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Guide for AuthorsWelcome to the electronic manuscript submission website for The ISME Journal. The instructions below are structured so you can quickly and easily answer the following questions:
Aims and ScopeThe ISME Journal seeks to promote diverse and integrated areas of microbial ecology spanning the breadth of microbial life, including bacteria, archaea, microbial eukaryotes, and viruses. Contributions of broad biological interest and impact are especially encouraged. Topics of particular interest within the journal’s scope include those listed below: Microbial population and community ecology
Microbe-microbe and microbe-host interactions
Evolutionary genetics
Integrated genomics and post-genomics approaches in microbial ecology
Microbial engineering
Geomicrobiology and microbial contributions to geochemical cycles
Microbial ecology and functional diversity of natural habitats
Microbial ecosystem impacts
Prior to SubmissionEditorial Policy Editors in Chief: Mark Bailey, John Heidelberg, Janet Jansson, George Kowalchuk. A manuscript will be considered for publication on the understanding that all named authors have agreed to its submission and that if accepted it will not be later published in the same or similar form in any language without the consent of the publishers. The editors also encourage submission of review articles, short communications and commentaries. The editors reserve the right to reject manuscripts without review. Such rejections must be approved by all editors-in-chief, and are intended to alleviate unnecessary workload for the editorial board, as well as provide authors the opportunity to seek other publishing options as soon as possible. To avoid unnecessary delays in the review process, please consider the following policies carefully before you submit your manuscript. Availability of published material It is understood that by publishing a paper in The ISME Journal the authors agree to make freely available to colleagues in academic research any of the organisms, viruses, cells, nucleic acids, antibodies, and other reagents that were used in the research reported and that are not available from commercial suppliers. Charges A Colour Artwork Form must be completed on acceptance of your article to indicate which figures should appear in colour for FREE in the HTML online version, and also which figures should be produced in colour in the print and PDF online version (please see the colour artwork form for pricing of print and PDF colour figures). You must also complete this form if all figures are to be reproduced in black and white. Authors will not incur page charges. Conflicts of interest In the interests of transparency and to help reviewers assess any potential bias, The ISME Journal requires authors of original research papers to declare any competing commercial interests in relation to the submitted work. Referees are also asked to indicate any potential conflict they might have reviewing a particular paper. Electronic manipulation of images Digital image enhancement is acceptable practice, although it can result in the presentation of quite unrepresentative data as well as in the loss of meaningful signals. During manipulation of images a positive relationship between the original data and the resulting electronic image must be maintained. If a figure has been subjected to significant electronic manipulation, the specific nature of the enhancements must be noted in the figure legend or in the 'Materials and methods' section. The Editors reserve the right to request original versions of figures from the authors of a paper under consideration. Submission to public databases The ISME Journal will only review and publish manuscripts if the authors agree to make all data that cannot be published in the journal itself (e.g. novel nucleotide sequences, structural data, or data from large-scale gene expression experiments) freely available in one of the public databases (see Submission to public databases below). Accession codes must be provided at the time a revised manuscript is returned to the Editorial Office. To avoid delays in publication of the manuscript, we encourage authors to deposit relevant data in public databases prior to submission. The authors may request that the data be stored in a confidential section of the database, in which they can request passwords from the database administrators, and these should be passed on to the Editorial Office to allow the editors and referees to anonymously access the information during the review process. Supplementary information for the editors and the reviewers Any manuscripts under review or accepted for publication elsewhere should accompany the submission if they are relevant to its scientific assessment. Authors should also provide upon submission any kind of supplementary material that will aid the review process. Content types The content types accepted by The ISME Journal are: Short communication Commentary Mini-Review Winogradsky review (by invitation only) Perspective Original article
Format of PapersPreparation of manuscripts Manuscripts are considered with the understanding that they have not been published previously in print or electronic format and are not under consideration by another publication or electronic medium. Copies of possibly duplicative materials that have been previously published or are being considered elsewhere must be provided at the time of manuscript submission. Cover Letter The uploaded covering letter must state that the material has not been submitted for publication elsewhere while under consideration for the The ISME Journal. Identify the name, full postal address, and fax number, of corresponding author. The authors are free to offer suggestions of suitable expert reviewers. The layout of the paper should be as follows; Short Communication Studies that fall short of the criteria for full research papers (eg preliminary experiments limited by sample size or duration, novel hypotheses or commentaries) may be submitted as Short Communications. They should contain no more than 1000 words of text, a maximum of two display items (tables and/or figures) and a maximum of 20 references. Apart from the Abstract (one paragraph of maximum 150 words) Keywords and Subject Category, there is no obligation to divide the text into sections. In all other respects, the directions for full papers should be followed. Commentary Commentaries are meant to discuss issues of particular significance to the field of microbial ecology. Commentaries may include highlights of significant papers, in the current issue or elsewhere, or comprise poignant opinions, responses to previously published items, or other timely information or comment. Commentaries should not exceed 900/1500 words and have 10 or fewer references. Commentaries may be either solicited by the editors or offered as an unsolicited submission. If you wish to offer an unsolicited commentary contribution, we ask you to first contact the editorial office with your request, including a short description of the content and implications of your commentary. Mini-Review Word limit of 3,000 words including abstract but excluding references, tables and figures. A number of mini-reviews will be solicited by the editors, however we also welcome timely, unsolicited mini-reviews. Authors with proposals for mini-reviews, should present information concerning the proposed content and authors of their mini-review to the editors prior to submission. Unless otherwise informed, all changes for color images will be the authors’ responsibility. Winogradsky Review (only by invitation of Editors) Word limit of 5,000 words including abstract but excluding references, tables and figures. Winogradsky reviews are a comprehensive analysis of specific topics in microbial ecology that are solicited by the Editors. Proposals for Reviews may be submitted; however, in this case authors should only send an outline of the proposed paper for initial consideration. Charges for color images will be negotiated with The ISME Journal. Perspective Perspective articles are a hybrid between a commentary and a review, providing an opinion-driven perspective on a particular research topic or field of interest to the ISMEJ readership. Authors should present a (provocative) view that can be supported by data and literature with the goal of sparking debate and stimulating future research avenues. Perspectives should not exceed 3,000 words, and typically contain 1-3 figures. Perspective articles are by invitation only, but authors wishing to contribute a perspective article are free to submit an unsolicited request to the editors with an outline or synopsis of the intended article. If the subject and content are deemed of interest, an invitation letter will then be extended by the editorial office. Original Articles Type preferably on A4 paper (210 x 297 mm) single-sided and double-spaced with 25 mm margins. Number each page following the title page and include line numbers (every 5 lines is sufficient) if this option is available. Please make spelling consistent with current editions of either Webster's Dictionary or Oxford English Dictionary. Word limit of 5,000 words including abstract but excluding references, tables and figures.
Manuscripts should be divided in to the following sections: Title page Abstract Introduction Materials and methods Results Discussion Acknowledgements References Figure legends Figures Tables Supplementary Information Title page Title page, giving a concise but informative title, and the first and last names, and other initials, and affiliations (but not degrees) of all contributors (formerly called authors). The order in which the contributors are listed should be agreed amongst the investigators, and should indicate that the first listed made the greatest contribution to the paper. Please provide a running title of no more than 50 characters including spaces. Three to six keywords, which may or may not appear in the title, should be given in alphabetical order, below the abstract, each separated by a slash (/). Subject Categories are used to structure the current and archived online content of The ISME Journal, and to help readers interested in particular areas of microbial ecology find relevant information more easily. Subject Categories are also indicated in the table of contents and on the title page of the published article. Authors should suggest an appropriate Subject Category for the submitted manuscript. One category may be selected from the following list:
Abstract An abstract of not more than 250 words. The Abstract should be comprehensible to readers before they have read the paper, and abbreviations and reference citations within the abstract should be avoided. Introduction This should give a short, clear account of the background and reasons for undertaking the study. It should not be a review of the literature. Materials and methods This section should contain sufficient detail so that all experimental procedures can be repeated by others, in conjunction with cited references. This section may be divided into subheadings to assist the reader. Extended protocol details can be submitted as supplementary information. Results The description of results should not simply reiterate data that appear in tables and figures and, likewise, the same data should not be displayed in both tables and figures. The results section should be concise and follow a logical sequence. If the paper describes a complex series of experiments, it is permissible to explain the protocol/experimental design before presenting the results. Do not discuss the results or draw any conclusions in this section. This section may be divided into subheadings to assist the reader. Large datasets or other cumbersome data pertinent to the manuscript may be submitted as supplementary information. Discussion Do not recapitulate the results, but discuss their significance against the background of existing knowledge, and identify clearly those aspects that are novel. The final paragraph should highlight the main conclusion(s), and provide some indication of the direction future research should take. This section may be divided into subheadings to assist the reader. Results and Discussion may be combined. Acknowledgments These should be brief, and should include sources of support, sources of material (eg novel compounds, strains, etc.) not available commercially. Units and Abbreviations Try to restrict the use of abbreviations to SI symbols and those recommended by the IUPAC. Abbreviations should be defined in brackets after their first mention in the text, not in a list of abbreviations. Standard units of measurements (SI symbols) and symbols of chemical elements may be used without definition in the body of the paper. Abbreviations of standard biochemical compounds, e.g. ATP, DNA, nucleotides in nucleic acids, and amino acids in proteins, need not be defined. References Authors are responsible for the accuracy of the references. Published articles as well as those in press (please state the name of the journal and enclose a copy of the manuscript) may be included. In the text of the manuscript, a reference should be cited by author and year of publication eg (Bailey & Kowalchuk, 2006) and (Heidelberg et al, 1994) and listed at the end of the paper in alphabetical order of first author. References should be listed and journal titles abbreviated according to the style used by Index Medicus, examples are given below. All authors should be quoted for papers with up to six authors; for papers with more than seven authors, the first six only should be quoted, followed by et al. Journal article: Cho JC, Kim MW, Lee DH, Kim SJ. (1997). Response of bacterial communities to changes in composition of extracellular organic carbon from phytoplankton in Daechung reservoir (Korea). Arch Hydrobiol 138:559–576. Journal article, e-pub ahead of print: Eng-Kiat L, Bowles DJ. A class of plant glycosyltransferases involved in cellular homeostasis. EMBO J 2004; e-pub ahead of print 8 July 2004, doi: 10.1038/sj.emboj.7600295. Journal article, in press: Lim E-K, Ashford DA, Hou B, Jackson RG, Bowles DJ. (2004). Arabidopsis glycosyltransferases as biocatalysts in fermentation for regioselective synthesis of diverse quercetin glucosides. Biotech Bioeng (in press). Complete book: Sambrook J, Fritsch E, Maniatis T. (1989). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor Press: New York. Chapter in book: Zinder, SH. (1998). Methanogens. In: Burlage, RS (ed). Techniques in Microbial Ecology. Oxford University Press: Oxford, pp 113–136. Figures These should be labeled sequentially as Figure 1, Figure 2, etc. Each figure should be saved in a separate file, numbered and titled and cited in the text. Figure legends should be printed, double spaced, on a separate sheet titled ‘Titles and legends to figures’. Figures should be referred to specifically in the text of the paper but should not be embedded within the text. The use of three-dimensional histograms is strongly discouraged when the addition of the third dimension gives no extra information. If a table or figure has been published before, the authors must obtain written permission to reproduce the material in both print and electronic formats from the copyright owner and submit it with the manuscript. This follows for quotes, illustrations and other materials taken from previously published works not in the public domain. The original source should be cited in the figure caption or table footnote. Colour figures can be reproduced if necessary, but the authors will be expected to contribute towards the cost of publication. A quote will be supplied upon acceptance of your paper. Artwork GuidelinesDetailed guidelines for submitting artwork can be found by downloading the guidelines PDF. Using the guidelines, please submit production quality artwork with your initial online submission. If you have followed the guidelines, we will not require the artwork to be resubmitted following the peer-review process, if your paper is accepted for publication. Colour on the web Authors who wish their articles to have FREE colour figures on the web (only available in the HTML (full text) version of manuscripts) must supply separate files in the following format. These files should be submitted as supplementary information and authors are asked to mention they would like colour figures on the web in their submission letter. For Single Images:
For Multi-part Images :
Authors may be asked to pay the full colour fee for figures that are not submitted in the format described above.A Colour Artwork Form must be completed on acceptance of your article to indicate which figures should appear in colour for FREE in the HTML online version, and also which figures should be produced in colour in the print and PDF online version. You must also complete this form if all figures are to be reproduced in black and white. TablesThese should be labeled sequentially as Table 1, Table 2, etc. Each table should be saved in a separate file, numbered and titled, and cited in the text. Reference to table footnotes should be made by means of Arabic numerals. Tables should not duplicate the content of the text. They should consist of at least two columns; columns should always have headings. Authors should ensure that the data in the tables are consistent with those cited in the relevant places in the text, totals add up correctly, and percentages have been calculated correctly. Unlike figures or images, tables may be embedded into the word processing software if necessary, or supplied as separate electronic files. House Style As the electronic submission will provide the basic material for typesetting, it is important that papers are prepared in the general editorial style of the journal.
File Formats: File formats for manuscript files, figures and tables that are acceptable for our electronic manuscript submission process are given on the online forms. Further advice on file types is also available from the Tips webpage. Please follow our artwork guidelines for submitting figures, and use a common word-processing package (such as Microsoft Word) for the text. Either embed tables converted into images at the end of your Word document, or as a separate files in which ever program you used to generate them. If you submit raw data, this can be done in Excel, or tab/comma delimited format. Saving files with Microsoft Office 2007 Microsoft Office 2007 saves files in an XML format by default (file extensions .docx, .pptx and xlsx). Files saved in this format cannot be accepted for publication. Save Word documents using the file extension .doc
These instructions also apply for the new versions of Excel and PowerPoint. Equations in Word must be created using Equation Editor 3.0 Equations created using the new equation editor in Word 2007 and saved as a "Word 97-2003 Document" (.doc) are converted to graphics and can no longer be edited. To insert or change an equation with the previous equation editor:
Do not use the "Equation" button in the "Symbols" section of the "Insert" tab.
Supplementary information
Supplementary information is peer-reviewed material directly relevant to the conclusion of an article that cannot be included in the printed version owing to space or format constraints. It is posted on the journal's web site and linked to the article when the article is published and may consist of data files, graphics, movies or extensive tables.
The printed article must be complete and self-explanatory without the supplementary information. Supplementary information enhances a reader’s understanding of the paper but is not essential to that understanding.
Supplementary information must be supplied to the editorial office in its final form for peer review. On acceptance the final version of the peer reviewed supplementary information should be submitted with the accepted paper.
To ensure that the contents of the supplementary information files can be viewed by the editor(s), referees and readers, please also submit a ‘read-me’ file containing brief instructions on how to use the file.
The supplementary information may not be altered, nor new supplementary information added, after the paper has been accepted for publication. Supplying supplementary information files Authors should ensure that supplementary information is supplied in its FINAL format becuase it is not subedited and will appear online exactly as originally submitted. It cannot be altered, nor new supplementary information added, after the paper has been accepted for publication.
Please supply the supplementary information via eJP, the electronic manuscript submission and tracking system, in an acceptable file format (see below).
Accepted file formats We cannot accept TeX and LaTeX.
File sizes must be as small as possible, so that they can be downloaded quickly. Images should not exceed 640 x 480 pixels (9 x 6.8 inches at 72 pixels per inch) but we would recommend 480 x 360 pixels as the maximum frame size for movies. We would also recommend a frame rate of 15 frames per second. If applicable to the presentation of the supplementary information, use a 256 colour palette. Please consider the use of lower specification for all of these points if the supplementary information can still be represented clearly. Our recommended maximum data rate is 150 KB/s.
The number of files should be limited to eight, and the total file size should not exceed 8 MB. Individual files should not exceed 1 MB. Please seek advice from the editorial office before sending files larger than our maximum size to avoid delays in publication. Further questions about the submission or preparation of supplementary information should be directed to the editorial office.
Conventions In general, the journal follows conventions given in Scientific Style and Format: The CBE Manual for Authors, Editors and Publishers (1994) Cambridge University Press, Cambridge, UK, 6th edn. Please follow Chemical Abstracts and its indexes for chemical names. For guidance in the use of biochemical terminology follow the recommendations issued by the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature. In general, genotypes should be indicated in italics; phenotypes should not be italicized. Non-Native Speakers of English Researchers who are not native speakers of English who submit manuscripts to international journals often receive negative comments from referees or editors about the English-language usage in their manuscripts, and these problems can contribute to a decision to reject a paper. To help reduce the possibility of such problems, we strongly encourage such authors to take at least one of the following steps:
Please note that the use of Nature Publishing Group Language Editing is at the author's own expense and in no way implies that the article will be selected for peer review or accepted by an NPG journal (or any other journal). The decisions that the editors of any NPG journal make based on the quality and suitability of a manuscript for that journal are entirely independent of whether that manuscript has been language-edited by Nature Publishing Group Language Editing. Submission to public databases The ISME Journal will only review and publish manuscripts if the authors agree to make all data that cannot be published in the journal itself (e.g. novel nucleotide sequences, structural data, or data from large-scale gene expression experiments) freely available in one of the public databases (see Submission to public databases below). Accession codes must be provided at the time a revised manuscript is returned to the Editors. To avoid delays in publication of the manuscript, we encourage authors to deposit relevant data in public databases prior to submission. The authors may request that the data be stored in a confidential section of the database, in which they can request passwords from the database administrators, and these should be passed on to the Editorial Office to allow the editors and referees to anonymously access the information anonymously during the review process. The ISME Journal requires submission of novel sequence and structural data to the appropriate public databases. We will not accept an article for publication until the relevant entry codes have been provided. These must be quoted in the text of the article. Sequence data Nucleotide sequence data can be submitted in electronic form to any one of the three major collaborative databases: DDBJ: DNA Data Bank of Japan, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411, Japan. Tel: +81 559 81 6853; Fax: +81 559 81 6849; E-mail: ddbjsub@ddbj.nig.ac.jp (for data submissions); WWW URL: http://www.ddbj.nig.ac.jp/ EMBL: EMBL Nucleotide Sequence Submissions, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Tel: +44 1223 494400; Fax: +44 1223 494472; E-mail: datasubs@ebi.ac.uk; WWW URL: http://www.ebi.ac.uk/ GenBank: National Center for Biotechnology Information, National Library of Medicine, Building 38A, Room 8N-803, Bethesda, MD 20894, USA. Tel: +1 301 496 2475; Fax: +1 301 480 9241; E-mail: gb-sub@ncbi.nlm.nih.gov; WWW URL: http://www.ncbi.nlm.nih.gov/ The suggested wording for referring to accession number information in journal articles is 'These sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession No. U12345'. Structural data The ISME Journal accepts and follows the recommendations of the International Union of Crystallography (IUCr), with regard to the deposition and release of macromolecular structural data. These guidelines are set out in the article by the IUCr Commission on Biological Macromolecules in Acta Crystallographica (2000), D56, 2. In summary, they state that all publications must be accompanied by deposition of both the atomic coordinates and the structure-factor amplitudes in the appropriate database (PDB or NDB). In the case of low-resolution structures for which only a chain trace is reported, a set of C alpha positions and structure-factor amplitudes may be sufficient. For NMR structures, data deposited should include resonance assignments, and all restraints used in structure determination (NOEs, spin-spin coupling constants, amide exchange rates, etc) and the derived atomic coordinates for both an individual structure and for a family of acceptable structures. Structures of biological macromolecules solved by electron microscopy must be submitted to the EMDB database at http://www.ebi.ac.uk/msd/Deposition.html For a brief description of the database, see Tagari et al. (2002) Trends Biochem Sci 27:589. Under exceptional circumstances and upon request, the Editors may grant a delay of up to 6 months for deposition or the release of deposited data. Microarray data Authors should refer to the MGED open letter specifying microarray standards (http://www.mged.org/Workgroups/MIAME/miame_checklist.html). The ISME Journal requires submission of microarray data to the ArrayExpress (http://www.ebi.ac.uk/arrayexpress/) or GEO (http://www.ncbi.nlm.nih.gov/geo/) databases, and provision of accession numbers before acceptance of the paper for publication
Submission of papersThe first thing you need to do, if you have not done so already, is register for an account. After this, please consult the instructions below to enable you to submit your article through our secure server. Please be sure that your browser is set to accept cookies. Our tracking system requires cookies for proper operation. (If you have Windows XP the defaults will need changing. For more details on this, please refer to the 'Tips' function on this site.)
Navigating the System
When you first access our tracking system, you will be taken to your Home page, where different categories of tasks are listed. If you are required to perform a pending action item or task, there will be a red arrow At any time please press HOME to go to the submission home page.
Process for Manuscript SubmissionPlease make sure you have gathered all the required manuscript information listed above BEFORE starting the submission process. The manuscript submission process starts by pressing the "Submit Manuscript" link on your "Home" page. The manuscript submission process is broken down into a series of 4 primary tasks that gather detailed information about your manuscript and allow you to upload the pertinent text and figure/image files. The sequence of screens is as follows:
You will need to have the following details for all authors before commencing online submission. Items in parenthesis may not be compulsory for co-authors:
In addition you will need:
Adobe Acrobat
Once you have submitted your files and the conversion is in progress, you may log off the Internet and come back later to check and approve the conversion. This process can take up to 5 - 10 minutes before the PDF, created in the conversion process, is ready for approval. Please remember that your manuscript will not be submitted until you have approved the converted files.
Getting Help If you need additional help, you can click on the help signs Welcome to The ISME Journal online manuscript submission and tracking system. Please be sure that your browser is set to accept cookies, our tracking system requires them for proper operation. If you are a first time user please read our Instructions to Authors or Reviewers. Experienced users please remember that passwords are case sensitive.
If you experience any problems, please contact the NPG Applications Helpdesk.
Manuscript Status After you approve your manuscript it is submitted and you will receive an acknowledgement email. You can check the status of your manuscript at any time in the review process by:
Licence to Publish The corresponding author must complete and sign the Licence to Publish form upon acceptance of the manuscript and return it to the editorial office. Failure to do so will result in delays to the publication of your paper. A copy of the Licence to Publish form can be found at http://mts-isme.nature.com/letters/isme_copyright.pdf ISME does not require authors of original research papers to assign copyright of their published contributions. Authors grant ISME an exclusive licence to publish, in return for which they can re-use their papers in their future printed work. NPG's author licence page provides details of the policy and a sample form. Authors are encouraged to submit their version of the accepted, peer-reviewed manuscript to their funding body's archive, for public release six months after publication. In addition, authors are encouraged to archive their version of the manuscript in their institution's repositories (as well as on their personal web sites), also six months after the original publication. Authors should cite the publication reference and doi number on any deposited version, and provide a link from it to the published article on the NPG website. This policy complements the policies of the US National Institutes of Health, the Wellcome Trust and other research funding bodies around the world. NPG recognizes the efforts of funding bodies to increase access of the research they fund, and strongly encourages authors to participate in such efforts. Advance Online Publication All original articles are published ahead of print on Advance Online Publication. This will be the final version of the manuscript and will subsequently appear, unchanged, in print.
Proofs Once the manuscript has been accepted, the corresponding author will receive PDF proofs and are responsible for proofreading and checking the entire article. Authors should correct only typesetting errors, no major alteration of the text will be accepted. Page proofs must be returned within 48 hours to avoid delays in publication along with the reprint order if required. Offprints Offprints may be ordered using the order form available for download with the proofs. Later orders submitted after the journal is printed are subject to increased reprint prices.
Business Matters To find out who to contact for business correspondence and enquiries such as advertising, subscriptions, permissions, papers in production or publishing a supplement, please visit our publisher’s contacts page. Alternatively, you can write to: The ISME Journal, Nature Publishing Group, The Macmillan Building, 4 Crinan Street, London, N1 9XW, UK. Please press HOME to continue. |
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