Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil

By Kathryn G. Eilers, Spencer J. Debenport, S. P. Anderson, Noah Fierer. 2012

784 citations recorded by the source corpus.

Abstract Microorganisms exist throughout the soil profile and those microorganisms living in sub-surface horizons likely play key roles in nutrient cycling and soil formation. However, the distributions of microbes through the soil profile remain poorly understood, as most studies focus only on those communities found in near-surface horizons. Here we examined how microbial community structure changes within soil profiles, whether these changes are similar across soils from different landscape positions, and how the community-level variation within individual soil depth profiles compares to the variation across surface soils from a wide range of biomes. We characterized changes in bacterial and archaeal community composition and diversity with depth through nine soil profiles located in a forested montane watershed in Colorado, USA. Microbial community composition was determined by barcoded pyrosequencing of the 16S rRNA gene employing a primer set that captures both bacteria and archaea. Relative microbial biomass and soil carbon concentrations decreased exponentially with depth while soil pH increased in nearly all of the profiles examined. Bacterial diversity was typically highest in the top 10 cm of the profile; diversity typically dropped by 20–40% from the surface horizons to the deepest horizons sampled. Community composition was significantly affected by soil depth in all profiles, driven primarily by a decline in the relative abundance of Bacteroidetes with depth and the peak in the relative abundance of Verrucomicrobia between 10 and 50 cm. Microbial community composition across the nine pits was most variable in the surface horizons; communities at deeper soil depths were relatively similar regardless of landscape position. When compared to the microbial communities from 54 previously-analyzed surface soils collected across a wide range of biome types, we found that there was as much variation within individual soil pits as across surface soils from different biomes, emphasizing the importance of soil depth as an environmental gradient structuring soil microbial communities.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7bacebc3a0770e41c0938c821e41b74a35b78fe2

How researchers see this paper

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In Ecology

1. Petr Baldrian
2. Haiyan Chu
3. R. López-Mondéjar
4. P. Grogan
5. S. Lladó
6. Gehong Wei
7. Shuo Jiao
8. Tomás Vetrovský

In Molecular Biology

1. Petr Baldrian
2. Haiyan Chu
3. P. Grogan
4. R. López-Mondéjar
5. S. Lladó
6. Gehong Wei
7. Shuo Jiao
8. Tomás Vetrovský

Citations in the corpus

• Culture-independent molecular tools for soil and rhizosphere microbiology (2013, methodology): “Recently, this method has been extensively used to characterize composition and diversity of soil microbial communities [20,107,160–163] and has also been applied to understand the effect of heavy metals and disturbances on soil microbial communities [162,164,165].”
• The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics (2015, background): “Contrary to the coniferous forest soil (Eilers et al., 2012), where bacterial diversity did not differ between litter and soil, here we observed a significantly higher bacterial diversity in litter compared to soil.”
• Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems (2018, background): “Previous work has demonstrated that the diversity of bacteria typically decreases with increasing soil depth [16].”
• Embracing the unknown: disentangling the complexities of the soil microbiome (2017, background): “Although most studies have focused exclusively on the microorganisms found in surface soil horizons (layers), communities found in the litter layer (or O-horizon) are often distinct from those found in underlying mineral soil horizons (A and B horizons) and deeper saprolite (C horizons) 123 .”
• Hydration and diffusion processes shape microbial community organization and function in model soil aggregates (2015, background): “As further elaborated in section 4, the focus was on exploration of a range of boundary conditions found in natural soils and known to influence the microbial community structure [Fierer et al., 2003; Eilers et al., 2012].”
• Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change (2017, background): “108), show an increased abundance with soil depth (109), but it is unclear whether this”
• Variation of Soil Microbial Population in Different Soil Horizons (2015, neutral): “8 trillion tons of carbon [5].”
• Soil fertility is associated with fungal and bacterial richness, whereas pH is associated with community composition in polar soil microbial communities (2014, background): “For example, studies along vertical soil profiles report considerable variation in microbial community structure because edaphic conditions change dramatically with depth (Eilers et al., 2012).”