Editorial Process

Summary of the editorial process

  • The author submits a manuscript and it receives a tracking number.
  • The editorial office performs an initial quality check on the manuscript to ensure that the paper is formatted correctly.
  • An Editor in Chief is assigned to the manuscript and decides whether to send the manuscript to a Senior Editor for assessment. If the decision is not to send the manuscript for assessment, the Editor in Chief contacts the author with the decision.
  • If the Editor in Chief decides the paper is within the Journal's scope and may be suitable for review, the Editor in Chief will assign the paper to a Senior Editor.
  • The Senior Editor then assesses the manuscript for its quality and perceived level of advance and then either recommends a reject decision or assigns peer reviewers. This can take some time depending on the responsiveness and availability of reviewers selected.
  • Reviewers are given 18 days from acceptance to submit their reports. Once the required reports are submitted the Senior Editor will make a decision recommendation to the Editor in Chief based on the rankings and comments received. 
  • The Editor in Chief makes the final decision. 

Authors are able to monitor the status of their paper throughout the peer review process.

Pre-submission Enquiries
Please note that, due to the increasing workload, our Editors-in-Chief cannot personally reply to pre-submission queries. Instead, the Editors-in-Chief would like to share the following statement:

When contemplating submission to The ISME Journal one should consider:

  • Is the research novel and does it represent a major advance for microbial ecology?
  • Does the work clearly fit within the scope of our journal? 
  • Has the research been conducted with state-of-the-art approaches? 

If the answer to these questions is yes, the study may well be appropriate for The ISME Journal, regardless of the system being studied. In this case, please feel free to submit the full manuscript via the online submission system. 

Submission
Papers should be submitted via the Journal's online submission system. 
Before submitting a manuscript, authors are encouraged to consult both the Guide to Authors and Editorial Policies sections of this website to ensure that the paper adheres to formatting and policy requirements - this will help to enable efficient processing of the manuscript once received. 

Peer review
​To expedite the review process, only manuscripts that seem likely to meet high reviewer rankings for publication priority, level of advance, and scientific merit are sent for external peer review. Manuscripts judged by the editors to be of insufficient general interest are rejected promptly without external review. 
Manuscripts sent out for peer review are evaluated by at least one independent reviewer (usually two or more). Authors are welcome to suggest independent reviewers without conflicts of interest (i.e., no current collaborations or co-authorship in the past 5 years) to evaluate their manuscript. All recommendations are considered, but it is at the Editor’s discretion to choose reviewers. ​Reviewers are not identified to the authors, except at the specific request of the reviewer.
Once a sufficient number of reviews are received, the Senior Editors then recommend a decision to the Editor-in-Chief based on the reviewer evaluations:

  • Provisional Acceptance - The manuscript is provisionally accepted. 
  • Minor or major revision - In cases where the editors determine that the authors should be able to address the referees’ concerns in a month or less the editors may request a revised manuscript that addresses concerns. The revised version may be sent back to some or all of the original reviewers for re-review especially if new data are requested. The decision letter will specify a deadline for receipt of the revised manuscript and link via which the author should upload to the online submission system. When submitting a revision authors are asked to upload (1) A rebuttal letter, indicating point-by-point how the comments raised by the reviewers have been addressed. If you disagree with any of the points raised, please provide adequate justification in your letter. (2) A marked-up version of the manuscript that shows changes made in response to the reviewers' comments in order to aid the editors and reviewers. (3) A "clean" (non-tracked) version of the manuscript.
  • Reject with the option to resubmit - In cases where reviewer concerns are more serious and appear unlikely to be addressed within a month, the editors will normally reject the manuscript. If the editors feel the work is of potential interest to the journal, however, they may express interest in seeing a future resubmission. The resubmitted manuscript may be sent back to the original referees or to new referees, at the Senior Editor’s discretion. If the authors decide to resubmit, the updated version of the manuscript must be submitted online as a new manuscript and should be accompanied by a cover letter that includes a point-by-point response to referees' comments and an explanation of how the manuscript has been changed. 
  • Reject - Typically on grounds of specialist interest, lack of novelty, insufficient conceptual advance or major technical and/or interpretational problems. In some cases, where the quality of the work is high but the level of advance does not meet the threshold for The ISME Journal, the editors may recommend transfer of the manuscript to our partner journal ISME Communications. The transfer would carry all manuscript history and reviewer information to facilitate subsequent consideration by editors of ISME Communications.

Post Acceptance
Once a manuscript is accepted and typeset, the corresponding author will be prompted to complete and sign a Licence to Publish form on behalf of all authors. Failure to complete the form will result in delay of publication.

Springer Nature does not require authors of original research papers to assign copyright of their published contributions. Authors grant Springer Nature an exclusive licence to publish, in return for which they can re-use their papers in their future printed work. Springer Nature’s author licence page provides details of the policy.

The corresponding author will be prompted to choose Standard or Open Access publication.

Standard Publication 
Manuscripts published under the standard method of publication will be behind a paywall, requiring readers to pay to view the article, either via their institutional or personal subscription or on a pay-per-view basis. Government employees from the United States and Crown are required to sign and submit the relevant license to publish form.

Open Access Publication (gold open access)
Once prompted, authors can indicate whether they wish to pay an optional article processing charge (APC) for their article to be made open access online immediately upon publication. Open access articles are published under a CC BY Creative Commons license, which allow authors to retain copyright to their work while making it open to readers.

The cost for open access publication in The ISME Journal is £2,500/ $3,300/ €2,700 (VAT or local taxes will be added where applicable)

If the authors opt to publish via the open access route, then the corresponding author will receive instructions to complete an open access License to Publish form on behalf of all authors, and will be contacted to arrange payment of the associated Article Processing Charge.
Please note that this process must be completed prior to publication and failure to do so will result in delay of publication.
Government employees from the United States and Crown are required to sign and submit the relevant government open access license to publish form. 

Please note with regards to payment that usual credit terms are 30 days from receipt of invoice. Failure to pay your invoice within the stated credit term may result in the Open Access status of the paper being rescinded, with the paper being placed behind the paywall. You may also be subject to such penalties as restrictions on your ability to publish with Springer Nature in the future, involvement of a third party debt collection agency and legal proceedings. 

Waiver of institutional open access policies
Please note that Harvard University FAS, MIT, Princeton, UCSF, University of Hawaii at Manoa, California Institute of Technology (Caltech) and the Georgia Institute of Technology have enacted Open Access policies that conflict with our own policy for articles published via the subscription route. If any corresponding or contributing authors are from these institutions, you will need to provide a waiver from the institution of every affected author, which can be obtained from the institution. This waiver should be submitted at the same time as the Licence to Publish form. This requirement does not apply to articles published via the open access route.

Self-archiving and digital preservation
Self-archiving of papers published open access
Authors publishing via the open access route are encouraged to deposit the final published PDF in their institutional repository or any suitable subject repository on publication.
Authors should provide a link from the deposited version to the URL of the published article on the journal's website; in all cases, the requirement to link to the journal’s website is designed to protect the integrity and authenticity of the scientific record, with the online published version on the journal’s website clearly identified as the definitive version of record.
Authors are advised to check their funders' deposition requirements to ensure compliance. Read our policy compliance FAQs to learn about how authors can ensure they meet funder self-archiving requirements. 

Self-archiving of papers published via the subscription route
Where articles are published via the subscription route, Springer Nature encourages authors to archive the author accepted version of their articles on their own personal website and/or in their funder’s or institution’s repository, for public release after an embargo period of six months after first publication. Where journals publish online in advance of print, the online publication date counts as the publication date.

Publisher deposition of papers published open access
Springer Nature automatically deposits open access articles in PubMed Central (PMC) and Europe PubMed Central (EPMC) on publication, if the article meets the PMC deposition guidelines.
Please note that there may be an interval of a few weeks between publication and the appearance of an article in PubMed Central and Europe PubMed Central, depending on the time required for PubMed Central to process the deposit and for PMC articles to be mirrored to Europe PubMed Central. Where a journal publishes content online ahead of publication in a print issue (known as advanced online publication, or AOP), open access articles will be deposited to PubMed Central at the point of issue publication, as PubMed Central requires that articles are deposited in their final format.
Authors are advised to check their funders' deposition requirements to ensure compliance. Read our policy compliance FAQs to learn about how authors can ensure they meet all their funders’ self-archiving requirements. If you believe your open access article is eligible to be deposited to PubMed Central but has not been, please contact us, or you can submit an open access article directly to PubMed Central or Europe PubMed Central through their submission systems: PubMed Central and Europe PubMed Central.

Digital preservation
Springer Nature ensures that publications are preserved and available for future scholars, researchers, and students. Find out more about archiving agreements with Digital Preservation organisations here.

Proofs 
The Springer Nature e-proofing system is a unique solution that will enable authors to remotely edit /correct article proofs. The corresponding author will receive an e-mail containing a URL linking to the e-proofing site. Proof corrections must be returned within 48 hours of receipt. Failure to do so may result in delayed publication. Extensive corrections cannot be made at this stage.
For more information and instructions on how to use the e-proofing too please see here.

Advance Online Publication (AOP)
The final version of the manuscript is published online in advance of print. AOP represents the official version of the manuscript and will subsequently appear unchanged, in print.