Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology:
Systematics: Theoretical and practical issues dealing with classification and taxonomy, i.e. (i) new descriptions or revisions of prokaryotic taxa, including descriptions of not-yet cultured taxa in the category Candidatus, (ii) innovative methods for the determination of taxonomical and genealogical relationships, (iii) evaluation of intra-taxon diversity through multidisciplinary approaches, (iv) identification methods.
Applied Microbiology: all aspects of agricultural, industrial, and food microbiology are welcome, including water and wastewater treatment.
Comparative biochemistry and genomics: studies concerning biochemical/metabolic and genomic diversity of cultured as well as yet-uncultured Bacteria and Archaea.
Ecology: descriptions of the microbial diversity in natural and man-made ecosystems; studies quantifying the size, dynamics, and function of microbial populations; innovative research on the interaction of microorganisms with each other and their biotic and abiotic environment.
Types of paper
Minireviews are short review papers, normally not exceeding 6 printed pages, concerned with matters of particular interest and current importance. They must be based on published articles.
Full-length papers should be as concise as possible.
Short communications should not exceed 3 printed pages, including illustrations. The paper should be preceded by a brief summary, and division of the text into various sections may be dispensed with.
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Please see our information pages on Ethics in publishing and Ethical guidelines for journal publication.
Declaration of interest
All authors must disclose any financial and personal relationships with other people or organizations that could inappropriately influence (bias) their work. Examples of potential conflicts of interest include employment, consultancies, stock ownership, honoraria, paid expert testimony, patent applications/registrations, and grants or other funding. If there are no conflicts of interest then please state this: 'Conflicts of interest: none'. More information.
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Changes to authorship
Authors are expected to consider carefully the list and order of authors before submitting their manuscript and provide the definitive list of authors at the time of the original submission. Any addition, deletion or rearrangement of author names in the authorship list should be made only before the manuscript has been accepted and only if approved by the journal Editor. To request such a change, the Editor must receive the following from the corresponding author: (a) the reason for the change in author list and (b) written confirmation (e-mail, letter) from all authors that they agree with the addition, removal or rearrangement. In the case of addition or removal of authors, this includes confirmation from the author being added or removed.
Only in exceptional circumstances will the Editor consider the addition, deletion or rearrangement of authors after the manuscript has been accepted. While the Editor considers the request, publication of the manuscript will be suspended. If the manuscript has already been published in an online issue, any requests approved by the Editor will result in a corrigendum.
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As an author you (or your employer or institution) have certain rights to reuse your work. More information.
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Our online submission system guides you stepwise through the process of entering your article details and uploading your files. The system converts your article files to a single PDF file used in the peer-review process. Editable files (e.g., Word, LaTeX) are required to typeset your article for final publication. All correspondence, including notification of the Editor's decision and requests for revision, is sent by e-mail.
Please submit your article via http://ees.elsevier.com/syapm.
Please submit the names and institutional e-mail addresses of several potential referees. For more details, visit our Support site. Note that the editor retains the sole right to decide whether or not the suggested reviewers are used.
Submitted taxonomic manuscripts must fulfill the following standards:
(i) For any new species of a genus a type strain must be designated, this strain must be deposited in two culture collections in different countries and the accession numbers must be available on the date of the submission. This strain must be comprehensively studied by means of a polyphasic approach, including genetic and phenotypic traits.(ii) It is highly encouraged that more than one single strain is used for descriptions of new genera and/or species. It is of the utmost importance that all strains are equally studied in order to describe intraspecific diversity. In addition, it is necessary to perform DNA-DNA hybridization analysis with the type strain of the species and those strains thought to belong to the same taxon. Alternatively, species identity may be demonstrated by a high degree of similarity in banding patterns after using genomic fingerprinting techniques, such as ERIC-, REP-, BOX-, (GTG)5- and/or RAPD-PCR, which in most cases may show clonality.
(iii) Any taxonomic paper should be accompanied by a fingerprint of the strain/strains used to classify a new taxon by means of methods like RAPD, PFGE, or even whole cell protein profiles. It is obligatory to show that the different strains in use, belonging to the same taxon, are not clonal varieties. The picture of the profiles showing the differences among the isolates of the same taxon should be submitted as supplementary material if they do not provide additional information. In cases of clonality, the fact should be discussed in order to understand the reasons to use multiple identical clones (mainly justifiable if they had been isolated from different samples). Finally, single strain species descriptions should be accompanied by a fingerprint of the new isolate and the closest relative type strains.(iv) The nearly complete 16S rRNA gene sequence (more than 1300 nucleotides) of the type strain of the species must be studied, and deposited in a public repository. The accession number must be given.
(v) The type strains of the most closely related taxa must be simultaneously investigated. It is of the utmost importance that all reference strains are tested with the same methods as the strains of the new taxon. Submissions where the discriminative tests of the reference strains are simply taken from the literature will not be reviewed, unless they are based on results obtained with the same methods. If possible, phenotypic tests should be performed by means of standardized methods.(vi) DNA-DNA hybridization experiments (DDH) must be carried out with the type strain of the new taxon and the closest relatives in any case where the 16S rRNA gene sequence similarities lie above 97%. Alternatively, the editors encourage authors to substitute DDH for average nucleotide identity (ANI) by means of complete pair wise genome comparisons, or by partially sequencing the genomes for about 20% of their length, as recommended in Richter and Rosselló-Móra (2009) PNAS 106 (45), 19126 – 19131.
(vii) It is highly recommended that chemotaxonomic markers are studied. It will be compulsory to show the chemical composition peculiarities for new genera descriptions. Recommended markers are fatty acid profiles, polar lipid composition, quinone types, polyamine patterns, and peptidoglycan type/composition (in particular for the description of Gram-positive bacteria, but also considering that Gram-negative bacteria may differ in their diamino acid composition).(viii) It is compulsory to give the G+C mole % values of the genome of the type strain of the type species of a new genus.
(ix) For other gene sequence analyses (e.g. MLSA), all accession numbers of the generated sequences must be given. In addition, it is compulsory to submit the full alignments used to generate the trees that are to be published. The alignments will be published as online supplementary material.
(x) For any new taxon, the etymology of the proposed name must be provided.(xi) For any new taxon, a protologue indicating the discriminative traits that are characteristic of the taxon should be clearly given. One should avoid linking tables to the protologue. The text should contain all the necessary information that explains how the taxon can be identified.
(xii) The discriminative phenotype should be summarized in a diagnostic table where the most closely related taxa are also indicated.Single strain descriptions. Single strain taxa descriptions are accepted only in exceptional cases. Exceptionalness may result from the relevance of the strain and of the work that has been done with it independently whether it has been published elsewhere. Cases such as full genome sequencing, ecological relevance in their environment, being a result of the isolation of a “candidatus” organism, or very especial metabolisms may be regarded as being of additional interest. Also, if the taxonomic work is done exhaustively and properly, adding new approaches, e.g. MLSA, ANI calculations, completing the phenotypic analyses by means of several chemotaxonomic markers and exhaustive metabolic studies, and any additional information that balances the lack of additional cultures (e.g. phage susceptibility, metabolic properties that are of biotechnological or industrial importance) would also be regarded as exceptionalness. Should this be the case, the authors must send a cover letter to the editor explaining why this new species deserves to be published in the journal, clarifying the uniqueness of the findings and the exceptionality of the new isolate. The manuscript should be submitted as a short communication with a maximum length of 2,000 words, including an abstract and references. Longer manuscripts with single strain descriptions may be allowed if they are accompanied by experimental information that is not necessarily of taxonomic value, but that may complement the taxonomic study (e.g. resistance to heavy metals, unexpected metabolic or genetic properties). Manuscripts not fulfilling the length and the exceptionality requirements will be directly rejected.
Organisation and style of taxonomic papers dealing with new classifications. In order to provide a succinct description of the new taxon, the manuscript should not be divided into sections in the body of the text (except for the Acknowledgements and References). The body of the text (compulsory for single strain species descriptions, and voluntary for other taxonomic papers) should be a continuous article that starts from the introduction to the subject, followed by clarification of the methods and the results obtained, and finishing with the protologue that should include the correct etymology and the strain deposition numbers from two international collections.
Use of word processing software
It is important that the file be saved in the native format of the word processor used. The text should be in single-column format. Keep the layout of the text as simple as possible. Most formatting codes will be removed and replaced on processing the article. In particular, do not use the word processor's options to justify text or to hyphenate words. However, do use bold face, italics, subscripts, superscripts etc. When preparing tables, if you are using a table grid, use only one grid for each individual table and not a grid for each row. If no grid is used, use tabs, not spaces, to align columns. The electronic text should be prepared in a way very similar to that of conventional manuscripts (see also the Guide to Publishing with Elsevier). Note that source files of figures, tables and text graphics will be required whether or not you embed your figures in the text. See also the section on Electronic artwork.
To avoid unnecessary errors you are strongly advised to use the 'spell-check' and 'grammar-check' functions of your word processor.
Subdivision - unnumbered sections
Divide your article into clearly defined sections. Each subsection is given a brief heading. Each heading should appear on its own separate line. Subsections should be used as much as possible when cross-referencing text: refer to the subsection by heading as opposed to simply 'the text'.
State the objectives of the work and provide an adequate background, avoiding a detailed literature survey or a summary of the results. Results
Results should be clear and concise.
This should explore the significance of the results of the work, not repeat them. A combined Results and Discussion section is often appropriate. Avoid extensive citations and discussion of published literature.
The main conclusions of the study may be presented in a short Conclusions section, which may stand alone or form a subsection of a Discussion or Results and Discussion section.
If there is more than one appendix, they should be identified as A, B, etc. Formulae and equations in appendices should be given separate numbering: Eq. (A.1), Eq. (A.2), etc.; in a subsequent appendix, Eq. (B.1) and so on. Similarly for tables and figures: Table A.1; Fig. A.1, etc.
• Title. Concise and informative. Titles are often used in information-retrieval systems. Avoid abbreviations and formulae where possible.
• Author names and affiliations. Please clearly indicate the given name(s) and family name(s) of each author and check that all names are accurately spelled. Present the authors' affiliation addresses (where the actual work was done) below the names. Indicate all affiliations with a lower-case superscript letter immediately after the author's name and in front of the appropriate address. Provide the full postal address of each affiliation, including the country name and, if available, the e-mail address of each author.
• Corresponding author. Clearly indicate who will handle correspondence at all stages of refereeing and publication, also post-publication. Ensure that the e-mail address is given and that contact details are kept up to date by the corresponding author.
• Present/permanent address. If an author has moved since the work described in the article was done, or was visiting at the time, a 'Present address' (or 'Permanent address') may be indicated as a footnote to that author's name. The address at which the author actually did the work must be retained as the main, affiliation address. Superscript Arabic numerals are used for such footnotes.
A concise and factual abstract is required. The abstract should state briefly the purpose of the research, the principal results and major conclusions. An abstract is often presented separately from the article, so it must be able to stand alone. For this reason, References should be avoided, but if essential, then cite the author(s) and year(s). Also, non-standard or uncommon abbreviations should be avoided, but if essential they must be defined at their first mention in the abstract itself.
Although a graphical abstract is optional, its use is encouraged as it draws more attention to the online article. The graphical abstract should summarize the contents of the article in a concise, pictorial form designed to capture the attention of a wide readership. Graphical abstracts should be submitted as a separate file in the online submission system. Image size: Please provide an image with a minimum of 531 × 1328 pixels (h × w) or proportionally more. The image should be readable at a size of 5 × 13 cm using a regular screen resolution of 96 dpi. Preferred file types: TIFF, EPS, PDF or MS Office files. You can view Example Graphical Abstracts on our information site.
Authors can make use of Elsevier's Illustration and Enhancement service to ensure the best presentation of their images and in accordance with all technical requirements: Illustration Service.
Highlights are a short collection of bullet points that convey the core findings of the article. Highlights are optional and should be submitted in a separate editable file in the online submission system. Please use 'Highlights' in the file name and include 3 to 5 bullet points (maximum 85 characters, including spaces, per bullet point). You can view example Highlights on our information site.
Immediately after the abstract, provide a maximum of 6 keywords, using American spelling and avoiding general and plural terms and multiple concepts (avoid, for example, 'and', 'of'). Be sparing with abbreviations: only abbreviations firmly established in the field may be eligible. These keywords will be used for indexing purposes.
You can enrich your article by providing a list of chemical compounds studied in the article. The list of compounds will be used to extract relevant information from the NCBI PubChem Compound database and display it next to the online version of the article on ScienceDirect. You can include up to 10 names of chemical compounds in the article. For each compound, please provide the PubChem CID of the most relevant record as in the following example: Glutamic acid (PubChem CID:611). Please position the list of compounds immediately below the 'Keywords' section. It is strongly recommended to follow the exact text formatting as in the example below:
Chemical compounds studied in this article
Ethylene glycol (PubChem CID: 174); Plitidepsin (PubChem CID: 44152164); Benzalkonium chloride (PubChem CID: 15865)
Define abbreviations that are not standard in this field in a footnote to be placed on the first page of the article. Such abbreviations that are unavoidable in the abstract must be defined at their first mention there, as well as in the footnote. Ensure consistency of abbreviations throughout the article.
Collate acknowledgements in a separate section at the end of the article before the references and do not, therefore, include them on the title page, as a footnote to the title or otherwise. List here those individuals who provided help during the research (e.g., providing language help, writing assistance or proof reading the article, etc.).
List funding sources in this standard way to facilitate compliance to funder's requirements:
Funding: This work was supported by the National Institutes of Health [grant numbers xxxx, yyyy]; the Bill & Melinda Gates Foundation, Seattle, WA [grant number zzzz]; and the United States Institutes of Peace [grant number aaaa].It is not necessary to include detailed descriptions on the program or type of grants and awards. When funding is from a block grant or other resources available to a university, college, or other research institution, submit the name of the institute or organization that provided the funding.
If no funding has been provided for the research, please include the following sentence:This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Nucleotide sequence data
New nucleotide data must be submitted and deposited in the DDBJ/EMBL/GenBank databases and an accession number obtained at the time of submission. Submission to any one of the three collaborating databanks is sufficient to ensure data entry in all. The accession number should be included in the manuscript e.g. as a footnote on the title page. For the evaluation of manuscripts containing gene sequences, sequence data have to be made available to the referees.
Please submit math equations as editable text and not as images. Present simple formulae in line with normal text where possible and use the solidus (/) instead of a horizontal line for small fractional terms, e.g., X/Y. In principle, variables are to be presented in italics. Powers of e are often more conveniently denoted by exp. Number consecutively any equations that have to be displayed separately from the text (if referred to explicitly in the text).
Footnotes should be used sparingly. Number them consecutively throughout the article. Many word processors can build footnotes into the text, and this feature may be used. Otherwise, please indicate the position of footnotes in the text and list the footnotes themselves separately at the end of the article. Do not include footnotes in the Reference list. Electronic artwork
• Make sure you use uniform lettering and sizing of your original artwork.
• Embed the used fonts if the application provides that option.
• Aim to use the following fonts in your illustrations: Arial, Courier, Times New Roman, Symbol, or use fonts that look similar.
• Number the illustrations according to their sequence in the text.
• Use a logical naming convention for your artwork files.
• Provide captions to illustrations separately.
• Size the illustrations close to the desired dimensions of the published version.
• Submit each illustration as a separate file.
A detailed guide on electronic artwork is available.
You are urged to visit this site; some excerpts from the detailed information are given here.
If your electronic artwork is created in a Microsoft Office application (Word, PowerPoint, Excel) then please supply 'as is' in the native document format.
Regardless of the application used other than Microsoft Office, when your electronic artwork is finalized, please 'Save as' or convert the images to one of the following formats (note the resolution requirements for line drawings, halftones, and line/halftone combinations given below):
EPS (or PDF): Vector drawings, embed all used fonts.
TIFF (or JPEG): Color or grayscale photographs (halftones), keep to a minimum of 300 dpi.
TIFF (or JPEG): Bitmapped (pure black & white pixels) line drawings, keep to a minimum of 1000 dpi.
TIFF (or JPEG): Combinations bitmapped line/half-tone (color or grayscale), keep to a minimum of 500 dpi.
Please do not:
• Supply files that are optimized for screen use (e.g., GIF, BMP, PICT, WPG); these typically have a low number of pixels and limited set of colors;
• Supply files that are too low in resolution;
• Submit graphics that are disproportionately large for the content.
Please make sure that artwork files are in an acceptable format (TIFF (or JPEG), EPS (or PDF), or MS Office files) and with the correct resolution. If, together with your accepted article, you submit usable color figures then Elsevier will ensure, at no additional charge, that these figures will appear in color online (e.g., ScienceDirect and other sites) regardless of whether or not these illustrations are reproduced in color in the printed version. For color reproduction in print, you will receive information regarding the costs from Elsevier after receipt of your accepted article. Please indicate your preference for color: in print or online only. Further information on the preparation of electronic artwork.
Elsevier's WebShop offers Illustration Services to authors preparing to submit a manuscript but concerned about the quality of the images accompanying their article. Elsevier's expert illustrators can produce scientific, technical and medical-style images, as well as a full range of charts, tables and graphs. Image 'polishing' is also available, where our illustrators take your image(s) and improve them to a professional standard. Please visit the website to find out more.
Ensure that each illustration has a caption. Supply captions separately, not attached to the figure. A caption should comprise a brief title (not on the figure itself) and a description of the illustration. Keep text in the illustrations themselves to a minimum but explain all symbols and abbreviations used.
Please submit tables as editable text and not as images. Tables can be placed either next to the relevant text in the article, or on separate page(s) at the end. Number tables consecutively in accordance with their appearance in the text and place any table notes below the table body. Be sparing in the use of tables and ensure that the data presented in them do not duplicate results described elsewhere in the article. Please avoid using vertical rules. Citation in text
Please ensure that every reference cited in the text is also present in the reference list (and vice versa). Any references cited in the abstract must be given in full. Unpublished results and personal communications are not recommended in the reference list, but may be mentioned in the text. If these references are included in the reference list they should follow the standard reference style of the journal and should include a substitution of the publication date with either 'Unpublished results' or 'Personal communication'. Citation of a reference as 'in press' implies that the item has been accepted for publication.
Increased discoverability of research and high quality peer review are ensured by online links to the sources cited. In order to allow us to create links to abstracting and indexing services, such as Scopus, CrossRef and PubMed, please ensure that data provided in the references are correct. Please note that incorrect surnames, journal/book titles, publication year and pagination may prevent link creation. When copying references, please be careful as they may already contain errors. Use of the DOI is encouraged.
As a minimum, the full URL should be given and the date when the reference was last accessed. Any further information, if known (DOI, author names, dates, reference to a source publication, etc.), should also be given. Web references can be listed separately (e.g., after the reference list) under a different heading if desired, or can be included in the reference list.
Please ensure that the words 'this issue' are added to any references in the list (and any citations in the text) to other articles in the same Special Issue.
References in the text should be:
_ Mitchell and Catalan  and Baird-Parker 
_...was discussed [6, 2]
_Ventosa et aI.  described
Reference to literature: The List of References should appear in alphabetical order, numbered consecutively with Arabic numbers.
Formats for citations:
 Fell, J.W., Boekhout, T., Fonseca, A., Scorzetti, G., Statzell-Tallman, A. (2000) Biodiversity and systematics of basidiomycetous yeasts as determined by large subunit rDNA D1/D2 domain sequence analysis. Int. J. Syst. Evolution. Microbiol. 50, 1351–1371.
 Fell, J.W., Statzell-Tallman, A. (1998) Cryptococcus Vuillemin. In: Kurtzman, C.P., Fell J.W. (Eds.), The Yeasts, A taxonomic study. Fourth Revised and Enlarged Edition, Elsevier, Amsterdam, pp. 742–767.
 Fry, M. (1987) A detailed characterisation of soils under different fynbos-climate-geology combinations in the southwesern Cape. M.Sc. Thesis, Department of Soil Science, University of Stellenbosch, Stellenbosch, South Africa.
Journal names should be abbreviated according to the List of Title Word Abbreviations.
Elsevier accepts video material and animation sequences to support and enhance your scientific research. Authors who have video or animation files that they wish to submit with their article are strongly encouraged to include links to these within the body of the article. This can be done in the same way as a figure or table by referring to the video or animation content and noting in the body text where it should be placed. All submitted files should be properly labeled so that they directly relate to the video file's content. In order to ensure that your video or animation material is directly usable, please provide the files in one of our recommended file formats with a preferred maximum size of 150 MB. Video and animation files supplied will be published online in the electronic version of your article in Elsevier Web products, including ScienceDirect. Please supply 'stills' with your files: you can choose any frame from the video or animation or make a separate image. These will be used instead of standard icons and will personalize the link to your video data. For more detailed instructions please visit our video instruction pages. Note: since video and animation cannot be embedded in the print version of the journal, please provide text for both the electronic and the print version for the portions of the article that refer to this content.
Supplementary material can support and enhance your scientific research. Supplementary files offer the author additional possibilities to publish supporting applications, high-resolution images, background datasets, sound clips and more. Please note that such items are published online exactly as they are submitted; there is no typesetting involved (supplementary data supplied as an Excel file or as a PowerPoint slide will appear as such online). Please submit the material together with the article and supply a concise and descriptive caption for each file. If you wish to make any changes to supplementary data during any stage of the process, then please make sure to provide an updated file, and do not annotate any corrections on a previous version. Please also make sure to switch off the 'Track Changes' option in any Microsoft Office files as these will appear in the published supplementary file(s). For more detailed instructions please visit our artwork instruction pages.
Elsevier encourages authors to connect articles with external databases, giving readers access to relevant databases that help to build a better understanding of the described research. Please refer to relevant database identifiers using the following format in your article: Database: xxxx (e.g., TAIR: AT1G01020; CCDC: 734053; PDB: 1XFN). More information and a full list of supported databases.
Elsevier encourages and supports authors to share raw data sets underpinning their research publication where appropriate and enables interlinking of articles and data. More information on depositing, sharing and using research data.
Google Maps and KML files
KML (Keyhole Markup Language) files (optional): You can enrich your online articles by providing KML or KMZ files which will be visualized using Google maps. The KML or KMZ files can be uploaded in our online submission system. KML is an XML schema for expressing geographic annotation and visualization within Internet-based Earth browsers. Elsevier will generate Google Maps from the submitted KML files and include these in the article when published online. Submitted KML files will also be available for downloading from your online article on ScienceDirect. More information.
You can enrich your article with visual representations, links and details for those chemical structures that you define as the main chemical compounds described. Please follow the instructions to learn how to do this.
Interactive Phylogenetic Trees
You can enrich your online articles by providing phylogenetic tree data files (optional) in Newick or NeXML format, which will be visualized using the interactive tree viewer embedded within the online article. Using the viewer it will be possible to zoom into certain tree areas, change the tree layout, search within the tree, and collapse/expand tree nodes and branches. Submitted tree files will also be available for downloading from your online article on ScienceDirect. Each tree must be contained in an individual data file before being uploaded separately to the online submission system, via the 'phylogenetic tree data' submission category. Newick files must have the extension .new or .nwk (note that a semicolon is needed to end the tree). Please do not enclose comments in Newick files and also delete any artificial line breaks within the tree data because these will stop the tree from showing. For NeXML, the file extension should be .xml. Please do not enclose comments in the file. Tree data submitted with other file extensions will not be processed. Please make sure that you validate your Newick/NeXML files prior to submission. More information.
The following list will be useful during the final checking of an article prior to sending it to the journal for review. Please consult this Guide for Authors for further details of any item.
Ensure that the following items are present:
One author has been designated as the corresponding author with contact details:
• E-mail address
• Full postal address
All necessary files have been uploaded, and contain:
• All figure captions
• All tables (including title, description, footnotes)
• Manuscript has been 'spell-checked' and 'grammar-checked'
• References are in the correct format for this journal
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