The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role.

Soil formation is the result of a complex network of biological as well as chemical and physical processes. The role of soil microbes is of high interest, since they are responsible for most biological transformations and drive the development of stable and labile pools of carbon (C), nitrogen (N) and other nutrients, which facilitate the subsequent establishment of plant communities. Forefields of receding glaciers provide unique chronosequences of different soil development stages and are ideal ecosystems to study the interaction of bacteria, fungi and archaea with their abiotic environment. In this review we give insights into the role of microbes for soil development. The results presented are based on studies performed within the Collaborative Research Program DFG SFB/TRR 38 (http://www.tu-cottbus.de/ecosystem ) and are supplemented by data from other studies. The review focusses on the microbiology of major steps of soil formation. Special attention is given to the development of nutrient cycles on the formation of biological soil crusts (BSCs) and on the establishment of plant–microbe interactions.

Nitrogen management in soils has been considered as key to the sustainable use of terrestrial ecosystems and a protection of major ecosystem services

Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions.