Harnessing Metagenomics To Study Microbial Ecology in Soils

Source: Janet Jansson

Combining “omics” approaches with cultivation and single-cell sequencing will help to address fundamental questions about soil microbial ecology.

Through soil metagenomics research, we can address fundamental questions about soil microbial ecology. For example, is there functional microbial redundancy in soil? Soil microbial community compositions differ in different soils in terms of dominant populations, according to 16S rRNA gene surveys. Although soil pH is a key driver of soil community composition, biogeography also plays a role.

Soil metagenomics methodology

As an illustration, we can compare soil microbial diversity to the diversity of microbial communities in the human gut. The gut microbiota from one individual to another differs at the 16S rRNA gene level, but at the broad functional level the communities are rather homogenous in healthy individuals. This pattern suggests that several different bacterial species can carry out the same functional roles in the human intestine. The situation in soil might be similar, but we have yet to explore and compare many soil metagenomes in depth to determine whether that possibility holds.

Metagenomics can help us determine whether microorganisms in soils embody a specialized cache of gene functions. Available metagenome sequence datasets are already providing clues as to what functions are predominant in soils. For example, genes for cellobiose phosphorylase, an enzyme that degrades plant carbohydrates, were identified in a Minnesota farm soil metagenome, but not in one from the Sargasso Sea. When we screened permafrost for other functional genes specifically involved in cycling carbon and nitrogen, the samples included several genes that were more or less prevalent after thaw.

Metagenomics can also help to address whether rare species play an important functional role in soils. For example, although methanogens may not be numerically dominant in permafrost, they play a key role in producing methane, which is 21 times more potent as a greenhouse gas than carbon dioxide. With deep sequencing, it should be possible to obtain genomes of some of the dominant species in soil and even some species of relatively low abundance, provided that they do not have large amounts of strain heterogeneities. As we collect soil metagenome sequence data, we need to improve how we mine such datasets. For example, the way we conduct BLAST searches might overlook valuable information, while the unassembled reads might be too short for annotating genes with confidence. Thus, we might well need to develop new assembly and annotation algorithms.

Another challenge is how to integrate different kinds of omics data, including metatranscriptomics and metaproteomics, to better understand functional processes of soil microbial communities. Metagenome sequence data, while informative, provides information about genes with the potential for being expressed, but cannot determine which ones are functional. Also, because we sequence total DNA, it is not possible to distinguish genes from actively growing cells from those in dormant or dead cells. Perhaps some analyses should be reserved for that fraction of DNA from active community members—for example, by extracting DNA that is allowed to incorporate stable isotopes or bromodeoxyuridine during replication. Ultimately, combining these approaches should enable us to gain a better understanding of which microbes are alive and active, and which enzymes and pathways function in soil microbial communities under different conditions. Then we can begin to truly comprehend soil microbial communities from the microscopic to the global scale.

 

More Information

• This article is a subsection (5 of 5) of the ESD Research Highlight: Soil Microbes: Metagenomic Approaches »
• As reported in Microbe Magazine »