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IMBeR IPO-China newsletter
Your news from the Integrated Marine Biosphere Research International Project Office - China
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Metagenomic probing toward an atlas of the taxonomic
and metabolic foundations of the global ocean genome
通过宏基因组探测构建全球海洋基因组的分类和代谢基础图谱
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Authors: Elisa Laiolo, Intikhab Alam, Mahmut Uludag, Tahira Jamil, Susana Agusti, Takashi Gojobori, Silvia G. Acinas, Josep M. Gasol, and Carlos M. Duarte
Journal: Frontiers in Science
The global ocean genome (the pool of genes in marine organisms and the functional information they encode) is a major, untapped resource for science and society with a growing range of biotechnology applications in sectors such as biomedicine, energy, and food. Shotgun sequencing and metagenomics can now be used to catalog the diversity of ocean microbial life and to explore its functional potential, but has been limited by sample coverage, access to suitable sequencing platforms, and computational capacity. Here we provide a novel synthesis of the global ocean genome based on analysis of 2,102 sampled ocean metagenomes, with gene assembly and annotation via the KAUST Metagenome Analysis Platform (KMAP) Global Ocean Gene Catalog 1.0 containing ~317.5 million gene clusters. Taxonomically, we report the distribution of marine genes across the tree of life and different ocean basins and depth zone biomes. Functionally, we map its relationship to protein families and biogeochemical processes, including the major microbial metabolic pathways that process three elements that play fundamental roles in biogeochemical cycles and are relevant to climate change. These data extend our understanding of the complex, dynamic nature of the ocean microbiome and its metabolic capabilities. Further research is of critical global importance both to unlock the potential of the ocean genome and to understand and predict the effects of human-induced changes, including pollution and climate change. Further hypothesis-driven research should target under-sampled deep sea and benthic microbial communities using enhanced metagenomic methods, to better understand marine ecosystem functioning. Investment in the necessary computational capacity is essential, as are suitable intellectual property frameworks.
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Fig. 1 Metagenomes sampling locations. (A) Pie chart showing the sample (number) distribution across basins. (B) Pie chart showing the sample (number) distribution across depth zones. (C) Map summarizing the distribution of the metagenomes across realms, indicated by the polygon shape, and depth zone, indicated by the filling color. The polygon indicates the realm (benthic or pelagic), while the filling color indicates the depth zone: upper ocean, 0–200 m, mesopelagic ocean, 200–1000 m, and dark ocean, >1000 m. The full list of metagenomes analyzed in this study is reported in Supplementary Table S2, including the above-mentioned classification. | |
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季节性层化陆架海是地球上最具生物生产力的海域之一。由此导致，较深的水域在夏末可能会发生缺氧。预测表明，全球变暖将加速这一缺陷。本文结合湍流时间序列与季节性层化陆架海水柱性状的垂直剖面，估算了氧通量和生物地球化学通量。剖面结果揭示了显著的次表层叶绿素最大值和相关的中层水氧最大值。本文发现，氧最大值同时支持向上及向下的氧通量。向上的通量进入表层混合层，而向下的通量进入深层水域，将部分抵消季节性缺氧。结果表明，通量对水柱结构和混合率都很敏感，表明季节性缺氧的形成是受跨等密度面混合调节。对海流切变的分析表明，向下的通量由潮汐混合支撑，向上的通量由风驱动的近惯性切变主导。因此，夏季风暴在季节性深水缺氧的形成中起重要作用。
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（实习生许若橦编译）
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Distribution, seasonal variation and influencing factors of total dissolved inorganic arsenic in the middle and lower reaches of the Yellow River
黄河中下游总溶解态无机砷的分布、季节变化及影响因素
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Authors: Mengyao He, Jingling Ren, Jiaqi Liu, Sumei Liu, Guiling Zhang, and Guodong Song
Journal: Marine Pollution Bulletin
The concentrations of dissolved arsenate in natural water has an important impact on human health. The distributions, seasonal variation and major influencing factors of total dissolved inorganic arsenic (TDIAs) were studied in the Yellow River. The concentrations of TDIAs in the middle and lower reaches of the Yellow River ranged from 4.3 to 42.4 nmol/L, which met the standards for drinking water of WHO. The seasonal variation of TDIAs concentration in the middle and lower reaches of the Yellow River was highest in summer, followed by autumn and winter, and lowest in spring. The influencing factors of TDIAs concentration in the middle and lower reaches of the Yellow River mainly include the hydrological conditions, topographical variation, the adsorption and desorption of suspended particulate matter (SPM) and the intervention of human activities. The absorption of TDIAs by phytoplankton in the Xiaolangdi Reservoir (XLD) is an important factor affecting its distributions and seasonal variation. The annual flux of TDIAs transported from the Yellow River into the Bohai Sea ranged from 1.1×105 to 4.5×105 mol from 2016 to 2018, which is lower than the flux in 1985 and 2009. The carcinogenic risks (CR) of TDIAs for children and adults were all within acceptable levels (<10−6).
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|  | Fig. 3 Graphical abstract | |
天然水体中溶解态砷酸盐浓度对人体健康有重要影响。本文研究了黄河流域总溶解态无机砷（Total Dissolved Inorganic Arsenic, TDIAs）的分布、季节变化及其主要影响因素。黄河中下游TDIAs浓度在4.3~42.4 nmol/L间，符合世界卫生组织（World Health Organisation, WHO）生活饮用水标准。黄河中下游TDIAs浓度的季节变化表现为：夏季最高，秋季和冬季次之，春季最低。黄河中下游TDIAs浓度的影响因素主要包括水文条件、地形变化、悬浮颗粒物（Suspended Particulate Matter, SPM）的吸附解吸以及人类活动的干预。小浪底水库浮游植物对TDIAs的吸附是影响其分布和季节变化的重要因素。2016-2018年黄河向渤海输送的TDIAs的年通量为1.1×105~4.5×105 mol，低于1985年和2009年的通量。TDIAs对儿童和成人的致癌风险（Carcinogenic Risks, CR）均在可接受水平内（<10−6）。
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（实习生刘熙茜编译）
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Redefining the scientific method:
as the use of sophisticated scientific methods that extend our mind
重新定义科学方法：利用复杂科学方法拓展我们的思维
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Authors: Alexander Krauss
Journal: PNAS Nexus
Scientific, medical, and technological knowledge has transformed our world, but we still poorly understand the nature of scientific methodology. Science textbooks, science dictionaries, and science institutions often state that scientists follow, and should follow, the universal scientific method of testing hypotheses using observation and experimentation. Yet, scientific methodology has not been systematically analyzed using large-scale data and scientific methods themselves as it is viewed as not easily amenable to scientific study. Using data on all major discoveries across science including all Nobel Prize and major non-Nobel Prize discoveries, we can address the question of the extent to which "the scientific method" is actually applied in making science's groundbreaking research and whether we need to expand this central concept of science. This study reveals that 25% of all discoveries since 1900 did not apply the common scientific method (all three features)-with 6% of discoveries using no observation, 23% using no experimentation, and 17% not testing a hypothesis. Empirical evidence thus challenges the common view of the scientific method. Adhering to it as a guiding principle would constrain us in developing many new scientific ideas and breakthroughs. Instead, assessing all major discoveries, we identify here a general, common feature that the method of science can be reduced to: making all major discoveries has required using sophisticated methods and instruments of science. These include statistical methods, particle accelerators, and X-ray methods. Such methods extend our mind and generally make observing, experimenting, and testing hypotheses in science possible, doing so in new ways and ensure their replicability. This provides a new perspective to the scientific method-embedded in our sophisticated methods and instruments-and suggests that we need to reform and extend the way we view the scientific method and discovery process.
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Fig. 4 Methods of science pyramid: share of each methodological approach used for making discoveries. Data reflect all 761 major discoveries. | |
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科学、医学和技术知识已经改变了我们的世界，但我们对科学方法论的本质仍然知之甚少。科学教科书、科学词典和科学机构经常声明，科学家遵循并应该遵循利用观察和实验来检验假设的普遍科学方法。然而，由于科学方法论被认为不容易用于科学研究，因此尚未使用大规模数据和科学方法对其进行系统分析。利用科学领域所有重大发现的数据，包括所有诺贝尔奖和非诺贝尔奖的重大发现，我们可以探讨“科学方法”在开展突破性科学研究中的实际应用程度，以及我们是否需要扩展这一科学核心概念的问题。本研究发现，自1900年以来，所有发现中有25%并没有采用常用的科学方法（所有三个特征），其中6%的发现没有采用观察，23%没有采用实验，17%没有验证假设。因此，经验证据对科学方法的普遍观点提出了挑战。坚持这一指导原则将会限制我们产生许多新的科学思想和突破。相反，通过评估所有重大发现，本文确定了一个普遍的、共同的特征，即科学方法可以归纳为：形成所有重大发现都需要使用科学的精实方法和仪器。这些方法包括统计方法、粒子加速器和X射线方法。这些方法拓展了我们的思维，通常使科学中的观察、实验和验证假设成为可能，以新的方式进行，并确保它们的重现性。这为科学方法提供了一个新的视角，嵌入在我们的精实方法和仪器中，并提示我们需要改革和拓展我们看待科学方法和发现过程的方式。
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（实习生周皓悦编译）
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Disclaimer: This column is a new trial to share cutting-edge research with wider academic community. The Chinese is not an official translation, while the English is invoked from original publication. If there is anything inappropriate, please contact imber@ecnu.edu.cn to correct us or request for a retraction.
声明：本版块为尝试性栏目，旨在传播分享最新科研动态。中文翻译仅供参考，中英文若有不符之处，请以英文为准。如有不妥之处，请联系 imber@ecnu.edu.cn 进行订正或要求撤稿。
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If you would like to put some recruitment information in the IMBeR bilingual monthly newsletter, please contact us through imber@ecnu.edu.cn.
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