title: The ecology and evolutionary history of the Deinococcaceae family

authors: Abbaszadeh, Jaber

subjects: Radiation resistance

abstract: Deinococcus radiodurans is the most studied member of the Deinococcaceae family for its outstanding capability to withstand extreme doses of gamma radiation and prolonged desiccation. D. radiodurans is also type species and the first described member of the Deinococcus genus. It demonstrates approximately 3000 times more radiation resistance capability than humans and 50 times more than Escherichia coli. The remarkable radiation resistance phenotype in D. radiodurans and certain members of this family has established the conventional belief that radiation resistance is the defining characteristic of Deinococcaceae. Consequently, microbiologists used gamma radiation as a pre-culture treatment to enrich radioresistant isolates in environmental samples before cultivation. However, a few studies did not use gamma radiation as an enrichment method and isolated sensitive Deinococcus species. These findings demonstrated that the radiation resistance capacity is highly diverse among Deinococcus species, with variations in the order of magnitude ranging from 1.5 kGy to 15 kGy. Because of this variability, the prevailing view is that genomic data cannot predict radiation resistance and that this phenotype remains without a genotype. Moreover, Deinococcus members have been isolated from diverse environments, including Antarctica, hot springs, deserts, atmospheric dust, animals, and garden soil. Nevertheless, the origins of this ubiquity have remained unexplored. Here, I discuss how the biased isolation methods and focus on highly resistant species created a gap in our understanding of the true ecology and evolution of Deinococcaceae. This thesis addresses this knowledge gap using comparative genomics methods by answering three questions. (I) What factors drive the ubiquity of the Deinococcus species? (ii) What drives the diversity of radiation resistance in the Deinococcus genus, and can we predict this phenotype using genomic data? (iii) How did the radiation resistance phenotype evolve, and what are the primary needs for the common ancestor of Deinococcaceae (proto-Deinococcus)? Our results indicate that the ubiquity of the Deinococcus genus arises from its large pangenome. A high abundance of transposase genes and efficient homologous recombination mechanisms enhanced their genetic flexibility and enabled Deinococcus to survive in diverse habitats. Conversely, this ecologically advantageous trait forms a dynamic accessory genome and impacts the radiation resistance phenotype. Phylogenomic and statistical analyses revealed a pattern in the radiation resistance level. The presence of 186 gene families, mainly related to metal and redox-related cofactors, can predict lower levels of resistance in two different clades of the Deinococcus genus. This observation contradicts the conventional wisdom that radiation resistance is the defining characteristic of the Deinococcaceae family because the accessory genome controls this phenotype. Furthermore, we used the gene tree-species tree reconciliation method to infer the evolutionary events that gave rise to the proto-Deinococcus. The ancestral reconstruction analysis indicated that the proto-Deinococcus underwent significant genome expansion by gaining 1000 gene families, which is about 50% of the genome size of its ancestor, while Thermaceae retained the same genome size as their common ancestor. Overall, we conclude that the ubiquity of Deinococcus species is the result of acquiring diverse functions and surviving in various environments. While this is a beneficial evolution for the family, gaining specific genes can lower the radiation resistance capability. Therefore, radiation resistance is not the defining characteristic of Deinococcaceae. Moreover, ancestral reconstruction reveals that this proto-Deinococcus underwent genome expansion and likely gained genes that induced radiation resistance traits and genomic flexibility.

text: The ecology and evolutionary history of the Deinococcaceae family Deinococcus radiodurans is the most studied member of the Deinococcaceae family for its outstanding capability to withstand extreme doses of gamma radiation and prolonged desiccation. D. radiodurans is also type species and the first described member of the Deinococcus genus. It demonstrates approximately 3000 times more radiation resistance capability than humans and 50 times more than Escherichia coli. The remarkable radiation resistance phenotype in D. radiodurans and certain members of this family has established the conventional belief that radiation resistance is the defining characteristic of Deinococcaceae. Consequently, microbiologists used gamma radiation as a pre-culture treatment to enrich radioresistant isolates in environmental samples before cultivation. However, a few studies did not use gamma radiation as an enrichment method and isolated sensitive Deinococcus species. These findings demonstrated that the radiation resistance capacity is highly diverse among Deinococcus species, with variations in the order of magnitude ranging from 1.5 kGy to 15 kGy. Because of this variability, the prevailing view is that genomic data cannot predict radiation resistance and that this phenotype remains without a genotype. Moreover, Deinococcus members have been isolated from diverse environments, including Antarctica, hot springs, deserts, atmospheric dust, animals, and garden soil. Nevertheless, the origins of this ubiquity have remained unexplored. Here, I discuss how the biased isolation methods and focus on highly resistant species created a gap in our understanding of the true ecology and evolution of Deinococcaceae. This thesis addresses this knowledge gap using comparative genomics methods by answering three questions. (I) What factors drive the ubiquity of the Deinococcus species? (ii) What drives the diversity of radiation resistance in the Deinococcus genus, and can we predict this phenotype using genomic data? (iii) How did the radiation resistance phenotype evolve, and what are the primary needs for the common ancestor of Deinococcaceae (proto-Deinococcus)? Our results indicate that the ubiquity of the Deinococcus genus arises from its large pangenome. A high abundance of transposase genes and efficient homologous recombination mechanisms enhanced their genetic flexibility and enabled Deinococcus to survive in diverse habitats. Conversely, this ecologically advantageous trait forms a dynamic accessory genome and impacts the radiation resistance phenotype. Phylogenomic and statistical analyses revealed a pattern in the radiation resistance level. The presence of 186 gene families, mainly related to metal and redox-related cofactors, can predict lower levels of resistance in two different clades of the Deinococcus genus. This observation contradicts the conventional wisdom that radiation resistance is the defining characteristic of the Deinococcaceae family because the accessory genome controls this phenotype. Furthermore, we used the gene tree-species tree reconciliation method to infer the evolutionary events that gave rise to the proto-Deinococcus. The ancestral reconstruction analysis indicated that the proto-Deinococcus underwent significant genome expansion by gaining 1000 gene families, which is about 50% of the genome size of its ancestor, while Thermaceae retained the same genome size as their common ancestor. Overall, we conclude that the ubiquity of Deinococcus species is the result of acquiring diverse functions and surviving in various environments. While this is a beneficial evolution for the family, gaining specific genes can lower the radiation resistance capability. Therefore, radiation resistance is not the defining characteristic of Deinococcaceae. Moreover, ancestral reconstruction reveals that this proto-Deinococcus underwent genome expansion and likely gained genes that induced radiation resistance traits and genomic flexibility.

year: 2024

title: Environmental Impacts of Effluent Containing EDTA from Dairy Processing Plants

authors: Xie, Congmin Zoe

subjects: EDTA

abstract: Ethylenediaminetetraacetic acid (EDTA) is a well-known chelating agent, and has numerous applications in industries, for example in dairy industry to improve the cleaning efficiency of plant and equipment.

As EDTA is water-soluble and not volatile, it is eventually released into the environment with wastewater effluent. In general, EDTA has a low toxic impact for both humans and natural environments. There are some concerns, however, about its poor biodegradation in conventional wastewater treatment plants and natural environments, and its effect in mobilizing heavy metals from solid phases to pose a risk to groundwater.

In the late 1980's the environmental impact of EDTA was scrutinized in Europe. Since then, treatment and discharge of wastewater containing EDTA is increasingly required as environmental regulations become more stringent. This is the first investigation into the effects of EDTA in New Zealand.

In the New Zealand dairy industry, EDTA has been used as an additive alongside caustic agents to improve cleaning efficiency within dairy processing plants and to minimize dairy wastewater discharge into the environment. There are two main disposal methods of dairy wastes; direct discharge into the local stream after treatment, and spray irrigation onto pasture land. The primary aim of this research is to identify whether EDTA is detectable in the environment after the release of dairy wastes containing EDTA into that environment.

For the first time in New Zealand, an analytical method using reversed-phase ion-pair liquid chromatography, was established to determine EDTA present in dairy wastewater, and then applied to surface water, soils and groundwater with appropriate modifications. Method detection limits were 5  g/L for dairy wastewater, 1  g/L for surface water, 0.15 mg/kg (dry weight) for soils, and 2  g/L for groundwater.

Significant concentrations of EDTA, as high as 83 mg/L, were observed in wastewater from dairy processing plants, when EDTA had been used alongside alkaline cleaning agents. The analyses have shown that approximate 93 % of EDTA was removed in the existing biological treatment process, which is an extended aeration activated sludge process, operated under alkaline pH 8.0-8.2 with a 3-week sludge retention time.

For surface water receiving the dairy effluent, 1 - 2.7  g/L of EDTA were found, and no particular concerns were suggested about the associated heavy metals. 

A quasi one-dimension vertical mixing model and a two-dimension (depth-averaged) 3DD hydrodynamic model were applied to simulate EDTA dispersion in the river. The modelling results for 'a worst case scenario' of high EDTA release combined with a low river flow, suggest that the dairy effluent discharge at the Fonterra Waitoa dairy site will not lead to a significant effect on the Waitoa River in terms of EDTA concentration. 

Investigation of EDTA and heavy metal concentrations in pastoral topsoil and groundwater following the land application of dairy biomass concludes that there are no specific concerns. In contrast, the analyses suggest that heavy metals may be built up over long periods of irrigation with dairy effluent in soils, and then transported to the groundwater in the presence of EDTA. However, more research would be required to clarify this matter.

text: Environmental Impacts of Effluent Containing EDTA from Dairy Processing Plants Ethylenediaminetetraacetic acid (EDTA) is a well-known chelating agent, and has numerous applications in industries, for example in dairy industry to improve the cleaning efficiency of plant and equipment.

As EDTA is water-soluble and not volatile, it is eventually released into the environment with wastewater effluent. In general, EDTA has a low toxic impact for both humans and natural environments. There are some concerns, however, about its poor biodegradation in conventional wastewater treatment plants and natural environments, and its effect in mobilizing heavy metals from solid phases to pose a risk to groundwater.

In the late 1980's the environmental impact of EDTA was scrutinized in Europe. Since then, treatment and discharge of wastewater containing EDTA is increasingly required as environmental regulations become more stringent. This is the first investigation into the effects of EDTA in New Zealand.

In the New Zealand dairy industry, EDTA has been used as an additive alongside caustic agents to improve cleaning efficiency within dairy processing plants and to minimize dairy wastewater discharge into the environment. There are two main disposal methods of dairy wastes; direct discharge into the local stream after treatment, and spray irrigation onto pasture land. The primary aim of this research is to identify whether EDTA is detectable in the environment after the release of dairy wastes containing EDTA into that environment.

For the first time in New Zealand, an analytical method using reversed-phase ion-pair liquid chromatography, was established to determine EDTA present in dairy wastewater, and then applied to surface water, soils and groundwater with appropriate modifications. Method detection limits were 5  g/L for dairy wastewater, 1  g/L for surface water, 0.15 mg/kg (dry weight) for soils, and 2  g/L for groundwater.

Significant concentrations of EDTA, as high as 83 mg/L, were observed in wastewater from dairy processing plants, when EDTA had been used alongside alkaline cleaning agents. The analyses have shown that approximate 93 % of EDTA was removed in the existing biological treatment process, which is an extended aeration activated sludge process, operated under alkaline pH 8.0-8.2 with a 3-week sludge retention time.

For surface water receiving the dairy effluent, 1 - 2.7  g/L of EDTA were found, and no particular concerns were suggested about the associated heavy metals. 

A quasi one-dimension vertical mixing model and a two-dimension (depth-averaged) 3DD hydrodynamic model were applied to simulate EDTA dispersion in the river. The modelling results for 'a worst case scenario' of high EDTA release combined with a low river flow, suggest that the dairy effluent discharge at the Fonterra Waitoa dairy site will not lead to a significant effect on the Waitoa River in terms of EDTA concentration. 

Investigation of EDTA and heavy metal concentrations in pastoral topsoil and groundwater following the land application of dairy biomass concludes that there are no specific concerns. In contrast, the analyses suggest that heavy metals may be built up over long periods of irrigation with dairy effluent in soils, and then transported to the groundwater in the presence of EDTA. However, more research would be required to clarify this matter.

year: 2009

title: Evaluation of land in Wairoa District for potential horticultural development

authors: Rau, Johnathon Taukiri

subjects: land suitability

abstract: The Wairoa District, on the East Coast of the North Island of New Zealand has less horticultural development than areas to the north and south. The objective of this study was to provide information to help inform landowners who may wish to invest in horticulture which could improve the economic situation of the district.
Field work involving local scale climate mapping and soil characterisation of areas with potential for horticulture in Wairoa District was completed in 2017. Constructed climate and topographical maps with existing soil maps were evaluated against known crop growth requirements to produce crop potential maps identifying areas with potential for crop production. Horticultural crops included in this study include kiwifruit, apples, cherries. Alternative crops include hemp and poppies.
Between mid-April – 31 October 2017, 45 portable iButton temperature loggers were deployed throughout Land Use Capability classes 1-3 in the Wairoa District and were set to record hourly temperature. When regressed against nearby climate stations, long term (18 -26 years) temperature datasets were derived from the short term iButton datasets. MODIS satellite images were also analysed to help identify areas prone to frost. From the long-term datasets local scale chill hour, growing degree days and October frost risk maps were constructed for the Wairoa District. For the central area from Wairoa to Frasertown, chill hours were estimated to range between 600 – 900, growing degree days 1300 – 1400 and October frost risk less than 25%.
From four representative soil types, horizon samples were taken to determine the soils physical properties including each horizons Total Available Water Holding Capacity (TAWHC). Horizon TAWHC for each soil type were summed to give TAWHC to 1 meter which along with 21 years of estimated daily rainfall and potential evapotranspiration were used in a soil water balance model to estimate seasonal crop irrigation requirements. Irrigation estimates for kiwifruit compared well against published values ranging between mean 204 – 247 mm.
The crop potential maps with seasonal crop irrigation estimates can enhance a land owner’s ability to make informed decisions resulting in economic benefit to whanau, community and the Wairoa District.

text: Evaluation of land in Wairoa District for potential horticultural development The Wairoa District, on the East Coast of the North Island of New Zealand has less horticultural development than areas to the north and south. The objective of this study was to provide information to help inform landowners who may wish to invest in horticulture which could improve the economic situation of the district.
Field work involving local scale climate mapping and soil characterisation of areas with potential for horticulture in Wairoa District was completed in 2017. Constructed climate and topographical maps with existing soil maps were evaluated against known crop growth requirements to produce crop potential maps identifying areas with potential for crop production. Horticultural crops included in this study include kiwifruit, apples, cherries. Alternative crops include hemp and poppies.
Between mid-April – 31 October 2017, 45 portable iButton temperature loggers were deployed throughout Land Use Capability classes 1-3 in the Wairoa District and were set to record hourly temperature. When regressed against nearby climate stations, long term (18 -26 years) temperature datasets were derived from the short term iButton datasets. MODIS satellite images were also analysed to help identify areas prone to frost. From the long-term datasets local scale chill hour, growing degree days and October frost risk maps were constructed for the Wairoa District. For the central area from Wairoa to Frasertown, chill hours were estimated to range between 600 – 900, growing degree days 1300 – 1400 and October frost risk less than 25%.
From four representative soil types, horizon samples were taken to determine the soils physical properties including each horizons Total Available Water Holding Capacity (TAWHC). Horizon TAWHC for each soil type were summed to give TAWHC to 1 meter which along with 21 years of estimated daily rainfall and potential evapotranspiration were used in a soil water balance model to estimate seasonal crop irrigation requirements. Irrigation estimates for kiwifruit compared well against published values ranging between mean 204 – 247 mm.
The crop potential maps with seasonal crop irrigation estimates can enhance a land owner’s ability to make informed decisions resulting in economic benefit to whanau, community and the Wairoa District.

year: 2018