological methods (alpha taxonomy), and to assess the use of molecular techniques for Demospongiae species identifications.
This was the first focused research on sponge diversity in the Bay of Plenty region. Fifty five species are described in this research. Of these, there are up to three new families, three new genera and thirty four species which are un-described and deemed new to science. However, a more conservative estimate with grouped specimens suggests that there is a minimum of at least one new family, one new genus, and eighteen new species that are un-described and deemed new to science. In summary, we conclude that for New Zealand Demospongiae, sequence variation present in the barcoding region of the COI gene is sufficient to allow for the identification individuals to their nominate species. The use of mtDNA barcoding can without doubt complement classical morphological taxonomy and accelerate the identification process and may in fact revive an interest classical morphological taxonomy.

year: 2015

title: The physiological characterisation of a novel Thermomicrobia strain WKT50.2, and a review of the characteristics of the class Thermomicrobia

authors: Houghton, Karen M.

subjects: Thermomicrobia

abstract: Thermomicrobia is a class of heterotrophic, obligate aerobes within the phylum Chloroflexi.  At the time of writing, it contained four distinct species, Thermomicrobium roseum, Sphaerobacter thermophilus, Nitrolancetus hollandicus and WKT50.2, the novel strain described in this study.  The physiology and ecology of this strain, and the description of the class Thermomicrobia was investigated as part of this study.

Strain WKT50.2 was isolated from the hot springs at Waikite, New Zealand. We investigated temperature and pH range and optima, analysed PLFA, and determined preferred carbon and energy sources, N-fixation, modes of growth and antibiotic sensitivity. As a general phenotype, WKT50.2 is a heterotrophic and thermophilic obligate aerobe with a preference for moderately alkaliphilic pH conditions. The possible ecology of WKT50.2 was discussed. 

WKT50.2 was able to oxidise methane to gain energy. This was an unexpected result as methanotrophy is a highly specialised phenotype restricted to the phyla Proteobacteria and Verrucomicrobia. Methanotrophs also tend to be metabolic specialists with no capability to oxidise substrates other than C1 compounds. In contrast, WKT50.2 was also able to oxidise ammonia and nitrite, along with a range of saccharides and protein rich substrates. WKT50.2 was sensitive to most of the antibiotics tested in this study, but metronidazole and trimethoprim both stimulated growth in a dosage-dependent manner. WKT50.2 is clearly a distinct genus from T. roseum and S. thermophilus, based on 16S rRNA gene sequence similarities (91 % and 88 % respectively), G+C content and metabolic capabilities.  

T. roseum and S. thermophilus were confirmed as heterotrophic, thermophilic, moderately alkaliphilic, obligate aerobes.  The temperature and pH optima and ranges for T. roseum and S. thermophilus were amended, along with expanding the known metabolic capabilities of both species. Of particular note was the discovery that both T. roseum and S. thermophilus were also able to oxidise both methane and ammonia for energy, and that both species possessed cellulolytic activity. 

In summary, the class Thermomicrobia can be redefined as comprising obligately aerobic, facultative heterotrophs.  Cells are non-motile, non-spore forming rods.  This study has shown that the cells have proteinaceous cell walls containing ornithine, and no lipopolysaccharide.  The major fatty acid is 12-Me-18:0, and lipids include ester-linked diols. The major isoprenoid quinone is MK-8.

Several of the observations in this study merit further research.  The discovery of methanotrophy in this class was unexpected and significant, and future work should include the identification of the enzymes involved in methanotrophy, and those involved in the oxidation of ammonia for energy. The mechanism for growth stimulation of WKT50.2 and T. roseum by antibiotics was also an interesting observation and warrants further analysis to determine the mode of action.

text: The physiological characterisation of a novel Thermomicrobia strain WKT50.2, and a review of the characteristics of the class Thermomicrobia Thermomicrobia is a class of heterotrophic, obligate aerobes within the phylum Chloroflexi.  At the time of writing, it contained four distinct species, Thermomicrobium roseum, Sphaerobacter thermophilus, Nitrolancetus hollandicus and WKT50.2, the novel strain described in this study.  The physiology and ecology of this strain, and the description of the class Thermomicrobia was investigated as part of this study.

Strain WKT50.2 was isolated from the hot springs at Waikite, New Zealand. We investigated temperature and pH range and optima, analysed PLFA, and determined preferred carbon and energy sources, N-fixation, modes of growth and antibiotic sensitivity. As a general phenotype, WKT50.2 is a heterotrophic and thermophilic obligate aerobe with a preference for moderately alkaliphilic pH conditions. The possible ecology of WKT50.2 was discussed. 

WKT50.2 was able to oxidise methane to gain energy. This was an unexpected result as methanotrophy is a highly specialised phenotype restricted to the phyla Proteobacteria and Verrucomicrobia. Methanotrophs also tend to be metabolic specialists with no capability to oxidise substrates other than C1 compounds. In contrast, WKT50.2 was also able to oxidise ammonia and nitrite, along with a range of saccharides and protein rich substrates. WKT50.2 was sensitive to most of the antibiotics tested in this study, but metronidazole and trimethoprim both stimulated growth in a dosage-dependent manner. WKT50.2 is clearly a distinct genus from T. roseum and S. thermophilus, based on 16S rRNA gene sequence similarities (91 % and 88 % respectively), G+C content and metabolic capabilities.  

T. roseum and S. thermophilus were confirmed as heterotrophic, thermophilic, moderately alkaliphilic, obligate aerobes.  The temperature and pH optima and ranges for T. roseum and S. thermophilus were amended, along with expanding the known metabolic capabilities of both species. Of particular note was the discovery that both T. roseum and S. thermophilus were also able to oxidise both methane and ammonia for energy, and that both species possessed cellulolytic activity. 

In summary, the class Thermomicrobia can be redefined as comprising obligately aerobic, facultative heterotrophs.  Cells are non-motile, non-spore forming rods.  This study has shown that the cells have proteinaceous cell walls containing ornithine, and no lipopolysaccharide.  The major fatty acid is 12-Me-18:0, and lipids include ester-linked diols. The major isoprenoid quinone is MK-8.

Several of the observations in this study merit further research.  The discovery of methanotrophy in this class was unexpected and significant, and future work should include the identification of the enzymes involved in methanotrophy, and those involved in the oxidation of ammonia for energy. The mechanism for growth stimulation of WKT50.2 and T. roseum by antibiotics was also an interesting observation and warrants further analysis to determine the mode of action.

year: 2013

title: Māori & Psychology Research Unit annual report 2011

authors: Rua, Mohi

subjects: Māori and Psychology Research Unit

abstract: Annual report of the Māori and Psychology Research Unit (MPRU) 2011. The unit was established in August of 1997. The unit is designed to provide a catalyst and support network for enhancing research concerning the psychological needs, aspirations, and priorities of Maori people. The MPRU is well situated to draw together skilled and experienced interdisciplinary research groups by networking and establishing working relationships with staff and students within the Faculty of Arts and Social Sciences, the University, and the wider community.

text: Māori & Psychology Research Unit annual report 2011 Annual report of the Māori and Psychology Research Unit (MPRU) 2011. The unit was established in August of 1997. The unit is designed to provide a catalyst and support network for enhancing research concerning the psychological needs, aspirations, and priorities of Maori people. The MPRU is well situated to draw together skilled and experienced interdisciplinary research groups by networking and establishing working relationships with staff and students within the Faculty of Arts and Social Sciences, the University, and the wider community.

year: 2012