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. Descriptions of the application of previously described technologies, including the cloning, amplification, and expression of вЂњforeignвЂќ genes, to a new genus or species of microbe will generally not be considered for independent publication. 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. 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. Invertebrate microbiology manuscripts should address interactions between invertebrates and microorganisms, ranging from commensalism and mutualism to parasitism and pathogenicity. Manuscripts focused on geological processes with only marginal links to microbiology will not qualify for AEM.

Topics include mineralization, the use of inorganic ions in energy metabolism, and growth in extreme environments. 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. The genetics and molecular biology section includes papers describing genetic organization, expression, mutation, and repair in organisms with environmental or practical significance. The food microbiology section covers manuscripts dealing with all aspects of food microbiology, including microbial food safety, microbial ecology of foods, predictive food microbiology, probiotics, food fermentations, and food spoilage. Topics include genomic analysis of established microorganisms and metagenomic investigation of microbial populations in the environment. Included in the evolutionary and genomic microbiology section are papers detailing newly described evolutionary processes and evolutionary relationships among microorganisms. The enzymology and protein engineering section covers the structure and function of environmentally or industrially significant proteins and how they can be modified to achieve practical catalytic objectives. 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. 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.

The environmental microbiology section covers manuscripts that focus on research related to microorganisms in the environment. Papers in the biotechnology section describe the use and modification of organisms in order to achieve socially beneficial objectives. The biodegradation section describes novel microbial processes for alteration, removal, or utilization of environmental or anthropogenic chemicals. 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. To best serve its readership, the journal must accept only those papers that are most significant to the field of applied and environmental microbiology.

Manuscripts should report new and significant findings that advance the understanding of microbiology and upon which other scientists may build. 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. Research must address salient microbiological principles, fundamental microbial processes, or basic questions in applied or environmental microbiology. 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.

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