Instructions to Authors

(revised March 2025)

1. Aims and Scope

Microbes and Environments (M&E) is an international, peer-reviewed and fully open-access journal published quarterly in an electronic version by Japanese Society of Microbial Ecology (JSME), Japanese Society of Soil Microbiology (JSSM), Taiwan Society of Microbial Ecology (TSME), Japanese Society of Plant Microbe Interactions (JSPMI) and Japanese Society for Extremophiles (JSE). Publication of M&E is open to members and non-members of JSME, JSSM, TSME, JSPMI, and JSE. M&E accepts articles related to cultured and non-cultured forms of any type of microorganism: Bacteria, archaea, fungi, yeasts, protists, algae and viruses in forms of Regular Papers, Short Communications, Reviews, Minireviews and Research Highlights (please also see the scope of M&E on the “About This Journal” page). The journal’s mission is to contribute primarily to the improvement of microbial ecology and environmental microbiology, through the publication of high-quality research results. M&E is broadly international both in its perspective and the country of origin of the authors it publishes. All articles receive a full and extensive peer review by recognized experts from the subject of research field.

2. Article Types

M&E publishes a variety of different article types. For each Article Type, authors are required to organize their content using the following formats. 

*¹ Word limit includes main body of the manuscript only (not including Title page, Abstract, Figure legends, Tables and References). 

*² Results and Discussion sections can be combined, if appropriate.

3. Manuscript Preparation

3.1 Editorial Standard

M&E requires that all manuscripts be prepared in accordance with the “Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly work in Medical Journals” as published by the International Committee of Medical Journal Editors (ICMJE Recommendations).

3.2 Language

Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language or engage a professional language editing service for help.

3.3 General Formatting

Manuscripts should be written in clear and simple English using size 12 with normal font (e.g. Times New Roman). All text shouldbe double-spaced with wide margin. All pages must be numbered consecutively, starting with the title page. The lines of the text should be numbered to aid the reviewers. 

3.4 File size and format

The total size of the uploaded files should be within 20 MB. Manuscript files can be in the following formats: 

• Main text: Microsoft Word (DOC, DOCX) or RTF
• Tables: Microsoft Word (DOC or DOCX). Excel is also acceptable.
• Figures: PPT (PowerPoint), EPS or TIFF

The unsatisfying manuscript may be editorially rejected and returned to the corresponding author.

3.5 Reproduction/Reuse of Copyright Material

The corresponding author is responsible for obtaining permission from both the original author(s) and the publishers (i.e., the copyright owner) to reproduce or modify figures and tables, and to reproduce text from previous publications. Statements indicating that the material is being reprinted with permission must be included in the relevant figure legend or table footnote of the manuscript. Reprinted text must be enclosed in quotation marks, and the permission statement must be included as running text or indicated parenthetically.

4. Manuscript Organization

The organization of the manuscript should be in the following order: Title Page; Abstract and key words; Main Text; Acknowledgements; References; Tables and footnotes; Figure Legends; Figures; Supplemental Files

Each figure and Supplemental Files must be saved in a separate file.

4.1 Title Page

The title page should be included as the first page of the manuscript file, and must include the following information:

• Article Title: The title should be as concise and informative as possible.  No abbreviations except for gene names or in common use.
• Topic(s) of the paper (see scope of M&E)
• Running headline: The abbreviated running headline should not exceed 40 characters.
• and affiliation(s) and address: Place an asterisk after the name of the corresponding author. Multiple authors with different addresses must indicate their respective addresses with numerals.
• The E-mail address and Tel. numbers of the author to whom all correspondence is to be addressed should also appear as a footnote.

4.2 Abstract and Key Words

The Abstract should be informative and completely self-explanatory, and briefly present the topic, major findings, and conclusions. See Article Type described above for word limits. The Abstract should be written in the past tense. Abbreviations and citations of literature should be avoided. Immediately following the Abstract, 2 to 5 Keywords should be given. 

4.3 Main Text

The arrangement of manuscripts for Regular Papers should be in the following order: Title, Author’s name and Address, Abstract, Keywords, Introduction, Materials and Methods, Results, Discussion, Acknowledgements, References, Tables, and Figure legends. Use section headings (e.g. Introduction, Materials and Methods, Results etc.) in the main text. Short Communications should include the same components as Regular Papers, but without section headings. Use of footnotes is not recommended, but abbreviations, when necessary, can be defined in a single footnote inserted in the first page of the text. Define abbreviations and acronyms not listed in the section “Common abbreviation” below when they first appear; thereafter directly use them. No need to define an abbreviation unless the term appears at least twice in the text. When appropriate, the Results and Discussion sections can be combined.

4.4 Acknowledgements (optional)

After the Discussion section, those who do not qualify for an authorship may be acknowledged individually or together as a group under a single heading with “Acknowledgements”. Examples of activities that do not qualify a contributor for authorship are acquisition of funding, general supervision of a research group, or general administrative support and writing assistance, technical editing, language editing, and proofreading.  Personal acknowledgements should only be made with the permission of the persons named.

4.5 Conflicts of Interest and Sources of Funding

If a manuscript concerns a commercial product, the manufacturer’s name must be indicated in the Materials and Methods section or elsewhere in the text, as appropriate, in an obvious manner.

Conflicts of Interest: 

All authors are expected to disclose (over the 3 years prior to submission), n the manuscript, any commercial affiliations as well as consultancies, stock or equity interests, and patent licensing arrangements that could be considered to pose a conflict of interest regarding the submitted manuscript (inclusion of a company name in the author address lines of the manuscript does not constitute disclosure). Authors must provide, in the Conflicts of Interest section, a statement disclosing financial or other relationships that are relevant to the study. Examples of potentially conflicting interests that should be disclosed include relationships that might detract from an author’s objectivity in presentation of study results and interests whose value would be enhanced by the results presented. 

Any possible COI related to the study presented in the manuscript must be disclosed before the Reference section under the heading “Conflicts of Interest” using the following examples: 

“A (author name) received honoraria from Z (entity name); B holds an advisory role in Y; C is an employee of Company X.”

If there are no COIs, the authors should state “The authors declare that there are no conflicts of interest”.

Sources of Funding: 

All funding sources for the project, institutional and corporate, should be credited in this section.　

4.6 References

Style and Format:

• List the references immediately after the main text. 
• The authors are responsible for the accuracy of their references. 
• Including AI-generated material as the primary source in the reference is not allowed.
• Only full articles that have been published or are ‘in press’ can be included in the reference list. Unpublished or submitted papers should be referred to as such (e.g., M. E. Smith, unpublished), or as a personal communication in the text. 
• In the text, references should be inserted in parentheses in date order, as follows: (McIntosh, 1996; Kamagata et al., 2000).
• The reference list should be in alphabetical order by first author. 
• If the first author is the same, arrange the citations by year of publication. 
• If both first author and published year are same, arrange them in alphabetical order of second (or third, fourth and fifth) author. 
• The references should not include personal communications, unpublished data or manuscripts in preparation (can be mentioned parenthetically in the text).
• Journal names should be abbreviated according to the Index Medicus. 
• Each citation must be complete: Do not use ibid., idem., etc. 
• Articles written by more than 8 authors should be edited to show the first 6 authors and ‘et al’. 

Acceptable styles are shown in the examples below. 

Examples:

Journal Article References:

Masuda, Y., Itoh, H., Shiratori, Y., Isobe, K., Otsuka, S., and Senoo, K. (2017) Predominant but previously-overlooked prokaryotic drivers of reductive nitrogen transformation in paddy soils, revealed by metatranscriptomics. Microbes Environ 32: 180–183.

Adam, P.S., Borrel, G., Brochier-Armanet, C., and Gribaldo, S. (2017) The growing tree of archaea: New perspectives on their diversity, evolution and ecology. ISME J 11: 2407–2425.

Kobayashi, S., Hira, D., Yoshida, K., Toyofuku, M., Shida, Y., Ogasawara, W., et al. (2018) Nitric oxide production from nitrite reduction and hydroxylamine oxidation by copper-containing dissimilatory nitrite reductase (NirK) from the aerobic ammonia-oxidizing archaeon, Nitrososphaera viennensis. Microbes Environ 33: 428–434.

Book/Ebook References:

Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Bernardet, J.-F., and Bowman, J.P. (2006) The genus Flavobacterium. In The Prokaryotes. New York, NY: Springer, pp. 481–531.

Chandler, M., and Mahillon, J. (2002) Insertion sequences revisited. In Mobile DNA II: American Society of Microbiology. Craig, N., Craigie, R., Gellert, M., Lambowitz, A. (eds). Washington, DC: ASM Press, pp. 305–366.

Conference Proceeding References:

Bachvaroff, T. R., Williams, E., Jagus, R. and Place, A. R. (2015) A noncryptic noncanonical multi‐module PKS/NRPS found in dinoflagellates. In Proceedings of the 16th International Conference on Harmful Algae. MacKenzie, A.L. (ed.) Wellington, New Zealand. Cawthron Institute, Nelson, New Zealand and International Society for the Study of Harmful Algae (ISSHA), pp. 101‐104.

Published Dissertation or Thesis References:

Zaikova, E. (2014) Molecular Mechanisms of Host‐Symbiont Recognition in a Highly Specific Sponge‐Archaeal Symbiosis. PhD Thesis, University of British Columbia.

Preprint Article References:

Hampton, S., Rabagliati, H., Sorace, A., and Fletcher-Watson, S. (2017). Autism and bilingualism: A qualitative interview study of parents’ perspectives and experiences. PsyArXiv. https://doi.org/10.31234/osf.io/76xfs

Website References:

Web-sites can be given as references, but only if the information is available without charge to readers. The format for citation is as follows:

Binniger, J., and Allen, J. (2014). General facts about the Gulf of Mexico.URL http://www.epa.gov/gmpo/about/facts.html

In-text Citations:

• For citing patent application or patent pending; …was measured by this new technique (Okabe, S. 24 December 2001, Japan Patent Office).
• For citing abstract of conference; …are important primary colonizers (Tojo, M., et al. 2002. Abstracts for XXV Symposium on Polar Biology. p. 210, Tokyo, in Japanese).

Important notice 1: The style for citing references in the main text changed from vol. 35, issue 1, 2020 in M&E as follows; “…as described previously (Takai et al., 2018; Nunoura et al., 2019).” and “ Takai et al. (2018) described…”.

Important notice 2: M&E is now accepting initial submission in any reference format to ease the submission process for authors. During the peer-review process, a revised/re-submitted manuscript will be required to follow the M&E reference format mentioned above.

4.7 Figures and Tables

Figures and Tables should be numbered with Arabic numerals (e.g. Figure 1, Figure 2, Table 1, Table 2), and must be cited in the text in bold in the order they are cited.

If any copyrighted or previously published material, edited or otherwise, are used in the manuscript, it is the author’s responsibility to obtain the permission from both the original author(s) and publishers (i.e., the copyright owner) prior to making a submission. Also, the authors must cite the source and indicate the permission to use such materials in the corresponding Figure or Table caption, as required by the copyright owner(s). Authors must submit permissions letters from the copyright owner(s) when submitting the manuscript.

Figures

All figures including drawings and photographs should be compact at their intended publication size, and numbered consecutively. Indicate the figure numbers and first-author’s name in the margin. Titles and legends of figures must be typed separately.

• File format: PPT (PowerPoint), EPS or TIFF.
• Resolution: 1,200 dpi for grayscales and color drawings, 300 dpi for photographs.
• File size: <20 MB 
• Give scales in microphotographs: do not report enlargement factors in legends. 
• Figures in 1-column (maximum width ca. 8.3 cm) of the printed page are strongly recommended. The maximum width for a 2-column figure is 17.6 cm.
• In-text citations: Figures should be referred to as ‘Fig. 1’ or ‘Fig. 1, 2 and 3,’ etc. throughout the manuscript. Small panels in each figure may also be referred to as ‘Fig. 1A’ or ‘Fig. 1A, B and C,’ etc.
• Graphs: should be made from finished drawings not requiring additional artwork or typesetting. 
• Photographs: should be glossy and rich in contrast. Give scales in microphotographs: do not report enlargement factors in legends. 

Figure Legends

Authors must list Figure Legends after the References section. Legends should be understandable without reference to the text. 

Tables

• File format: Microsoft Word or RTF as editable files. 
• Each table must be typed on a separate page, and all tables should have titles.
• Table title/caption: should be understandable without reference to the text.
• Abbreviations and footnotes: when necessary, should be defined in table footnotes. 
• The maximum width of a table on the printed page should be 17.6 cm, and thus the author should prepare tables as concisely as possible.

Supplementary Materials

Supplemental material may be posted by M&E for any type of paper. A figure for large phylogenetic tree should be basically supplied as a supplemental material. Any previously published copyrighted material, in any form of media (print or online), is not permitted for posting as supplemental material without obtaining permission from the copyright holder. Supplementary materials are published exactly as they are received and not edited by the journal.

• Recommended File formats: a single PDF file, an Excel file for materials that contain large data sets or raw data, or a video image file. 
• File size: <20 MB 
• Supplemental figures and tables should be referred to as Fig. S1 and Table S1, respectively.
• References related to supplemental material only should not be listed in the References section of an article.
• Material that has been published previously (print or online) is not accepted.
• A figure for large phylogenetic tree should be basically supplied as a supplemental material.

4.8 Data Sharing Statement

M&E strongly encourages that all datasets upon which the conclusions of the manuscript are based should be available to readers. The authors should include a data sharing statement in the manuscript detailing where the data supporting their findings can be found (if applicable). The data sharing statement should indicate the following: available types of data (study protocol, statistical analysis plan, informed consent form, clinical study report, or analytic code); with whom the data are available; types of analyses the authors are willing to share the data; method of requesting the data. For datasets containing clinical data, M&E requires registration of clinical trials in a public trials registry at or before the time of first patient enrollment as a condition of consideration for publication in accordance with the standards set out in the ICMJE recommendations on clinical trial data sharing.

5. Additional Requirements at Submission

5.1 Reporting numerical data

Standard metric units are used for reporting length, weight, and volume. For these units and for molarity, use the prefixes m, μ, n, and p for 10-3, 10-6, 10-9, and 10-12, respectively. Likewise, use the prefix k, M, and G for 103, 106, and 109, respectively. Avoid compound prefixes such as mμ or μμ. Parts per million (ppm) or parts per billion (ppb) may be used when that is the common measure for the science in that field. Units of temperature are presented as follows: 37°C or 310K. When fractions are used to express such units as enzyme activities, it is preferable to use whole units, such as g or min, in the denominator instead of fractional or multiple units, such as μg or 10 min. For example, “pmol min-1” is preferable to “nmol (10 min)-1,” and “μmol (g soil)-1” is preferable to “nmol (μg soil)-1.” It is not preferable to use units in combination with slash; for example, “μmol (g protein)-1min-1” is preferable to “μmol/g protein/min.” Always report numerical data in the applicable SI units. “L” with an uppercase letter should be used for the unit of liter; e.g., mL, μL, and nL. Seconds, minutes, hours, and days should be abbreviated as s, min, h, and d. A single space should be placed between the number and the units, but for the units for temperature (°C and K) and the symbols of “%” and “‰. For the presentation of percentages or ratios of chemicals, “w/w,” “w/v,” “v/v,” or “mol/mol” should be presented in combination with “%” or “:”; e.g., “10% (w/w)” and “25:24:1 (v/v/v)” are appropriate. Representation of data as accurate to more than two significant figures must be justified by presentation of appropriate statistical analysis with indicating sample number as (n=3), etc.

Equations: In mathematical equations, indicate the order of operations clearly by enclosing operations in parentheses, brackets, and braces. No spaces should be placed between “+,” “-,” “×,” “÷,” “?,” “=,” “<,” “>,” “=” “=,” and the symbols and the numbers.

5.2 Common Abbreviations

The following abbreviations can be used in tables and figures without definition: avg (average), concn (concentration), no. (number), OD (optical density), ORF (open reading frame), P (probability), SD (standard deviation), SE (standard error), temp (temperature), sp act (specific activity), tr (trace), U (enzyme unit), vol (volume), vs (versus), wt (weight). In addition to abbreviations for common units (e.g., bp, Da, kb, ppm and rpm) and chemical symbols for the elements, the following common acronyms should be used without definition in the title abstract, text, tables and figures: ATP, ADP, AMP, GTP, etc. (for the respective 52 phosphate of adenosine and other nucleotides); DNA, cDNA, RNA, mRNA, rRNA, etc. (for nucleic acids); ATPase, RNase, etc. (adenosine triphosphatase, ribonuclease, etc.); NAD+ (nicotinamide adenine dinucleotide, oxidized); NADH (nicotinamide adenine dinucleotide, reduced); NADP (nicotinamide adenine dinucleotide phosphate); NADPH (nicotinamide adenine dinucleotide phosphate, reduced); NADP+(nicotinamide adenine dinucleotide phosphate, oxidized); CFU (colony-forming units); MIC (minimum inhibitory concentration); PFU (plaque-forming units); HPLC (high-performance liquid chromatography); PCR (polymerase chain reaction); EDTA (ethylenediaminetetraacetic acid); Tris (tris(hydroxymethyl)aminomethane); and UV (ultraviolet).

5.3 Sequence data

Authors are required to provide accession numbers to the three major collaborative databases-DDBJ/EMBL/GenBank for all nucleic acid sequence data reported in their manuscripts. Sequence data should be available in the reviewing process and publicly available upon publication. The accession number should be included in a separate paragraph at the end of the Materials and Methods section for Regular Papers or at the end of the text for Short Communications.

5.4 Chemical and biochemical nomenclature

The rules and recommendations of the International Union of Pure and Applied Chemistry (IUPAC) will be used for abbreviations of chemical names, and the nomenclature of chemical compounds, enzymes, isotopic compounds, and optically active isomers. Information can be obtained at the Web page <http://www.chem.qmw.ac.uk/iupac/>. Use the EC number when one has been assigned.

5.5 Nomenclature of microorganisms

Binary names consisting of generic and species names (e.g., Bacillus subtilis) must be used. A generic name followed by a specific epithet should be written out in full in the title and at first use in the text, and at first use in each legend and each title of figures and tables. Thereafter, it may be abbreviated to its capitalized initial letter (e.g., B. subtilis). If there are several generic names in the text with the same initial letter, the names should be spelled out at each occurrence. Names of all taxa (phyla, classes, families, genera, species, etc.) are printed in italics and should be italicized. For the bacterial names that have standing in nomenclature, authors should follow the Approved Lists of Bacterial Names (amended edition) (edited by V. B. D. Skerman, V. McGowan and P. H. A. Sneath) and the validation lists published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) (http://ijs.sgmjournals.org/). Information about bacterial nomenclature is also available online at http://www.bacterio.cict.fr/ (List of Prokaryotic Names with Standing in Nomenclature). If there is a need to use a non-valid name of bacteria, the name must be enclosed in quotation marks. Since the classification of fungi is incomplete, it is the responsibility of the author to determine the accepted binomial for a given organism.

5.6 Culture deposition

The Societies encourage authors to deposit studied strains in publicly accessible culture collections (ATCC, DSMZ, JCM, NBRC, etc.) and to refer to the collections and strain numbers in the text. In the case of materials that have been provided by individuals, authors should indicate the laboratory strain designations and the name and address of the donor, as well as the original culture-collection identification-number. WFCC-MIRCEN World Data Centre for Microorganisms (WDCM, http://wdcm.nig.ac.jp/) provides a comprehensive directory of culture collections.

5.7 Using Italic letters

Italic letters should be used for the running headline, and the subheadings. Italic letters should also be used for the followings: Latin names, first three letters of the names of restriction enzymes, names of loci, the Italic letters appropriately presented in IUPAC names, “e.g.,” “i.e.,” “ca.,” “et al.,” “in vitro,” “in vivo,” “in situ,” “in silico,” symbols for expressing probability, “n” for expressing the number of samples, and “g” for expressing the gravitational acceleration. These letters should also be written in Roman Type only when written in the running headline, and the subheadings.

6. Online Manuscript Submission

Manuscripts may only be submitted electronically via the journal’s ScholarOne system.

You need to register before your first submission to M&E. If you have any technical problems or questions related to the electronic submission process or uploading your files, please contact our Support Desk. For other inquiries, please contact ScholarOne Manuscripts Support Desk (Japan): s1-support@kyorin.co.jp

The total size of the uploaded files should be within 20 MB.  

7. Peer Review Process

Articles submitted to M&E operates a single-anonymized peer review process where reviewers know who the authors are, but the reviewer’s identity is not revealed to the authors. Manuscripts that do not adhere to the journal’s requirements may be editorially rejected or returned to the corresponding author for technical revision before undergoing peer review.  A received manuscript is sent to a Senior Editor of the Editorial Board, who is responsible for making a final decision on its acceptability. The Senior Editor will choose an Associate Editor who is in charge of sending the manuscript to at least two referees for criticism and further communication with authors. The editors of M&E will review the peer review comments and make all decisions on the manuscriptpublication, which include acceptance, major or minor revisions, and rejection.  The primary criteria for judging the acceptability of a manuscript are its originality and scientific importance.

7.1 Revised Manuscript

Revised manuscript should be submitted within 3 weeks from the date of prior decision. Otherwise it may be considered withdrawn or treated as a new submission.  Authors must include a detailed point-by-point response letter to the editor(s) and reviewer(s). Revisions must be approved by all authors prior to submission of the revised manuscript.

7.2 Editors and Journal Staff as Authors

Manuscripts submitted by editors, Editorial Board members, or journal staff will follow the same process as outlined above. However, they are excluded from any editorial decision process of their own manuscript and have neither access to that manuscript nor any information about the review process other than what is provided in the editor’s decision letter. Additionally, ScholarOne, the journal’s online submission and peer review system is designed to anonymize a person in other roles (editor/reviewer) from any paper he/she has authored. The manuscript submitted by editors, Editorial Board, and journal staff of M&E should include a statement that declares their personal conflict of interest with the journal.

8. Editorial Policy

8.1 Authorship/Contributorship

All authors listed in the manuscript must meet the following four contribution criteria as defined by the ICMJE Recommendations.

1. Substantial contributions to the conception or design of the research or the acquisition and analysis of data; and
2. Drafting the work or reviewing it critically for important intellectual content; and
3. Final approval of the version to be published; and
4. Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Contributors who do not meet all four criteria above should not be listed as authors. Guest or honorary authorship is strictly prohibited. Those who do not qualify for authorship may be acknowledged individually or together as a group. Any authorship changes such as order, addition, and deletion of authors between the initial manuscript submission and the final decision should be discussed and approved by all authors. Adding, deleting, or changing the author names and their order is not permitted after the acceptance of the manuscript for publication.

8.2 Use of Artificial Intelligence (AI)-Assisted Tools/Technologies

In consonance with the COPE’s position statement, WAME’s recommendations, and ICMJE’s Recommendation, M&E does not allow artificial intelligence (AI)-assisted tools/technologies such as Large Language Models (LLMs), chatbots, or image creators to be listed as author or co-author. The authors (humans) are fully responsible for any materials of the submitted work, including the use of AI-assisted tools or technologies, and should carefully review and edit the result because AI can generate authoritative-sounding output that can be incorrect, incomplete, or biased. Authors should not list AI and AI-assisted technologies as an author or co-author, nor cite AI as an author. Authors (humans) are also responsible for plagiarism including in text and AI-produced images. If AI was used for data collection, analysis, or figure generation, authors should describe this use in the methods. Authors who used AI technology to conduct the study should describe its use in the methods section in sufficient detail to enable replication of the approach. Including the tool used, version, and prompts where applicable. For example, if AI was used for writing assistance, describe this in the acknowledgment section.

8.3 Exclusive Submission

Articles that have been previously published or are being considered for publication in another journal in any language will not be accepted. Submission of a manuscript implies that: the work described has not been previously published; it is not under consideration for publication elsewhere; its publication has been approved by all co-authors. The editors make all decisions on the acceptance of the peer-reviewed manuscripts.

8.4 Redundant or Duplicate Publication

Articles that are being considered for publication in another journal including advanced publications such as “in-press” or “E-pub ahead of print” articles in any language might be regarded as redundant or duplicate publication. The author should notify the editorformally about all submission and the previous reports that could be regarded as redundant or duplicate publication of the same or similar work. Any such material must be referred to and referenced in the new work. Editorial actions should be expected if redundant or duplicate publication is attempted or occurs without such notification. For acceptable secondary publication M&E accepts secondary publications of only those that meet the criteria and conditions described in the ICMJE Recommendations.

8.5 Preprints

M&E will consider publication of manuscripts previously available as preprints on non-commercial servers such as ArXiv, bioRxiv, Jxiv. Also, M&E welcomes the manuscripts that have been previously reviewed by PCI Microbiol, a community of recommenders. It is the responsibility of authors to inform M&E at the time of submission if and where their article has been previously posted, and if the manuscript is accepted for publication in M&E, authors are required to update the preprint with a citation to the final published article that includes the URL along with a link.

8.6 Use of Human Subjects or Animals in Research

The use of human subjects or other animals for research purposes is regulated by the government and individual institutions. Manuscripts containing information related to human or animal use should clearly state in the manuscript that the research has complied with all relevant guidelines and institutional policies. Clinical research included in articles that report on human subjects or materials of human origin, must comply with the provisions of the Declaration of Helsinki.

8.7 Informed Consent

All investigations on human subjects must include a statement that the subject gave informed consent in Acknowledgement section. Patient anonymity should be preserved. Photographs need to be cropped sufficiently to prevent human subjects being recognized (or an eye bar should be used). When isolates are derived from patients in clinical studies, do not identify them by using the patients’ initials, even as part of a strain designation. Change the initials to numerals or use randomly chosen letters. Do not give hospital unit numbers; if a designation is needed, use only the last two digits of the unit. (Note: established designations of some viruses and cell lines, although they consist of initials, are acceptable [e.g., JC virus, BK virus, and HeLa cells].

9. Proofing and Revision after Acceptance

When a manuscript has been accepted, it will undergo a copy-editing process during which the Managing Editor will correct the style and the format of the manuscript, and the English will be proofread. The editing processes usually take about one to two months.  The author should revise the copy-edited manuscript according to the instruction and return the final version of the manuscript to the Managing Editor. The main text should contain the title page, abstract, references, tables, and figure legends, but no figures. Each figure must be saved in a separate file. Galley proofs will be available to the authors for corrections of minor errors such as spelling errors and omitted characters or letters. Any other corrections and revisions after the acceptance of a manuscript are not permitted unless requested by the Editorial Board of M&E. The corresponding author will receive a galley proof for one revision. If the galley proof is not returned before the deadline, the paper may be printed without corrections.

Only after completion of article processing charge payment (see section 12 for detail), the accepted manuscript will proceed to publishing process, except for the case that the corresponding author is a JSME/JSSM/TSME/JSPMI/JSE member.

Press release: Authors who plan for a press release, please contact by email to a production editor during an editing process of your accepted manuscript. Press release day should be set after completing the editing process.

After publication, further changes, or corrections, can only be made in the form of an Erratum which will be hyperlinked to the original article.

10. Errata, Author’s corrections, and Retractions

10.1 Errata

The Erratum section provides a means of correcting errors that occurred during the writing, typing, editing, or printing (e.g., a misspelling, a dropped word or line, or mislabeling in a figure) of a published article. Submit your Errata as a MS Word file directly to Editor-in-Chief via E-mail (microb.environ@microbial-ecology.jp). Please see a recent issue for correct formatting. 

10.2 Authors’ corrections

The Author’s Correction section provides a means of correcting errors of omission (e.g., author names or citations) and errors of a scientific nature that do not alter the overall basic results or conclusions of a published article (e.g., an incorrect unit of measurement or order of magnitude used throughout, contamination of one of numerous cultures, or misidentification of a mutant strain, causing erroneous data for only a portion [noncritical] of the study). Note that the addition of new data is not permitted. Submit your Author’s correction as a MS Word file directly to Editor-in-Chief via E-mail (microb.environ@microbial-ecology.jp). Please see a recent issue for correct formatting.

10.3 Retractions

Retractions are reserved for major errors or breaches of ethics that, for example, may call into question the source of the data or the validity of the results and conclusions of an article. Letters of agreement signed by all of the authors must be supplied as supplemental material (scanned PDF files). The Retraction will be assigned to the Editor-in-Chief of M&E, and the editor who handled the paper will be consulted. If all parties agree to the publication and content of the Retraction, it will be sent to the Editor-in-Chief for publication.

11. Copyright and Agreement for Publication

All the authors of a manuscript must have agreed to its submission and are responsible for its contents, including appropriate citations and acknowledgements. All authors also must have agreed that the corresponding author has authority to act on their behalf in all matters pertaining to publication of the manuscript. If the manuscript is accepted for publication in M&E, a Copyright Transfer Agreement is sent to the corresponding author. The corresponding author will sign this agreement on behalf of all the authors. Unless this agreement is executed, M&E will not publish the article. After signing the Copyright Transfer Agreement, the copyright to articles and their contents published in M&E belongs to the Japanese Society of Microbial Ecology, The Japanese Society of Soil Microbiology, Taiwan Society of Microbial Ecology, Japanese Society of Plant Microbe Interactions and Japanese Society for Extremophiles. However, M&E applies the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) to all works published by the journal. Anyone may download, reuse, copy, reprint, distribute, or modify articles published in the journal, if they cite the original authors and source. The author guarantees that the manuscript will not be published elsewhere in any other language without the written permission of the copyright holders. Copyright for supplemental material remains with the authors, but a license permitting the posting by M&E (Supplementary Material License Agreement) must be signed by the corresponding author.

Special note to US government employees: Material prepared by a US federal government employee as part of the employee’s official duties is in the public domain in the United States. In this case, the employee does not need to have the assignment of copyright transferred.

12. Charges

Upon acceptance of the manuscript, authors are required to pay article processing charges (APC) to cover the cost of publication. The APC is non-refundable. The Corresponding author will receive an e-mail notification regarding the payment of the APC. This will include all necessary instructions for completing the payment process. 

For Members:

For a corresponding author who is a JSME/JSSM/TSME/JSPMI/JSE member, article processing charge is ¥60,000 per article (subject to change, without notice).

For Non-members:

For a nonmember corresponding author, article processing charge is ¥140,000 per article (subject to change, without notice). 

Notes: 

• Only after confirmation of payment of page charges, the accepted article will proceed to publication process.
• Invited articles, Letters to the Editor and Corrections are not subject to publication charges.

For inquiries:

Microbes and Environments Editorial Office

E-mail: microb.environ@microbial-ecology.jp

Copyright (c) 2025 Japanese Society of Microbial Ecology (JSME) / Japanese Society of Soil Microbiology (JSSM) / Taiwan Society of Microbial Ecology (TSME) / Japanese Society of Plant Microbe Interactions (JSPMI) / Japanese Society for Extremophiles (JSE). All rights reserved.