cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20343336
title: Characterization of vanadium-dependent bromoperoxidases involved in the production of brominated sesquiterpenes by the red alga <i>Laurencia okamurae</i>

description: The red algal genus <i>Laurencia</i> produces abundant brominated metabolites, including cuparane- and laurane-type brominated sesquiterpenes. In order to gain insights into the biosynthesis mechanisms for brominated compounds, we focused on the vanadium-dependent bromoperoxidase (V-BPO). Four members of the homologous genes encoding for V-BPO were obtained from <i>L. okamurae</i> by PCR amplification. The recombinant V-BPO protein produced in <i>Escherichia coli</i> exhibited a significant brominating activity to monochlorodimedone. The function of V-BPO was examined by an assay using nerolidol as a relevant natural substrate. The enzyme properties of V-BPO were compared with those of related halogenating enzymes. The results indicate that V-BPO is one of the key enzymes responsible for the production of brominated compounds in <i>Laurencia</i>.
DOI: 10.6084/m9.figshare.20408076
title: A resilience lens to explore seaweed farmers’ responses to the impacts of climate change in Tanzania

description: Seaweed-based mariculture is an important source of livelihoods for impoverished coastal communities in Tanzania. However, the impacts of climate change across East Africa are putting a strain on the growth of the seaweed industry. Smallholder farmers are already mobilizing strategies to cope with challenges such as disease outbreaks, but they are struggling to maintain seaweed production and derive sufficient income. A better understanding of the challenges they face and the factors inhibiting their ability to build resilience is needed to inform policies and development programmes to achieve the Sustainable Development Goals, particularly Goal 13 on Climate action and Goal 14 on Life Below Water. The global demand for seaweed is expanding rapidly. Strengthening the adaptability of seaweed production to climate change is important for farmers to rely on it as a source of livelihoods on which they can build their own resilience to climate change. Drawing on qualitative data from key informant interviews in four Tanzanian seaweed-producing areas, this paper assesses the long-term resilience capacities of seaweed farmers to respond to one of the main hazards: diseases affecting seaweed crops. While several strategies help farmers maintain their income, most of them only support resilience in the short term. The increasing pressure on marine resources and the lack of regulations for supporting an equitable and sustainable seaweed-based mariculture sector do not bode well for farmers’ long-term adaptation to climate change and environmental degradation. Seaweed farming remains a crucial source of livelihoods for poor coastal communities in Tanzania, but it does not currently lead to positive transformative changes in their socio-economic conditions. Policies aiming to support sustainable aquaculture, particularly in tropical ecosystems that are highly vulnerable to climate change, must address the existing social, economic and knowledge inequities that prevent poor communities from building their resilience.
DOI: 10.6084/m9.figshare.19768553.v1
title: Viruses of Rhodophyta: lack of cultures and genomic resources pose a threat to the growing red algal aquaculture industry

description: There is a growing global demand for algal-derived products as they offer alternatives that can help to mitigate climate change, support coastal biodiversity and reach food sovereignty. Red algae (Rhodophyta) have been cultivated for hundreds of years and currently support an economically important industry worldwide. However, pathogen outbreaks pose a major potential threat to this growing industry, in some cases already causing more than $1 million loss annually, as in <i>Pyropia</i> (Bangiaceae) farms. Some of the most destructive algal pathogens, although poorly understood, are viruses. They are highly diverse and abundant, exerting strong pressure on the life cycle of their hosts. Knowledge of red algal viruses has developed at a much slower pace than for their green algal counterparts, even though it was in a red algal species, <i>Sirodotia tenuissima</i> (Batrachospermaceae), that the first observation of viruses in eukaryotic algae was made. Furthermore, it was only in 2016 that the first Rhodophyta viruses were isolated, and to date only three have sequenced genomes, all RNA viruses, isolated from the hosts <i>Delisea pulchra, Chondrus crispus</i> and <i>Pyropia suborbiculata</i>. Given that viruses are prevalent and constitute major threats to all groups of life and that genomic resources are still lacking, they could pose a serious menace to ongoing aquaculture endeavours. Therefore, here we report a thorough and comprehensive (though not exhaustive) review of studies on Rhodophyta viruses, suggesting a set of propositions to advance knowledge in the field and to encourage more active focussed investigation. This will benefit not only red algal aquaculture but also shed light on the associated viral diversity, evolution and viral impacts on the life history of their red algal hosts.
DOI: 10.6084/m9.figshare.19768553
title: Viruses of Rhodophyta: lack of cultures and genomic resources pose a threat to the growing red algal aquaculture industry

description: There is a growing global demand for algal-derived products as they offer alternatives that can help to mitigate climate change, support coastal biodiversity and reach food sovereignty. Red algae (Rhodophyta) have been cultivated for hundreds of years and currently support an economically important industry worldwide. However, pathogen outbreaks pose a major potential threat to this growing industry, in some cases already causing more than $1 million loss annually, as in <i>Pyropia</i> (Bangiaceae) farms. Some of the most destructive algal pathogens, although poorly understood, are viruses. They are highly diverse and abundant, exerting strong pressure on the life cycle of their hosts. Knowledge of red algal viruses has developed at a much slower pace than for their green algal counterparts, even though it was in a red algal species, <i>Sirodotia tenuissima</i> (Batrachospermaceae), that the first observation of viruses in eukaryotic algae was made. Furthermore, it was only in 2016 that the first Rhodophyta viruses were isolated, and to date only three have sequenced genomes, all RNA viruses, isolated from the hosts <i>Delisea pulchra, Chondrus crispus</i> and <i>Pyropia suborbiculata</i>. Given that viruses are prevalent and constitute major threats to all groups of life and that genomic resources are still lacking, they could pose a serious menace to ongoing aquaculture endeavours. Therefore, here we report a thorough and comprehensive (though not exhaustive) review of studies on Rhodophyta viruses, suggesting a set of propositions to advance knowledge in the field and to encourage more active focussed investigation. This will benefit not only red algal aquaculture but also shed light on the associated viral diversity, evolution and viral impacts on the life history of their red algal hosts.
DOI: 10.6084/m9.figshare.20408076.v1
title: A resilience lens to explore seaweed farmers’ responses to the impacts of climate change in Tanzania

description: Seaweed-based mariculture is an important source of livelihoods for impoverished coastal communities in Tanzania. However, the impacts of climate change across East Africa are putting a strain on the growth of the seaweed industry. Smallholder farmers are already mobilizing strategies to cope with challenges such as disease outbreaks, but they are struggling to maintain seaweed production and derive sufficient income. A better understanding of the challenges they face and the factors inhibiting their ability to build resilience is needed to inform policies and development programmes to achieve the Sustainable Development Goals, particularly Goal 13 on Climate action and Goal 14 on Life Below Water. The global demand for seaweed is expanding rapidly. Strengthening the adaptability of seaweed production to climate change is important for farmers to rely on it as a source of livelihoods on which they can build their own resilience to climate change. Drawing on qualitative data from key informant interviews in four Tanzanian seaweed-producing areas, this paper assesses the long-term resilience capacities of seaweed farmers to respond to one of the main hazards: diseases affecting seaweed crops. While several strategies help farmers maintain their income, most of them only support resilience in the short term. The increasing pressure on marine resources and the lack of regulations for supporting an equitable and sustainable seaweed-based mariculture sector do not bode well for farmers’ long-term adaptation to climate change and environmental degradation. Seaweed farming remains a crucial source of livelihoods for poor coastal communities in Tanzania, but it does not currently lead to positive transformative changes in their socio-economic conditions. Policies aiming to support sustainable aquaculture, particularly in tropical ecosystems that are highly vulnerable to climate change, must address the existing social, economic and knowledge inequities that prevent poor communities from building their resilience.
DOI: 10.6084/m9.figshare.20364709
title: Identification of the quorum sensing signal of the opportunistic pathogen inducing bleaching disease in the red macroalga <i>Halymenia floresii</i> holobiont

description: Seaweed surface provides a suitable substratum for the settlement of microorganisms (bacteria, viruses, and plankton). These microbial partners may have either beneficial or detrimental effects on the host since surface microbiota can act either as a protective layer to the macroalgae (symbiotic beneficial relations) or, under changing environmental conditions, the microbial equilibrium may shift to a detrimental, pathogenic state thus inducing diseases in the host. In commercial aquaculture, seaweed diseases feature a growing concern. Pathogenicity of microorganisms that infect algal hosts is closely related to the release of virulence factors and the formation of biofilms, both of which are regulated by <i>Quorum Sensing</i> (QS). The main focus of this study is to determine the pathogenicity of the surface-associated bacteria of <i>Halymenia floresii</i>, a carrageenophyte that originated from distinct habitats. Twenty-five bacterial species isolated from the surface of <i>H. floresii</i> were individually tested for tip bleaching assay to evaluate their potential pathogenicity. Ten isolates significantly reduced the risk of tip bleaching in <i>H. floresii</i> and were designated as “significantly non-pathogenic”. <i>Vibrio owensii</i> was identified as a “significant pathogen” inducing bleaching disease in <i>H. floresii</i>. By using LC-MS, we here identified its HomoSerine Lactones (HSL) QS signal, as a C4-HSL (short-chain). This study thus suggests a possible involvement of QS signal (short-chain) in the disease-inducing bacterium from the aquaculture ponds (an integrated multitrophic aquaculture system). This study firstly reports on the surface-associated bacteria of a lambda-carrageenophyte. This study must contribute to the development of dedicated strategies for disease control based on HSL disruption in aquaculture.
DOI: 10.6084/m9.figshare.20364709.v1
title: Identification of the quorum sensing signal of the opportunistic pathogen inducing bleaching disease in the red macroalga <i>Halymenia floresii</i> holobiont

description: Seaweed surface provides a suitable substratum for the settlement of microorganisms (bacteria, viruses, and plankton). These microbial partners may have either beneficial or detrimental effects on the host since surface microbiota can act either as a protective layer to the macroalgae (symbiotic beneficial relations) or, under changing environmental conditions, the microbial equilibrium may shift to a detrimental, pathogenic state thus inducing diseases in the host. In commercial aquaculture, seaweed diseases feature a growing concern. Pathogenicity of microorganisms that infect algal hosts is closely related to the release of virulence factors and the formation of biofilms, both of which are regulated by <i>Quorum Sensing</i> (QS). The main focus of this study is to determine the pathogenicity of the surface-associated bacteria of <i>Halymenia floresii</i>, a carrageenophyte that originated from distinct habitats. Twenty-five bacterial species isolated from the surface of <i>H. floresii</i> were individually tested for tip bleaching assay to evaluate their potential pathogenicity. Ten isolates significantly reduced the risk of tip bleaching in <i>H. floresii</i> and were designated as “significantly non-pathogenic”. <i>Vibrio owensii</i> was identified as a “significant pathogen” inducing bleaching disease in <i>H. floresii</i>. By using LC-MS, we here identified its HomoSerine Lactones (HSL) QS signal, as a C4-HSL (short-chain). This study thus suggests a possible involvement of QS signal (short-chain) in the disease-inducing bacterium from the aquaculture ponds (an integrated multitrophic aquaculture system). This study firstly reports on the surface-associated bacteria of a lambda-carrageenophyte. This study must contribute to the development of dedicated strategies for disease control based on HSL disruption in aquaculture.
DOI: 10.6084/m9.figshare.19705972.v1
title: New temperate seaweed targets for mitigation of ruminant methane emissions: an in vitro assessment

description: Methane is a potent greenhouse gas with a comparatively short (9 yr) atmospheric lifetime; therefore effective strategies for methane mitigation will contribute significantly to meeting the UN Sustainable Development Goal #13 of taking rapid action against climate change. Methane emissions from enteric fermentation constitute a large proportion of agricultural greenhouse gas emissions. Low inclusions of red seaweed from the genus <i>Asparagopsis</i> have demonstrated near elimination of enteric methane from ruminants; however, only a limited number of other seaweeds have been assessed for their anti-methanogenic potential. New Zealand red seaweed species <i>Bonnemaisonia hamifera, Euptilota formisissima, Plocamium cirrhosum, Vidalia colensoi</i>, and identified aquaculture target species <i>Ecklonia radiata</i> and <i>Ulva</i> sp. B were investigated as anti-methanogenic feed additives. Seaweeds were included at 0%, 2%, 6%, or 10% of feed organic matter (OM, ryegrass hay) during <i>in vitro</i> fermentation assays using rumen inoculant from non-lactating Friesian x Jersey dairy cows, using <i>Asparagopsis armata</i> as a positive control. Total gas, methane, hydrogen, volatile fatty acids, and organic matter degradation were measured over a 48 h incubation. Inclusion of all seaweeds except <i>Ulva</i> sp. B reduced the production of methane at either 6 or 10% OM. <i>Bonnemaisonia hamifera</i> was the best performing seaweed, reducing the production of methane by 17.1%, 95.4%, and 98.8% relative to the basal feed substrate control at inclusion levels of 2%, 6%, and 10% OM, respectively, with notable increases in the production of hydrogen. <i>Euptilota formisissima</i> and <i>P. cirrhosum</i> reduced the production of methane by up to 50.5 and 39.5%, respectively, at an inclusion level of 10%, with minimal effects on measured fermentation parameters. Bromoform, the primary bioactive component in <i>Asparagopsis</i>, was not detected in any of the new seaweeds tested. Our results therefore identify potential alternative anti-methanogenic seaweed targets that are less susceptible to the loss of volatile bioactives during processing.
DOI: 10.6084/m9.figshare.20163620
title: Establishing and validating axenic cultures of the microalga <i>Haematococcus lacustris</i> (Chlorophyceae)

description: Although many isolation techniques for algaeaxenic cultures of algae are known, successful isolation approaches are species and contaminant-specific. The commercially important alga <i>Haematococcus lacustris</i> has been intensively studied due to its natural production of the high-value carotenoid astaxanthin, yet there are no reports of axenic <i>H. lacustris</i> cultures. In this article, we describe the successful isolation of axenic <i>H. lacustris</i>, originally isolated in non-axenic form from its natural habitat and adopted to be used daily <i>in vitro</i>, in our laboratory. We verify the absence of bacteria and identify the bacterial communities in the non-axenic algal culture. using PCR amplification with selected universal primers for 16S rRNA gene amplification in the gDNA. Amplification of the 16S rRNA gene of the non-axenic culture showed the presence of bacteria with high identity to <i>Massilia, Blastococcus</i> and <i>Deinococcus</i> species. The bacteria which were identified in our strain further expand our knowledge of bacterial communities on algae, and because we established axenic <i>H. lacustris</i> culture, testing their effect on growth or astaxanthin accumulation in controlled co-cultures is now available. The isolation technique described herein can be applied to other green algal species to eliminate bacteria, and the selected primers can be used to verify the axenic nature of other green algal cultures. The resulting axenic culture is required for molecular genetics research and will be very valuable for establishing heterotrophic growth in laboratory or industrial bioreactors.
DOI: 10.6084/m9.figshare.20163620.v1
title: Establishing and validating axenic cultures of the microalga <i>Haematococcus lacustris</i> (Chlorophyceae)

description: Although many isolation techniques for algaeaxenic cultures of algae are known, successful isolation approaches are species and contaminant-specific. The commercially important alga <i>Haematococcus lacustris</i> has been intensively studied due to its natural production of the high-value carotenoid astaxanthin, yet there are no reports of axenic <i>H. lacustris</i> cultures. In this article, we describe the successful isolation of axenic <i>H. lacustris</i>, originally isolated in non-axenic form from its natural habitat and adopted to be used daily <i>in vitro</i>, in our laboratory. We verify the absence of bacteria and identify the bacterial communities in the non-axenic algal culture. using PCR amplification with selected universal primers for 16S rRNA gene amplification in the gDNA. Amplification of the 16S rRNA gene of the non-axenic culture showed the presence of bacteria with high identity to <i>Massilia, Blastococcus</i> and <i>Deinococcus</i> species. The bacteria which were identified in our strain further expand our knowledge of bacterial communities on algae, and because we established axenic <i>H. lacustris</i> culture, testing their effect on growth or astaxanthin accumulation in controlled co-cultures is now available. The isolation technique described herein can be applied to other green algal species to eliminate bacteria, and the selected primers can be used to verify the axenic nature of other green algal cultures. The resulting axenic culture is required for molecular genetics research and will be very valuable for establishing heterotrophic growth in laboratory or industrial bioreactors.
DOI: 10.6084/m9.figshare.19705972
title: New temperate seaweed targets for mitigation of ruminant methane emissions: an in vitro assessment

description: Methane is a potent greenhouse gas with a comparatively short (9 yr) atmospheric lifetime; therefore effective strategies for methane mitigation will contribute significantly to meeting the UN Sustainable Development Goal #13 of taking rapid action against climate change. Methane emissions from enteric fermentation constitute a large proportion of agricultural greenhouse gas emissions. Low inclusions of red seaweed from the genus <i>Asparagopsis</i> have demonstrated near elimination of enteric methane from ruminants; however, only a limited number of other seaweeds have been assessed for their anti-methanogenic potential. New Zealand red seaweed species <i>Bonnemaisonia hamifera, Euptilota formisissima, Plocamium cirrhosum, Vidalia colensoi</i>, and identified aquaculture target species <i>Ecklonia radiata</i> and <i>Ulva</i> sp. B were investigated as anti-methanogenic feed additives. Seaweeds were included at 0%, 2%, 6%, or 10% of feed organic matter (OM, ryegrass hay) during <i>in vitro</i> fermentation assays using rumen inoculant from non-lactating Friesian x Jersey dairy cows, using <i>Asparagopsis armata</i> as a positive control. Total gas, methane, hydrogen, volatile fatty acids, and organic matter degradation were measured over a 48 h incubation. Inclusion of all seaweeds except <i>Ulva</i> sp. B reduced the production of methane at either 6 or 10% OM. <i>Bonnemaisonia hamifera</i> was the best performing seaweed, reducing the production of methane by 17.1%, 95.4%, and 98.8% relative to the basal feed substrate control at inclusion levels of 2%, 6%, and 10% OM, respectively, with notable increases in the production of hydrogen. <i>Euptilota formisissima</i> and <i>P. cirrhosum</i> reduced the production of methane by up to 50.5 and 39.5%, respectively, at an inclusion level of 10%, with minimal effects on measured fermentation parameters. Bromoform, the primary bioactive component in <i>Asparagopsis</i>, was not detected in any of the new seaweeds tested. Our results therefore identify potential alternative anti-methanogenic seaweed targets that are less susceptible to the loss of volatile bioactives during processing.
DOI: 10.5281/zenodo.7223114
title: Dataset used for "On-demand electrical control of spin qubits'

description: Dataset used to generate figures in 'On-demand electrical control of spin qubits'.
DOI: 10.5281/zenodo.7223113
title: Dataset used for "On-demand electrical control of spin qubits'

description: Dataset used to generate figures in 'On-demand electrical control of spin qubits'.
DOI: 10.5281/zenodo.7528557
title: Tepe Sadegh's database

description: A typological study of potsherds collected from different trenches at Tepe Sadegh was carried out based on those collected during the first, fourth, fifth, and sixth excavation seasons. Since all potsherds in this study are wheel-made and have a mineral temper, these two factors are not included in the catalogs. As a result of the large size of the tables and pictures, this section has been published online, as an open data source.
DOI: 10.5281/zenodo.7528558
title: Tepe Sadegh's database

description: A typological study of potsherds collected from different trenches at Tepe Sadegh was carried out based on those collected during the first, fourth, fifth, and sixth excavation seasons. Since all potsherds in this study are wheel-made and have a mineral temper, these two factors are not included in the catalogs. As a result of the large size of the tables and pictures, this section has been published online, as an open data source.
DOI: 10.5281/zenodo.7528678
title: Tepe Sadegh's database

description: A typological study of potsherds collected from different trenches at Tepe Sadegh was carried out based on those collected during the first, fourth, fifth, and sixth excavation seasons. Since all potsherds in this study are wheel-made and have a mineral temper, these two factors are not included in the catalogs. As a result of the large size of the tables and pictures, this section has been published online, as an open data source.