A note on oligotrophic microbes and life at low nutrient concentrations.

1. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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Oligotrophic Microbes – Life at Low
Nutrient Concentrations
Low nutrient concentration in the environment serves as a limiting factor for microbial
growth. Most of the microbes, present in the environment are heterotrophs and hence
they depend on the available nutrients. Cells mainly use nutrients for two purposes:
maintenance of cellular functions and growth (in both size and number). Heterotrophic
microbes may be either oligotrophs (which live in nutrient-deprived environments) or
corticotrophs (which live in nutrient-rich environments), depending on how much
nutrients they need to survive.
“Oligotrophs are organisms that can live in environments that offer very low levels of
nutrients. While, copiotrophs are organisms found in environments rich in nutrients,
particularly carbon.”
The following table compares the characteristics of oligotrophic and copiotrophic
microorganisms:
OLIGOTROPHIC MICROBES COPIOTROPHIC MICROBES
 They have low growth and metabolic
rates.
 They are highly efficient in substrate
scavenging.
 They frequently live attached to
surfaces.
 They form polymers and storage
products even while starving, and
often aggregate.
 Many oligotrophs alter their
morphology (surface to volume ratio)
with changing nutrient concentrations.
 They have a low substrate affinity.
 They have high growth and
metabolic rates.

2. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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Figure: General comparisons between oligotrophs and copiotrophs.
Culturing a sample of microbes from its natural context (soil, water, etc.) to a nutrient
medium will not allow one to observe all of the species, as the oligotrophs will be
unable to grow in such a nutrient-rich medium, only copiotrophs can be detected via
this method.
There are also certain bacteria such as Aeromonas hydrophila (which is a pathogenic
gram-negative bacteria) which can adapt to a wide range of nutrient concentrations
due to its low level of endogenous metabolism and a low maintenance energy level.
GENERAL RESPONSE OF MICROBES TO STARVATION
The life cycle of some specialized prokaryotes, fungi, and protozoa includes a
resistant, quiescent stage, variously termed endospore, myxospore, cyst, conidium,
etc. Such developmental stages in microbial life cycles are triggered by environmental
cues, especially starvation, received by the microorganism. The resulting resting
stages typically surround vital cytoplasmic constituents with a thick-walled structure
that confers resistance not only to starvation but also to extreme environmental
conditions ranging from heat, to desiccation, to acidity, to γ-irradiation, to salinity, to
UV light.

3. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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Information about the chemical, physical, and nutritional status of a microorganism’s
habitat must be transmitted to the genetic regulatory networks within. Thus, sensing
the environment is a well-honed ability in prokaryotes. Commonly the sensor is a
protein embedded within, but extending out from, the cytoplasmic membrane of the
cell. The environmental change causes an allosteric (structural) alteration in protein
conformation which leads to its self-catalyzed binding to a phosphate molecule. The
term “sensor kinase” applies. The phosphorylation triggers a subsequent series of
phosphorylation events that influence the activity of one or more regulatory proteins.
These, in turn, control gene transcription by binding to the promoter or attenuator
regions of one or more operons. Following translation of the transcribed genes,
protein-catalyzed metabolic changes in the cell eventually deliver negative feedback
to the regulatory circuit.
Figure: Cellular response to environmental stress, i.e. starvation.

4. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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Overall, the cell’s response is matched to the severity of the nutritional stress.
Furthermore, when the stress is relieved, the cytoplasmic sensor resumes its previous
non-phosphorylated state.
The following five processes render microbial populations “fit” for starvation survival:
 All metabolic processes are reduced to a dormant or near-dormant state.
 When starved, many species will increase in cell number via reductive division,
resulting in reduced cell size – hence forming ultramicrobacteria.
Ultramicrobacteria are bacteria that are smaller than 0.1 μm3 under all growth
conditions. They possess a relatively high surface-area-to-volume ratio due to their
small size, which aids in growth under oligotrophic (i.e. nutrient-poor) conditions.
 In the starvation/survival process, any cellular energy reserve material is used to
prepare the cell for survival.
 All metabolic mechanisms are directed to the formation of specific proteins, ATP,
and RNA so that the cell, when it encounters a substrate is equipped to use it
immediately without a delay that otherwise would occur if initial amounts of energy
had to be expended for the synthesis of RNA and protein. Both RNA and protein
synthesis are high energy-consuming processes, and the high ATP level per viable
cell is thus available and used primarily for active transport of substrates across
the membrane. Protective starvation proteins are synthesized and substrate
capturing is enhanced (i.e. amino acid uptake).
 The change to a smaller cell size on starvation (miniaturization) permits greater
efficiency in scavenging what little energy-yielding substrates there are in the
environment and also enhances survival prospects against other adverse
environmental factors.
NUTRIENT DEFICIENT ENVIRONMENTS
The word oligotrophic may also be used as an adjective to refer to environments that
offer little to sustain life, organisms that survive in such environments, or the

5. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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adaptations that support survival. The word “oligotroph” is a combination of the Greek
adjective “oligos” meaning “few” and the adjective “trophikos” meaning “feeding”.
Oligotrophic environments include deep oceanic sediments, caves, glacial and polar
ice, deep subsurface soil, aquifers, ocean waters, and leached soils. Details of some
of these are as follows:
1. Oligotrophic Soils
The oligotrophic soil environments include agricultural soil, frozen soil, etc. Various
factors, such as decomposition, soil structure, fertilization, and temperature, can affect
the nutrient availability in the soil environments.
Deep Subsurface Soils: Generally, the nutrient becomes less available along the depth
of the soil environment, because on the surface, the organic compounds decomposed
from the plant and animal debris are consumed quickly by other microbes, resulting in
the lack of nutrient in the deeper level of the soil. The metabolic waste produced by
the microorganisms on the surface also causes the accumulation of toxic chemicals in
the deeper area. Furthermore, it is difficult for water and oxygen to diffuse to lower
depths. Moreover, the presence of mineral under the soil provides alternative sources
for the species living in the oligotrophic soil.
Frozen Soils: In terms of polar areas, such as the Antarctic and Arctic region, the soil
environment is considered oligotrophic because the soil is frozen with low biological
activities. The most abundant species in the frozen soil are those of Actinobacteria,
Proteobacteria, Acidobacteria, and Cyanobacteria, together with a small amount of
archaea and fungi. Actinobacteria can maintain the activity of their metabolic enzymes
and continue their biochemical reactions under a wide range of low temperatures.
Besides, the DNA repairing machinery in Actinobacteria protects them from lethal DNA
mutations at low temperatures.
2. Oligotrophic Lakes
An oligotrophic lake is a lake with low primary productivity, as a result of low nutrient
content. These lakes have low algal production, and consequently, often have very

6. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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clear waters, with high drinking-water quality. The bottom waters of such lakes typically
have ample oxygen; thus, such lakes often support many fish species such as lake
trout, which require cold, well-oxygenated waters. The term oligotrophic is used to
distinguish unproductive lakes, characterized by nutrient deficiency, from productive,
eutrophic lakes, with an ample or excessive nutrient supply. Oligotrophic lakes are
most common in cold regions underlain by resistant igneous rocks (especially granitic
bedrock).
Figure: Features of an oligotrophic lake.
Some examples of oligotrophic lakes of Antarctica are as follows:
Lake Vostok: It is a freshwater lake that has been isolated from the world beneath 4 km
of Antarctic ice and is frequently held to be a primary example of an oligotrophic
environment. The average water temperature of Lake Vostok is calculated to be
around −3 °C (27 °F); it remains liquid below the normal freezing point because of high
pressure from the weight of the ice above it. Geothermal heat from the Earth's interior
may warm the bottom of the lake, while the ice sheet itself insulates the lake from cold

7. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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temperatures on the surface. Lake Vostok is an oligotrophic extreme environment, one
that is expected to be supersaturated with nitrogen and oxygen, around 50 times more
than ordinary freshwater lakes on Earth's surface. The sheer weight and pressure of
the continental ice cap on top of Lake Vostok is estimated to contribute to the high gas
concentration. Analysis of ice samples showed ecologically separated
microenvironments. Isolation of microorganisms from each microenvironment led to
the discovery of a wide range of different microorganisms present within the ice sheet.
Traces of fungi have also been observed which suggests the potential for unique
symbiotic interactions. The lake's extensive oligotrophy has led some to believe parts
of the lake are completely sterile. This lake is a helpful tool for simulating studies
regarding extraterrestrial life on frozen planets and other celestial bodies.
Figures: Left – a map of Lake Vostok (Antarctica) & Right – layers of the lake.
Krok (Crooked) Lake: Krok Lake is an irregular-shaped glacial lake about 7 km long in
Antarctica. The lake was partially mapped by Norwegian cartographers from air photos
taken by the Lars Christensen Expedition (1936–37) and named “Krokvatnet” (the
crooked lake). It is an ultra-oligotrophic glacial lake with a thin distribution of
heterotrophic and autotrophic microorganisms. The microbial loop plays a big role in
cycling nutrients and energy within this lake, despite particularly low bacterial

8. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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abundance and productivity in these environments. The little ecological diversity can
be attributed to the lake's low annual temperatures.
3. Oligotrophic Oceans
In the ocean, the subtropical regions north and south of the equator are regions in
which the nutrients required for phytoplankton growth (for instance, nitrate, phosphate,
and silicic acid) are strongly depleted all year round. These areas are described as
oligotrophic and exhibit low surface chlorophyll. They are occasionally described as
"ocean deserts".
North Pacific Subtropical Gyre: The North Pacific Subtropical Gyre (NPSG) is the largest
contiguous ecosystem on Earth. Low nutrient concentrations and thus a low density
of living organisms characterize the surface waters of the NPSG. The low biomass
results in clear water, allowing photosynthesis to occur to a substantial depth. The
NPSG is classically described as a two-layered system. The upper, nutrient-limited
layer accounts for most of the primary production, supported primarily by recycled
nutrients. The lower layer has nutrients more readily available, but photosynthesis is
light-limited.
4. Deep Oceanic Sediments
The deep benthic habitats of the ocean consist of some of the most food-poor regions
on the planet. One of the sources of nutrients to this deep ocean habitat is marine
snow, which consists of detritus (dead organic matter) which falls from the surface
waters where productivity is highest.
EXAMPLES OF OLIGOTROPHIC BACTERIA
The details of some notable oligotrophic bacteria are as follows:
Pelagibacter ubique
The bacterium, Pelagibacter ubique, is the most abundant organism in the oceans and
quite possibly the most abundant bacteria in the entire world. The total abundance of
P. ubique and its relatives is estimated to be about 2 × 1028 microbes. They have
sensors for nitrogen, phosphate, and iron limitation, and a very unusual requirement

9. SYED MUHAMMAD KHAN (BS HONS. ZOOLOGY)
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for reduced sulfur compounds. They have been molded by evolution in a low nutrient
ecosystem. A population of P. ubique cells can double every 29 hours, which is fairly
slow, but they can replicate under low nutrient conditions. P. ubique can be grown on
a defined, artificial medium with additions of reduced sulfur, glycine, pyruvate, and
vitamins.
Collimonas spp. (Collimonas fungivorans)
Collimonas spp. is one of the oligotrophic microbes capable of living in nutrient-
deficient soils. One common feature of the environments where Collimonas live in the
presence of fungi because Collimonas cannot only hydrolyzing the chitin produced by
fungi for nutrients but also producing materials to protect themselves from fungal
infection. Additionally, Collimonas can also obtain electron sources from rocks and
minerals by weathering.
Pelagibacter ubique (SEM) Collimonas spp.