Journal Article

Embracing the unknown: disentangling the complexities of the soil microbiome

Fierer, Noah

2017

Overview

Key Points Soils can contain large amounts of microbial biomass, including fungi, protists, viruses, bacteria and archaea. Most of these taxa currently remain undescribed, and have physiological and ecological attributes that are unknown. Soil microbial communities are highly diverse, in part because soil environmental conditions are so heterogeneous. In a single soil there is a wide range of distinct microbial habitats that contain unique microbial assemblages. Spatial variability in the structure of soil microbial communities is typically larger than the temporal variability. The composition of soil bacterial communities and the abundances of specific taxa are often predictable from soil and site characteristics, including soil pH, climate and organic carbon availability. Plants can clearly have important direct or indirect effects on soil microbial communities and vice versa. However, the effects of plant species on microbial taxa are often difficult to predict a priori owing, in part, to plant associations with soil microorganisms being highly context-dependent. Linking specific soil microbial processes to specific microbial taxa remains difficult. One way to tackle this problem is to use genomic data to group microbial taxa according to shared similar life-history strategies and functional attributes. Given recent methodological and conceptual advances, the field is poised to rapidly advance our understanding of the soil microbiome. Promising future research directions include cultivation-based analyses of soil microbial taxa, studies of soil viruses and investigations into the importance of horizontal gene transfer in shaping the soil microbiome. Soil contains a vast diversity of microorganisms that can directly or indirectly modulate soil processes and terrestrial ecosystems. In this Review, Fierer summarizes the challenges in characterizing the composition and functions of the soil microbiome, and discusses key future research directions. Soil microorganisms are clearly a key component of both natural and managed ecosystems. Despite the challenges of surviving in soil, a gram of soil can contain thousands of individual microbial taxa, including viruses and members of all three domains of life. Recent advances in marker gene, genomic and metagenomic analyses have greatly expanded our ability to characterize the soil microbiome and identify the factors that shape soil microbial communities across space and time. However, although most soil microorganisms remain undescribed, we can begin to categorize soil microorganisms on the basis of their ecological strategies. This is an approach that should prove fruitful for leveraging genomic information to predict the functional attributes of individual taxa. The field is now poised to identify how we can manipulate and manage the soil microbiome to increase soil fertility, improve crop production and improve our understanding of how terrestrial ecosystems will respond to environmental change.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/158/855 / 631/326/2565/2134 / 631/326/47 / Bacteria - classification / Bacteria - genetics / Crop production / Environmental changes / Eukaryota - classification / Eukaryota - genetics / Fungi - classification / Fungi - genetics / Genotypes / Identification and classification / Infectious Diseases / Life Sciences / Medical Microbiology / Microbial activity / Microbiological research / Microbiology / Microbiota - genetics / Microorganisms / Parasitology / review-article / Soil - parasitology / Soil fertility / Soil improvement / Soil Microbiology / Soil microorganisms / Soils / Terrestrial ecosystems / Virology