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.