CHAPTER 9
COMMUNITY STRUCTURE
OF MICROBE IN NATURAL
ENVIRONMENTS
海洋微生物生態学
NGUYEN CHI
Types of bacteria in soils, freshwater, and the oceans
Alphaproteobacterium: Rhizobium
Betaproteobacterium: Burkholderia
Gammaproteobacterial: Alteromonas, Escherichia, Pseudomonas, Salmonella, and Vibrio
Of the 50-100 phyla of bacteria found in the biosphere, only a few (<10) are abundant in any
particular habitat.
Microbial communities are usually dominated by a few phylotypes and clades while most are in
low abundance, making up a rare biosphere.
Types of bacteria in soils, freshwater, and the oceans
Only about 70 have have been classified as being in the Acidobacteria phylum
Over 50% of the total community in low pH soils
Low pH values are less common in lakes than in soils and very rare marine systems, explaining
why this phylum is not abundant in most aquatic systems.
Archaea in non-extreme environments
In soils and surface waters of the oceans –
archaea make up <5% of total microbial
abundance.
The big exception is the deep ocean.
In waters below about 500m, archaea can
account for as much as 50% of all microbes
Many archaea appear to be chemoautotrophs that oxidize ammonia to obtain energy.
This help to explain the apparent negative relationship between archaea and phytoplankton and
light in the oceans.
Everything, Everywhere?
With many large organisms, the same
environmental conditions – different
continents => the same communities
With microbes in soils or water?
Depending on the Bass Becking hypothesis
Similar soil environments & different latitudes
- Bacteria in the Artic Ocean and artic lakes = Antarctic waters
- Archaes in soda lakes of Mongolia and Argentina
- On the giant marine ciliate - Zoothamnium niveum (the 16sRNA genes and genes for carbon
and sufur metabolism) in the Mediterranean Sea = in the Caribean Sea
However, arguments against the Bass becking hypothesis – for Protist
What controls diversity levels and bacterial community structure
Different environments => different microbial communities
Temperature, salinity, and pH
These three physical factors – the
potential to shape bacterial community
structure, although not necessarily the
same for soils and aquatic habitats
Microbial communities – more diverse in warmer water because faster metabolic rates lead to
higher rates of speciation. Even in cold water- can develop high diversity.
Diversity of soil communities varies primarily with pH
Salinity – affect communities structure ( Betaproteobacteria in lakes and in the oceans)
However, Extremes in salinity and in other physical factors do lead to low diversity
What controls diversity levels and bacterial community structure
Moisture and soil microbial communities
Water content has a large impact om microbial activity and diversity in soils
Results from cultivation-independent approaches indicate that bacterial communities are more
even with higher phylotype richness in unsaturated surface soils than in saturated soils which are
dominated by a few bacterial types
What controls diversity levels and bacterial community structure
Organic material and primary production
Diversity of soil bacterial communities does not seem vary with soil organic content or with plant
diversity, although organic carbon additions do affect the make up of soil communities.
In addition to amounts, the type of organic compounds in an environment may effect bacterial
communities.
What controls diversity levels and bacterial community structure
Predation and viral lysis
Top-down control by grazers and viruses limits
standing stocks of microbes and can affect their
growth rates in natural environments.
Both grazing and viral lysis have the potential
for determining the success of specific
microbes and thus in shaping diversity levels
and overall community structure of microbes
The impact of viruses is probably stronger than that of grazers.
Viruses are more abundant than prospective hosts by about tenfold.
Grazers are much less abundant than their prey.
Another important point is that viral lysis increases as the abundance of the host microbe goes up
because encounter rates between viruses and hosts. Depend on the abundance of each
Problems with 16S rRNA as a taxonomic and phylogenetic tool
16S rRNA gene tool problem
One is that many bacteria have several copies of this gene.
For example: Pelagibacter ubique to as many as 15, a record now held by Clostridium
paradoxum and Photobacterium profundum.
However, about the number of 16S rRNA genes/bacterium puts limits on using the abudance of a
16S rRNA gene to estimate the abundance of that bacterium in nature.
Another problem is that 2 microbes that differ substantially in physiology and ecology can have
similar 16S rRNA genes
Problems with 16S rRNA as a taxonomic and phylogenetic tool
Solution
Use other phylogenetic markers
Another marker is intergenic spacer (ITS)
Other phylogenetic markers are genes for various proteins
Community structure of protists and other eukaryotic microbes
Protist can be identified by morphology – by their physical appearance
Problem: different sequences of a phylogenetic marker gene
Community structure of protists and other eukaryotic microbes
Types of protists and other eukaryotic microbes in nature
Cultivation-independent methods that examine various rRNA genes have revealed an even more
diverse that the diversity world of eukaryotic microbes – the phylum Alveolata
Fungi account for a large proportion of the rRNA genes recovered by cultivation-independent
approaches from soils, with protists a close second in one study
Relevance of community structure to understanding processes
In every other field of ecology, identifying the organisms is essential for understanding the role
of organisms in the environment.
The ecology of microbes is likely to be no different, but the connection between community
structure and biogeochemical processes is an open question.
The diversity of microbial communities may be key to the maintenance of biogeochemical
cycles in the biosphere.
Thank you for listening