title: Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

authors: Lear, Gavin

subjects: Science & Technology

abstract: Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

text: Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil® and PowerMax® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

year: 2018

title: The lithospheric geodynamics of plate boundary transpression in New Zealand: Initiating and emplacing subduction along the Hikurangi margin, and the tectonic evolution of the Alpine Fault system

authors: Furlong, Kevin P.

subjects: plate tectonics of New Zealand

abstract: In contrast to the normal ‘Wilson cycle’ sequence of subduction leading to continental collision and associated mountain building, the evolution of the New Zealand plate boundary in the Neogene reflects the converse—initially a period of continental convergence that is followed by the emplacement of subduction. Plate reconstructions allow us to place limits on the location and timing of the continental convergence and subduction zones and the migration of the transition between the two plate boundary regimes. Relative plate motions and reconstructions since the Early to Mid-Miocene require significant continental convergence in advance of the emplacement of the southward migrating Hikurangi subduction—a sequence of tectonism seen in the present plate boundary geography of Hikurangi subduction beneath North Island and convergence in the Southern Alps along the Alpine Fault. In contrast to a transition from subduction to continental convergence where the leading edge of the upper plate is relatively thin and deformable, the transition from a continental convergent regime, with its associated crustal and lithospheric thickening, to subduction of oceanic lithosphere requires substantial thinning (removal) of upper plate continental lithosphere to make room for the slab. The simple structure of the Wadati–Benioff zone seen in the present-day geometry of the subducting Pacific plate beneath North Island indicates that this lithospheric adjustment occurs quickly. Associated with this rapid lithospheric thinning is the development of a series of ephemeral basins, younging to the south, that straddle the migrating slab edge. Based on this association between localized vertical tectonics and slab emplacement, the tectonic history of these basins records the effects of lithospheric delamination driven by the southward migrating leading edge of the subducting Pacific slab. Although the New Zealand plate boundary is often described as simply two subduction zones linked by the transpressive Alpine Fault, in actuality the present is merely a snapshot view of an ongoing and complex evolution from convergence to subduction.

text: The lithospheric geodynamics of plate boundary transpression in New Zealand: Initiating and emplacing subduction along the Hikurangi margin, and the tectonic evolution of the Alpine Fault system In contrast to the normal ‘Wilson cycle’ sequence of subduction leading to continental collision and associated mountain building, the evolution of the New Zealand plate boundary in the Neogene reflects the converse—initially a period of continental convergence that is followed by the emplacement of subduction. Plate reconstructions allow us to place limits on the location and timing of the continental convergence and subduction zones and the migration of the transition between the two plate boundary regimes. Relative plate motions and reconstructions since the Early to Mid-Miocene require significant continental convergence in advance of the emplacement of the southward migrating Hikurangi subduction—a sequence of tectonism seen in the present plate boundary geography of Hikurangi subduction beneath North Island and convergence in the Southern Alps along the Alpine Fault. In contrast to a transition from subduction to continental convergence where the leading edge of the upper plate is relatively thin and deformable, the transition from a continental convergent regime, with its associated crustal and lithospheric thickening, to subduction of oceanic lithosphere requires substantial thinning (removal) of upper plate continental lithosphere to make room for the slab. The simple structure of the Wadati–Benioff zone seen in the present-day geometry of the subducting Pacific plate beneath North Island indicates that this lithospheric adjustment occurs quickly. Associated with this rapid lithospheric thinning is the development of a series of ephemeral basins, younging to the south, that straddle the migrating slab edge. Based on this association between localized vertical tectonics and slab emplacement, the tectonic history of these basins records the effects of lithospheric delamination driven by the southward migrating leading edge of the subducting Pacific slab. Although the New Zealand plate boundary is often described as simply two subduction zones linked by the transpressive Alpine Fault, in actuality the present is merely a snapshot view of an ongoing and complex evolution from convergence to subduction.

year: 2009

title: William Grey Nicholls and Rihitoto Mataia

authors: Hart, Philip

abstract: The son of a Pakeha Maori, Nicholls had an illustrious ancestry on his mother’s side, and his wife Rihitoto Mataia also had a distinguished whakapapa. From the 1870s Nicholls farmed in Ohinemuri, and as a licensed interpreter played an important role in land transactions at the same time as he was becoming prominent in the Pakeha community. For over 30 years he invested in mining, starting at Te Aroha in 1880. He also invested in a variety of other enterprises, becoming prosperous through these investments, his farming, and in particular by acquiring and selling land. Over a 40-year period, Nicholls conducted many cases in the land court, and assisted Pakeha to acquire Maori land, and also acquired a considerable amount of land for himself and Rihitoto, who inherited many blocks from her father (but had to pay off his massive debts).
         Whereas Rihitoto was a prominent leader in the Maori community of Hauraki, Nicholls had the same role in Pakeha society. Active in a variety of initiatives to benefit the Ohinemuri community, he was a popular member and chairman of the Ohinemuri County Council, and late in life was elevated to the Legislative Council. Reputedly he assisted Maori in various ways, but clearly he identified rather more with his Pakeha ancestry. His career was a remarkably successful one, and his wife was also successful in maximizing the benefits that could be derived from her ancestry.

text: William Grey Nicholls and Rihitoto Mataia The son of a Pakeha Maori, Nicholls had an illustrious ancestry on his mother’s side, and his wife Rihitoto Mataia also had a distinguished whakapapa. From the 1870s Nicholls farmed in Ohinemuri, and as a licensed interpreter played an important role in land transactions at the same time as he was becoming prominent in the Pakeha community. For over 30 years he invested in mining, starting at Te Aroha in 1880. He also invested in a variety of other enterprises, becoming prosperous through these investments, his farming, and in particular by acquiring and selling land. Over a 40-year period, Nicholls conducted many cases in the land court, and assisted Pakeha to acquire Maori land, and also acquired a considerable amount of land for himself and Rihitoto, who inherited many blocks from her father (but had to pay off his massive debts).
         Whereas Rihitoto was a prominent leader in the Maori community of Hauraki, Nicholls had the same role in Pakeha society. Active in a variety of initiatives to benefit the Ohinemuri community, he was a popular member and chairman of the Ohinemuri County Council, and late in life was elevated to the Legislative Council. Reputedly he assisted Maori in various ways, but clearly he identified rather more with his Pakeha ancestry. His career was a remarkably successful one, and his wife was also successful in maximizing the benefits that could be derived from her ancestry.

year: 2016