Dear Colleagues,

The soil and water microbiome plays a crucial role in nutrient cycling within an environmental ecosystem. In recent years, thanks to metagenomic next-generation sequencing, we have begun to understand more about the vast diversity of microorganisms in many ecosystems on the planet. There is much more to be discovered and documented, however it has become clear that no cell lives and dies alone. There is a complex network of interactions between all forms of life, much of which still needs to be discovered.

Past research has mainly focused on parasitic or pathogenic interactions, but more recently we are starting to shed light on the complex syntrophic and other symbiotic interactions that occur between bacteria, protists, plants, and animals in environmental systems. With metagenomic analysis becoming more accessible, we can now also start comparing seasonal, temporal and spactial variations of microorganisms within an ecosystem. This presents a new level of understanding of the adaptation, resilience, and evolution of microbial ecosystems.

The aim of this Special Issue is to present advances in our understanding of microbial interactions (amongst each other or with plant or animal systems), in the fluctuations and resilience of microbial ecosystems, and broaden our understanding of the complex environmental microbiome in the era of metagenomics.

For this purpose, we welcome the submission of research articles, review articles, and short communications that provide novel insights into the various aspects of the environmental microbiome: the metagenomic analysis of microbiomes of novel or extreme environments, studies on microbial resilience or temporal fluctuations, symbiosis and co-evolution of the microbiome, novel microbial interactions (bacterial-–host interactions or symbiosis), modeling of nutrient cycling within environmental microbiomes, and technical challenges and interpretation issues of mNGS.

Dr. John Kyndt
Guest Editor

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• Microbial ecosystems
• Metagenomics
• Microbial interactions
• Symbiosis
• Microbiome resilience
• Nutrient cycling
• Next-generation sequencing