Microbial Diversity, Ecology, and Biogeochemistry
Microorganisms are the most diverse form of life on the planet due to the fact that they have been
around for 3.8 billion years of Earth history, their abundance, their short growth time, and the fact
that they can carry genes from other microorganisms. As a result, they can change rapidly to adapt to
new environments and occupy nearly any available niche. Determining microbial diversity can be
complex, as a good definition of microbial species does not exist. Based on the competitive
exclusion principle, each niche should only be able to be occupied by a single microbial species. The
niche that a microorganism can fill is determined by negative and positive interactions with a large
number of different factors, both biotic and abiotic. The main method currently used to examine
relationships between organisms (now both microorganisms and multicellular organisms) is based on
the sequence of the ribosomal RNA. These sequences led to the discovery of theArchaea as a
separate domain of life and demonstrate very clearly the diversity within the microorganisms relative
to the plants and animals. The interactions between microorganisms can be very complex and can
lead to dividing up niches, i.e. resource partitioning. High levels of biodiversity often lead to high
levels of functional redundancy, which leads to a very resilient ecosystem. It also leads to complex
interactions with their environment. The C, N, S, and Fe cycles are highly dependent upon the
interactions between complex microbial ecosystems and the environment. These cycles have
significant impacts on the world around us, including important implications for global warming.
If you understand this chapter you should be able to explain:
1. The reasons why microorganisms are highly diverse
2. The concepts of species richness, species evenness, and species dominance
3. Explain how the microenvironment of an organism defines its niche.
4. The concept of ecotypes and why they are considered to be the closest to a biological species
5. How 16S rRNAgene sequences are useful for identification of microorganisms from environmental
samples using phylogenetic analysis
6. How negative and positive interactions help to determine a microbial niche
7. The mechanisms that maintain specific levels of microbial diversity in microbial systems, both top-
down and bottom-up regulation.
8. The concept of functional redundancy in microbial ecosystems and how it contributes to ecosystem
9. Understand why life on earth would not be possible without the presence and activities of
10. Explain how the balance between aerobic and anaerobic metabolism of microorganisms cycles and
recycles carbon, nitrogen, sulfur, iron, and manganese.
11. Understand the concept of syntrophy.
12. Explain how and why microorganisms participating in the carbon and nitrogen cycles produce the
greenhouse gases, methane and nitrous oxide. OUTLINE
I. Why are microorganisms so diverse?
1. Microorganisms have been around a long time. Fossilized remains of bacterial cells date back to
around 3.5 to 3.8 billion years ago, while multicellular eukaryotes have only been around for ~1 billion years
and the earliest animals for only about 500 million years. Humans have only been around for <40,000 years.
The antiquity of microorganisms has provided them with a long, long time to differentiate.
2. There are a lot of microorganisms. It is estimated that there are ~5 x 10 prokaryotic (Bacteria and
Archaea) on Earth—enough to stretch across the Milky Way galaxy if laid end to end. This means that even
rare events happen often. For example, an event that happens only one in a trillion times (10 ) will happen
10 times in the microbial world.
3. Microorganisms replicate rapidly, with doubling times as short as 15-30 minutes. This also allows
events that happen rarely (say, once in 10,000 generations) to happen rapidly (in this case, about once every
7 months if the divisions are happening that often).
4. Microorganisms can transfer DNAfrom organism to organism, allowing them to pick up new
features that provide them with increased evolutionary fitness (i.e. a selective growth advantage) without
having to develop the mechanism themselves. Although this happens relatively rarely, it is still a significant
driver of evolution in the microorganisms (see #2 and #3 above). See below for more information on
horizontal gene transfer.
5. Laboratory experiments help demonstrate how rapidly microorganisms can differentiate. Rainey and
Travisano (1998) incubated a single, genetically identical bacterial strain without shaking. Within a single
culture round (approximately 20-25 generations), the strain had differentiated into three separate,
phenotypically distinct strains. One preferred to live on the bottom of the flask, a second preferred to live at
the surface, and a third preferred to live throughout the liquid. The colony morphology of these strains were
distinct and the preferences were heritable, indicating that there was a genetic shift. In a separate
experiment, Treves et al. (1998) showed that a strain developed in an apparently stationary phase culture that
was capable of eating the waste product (acetate) of the parent strain (which was unable to grow on acetate).
Since there was no change in the abundance of cells during the stationary phase and evolutionary processes
require growth, they concluded that the development of the new phenotype must be the result of cryptic
growth (see the growth lectures for information on cryptic growth).
6. Biofilms are organized microbial ecosystems where layers of microbial cells form by associating
with surfaces. Biofilms can be complex communities comprised of many different types of microbes, or they
can be made of a single organism. Microbial mats are extremely dense biofilms where several niches are
formed by microbial communities layering on top of one another. In a microbial mat, the communities
underneath rely on diffusion of nutrients in (e.g. organic carbon from photosynthetic microbes) and waste
out (which acts as nutrient to the next layer) to survive. Some of the oldest fossils of microbes on Earth are
extinct microbial mats called stromatolites. Microcolonies are small biofilms formed by soil microbes
attached to soil particles.As water diffusion is the main limitation to soil microbes, microcolonies will form
where water can easily flow and are most common near plant roots due to the high levels of available
II. How do we measure diversity—phylogeny
Organisms are grouped together based on probable evolutionary relationships. The evolution of bacteria is difficult to track because they are so ancient and the fossil record does not go back that far due to plate
tectonics and turn-over of the Earth’s crust.
The work of Carl Woese suggests that organisms fall into one of three domains into which the traditional
kingdoms are distributed
1. Eukarya - contains all eukaryotic organisms
2. Bacteria (Eubacteria) - contains prokaryotic organisms with eubacterial rRNAand membrane lipids
that are primarily diacyl glycerol ethers
3. Archaea - contains prokaryotic organisms with archaeal rRNAand membrane lipids that are
primarily isoprenoid glycerol diether or diglycerol tetraether derivatives.
Prokaryotes have a 70S ribosome, and eukaryotes an 80S ribosome. The respective subunits that are
important in phylogenetic relationships are the 16S and 18S rRNAmolecules, respectively. The 16S and
18S rRNAhave very specific sequence arrangements, which can be used to describe molecular relatedness.
It is thought that the mutation rate of 16/18S rRNAmolecules is constant through time such that the
evolutionary distance between organisms is equivalent to the mutation plus fixation rate of these molecules.
Hence, 16/18S rRNA is considered the best “molecular clock” to time the divergence of organisms from one
another. Phylogenetic methodology based on 16/18S rRNAsequence comparisons has become extremely
important in identification of microorganisms from the environment without need of culturing.
Differences in 16/18S rDNAsequences can be arranged mathematically to determine an evolutionary
relatedness for construction of the branches that connect evolutionary nodes on the “tree of life.” Those
having the closer relationships will be closer in distance on the evolutionary tree. The branches of the tree
may represent taxonomic units such as species or genera, although neither has can be precisely defined using
III. Bacterial species—is there such a thing?
1. In plants and animals, the biological species definition (i.e. the species definition based on
biological, rather than morphological or operational, parameters) is “a population of individuals that can
interbreed under natural conditions, produce fertile offspring, and are reproductively isolated from other
populations”. However, this definition does not work well for microorganisms. Microorganisms reproduce
clonally, so they don’t interbreed, and when they do HGT, they can transfer across very large evolutionary
distances (although this happens more rarely than between closely related species). During binary fission, it
is often unclear which the “offspring” and which the “parent” cell is. And microorganisms are so small, they
are easily moved around and thus show few signs of being reproductively isolated.
2. Without a working biological species definition, microbiologists have had to resort to the use of
operational definitions (i.e. definitions based on morphological, genetic, or biochemical parameters). The
problem with this approach is that there is no clear dividing line between species; thus, researchers often
disagree on whether a new feature (e.g. pathogenic vs. non-pathogenic, with everything else essentially
identical) is sufficient to designate two strains as separate species. Even genetic parameters (e.g. rRNAgene
sequence or DNA-DNAreassociation) use arbritrary cut-offs to determine species and/or genus level
differences. The compromise position has been to use polyphasic taxonomy, where a number of different
parameters, both genetic and phenotypic, must agree in order to designate a new species. However, this is
still only for the convenience of the researchers and may have no biological significance. 3. Anew species definition based on the concept of ecotypes was proposed by Cohan in a series of
papers starting in the late 1990s. In this concept, a population is a new species if it occupies a new niche.
The role an organism plays in its environment is known as its niche. Niche is defined by a variety of
overlapping parameters determined by environmental conditions and biological interactions. The
exclusionary principle says that only one species can occupy each niche. The niche is determined by
negative and positive interactions with biotic and abiotic components of the environment. For example, a
species will have a specific temperature (or moisture, or pH, or redox potential, or salinity, or light, or…..)
range. There is an optimal range, in which the species will be abundant, zones at either end of physiological
stress (where the species is present but at low levels), and zones below or above which the species is absent
because it is unable to grow. If we think about all of the possible environmental components and the optimal
range for a particular species (i.e. graph each parameter in a single dimension, and then project those in
overlapping n-dimensions, where n is the number of different parameters), these determine the niche of that
The ecotype concept turns the exclusionary principle on its head—it says that the thing that
defines a species is that it occupies a niche. You can tell whether two similar populations are
different ecotypes if they respond differently to a periodic selection event. For example, in a
community consisting of three ecotypes (ecotype I, II, and III), a cell in ecotype I has an adaptive
mutation that makes it better adapted to it’s niche than its siblings. Thus, it takes over the niche,
eliminating the cells that do not have the mutation by out competing them for substrates and out
growing them. However, this adaptation has no effect on the other ecotypes—the adaptive mutation
does not affect them and they are not eliminated from the system. If this happens enough times, then
the population is sufficiently different from the original one that it occupies a different niche and
hence becomes a different ecotype. This definition has the advantage that it has a biological basis
and directly links species definitions to their ecology. However, if we use this definition, most
groups that we currently call “species” should be redefined as genera, and most groups that we
currently call “strains” are really species. This greatly complicates our understanding of ecosystems
(including the human ecosystem) and the interactions of microbes with their environments.
4. It is unknown how many bacterial species exist—only about 6,000 have been formally named based
on the strict criteria necessary for naming new organisms. However, a conservative estimate is that there are
between 100,000 and 200,000 microbial species, and there may be several million. As a result, it is very
easy to find a microorganism that is “new to science”—including at the species, genus, family, or even
phylum level. Note that there is much less diversity in physiology than in genomes: metabolism is restricted
to the periodic table, whereas genetic diversity is nearly unlimited.
IV. What is diversity?
Species richness is the total number of species in a particular sample. Species evenness is the relative
abundance of those species. Species composition is which species are present. It is possible to have two
communities (i.e. a group of species living in the same place at the same time) that have identical species
richness, yet very different species evenness or species composition. In a community showing dominance
of one or a few species, the community shows much lower overall diversity than one with evenly distributed
species abundance. In two communities with identical richness and evenness, but different composition,
entirely different processes may occur. Thus all three concepts are necessary to fully describe overall
diversity. V. Microbial ecology
The exclusionary principle assumes that each species will be able to grow to its maximum population
density, thereby pushing all competing species out of that niche. Microorganisms have both positive and
negative interactions with their environment. Positive interactions (e.g. availability of nutrients) allow the
population density to increase with increasing growth rate to a maximum growth rate. On the other hand,
there are negative interactions (such as competition or predation) that lead to a decrease in the growth rate
with increasing population density. The combination of these factors leads to a situation where the