title: Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep-sea habitats

authors: Knox, Matthew Andrew

subjects: Biodiversity

abstract: The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep-sea habitats due to under-sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau) of New Zealand were sampled to depths of 200–1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6% and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n = 297) revealed high total diversity (n = 49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxocephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of interstation assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher surface productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under-sampled and/or under-studied taxa.

text: Mitochondrial DNA (COI) analyses reveal that amphipod diversity is associated with environmental heterogeneity in deep-sea habitats The relationship between species diversity and environmental parameters is poorly understood for the mobile macrofauna of deep-sea habitats due to under-sampling and subsequent lack of accurate taxonomic information. To redress this, cytochrome oxidase c subunit I (COI) DNA sequences were used to estimate species diversity and to compare phoxocephalid amphipod assemblages among 20 stations encompassing a range of environmental conditions. Two regions, east (Chatham Rise) and west (Challenger Plateau) of New Zealand were sampled to depths of 200–1200 m with an epibenthic sled. Using a comparison among identified morphospecies, we found a clear gap in sequence divergences between 6% and 13% and used a 6% threshold to designate molecular operational taxonomic units (MOTUs), as a surrogate to putative species. DNA sequences (n = 297) revealed high total diversity (n = 49 MOTUs), as well as high beta diversity (28 MOTUs found at single location only). Novel phoxocephalid MOTUs were found at most stations, especially on Challenger Plateau and the flanks of Chatham Rise. Analyses of interstation assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions. A cluster of highly similar stations was identified, broadly distributed over the crest of Chatham Rise, in association with elevated food availability, probably resulting from higher surface productivity and relatively shallow depth. Accordingly, multivariate analysis revealed a strong correlation between phoxocephalid assemblages and food supply. This study highlights the value of molecular approaches, in particular COI sequences, for quantifying and comparing diversity in under-sampled and/or under-studied taxa.

year: 2012

title: Grainyhead-like 2 is required for morphological integrity of mouse embryonic stem cells and orderly formation of inner ear-like organoids

authors: Forrester-Gauntlett, Blaise

abstract: Mutations in the transcription factor gene grainyhead-like 2 (GRHL2) are associated with progressive non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28) in humans. Since complete loss of Grhl2 is lethal in mouse embryos, we studied its role during inner ear pathology and hearing loss in vitro. To this end, we generated different homozygous deletions to knockout Grhl2 in mouse embryonic stem cells (Grhl2-KO ESCs), including some mimicking naturally occurring truncations in the dimerisation domain related to human DFNA28. Under naïve culture conditions, Grhl2-KO cells in suspension were more heterogenous in size and larger than wild-type controls. Adherent Grhl2-KO cells were also larger, with a less uniform shape, flattened, less circular morphology, forming loose monolayer colonies with poorly defined edges. These changes correlated with lower expression of epithelial cadherin Cdh1 but no changes in tight junction markers (Ocln, Tjp2) or other Grhl isoforms (Grhl1, Grhl3). Clonogenicity from single cells, proliferation rates of cell populations and proliferation markers were reduced in Grhl2-KO ESCs. We next induced stepwise directed differentiation of Grhl2-KO ESCs along an otic pathway, giving rise to three-dimensional inner ear-like organoids (IELOs). Quantitative morphometry revealed that Grhl2-KO cells initially formed larger IELOs with a less compacted structure, more eccentric shape and increased surface area. These morphological changes persisted for up to one week. They were partially rescued by forced cell aggregation and fully restored by stably overexpressing exogenous Grhl2 in Grhl2-KO ESCs, indicating that Grhl2 alters cell-cell interactions. On day 8, aggregates were transferred into minimal maturation medium to allow self-guided organogenesis for another two weeks. During this period, Grhl2-KO cells and wild-type controls developed similarly, expressing neural, neuronal and sensory hair cell markers, while maintaining their initial differences in size and shape. In summary, Grhl2 is required for morphological maintenance of ESCs and orderly formation of IELOs, consistent with an essential role in organising epithelial integrity during inner ear development. Our findings validate quantitative morphometry as a useful, non-invasive screening method for molecular phenotyping of candidate mutations during organoid development.

text: Grainyhead-like 2 is required for morphological integrity of mouse embryonic stem cells and orderly formation of inner ear-like organoids Mutations in the transcription factor gene grainyhead-like 2 (GRHL2) are associated with progressive non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28) in humans. Since complete loss of Grhl2 is lethal in mouse embryos, we studied its role during inner ear pathology and hearing loss in vitro. To this end, we generated different homozygous deletions to knockout Grhl2 in mouse embryonic stem cells (Grhl2-KO ESCs), including some mimicking naturally occurring truncations in the dimerisation domain related to human DFNA28. Under naïve culture conditions, Grhl2-KO cells in suspension were more heterogenous in size and larger than wild-type controls. Adherent Grhl2-KO cells were also larger, with a less uniform shape, flattened, less circular morphology, forming loose monolayer colonies with poorly defined edges. These changes correlated with lower expression of epithelial cadherin Cdh1 but no changes in tight junction markers (Ocln, Tjp2) or other Grhl isoforms (Grhl1, Grhl3). Clonogenicity from single cells, proliferation rates of cell populations and proliferation markers were reduced in Grhl2-KO ESCs. We next induced stepwise directed differentiation of Grhl2-KO ESCs along an otic pathway, giving rise to three-dimensional inner ear-like organoids (IELOs). Quantitative morphometry revealed that Grhl2-KO cells initially formed larger IELOs with a less compacted structure, more eccentric shape and increased surface area. These morphological changes persisted for up to one week. They were partially rescued by forced cell aggregation and fully restored by stably overexpressing exogenous Grhl2 in Grhl2-KO ESCs, indicating that Grhl2 alters cell-cell interactions. On day 8, aggregates were transferred into minimal maturation medium to allow self-guided organogenesis for another two weeks. During this period, Grhl2-KO cells and wild-type controls developed similarly, expressing neural, neuronal and sensory hair cell markers, while maintaining their initial differences in size and shape. In summary, Grhl2 is required for morphological maintenance of ESCs and orderly formation of IELOs, consistent with an essential role in organising epithelial integrity during inner ear development. Our findings validate quantitative morphometry as a useful, non-invasive screening method for molecular phenotyping of candidate mutations during organoid development.

year: 2023-01-01

title: Spatial and temporal characteristics of the underwater soundscape around the Motiti Protection Area: Ōtaiti/Astrolabe Reef and Motiti Island

authors: Riegel, Maria Sophie

subjects: Underwater Soundscapes

abstract: Marine ecosystems around the world have been impacted by degradation and loss of biodiversity as a result of human impacts and climate change. The monitoring and management of ecologically significant areas is vital in understanding the effects of habitat degradation on marine ecosystems. Traditional monitoring methods are often expensive, time consuming, labour intensive and invasive. Soundscapes offer a unique opportunity for monitoring habitats in a way that is cost effective, minimally invasive and efficient. The aim of this study was to use passive acoustic monitoring to create a baseline data set using ambient sound data to investigate the spatial and temporal changes in ambient sound pressure levels, and to identify biotic, abiotic and anthropogenic sound sources which make up the marine soundscapes at the Motiti Island and Ōtaiti/Astrolabe Reef. Five diverse and ecologically significant sites in the Motiti Protection Area – at Ōtaiti/Astrolabe Reef and Motiti Island, in the Bay of Plenty, New Zealand were selected and monitored over the course of a year. This provided a wide variety of data to show the diel, lunar and seasonal patterns and trends in acoustic biological activity in order to represent the ecosystems accurately. The results showed that all sites showed strong diel patterns, with a sound pressure level increase of ~6-10dB during daylight hours compared to dark hours, and evident peaks during dawn and dusk hours as a result of biological choruses composed largely of sea urchins. There were also strong seasonal trends among the five sites, with Summer having the overall highest sound pressure level compared to Spring, Autumn and Winter, this also had an effect on the peaks in dusk choruses, which were also found to be highest during Summer. Lunar phases were also found to have an impact on the sound pressure levels of all five sites, with increased sound pressure levels during the new moon, compared to sound pressure levels during the full moon. This study created a baseline data set for a culturally, ecologically, and economically valuable area. Passive acoustic monitoring was found to be an incredibly useful tool in understand the ecosystems health and biological condition, and offers an alternative to traditional monitoring which is an effective, minimally invasive, and less labour intensive way of monitoring marine ecosystems.

text: Spatial and temporal characteristics of the underwater soundscape around the Motiti Protection Area: Ōtaiti/Astrolabe Reef and Motiti Island Marine ecosystems around the world have been impacted by degradation and loss of biodiversity as a result of human impacts and climate change. The monitoring and management of ecologically significant areas is vital in understanding the effects of habitat degradation on marine ecosystems. Traditional monitoring methods are often expensive, time consuming, labour intensive and invasive. Soundscapes offer a unique opportunity for monitoring habitats in a way that is cost effective, minimally invasive and efficient. The aim of this study was to use passive acoustic monitoring to create a baseline data set using ambient sound data to investigate the spatial and temporal changes in ambient sound pressure levels, and to identify biotic, abiotic and anthropogenic sound sources which make up the marine soundscapes at the Motiti Island and Ōtaiti/Astrolabe Reef. Five diverse and ecologically significant sites in the Motiti Protection Area – at Ōtaiti/Astrolabe Reef and Motiti Island, in the Bay of Plenty, New Zealand were selected and monitored over the course of a year. This provided a wide variety of data to show the diel, lunar and seasonal patterns and trends in acoustic biological activity in order to represent the ecosystems accurately. The results showed that all sites showed strong diel patterns, with a sound pressure level increase of ~6-10dB during daylight hours compared to dark hours, and evident peaks during dawn and dusk hours as a result of biological choruses composed largely of sea urchins. There were also strong seasonal trends among the five sites, with Summer having the overall highest sound pressure level compared to Spring, Autumn and Winter, this also had an effect on the peaks in dusk choruses, which were also found to be highest during Summer. Lunar phases were also found to have an impact on the sound pressure levels of all five sites, with increased sound pressure levels during the new moon, compared to sound pressure levels during the full moon. This study created a baseline data set for a culturally, ecologically, and economically valuable area. Passive acoustic monitoring was found to be an incredibly useful tool in understand the ecosystems health and biological condition, and offers an alternative to traditional monitoring which is an effective, minimally invasive, and less labour intensive way of monitoring marine ecosystems.

year: 2022