Limitations in the Use of Archived Vent Mussel Samples to Assess Genetic Connectivity Among Seafloor Massive Sulfide Deposits: A Case Study with Implications for Environmental Management

Genetic connectivity studies can inform the design of mitigation strategies used in environmental management. However, the expense of developing species-specific molecular markers and collecting samples at appropriate spatial and temporal scales can be prohibitive. Using archived material and existing molecular markers may provide a cost-effective way to assess population connectivity. Genetic connectivity studies are increasingly in demand in the deep sea in response to mounting anthropogenic pressures, including seafloor massive sulfide (SMS) mining. The feasibility of using archived material was assessed using the New Zealand-endemic vent mussel Gigantidas gladius, which inhabits areas licensed for the prospecting phase of SMS mining. Four molecular markers were tested, but only one (mitochondrial COI) provided suitable sequences. Of 942 specimens, only 150 individuals were informative, largely due to poor tissue quality of archived samples. Seven populations spanning the distributional range of G. gladius were assessed. The results indicate that G. gladius has high levels of gene flow among sites 10s to 100s km apart and limited genetic structure. Haplotypic diversity was not equally distributed among populations, with lower diversity for the Macauley Volcano population at the northern extent of the species distribution and greater diversity within central populations. Migrant exchange was also greatest between central populations, with one population at Rumble V Seamount appearing important in terms of maintaining genetic diversity within the Kermadec Volcanic Arc region. However, interpretation of the results should be viewed with caution as small sample sizes may have limited the ability to detect genetic structure. Despite these limitations, mitigation strategies that protect areas of seabed from mining activities should consider the genetic vulnerability of the population at the northern edge of the species’ distribution and the significance of certain central populations

A primer for use of genetic tools in selecting and testing the suitability of set-aside sites protected from deep-sea seafloor massive sulfide mining activities

AbstractSeafloor massive sulfide (SMS) mining will likely occur at hydrothermal systems in the near future. Alongside their mineral wealth, SMS deposits also have considerable biological value. Active SMS deposits host endemic hydrothermal vent communities, whilst inactive deposits support communities of deep water corals and other suspension feeders. Mining activities are expected to remove all large organisms and suitable habitat in the immediate area, making vent endemic organisms particularly at risk from habitat loss and localised extinction. As part of environmental management strategies designed to mitigate the effects of mining, areas of seabed need to be protected to preserve biodiversity that is lost at the mine site and to preserve communities that support connectivity among populations of vent animals in the surrounding region. These “set-aside” areas need to be biologically similar to the mine site and be suitably connected, mostly by transport of larvae, to neighbouring sites to ensure exchange of genetic material among remaining populations. Establishing suitable set-asides can be a formidable task for environmental managers, however the application of genetic approaches can aid set-aside identification, suitability assessment and monitoring. There are many genetic tools available, including analysis of mitochondrial DNA (mtDNA) sequences (e.g. COI or other suitable mtDNA genes) and appropriate nuclear DNA markers (e.g. microsatellites, single nucleotide polymorphisms), environmental DNA (eDNA) techniques and microbial metagenomics. When used in concert with traditional biological survey techniques, these tools can help to identify species, assess the genetic connectivity among populations and assess the diversity of communities. How these techniques can be applied to set-aside decision making is discussed and recommendations are made for the genetic characteristics of set-aside sites. A checklist for environmental regulators forms a guide to aid decision making on the suitability of set-aside design and assessment using genetic tools. This non-technical primer document represents the views of participants in the VentBase 2014 workshop

sFDvent: A global trait database for deep‐sea hydrothermal‐vent fauna

Motivation: Traits are increasingly being used to quantify global biodiversity patterns, with trait databases growing in size and number, across diverse taxa. Despite grow‐ ing interest in a trait‐based approach to the biodiversity of the deep sea, where the impacts of human activities (including seabed mining) accelerate, there is no single re‐ pository for species traits for deep‐sea chemosynthesis‐based ecosystems, including hydrothermal vents. Using an international, collaborative approach, we have compiled the first global‐scale trait database for deep‐sea hydrothermal‐vent fauna – sFD‐ vent (sDiv‐funded trait database for the Functional Diversity of vents). We formed a funded working group to select traits appropriate to: (a) capture the performance of vent species and their influence on ecosystem processes, and (b) compare trait‐based diversity in different ecosystems. Forty contributors, representing expertise across most known hydrothermal‐vent systems and taxa, scored species traits using online collaborative tools and shared workspaces. Here, we characterise the sFDvent da‐ tabase, describe our approach, and evaluate its scope. Finally, we compare the sFD‐ vent database to similar databases from shallow‐marine and terrestrial ecosystems to highlight how the sFDvent database can inform cross‐ecosystem comparisons. We also make the sFDvent database publicly available online by assigning a persistent, unique DOI. Main types of variable contained: Six hundred and forty‐six vent species names, associated location information (33 regions), and scores for 13 traits (in categories: community structure, generalist/specialist, geographic distribution, habitat use, life history, mobility, species associations, symbiont, and trophic structure). Contributor IDs, certainty scores, and references are also provided. Spatial location and grain: Global coverage (grain size: ocean basin), spanning eight ocean basins, including vents on 12 mid‐ocean ridges and 6 back‐arc spreading centres. Time period and grain: sFDvent includes information on deep‐sea vent species, and associated taxonomic updates, since they were first discovered in 1977. Time is not recorded. The database will be updated every 5 years. Major taxa and level of measurement: Deep‐sea hydrothermal‐vent fauna with spe‐ cies‐level identification present or in progress. Software format: .csv and MS Excel (.xlsx).This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited

The Ecological Impacts of Mining at Seafloor Massive Sulfide Deposits on Megafaunal Assemblage Structure and Population Connectivity

Deep-sea mining is rapidly becoming a reality, yet there are considerable gaps in our knowledge of the seabed assemblages that could be affected by mining activities. Seafloor Massive Sulfide (SMS) mining is expected to remove nearly all organisms in the immediate area and alter the remaining habitat, so that mitigation strategies for SMS mining will most likely need to include the establishment of protected areas to preserve the biodiversity that is lost at mine sites. Prospecting licences have been issued previously for SMS deposits within the New Zealand Exclusive Economic Zone (EEZ), however little is known about the seabed assemblages potentially at risk from SMS mining, particularly with respect to their structure (at multiple spatial scales) and the connectivity of assemblages at different sites. Designing studies to provide this information can be aided by turning to terrestrial, freshwater and shallow marine systems, where the fields of ecological theory, environmental management and conservation theory are better developed (Chapter 1).  Prior to detailed investigations into the assemblage structure and population connectivity of New Zealand SMS deposits, it is essential to understand the global context of SMS mining. This was undertaken through an extensive literature review of SMS deposits, including their geology, seafloor communities, impacts from mining, international and national regulation, and environmental management (Chapter 2).  In order to investigate the large-scale spatial distribution and structure of seafloor assemblages at SMS deposits, three New Zealand seamounts previously licenced for the prospecting phase of SMS mining were surveyed. Video footage from a towed camera was analysed to identify and characterise assemblages, and their association with environmental variation was investigated. Analysis of 249 video samples (each 250 m in length) distributed amongst the three seamounts indicated that SMS deposits support unique assemblages and that there were strong links between assemblage structure and environmental variation at a range of spatial scales. There was also a complex distribution of assemblages amongst the seamounts, suggesting a network of protected areas would be the most effective method for spatial management. Such networks should include sites that support the unique assemblages found in association with SMS deposits (Chapter 3).  The fine-scale distribution and structure of assemblages at SMS deposits was investigated by using data from a single SMS deposit, Proteus 1, and comparing it to a Reference Site selected to have similar size and seabed characteristics to the deposit. Video footage from a Remotely Operated Vehicle (ROV) was used to identify and characterise assemblages, and their association with environmental conditions. Analysis of 153 video samples (each 15 m in length) confirmed the existence of assemblages unique to SMS deposits, and indicated that environmental characteristics specific to the deposit are responsible for the observed patterns of faunal distribution. Although five assemblages were shared between Proteus 1 and the Reference Site, six assemblages were unique to Proteus 1. This suggested that the proposed Reference Site would be inadequate on its own in terms of protecting the biological diversity present at the mine site but could contribute to a network of protected areas (Chapter 4).  The issue of connectivity was addressed by examining the genetic connectivity of populations of the endemic hydrothermal vent mussel, Gigantidas gladius. Universal markers, archived material and off-the-shelf DNA extraction kits were used to investigate a cost effective approach. The assessment utilised variation in 586 base pairs of the mitochondrial cytochrome oxidase I subunit (COI) from 150 individuals in seven populations of G. gladius. Small sample sizes limited the recommendations that could be made for environmental management; however interpretation of the available sequences indicated panmixia with limited genetic structure and high connectivity amongst populations. Central Kermadec Volcanic Arc populations had particularly high haplotypic diversity and migrant exchange, suggesting they could be important for maintaining regional genetic connectivity and would merit inclusion in seabed protection measures (Chapter 5).  Establishing protected areas for biodiversity needs to utilise all of the available information. The integrated findings of this thesis highlight the need for a network of protected seabed areas along the Kermadec Volcanic Arc to help mitigate the impacts of any future SMS mining activities. These networks should be highly connected (as determined by genetic connectivity) and include both active and inactive SMS areas to conserve 1) the endemic vent fauna in active areas and 2) the unique assemblages found in both environments (Chapter 6).</p

Distribution, population structure, reproduction and diet of Ophiolimna antarctica (Lyman, 1879) from Kemp Caldera in the Southern Ocean

A new population of Ophiolimna antarctica (Lyman, 1879) was discovered at 1546 m in Kemp Caldera, a topographic feature with active hydrothermal venting at the southern end of the South Sandwich Islands, Southern Ocean. The distribution, population structure, reproduction, and diet of O. antarctica were investigated. O. antarctica were found predominantly on basalt with an over-dispersed distribution. The mean density was 17 individuals m?2 with a range of 9–24 individuals m?2. There was a bimodal population structure, with separate juvenile and adult peaks. Sexes were separate and the sex ratio was not significantly different from equality. The maximum oocyte diameter was 520 ?m, suggesting direct or lecithotrophic development, whilst individual females reproduced asynchronously. Stomach contents included crustacean fragments, flocculate material, diatoms, forams, fish scales, and ophiuroid tissues and spines, which was indicative of omnivory. There was no apparent influence of hydrothermal vents &lt;500 m away on the diet of Ophiolimna antarctica. The ecology of Ophiolimna antarctica is consistent with what is known for other Antarctic and deep-sea ophiuroid species

北部ケルマディック島弧の熱水性魚類から同定された新規の恒常性維持システム ―極限環境適 応に注目した医生物学モデルの開拓にむけて.

http://www.godac.jamstec.go.jp/darwin/cruise/yokosuka/yk13-11/

ATLAS Submission to the International Seabed Authority regarding Draft Regulations for Exploitation

This is the ATLAS submission to the International Seabed Authority regarding Draft Regulations for Exploitation. The individuals within ATLAS who provided comments as part of this response include: Dr Rachel Boschen-Rose, Seascape Consultants – United Kingdom Prof. David Johnson (ATLAS Marine Policy Work Package Lead) Seascape Consultants - United Kingdom Dr Sophie Arnaud-Haond (ATLAS Connected Resources Work Package Lead) French Research Institute for Exploitation of the Sea (Ifremer) – France Dr Dick van Oevelen, Royal Netherlands Institute for Sea Research (NIOZ) - Netherlands Dr Anthony Grehan (ATLAS Maritime Spatial Planning Work Package Lead) National University of Ireland Galway – Ireland Prof. Murray Roberts (ATLAS Project Lead) University of Edinburgh – United Kingdom Prof. Alex Rogers, University of Oxford – United Kingdo

Osteoclast-mediated bone loss observed in a COVID-19 mouse model

This article is made available for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.The consequences of SARS-CoV-2 infection on the musculoskeletal system represent a dangerous knowledge gap. Aging patients are at added risk for SARS-CoV-2 infection; therefore, a greater understanding of the resulting musculoskeletal sequelae of SARS-CoV-2 infection may help guide clinical strategies. This study examined fundamental bone parameters among mice treated with escalating viral loads. Male C57BL/6J (WT, n = 17) and B6.Cg-Tg(K18-ACE2)2Prlmn/J mice (K18-hACE2 transgenic mice, n = 21) expressing human ACE2 (TG) were divided into eight groups (n = 4-6/group) and subjected to intranasal dosing of 0, 1 × 103, 1 × 104, and 1 × 105 PFU (plaque forming units) of human SARS-CoV-2. Animal health was assessed daily by veterinary staff using established and validated scoring criteria (activity, posture, body condition scores and body weight). We report here that mock and WT infected mice were healthy and completed the study, surviving until 12-14 days post infection (dpi). In contrast, the TG mice infected with 1 × 105 PFU all experienced severe health declines that necessitated early euthanasia (6-7 dpi). For TG mice infected with 1 × 104 PFU, 2 mice were also euthanized after 7 dpi, while 3 mice showed signs of moderate disease at day 6 dpi, but recovered fully by day 11 dpi. Four of the 5 TG mice that were infected with 1 × 103 PFU remained healthy throughout the study. This suggests that our study mimics what is seen during human disease, where some patients develop severe disease resulting in death, while others have moderate to severe disease but recover, and others are asymptomatic. At necropsy, femurs were extracted and analyzed by μCT. No difference was found in μCT determined bone parameters among the WT groups. There was, however, a significant 24.4% decrease in trabecular bone volume fraction (p = 0.0009), 19.0% decrease in trabecular number (p = 0.004), 6.2% decrease in trabecular thickness (p = 0.04), and a 9.8% increase in trabecular separation (p = 0.04) among surviving TG mice receiving any viral load compared to non-infected controls. No differences in cortical bone parameters were detected. TRAP staining revealed surviving infected mice had a significant 64% increase in osteoclast number, a 27% increase in osteoclast surface, and a 38% increase in osteoclasts per bone surface. While more studies are needed to investigate the long-term consequences of SARS-CoV-2 infection on skeletal health, this study demonstrates a significant reduction in several bone parameters and corresponding robust increases in osteoclast number observed within 2 weeks post-infection in surviving asymptomatic and moderately affected mice

VentBase: Developing a consensus among stakeholders in the deep-sea regarding environmental impact assessment for deep-sea mining – A workshop report

Mining seafloor massive sulfides for metals is an emergent industry faced with environmental management challenges. These revolve largely around limits to our current understanding of biological variability in marine systems, a challenge common to all marine environmental management. VentBase was established as a forum where academic, commercial, governmental, and non-governmental stakeholders can develop a consensus regarding the management of exploitative activities in the deep-sea. Participants advocate a precautionary approach with the incorporation of lessons learned from coastal studies. This workshop report from VentBase encourages the standardization of sampling methodologies for deep-sea environmental impact assessment. VentBase stresses the need for the collation of spatial data and importance of datasets amenable to robust statistical analyses. VentBase supports the identification of set-asides to prevent the local extirpation of vent-endemic communities and for the post-extraction recolonization of mine sites.<br/