万维提示：
1、投稿方式：在线投稿。
2、期刊网址：https://aem.asm.org/
3、投稿网址：
https://aem.msubmit.net/cgi-bin/main.plex
4、官网邮箱：aem@uni-bayreuth.de（主编）
更多编辑邮箱请查看期刊官网信息。
5、期刊刊期：半月刊，一年出版二十四期。
2021年4月27日星期二
投稿须知【官网信息】
For Authors
SCOPE
Applied and Environmental Microbiology® (AEM) publishes descriptions of all aspects of applied microbial research, basic research on microbial ecology, and research of a genetic and molecular nature that focuses on microbial topics of practical value. Research must address salient microbiological principles, fundamental microbial processes, or basic questions in applied or environmental microbiology. Topics that are considered include microbiology in relation to foods, agriculture, industry, biotechnology, public health, plants, and invertebrates and basic biological properties of bacteria, fungi, algae, protozoa, and other simple eukaryotic organisms as related to microbial ecology. Manuscripts should report new and significant findings that advance the understanding of microbiology and upon which other scientists may build. To best serve its readership, the journal must accept only those papers that are most significant to the field of applied and environmental microbiology. Thus, the editors will reject manuscripts that, while scientifically sound, represent only incremental extensions of other studies, are mainly confirmatory, or do not pursue a question in sufficient depth.
AEM publishes minireviews that provide forward-reaching assessments of topics of current relevance to the diverse sections of the journal. Additional information on minireviews can be found in a subsequent part of these Instructions.
AEM welcomes microbiome studies that address the microbiology and functions of natural or experimental systems. The nature of the microbiome study will determine in which section of the journal it will be published.
The biodegradation section describes novel microbial processes for alteration, removal, or utilization of environmental or anthropogenic chemicals.
Papers in the biotechnology section describe the use and modification of organisms in order to achieve socially beneficial objectives.
The environmental microbiology section covers manuscripts that focus on research related to microorganisms in the environment. This is distinct from the microbial ecology section, which focuses on ecological relationships, such as interactions among organisms, their structure and functional role in an ecosystem, and community-level studies. Thus, the environmental microbiology section features articles that focus on specific organisms in the environment, rather than a whole community, as well as those in which the study is not focused on implied or stated underlying ecological relationships.
The enzymology and protein engineering section covers a broad range of topics relative to microbial catalysis and includes papers describing (i) the structure and function of environmentally or industrially significant proteins and how they can be modified to achieve practical catalytic objectives and (ii) the enzymology or biosynthesis of fungal, algal, and bacterial metabolites or toxins of importance to the environment or to society.
Included in the evolutionary and genomic microbiology section are papers detailing newly described evolutionary processes and evolutionary relationships among microorganisms. Topics include genomic analysis of microorganisms and metagenomic investigation of microbiomes in the environment. (Meta)genome analyses that do not provide significant new insights into the microbiology of the system(s) under study will normally not be acceptable for publication in AEM.
The food microbiology section covers manuscripts dealing with all aspects of food microbiology, including microbial food pathogens, microbial ecology of foods, predictive food microbiology, food fermentations, food spoilage, probiotics, and prebiotics. Manuscripts reporting on the effects of probiotics or prebiotics should provide new insights into the mechanism(s). Manuscripts detailing the occurrence of microbial toxins or microbial metabolites are suitable if the work includes significant information on the microbe and its toxin or metabolite production. This section also includes studies on the gastrointestinal tract microbiome as it relates to molecular toxicology, diet, and nutrition. Molecular assessments of food microbiomes should follow guidelines for the microbial ecology section.
The genetics and molecular biology section includes papers describing genetic organization, expression, mutation, and repair in organisms with environmental or practical significance.
Manuscripts for the geomicrobiology section must emphasize the role of microorganisms in geobiochemical processes in terrestrial or aquatic ecosystems, including subsurface, aquifer, and oceanic environments. Topics include mineralization, the use of inorganic ions in energy metabolism, and growth in extreme environments. Manuscripts focused on geological processes with only marginal links to microbiology will not qualify for AEM.
Invertebrate microbiology manuscripts should address interactions between invertebrates and microorganisms, ranging from commensalism and mutualism to parasitism and pathogenicity. Manuscripts describing work dealing with the metabolites or toxins from animal, plant, or insect cells or the physiology of such cells are not suitable for AEM unless the work concerns a microbial community or individual microorganisms.
New microbiological methods must provide novel avenues to address fundamental biological questions and will be considered for publication in AEM when accompanied by a demonstrated application. Descriptions of the application of previously described technologies, including the cloning, amplification, and expression of "foreign" genes, to a new genus or species of microbe will generally not be considered for independent publication. Manuscripts that describe the construction of engineered strains for innovative process application, development, or enhancement must present results to authenticate the utility, superiority, and uniqueness of such strains.
The microbial ecology section covers a wide range of topics on the ecology of microorganisms, including culture-independent molecular assessments that provide new insights into (i) the structure-function relationships of microorganisms, (ii) the impact of in situ conditions on community structure, or (iii) the effect of changes in microbial community composition on ecosystem function. Phylogenetic assessments that do not provide such insights will normally not be acceptable for publication in AEM.
The physiology section addresses questions about how organisms adapt to changes in their environment, including bioenergetics, stress, starvation, metabolic challenges, and responses to nutritional variation.
The plant microbiology section covers manuscripts dealing with all aspects of plant-microorganism interactions, including symbiotic and rhizosphere bacteria as well as phytopathogenic microorganisms.
The public and environmental health microbiology section is focused primarily on environmentally transmitted microorganisms that affect human health. Environmental health microbiology is a branch of public health concerned with the environmental occurrence of disease-causing microbes and with creating health-supportive environments. Microbes of a zoonotic nature or microbes transmitted through water, soil, or environmental surfaces are of special interest.
AEM is not specialized in the systematics of prokaryotes, but taxonomic papers that describe a new prokaryotic taxon are welcome when phylogenetic or genotypic data are accompanied by a significant amount of information that goes beyond the taxonomic description of the new taxon. Such additional information might include information on the novel ecological, physiological, biotechnological, or evolutionary features of the new taxa. Description of a new taxon should include an amount of information adequate to allow the new taxon to be validated and must include genus and species descriptions, which should be placed at the end of the Discussion section. Likewise, the new taxon must be deposited in two publically available culture collections that are in separate countries. Large data sets of comparative phenotypic and genotypic features (e.g., fatty acid compositions, substrate profiles, sequence similarities) or related species that might be of value for the taxonomic evaluation of the new taxon should normally be placed in supplemental material. The section of the journal in which such a paper will be placed will depend on the nature of the new taxon and the environment from which it was isolated.
ASM publishes a number of different journals covering various aspects of the field of microbiology. Each journal has a prescribed scope which must be considered in determining the most appropriate journal for each manuscript. The following guidelines may be of assistance.
(i) AEM will consider manuscripts describing properties of enzymes and proteins that are produced by either wild-type or genetically engineered microorganisms and that are significant or have potential significance in industrial or environmental settings. Studies dealing with basic biological phenomena of enzymes or proteins or in which enzymes have been used in investigations of basic biological functions are more appropriate for the Journal of Bacteriology®.
(ii) AEM will consider papers which describe the use of antimicrobial agents as tools for elucidating aspects of applied and environmental microbiology. Other papers dealing with antimicrobial agents, including manuscripts dealing with the biosynthesis and metabolism of such agents, are more appropriate for Antimicrobial Agents and Chemotherapy®.
(iii) AEM will consider manuscripts that concern bacteriophages or other viruses in relation to the environment, public health, or industrial microbiology. Papers that primarily concern attachment and intracellular replication of viruses, virus interactions with host metabolism, virus structure, or virus genomics are more appropriate for the Journal of Virology®.
(iv) Manuscripts dealing with the immune system or with topics of basic medical interest or oral microbiology are more appropriate for Infection and Immunity®. Reports of clinical investigations and environmental biology applied to hospitals should be submitted to the Journal of Clinical Microbiology®.
(v) AEM and mSphere® accept manuscripts on population dynamics and the ecology of eukaryotic microbes. Studies of microbial communities and of microbial populations with identified economic or ecological significance, e.g., plant pathogens or symbionts, are usually more appropriate for AEM.
(vi) Manuscripts dealing with the purification and characterization of enzymes or cloning of genes that have already been extensively described for other organisms will be considered for publication only if they offer experimentally supported new insights into the biological role, properties, or applications of these enzymes. Descriptions of genes or enzymes that differ only in minor ways from the prototypes are not suitable for AEM.
Questions about these guidelines may be directed to the editor in chief of the journal being considered.
If transfer to another ASM journal is recommended by an editor, the corresponding author will be contacted.
Note that a manuscript rejected by one ASM journal on scientific grounds or on the basis of its general suitability for publication is considered rejected by all other ASM journals.
SUBMISSION, REVIEW, AND PUBLICATION PROCESSES
Initial Submissions
For initial submissions, AEM welcomes papers in any format ("format-neutral submission"). At this stage, authors are encouraged to upload a single PDF that incorporates the full text, tables, and figures. The reference style, the arrangement of sections of the paper, and other formatting issues are at the discretion of the author. However, to assist the reviewers, manuscript pages should have continuous line numbers and page numbers. (For revised submissions and resubmissions, formatting guidelines are described in detail below.)
Submission Process
All submissions to AEM must be made electronically via the eJournalPress (eJP) online submission and peer review system at the following URL: https://aem.msubmit.net/cgi-bin/main.plex. (E-mailed submissions will not be accepted.) First-time users must create an Author account, which may be used for submitting to all ASM journals. Instructions for creating an Author account are available at the above URL via the "help for authors" link, and step-by-step instructions for submitting a manuscript via eJP are also available through the same link on the log-in screen or on the account holder's home page. Information on file types acceptable for electronic submission can be found under the Files heading in the help for authors screen.
Review Process
All manuscripts are considered to be confidential and are reviewed by the editors, members of the editorial board, or qualified ad hoc reviewers.
To expedite the review process, authors must recommend at least three reviewers who have expertise in the field, who are not members of their institution(s), who have not recently been associated with their laboratory(ies), and who could not otherwise be considered to pose a conflict of interest regarding the submitted manuscript. Impersonation of another individual during the review process is considered serious misconduct. Please provide, where indicated on the submission form, contact information for suggested reviewers who are not editorial board members.
To facilitate the review, copies of in-press and submitted manuscripts that are important for judgment of the present manuscript should be included as Miscellaneous Files Not for Publication.
When a manuscript is submitted to the journal, it is given a control number (e.g., AEM00123-20) and assigned to one of the editors. (Always refer to this control number in communications with the editor and the Journals Department.) From there it is assigned to at least two independent experts for peer review. A single-blind review, where authors’ identities are known to reviewers, is applied. It is the responsibility of the corresponding author to inform the coauthors of the manuscript's status throughout the submission, review, and publication processes. The reviewers operate under strict guidelines set forth in "Reviewer Guidelines" (https://journals.asm.org/content/reviewer-guidelines) and are expected to complete their reviews expeditiously.
The corresponding author is notified, generally within 4 to 6 weeks after submission, of the editor's decision to accept, reject, or require modification. When modification is requested, the corresponding author must either submit the modified version within 45 days or withdraw the manuscript. A point-by-point response to all of the reviews must be uploaded as a separate Response to Reviewer Comments file. Additionally, a Marked Up Manuscript file (without figures) highlighting all of the changes from the original manuscript submission must be uploaded as a separate file. For the benefit of editors and reviewers assessing revisions, all changes in this file should be highlighted, no matter how minor. Please note that a manuscript may not necessarily be processed editorially until a version with all changes noted has been submitted.
Manuscripts that have been rejected with the option to resubmit, or withdrawn after being returned for modification, may be resubmitted to the same ASM journal if the major criticisms have been addressed. A manuscript rejected on scientific grounds or on the basis of its general suitability for publication by one ASM journal, with the exception of mBio® (see below), is considered rejected by all other ASM journals. A manuscript rejected solely on the basis of scope may be resubmitted to a more appropriate ASM journal.
The cover letter of every resubmitted manuscript must state that the manuscript is a resubmission, and the former manuscript control number must be provided. A point-by-point response to the review(s) must be uploaded as a separate file (identified as such), and a copy of the revised manuscript tracking the changes must be included as a Marked Up Manuscript. Manuscripts resubmitted to the same journal are normally handled by the original editor. Manuscripts rejected with the option to resubmit may be resubmitted only once unless permission has been obtained from the original editor or from the editor in chief.
For manuscripts rejected from mBio and resubmitted to AEM, the author is not required to disclose the details of the previous submission. It is the author's option whether to disclose the mBio submission in the cover letter and/or provide a response to the mBio reviews.
Manuscripts Reviewed by Non-ASM Journals
AEM offers expedited review for manuscripts previously reviewed by non-ASM journals. Such submissions will receive a final decision without review if possible, or they may be sent for peer or editorial review. You may send a presubmission inquiry to the editor in chief if you wish to discuss whether your manuscript is a good candidate for this submission track. To submit your manuscript to AEM, please include the following items in your submission:
A cover letter declaring the previous submission and requesting expedited review
A PDF file of the entire previously submitted manuscript uploaded as a Miscellaneous File Not for Publication
A Response to Reviewer Comments file containing the previous decision letter(s), all previous reviews, any manuscript correspondence, and your point-by-point response to the reviews, including page numbers where changes have been made
A tracked-changes file showing the revisions made, uploaded as a Marked Up Manuscript file
Notification of Acceptance
When an editor has decided that a manuscript is acceptable for publication on the basis of scientific merit, the author and the Journals Department are notified. A PDF version of the accepted manuscript is posted online as soon as possible (see below).
The text files undergo an automated preediting, cleanup, and tagging process specific to the particular article type, and the illustrations are examined. If all files have been prepared according to the criteria set forth in these Instructions and those in the eJP online manuscript submission system, the acceptance procedure will be completed successfully. If there are problems that would cause extensive corrections to be made at the copyediting stage or if the files are not acceptable for production, ASM Journals staff will contact the corresponding author. Once all the material intended for publication has been determined to be adequate, the manuscript is scheduled for the next available issue. The editorial staff of the ASM Journals Department completes the editing of the manuscript to bring it into conformity with prescribed standards.
Accepted Manuscripts
For its primary-research journals, ASM posts online PDF versions of manuscripts that have been peer reviewed and accepted but not yet copyedited. Accepted manuscripts are accessible from the Journals website. The manuscripts are published online as soon as possible after acceptance, on a weekly basis, before the copyedited, typeset articles are published. They are posted "as is" (i.e., as submitted by the authors at the modification stage) and do not reflect ASM editorial changes. No corrections/changes to the PDF manuscripts are accepted. Accordingly, there likely will be differences between the accepted AEM manuscripts and the final, typeset articles. The manuscripts remain listed on the Accepted Manuscripts page until the final, typeset articles are posted. At that point, the manuscripts are removed from the Accepted Manuscripts page. The manuscripts are under subscription access control until 6 months after the typeset articles are posted, when free access is provided to everyone (subject to the applicable ASM license terms and conditions). Supplemental material intended, and accepted, for publication is not posted until publication of the final, typeset article.
The ASM embargo policy allows a press release to be issued as soon as the accepted manuscript is posted on the Accepted Manuscripts page. To be notified as soon as your manuscript is posted, please sign up for e-Alerts.
Instructions on how to cite such manuscripts may be found in "References."
Page Proofs
Page proofs, together with a query sheet and instructions for handling proofs, will be made available to the corresponding author electronically. Queries must be answered on the query page, and any changes related to the queries, as well as any additional changes, must be indicated on the proofs. Note that the copy editor does not query at every instance where a change has been made. Queries are written only to request necessary information or clarification of an unclear passage or to draw attention to edits that may have altered the sense. It is the author's responsibility to read the entire text, tables, and figure legends, not just items queried. Corrected proofs must be returned within two business days after notification of availability.
The proof stage is not the time to make extensive corrections, additions, or deletions. Figures as they appear in the proofs are for validation of content and placement, not quality of reproduction or color accuracy. Print output of figures in the PDF page proofs will be of lower quality than the same figures viewed on a monitor. Please avoid making changes to figures based on quality of color or reproduction in proof.
Important new information that has become available between acceptance of the manuscript and receipt of the proofs may be inserted as an addendum in proof with the permission of the editor. If references to unpublished data or personal communications are added, it is expected that written assurance granting permission for the citation will be included. Limit changes to correction of spelling errors, incorrect data, and grammatical errors and updated information for references to articles that have been submitted or are in press. If URLs have been provided in the article, recheck the sites to ensure that the addresses are still accurate and the material that you expect the reader to find is indeed there.
Questions about proofs should be directed to the ASM Journals Department (e-mail, bslinker@asmusa.org; telephone, 202-942-9219).
PDF Files
The corresponding author will have limited access (10 downloads, total) to the PDF file of his/her published article. An e-mail alert will automatically be sent to him/her on the day the issue is posted. It will provide a URL, which will be required to obtain access, and instructions. An article may be viewed, printed, or stored, provided that it is for the author's own use.
Should coauthors or colleagues be interested in viewing the paper for their own use, the corresponding author may provide them with the URL; a copy of the article may not be forwarded electronically. However, they must be made aware of the terms and conditions of the ASM copyright. (For details, go to https://journals.asm.org/content/copyright-and-license-information.) Note that each such download will count toward the corresponding author's total of 10. After 10 downloads, access will be denied and can be obtained only through a subscription to the journal (either individual or institutional) or after the standard access control has been lifted (i.e., 6 months after publication).
Funding Agency Repositories
The National Institutes of Health (NIH) requests that its grantee and intramural authors provide copies of their accepted manuscripts to PubMed Central (PMC) for posting in the PMC Public Access Repository. AEM authors are automatically in compliance with this policy and need take no action themselves. For the past several years, ASM has deposited in PubMed Central all publications from all ASM journals. Further, ASM policy is that all primary-research articles are made available to everyone, free, 6 months after publication through PubMed Central, HighWire, and international PubMed Central-like repositories. By having initiated these policies, ASM is in full compliance with NIH Policy. For more information, see https://publicaccess.nih.gov/.
ASM also allows AEM authors whose work was supported by funding agencies that have public access requirements like those of the NIH (e.g., the Wellcome Trust) to post their accepted manuscripts in publicly accessible electronic repositories maintained by those funding agencies. If a funding agency does not itself maintain such a site, then ASM allows the author to fulfill that requirement by depositing the manuscript (not the typeset article) in an appropriate institutional or subject-based open repository established by a government or noncommercial entity.
Since ASM makes the final, typeset articles from its primary-research journals available free of charge on the ASM Journals and PMC websites 6 months after final publication, ASM requests that when submitting the accepted manuscript to PMC or a similar public access site, the author specify that the posting release date for the manuscript be no earlier than 6 months after publication of the typeset article by ASM and that a link to the published manuscript on the journal website be provided.
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