Author Guidelines

Environmental Microbiology (EMI) and Environmental Microbiology Reports (EMIR) publish articles reporting original experimental or theoretical work that substantively advances our understanding of the lives and activities of microorganisms in the environment, microbial communities, microbial interactions and microbially driven environmental processes. A key acceptance criterion for publication in the Journals is that the originality and significance of the work places it in the upper 10 % of research in the field.

EMI, which is published monthly, and EMIR, which is published bimonthly, share the same:

• Scope
• Submission website:
• International editorial team
• Acceptance criteria
• Rigorous peer-review process
• Submission guidelines


The scope of EMI and EMIR includes, but is not restricted to:

• microbial communities: structure:function relationships and communal behavior
• microbial interactions and interactions with plants, animals and abiotic factors, including systems analysis of interactions and their component networks
• pathogen ecology and environmental epidemiology
• genomics, functional genomics, environmental genomics/metagenomics, bioinformatic analyses and comparative genomics
• responses to environmental signals and stress factors
• primary and secondary production
• element cycles and biogeochemical processes
• microbial physiological, metabolic and structural diversity
• extremophiles and life in extreme and unusual little-explored habitats
• pollution microbiology
• microbially-influenced global changes
• growth and survival
• microbes and surfaces, adhesion, biofilm biology, biofouling
• population biology and clonal structure
• microbial community genetics and evolutionary processes
• modelling and theory development
• new technological developments in microbial ecology, in particular for the study of activities of microbial communities and of non-culturable microorganisms

Interdisciplinary studies of fundamental problems are particularly appropriate.

Article Types

The types of article published in both Journals reflect the Editors’ endeavour to actively promote the field of environmental microbiology, the broad scope of the subject, and the impact of socio-political, health, nutritional and economic issues and developments. Thus, in addition to the principal content of full-length (EMI) and compact (EMIR) research papers, issues may include Editorials/Opinions, Minireviews, Web Alerts, and Correspondence (general, scientific). The importance of genomics to the field is recognized by the Genomics Update feature.

Research Papers and Brief Reports

These report new original findings that significantly advance the field of environmental microbiology/microbial ecology. A principal criterion for judging the potential acceptability of a paper is that the advance reported places it in the top 10 % of research in the field. Papers may either be Full Papers or Brief Reports. In both cases, the work must be complete (preliminary communications will not be considered) and represent the indicated level of originality and accomplishment. Research papers documenting major studies should be submitted to EMI; Brief Reports reporting significant research in compact form should be submitted to EMIR. In all cases, manuscripts should be as concise as permitted by good scientific reporting. Essential material (e.g. primer sequences; strain lists, etc.) not crucial to an understanding of the main findings should be submitted as Supplementary Information.

The ultimate decision of whether a submission may be published as a Research Article or Brief Report is not dictated by the length of the initial submission, but rather by the length considered by the reviewers and Editor to be appropriate for the significance of the advance described and for its proper scientific documentation.


These bring to the attention of our readership exciting new developments and/or concepts in a timely fashion. They are selective in scope, focused and concise, rather than being comprehensive or historical, and may be somewhat speculative, if this is likely to provoke interesting discussions and stimulate new lines of creative experimentation. There is no strict format for minireviews, but they should include a Summary, Introduction, and Concluding Remarks, which bracket the main text. Literature citations should be balanced but not exhaustive. Most, but not all, minireviews are invited; authors wishing to submit a minireview should first contact the Minireview Editor, Juan Luis Ramos, to ascertain whether or not their topic is appropriate.


Submissions should contribute to discussions of topical issues in or impacting environmental microbiology, advance new hypotheses or provide new interpretations of existing hypotheses.


Environmental Microbiology will consider for review articles previously available as preprints on non-commercial servers such as ArXiv, bioRxiv, psyArXiv, SocArXiv, engrXiv, etc. Authors may also post the submitted version of their manuscript to non-commercial servers at any time. Authors are requested to update any pre-publication versions with a link to the final published article.

Exclusivity, copyright and author ethical obligations

Papers must be submitted exclusively to EMI or EMIR and are accepted on the understanding that they are entirely original and have not been, and will not be, published elsewhere. If accepted, authors will retain copyright of the article, and grant the Publisher the exclusive right to publish.

In submitting a manuscript to EMI/EMIR, the corresponding author must explicitly state in a cover letter that the content and authorship of the submitted manuscript has been approved by all authors, and that all prevailing local, national and international regulations and conventions, and normal scientific ethical practices, have been respected. Authors are reminded of the need to avoid plagiarism, and are strongly advised to employ one of the available plagiarism detection softwares. Failure to respect ethical norms may result in imposition of sanctions.

Conflict of Interest

EMI requires that all authors disclose any potential sources of conflict of interest. Any interest or relationship, financial or otherwise, that might be perceived as influencing an author’s objectivity is considered a potential source of conflict of interest. These must be disclosed when directly relevant or indirectly related to the work that the authors describe in their manuscript. Potential sources of conflict of interest include but are not limited to patent or stock ownership, membership of a company board of directors, membership of an advisory board or committee for a company, and consultancy for or receipt of speaker’s fees from a company. The existence of a conflict of interest does not preclude publication in this journal.

If the authors have no conflict of interest to declare, they must also state this at submission.
It is the responsibility of the corresponding author to review this policy with all authors and to collectively list in the cover letter to the Editor, in the manuscript (under the Acknowledgment section), and in the online submission system ALL pertinent commercial and other relationships.

Pre-submission English-language editing

Authors for whom English is a second language may choose to have their manuscript professionally edited before submission to improve the English. A list of independent suppliers of editing services can be found here. All services are paid for and arranged by the author, and use of one of these services does not guarantee acceptance or preference for publication.

Presentation of manuscripts

Authors should ensure that manuscripts submitted online have line numbers.

Lengths of printed articles

Papers should be focused and succinct, and as concise as possible consistent with clarity and good scientific reporting practice. Material essential for the paper, but not for an understanding of the advance reported, such as lists of primer sequences, strain characteristics, or material too large to be part of the main text (such as multimedia adjuncts, large data sets, extra colour illustrations, bibliographies, or any other material for which insufficient space in the journals is available) etc., must be submitted as Supporting Information, for publication online. The lengths of printed articles will generally not exceed the following: Research Articles: 10 printed pages (approx. 20 double line-spaced manuscript pages with 5 displays); Brief Reports: 5 printed pages; Minireviews: 6 printed pages; Correspondence: 2 printed pages. However, longer manuscripts will be considered if the extra length is dictated by good scientific reporting practice.

Supporting information
Supporting Information can be a useful way for an author to include important but ancillary information with the online version of an article. Examples of Supporting Information include additional tables, data sets, figures, movie files, audio clips, 3D structures, and other related nonessential multimedia files. Supporting Information should be cited within the article text, and a descriptive legend should be included. It is published as supplied by the author, and a proof is not made available prior to publication; for these reasons, authors should provide any Supporting Information in the desired final format. For further information on recommended file types and requirements for submission, please visit:

Title page. The title page should include: (1) a concise informative title for the work reported, (2) the names of all authors and their affiliation(s) where the work was conducted, (3) the name, full postal address, telephone and fax numbers, and email address of the corresponding author (one only), to whom all correspondence and proofs should be sent and (4) a running title of not more than 50 characters. Different current addresses of authors should appear as a footnote. Titles encapsulating the main advance ('Methylation is the initial reaction in anaerobic naphthalene degradation') are prefered over less informative general titles ('A study of . . .' 'Characterization of . . .' 'Diversity of . . .').

Originality-Significance Statement. Identify the key aspects of originality and significance that place the work within the top 10% of current research in environmental microbiology.

Summary. All papers must include a summary, not exceeding 200 words, that succinctly describes the principal findings of the work. Background information, and descriptions of what was done and how, should be avoided as redundant, unless essential to an understanding the findings, and then should be restricted to a sentence or two.

The main text. For Research Articles, the main text should be subdivided into Introduction, Results, Discussion, Experimental Procedures, Acknowledgments, References, Table and Figure legends. The Results and Discussion sections may be combined and can include additional subheadings. New or unfamiliar experimental procedures should be described in sufficient detail to enable the experiments to be reproduced. Well documented procedures should be adequately cited. For Brief Reports, Results and Discussion are combined, there is no section on Experimental Procedures, and essential experimental details should be incorporated into the corresponding figure and table legends. The preferred position of tables and figures should be indicated at the appropriate places in the manuscript. Footnotes should be avoided.



The text should be formatted double-spaced, typed consistently [e.g. care taken to distinguish between '1' (one) and 'l' (lower-case L), '0' (zero) and 'O' (capital O), etc.] with no hyphenation and automatic word-wrap (no hard returns within paragraphs), and line and page numbered consecutively.


Authors should use the system of citing references illustrated below. Only full articles that have been published or are 'in press' may be included in the reference list. In the text, unpublished or submitted studies should be referred to as such (e.g. J. M. Smith, unpublished), or as a personal communication. It is the author's responsibility to obtain permission from colleagues to include their work as a personal communication. In the text, references should be inserted in parentheses in date order, as follows: (Pugsley, 1996; Matsunaga et al., 1997). The reference list should be in alphabetical order according to the first-named author. Papers with two authors should follow those of the first-named author, arranged in alphabetical order according to the name of the second author. Articles with more than two authors should follow those of the first named author in chronological order; with multiple references from the same first author in a given year, please list the references in cited order. The title of the article must be included. For papers with up to seven authors, the names of all authors should be listed. For papers with eight or more authors, the first six names should be listed, followed by 'et al.'. Standard abbreviations of journal titles should be used, as in the Index Medicus.

The following provide examples:

Sahm, K., MacGregor, B.J., Jørgensen, B.B., and Stahl, D.A. (1999) Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slotblot hybridization in a coastal marine sediment. Environ Microbiol 1: 65-74.

Madigan, M.T., Martinko, J.M., Dunlap, P.V., and Clark, D.P. (2008) Brock Biology of Microorganisms, 12th edn. New York, USA: Pearson Higher Education.

Finlay, B.I., Fenchel, T., and Embley, T.M. (1993) Methanogen endosymbiosis in anaerobic climates. In Trends in Microbial Ecology. Guerrero, R., and Pedros-Alio, C. (eds). Barcelona: Spanish Society for Microbiology, pp. 285-288.

References to material available on the World Wide Web can be given, but only if the information is available without charge to readers on an official site. Authors will be asked to provide electronic copies of the cited material for inclusion on the journal websites at the discretion of the Editors. The format for citations is as follows:

Beckleheimer, J. (1994). How do you cite URLs in a bibliography? [WWW document]. URL
Nevertheless, as web site content and addresses are constantly changing, authors are discouraged from citing key information available only on the web.


In-line equations should be typed as text. The use of graphics programs and 'equation editors' should be avoided. Displayed equations are rekeyed by our typesetter.


Tables should be typed as text, using either 'tabs' or a table editor for layout. Do not use graphics software to create tables.


Please supply high quality digital versions of figures, preferably in EPS or TIFF format. TIFF files should not be produced by transferring images from a previous Powerpoint file, as this results in major loss in resolution. Photomicrographs should include a scaled bar and indicate the size (descriptions of magnification alone are not sufficient). Submitted photographic images should be scaled to publication size and must have an image resolution of 300 dpi or greater in TIFF format. Annotated photographs, line graphs and bar charts should be generated in EPS format for best quality of reproduction. For more detailed guidelines, please refer to

Provide methodological details on image acquisition and image processing, including software and operations such as colourizing and other modifications.

Authors are reminded that it is not acceptable scientific conduct to modify any separate element within an image. Sometimes adjustments of the entire image in brightness, contrast and colour balance are justified if they do not misrepresent the original, observed data. Composite figures composed of grouped images such as insets from different fields or separate parts of gels must be explained in the figure legend and differentiated by use of dividing lines or other means to make composites unambiguous.

Please ensure that electronic artwork is prepared such that, after reduction to fit across one or two columns or two-thirds page width (80 mm, 169 mm or 110 mm respectively) as required, all lettering will be clear and easy to read, i.e. no labels should be too large or too small. Avoid using tints if possible; if they are essential to the understanding of the figure, try to make them coarse. No artwork should be incorporated into the text files. In the full-text online edition of the journal, figure legends may be truncated in abbreviated links to the full-screen version. Therefore, the first 100 characters of any legend should inform the reader of key aspects of the figure.

Authors are encouraged to use colour displays, where appropriate:

Cover Photographs

The Editors welcome proposals of images related to the content of submitted papers that may be suitable for the covers of EMI and EMIR. If such an image is accepted and used as a cover, a free pdf offprint of the cover will be provided to the author.



Standard abbreviations should be as recommended in Quantities, Units, and Symbols (The Royal Society, 1988). Abbreviations of non-standard terms should follow, in parentheses, their first full usage.

Genetic nomenclature

Standard genetic nomenclature should be used. For more detailed information, authors should consult Bachman (Microbiol Rev 47: 180-230, 1983) for E. coli K-12; Sanderson and Roth (Microbiol Rev 47: 310-453, 1983) for Salmonella typhimurium; Holloway et al. (Microbiol Rev 43: 73-102, 1979) for Bacillus subtilis; Perkins et al. (Microbiol Rev 46: 426-570, 1982) for Neurospora crassa; and the Handbook of Genetics Vol. 1 (R. C. King, ed., Plenum Press, 1974) for Saccharomyces cerevisiae.

Restriction enzymes

EMI and EMIR have adopted the revised convention of naming restriction enzymes without italics. Previous designations like EcoRI, KpnI HindIII, SacII, etc., are thus supplanted by EcoRI, KpnI, HindIII, SacII, etc. For more information on the updatedguidelines to naming restriction enzymes, please consult Roberts et al. (Nucleic Acids Res 31: 1805-1812).

Submission of Manuscripts

Cover letter

In the cover letter, (a) specify the title and authors, (b) provide a 1-2 sentence description of the advance reported and its significance, and confirm that (c) all of the reported work is original, (d) all authors have seen and approved the final version submitted, (e) all prevailing local, national and international regulations and conventions, and normal scientific ethical practices, have been respected, and (f) consent is given for publication in EMI/EMIR, if accepted.

Online submission

All manuscripts should be submitted online at A user ID and password are required and can be obtained on the first use of the site. All file types are supported, but the following types are recommended: text in Microsoft Word or generic rich text format (RTF), figures in high resolution EPS or TIFF. Macintosh users are advised to add the correct three-letter filename suffix.


Authors may nominate up to five referees appropriately qualified to judge the manuscript, though the Editors may or may not ultimately select some of these. Authors may also request that one or two specified persons do not act as reviewers. Should authors feel that they have a significant conflict with another PI, they should explain this in the cover letter and this information may be taken into consideration by the assigned editor.

Manuscript revision and re-submission

There are four basic editorial decisions: Accept, Minor Revision, Reject with a possibility of submission of a new version, and Reject. A Reject decision is definitive and authors may not submit a new version of the manuscript to EMI/EMIR. A Reject with a possibility of submission of a new version requires a major re-write of the manuscript and/or inclusion of significant new data, and thus the creation of a new manuscript, which will thus be asigned a new submission date. A Minor Revision decision implies that the paper can in principle attain the required standard of the Journal without major change. Editors may or may not have a revised manuscript reviewed (generally, by the original reviewers), in order to ascertain whether changes to the original manuscript adequately respond to the criticisms. If changes made do not result in a paper of the required standard, the revised manuscript will be definitively rejected; iterative improvements are not permitted. If a revised manuscript is accepted, the original submission date will be retained.

If any part of a study submitted to EMI/EMIR is resubmitted at a later date, it must be sent to the same handling editor, noting the EM number of the previous version of the manuscript.

Files of re-submitted manuscripts must be supplied editable formats, such as Word, for text and tables (authors should avoid embedding non-editable displays in their texts), and EPS or TIFF formats for figures. Submitted manuscripts containing non-editable files will be unsubmitted and authors will experience unnecessary delays in publication of their papers.

Accepted Manuscripts

Copyright Assignment

Authors submitting a paper do so on the understanding that the work and its essential substance have not been published before and is not being considered for publication elsewhere. The submission of the manuscript by the authors means that the authors automatically agree to assign exclusive copyright to Wiley Blackwell if and when the manuscript is accepted for publication. The work shall not be published elsewhere in any language without the written consent of the publisher. The articles published in this journal are protected by copyright, which covers translation rights and the exclusive right to reproduce and distribute all of the articles printed in the journal. No material published in the journal may be stored on microfilm or videocassettes or in electronic database and the like or reproduced photographically without the prior written permission of the publisher.

Authors will be required to sign a Copyright Transfer Agreement (CTA) for all papers accepted for publication. Signature of the CTA is a condition of publication and papers will not be passed for production unless a signed form has been received. Please note that signature of the Copyright Transfer Agreement does not affect ownership of copyright in the material. (Government employees need to complete the Author Warranty sections, although copyright in such cases does not need to be assigned). After submission authors will retain the right to publish their paper in various medium/circumstances

For questions concerning copyright, please visit Copyright FAQ.

Colour Work Agreement Form

Once a manuscript is accepted, authors will be required to complete and return a Colour Work Agreement form, if the manuscript contains colour displays. This form can be downloaded as a pdf here.

Please post the completed forms back to the Customer Services at:

Customer Services (OPI)
John Wiley & Sons Ltd, European Distribution Centre
New Era Estate
Oldlands Way
Bognor Regis
West Sussex
PO22 9NQ


Page charges

No page charges will be levied on papers published in the normal way.

Colour displays

Authors pay the full cost of reproduction of their colour artwork. Exceptionally, if the authors cannot meet these charges, and the editors feel that colour figures are essential for a manuscript, then it may be possible to waive part or all of these charges.


A PDF offprint of the online published article will be provided free of charge, and may be distributed subject to the Publisher's terms and conditions. The electronic offprint is sent to the corresponding author, unless advised otherwise; therefore please ensure that the name, address and e-mail of the receiving author are clearly indicated on the manuscript title page. Paper offprints of the printed published article may be purchased if ordered via the method stipulated on the instructions that accompany the proofs. Printed offprints are posted to the correspondence address given for the paper unless a different address is specified when ordered. Note that it is not uncommon for printed offprints to take up to eight weeks to arrive after publication of the journal.

Open Access

If your paper is accepted, the author identified as the formal corresponding author for the paper will receive an email prompting them to login into Author Services; where via the Wiley Author Licensing Service (WALS) they will be able to complete the license agreement on behalf of all authors on the paper.

For authors signing the copyright transfer agreement

If the OnlineOpen option is not selected the corresponding author will be presented with the copyright transfer agreement (CTA) to sign. The terms and conditions of the CTA can be previewed in the samples associated with the Copyright FAQs below:

CTA Terms and Conditions

For authors choosing OnlineOpen

If the OnlineOpen option is selected the corresponding author will have a choice of the following Creative Commons License Open Access Agreements (OAA):

Creative Commons Attribution License OAA
Creative Commons Attribution Non-Commercial License OAA
Creative Commons Attribution Non-Commercial -NoDerivs License OAA

To preview the terms and conditions of these open access agreements please visit the Copyright FAQs hosted on Wiley Author Services and visit

If you select the OnlineOpen option and your research is funded by The Wellcome Trust and members of the Research Councils UK (RCUK) or the Austrian Science Fund (FWF) you will be given the opportunity to publish your article under a CC-BY license supporting you in complying with your Funder requirements. For more information on this policy and the Journal’s compliant self-archiving policy please visit:

Referrals to the Open Access Journal MicrobiologyOpen

This journal works together with Wiley’s open access journal, MicrobiologyOpen, to enable rapid publication of good quality research that is unable to be accepted for publication by our journal. Authors will be offered the option of having the paper, along with any related peer reviews, automatically transferred for consideration by the Editor of MicrobiologyOpen. Authors will not need to reformat or rewrite their manuscript at this stage, and publication decisions will be made a short time after the transfer takes place. The Editor of MicrobiologyOpen will accept submissions that report well-conducted research which reaches the standard acceptable for publication. The journal seeks to publish research, pure or applied, that furthers our understanding of microbial interactions and microbial processes. MicrobiologyOpen is compliant with open access mandates and will facilitate wide dissemination of your research findings, while continuing to uphold the Wiley tradition of publishing excellence. Accepted papers can be published rapidly, typically within 15 days of acceptance. MicrobiologyOpen is a Wiley open access journal and article publication fees apply. For more information, please go to


Accepted manuscripts are transmitted directly to the Production Office, which deals with all enquiries related to publication. Wiley Blackwell's Author Services enables authors to track their article through the production process to publication online and in print, and to choose to receive automated e-mails at key stages of production, so they don't need to contact the production editor to check on progress. The author will receive an e-mail with a unique link that enables them to register and have their article automatically added to the system. Please ensure that a correct, regularly accessed e-mail address is provided when submitting the manuscript. Visit for more details on online production tracking and for a wealth of resources including FAQs and tips on article preparation, submission and more.


Page proofs will be despatched via e-mail notification of a link with a downloadable Acrobat PDF file, about 4 weeks after acceptance of papers, and should be corrected and returned within 3 days of receipt. Only corrections and essential changes can be made at this stage. The cost of any extensive changes will be charged to the authors. The Journal reserves the right to make minor modifications to manuscripts that do not conform to accepted standards. Such alterations will always be submitted to the authors for approval at the proof stage. Online publication will normally be within 2 weeks of receipt of corrected proofs by the production office.

Accepted Articles

'Accepted Articles' have been accepted for publication and undergone full peer review but have not been through the copyediting, typesetting, pagination and proofreading process. Accepted Articles are published online a few days after final acceptance, appear in PDF format only, are given a Digital Object Identifier (DOI), which allows them to be cited and tracked, and are indexed by PubMed. A completed copyright form is required before a manuscript can be processed as an Accepted Article.

Early View

Both EMI and EMIR are covered by Wiley Blackwell's Early View service. Early View articles are complete full-text articles published online in advance of their publication in a printed issue. Articles are therefore available as soon as they are ready, rather than having to wait for the next scheduled print issue. Early View articles are complete and final. They have been fully reviewed, revised and edited for publication, and the authors' final corrections have been incorporated. Because they are in final form, no changes can be made after online publication. The nature of Early View articles means that they do not yet have volume, issue or page numbers, so Early View articles cannot be cited in the traditional way. They are therefore given a Digital Object Identifier (DOI), which allows the article to be cited and tracked before it is allocated to an issue. After print publication, the DOI remains valid and can continue to be used to cite and access the article. More information about DOIs can be found at

Peer Access to Data and Materials

Data that is integral to the paper must be made available in such a way as to enable readers to replicate, verify and build upon the conclusions published in the paper. Any restriction on the availability of this data must be disclosed at the time of submission. Data may be included as part of the main article where practical.

We recommend that data for which public repositories are widely used, and are accessible to all, should be deposited in such a repository prior to publication. The appropriate linking details and identifier(s) should then be included in the publication and where possible the repository, to facilitate linking between the journal article and the data. If such a repository does not exist, data should be included as supporting information to the published paper or authors should agree to make their data available upon reasonable request.

Distribution of Strains and Experimental Materials

In accordance with good scientific practice, and the need for important findings to be independently confirmed, the publication of an article in EMI or EMIR is subject to the understanding that authors will distribute freely any strains, clones, antibodies or other reagents not readily available described therein, for use in academic research.

Sequence data

Any nucleotide sequence data reported or referred to in a submitted manuscript must be accessible to reviewers (genbank now offers for certain genome, transcriptome or ptoteome databases a reviewer accession via temporary password) in one of the three major collaborative databases-DDBJ/EMBL/GenBank-which exchange data on a daily basis. If the manuscript is subsequently accepted and published, such data must become immediately available to the scientific community. The suggested wording for referring to accession number information is: These sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession number U12345. Addresses are as follows:

DNA Data Bank of Japan
Center for Information Biology
National Institute of Genetics
Mishima, Shizuoka 411
Tel: +81 559 81 6853
Fax: +81 559 81 6849
email: (for data submissions)

EMBL Nucleotide Sequence Submissions
European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge, CB10 1SD
Tel: +44 1223 494400
Fax: +44 1223 494472

National Center for Biotechnology Information
National Library of Medicine
Bldg. 38A, Rm 8N-803
Bethesda, MD 20894
Tel: +1 301 496 2475
Fax: +1 301 480 9241

Functional genomics data sets
Where possible, authors should submit functional genomics primary data sets to public data bases, such as the Gene Expression Omnibus (GEO), for micro-array data:

National Center for Biotechnology Information
National Library of Medicine
Bethesda, MD 20894