title: Electrofishing survey of the Manawatu, Whanganui, and Mokau rivers and Lake Rotorangi, Petea River

authors: Hicks, Brendan J.

subjects: electrofishing

abstract: We used New Zealand’s first successful electrofishing boat to survey fish in three large North Island rivers and in Lake Rotorangi, hydro-electric impoundment on the Patea River. The primary objective of the fishing was to see if undesirable fish species such as koi carp (Cyprinus carpio haemaotopterus; Zhou et al. 2003), brown bullhead catfish(Ameiurus nebulosus), and rudd (Scardinius erythophthalmus) have become established in the Manawatu, Whanganui, Petea, and Mokau rivers. Koi carp are known to be present in several ponds within the Manawatu and Whanganui River catchments, and a juvenile rudd was caught by a whitebaiter near the mouth of the Mokau River. Lake Rotorangi has an established trout fishery, but European perch (Perca fluviatilis) have been illegally released into the lake, and are numerous near Stratford. This lake is also vulnerable to illegal releases of other fish species, so it was included in the survey. A secondary objective was a general survey of native and sports fish.
Nine species of native fish and three introduced species were captured during the survey of 27 sites in four river systems. Fish habitat was generally poor, with little in-water obvious at the shoreline. Aquatic macrophytes were only in Manawatu River tributaries (the Koputaroa and Tokomaru streams). All three rivers had U-shaped channels with soft banks generally of clay and mud. Poor water visibility made observations difficult in the mainstreams of all the rivers.
Common smelt were the most abundant and widespread fish species, and were present at all sites except those in the Tokomaru Stream and Lake Rotorangi. High water conductivity prevented effective electrofishing at Site 25 in the Mokau River mainstem, where the juvenile rudd was found.
Some unexpected catches in this survey were stargazers in the Manawatu River at Site 1 and 3, 10 km upstream from the sea, and black flounder in tributaries of the Manawatu (Sites 4 and 5), up to 23 km inland. Black flounder were found in the Whanganui River at Site 13, 30 km from the sea. Rainbow trout were caught in the Manawatu River at several sites (Table 4, Figure 3).
No recognised pest fish species were caught, but we cannot exclude the possibility that pest fish might occur at sites that were not fished. Despite these limitations, we are confident that our study has provided a good summary of the fish species present in the three rivers and Lake Rotorangi, and has provided estimates of minimum densities for the sites that were fished.

text: Electrofishing survey of the Manawatu, Whanganui, and Mokau rivers and Lake Rotorangi, Petea River We used New Zealand’s first successful electrofishing boat to survey fish in three large North Island rivers and in Lake Rotorangi, hydro-electric impoundment on the Patea River. The primary objective of the fishing was to see if undesirable fish species such as koi carp (Cyprinus carpio haemaotopterus; Zhou et al. 2003), brown bullhead catfish(Ameiurus nebulosus), and rudd (Scardinius erythophthalmus) have become established in the Manawatu, Whanganui, Petea, and Mokau rivers. Koi carp are known to be present in several ponds within the Manawatu and Whanganui River catchments, and a juvenile rudd was caught by a whitebaiter near the mouth of the Mokau River. Lake Rotorangi has an established trout fishery, but European perch (Perca fluviatilis) have been illegally released into the lake, and are numerous near Stratford. This lake is also vulnerable to illegal releases of other fish species, so it was included in the survey. A secondary objective was a general survey of native and sports fish.
Nine species of native fish and three introduced species were captured during the survey of 27 sites in four river systems. Fish habitat was generally poor, with little in-water obvious at the shoreline. Aquatic macrophytes were only in Manawatu River tributaries (the Koputaroa and Tokomaru streams). All three rivers had U-shaped channels with soft banks generally of clay and mud. Poor water visibility made observations difficult in the mainstreams of all the rivers.
Common smelt were the most abundant and widespread fish species, and were present at all sites except those in the Tokomaru Stream and Lake Rotorangi. High water conductivity prevented effective electrofishing at Site 25 in the Mokau River mainstem, where the juvenile rudd was found.
Some unexpected catches in this survey were stargazers in the Manawatu River at Site 1 and 3, 10 km upstream from the sea, and black flounder in tributaries of the Manawatu (Sites 4 and 5), up to 23 km inland. Black flounder were found in the Whanganui River at Site 13, 30 km from the sea. Rainbow trout were caught in the Manawatu River at several sites (Table 4, Figure 3).
No recognised pest fish species were caught, but we cannot exclude the possibility that pest fish might occur at sites that were not fished. Despite these limitations, we are confident that our study has provided a good summary of the fish species present in the three rivers and Lake Rotorangi, and has provided estimates of minimum densities for the sites that were fished.

year: 2003

title: Regulation of Metabolism in Mycobacteria and Cyanobacteria

authors: Vickers, Chelsea

subjects: AmtR

abstract: Bacteria encounter changes in their environment and must adapt to these changes in order to survive. Their ability to adapt is determined by their capacity to efficiently regulate their cellular processes. The mechanisms of bacterial regulation at the transcriptional level have been investigated by structural and functional characterisation of the transcription factor AmtR from Mycobacterium smegmatis. M. smegmatis is a soil bacteria capable of utilising alternative nitrogen sources during nitrogen limitation. AmtR is an important transcription factor that regulates the cellular machinery involved in alternative nitrogen metabolism via a novel co-repressor induced mode of regulation. A second pathway that involves post-transcriptional regulation was investigated by preliminary characterisation of a previously unexplored VapBC family of Type II Toxin Antitoxin (TA) systems found in the cyanobacteria Microcystis aeruginosa and Synechocystis sp. PCC6803 (Synechocystis). Investigation of the biochemistry of M. aeruginosa VapBC systems was limited by poor expression, however a single TA system, VapBCMAE43230/20, was successfully purified by incorporating the SUMO fusion protein into the expression construct. VapBMAE43230 and VapCMAE43220 are coexpressed and form a tetrameric complex that appears to be copurified with DNA. Similar to M. aeruginosa, only one system, VapBCslr1209/1210, in Synechocystis was successfully purified and investigated in vitro. Preliminary EMSA assays indicate VapBCslr1209/1210 is autoregulatory and binds to the promoter region of its operon by recognising palindromic sequences. The RNA pentaprobe system demonstrates that VapCslr1210 has metal dependent endoribonuclease activity that can be inhibited by VapBslr1209. Markerless deletion strains of five Synechocystis vapBC operons were made and growth experiments of three of the deletion strains were conducted. Growth experiments identified a reduced growth rate in two of the deletion strains (when compared to the WT strains): ΔvapBCslr1209/1210 and ΔvapBCssl2138/sll1092. Transcriptomic analyses of both deletion strains were conducted. Preliminary data show that both VapBC systems appear to target genes involved in carbon assimilation and metabolism via both photosynthetic and heterotrophic processes. Interestingly, VapBCslr1209/1210 targets an operon involved in glucose transport, which is also the cellular process targeted by the only other well characterised VapBC system from M. smegmatis (VapBC1283/4). These preliminary results point toward a possible similarity in biological function for VapBC systems across the prokaryotic tree.

text: Regulation of Metabolism in Mycobacteria and Cyanobacteria Bacteria encounter changes in their environment and must adapt to these changes in order to survive. Their ability to adapt is determined by their capacity to efficiently regulate their cellular processes. The mechanisms of bacterial regulation at the transcriptional level have been investigated by structural and functional characterisation of the transcription factor AmtR from Mycobacterium smegmatis. M. smegmatis is a soil bacteria capable of utilising alternative nitrogen sources during nitrogen limitation. AmtR is an important transcription factor that regulates the cellular machinery involved in alternative nitrogen metabolism via a novel co-repressor induced mode of regulation. A second pathway that involves post-transcriptional regulation was investigated by preliminary characterisation of a previously unexplored VapBC family of Type II Toxin Antitoxin (TA) systems found in the cyanobacteria Microcystis aeruginosa and Synechocystis sp. PCC6803 (Synechocystis). Investigation of the biochemistry of M. aeruginosa VapBC systems was limited by poor expression, however a single TA system, VapBCMAE43230/20, was successfully purified by incorporating the SUMO fusion protein into the expression construct. VapBMAE43230 and VapCMAE43220 are coexpressed and form a tetrameric complex that appears to be copurified with DNA. Similar to M. aeruginosa, only one system, VapBCslr1209/1210, in Synechocystis was successfully purified and investigated in vitro. Preliminary EMSA assays indicate VapBCslr1209/1210 is autoregulatory and binds to the promoter region of its operon by recognising palindromic sequences. The RNA pentaprobe system demonstrates that VapCslr1210 has metal dependent endoribonuclease activity that can be inhibited by VapBslr1209. Markerless deletion strains of five Synechocystis vapBC operons were made and growth experiments of three of the deletion strains were conducted. Growth experiments identified a reduced growth rate in two of the deletion strains (when compared to the WT strains): ΔvapBCslr1209/1210 and ΔvapBCssl2138/sll1092. Transcriptomic analyses of both deletion strains were conducted. Preliminary data show that both VapBC systems appear to target genes involved in carbon assimilation and metabolism via both photosynthetic and heterotrophic processes. Interestingly, VapBCslr1209/1210 targets an operon involved in glucose transport, which is also the cellular process targeted by the only other well characterised VapBC system from M. smegmatis (VapBC1283/4). These preliminary results point toward a possible similarity in biological function for VapBC systems across the prokaryotic tree.

year: 2015

title: Analysis of multibeam sonar data for benthic habitat characterization of the Port of Tauranga, New Zealand.

authors: Boulay, Sebastien O. C.

subjects: Tauranga

abstract: Tauranga Harbour is a mesotidal lagoon located within the Bay of Plenty, New Zealand, and is subject to an ongoing maintenance dredging program to remove mud deposits coming from various sources in the catchment. At the southern end of the commercial port, the Tauranga Bridge Marina was built adjacent to the bridge causeway, with 500 floating concrete berths, enclosed by concrete floating breakwaters. It is proposed to convert these floating breakwaters into solid ones to stop waves entering the marina. This is expected to influence tidal circulation around the Tauranga bridge causeway, and potentially affect sedimentation and marine habitats. The region is an important source of "kai moana" (seafood) for local iwi, and is a source of juvenile shellfish for the large beds located on the flood tidal delta and surrounding channels.

This study investigates the impact of the successive harbour constructions on the local sedimentology. The overall goal of the mapping part of this project is to identify and locate the different seabed facies and features within the study site, which may be affected by the sediment transport potentially resulting from the past and future harbour developments. 

To investigate the impacts of the harbour modifications, a habitat-mapping survey using acoustic mapping techniques was undertaken in July and August 2011. The hydrographic survey was simultaneously performed using a multibeam echosounder (Kongsberg-Simrad EM3000) and a Starfish 452F sidescan sonar. The backscatter/imagery data from both systems was then used for habitat mapping, using a combination of Angular Response Analysis and image-based segmentation. An underwater camera survey and seabed sampling were also performed to ground-truth the morphologies identified from the acoustic backscatter analysis. The most recent habitat map was then compared to the previous studies to identify changes in response to the different modifications of the estuary.

text: Analysis of multibeam sonar data for benthic habitat characterization of the Port of Tauranga, New Zealand. Tauranga Harbour is a mesotidal lagoon located within the Bay of Plenty, New Zealand, and is subject to an ongoing maintenance dredging program to remove mud deposits coming from various sources in the catchment. At the southern end of the commercial port, the Tauranga Bridge Marina was built adjacent to the bridge causeway, with 500 floating concrete berths, enclosed by concrete floating breakwaters. It is proposed to convert these floating breakwaters into solid ones to stop waves entering the marina. This is expected to influence tidal circulation around the Tauranga bridge causeway, and potentially affect sedimentation and marine habitats. The region is an important source of "kai moana" (seafood) for local iwi, and is a source of juvenile shellfish for the large beds located on the flood tidal delta and surrounding channels.

This study investigates the impact of the successive harbour constructions on the local sedimentology. The overall goal of the mapping part of this project is to identify and locate the different seabed facies and features within the study site, which may be affected by the sediment transport potentially resulting from the past and future harbour developments. 

To investigate the impacts of the harbour modifications, a habitat-mapping survey using acoustic mapping techniques was undertaken in July and August 2011. The hydrographic survey was simultaneously performed using a multibeam echosounder (Kongsberg-Simrad EM3000) and a Starfish 452F sidescan sonar. The backscatter/imagery data from both systems was then used for habitat mapping, using a combination of Angular Response Analysis and image-based segmentation. An underwater camera survey and seabed sampling were also performed to ground-truth the morphologies identified from the acoustic backscatter analysis. The most recent habitat map was then compared to the previous studies to identify changes in response to the different modifications of the estuary.

year: 2012