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From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?

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PubMed ID: 29882154

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Kerfahi D, Tripathi BM, Dong K, Kim M, Kim H, Ferry Slik JW, Go R, Adams JM

Microb Ecol. Jan 2019. doi: 10.1007/s00248-018-1215-z

COMMENT: In this work soil metagenomes from Arctic regions are compared with those from Equatorial tropics. The results in some cases confirm the predictions of the authors but in others cases are unexpected and to understand why the actual features of both extreme environments differ in that way supposes a challenge. The findings of this work, considered in a more broad context, suggest that it is needed to review many classical concepts about the differences between tropical and higher latitude ecosystems.

OBJECTIVE

Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates.

MAIN RESULTS

We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing.

We made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct and in other ones not.

The predictions and the findings about them are sumarized in the following lines.

1)Is there greater diversity of taxa and gene functions in the tropics?

- NO.

We expected to find higher alpha diversity of both taxa and gene functions in tropical equatorial forest than in high Arctic tundra. In fact, we found greater microbial diversity—based on both taxa and gene functions—in high Arctic sites compared to tropical sites. We hypothesized that there would be a latitudinal difference in taxonomic alpha diversity between high Arctic and tropical environments, with microbial diversity being lower in the high Arctic. There was, surprisingly, a higher diversity in the high Arctic samples compared to the tropical ones.

2) Are genes for dormancy/sporulation more common in the high Arctic?

- YES

Here, the result conforms to our expectations based on classical ecological theory: dormancy genes were more common in the Arctic samples than in the tropical samples

3) Are stress response genes more common in the high Arctic?

- NO

Contrary to our expectations, stress response genes were no more common in the high Arctic sites than in the equatorial tropics. It appears that a priori expectations about how much stress soil biota is exposed to may not be accurate. At least if there is more stress in the high Arctic, the genes that are needed are not those identified by MG-RAST.

4) Are genes associated with replication and cell division more common in the tropics?

- NO

In contrast to our predictions, relative abundance of genes associated with cell division did not differ between the high Arctic and tropical sites. Our results parallel those of Fierer et al. who (in a more limited set of samples) found higher abundance of genes associated with cell division and cell cycle in polar desert soils than non-desert soils. This difference may be related to the extreme environmental conditions in the high Arctic, leading to higher abundance of the products of these core genes to facilitate the genomic stability in microbial communities.

5) Are genes associated with viruses and anti-virus defenses more common in the equatorial tropics?

- NO

 In contrast to our hypothesis, the results showed significantly greater relative abundance of virus and virus-like elements in the polar soils compared to the tropical sites. Likewise, CRISPR elements (an anti-viral defense) were significantly more abundant in the polar soils. It appears that the assumption of greater disease pressure in the tropics may be incorrect.

6) Are genes associated with metabolism of aromatic compounds more common in the equatorial tropics?

- YES

As predicted, these genes are relatively more common in the tropical sites, which may reflect the much higher levels of vascular plant biomass—the main source of carbon in most soils and especially tropical soils —together with the lignin and aromatic secondary compounds that they bring to the soil.

7) Are genes associated with secondary metabolism more abundant in the equatorial tropics?

- NO

Contrary to our prediction, genes associated with secondary metabolism did not vary in relative abundance between polar and tropical sites.

8) Will there be greater abundance of genes associated with respiration in the tropics?

- YES

These results conform to our expectations, with respiration-related genes more common in the tropical sites. Previous studies showed that soil respiration and microbial growth rate are greater in warmer climates. However although this could simply be achieved by the same enzymes working faster in warmer temperatures, it is possible that respiration-related genes are present in greater copy numbers in warmer conditions to enable cells to take advantage of the conditions.

9) Are antibiotic resistance genes more common in the tropics?

- NO

Contrary to our expectations, in our samples, antibiotic resistance genes appear to be no more common in the polar arctic sites than in the equatorial tropics.

 

10) Will there be a greater abundance of genes associated with virulence/disease and defense in the tropics?

- NO

Contrary to our hypothesis, the high Arctic sites had a greater abundance of these genes involved in cell-cell interactions than the tropical sites.

11) Is there greater connectedness in the tropics?

- YES

Our results indicated that the Brunei tropical rainforest soils do have higher network complexity than Svalbard high Arctic soils (Figs. 5 and 6). Thus, our hypothesis is supported.

CONCLUSIONS

In many instances the expected difference between tropical and polar soil biota was not found, and in other instances the polar-to-tropical difference was the opposite of what we had predicted. This adds an intriguing new perspective on how ecological and evolutionary processes vary around the world.

Contributor

Raquel Tobes