title: The First Insights into the Phylogeny, Genomics, and Ecology of the Novel Bacterial Phylum Armatimonadetes

authors: Lee, Chien-Yu Kevin

subjects: Microbiology

abstract: Currently, a large proportion of novel microbial evolutionary lineages is poorly understood due to limited coverage of representative species. These “candidate” lineages represent significant gaps in our understanding of microbial function and ecology. This study focused on Chthonomonas calidirosea, the earliest isolated species within Armatimonadetes, the most recently-recognised bacterial phylum. The overall aim of this research was to start to understand the ecology and phylogeny of Armatimonadetes, and provide a foundation for future research into the phylum, with the benefit of narrowing the current knowledge gaps on microbial diversity. This was achieved by integrating multiple data types (phylogenetics, genomics, and community profiling metagenomics).

The initial stage of this research aimed to address and clarify conflicts in reported phylogeny of the phylum Armatimonadetes. This study generated a comprehensive reference phylogenetic tree of 16S rRNA genes for the phylum, so that the phylogenetic position of newly-identified phylotypes can be reliably associated across studies. Multiple robust statistical methods were used to arrive at a consensus on the partitioning of classes and neighbouring phyla. The process also helped to identify and exclude candidate phyla previously misattributed to Armatimonadetes, thus better defining the phylum for future studies.

The deeply-branching phylogenetic relationship of Armatimonadetes with other bacterial phyla was resolved by the sequencing of C. calidirosea T49T genome and analysing concatenated amino acid sequences of conserved genes against homologs in other prokaryotic genomes. The phylogenomic analysis showed Chloroflexi to be the most closely related formal phylum to Armatimonadetes. This publication was the first analysis of a genome from the phylum Armatimonadetes, and provided evolutionarily- and genetically-distinct insights to the overall knowledge of microbial genetic diversity. Analysis of the genome showed a metabolism geared towards non-cellulosic carbohydrates as the carbon and energy source, which coincides with previous culture-based physiological experiments (Lee et al., 2011). Genetic mechanisms behind leucine auxotrophy and narrow pH growth range were also identified. These observations supported the theory that C. calidirosea T49T occupies the niche of a scavenger of diverse species of carbohydrates within geothermal environments, in association with cellulolytic community members. In addition, the genome exhibited an unusual disorganisation of functionally-related genes typically found in conserved operons. The relatively high abundance of sigma factors (relative to genome size) in strain T49T may play an important role in gene regulation and coordination of metabolic pathways to compensate for the scattering of operons. Overall, this research built upon the previous physiological characterisation C. calidirosea T49T (Lee et al., 2011), resulting in a more in-depth and integrated analysis of the bacterium through both phenotypic and genotypic information.

Finally, to investigate the genome dynamics of the species (particularly in genome organisation and adaptation to various environments as a scavenger), and to provide ecological and evolutionary context beyond the single genome analysed, the genomes of three additional C. calidirosea isolates cultured from diverse locations across the Taupō Volcanic Zone were extracted, sequenced, and compared to T49T. The genomes exhibited higher within-species conservation than other thermophilic species such as Thermus thermophilus (Henne et al., 2004; Jiang et al., 2013; Oshima & Ariga, 1975) and Sulfolobus islandicus (Reno et al., 2009) isolated from similar geographical distance. No genomic rearrangements were identified between C. calidirosea isolates. The majority of variation was limited to single nucleotide polymorphisms, with a limited number of horizontally-transferred genes and differentially-present fast-evolving genes, such as restriction modification system. The phylogeny and carbohydrate utilisation profiles of the isolates correlated with the geographical relationship between the sample sites rather than with other factors, such as soil geochemistry or microbial communities of the sites. The correlation between geography and phylogeny, low abundance of C. calidirosea at all sample sites (ranging from 0.006 % to 0.3 %), and the high genomic conservation indicated rapid aeolian dispersal and localised extinction as the most probable causes of homogeneity between the populations. The findings contribute to a better understanding of the genome dynamics and ecology of C. calidirosea, as well as the dispersal possibilities of free-living bacteria between distinct and discrete habitats.

These studies addressed the overarching aim to investigate the ecology and phylogeny of Armatimonadetes through the research outlined above. This body of work contributed greatly to our understanding of Armatimonadetes phylogeny, both by clarifying its internal taxonomy and its position relative to neighbouring clades. Furthermore, it contributed to understanding of Armatimonadetes ecology by richly describing the ecological niche, genome, and lifestyle of C. calidirosea. Not only does this work greatly increase our understanding of the newest of the 30 prokaryotic phyla (Euzéby, 2011, Retrieved in December 2014), it also provides a rich foundation for future study.

text: The First Insights into the Phylogeny, Genomics, and Ecology of the Novel Bacterial Phylum Armatimonadetes Currently, a large proportion of novel microbial evolutionary lineages is poorly understood due to limited coverage of representative species. These “candidate” lineages represent significant gaps in our understanding of microbial function and ecology. This study focused on Chthonomonas calidirosea, the earliest isolated species within Armatimonadetes, the most recently-recognised bacterial phylum. The overall aim of this research was to start to understand the ecology and phylogeny of Armatimonadetes, and provide a foundation for future research into the phylum, with the benefit of narrowing the current knowledge gaps on microbial diversity. This was achieved by integrating multiple data types (phylogenetics, genomics, and community profiling metagenomics).

The initial stage of this research aimed to address and clarify conflicts in reported phylogeny of the phylum Armatimonadetes. This study generated a comprehensive reference phylogenetic tree of 16S rRNA genes for the phylum, so that the phylogenetic position of newly-identified phylotypes can be reliably associated across studies. Multiple robust statistical methods were used to arrive at a consensus on the partitioning of classes and neighbouring phyla. The process also helped to identify and exclude candidate phyla previously misattributed to Armatimonadetes, thus better defining the phylum for future studies.

The deeply-branching phylogenetic relationship of Armatimonadetes with other bacterial phyla was resolved by the sequencing of C. calidirosea T49T genome and analysing concatenated amino acid sequences of conserved genes against homologs in other prokaryotic genomes. The phylogenomic analysis showed Chloroflexi to be the most closely related formal phylum to Armatimonadetes. This publication was the first analysis of a genome from the phylum Armatimonadetes, and provided evolutionarily- and genetically-distinct insights to the overall knowledge of microbial genetic diversity. Analysis of the genome showed a metabolism geared towards non-cellulosic carbohydrates as the carbon and energy source, which coincides with previous culture-based physiological experiments (Lee et al., 2011). Genetic mechanisms behind leucine auxotrophy and narrow pH growth range were also identified. These observations supported the theory that C. calidirosea T49T occupies the niche of a scavenger of diverse species of carbohydrates within geothermal environments, in association with cellulolytic community members. In addition, the genome exhibited an unusual disorganisation of functionally-related genes typically found in conserved operons. The relatively high abundance of sigma factors (relative to genome size) in strain T49T may play an important role in gene regulation and coordination of metabolic pathways to compensate for the scattering of operons. Overall, this research built upon the previous physiological characterisation C. calidirosea T49T (Lee et al., 2011), resulting in a more in-depth and integrated analysis of the bacterium through both phenotypic and genotypic information.

Finally, to investigate the genome dynamics of the species (particularly in genome organisation and adaptation to various environments as a scavenger), and to provide ecological and evolutionary context beyond the single genome analysed, the genomes of three additional C. calidirosea isolates cultured from diverse locations across the Taupō Volcanic Zone were extracted, sequenced, and compared to T49T. The genomes exhibited higher within-species conservation than other thermophilic species such as Thermus thermophilus (Henne et al., 2004; Jiang et al., 2013; Oshima & Ariga, 1975) and Sulfolobus islandicus (Reno et al., 2009) isolated from similar geographical distance. No genomic rearrangements were identified between C. calidirosea isolates. The majority of variation was limited to single nucleotide polymorphisms, with a limited number of horizontally-transferred genes and differentially-present fast-evolving genes, such as restriction modification system. The phylogeny and carbohydrate utilisation profiles of the isolates correlated with the geographical relationship between the sample sites rather than with other factors, such as soil geochemistry or microbial communities of the sites. The correlation between geography and phylogeny, low abundance of C. calidirosea at all sample sites (ranging from 0.006 % to 0.3 %), and the high genomic conservation indicated rapid aeolian dispersal and localised extinction as the most probable causes of homogeneity between the populations. The findings contribute to a better understanding of the genome dynamics and ecology of C. calidirosea, as well as the dispersal possibilities of free-living bacteria between distinct and discrete habitats.

These studies addressed the overarching aim to investigate the ecology and phylogeny of Armatimonadetes through the research outlined above. This body of work contributed greatly to our understanding of Armatimonadetes phylogeny, both by clarifying its internal taxonomy and its position relative to neighbouring clades. Furthermore, it contributed to understanding of Armatimonadetes ecology by richly describing the ecological niche, genome, and lifestyle of C. calidirosea. Not only does this work greatly increase our understanding of the newest of the 30 prokaryotic phyla (Euzéby, 2011, Retrieved in December 2014), it also provides a rich foundation for future study.

year: 2015

title: Mitigating FMCG transport bottlenecks following an extended Cook Strait ferry outage in Aotearoa New Zealand

authors: Brutsch, Nathan

subjects: fast-moving consumer goods

abstract: This research aims to understand how an extended Cook Strait ferry outage would impact the movement of fast-moving consumer goods (FMCGs) in New Zealand (NZ). The Cook Strait ferries are critical to the country’s freight system, serving as an extension of the main state highway and rail line connecting the North and South Islands. Despite the significance of the ferries, the ferry terminals are aged and lack redundancy, and they could fail in an earthquake. To understand how an extended terminal outage would impact the movement of FMCGs, data was collected through interviews with 30 industry experts in the transport and FMCG sectors, which was thematically analysed and supplemented with quantitative details to further understand the impact. The findings revealed numerous transport bottlenecks would surface in an extended terminal outage and a lack of preparedness in NZ’s freight system. To guide this research, a set of management tools known as the Theory of Constraints Thinking Process were used, enabling sense to be made of NZ’s domestic freight system following a Cook Strait ferry outage. Using these tools to generate visual diagrams, the cause-and-effect relationships between bottlenecks were identified, root causes were uncovered, and potential solutions were explored. Given that it is not a case of if a major disaster will occur, but when, it is important that progress is made towards addressing the identified root causes so that the impact from future disruptions is minimised and goods can continue moving.

text: Mitigating FMCG transport bottlenecks following an extended Cook Strait ferry outage in Aotearoa New Zealand This research aims to understand how an extended Cook Strait ferry outage would impact the movement of fast-moving consumer goods (FMCGs) in New Zealand (NZ). The Cook Strait ferries are critical to the country’s freight system, serving as an extension of the main state highway and rail line connecting the North and South Islands. Despite the significance of the ferries, the ferry terminals are aged and lack redundancy, and they could fail in an earthquake. To understand how an extended terminal outage would impact the movement of FMCGs, data was collected through interviews with 30 industry experts in the transport and FMCG sectors, which was thematically analysed and supplemented with quantitative details to further understand the impact. The findings revealed numerous transport bottlenecks would surface in an extended terminal outage and a lack of preparedness in NZ’s freight system. To guide this research, a set of management tools known as the Theory of Constraints Thinking Process were used, enabling sense to be made of NZ’s domestic freight system following a Cook Strait ferry outage. Using these tools to generate visual diagrams, the cause-and-effect relationships between bottlenecks were identified, root causes were uncovered, and potential solutions were explored. Given that it is not a case of if a major disaster will occur, but when, it is important that progress is made towards addressing the identified root causes so that the impact from future disruptions is minimised and goods can continue moving.

year: 2024

title: Machine translation for te reo Māori

authors: Keegan, Te Taka Adrian Gregory

abstract: What is Machine Translation? Machine Translation (MT) is a process where computer software is used to translate texts from one natural (or spoken) language to another. Early research centred on two distinct approaches: Rules Based Machine Translation (RBMT) and Statistical Machine Translation (SMT). In simple terms RBMT makes use of large sets of linguistic rules that define languages whereas SMT uses statistical techniques to build language models from large language corpora. Increases in computing power and the amount of language corpora available has meant that SMT had become the preferred option with recent advances in neural networks also being applied to improve the accuracy of SMT. For commercial reasons, this is an area of research that has generated a lot of interest and funding support from some major international computer companies, including Google¹,Microsoft² and Facebook³.
Why is Machine Translation important for te reo Māori? A te reo Māori purist may argue that it is not important to focus activities on having a machine undertake translations for te reo Māori; if people want to understand te reo Māori then they should put in the effort to learn the language. This line of reasoning is difficult to argue with. But, from a Māori language activist perspective the value of MT is not so much in the translation of te reo Māori to (say) English, but rather the translation of English to te reo Māori. If this translation can be done efficiently, with low costs, it will assist in the proliferation of te reo Māori into new contexts, new environments and will assist its normalisation in New Zealand's society.
At this time, two of the major international companies, Google and Microsoft, have invested significantly in MT for te reo Māori. This paper summarises their endeavours and reports on the quality of translations they have been able to generate.

text: Machine translation for te reo Māori What is Machine Translation? Machine Translation (MT) is a process where computer software is used to translate texts from one natural (or spoken) language to another. Early research centred on two distinct approaches: Rules Based Machine Translation (RBMT) and Statistical Machine Translation (SMT). In simple terms RBMT makes use of large sets of linguistic rules that define languages whereas SMT uses statistical techniques to build language models from large language corpora. Increases in computing power and the amount of language corpora available has meant that SMT had become the preferred option with recent advances in neural networks also being applied to improve the accuracy of SMT. For commercial reasons, this is an area of research that has generated a lot of interest and funding support from some major international computer companies, including Google¹,Microsoft² and Facebook³.
Why is Machine Translation important for te reo Māori? A te reo Māori purist may argue that it is not important to focus activities on having a machine undertake translations for te reo Māori; if people want to understand te reo Māori then they should put in the effort to learn the language. This line of reasoning is difficult to argue with. But, from a Māori language activist perspective the value of MT is not so much in the translation of te reo Māori to (say) English, but rather the translation of English to te reo Māori. If this translation can be done efficiently, with low costs, it will assist in the proliferation of te reo Māori into new contexts, new environments and will assist its normalisation in New Zealand's society.
At this time, two of the major international companies, Google and Microsoft, have invested significantly in MT for te reo Māori. This paper summarises their endeavours and reports on the quality of translations they have been able to generate.

year: 2017