It was not long ago that nucleic-acid sequencing was prohibitively expensive and inaccessible to many researchers in environmental science and technology fields. Bioinformatics tools were limited. There were limited sequencing data in the literature, and highly descriptive studies that used amplicon sequencing, metagenomics, or meta-transcriptomics to characterize biological communities or organisms in the natural and built environments were state-of-the-art. Nucleic-acid sequencing technologies have come a long way in the past few decades. Costs have decreased significantly allowing relatively affordable, deeper sequencing efforts that include low-abundance populations and functions, as well as the acquisition of longer sequences with low error rates. Analysis centers with specialized equipment run by highly trained staff have made sequencing data within reach of most researchers, even those with limited molecular biology experience. Single-molecule, real-time sequencers are now available to individual researchers for the collection of sequences in their lab experiments or field studies. Bioinformatic pipelines with analysis and visualization packages, each with their own approaches and assumptions, are vast and readily available to most researchers for free and can be readily implemented using R and Python, which are also free. Genomic, transcriptomic, and other (meta-)omic methods are now as accessible as amplicon sequencing methods were a decade ago, encouraging researchers to widely use these methods. As a result, we are experiencing an explosion of new biological insights at scales from viruses to single cells to multicellular organisms to entire biological communities across multiple domains of life. This is an exciting time to be working in the environmental biotechnology, microbial ecology, and bioremediation fields! Nucleic-acid sequencing tools are critical in the field of environmental science and technology. They have provided insights into the role of microorganisms in wastewater treatment processes, (1,2) drinking water systems, (3) and consortia capable of degrading chemical pollutants. (4,5) They have provided important insights into anthropogenic impacts on aquatic food webs (6) and the response of model organisms to chemical exposures. (7) At Environmental Science & Technology (ES&T) and Environmental Science & Technology Letters (ES&T Letters), we receive large numbers of papers utilizing nucleic-acid sequencing tools, but these papers do not always effectively address research questions or evaluate hypotheses. Most such manuscripts are rejected without sending them out for peer review, and many of those sent out for peer review do not attract favorable comments and are also rejected. As ES&T and ES&T Letters associate editors, we feel it is important to share with the community the insights we gained from handling these papers, so that researchers may make more informed decisions about whether to submit their manuscripts to the journals and even make decisions during study design and implementation that will ensure their work is more impactful and likely to receive favorable feedback from editors, peer reviewers, and readers. Many of the rejected papers that use nucleic-acid sequencing tools share distinctive characteristics. They often provide highly descriptive information about an environmental system using sequencing data alone but do not advance basic understanding, evaluate hypotheses, or advance technology by using insights from ecosystem characterization. Such manuscripts do not fare well in peer review, and ES&T and ES&T Letters do not encourage researchers to submit papers that fit this description. However, studies that characterize highly novel biological systems or are used to evaluate carefully articulated and compelling hypotheses will continue to be within the scope of the journals. Work that uses nucleic-acid sequencing approaches to characterize a microbial community should provide a fundamental or predictive understanding of community function. Studies that use off-the-shelf bioinformatics software to create network plots or infer community function and interactions from amplicon sequencing data also often do not fare well in peer review, as inferences derived using such approaches are viewed as unsubstantiated and lacking validation. To infer a functional gene role, RNA-based sequencing and not DNA-based sequencing should be used, and the functional gene roles elucidated from the sequencing approaches can be further strengthened by including other metadata (e.g., biodegradation intermediates, nutrient removal rates, etc.). Additional methods, such as stable isotope probing, and traditional community characterization approaches, including microbial cultivation and biochemical characterizations, should not be shunned but instead combined with (meta-)omic approaches to provide validation of key inferences. In short, we encourage authors to use a suite of complementary approaches in their studies rather than just relying solely on sequencing data. We remind authors that ES&T and ES&T Letters have a Research Data Policy and have Data Requirements. As part of these guidelines, authors should review the need for replication, and negative and positive controls, and clearly report on those in their manuscripts. We have noticed that as authors outsource sequencing and bioinformatics to third-party laboratories, they frequently neglect to provide enough methodological details to allow others to replicate the work. Finally, as is required by all high-quality journals publishing on biological systems, sequences and associated metadata should be deposited in open access databases as described in detail in the Database Deposition, Sequence Data, Omics Data, and Proteomics Data sections of the Data Requirements in ES&T and ES&T Letters Author Guidelines. As authors aim to adhere to these guidelines, they may benefit from reviewing guidance provided by societies other than the American Chemical Society, such as the American Society of Microbiology, which also may be helpful when it comes to microbiological nomenclature. This article references 7 other publications. This article has not yet been cited by other publications. This article references 7 other publications.

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最大限度地发挥核酸测序方法研究在环境科学与技术和环境科学与技术快报中的影响

不久前，核酸测序还非常昂贵，许多环境科学和技术领域的研究人员无法获得。生物信息学工具有限。文献中的测序数据有限，并且使用扩增子测序、宏基因组学或元转录组学来表征自然和建筑环境中的生物群落或生物体的高度描述性研究是最先进的。过去几十年来，核酸测序技术取得了长足的进步。成本显着下降，允许相对负担得起的、更深入的测序工作，包括低丰度群体和功能，以及以低错误率获取更长的序列。分析中心配备了由训练有素的工作人员运行的专用设备，使大多数研究人员（甚至那些分子生物学经验有限的研究人员）都能获得测序数据。现在，单个研究人员可以使用单分子实时测序仪在实验室实验或现场研究中收集序列。带有分析和可视化包的生物信息学管道数量庞大，每个都有自己的方法和假设，大多数研究人员都可以免费使用，并且可以使用同样免费的 R 和 Python 轻松实现。基因组学、转录组学和其他（元）组学方法现在与十年前的扩增子测序方法一样容易使用，这鼓励研究人员广泛使用这些方法。因此，我们正在经历从病毒到单细胞到多细胞生物再到跨生命多个领域的整个生物群落的新生物学见解的爆炸式增长。这是在环境生物技术、微生物生态学和生物修复领域工作的激动人心的时刻！核酸测序工具在环境科学技术领域至关重要。他们深入了解了微生物在废水处理过程、(1,2) 饮用水系统、(3) 以及能够降解化学污染物的联盟中的作用。 (4,5) 他们为人为对水生食物网的影响 (6) 以及模式生物对化学品暴露的反应提供了重要见解。 (7) 在环境科学与技术( ES&T ) 和环境科学与技术快报( ES&T Letters ) 中，我们收到了大量利用核酸测序工具的论文，但这些论文并不总能有效地解决研究问题或评估假设。大多数此类稿件在没有送去同行评审的情况下就被拒绝了，而且许多送去同行评审的稿件没有引起好评，也被拒绝了。作为ES&T和ES&T 字母副主编，我们认为与社区分享我们从处理这些论文中获得的见解非常重要，以便研究人员可以就是否将手稿提交给期刊做出更明智的决定，甚至在研究设计和实施过程中做出决定确保他们的工作更具影响力，并可能获得编辑、同行评审员和读者的积极反馈。许多使用核酸测序工具的被拒绝论文都有着独特的特征。它们通常仅使用测序数据来提供有关环境系统的高度描述性信息，但不会通过使用生态系统特征的见解来推进基本理解、评估假设或推进技术。此类手稿在同行评审中表现不佳，ES&T和ES&T Letters不鼓励研究人员提交符合此描述的论文。然而，表征高度新颖的生物系统或用于评估仔细阐述和令人信服的假设的研究将继续在期刊的范围内。使用核酸测序方法来表征微生物群落的工作应该提供对群落功能的基本或预测性理解。使用现成的生物信息学软件创建网络图或从扩增子测序数据推断群落功能和相互作用的研究通常在同行评审中表现不佳，因为使用此类方法得出的推论被视为未经证实且缺乏验证。为了推断功能基因的作用，应使用基于 RNA 的测序而不是基于 DNA 的测序，并且可以通过包含其他元数据（例如生物降解中间体、营养物去除率等）进一步加强从测序方法阐明的功能基因作用.)。不应回避其他方法，例如稳定同位素探测和传统的群落表征方法，包括微生物培养和生化表征，而应与（宏）组学方法相结合，以验证关键推论。简而言之，我们鼓励作者在他们的研究中使用一套互补的方法，而不是仅仅依赖测序数据。我们提醒作者ES&T和ES&T Letters有研究数据政策和数据要求。作为这些指南的一部分，作者应审查复制的必要性以及阴性和阳性对照，并在手稿中清楚地报告这些内容。我们注意到，当作者将测序和生物信息学外包给第三方实验室时，他们经常忽略提供足够的方法细节以允许其他人复制工作。最后，按照所有发表生物系统的高质量期刊的要求，序列和相关元数据应存放在开放存取数据库中，如数据要求的数据库存放、序列数据、组学数据和蛋白质组数据部分中详细描述的那样ES &T和ES&T Letter作者指南。由于作者旨在遵守这些指南，他们可能会受益于审查美国化学会以外的协会（例如美国微生物学会）提供的指南，这在微生物命名法方面也可能有所帮助。本文参考了其他 7 篇出版物。这篇文章尚未被其他出版物引用。本文参考了其他 7 篇出版物。