Every journal has specific policies for the preparation of a manuscript for submission and possible publication. However, a general, common structure is generally shared among publishers and journals. This article serves as a list of suggestions that I consider to be best practices. For this, I merged the instructions to authors of five high-impact journals in my research field (Hydrogeology Journal – Springer; Hydrology and Earth System Sciences – Copernicus; Journal of Hydrology – Elsevier; Water – MDPI; Water Resources Research – Wiley) with some suggestions and remarks of mine.
Title page
The title page includes the following.
- A concise but informative title. Abbreviations and formulae should be avoided if possible.
- Authors’ names. Different research groups use different policies, but my opinion is that the list of authors should include those who contributed significantly to the work. In other words, those whose work has not been essential to obtain the results shouldn’t appear in the author list. Also, different policies might be used for the list, For example, alphabetical order, authors who gave a major contribution first, etc. If the manuscript has been co-authored by a large team, the team name could be indicated in the author list on the title page and then a specific section can be added to provide the names and affiliations of all authors.
- The affiliations and addresses where the work was carried out should be included. Then, present or permanent address could be added if relevant.
- Clear indication of the corresponding author. This is the person who will handle correspondence for the article at all stages of the process (as well as post-publication). This responsibility includes answering any future queries about results, data, methodology, and materials.
Highlights
Highlights are a small collection of short bullet points, usually 3 to 5 points. These are usually less than 90 characters. They should capture the novel results of the research, as well as any innovative methods used.
I recommend to avoid repeating sentences in the abstract. This isn’t as useful and doesn’t really help to attract the readers’ attention.
Index terms and/or keywords
Index terms, which refer to disciplinary lists, or free keywords can be given. These are often used for online searches.
The maximum number of index terms or keywords usually varies according to the journal. Usually, it’s between five and seven.
The best keywords are a good compromise between generic and specific keywords.
Graphical abstract
The inclusion of graphical abstracts depends on the format of the publication. It is usually optional. A graphical abstract should be a high-quality, well-designed, self-explaining picture that summarizes the content of the manuscript.
Preparing a good graphical abstract is not easy. Most of the graphical abstracts are usually obtained by putting together a few pictures from the manuscript, but they do not grasp the attention of potential readers
Abstract
An abstract should be concise. It should be easily understood without needing to read the text.
The abstract is not a summary of the manuscript. It should briefly state the research question, the principal results, and major conclusions.
An abstract should not include references to figures and tables. While citations should be avoided, if the manuscript is heavily dependent on (or directly related to another paper) they might be needed. Abbreviations should not be included without the term in full.
Main Text
Coming to the main body of a manuscript, it is divided into sections and subsections. These are numbered, unless a journal does not permit this.
Figures, tables, and equations will be addressed in a future article.
Introduction
This section should lead the readers to understand the research question. And its relevance in a relatively broad context.
Discussing the general relevance of the work should be avoided. This is often trivial and not important from a scientific point of view. Scientists know the social and economical impacts of their research field, as do most well-educated stakeholders. As such, there is no need to spend time doing this.
Instead, it is crucial to provide a good summary of the state-of-the-art. This way, the open research question can emerge in a clear way.
The introduction should include a clear definition of the research question and of the methods used to address it. This should be done in such a way that the innovative content of the work is apparent.
Materials and methods
The second section is usually devoted to a description of materials and methods used. Here, the authors should provide all necessary information for other researchers to replicate the results.
It is fundamental to clearly and thoroughly state the assumptions and the approximations upon which the work is based. This issue is often underestimated, but is crucial for a proper illustration of scientific results, especially in physical and natural sciences and in engineering.
New methods and protocols should be described in detail. Well-established methods can be briefly described (and appropriately cited). In the latter case, references to textbooks are very appropriate.
For experimental work, it is necessary to describe all the preparation steps and the conditions under which the tests were conducted. For modeling work, all the details about the computer codes and the input parameters should be given.
This may yield a long list of technical information. As such, it is good practice to provide such information with a thorough description in an appendix or as supplementary material.
Generally, many scholars strongly recommend to separate the methods from the results. In other words, the methodologies should be described in a way that is independent of the specific tests that were conducted. This allows to assess the validity of applied methods.
Results
This central section is devoted to a concise, but thorough and precise description and interpretation of the results.
Discussion
Authors should discuss the results and how they can be interpreted under the light of previous studies. They should also discuss the working hypotheses and any assumptions and approximations introduced in the materials and methods section. This is crucial to emphasize the strength and weaknesses of the work.
Conclusions
This last section should highlight how the results are in agreement with the expectations. Namely, if the approach proposed solved the open research question or not. If yes, with which limitations. If not, why.
Some authors tend to use this section also to suggest future research directions, but this often remains wishful thinking, and therefore I would discourage this.
Appendices
Appendices can be very useful to provide details about experimental methods, data, and mathematical manipulations, which could make it difficult to follow the workflow if left in the main text. These can include additional figures, tables, as well as technical and theoretical developments. They might not be critical in supporting the conclusions of the paper, but can provide extra details useful for replicating the results.
References
Different formats are given by different journals for citations and references. The following are only some general remarks.
The list of references should include all papers that are cited in text or in captions of figures and tables. When well-established methods are used, I’d recommend references to the original works where the methods were proposed.
Every reference must be available online or in print, and full details should be given in such a way that everybody can easily find the paper, the book, or the map (online or in libraries). For this, a DOI is strongly encouraged by many journals.
Citations to papers in languages other than English should be limited, and the translation of the title in English should be added if necessary.
There is no common format for web references currently. However, the minimum information is the full URL and the date of access. Further information may be less relevant.
Author contributions
For research articles with several authors, a section specifying individual contributions must be provided. Most journals recommend using the CRediT contributor roles taxonomy.
In particular, the considered steps are the following, in alphabetical order: conceptualization; data curation; formal analysis; funding acquisition; investigation; methodology; project administration; resources; software; supervision; validation; visualization; writing—original draft; writing—review and editing.
A fair description of the roles played by each author is very important, as this is becoming crucial in enrollment procedures in the academic world.
Funding
All sources of funding of the research should be disclosed in a specific section or in the acknowledgements section, depending on the journal’s policy. It is very important to mention the funds received to cover any article processing charges (APC) and/or publication costs. Of course, the sentence “This research received no external funding” can be used if there is nothing to disclose.
Open Science statements (data and software availability)
The increasing role of open science causes many journals to request Open Science statements. These refer mostly to data and computer code availability.
Details about where data supporting the results are stored and how they can be retrieved should be given. Basically, the FAIR (Findability, Accessibility, Interoperability, and Reuse) principles should apply, unless there are strong reasons to keep a dataset confidential.
Very similar principles also apply to software. If original software is developed in the work, it is also very important to provide tutorials, which can help other researchers to use the computer codes.
Acknowledgments
This section should be focused on acknowledging any support not covered by the author contributions or funding sections. This may include administrative and technical support, or acknowledgement of discussions with colleagues who helped to trigger some of the ideas on which the work is based, but whose contributions are not so relevant to include them as authors.
In the future, the use of generative artificial intelligence (GenAI) may become more relevant. I expect that a specific statement along one of two possible paths will be required. Authors may be asked to declare that no GenAI tool has been used in the research and in the preparation of the manuscript; otherwise the authors may need to specify where and how GenAI has been used (writing text; drawing graphics; data collection; analysis and interpretation of the results), and all the details should be given. When GenAI is accepted by publishers and used by authors, it will nevertheless be mandatory to include disclaimers stating that the authors have reviewed and edited the work and take full responsibility for its content.
Acknowledgements could also include information on patents, submission for publication in special issues, submission by invitation, or other such things.
Conflicts of Interest
Authors must identify and declare any personal circumstances or interest that may be perceived as influencing the representation or interpretation of reported research results. Particular care should be given when funding agencies or private companies supported the work and had some roles in the research design and realization—or worse, in address the conclusions.
A statement of absence of conflicts of interest can apply in many cases. Something like, “the authors declare no conflict of interest” would be sufficient.
If some authors are members of the editorial board of the journal to which the manuscript is submitted, this should be explicitly stated.
Supplementary material
Supplementary material can provide details which would make the text excessively long, or which could interrupt the flow.
These are similar to appendices, it is very important for authors to consider what is more appropriate: appendices or supplementary materials?
Remember that supplementary materials are available as additional material in the online version of papers, whereas appendices will be part of the published text. Therefore, appendices should strictly respect the lengths and formats required by a journal, whereas supplementary materials usually allow the author more freedom. Supplementary materials can also include audio and video materials.
All supplementary files should be cited in the manuscript text.
I hope that you have found some useful information that you can use in the preparation of a manuscript.
In the future, we will discuss specific items like figures, tables, equations, measurement units, and significant digits.
Disclaimer
The views, thoughts, and opinions expressed in this article belong solely to the author, and do not necessarily reflect the position or opinions of MDPI or its employees. MDPI takes no responsibility for the content or ideas expressed in this article.
Last updated on: July 25, 2026