Instructions for Authors (revised May 2015)

1. Editorial Policy

Microbes and Environments (M&E) is an international journal devoted to the publication of original and review articles regarding all aspects of research on microbial ecology and environmental microbiology. It is published quarterly in a printed and an electronic version by Japanese Society of Microbial Ecology (JSME), Japanese Society of Soil Microbiology (JSSM), Taiwan Society of Microbial Ecology (TSME), and Japanese Society of Plant Microbe Interactions (JSPMI). Information about M&E is available online at:

Publication of M&E is open to members and non-members of JSME, JSSM, TSME, and JSPMI. Articles can deal with cultured and non-cultured forms of any type of microorganism: Bacteria, archaea, fungi, yeasts, protozoa, algae and viruses. Topics including ecology of microorganisms in natural and engineered environments, microbial interactions and interrelations with other organisms (symbiosis and pathogenesis for plants, animals, and human), public health, pollution microbiology and microbial biocontrol are encouraged for publication. Articles on microbial physiology, molecular genetics, microbial genomics, microbial biotechnology, food microbiology, microbial systematics and microbiological methods are also considered for publication if they have an ecological perspective. All manuscripts must be submitted electronically via the online manuscript submission and peer review system at the following URL:

The Editorial Office will confirm the editorial style of a submitted manuscript. Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language. The unsatisfying manuscript may be editorially rejected, and returned to the corresponding author. 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 two referees for criticism and further communication with authors. The primary criteria for judging the acceptability of a manuscript are its originality and scientific importance. A manuscript returned for revision should be resubmitted to the Associate Editor within 6 weeks; otherwise it may be considered withdrawn or treated as a new submission. On acceptance of a manuscript, the corresponding author will be sent page proofs by the Managing Editor. To avoid delays in the publication process, the proofs should be checked immediately only for typographical errors and returned to the Editor.

2. Types of Papers Published and Supplemental Material

Four types of papers are published: Full-length Regular Papers, Short Communications, Reviews and Short reviews. Regular Papers and Short Communications must represent a report of original research that has not been published before (except in the form of an abstract or as part of a published lecture, review, or thesis) and is not under consideration for publication elsewhere. Only complete papers will be published; preliminary reports will not be considered. Papers published as Short Communications should not be longer than 4 printed pages (12 pages of double-spaced typescript, including tables and figures). The editors reserve the right to decide what constitutes a short communication. Review articles are summaries of developments in a fast-growing area, addressing any subject within the scope of M&E. Review articles are normally invited. Authors interested in submitting a Review should send the title and a short summary of the proposed topic to the Editor-in-Chief (E-mail: y.kamagata@aist.go.jp) for approval before its submission. Short review articles are invited brief communications concerning topics relevant to the readership of M&E.

Supplemental material may be posted by M&E for any types of paper. M&E encourages that supplemental material intended for posting by M&E be uploaded via the online submission system as a single PDF file or a single video imaging file. The maximum size permitted for an individual file is 10 MB. 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 on-line) is not accepted for posting as supplemental material. Supplemental figures and tables should be referred to as Fig. S1 and Table S1, respectively. A figure for large phylogenetic tree should be basically supplied as a supplemental material.

3. 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. 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.

4. Submission of Manuscripts

Electronic submission to M&E is strongly encouraged via the JST online submission and peer review system at the following URL: http://mc.manuscriptcentral.com/jsme2. Step-by-step instructions for submitting a manuscript via the online submission system are available. Authors in Japan should give their address in Japanese as well as in English.

5. Accepted Manuscripts

When a manuscript has been accepted, the Managing Editor will correct the style and the format of the manuscript, and the English will be proofread. The author should check the corrected manuscript and submit final version of the manuscript according to the instruction of 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.

Saving the text and tables : Microsoft Word is acceptable. Only for a large table, Excel is acceptable.

Saving the figures : Digital images in the PPT (PowerPoint), EPS or TIFF format are acceptable. The minimum resolution is 1,200 dpi for grayscales and color drawings, and 300 dpi for photographs.
The corresponding author will receive a galley proof for one revision. Only printing errors can be corrected. If the galley proof is not returned before the deadline, the paper may be printed without corrections.

6. Advance Publication Online

M&E posts online PDF file versions of manuscripts that have been peer reviewed, accepted and copy edited. Advance publication manuscripts are accessible from the M&E website (https://www.jstage.jst.go.jp/browse/jsme2/advpub/0/_contents). Supplemental material for publication is not posted until the final, typeset article.

7. Preparation of Manuscripts

Manuscripts should be written in clear and simple English and be double-spaced for all text, on 280×210 mm (A4) or 8.5×11 inch sheets. A margin of at least 2 cm should be left around the text, and the right hand margin justification should be switched off. All pages must be numbered consecutively, starting with the title page. The lines of the text should be numbered to aid the reviewers. The arrangement of manuscripts for Regular Papers should be in the following order: Title, Author’s name and Address, Abstract, Key words, Introduction, Materials and Methods, Results, Discussion, Acknowledgements, References, Tables, Figure legends and Figures. 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. The References section of Short Communications should be the same as that of Regular Papers.

Title page : The title page must include the title of the paper, the author’s full name, affiliations, address, the topic(s) of the manuscript (see section 1) and the running headline. The E-mail address, and Tel. and Fax. numbers of the author to whom all correspondence is to be addressed should also appear as a footnote. The title should be as concise and informative as possible. Multiple authors with different addresses must indicate their respective addresses with numerals. Place an asterisk after the name of the corresponding author. The abbreviated running headline should not exceed 40 characters.

Abstract : The Abstract should be informative and completely self-explanatory, and briefly present the topic, major findings, and conclusions. It should not exceed 250 words for a Regular Paper, and 100 words for a Short Communication. The Abstract should be written in the past tense. Abbreviations and citation of literature should be avoided. Immediately following the Abstract, up to 5 Key words should be given.

Main text : Subheadings can be used in the Materials and Methods and Results sections of Regular Papers. 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” when they first appear; thereafter directly use them. No need to define if they are no longer used. When appropriate, the Results and Discussion sections can be combined.

Acknowledgements : After the Discussion section, Acknowledgements should be presented. Personal acknowledgements should only be made with the permission of the persons named.

References : Arrange the citations in alphabetical order by first author, and number consecutively. If first author is 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, forth 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 Chemical Abstracts Service Source Index (CASSI). Each citation must be complete: Do not use ibid., idem., etc.Articles written by more than 10 authors should be edited to show the first three authors and ‘et al’. Acceptable styles are shown in the examples below. For additional styles and formats, consult recent issues of M&E.

  1. Amann, R.I., B.J. Binder, R.J. Olson, S.W. Chisholm, R. Devereux, and D.A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
  2. Okubo, T., T. Tsukui, H. Maita, et al. 2011. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ. 27:306-315.
  3. Ling, F., and W.-T. Liu. 31 October 2011. Impact of chloramination on the development of laboratory-grown biofilms fed with filter-pretreated groundwater. Microbes Environ. doi:10.1264/jsme2.ME12095.
  4. Sambrook, J., and D.W. Russell. 2001. Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory Press, New York.
  5. Hiraishi, A. 1989. Isoprenoid quinone profiles for identifying and classifying microorganisms in the environment, p. 663- 668. In T. Hattori, Y. Ishida, Y. Maruyama, R. Y. Morita, and A. Uchida (ed.), Recent Advances in Microbial Ecology. Japan Scientific Societies Press, Tokyo.
  6. Sako, Y., and N. Nomura. 2001. Genus II, Aeropyrum Sako, Nomura, Uchida, Ishida, Morii, Koga, Hoaki, and Maruyama 1996, 1075VP. p. 183-184. In D.R. Boone, R.W. Castenholz, and G.M. Garity (ed.), Bergey’s Manual of Systematic Bacteriology, 2nd ed., vol. 1. Springer, New York.
  7. Narita, M., T. Sawabe, P. Gacesa, and Y. Ezura. 2003. Rapid PCR detection of Pseudoalteromonas elyakovii, which is the causative bacterium of Laminaria spot-wounded disease in Japan, p. 389-394. In A.R.O. Chapman, R.J. Anderson, V.J. Vreeland, and I.R. Davidson (ed.), Proceedings of the XVIIth International Seaweed Symposium, Oxford University Press, London.
  8. Hu, H.-I. 1993. Kinetic and ecological studies on aerobic submerged biofilter for wastewater treatment. Ph.D. thesis. Yokohama National University, Yokohama, Japan (In Japanese).

Important notice: The style for citing references in the main text changed from vol. 24, issue 1, 2009 in M&E as follows; “...as described previously (3, 6, 9).” and “ Minamisawa et al. (5) described...”.

References to unpublished data, articles submitted for publication, abstracts of conferences, personal communications, letters, company publications, patent applications or patents pending, and web-sites should be made parenthetically in the text, not as footnotes or references. Authors may indicate the URLs of web-sites if they contain data that might supplement the article itself and/or be of interest or assistance to readers. Such addresses should be included parenthetically in the relevant text, not as footnotes or references. The URLs provided in the article must be permanent sites to ensure that the addresses are accurate and the material referred to is indeed there.

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)...

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. 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. 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. 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.

Tables : Each table must be typed on a separate page, and all tables should have titles. Abbreviations, 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.

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)−1 min−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 litter; 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.

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).

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. 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.

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.

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.

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.

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.

8. Errata, Author’s correction, and Retraction

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. Please see a recent issue for correct formatting.

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. Please see a recent issue for correct formatting.

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.

9. Page Charges

Starting January 1st, 2013, authors will be required to pay page charges for accepted manuscripts submitted after the start date. Instead, authors will NOT be charged for English proofreading. For a corresponding author who is a JSME/JSSM/TSME/JSPMI member, page charges are currently ¥4,000 per page. For a nonmember corresponding author, page charges are currently ¥8,000 per page. Color pages will be printed at the author’s expense. The cost of publishing colored figures needs to be borne by the authors. The costs are ¥50,000 for each printed color page. The authors may choose a lower- cost color page only for publication in the online version of M&E. In this publication style, the page in the printed journal is in black and white, however the web page of the online journal is in full-color. The cost is dependent on page arrangement, thus authors are requested to contact the Managing Editor for details. An order form that includes a table showing the cost of reprints will be sent with the proofs to the corresponding author.

10. Permission

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.

11. Conflict-of-Interest

All authors are expected to disclose, in the manuscript submittal letter, 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). Details of the disclosure to the editor will remain confidential. However, it is the responsibility of authors to provide, in the Acknowledgements section, a general 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. All funding sources for the project, institutional and corporate, should be credited in the Acknowledgements section, as described above. In addition, 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.

12. 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 that the research has complied with all relevant guidelines and institutional policies.

13. 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].

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