Soil Equality

Forest soil under lodegpole pine in Lyons, Colorado. Photo courtesy of Andrea Borkenhagen, 2013.

By Kelly S. Ramirez, PhD

As a soil ecologist, I am inevitably asked about dirt (and lawn care), but mainly dirt. Depending on the person and my mood and the event, I may quip back, ‘dirt is under your fingernails.’* Some inquirer’s eyes will glaze over, realizing I was the wrong person to make small talk with at said event. Others will eye me apologetically.

Soil, not dirt, is the foundation of our terrestrial ecosystems, maintains our food sources, cleans and cycles our water, regulates climate change, controls disease, and supports our cultural activities and recreation (Wall and Nielsen, 2012). Soil is not an inert, static substance, rather it is a complex dynamic system and its formation is controlled by 5 factors (climate, organisms, parent material, time and topography)… Are you dozing off?? Watch here for the lovely story of soils and here for the classic explanation of soil formation.

Long story short, not all soils are created equal. We can visually see the fertility of a grassland soil in Kansas (a) versus one on the side of a 14,000 ft peak in Colorado (b). And just like we don’t find the same plants in a cold desert (c) as we do forest (d), we find a different microbial community in a desert soil versus a forest soil.

The differences in soils extend beyond the organisms present. Not only do the four soils pictured have different soil microbial communities, but each community also functions differently (or at least not all in the same way). One way to measure the functional potential of a soil is through shotgun-metagenomics**—looking at all of the traits in a soil system (traits like cell division, nitrogen metabolism, and virulence, disease and defense) that can be related to ecosystem traits. For example, desert systems have lower nitrogen cycling rates and in the functional trails we would expect to observe lower levels of nitrogen metabolism. While some differences in function are due to precipitation, nutrient levels, pH, temperature, and plant life (to name a few), what remains a major research question is how the functional differences between soils relate back to the millions of organisms living in each gram of soil and how these functional differences may change across the landscape.

A recent paper in PNAS, Cross-biome metagenomic analyses of soil microbial communities and their functional attributes, by Fierer et al, explores just that: how does microbial community composition and function vary across five very different ecosystems- hot deserts, cold deserts, forests, grasslands, and tundra?

Briefly, the authors collected soils from 16 locations across the five biomes. They then used high-throughput sequencing methods*** to analyze both the diversity (who is there and how they are related) and the function (what can they do) of the community.

How different are deserts from forests from tundra from grasslands?

Before we dive into results, let me state (an only slightly biased opinion) that this is an impressive paper:

·      First, this is the first study to compare metagenomes from across multiple biomes. The sheer volume of information from the sequencing is impressive. And while I know next year we will say, ‘What? Only 16 samples?!?‘ This year, it is impressive. The team used shotgun metagenomics to compare 16 sites with ~688,000 annotated sequences per sample (from >390 Million base pairs from each soil!). While I am sure in just a few years time the number of sequences in this study will seem trivial, lets appreciate, for this minute, that 688,000 annotated reads per sample is a lot of information!

·      Second, this paper demonstrates the ability to go beyond surveys of who is there, and works to integrate the functional contribution of the community to ecosystem processes. By relating taxonomic and phylogentic diversity (who is there) to shotgun metagenomics (functional diversity and functional potential), we gain insight into what the organisms are doing in each soil and, therefore, why distinct communities are important for their individual biomes.

What are the take home messages? I am only going to mention three, though there were quite a few interesting points.

1.     Overall, and not super surprisingly, biomes separate out by biomes, especially deserts from nondeserts. We would expect soils with harsher conditions, fewer nutrients, less plant life to have different soil microbial communities, and they do – both in community composition (16S rRNA genes) and by functional capability (metagenomes).

2.     One function driving this separation is the large difference in antibiotic resistance genes, which are much lower in desert environments. The authors hypothesize that this large discrepancy is a result of desert soil communities having fewer competitive interactions because there are simply less microbes (similar to the plant communities). Other functions that were different included nutrient cycling rates (lower in deserts), stress proteins (higher in deserts), and degradation of plant materials (lower in deserts).

3.     Taxonomic diversity does not necessarily correlate with functional diversity (in other words, just because there are more types of organisms doesn’t necessarily mean they can perform more functions). So while the cold deserts have lower species diversity, the authors did not consistently find lower functional diversity, suggesting that it is not merely the number of species that dictates the functional diversity but also the type of those species.

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^*Sarcastic comment credit to @NoahFierer

^**The authors use both 16S rRNA amplicon sequencing and shotgun-metagenomic gene sequencing to address this question. Briefly, 16S rRNA sequencing allows for survey of bacteria and arachea only, and shot-gun metagenomic sequencing allows for the survey of all genes in a given sample, including 16S and 18S rRNA genes.

^***Metagenomics references:

http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050082

http://mmbr.asm.org/content/72/4/557.abstract

References:

Fierer et al. (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. PNAS 109(52), 21390-21395

Wall, D. H. & Nielsen, U. N. (2012) Biodiversity and Ecosystem Services: Is It the Same Below Ground? Nature Education Knowledge 3(12):8