Microbes and mountains: metagenetics on Mount Fuji, Japan and Mountains Metagenetics on Moun… ·...
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Microbes and mountains: metagenetics on Mount Fuji, Japan Jonathan Adams, Biology Department, SNU, Korea [email protected]
Transcript of Microbes and mountains: metagenetics on Mount Fuji, Japan and Mountains Metagenetics on Moun… ·...
Microbes and mountains: metagenetics on Mount Fuji, Japan
Jonathan Adams, Biology Department, SNU, Korea
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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Correlation with PotassiumTh
aum
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aW
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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
