Manuscript Preparation

Manuscripts may be rejected without review for several reasons. These include (but are not limited to) inadequate evidence that the method is substantially new and promising, a lack of focus on methods rather than their application, poor preparation, an insufficiently clear and detailed presentation, and a lack of adherence to the following rules for preparation. It is in your own best interest to read the manuscript preparation guidelines carefully and conform to them as closely as possible. It may be helpful to refer to articles previously published in the journal as examples. Questions regarding presentation style may be sent to lomethods@aslo.org.

Basic structure of a manuscript

Manuscripts submitted to the journal may range from descriptions of a new analytical method, to experiments conducted to test an existing method, to metaanalyses of published data, to critical reviews of the methods used in a particular field of study. It should be no surprise that no single structure can fit all possible manuscripts. The following is a general template for constructing your manuscript, and should be followed as closely as possible. Different sections may be emphasized or deemphasized as needed. Please note that the structure of an L&O: Methods manuscript differs somewhat from the familiar sequence of abstract-introduction-methods-results-discussion.

Title page
Contains the title, authors and addresses, and a running head.
Acknowledgments
Contains brief statements about granting agencies, notable aid from individuals and institutions, and potential conflicts of interest.
Abstract
Briefly summarizes the need for a new method, calibration, intercomparison, or metaanalysis; the approach described in the article; and the principal conclusions reached.
Introduction
Establishes the need for a new or improved method and introduces the method in concept. Discusses problems with existing methods that will be evaluated. Establishes need for intercomparison or intercalibration studies. Discusses the current status of a field and establishes the need for a critical review or metaanalytical study.
Materials and Procedures
Provides a detailed set of instructions for implementing the method, including all materials required and all procedures followed. Describes methods used in evaluation and intercalibration or intercomparison studies. Presents data sources, data extraction protocols and analytical methods used in reviews and metaanalyses.
Assessment
Presents the critical experiments or studies that were conducted during methods testing, the results of those studies, including the interpretation of results, and the proof of concept they provide. Presents results and principal conclusions reached in evaluation or comparison studies, and metaanalyses.
Discussion
Discusses the degree to which a new method meets the need defined in the introduction, and argues for the potential for the method to lead to new insight. Discusses the potential impact of comparative studies, evaluations and metaanalyses on the conclusions reached in previously published work.
Comments and recommendations
Comments on particularly critical aspects of new procedures, and suggests adaptations needed for potential applications to other environments. Recommends changes to existing methods.
References
Figures and figure legends
Tables
Multimedia files and other appendices

Manuscript checklist

General style
  1. Line spacing should be set to double-spaced throughout.
  2. All pages are numbered, starting with 1 on the title page. If supported by the program used to prepare the manuscript, the lines on each page of text are also numbered (this facilitates commenting on the manuscript).
  3. The right-hand margin is not justified, there are no hyphenated words at the ends of lines, and the first line of each paragraph is indented.
  4. Sections of the manuscript are not numbered.
  5. The text has been thoroughly proofread and spell-checked with a computer program.
  6. A single serifed font is used (Times New Roman is preferred). The same font is used for mathematical symbols that appear anywhere in the manuscript (text, displayed equations, tables, figures, and figure legends). If special mathematical or Greek symbols not available in that font are needed, the Symbol font is used. Note: superscripts, subscripts, italic, boldface, underline, and changes of font size are not considered to be different fonts, and may be used judiciously as needed for clarity.
  7. All figures and tables are cited in the text and numbered in the order that they appear.
  8. Numbered equations contain no punctuation (commas or periods).
  9. Literature citations in the text are given in chronological followed by alphabetical order and are formatted similarly to these examples: "Campbell (1983, 1987b)" or "(Smith et al. 1984; Karl and Craven 1988; Korobi 1997, 1998)." The References are listed in alphabetical, then chronological order.
  10. The manuscript is written in English and proofread by a person fluent in English.
  11. The manuscript contains only metric and Celsius units, Standard International units preferred. Exponents are used to signify the multiplication or division of units.
  12. Common Latin terms and abbreviations (i.e., e.g., in situ, in vivo, and et al.) are not italicized.
  13. Degrees of freedom for F-tests are given as subscripts (e.g., F3,4, p=0.035); for other statistics they are reported as "df= n" following the test result (e.g., t=3.4, df=20, p=0.02).
Abbreviations and acronyms
  1. Abbreviations are used sparingly. Periods are used after all abbreviations except for metric measures, compass directions, and time (min, h, d, yr).
  2. All acronyms are spelled out upon first use.
  3. Dates are formatted as "Day Month Year" (e.g. 15 June 1999) throughout the text, figures, and tables. If necessary to conserve space, month names are abbreviated to the first 3 letters of the month (no period) and the year is abbreviated to two digits.
  4. State, province, and city names are spelled out in full.
Title page
  1. Only the first word, proper nouns, and acronyms are capitalized.
  2. No abbreviations appear in the title (i.e., use 'iron', not 'Fe'; and 'southeast', not 'SE').
  3. The names of all authors are listed below the title. Footnotes indicate the corresponding author (if different than the first author listed) and author addresses at the time that the work presented in the paper was done. If any addresses have changed since that time, the current address should be listed in a separate footnote. State or province names are spelled out in full and include postal codes. All footnotes on the title page are double-spaced paragraphs and no other footnotes occur anywhere in the manuscript (except when they are unavoidable in tables).
  4. A condensed running head of no more than 40 characters (including spaces) is provided at the bottom of the page.
Acknowledgments
  1. Acknowledgements should be typed double spaced on a separate page. They should contain brief statements about granting agencies, notable aid from individuals and institutions, and potential conflicts of interest. More information on conflicts of interest is provided in the Ethics Statement.
  2. Acknowledgements should name anyone who made a substantial contribution to the work (e.g., data collection, analysis, or writing or editing assistance) but who did not fulfill the authorship criteria, along with their specific contributions.
  3. Because citation in the Acknowledgements may be interpreted as endorsement of the data or conclusions, all persons named in the Acknowledgment section must have given permission to be named.
Abstract
  1. For new methods, the abstract should succinctly summarize the most important properties of the method, and the need it addresses. For evaluation, intercalibration and intercomparison, or metaanalytical studies, the abstract summarizes the approach used to address a problem, the principal conclusions reached, and the impact of those conclusions.
  2. Abstracts are limited to a single paragraph containing no more than 250 words (15 to 17 lines of text in a 12-point Times New Roman font, where the line width is 16.5 cm [=6.5 inches]).
  3. The abstract will be included with the rest of the article in a single PDF file. In addition, it will be presented separately in HTML format (i.e. as a web page). The web page version may not contain special symbols that cannot be displayed directly, and is limited to the ANSI character set. During submission, you will be asked to provide an ANSI-only version of your manuscript abstract. The version of your abstract included with your main manuscript document can include non-ANSI characters.
Introduction
  1. Manuscripts must include a succinct introduction in which the need for a new or improved method is established, and the method is introduced in concept. The introduction may be used to introduce problems with existing methods that will be tested or evaluated; or to establish the need for intercomparison, intercalibration or metaanalytical studies.
Materials and Procedures
  1. Whenever possible and appropriate, manuscripts must present complete instructions for the recommended procedure, analogous to a good cookbook or an easy-to-use laboratory manual. Descriptions of equipment and apparatus must provide a similar level of detail regarding the contruction and operation of the device. Evaluation and intercalibration or intercomparison studies may refer to published descriptions of existing methods, but should describe in reproducible detail how the present study was conducted. Metaanalytical studies should provide details regarding data sources and extraction, and analytical methods used.
    Materials
    "Materials" includes expendible and non-expendible supplies, equipment, and solutions. Materials should be listed as completely as possible, with careful attention to providing enough information to assist new users in adopting the method. Descriptions of needed equipment must note the essential features of the equipment in sufficient detail to allow users to obtain similar devices, or authors may refer to specific commercial products in lieu of a detailed description. The composition of any solutions must be stated explicitly (e.g. grams per liter of a specific compound).
    Procedures
    A stepwise description of all procedures used, divided into sub-procedures as necessary for clarity. Sufficient detail must be provided that a reader may readily adopt and employ the method as described, at least under the conditions described.
  2. Limnology and Oceanography: Methods will not accept manuscripts that describe laboratory and field techniques, equipment, analyses, and other methods, in insufficient detail to be reproduced by others.
Assessment
  1. Typically, authors will present in this section the critical experiments or studies that were conducted in the process of methods testing, the results of those studies, and the proof of concept they provide. The Assessment section may also be used to present the results of re-evaluations of existing methods, intercomparison and intercalibration experiments, and metaanalyses. It should include not only the factual results, but their interpretation and the conclusions reached from them. The assessment should provide the answers to such basic questions as:
    • How do you know that your method really works?
    • How well does your method work?
    • What are the method's strengths and limitations?
    • How difficult or expensive is your method to adopt and use?
    • Does an existing method indeed have a fundamental flaw that needs to be addressed?
    • How well did alternative methods agree?
  2. The methods assessment must address statistical properties of new methods, such as precision, accuracy, and detection limits. These elements are particularly important if a new method is intended to supplant an established procedure.
  3. If a method involves any subjective decision by an operator, or is dependent on operator skill, the manuscript must address explicitly the extent to which operator performance affects the statistical properties of the method. As an example: epifluorescence microscopy is often used to enumerate aquatic bacteria, but usually requires subjective decisions on the part of the individual doing the counting. The extent to which such subjective decisions influence results would need to be measured.
  4. Authors should assess the ease or difficulty of setting up and employing the method.
  5. One effective and persuasive technique to demonstrate the utility of a new method is to apply it successfully to a real-world problem. Authors are not required to demonstrate proof-of-concept through a real-world application, in order to submit a methods manuscript to Limnology and Oceanography: Methods. Demonstrations of the effectiveness of a method under controlled experimental conditions are equally acceptable, provided that the authors can argue successfully that the transition to real-world applications should not present potentially insurmountable obstacles.
Discussion
  1. You should have already described the results and conclusions of any tests and analyses conducted in the Assessment section.
  2. For new methods: Authors should discuss the degree to which a new method meets the need defined in the introduction. Authors must address and establish the potential for the method to lead to new insight, based on the demonstrated properties as tested and described in the assessment section. What does this method offer? Is it a fundamentally new approach, or a breakthrough advance in comparison with the capabilities and properties of alternative approaches? What questions and problems might be addressed that were previously intractable? What new questions are raised? Again, you must make plain to the editors and reviewers why you believe that your work will advance the aquatic sciences. Manuscripts that only report modest improvements upon methods already in use are unlikely to be accepted.
  3. For evaluation, comparison and intercalibration studies, and metaanalyses: Having presented the tests conducted and the conclusions reached, authors should now discuss the impact of their conclusions. How will these conclusions change the interpretation of past work? Have past methodological errors led to any probably-incorrect conclusions? What needs to be changed in future work? Authors must demonstrate that their work will have a substantial impact on the way published work should be interpreted, and on the way future work should be conducted.
Comments and recommendations
  1. Real-world applications will often require modifications to procedures. Authors are encouraged to conclude with brief comments on particularly critical aspects of the procedure, and suggestions for adapting the method to various potential applications or environments. If an existing method has been re-evaluated, authors should make recommendations for any changes to the method for future work.
References
  1. All references cited in the text appear in the References, and vice versa.
  2. The spelling of author(s) name(s), and the year of publication have been double-checked in the text and in the References.
  3. Citations to personal communications, manuscripts in preparation or submitted, unpublished thesis, and other inaccessible sources are not included in the References. These should be used sparingly and are cited parenthetically in the text.
  4. All entries have been verified against original sources; check especially journal titles, accents, diacritical marks, and spelling in languages other than English.
  5. Each citation is complete, according to the following examples:
    Article
    Fenchel, T. 1986. Protozoan filter feeding. Prog. Protistol. 1:65-113.
    Book
    Stumm, W., and J. Morgan. 1981. Aquatic chemistry, 2nd ed. Wiley.
    Chapter
    Codispoti, L. A. 1983. Nitrogen in upwelling systems, p. 513-564. In E. J. Carpenter and G. Capone [eds.], Nitrogen in the marine environment. Academic.
    Thesis
    Kimmance, S. A. 2001. The interactive effect of temperature and food concentration on plankton grazing and growth rates. Ph.D. thesis. Univ. of Liverpool.
  6. Author names may not be presented entirely in capital letters because doing so makes it impossible to properly recognize names like "MacKenzie."
  7. References are abbreviated according to Chemical Abstracts Service Source Index (CASSI) or Biosis.
  8. Issue numbers are not necessary if pagination is continuous through a volume, but may be included in parentheses following the volume number.
  9. We encourage the use of Digital Object Identifers in citations. They should be included in square brackets at the end of the standard citation; e.g. [doi: 10.100/xxxxxxxxxx]. If no volume or page numbers have been assigned to a cited article, as for example in some electronic-only publications, include the DOI in square brackets as the last item in the citation.
Figures and figure legends
  1. The most common problems with figures are:
    1. Text labels are too small when reduced to single column width.
    2. Symbols in figures are too small when reduced to single column width.
    3. Figure resolution is too low.
    4. Color is used unnecessarily.
    Please follow these guidelines to avoid delays in reviewing and publishing your manuscript.
  2. Authors have the option of either embedding figures in the manuscript, or uploading them as separate files. For review purposes only, the preferred method is to embed all figures. If embedded, figures should appear in the order cited and as close as possible to the text in which they are first cited. Figure legends should appear beneath embedded figures. If uploaded separately, figure legends should follow the references in the manuscript. Please take note: figures MUST be uploaded as separate high-resolution files for revised manuscripts. Embedded figures cannot be used to prepare a manuscript for publication.
  3. For preliminary versions of figures used in the review process, we accept black and white, grayscale and color figures in virtually any common graphics file format. All formats are automatically converted to JPG to reduce file size during the review process.
  4. Please note that all materials that pertain to a revised manuscript must be resubmitted even if they have not changed from the original version. For example, if figures and tables are in separate files and not embedded in the main manuscript body, you must upload all such files again for the revised version.
  5. The final versions of figures must adhere to more demanding standards to ensure that figure quality is acceptable for composition. Final versions should be submitted in TIFF format. TIFF images may be saved as compressed or uncompressed files. Uncompressed TIFF files can be very large (e.g. 50 MB); compressed TIFF files are much smaller and usually yield satisfactory results.
  6. There is no surcharge for the use of color versus black and white or grayscale figures. However, color should be used only when it is needed to carry information, and not merely to make figures more colorful. Line art, for example, should rarely need colored lines to be clear and unambiguous. Authors are expected to use color sparingly.
  7. Color figures must be set to CMYK mode, with a minimum resolution of 350 dpi. Line art generally should be set to a higher resolution, e.g. 1200 dpi. Grayscale images should be set to 350 dpi or higher.
  8. Figures are usually displayed on computer screens at 72 dpi. Thus, a figure that appears the "right size" on your computer screen is almost certainly inadequate for publication, though it may be acceptable for the review process.
  9. Use the following to estimate the appropriate pixel dimensions for your figures:
    1. The maximum width for a 1-column figure is 8.9 cm = 3.5 inches = 1225 pixels at 350 dpi resolution.
    2. For a 2-column full-width figure, the maximum width is 18.4 cm = 7.25 inches = 2535 pixels at 350 dpi resolution.
    3. The maximum height of a figure is 23.2 cm = 9.13 inches = 3196 pixels at 350 dpi resolution.
    4. Thus, the maximum size for a figure is 18.4 x 23.2 cm = 7-1/4 x 9-1/8 inches = 2535 x 3196 pixels at 350 dpi resolution. However, some room must be allowed for the figure legend, which will be displayed under the figure.
  10. All figures will be checked during composition, and may undergo image highgrading to adjust resolution, dimensions, color space, and cross-platform compatibility. Figures that do not meet minimum standards must be replaced.
  11. The text labels on the axes of the figures are sized so that they will be of similar size in all figures in the journal, after reduction.
  12. Figures are as simple as possible. For example, there are no grid lines or boxes around symbol definitions, and hatching patterns are solid lines.
  13. All text and numerals on the figures are in the Times New Roman font and are at least 8 points (0.1 inch, 2.8 mm) high after reduction to the size that they will appear in the journal.
  14. Figures are numbered in Arabic numerals in the order of their citation in the text. When panels are labeled (A, B, ...) references to these panels in the text use the same case (A, B, ..., not a, b,...). Panel labels are separated from all lines in the figure. Scale bars are on the figure, not in the figure legend.
  15. Figure legends (one paragraph per figure) explain all panels (A, B, ...). Symbols used in the figure (e.g., circles, squares, ...) are explained in a symbol table on the figure itself, and not in the legend. The symbol table should not be surrounded by a box.
  16. For figures that consist of multiple panels, all panels are displayed on one page, and axis titles are repeated on each panel only if different.
  17. Maps include reference to latitude, longitude and direction (e.g., 42ºN, 18ºW) and are bounded by a fine border. Symbols are legible and reduction has been taken into consideration.
  18. PC or Macintosh versions of Adobe Postscript fonts should be used to label figures. Do not use TrueType fonts or system "bitmap" fonts.
Tables
  1. Authors have the option of either embedding tables in the manuscript, or uploading them as separate files. The preferred method is to embed all tables.
  2. Each table should start on a new page.
  3. Tables are laid out to fit either one or two columns of a standard two-column layout. A one-column table can be up to 60 characters wide, and a two-column table up to 130.
  4. Captions are typed double-spaced as paragraphs at the top of each table.
Multimedia files and other appendices
  1. In addition to color, grayscale and black and white figures, Limnology and Oceanography: Methods will publish multimedia graphic files as appendices to articles, when needed to support an author's presentation of a method. Any such appendices should be used sparingly and only when absolutely required. The Manuscript Submission and Review system allows authors to upload ancillary files during manuscript submission.
  2. In rare cases, other file types may be considered, such as executable programs. Inevitably, some file types will become obsolete over time. The journal's policy is to take a very conservative approach to the use of file formats that seem likely to become obsolete. Authors who wish to include such ancillary files should include a strong argument for their use in the manuscript cover letter.