FEMS微生物生態學發表高質量的論文，對該領域做出了重大貢獻。它涵蓋了土壤、aqautic和大氣棲息地的微生物群落，包括極端環境，還包括自然、人工和管理系統。FEMS微生物生態學的目標是發表高質量的原創論文，為理解微生物生態學做出重要貢獻。該雜志包含了關于自然土壤、水生和大氣棲息地(包括極端環境)以及人工或管理環境中微生物生態學基本方面的研究文章和小型評論。關于純培養和植物病理學、醫學、食品或獸醫微生物學領域的研究論文將在提供有關微生物生態學的寶貴一般信息的地方發表。論文可以處理任何類型的微生物的可培養和不可培養形式:細菌、古生菌、絲狀真菌、酵母菌、原生動物、藍藻、藻類或病毒。此外，該雜志出版觀點，當前的意見和爭議文章，評論和信件的編輯在微生物生態學的熱點問題。

FEMS Microbiology Ecology publishes high quality papers that make a significant contribution to the field. It covers microorgansims in soil, aqautic, and atmospheric habitats - including extreme environments - and includes natural, artificial and managed systems.FEMS Microbiology Ecology aims to publish high-quality papers that are original and provide a significant contribution to the understanding of microbial ecology. The journal contains Research Articles and MiniReviews on fundamental aspects of the ecology of microorganisms in natural soil, aquatic and atmospheric habitats, including extreme environments, and in artificial or managed environments. Research papers on pure cultures and in the areas of plant pathology and medical, food or veterinary microbiology will be published where they provide valuable generic information on microbial ecology. Papers can deal with culturable and non-culturable forms of any type of microorganism: bacteria, archaea, filamentous fungi, yeasts, protozoa, cyanobacteria, algae or viruses. In addition, the journal publishes Perspectives, Current Opinion and Controversy Articles, Commentaries and Letters to the Editor on topical issues in microbial ecology.