Abstract
Studies in microbiology have long been mostly restricted to small spatial scales. However, recent technological advances, such as new sequencing methodologies, have ushered an era of large-scale sequencing of environmental DNA data from multiple biomes worldwide. These global datasets can now be used to explore long standing questions of microbial ecology. New methodological approaches and concepts are being developed to study such large-scale patterns in microbial communities, resulting in new perspectives that represent a significant advances for both microbiology and macroecology. Here, we identify and review important conceptual, computational, and methodological challenges and opportunities in microbial macroecology. Specifically, we discuss the challenges of handling and analyzing large amounts of microbiome data to understand taxa distribution and co-occurrence patterns. We also discuss approaches for modeling microbial communities based on environmental data, including information on biological interactions to make full use of available Big Data. Finally, we summarize the methods presented in a general approach aimed to aid microbiologists in addressing fundamental questions in microbial macroecology, including classical propositions (such as “everything is everywhere, but the environment selects”) as well as applied ecological problems, such as those posed by human induced global environmental changes.
Highlights
The purpose of macroecology is to describe spatial patterns of species distribution and abundance, as well as the mechanisms underlying such patterns (McGill, 2003; McGill and Nekola, 2010)
We outlined the main questions in macroecology, community ecology and addressed how microbial ecologists can address them with bioinformatics, statistical and modeling tools
We covered fundamental aspects of biodiversity, reviewed classical approaches used in microbial ecology in a macroecological context, and highlighted the existing caveats and solutions to implement ecological modeling of microbial communities, which is a crucial research area for both the theoretical and practical aspects of macroecology
Summary
The purpose of macroecology is to describe spatial patterns of species distribution and abundance, as well as the mechanisms underlying such patterns (McGill, 2003; McGill and Nekola, 2010). The availability of large amounts of data (Hampton et al, 2013) has helped to uncover global ecological patterns in species distribution and abundance, greatly advancing the field of macroecology. This is highlighted by several studies discussing the contribution of microbial community investigations to a unified macroecological theory (Barberán et al, 2014; Blaser et al, 2016; Nelson et al, 2016; Shade et al, 2018). The field of microbial macroecology has emerged as a promising research path to the unified understanding of ecological processes shaping patterns across different branches in the tree of life
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