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Welcome to Environmental Microbiome
Environmental Microbiome ( IF 7.9 ) Pub Date : 2019-04-01 , DOI: 10.1186/s40793-019-0340-8
Joy E M Watts ₁

Affiliation

I am delighted to serve as Editor-in-Chief for Environmental Microbiome, sister publication to Microbiome and Animal Microbiome. We are kicking off Environmental Microbiome with a research article by Barbara Cania and colleagues: A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides [1]. This article looks at how the common agricultural practice of tilling can disrupt the potential of bacteria to produce the natural compounds that ‘glue’ soil particles together – this ‘gluing’ effect helps prevent soil erosion.

Environmental microbiology can be loosely defined as the study of microbes, their functions, and interactions in all habitats on Earth (and beyond). This is a burgeoning research area that covers air, soil and aquatic systems, astrobiology, biogeochemical cycles, plant-soil interactions, extreme environments, and spatial, temporal and perturbation studies. Unfortunately, due to the non-culturability of most environmental species, our understanding of microbial community composition and function is somewhat driven by technological innovation. A proliferation of 16S rRNA gene studies in the 1990s started to reveal the diversity present in environmental systems. The increasing ease and availability of sequencing-based approaches enabled larger fragments of environmental DNA to be cloned [2]. This was followed shortly after by early metagenomics studies such as Rondon et al. 2000 [3], and genome reconstruction from environmental samples [4]. These omics-based tools have enabled new insights into microbial diversity, function, and the complex ecological interactions therein. This is an exciting time and continuing innovations in sequencing technology and downstream analysis have now made assessments of complex environmental microbiomes commonplace and also revealed how much diversity is left to discover!

This journal will provide a forum to publish hypothesis-driven environmental microbiome studies such as marker gene surveys, metagenomes, metatranscriptomes, metaproteomes, metabolomes, microbial genome reconstruction, and single-cell analysis from environmental habitats. Previously, many studies have focused on bacterial and archaeal microbiome analysis, but to obtain a more holistic view of ecological interactions we should aim to include the environmental mycobiome and virome to better understand different systems. Understanding the function and activities of microbial dark matter and the rare biosphere will be a major focus for the journal, and utilising improved technologies such as single-cell sequencing analysis will also provide valuable insights. New methodologies, theoretical community analysis, and development of bioinformatics tools are also welcome due to their importance in moving our understanding forward.

The journal is transitioning from Standards in Genomic Sciences and, as such, we are in the fortunate position of already having an Impact Factor that we can build upon. The Editorial team for this journal is diverse and reflects the broad research areas that will be reflected in this publication. As a sister journal to Microbiome and Animal Microbiome the same high standards of openness and transparency will be employed. To promote open access science, which is crucial for ensuring the most impact from published research, all articles published in Environmental Microbiome will be freely available through the journal web portal and within major research publication databases such as PubMed Central. Also, because authors, not the publisher will hold the copyright to their work, they will be free to distribute published articles.

The editorial team at Environmental Microbiome hope that you will support this endeavour by submitting your research studies and furthering our understanding of environmental microbiology.

1.
Cania B, Vestergaard G, Krauss M, Fliessbach A, Schloter M, Schulz S. A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides. Environmental Microbiome. 2019; [production to add citation].
2.
Stein JL, Marsh TL, Wu KY, Shizuya H, Delong EF. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol. 1996;178:591–9.
CAS Article Google Scholar
3.
Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, Macneil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol. 2000;66:2541–7.
CAS Article Google Scholar
4.
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428(6978):37.
CAS Article Google Scholar

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University of Portsmouth, University House, Winston Churchill Ave, Portsmouth, PO1 2UP, UK
Joy E. M. Watts

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All authors read and approved the final manuscript.

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Correspondence to Joy E. M. Watts.

Authors’ information

Joy Watts is the Editor-in-Chief of Environmental Microbiome and a Senior Editor of Microbiome.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Watts, J.E.M. Welcome to Environmental Microbiome. Environmental Microbiome 14, 2 (2019). https://doi.org/10.1186/s40793-019-0340-8

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Published: 01 April 2019
DOI: https://doi.org/10.1186/s40793-019-0340-8

中文翻译：

欢迎来到环境微生物组

我很高兴担任《微生物组》和《动物微生物组》的姊妹刊物《环境微生物组》的主编。我们通过 Barbara Cania 及其同事的一篇研究文章启动了环境微生物组：一项长期田间实验证明了耕作对细菌产生土壤结构稳定剂（如胞外多糖和脂多糖）潜力的影响 [1]。本文着眼于常见的耕作农业实践如何破坏细菌产生将土壤颗粒“粘合”在一起的天然化合物的潜力 - 这种“粘合”效应有助于防止土壤侵蚀。

环境微生物学可以宽泛地定义为对微生物、其功能以及地球上（及其他）所有栖息地中相互作用的研究。这是一个新兴的研究领域，涵盖空气、土壤和水生系统、天体生物学、生物地球化学循环、植物-土壤相互作用、极端环境以及空间、时间和扰动研究。不幸的是，由于大多数环境物种的不可培养性，我们对微生物群落组成和功能的理解在某种程度上是由技术创新驱动的。20 世纪 90 年代，16S rRNA 基因研究的激增开始揭示环境系统中存在的多样性。基于测序的方法日益简便和实用，使得环境 DNA 的更大片段得以克隆 [2]。不久之后，Rondon 等人进行了早期的宏基因组学研究。2000年[3]，以及从环境样本中重建基因组[4]。这些基于组学的工具使人们对微生物多样性、功能及其复杂的生态相互作用有了新的认识。这是一个激动人心的时刻，测序技术和下游分析的持续创新现已使复杂环境微生物组的评估变得司空见惯，同时也揭示了还有多少多样性有待发现！

该期刊将提供一个论坛来发表假设驱动的环境微生物组研究，例如标记基因调查、宏基因组、宏转录组、宏蛋白质组、代谢组、微生物基因组重建和环境栖息地的单细胞分析。此前，许多研究都集中在细菌和古菌微生物组分析上，但为了获得生态相互作用的更全面的观点，我们应该致力于将环境真菌组和病毒组包括在内，以更好地了解不同的系统。了解微生物暗物质和稀有生物圈的功能和活动将是该杂志的主要关注点，利用单细胞测序分析等改进技术也将提供有价值的见解。新方法、理论群体分析和生物信息学工具的开发也受到欢迎，因为它们对于推动我们的理解具有重要意义。

该期刊正在从基因组科学标准过渡，因此，我们很幸运，已经拥有了可以借鉴的影响因子。该期刊的编辑团队是多元化的，反映了本出版物将反映的广泛研究领域。作为《微生物组》和《动物微生物组》的姊妹期刊，将采用同样高标准的开放性和透明度。为了促进开放获取科学（这对于确保已发表的研究产生最大影响至关重要），《环境微生物组》中发表的所有文章都可以通过期刊门户网站和 PubMed Central 等主要研究出版数据库免费获取。此外，由于作者（而不是出版商）拥有其作品的版权，因此他们可以自由分发已发表的文章。

Environmental Microbiome的编辑团队希望您能够提交您的研究报告并加深我们对环境微生物学的理解，以支持这一努力。

1.
Cania B、Vestergaard G、Krauss M、Fliessbach A、Schloter M、Schulz S。长期田间实验证明了耕作对细菌产生土壤结构稳定剂（如胞外多糖和脂多糖）潜力的影响。环境微生物组。2019；[制作添加引文]。
2.
Stein JL，Marsh TL，吴 KY，Shizuya H，德龙 EF。未培养的原核生物的表征：从浮游海洋古菌中分离和分析 40 KB 对基因组片段。J细菌。1996；178：591-9。
CAS 文章谷歌学术
3.
Rondon MR、August PR、Bettermann AD、Brady SF、Grossman TH、Liles MR、Loiacono KA、Lynch BA、Macneil IA、Minor C、Tiong CL、Gilman M、Osburne MS、Clardy J、Handelsman J、Goodman RM。克隆土壤宏基因组：一种获取未培养微生物遗传和功能多样性的策略。应用环境微生物。2000；66：2541–7。
CAS 文章谷歌学术
4.
Tyson GW、Chapman J、Hugenholtz P、Allen EE、Ram RJ、Richardson PM、Solovyev VV、Rubin EM、Rokhsar DS、Banfield JF。通过从环境中重建微生物基因组来研究群落结构和代谢。自然。2004；428(6978):37。
CAS 文章谷歌学术

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朴茨茅斯大学，University House, Winston Churchill Ave, Portsmouth, PO1 2UP, UK
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Joy Watts 是《Environmental Microbiome》的主编和《Microbiome》的高级编辑。

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