Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change—A review

Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy‐making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain process‐oriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science‐based policy formulation.     

Meeting report: Ocean ‘omics science,technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013)

The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.     

Climate impacts and oceanic top predators: moving from impacts to adaptation in oceanic systems

Climate impacts are now widely reported from coastal marine systems, but less is known for the open ocean. Here we review progress in understanding impacts on large pelagic species presented at an international workshop for the Climate Impacts on Oceanic Top Predators programme, and discuss the future with regard to the next phase of adaptation-focused research. Recent highlights include a plan to map the distribution of key species in the foodweb using both acoustics and biochemical techniques, and development of a new data sharing and access tool for fisheries and associated data, including socio-economic information. A common research focus in pelagic ecosystems is on understanding climate variability and climate change impacts on marine species, but a greater emphasis on developing future scenarios and adaptation options is needed. Workshop participants also concluded that engagement with and provision of science support to regional fisheries management organisations are critical elements for ensuring successful uptake of research. This uptake will be required for future management of fisheries as global warming continues such that some open ocean top predators can be sustainably harvested, impacts on conservation-dependent species can be avoided, and ecosystem function is not compromised.     

Training the next generation of protein scientists

Carl Brändén made significant contributions in areas of protein X‐ray crystallography and science education. As the 2011 recipient of the Protein Society award honoring Carl's contributions, I had the opportunity to reflect on the undergraduate educational activities that have been practiced in my own laboratory over the past 24 years at the University of Maryland Baltimore County, an institution that emphasizes both research and undergraduate education. A system has been developed that attempts to minimize the tension that can exist between conflicting graduate research and undergraduate mentoring goals. The outcomes, as measured not only by subsequent activities of the participating undergraduates, but also by the activities of the graduate students and postdocs that worked with the undergraduates, indicate a general overall benefit for all participants, particularly for women and underrepresented minorities who are traditionally poorly retained in the sciences. Greater participation of undergraduates in research activities of active scientists who often focus primarily on graduate and postdoctoral training could have a positive impact on the leaky undergraduate science pipeline.     

Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs

Extracellular enzymes produced by heterotrophic microbial communities are major drivers of carbon and nutrient cycling in terrestrial, freshwater, and marine environments. Although carbon and nutrient cycles are coupled on global scales, studies of extracellular enzymes associated with terrestrial, freshwater, and marine microbial communities are not often compared across ecosystems. In part, this disconnect arises because the environmental parameters that control enzyme activities in terrestrial and freshwater systems, such as temperature, pH, and moisture content, have little explanatory power for patterns of enzyme activities in marine systems. Instead, factors such as the functional diversity of microbial communities may explain varying patterns of enzyme activities observed in the ocean to date. In any case, many studies across systems focus on similar issues that highlight the commonalities of microbial community organization. Examples include the effective lifetime of enzymes released into the environment; the extent to which microbial communities coordinate enzyme expression to decompose complex organic substrates; and the influence of microbial community composition on enzyme activities and kinetics. Here we review the often-disparate research foci in terrestrial, freshwater, and marine environments. We consider the extent to which environmental factors may regulate extracellular enzyme activities within each ecosystem, and highlight commonalities and current methodological challenges to identify research questions that may aid in integrating cross-system perspectives in the future.     

Mobilizing and integrating big data in studies of spatial and phylogenetic patterns of biodiversity

The current global challenges that threaten biodiversity are immense and rapidly growing. These biodiversity challenges demand approaches that meld bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification, and other ecological analyses). Recent developments in phylogenetics coupled with emerging cyberinfrastructure and new data sources provide unparalleled opportunities for mobilizing and integrating massive amounts of biological data, driving the discovery of complex patterns and new hypotheses for further study. These developments are not trivial in that biodiversity data on the global scale now being collected and analyzed are inherently complex. The ongoing integration and maturation of biodiversity tools discussed here is transforming biodiversity science, enabling what we broadly term “next-generation” investigations in systematics, ecology, and evolution (i.e., “biodiversity science”). New training that integrates domain knowledge in biodiversity and data science skills is also needed to accelerate research in these areas. Integrative biodiversity science is crucial to the future of global biodiversity. We cannot simply react to continued threats to biodiversity, but via the use of an integrative, multifaceted, big data approach, researchers can now make biodiversity projections to provide crucial data not only for scientists, but also for the public, land managers, policy makers, urban planners, and agriculture.     

How to work with children and animals: A guide for school‐based citizen science in wildlife research

Engaging school students in wildlife research through citizen science projects can be a win–win for scientists and educators. Not only does it provide a way for scientists to gather new data, but it can also contribute to science education and help younger generations become more environmentally aware. However, wildlife research can be challenging in the best of circumstances, and there are few guidelines available to help scientists create successful citizen science projects for school students. This paper explores the opportunities and challenges faced when developing school‐based citizen science projects in wildlife research by synthesising two sources of information. First, we conducted a small, school‐based citizen science project that investigated the effects of supplementary feeding on urban birds as a case study. Second, we reviewed the literature to develop a database of school‐based citizen science projects that address questions in wildlife ecology and conservation. Based on these activities, we present five lessons for scientists considering a school‐based citizen science project. Overall, we found that school‐based citizen science projects must be carefully designed to ensure reliable data are collected, students remain engaged, and the project is achievable under the logistical constraints presented by conducting wildlife research in a school environment. Ultimately, we conclude that school‐based citizen science projects can be a powerful way of collecting wildlife data while also contributing to the education and development of environmentally aware students.     

基于文献计量的全球海洋酸化研究状况分析

海洋酸化(Ocean acidification)为目前备受人们关注的全球性问题。因此为了能够客观地揭示海洋酸化的研究态势,研究采用文献计量分析(Bibliometric analysis)的方法,以海洋酸化概念提出后(2004年以后)ISI Web of Science期刊引文数据库中涉及到海洋酸化研究的所有文献为样本,对文献的增长趋势及期刊分布进行描述统计,并基于关键词的知识图谱及突变分析的方法探究海洋酸化的热点关注方向随时间的变动及研究前沿。描述统计表明:海洋酸化概念提出的这十多年来,涉及海洋酸化的研究文献数量呈现激增的态势,研究学科交叉明显,海洋酸化对珊瑚礁的影响是这十年来的重点研究领域。从基于关键词的知识图谱可以看到,在海洋酸化研究初期(2004—2009年),研究内容主要分为两个部分,一是海洋酸化对海洋生物(尤其是珊瑚礁生物及浮游植物)及生态系统的影响;二是对海洋酸化现象的认识;中期(2010—2015年),研究内容与初期相似,研究重点往海洋生物上倾斜,同时有新的热点研究区域和研究方向的出现;近期(2016年以后),海洋酸化对海洋生物影响的研究依旧占据着主流研究方向。对基于突变分析得到的当前(2018年2月)海洋酸化研究的热点关注的文献分析发现,当前海洋酸化的研究存在以下5个前沿方向:(1)在探究海洋酸化与生物的关系之时需结合多因子讨论;(2)探索生物在海洋酸化下的内在应对机制;(3)海洋酸化影响下的生物响应的综合评估及预测;(4)探索海洋酸化对海洋生态系统的影响;(5)对海洋酸化概念的挑战——海洋酸化形成原因的探索。     

Solutions for ecosystem‐level protection of ocean systems under climate change

The Paris Conference of Parties (COP21) agreement renewed momentum for action against climate change, creating the space for solutions for conservation of the ocean addressing two of its largest threats: climate change and ocean acidification (CCOA). Recent arguments that ocean policies disregard a mature conservation research field and that protected areas cannot address climate change may be oversimplistic at this time when dynamic solutions for the management of changing oceans are needed. We propose a novel approach, based on spatial meta‐analysis of climate impact models, to improve the positioning of marine protected areas to limit CCOA impacts. We do this by estimating the vulnerability of ocean ecosystems to CCOA in a spatially explicit manner and then co‐mapping human activities such as the placement of renewable energy developments and the distribution of marine protected areas. We test this approach in the NE Atlantic considering also how CCOA impacts the base of the food web which supports protected species, an aspect often neglected in conservation studies. We found that, in this case, current regional conservation plans protect areas with low ecosystem‐level vulnerability to CCOA, but disregard how species may redistribute to new, suitable and productive habitats. Under current plans, these areas remain open to commercial extraction and other uses. Here, and worldwide, ocean conservation strategies under CCOA must recognize the long‐term importance of these habitat refuges, and studies such as this one are needed to identify them. Protecting these areas creates adaptive, climate‐ready and ecosystem‐level policy options for conservation, suitable for changing oceans.     

Factors Affecting Women's Autonomous Decision Making In Research Participation Amongst Yoruba Women Of Western Nigeria

Research is a global enterprise requiring participation of both genders for generalizable knowledge; advancement of science and evidence based medical treatment. Participation of women in research is necessary to reduce the current bias that most empirical evidence is obtained from studies with men to inform health care and related policy interventions. Various factors are assumed to limit autonomy amongst the Yoruba women of western Nigeria. This paper seeks to explore the experience and understanding of autonomy by the Yoruba women in relation to research participation. Focus is on factors that affect women's autonomous decision making in research participation. An exploratory qualitative approach comprising four focus group discussions, 42 in‐depth interviews and 14 key informant interviews was used. The study permits a significant amount of triangulation, as opinions of husbands and religious leaders are also explored. Interviews and discussions were audiotaped and transcribed verbatim. Content analysis was employed for data analysis. Findings show that concepts of autonomy varied amongst the Yoruba women. Patriarchy, religion and culture are conceived to have negative impact on the autonomy of women in respect to research participation. Among the important findings are: 1) male dominance is strongly emphasized by religious leaders who should teach equality, 2) while men feel that by making decisions for women, they are protecting them, the women on the other hand see this protection as a way of limiting their autonomy. We recommend further studies to develop culturally appropriate and workable recruitment methods to increase women's participation in research.     

Perceived challenges in the informed consent process: Mismatches between enrollers and researchers at a South African clinical research site

Enrollers play a critical yet often overlooked role in clinical research, particularly in informed consent processes. Study retention may depend in part on how complex information is conveyed to potential participants. This qualitative study aimed to assess communicative barriers during consent and enrolment in two South African TB/HIV clinical studies. In particular, we compared our own perceptions of potential challenges to consent with that of thirteen enrollers, gained via reflective journaling and focus group discussions. Some overlap of identified challenges was evident, including terminology, jargon and consent document format. However there were mismatches to identified challenges. Enrollers provided further insights into potential challenges to consent, in particular, blood withdrawal, discussion of sexual issues and misunderstanding of study participation. Enrollers also reported feeling ill‐equipped to provide counselling when participants became distressed. We offer several recommendations for strengthening the inclusion of enrollers in the development of clinical research protocols and consent documents.     

A Perspective on the History and Evolution of an Oceans and Human Health “Metadiscipline” in the USA

We review recent history and evolution of Oceans and Human Health programs and related activities in the USA from a perspective within the Federal government. As a result of about a decade of support by the US Congress and through a few Federal agencies, notably the National Science Foundation, National Institute of Environmental Health Sciences, and National Ocean and Atmospheric Administration, robust Oceans and Human Health (OHH) research and application activities are now relatively widespread, although still small, in a number of agencies and academic institutions. OHH themes and issues have been incorporated into comprehensive federal ocean research plans and are reflected in the new National Ocean Policy enunciated by Executive Order 13547. In just a decade, OHH has matured into a recognized “metadiscipline,” with development of a small, but robust and diverse community of science and practice, incorporation into academic educational programs, regular participation in ocean and coastal science and public health societies, and active engagement with public health decision makers. In addition to substantial increases in scientific information, the OHH community has demonstrated ability to respond rapidly and effectively to emergency situations such as those associated with extreme weather events (e.g., hurricanes, floods) and human-caused disasters (e.g., the Deep Water Horizon oil spill). Among many other things, next steps include development and implementation of agency health strategies and provision of specific services, such as ecological forecasts to provide routine early warnings for ocean health threats and opportunities for prevention and mitigation of these risks.     

Challenges Facing the Adoption of Ecosystem Health as a Core Component in Professional Curricula

While there has been considerable success in introducing ecosystem health into professional curricula at a number of universities, there have been significant challenges to its introduction. There are difficulties relating to pervading attitudes within universities. Ecosystem health deals with uncertainty whereas most other disciplines cherish certainty. Ecosystem health is often considered a “soft science” lacking in specifics. The enormity and complexity of ecosystem health problems are often perceived as discouraging and impossible to solve. The university structure can present challenges in that transdisciplinary problem solving requires the participation of many different departments, with several levels of approval required. There are also challenges in the teaching of ecosystem health given its extremely broad focus, limited experience in ecosystem health curricula, and almost no experience in effective evaluation of a field that emphasizes attitudes as much as it does information. This article describes each of these challenges, draws on the experience of the conference, and provides potential solutions to overcoming these challenges.     

Radwaste at sea: A new era of polarization or a new basis for consensus?

Abstract

A coalition of third world nations, led by the Pacific island countries and those European nations who have developed land‐based disposal programs for their radioactive wastes, seek to amend the London Convention on Dumping (the international treaty controlling ocean disposal of radioactive and other wastes) in order to ban ocean disposal of low‐level radioactive wastes. Pro‐dumping nations maintain that the treaty may only be amended based on science and that current scientific research indicates that low‐level waste represents neither a threat to the integrity of the marine environment nor human health. Anti‐dumping nations, on the other hand, argue that the same science, particularly the models used to predict the fate and the effects of these wastes, exhibits sufficient uncertainty to preclude judgments about the absence of harm from future disposal activities. These differing conclusions mirror differing assessments of risk. These assessments build on the differing social, political, and economic values placed on use of the ocean and on conflicting conceptions of the fundamental rights and obligations of nations whose use of the ocean may impinge on the resources of others. Each side's continued intransigence may result in unilateral ocean disposal activities with serious consequences for the London Convention on Dumping (LDC) and its control over other wastes transported to sea for disposal. Initiatives of anti‐dumping nations to expand the LDC's decision‐making framework to examine the social, economic, and political issues underlying each side's interpretation of scientific evidence offer hope to address the underlying non‐scientific issues and perhaps to strengthen decision‐making within the LDC.     

全球变化对海洋生态系统初级生产关键过程的影响

工业革命以来, 不断加剧的人类活动所引起的大气CO₂浓度增加、温度上升等全球变化问题, 正使得海洋生态系统面临着前所未有的压力。该文通过文献计量的方法分析了国内外的研究现状, 简要地回顾了全球变化对海洋生态系统影响研究的发展简史, 并聚焦海洋暖化、海洋酸化和富营养化与缺氧这三个核心研究方向, 重点阐述了它们对海洋生态系统初级生产的关键过程的影响, 总结了已取得的重要进展以及存在的主要问题, 最后提出前沿展望。     

Synthetic biology: an emerging research field in China

Synthetic biology is considered as an emerging research field that will bring new opportunities to biotechnology. There is an expectation that synthetic biology will not only enhance knowledge in basic science, but will also have great potential for practical applications. Synthetic biology is still in an early developmental stage in China. We provide here a review of current Chinese research activities in synthetic biology and its different subfields, such as research on genetic circuits, minimal genomes, chemical synthetic biology, protocells and DNA synthesis, using literature reviews and personal communications with Chinese researchers. To meet the increasing demand for a sustainable development, research on genetic circuits to harness biomass is the most pursed research within Chinese researchers. The environmental concerns are driven force of research on the genetic circuits for bioremediation. The research on minimal genomes is carried on identifying the smallest number of genomes needed for engineering minimal cell factories and research on chemical synthetic biology is focused on artificial proteins and expanded genetic code. The research on protocells is more in combination with the research on molecular-scale motors. The research on DNA synthesis and its commercialisation are also reviewed. As for the perspective on potential future Chinese R&D activities, it will be discussed based on the research capacity and governmental policy.     

Effects of global change on key processes of primary production in marine ecosystems

工业革命以来, 不断加剧的人类活动所引起的大气CO₂浓度增加、温度上升等全球变化问题, 正使得海洋生态系统面临着前所未有的压力。该文通过文献计量的方法分析了国内外的研究现状, 简要地回顾了全球变化对海洋生态系统影响研究的发展简史, 并聚焦海洋暖化、海洋酸化和富营养化与缺氧这三个核心研究方向, 重点阐述了它们对海洋生态系统初级生产的关键过程的影响, 总结了已取得的重要进展以及存在的主要问题, 最后提出前沿展望。     

An integrated,modular approach to data science education in microbiology

We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, postsecondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has the potential to improve research and learning outcomes as well as better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated cocurricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants (TAs), postdocs, instructors, and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences.     

Dive Europa: a search-for-life initiative.

Liquid water, underwater volcanoes and possibly life forms have been suggested to be present beneath the estimated 10 km-thick ice shell of Europa the Jovian satellite J2. Europa's possible ocean is estimated to be 100-200km deep. Despite the great depth of the Europa's ocean, hydrostatic pressure at the seafloor would be 130-260 MPa, corresponding to 13-26 km depth of a theoretical Earth's ocean. The hydrostatic pressure is not beyond the edge of existing deep-sea technology. Here we propose exploration of Europa's deep-sea by the use of current technologies, taking a symbolic example of a deep submergence vehicle Shinkai 6500 which dives to a depth of 6.5 km deep (50 km depth of Europa's ocean). Shinkai 6500 is embarkable in the payload bay of the Space Shuttles in terms of size and weight for the transportation to a Low Earth Orbit (LEO). Secondary boost is needed for interplanetary flight from the LEO. On-orbit assembly of the secondary booster is a technological challenge. The International Space Station (ISS) and ISS-related technologies will facilitate the secondary boost. Also, ice shell drilling is a challenge and is needed before the dive into Europa's ocean. These challenges should be overcome during a certain leading time for matured experience in the ISS operation.