Microbes and mountains: metagenetics on Mount Fuji, Japan. Jonathan Adams, Biology Department, SNU, Korea

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1 Microbes and mountains: metagenetics on Mount Fuji, Japan Jonathan Adams, Biology Department, SNU, Korea

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

3 New techniques DNA sequencing and computing - capable of analysing vast amounts of information in DNA at rates unimaginable 20 years ago

4 As a result of metagenetic methods we are in a new age of discovery analogous to the time years ago when modern science first documented the life forms of the planet, and the patterns of their variation

5 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

6 Today I ll talk just about our exploration of prokaryotes in one particular location

7 Adams lab members

8 16S RNA subunit a vital part of every prokaryotic cell Its gene varies by just enough that we can usually distinguish species by their different 16S gene sequences

9 We studied Mount Fuji as a relatively simple environmental system

10 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

11 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?)

12 On Fuji: middle elevations on mountain favour greater soil bacterial diversity Mt Fuji, Japan (Singh et al. 2011) (Phylotype Richness (OTUs) Elevation (meters)

13 PCoA bacterial community vs elevation 1000masl 1500masl 2000masl 2500masl 3000masl 3700masl Discrete bacterial community for each elevational zone

14 Lower slopes with forest have low bacterial diversity

15 Increasing into the upper forests

16 Mid-altitudes above tree line most diverse In terms of bacteria

17 Barren upper slopes, less bacterial diversity again

18 Another area of revelation from metagenetics: the diversity and abundance of Archaea

19 Archaea (Total archaea, above, and Thaumarcheota only)

20 Best fit for all Archaea and Thaumarcheota

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

22 Thaumarchaeota Whole Community Correlation with Ammonia

23 Thaumarchaeota Whole Community Correlation with nitrate

24 Thaumarchaeota Whole Community Correlation with Potassium

25 Relative Abundance m 1500m 2000m 2500m 3000m 3700m Archaea_uc Thaumarchaeota Euryarchaeota m 1500m 2000m 2500m 3000m 3700m Group1b Marine Group1a FFSB Thaumarchaeota_uc Thermoplasmata DHVEG Euryarchaeota_uc Phylum Class 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.

26 NMDS 2D Stress: D Stress: 0.08 Thaumarchaeota Elevation Whole archaeal Community

27 Humpback curve on mountain: An optimal environment needs less physiological specialization, and species fall into it?

28 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

29 Or greatest diversity where lower forest communities mix in a fine mosaic with barren upper slope environments? (for bacteria, anyway)

30 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