Microbes and mountains: metagenetics on Mount Fuji, Japan

Jonathan Adams, Biology Department, SNU, Korea

jonadams@snu.ac.kr

Until about a decade ago, culturing could only yield 8,000 described species of prokaryotes

New techniques – DNA sequencing and computing - capable of analysing vast amounts

of information in DNAat rates unimaginable 20 years ago

As a result of metagenetic methods we are in a new ‘age of discovery’ analogous to the time 200-300 years ago when modern science first documented the life forms of the planet, and

the patterns of their variation

As in the ‘age of discovery’, much work with metagenetics at present is about initial exploration and description of

patterns

From which mechanistic understanding of microbial

communities can eventually result

Today I’ll talk just about our exploration of prokaryotes in

one particular location

Adams lab members

16S RNA subunit – a vital part of everyprokaryotic cell

Its gene varies by just enough thatwe can usually distinguish ‘species’

by their different 16S gene sequences

We studied Mount Fuji as a relatively ‘simple’ environmental system

Mount Fuji

• Is very high, up to 3,770m, wide range of temperature and vegetation

• Geologically uniform (late Quaternary volcanic ash cover formed all at same time)

• Topographically simple: ‘perfect’ monotonous cone

• A nice environmental gradient to begin exploring soil microbial diversity patterns

Questions we asked

• What are the diversity patterns?

• Why do whatever patterns we see occur? (i.e. what favours high diversity in a prokaryotic community?)

• Are there discrete communities at each altitudinal zone? (i.e. are prokaryotes finely partitioned by niche in relation to environmental gradients?)

On Fuji: middle elevations on mountain favourgreater soil bacterial diversity

Mt Fuji, Japan (Singh et al. 2011)

1000 1500 2000 2500 3000 3500

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Elevation (meters)

(Phy

loty

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ess

(OTU

s)

PCoA bacterial community vs elevation

1000masl1500masl2000masl2500masl3000masl3700masl

Discrete bacterial community for each elevational zone

Lower slopes with forest have low bacterial diversity

Increasing into the upper forests…

Mid-altitudes above tree line most diverseIn terms of bacteria

Barren upper slopes, less bacterial diversity again

Another area of revelation from metagenetics: the diversity and

abundance of Archaea

Archaea(Total archaea, above, and

Thaumarcheota only)

Best fit for all Archaea

and Thaumarcheota

With Archaea, the greatest diversity is in the upper forests…(why??)

Correlation with AmmoniaTh

aum

arch

aeot

aW

hole

Com

mun

ity

Correlation with nitrateTh

aum

arch

aeot

aW

hole

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mun

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Correlation with PotassiumTh

aum

arch

aeot

aW

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Com

mun

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Relative Abundance

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1000m 1500m 2000m 2500m 3000m 3700m

Archaea_uc

Thaumarchaeota

Euryarchaeota

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1000m 1500m 2000m 2500m 3000m 3700m

Group1b

Marine Group1a

FFSB

Thaumarchaeota_uc

Thermoplasmata

DHVEG

Euryarchaeota_uc

Figure.2. Percent relative abundance at phylum (left) and class (right) levels.*green color is for thaumarchaeota and red is for euryarchaeota.* No seq. could be classified up to crenarchaeota ( at 80% cut off) although at a cut off of 50% there were 3 sequences.

Phylum Class

NMDS

2D Stress: 0.08

Thaumarchaeota Whole archaealCommunity

2D Stress: 0.08

Elevation100015002000250030003700

Humpback curve on mountain: An ‘optimal’ environment needs less physiological

specialization, and species ‘fall into’ it?

An intermediate disturbance effect (Mount Fuji) ?

• Low intensities of disturbance lower on mountain, out-competition

• Moderate intensities mid-altitudes, allow co-existence

• Upper slopes – too ‘stressful’, low diversity

Or greatest diversity where lower forest communities mix in a fine mosaic with barren

upper slope environments? (for bacteria, anyway)

Conclusions

• Striking patterns in diversity of prokaryotic communities along an environmental gradient

• Intermediate environments seem to promote maximum prokaryotic diversity

• Prokaryotic community character partitioned by elevational zone

• More studies needed to ‘tease apart the threads’ of microbial diversity along gradients