Microbial diversity on Earth

The Shapiro Team

March 27th 2019 - University of Montreal

Pictures: https://www.cafepress.com/microbesrule
 PLoS Biology (2019)

- Predict 0.8-1.6 million of prokaryotes (Bacteria and Archaea) on Earth

- Approach: census-based estimate (Global Prokaryotic Census (GPC))
- Data set: 1.7 billion 16S ribosomal RNA amplicon sequences data from
34,368 samples across 492 studies, covering a wide range of environments
from over 2,800 distinct geographical locations worldwide.

- Results: The resulting GPC comprises 739,880 prokaryotic OTUs (690,474

bacterial and 49,406 archaeal).
 The accumulation curves of OTUs discovered by the GPC
show a deceleration with increasing number of studies
About 93% of
bacterial OTUs
and 83% of
archaeal OTUs
found in any
additional
study are
expected to be
already included
in the GPC.

The same
OTU richness
is recovered
from the
Americas as
from the full
GPC

Comparable estimates for global prokaryotic OTU richness ( 1–2 million prokaryotic OTUs)
The rapid decline of the number of OTUs for lower MRAs suggests that the
number of much more rare OTUS is relatively small and that the GPC did not miss
vast numbers of extremely rare OTUs

Mean relative OTU abundances

 PNAS (2016)

- Predict 1 trillion of microbial species on Earth

- Approach: inference of scaling law combined with the lognormal model of diversity

Data Set
20,376 sites of bacterial, archaeal, and microscopic fungal communities
from the Earth Microbiome Project (EMP), Human Microbiome Project
(HMP), and from the metagenomics RAST server (MG-RAST, which
include arctic aquatic systems, hydrothermal vents, bovine fecal
samples, etc)
 PNAS (2016)

- Predict 1 trillion of microbial species on Earth

- Approach: inference of scaling law combined with the lognormal model of diversity

S=cAZ
Examples of scaling laws:
Rate at which species richness scale with area (S=cAz), or that metabolic
rate (B) increases with body size/mass (M) (B=BoM3/4)
 Approach: scaling law combined and the lognormal model of biodiversity

- Unified scaling law was inferred, based on the

prediction of Nmax (number of individuals belonging to
the most abundant species) according to N (total
abundance) at different environments/scales

Nmax = 0.38*N0.93

- Then the lognormal distribution model was used to

predict S (species richness) using N and N max
- The lognormal predicts that the distribution of
abundances among species is ~normal when
species abundances are log-transformed
 1011-1012 species
The microbial richness-abundance scaling
relationship (dashed red line) supports values
of S predicted from the lognormal model:

- either using the published ranges of N

and Nmax (gray dots)
- or using ranges of Nmax predicted from
the dominance scaling law (blue dots,
formula also shown in the previous
figure)

Potentially 99.999% of microbial

taxa remain undiscovered
 Questions to discuss in group:
- Why is it important to have an accurate estimate of the microbial biodiversity on
Earth?
- What should be an acceptable confidence interval of such an estimate?
- How to explain the gap in the global diversity estimates between the two papers?
- How these different estimates could affect the interpretation of biodiversity
theories?
- What are the main constraints of the methods at each paper?
- How we could improve the accuracy of microbial diversity estimates on Earth?
- What are the challenges faced for those studying microbial diversity?
- How important are space and time variation to estimate the global microbial
diversity?
In red more methodological questions and in blue more theoretical questions