title: Intra-species genomic variations in hydrogen-oxidising bacteria is delineated by horizontal gene flow

authors: Cabria, Gamaliel Lysander

subjects: Bacterial speciation

abstract: Species are the fundamental unit of ecology and evolutionary biology. However, there is no universal definition of a species that spans all domains of life. Eukaryotic species are traditionally defined through reproductive isolation, where reproductive barriers result in adaptive traits being shared only within the isolated population. Therefore, discontinuities in gene flow in eukaryotes generally result in the formation of an ecologically and genotypically cohesive unit. In contrast, delineating asexual bacterial species is often hampered by extensive horizontal gene flow and is further confounded by the difficulty of identifying a bacteria’s ecological niche. Therefore, the working definition of a prokaryotic species is based on arbitrary standards of relatedness and often lacks a cohesive ecological niche. To address this problem, the ecological population theory, which defines bacterial ‘species’ as ecologically distinct populations delineated through discontinuities in total gene flow, was proposed. It postulates that, rather than a hindrance, the prevalence of horizontal gene flow, primarily through homologous recombination, plays a significant role in bacterial speciation. Horizontal gene flow allows gene-specific sweeps in bacterial populations, where adaptive genes are shared preferentially between recombining bacteria independent of their genomic background. Thus, discontinuities in horizontal gene flow can be utilised to demarcate a genotypically and ecologically cohesive bacterial species. 
Previous studies have demonstrated that ecological populations exist in heterotrophic bacteria. However, examining the generalisability of the ecological population theory requires understanding the role of horizontal gene flow in delineating populations from extreme bacterial communities, especially bacteria with limited metabolic redundancy due to their higher impact of deleterious consequences (e.g., pathway dysregulation by recombination of a maladaptive gene) during horizontal gene flow. Therefore, in this work, I utilised the chemolithoautotrophic hydrogen-oxidising Aquificota bacteria from natural populations as a model system to test the generalisability of the ecological population theory. Utilising a novel high-throughput isolation method, I isolated co-habiting Aquificota bacteria with minimal enrichment from geothermal springs. Sequencing and comparative analysis of the Aquificota genomes reveal intra-species genomic variations driven by varying degrees of horizontal gene flow and a population structure composed of co-occurring clonal lineages and recombinogenic bacteria. To examine whether these Aquificota populations exhibit ecological and evolutionary patterns akin to eukaryotic species, I investigated the changes in their population structure across four additional time points (1 year). Analysis of recent horizontal gene flow and mutations in Aquificota populations show that clonal lineages remain clonal across time, with minimal changes in their genomic background diversity. In contrast, recombining populations experience variation in intra-population diversity and a shift in the dominant genomic background across time—implying an intra-population turnover. Lastly, I also investigated the role of both non-homologous and homologous recombination in maintaining ecological populations in Aquificota by analysing the presence and function of mobile genetic elements (MGEs) in its different populations. The lack of spatial and functional overlap between MGEs and horizontally swept regions confirms that homologous recombination drives horizontal gene flow in Aquificota populations.
This work demonstrated that ecological populations in Aquificota can be delineated through discontinuities in horizontal gene flow driven primarily by homologous recombination. Thus, ecological population theory can be a generalisable model for speciation and evolution in bacteria.

text: Intra-species genomic variations in hydrogen-oxidising bacteria is delineated by horizontal gene flow Species are the fundamental unit of ecology and evolutionary biology. However, there is no universal definition of a species that spans all domains of life. Eukaryotic species are traditionally defined through reproductive isolation, where reproductive barriers result in adaptive traits being shared only within the isolated population. Therefore, discontinuities in gene flow in eukaryotes generally result in the formation of an ecologically and genotypically cohesive unit. In contrast, delineating asexual bacterial species is often hampered by extensive horizontal gene flow and is further confounded by the difficulty of identifying a bacteria’s ecological niche. Therefore, the working definition of a prokaryotic species is based on arbitrary standards of relatedness and often lacks a cohesive ecological niche. To address this problem, the ecological population theory, which defines bacterial ‘species’ as ecologically distinct populations delineated through discontinuities in total gene flow, was proposed. It postulates that, rather than a hindrance, the prevalence of horizontal gene flow, primarily through homologous recombination, plays a significant role in bacterial speciation. Horizontal gene flow allows gene-specific sweeps in bacterial populations, where adaptive genes are shared preferentially between recombining bacteria independent of their genomic background. Thus, discontinuities in horizontal gene flow can be utilised to demarcate a genotypically and ecologically cohesive bacterial species. 
Previous studies have demonstrated that ecological populations exist in heterotrophic bacteria. However, examining the generalisability of the ecological population theory requires understanding the role of horizontal gene flow in delineating populations from extreme bacterial communities, especially bacteria with limited metabolic redundancy due to their higher impact of deleterious consequences (e.g., pathway dysregulation by recombination of a maladaptive gene) during horizontal gene flow. Therefore, in this work, I utilised the chemolithoautotrophic hydrogen-oxidising Aquificota bacteria from natural populations as a model system to test the generalisability of the ecological population theory. Utilising a novel high-throughput isolation method, I isolated co-habiting Aquificota bacteria with minimal enrichment from geothermal springs. Sequencing and comparative analysis of the Aquificota genomes reveal intra-species genomic variations driven by varying degrees of horizontal gene flow and a population structure composed of co-occurring clonal lineages and recombinogenic bacteria. To examine whether these Aquificota populations exhibit ecological and evolutionary patterns akin to eukaryotic species, I investigated the changes in their population structure across four additional time points (1 year). Analysis of recent horizontal gene flow and mutations in Aquificota populations show that clonal lineages remain clonal across time, with minimal changes in their genomic background diversity. In contrast, recombining populations experience variation in intra-population diversity and a shift in the dominant genomic background across time—implying an intra-population turnover. Lastly, I also investigated the role of both non-homologous and homologous recombination in maintaining ecological populations in Aquificota by analysing the presence and function of mobile genetic elements (MGEs) in its different populations. The lack of spatial and functional overlap between MGEs and horizontally swept regions confirms that homologous recombination drives horizontal gene flow in Aquificota populations.
This work demonstrated that ecological populations in Aquificota can be delineated through discontinuities in horizontal gene flow driven primarily by homologous recombination. Thus, ecological population theory can be a generalisable model for speciation and evolution in bacteria.

year: 2024

title: Axial Variations and Entry Effects in a Pressure Screen

authors: Atkins, Martin John

subjects: Pressure Screening

abstract: Pressure screens are used for contaminant removal and fibre length fractionation in the production of pulp and paper products.  Axial variations and entry effects in the screen are known to occur and these variations have not been adequately quantified.  This thesis describes a fundamental study of the axial variations of several factors that occur within an industrial pressure screen; namely, pulp consistency, fibre length distribution, rotor pressure pulse, and feed annulus tangential velocity.

Axial variations of pulp consistency in the screen annulus and the accept chamber of the screen were studied using an internal radial sampling method.  Localised pulp samples were taken and evaluated and common measures of screen performance such as fibre passage ratio and fractionation efficiency were calculated along the screen.  Consistency generally increased along the length of the screen although under certain conditions the consistency toward the front of the screen was lower than the feed consistency.  A two passage ratio model that incorporated forward and reverse passage ratio was derived to elucidate the flow of both fibre and fluid through the screen and their effects on overall screen performance.  The passage of fibre through the screen decreased with screen length which generally had a positive effect on the fractionation efficiency toward the back of the screen.  The passage of individual fibre length fractions was also studied and it was found that long fibre had a much lower passage than short fibre which caused the average fibre length in the annulus to increase.  

Rotor induced pressure pulse variations along the screen length were also investigated.  The magnitude of the pressure pulse was significantly lower (up to 40 %) at the rear of the screen.  The variation in pressure caused by the rotor is due to a Venturi effect and the shape of the rotor.  The relative velocity of the fluid and the rotor, called the slip factor, also directly affects the size of the pressure pulse in the annulus.  The slip factor decreases along the length of the screen due to the increase in tangential velocity of the fluid.  Pressure pulse data was also used to estimate the instantaneous aperture velocity and back-flush ratio.  The instantaneous aperture velocity was calculated to vary considerably from the superficial aperture velocity by up to 5 m/s in the forward direction and 10 m/s in the reverse direction.   
Computational Fluid Dynamics (CFD) was used to model tangential velocity changes in simplified screen annuli with axial through flow.  For a smooth screen rotor the mean tangential velocity increased over the entire length of the annulus without reaching a maximum value.  A step and bump rotor were modelled and the shape of the pressure pulses showed good agreement with experimentally measured pulses.  The mean tangential velocity and the entrance length were found to be heavily dependant on the screen rotor used.

text: Axial Variations and Entry Effects in a Pressure Screen Pressure screens are used for contaminant removal and fibre length fractionation in the production of pulp and paper products.  Axial variations and entry effects in the screen are known to occur and these variations have not been adequately quantified.  This thesis describes a fundamental study of the axial variations of several factors that occur within an industrial pressure screen; namely, pulp consistency, fibre length distribution, rotor pressure pulse, and feed annulus tangential velocity.

Axial variations of pulp consistency in the screen annulus and the accept chamber of the screen were studied using an internal radial sampling method.  Localised pulp samples were taken and evaluated and common measures of screen performance such as fibre passage ratio and fractionation efficiency were calculated along the screen.  Consistency generally increased along the length of the screen although under certain conditions the consistency toward the front of the screen was lower than the feed consistency.  A two passage ratio model that incorporated forward and reverse passage ratio was derived to elucidate the flow of both fibre and fluid through the screen and their effects on overall screen performance.  The passage of fibre through the screen decreased with screen length which generally had a positive effect on the fractionation efficiency toward the back of the screen.  The passage of individual fibre length fractions was also studied and it was found that long fibre had a much lower passage than short fibre which caused the average fibre length in the annulus to increase.  

Rotor induced pressure pulse variations along the screen length were also investigated.  The magnitude of the pressure pulse was significantly lower (up to 40 %) at the rear of the screen.  The variation in pressure caused by the rotor is due to a Venturi effect and the shape of the rotor.  The relative velocity of the fluid and the rotor, called the slip factor, also directly affects the size of the pressure pulse in the annulus.  The slip factor decreases along the length of the screen due to the increase in tangential velocity of the fluid.  Pressure pulse data was also used to estimate the instantaneous aperture velocity and back-flush ratio.  The instantaneous aperture velocity was calculated to vary considerably from the superficial aperture velocity by up to 5 m/s in the forward direction and 10 m/s in the reverse direction.   
Computational Fluid Dynamics (CFD) was used to model tangential velocity changes in simplified screen annuli with axial through flow.  For a smooth screen rotor the mean tangential velocity increased over the entire length of the annulus without reaching a maximum value.  A step and bump rotor were modelled and the shape of the pressure pulses showed good agreement with experimentally measured pulses.  The mean tangential velocity and the entrance length were found to be heavily dependant on the screen rotor used.

year: 2007

title: He whakanui i ēnei tau, e rima tekau o Te Whare Wānanga o Waikato

authors: Rewi, Poia

subjects: Tohu mātauranga

abstract: Aku tau ki Waikato: 1986-2003

A Block

Koia tērā, ko te Tari Māori (Māori Department), ko Timoti Kāretu te tumuaki, ko tōna kāhui kawe i ngā mahi ko te momo he wā tōna he pūkenga, he ahonuku, he ahorangi, he tākuta, he tohunga; he wā anō he pāpā, he whaea, he matua kēkē, he whaea kēkē; he wā anō he haututū, he hangarau, he whakatoi, he hoa tonu. Ko te tohu kē ia e whakaatuhia nei, ko te mātau o tēnei hanga ki te hāpai i te momo taera e hua ai te pai ki te ākonga, ki te mahi, ki te hapori.

Koia hoki te momo e whakamātauhia ana e te ao Pākehā; te mōhio kē, te tirohanga kē, te pōhēhē, te ture, te kawa me ngā tini aha kē. Koia tonu te momo e whakamātauhia ana e te ao Māori; ōna manako, ōna wawata, ōna taumahatanga, ōna piki, ōna heke. Ko te wā hui ki ngā kaimahi i Te Tari Māori he whakamoemoe i ngā utanga a te whare wānanga me ā te iwi kia whakapōtaehia he ākonga, me te mea, kia puta tonu hei tamāhine, hei tāhae, hei irāmutu, hei mokopuna e “toa ai rātou hei iti kotahi harakoa mō te iwi”. Kātahi nā te whiu ko tēnā, he taumahatanga kāore e pērā rawa te wahatanga e ngā kaimahi Pākehā i roto i ngā kura wānanga pēnei. Heoi anō, ko ia tērā ngā wheako o te wā, ahakoa nō nākua rawa nei i mārama ai taua here ki aua kaimahi, ka mahara iho au ki taua wā, ka mīharo tonu i te kaha o ērā pūkenga2 ki te whakatutuki i te wāhi ki a rātou. I tēnei punua hokinga mahara, ka aro ki ēnei mātua marau e rua, arā, ko te kawea o ngā mahi e taea ai e te Māori, ākonga mai, pūkenga mai, kaupapa mai, i te ao whare wānanga Pākehā, ka tahi; ka rua, ka aro ki ētahi o ngā āhuatanga e honohono ana ki te iwi.

text: He whakanui i ēnei tau, e rima tekau o Te Whare Wānanga o Waikato Aku tau ki Waikato: 1986-2003

A Block

Koia tērā, ko te Tari Māori (Māori Department), ko Timoti Kāretu te tumuaki, ko tōna kāhui kawe i ngā mahi ko te momo he wā tōna he pūkenga, he ahonuku, he ahorangi, he tākuta, he tohunga; he wā anō he pāpā, he whaea, he matua kēkē, he whaea kēkē; he wā anō he haututū, he hangarau, he whakatoi, he hoa tonu. Ko te tohu kē ia e whakaatuhia nei, ko te mātau o tēnei hanga ki te hāpai i te momo taera e hua ai te pai ki te ākonga, ki te mahi, ki te hapori.

Koia hoki te momo e whakamātauhia ana e te ao Pākehā; te mōhio kē, te tirohanga kē, te pōhēhē, te ture, te kawa me ngā tini aha kē. Koia tonu te momo e whakamātauhia ana e te ao Māori; ōna manako, ōna wawata, ōna taumahatanga, ōna piki, ōna heke. Ko te wā hui ki ngā kaimahi i Te Tari Māori he whakamoemoe i ngā utanga a te whare wānanga me ā te iwi kia whakapōtaehia he ākonga, me te mea, kia puta tonu hei tamāhine, hei tāhae, hei irāmutu, hei mokopuna e “toa ai rātou hei iti kotahi harakoa mō te iwi”. Kātahi nā te whiu ko tēnā, he taumahatanga kāore e pērā rawa te wahatanga e ngā kaimahi Pākehā i roto i ngā kura wānanga pēnei. Heoi anō, ko ia tērā ngā wheako o te wā, ahakoa nō nākua rawa nei i mārama ai taua here ki aua kaimahi, ka mahara iho au ki taua wā, ka mīharo tonu i te kaha o ērā pūkenga2 ki te whakatutuki i te wāhi ki a rātou. I tēnei punua hokinga mahara, ka aro ki ēnei mātua marau e rua, arā, ko te kawea o ngā mahi e taea ai e te Māori, ākonga mai, pūkenga mai, kaupapa mai, i te ao whare wānanga Pākehā, ka tahi; ka rua, ka aro ki ētahi o ngā āhuatanga e honohono ana ki te iwi.

year: 2016