Microbial Habitat

BY: DR WAN ZUHAINIS BT MOHD SAAD

Microbial Habitat and its Microbial Inhabitants
- Three major divisions
a) atmosphere
b) hydrosphere c)
lithosphere
- Influenced by physical and chemical characteristics
- M/os can be
a) autochthonous (indigenous)
adaptive features
functional (metabolically active)
competitive

b) Allochthonous (foreign)
transient members
great variation in length of time of survival
Hydrosphere
- Ecosystem which contains water
- General characteristics of m/os that survive in water
a) grow at low nutrient concentrations
b) motile
c) some exhibit unusual shapes
- Divided into
a) freshwater habitat
b) marine habitat
General influencing factors in aquatic
environments:
a) Light
- Determine the rate of photosynthesis
- Dependent on clarity of water, season and latitude

b) Temperature
- Determined by the latitude and weather condition
- Distribution of heat dependent upon mixing of
water
- Large body of water more stable in temperature
c) Pressure
- Inland water (not important), oceans (important)
- Increases 1 atm with each 10 m in depth
- Affects metabolism of organisms and dissociation of
carbonic acids decrease in pH

d) Nutrient
- Varies.extremely low to high.
e) Dissolved gas
- Two most important gasses:
i. Oxygen: for aerobic biological processes

ii. CO2 : for photosynthetic processes

pH equilibrium
Oxygen
- Deep aquatic environment low O2 diffusion
environment.
- Thin water film high O2 diffusion environment
- O2 in water:
i) Slow diffusion
ii) Influencing factor: temperature and pressure.
- Rate of usage is faster than it can be replenished
- Aeration facilitated by surface turbulence
CO2
- Increase in CO2 will decrease pH
- Solubility affected by temperature
- Solubility is 3x higher than O2

Other gases
- N2 gas: N source for N2 fixers
Solubility is half of O2
- Methane: waste product
least soluble among the gasses.
Freshwater habitats
- Classification
a) lentic habitats
b) lotic habitats
- With higher vertical gradients over much shorter
distances
The neuston layer of freshwater habitat
- Neuston layer
uppermost layer of hydrosphere
interface between hydrosphere and atmosphere
- Microbial populations
photoautotrophic m/os
aerobic heterotropic m/os
- Usually 10 to 100-fold higher than underlaying water
Lakes/Ponds
- 4 zones based on penetration of sunlight
a) Littoral zone Combination = euphotic zone
with photosynthetic
b) Limnetic zone
activity
c) Light compensation level
d) Profundal zone - Beyond the depth of effective
light penetration
- Not observed in shallow ponds
a) Littoral zone
- Full light penetration
- Shallow water near shore
- Dominated by submerged or partially submerged
higher plants, algae and cyanobacteria

b) Limnetic zone
- Open water away from shore
- Full penetration of light
- Primary producers algae and
cyanobacteria
c) Light compensation point (LCP)
- Lowest level having effective light penetration
- Photosynthetic activity = respiratory
activity - Green nonsulfur and purple sulfur
d) Profundal zone
- Very low penetration of sunlight
- High in organic nutrients
- Mostly anaerobic heterotrophs
- Zonation of lakes based on temperature
a) epilimnion
- warm and O2 rich
b) thermocline
- rapid decrease of temperature
c) hypolimnion
- below thermocline
- low temperature
- low O2 concentrations
- poor light penetration
- Zonation of lakes based on temperature
a) epilimnion
- warm and O2 rich
b) thermocline
- rapid decrease of temperature
c) hypolimnion
- below thermocline
- low temperature
- low O2 concentrations
- poor light penetration
 Stratification and productivity
during summer stratification, phytoplankton confined to
epilimnion
phytoplankton (free-floating algae) contribute most of
primary production
productivity dependent on nutrient inputs to lake
(ground- and surface-water inputs), and nutrient
recycling in epilimnion
decomposition rates typically high in epilimnion
(aerobic environment)
rapid nutrient uptake by phytoplankton results in low
nutrient availability in epilimnion
dead organic matter sinks to hypolimnion
decay depletes O2, causing anaerobic environment
Factors affecting growth of m/os in ponds
and lakes
a. Temperature (0-100oC) moderate temperature

b. pH preferable neutral
c. Oxygen
Limiting factor
d. Sunlight penetration
e. Nutrients
- Oligotrophic
Nutrient-poor
O2 saturated
low microbial population Lake Vostok

- Eutrophic nutrient-rich
Nutrient-rich
Sediments of organic matter
Epilimnion: aerobic
Hypolimnion: anaerobic
Oligotrophic
-Water is clear
- Deep
- Free of weeds
- No algae blooms
- Low nutrients
- Do not support big fishes
Eutrophic
-Water is not clear
- Shallow (sediments)
- Weeds
- Algae blooms
- High nutrients
- Support big fishes
- Eutrophication nutrient-enrichment
- Stimulates growth of plants, algae and bacteria

Eutrophication is apparent as increased

turbidity in the northern part of the
Caspian Sea, imaged from orbit.
Effects of
eutrophication

Nu ru
in
tr nof
ie f
nt
s
Nutrients fertilize small
floating aquatic plants

Light penetration is reduced

Reduced
submerged
aquatic Plants die off decompose
vegetation depletion of O2 in water

Lack of O2 animals die

 Composition and Activity of Microbial Communities in Lakes/Ponds

0 O2
Cyanobacteria
Epilimnion

Chlorobiaceae and
Chromatiaceae
Depth (m)

10
Hypolimnion

Colorless sulfur Heterotrophic H2S

bacteria and sulfate- bacteria
reducing organisms
20
- Surface with full light penetration autochthonous
photoautotrophic bacteria e.g. cyanobacteria
- Photoautotrophic members e.g. Chlorobiaceae and
Chromatiaceae
- Heterotrophic bacterial are distributed throughout
- In the sediments:
Anaerobic photoautotrophic bacteria
Anaerobic bacteria e.g. Pseudomonas
Obligate anaerobic bacteria e.g. endospore forming
Clostridium spp., methanogenic bacteria and Desulfovibrio
spp.
- Other microorganisms
Algae autochthonous, contribute most of the organic C
Protozoa autochthonous, graze on algae and bacteria.
Allochthonous m/os e.g. cellulolytic form of fungi
Nutrient cycles in Lakes and Ponds
- Phytoplankton grow and fix CO2 to form organic matter, acquire N
and P from water.
- Biomass of phytoplankton enter microbial loop
- Phytoplankton release dissolved organic matter (DOM).
- DOM used by heterotrophic bacteria transformed to
bacteria [particulate organic matter (POM)].
- Heterotrophic bacteria (POM) consumed and digested by large
predators release C as CO2 and other nutrients recycled to
phytoplankton.
 CO2

Phytoplankton
N, P

DOM

Heterotrophic
bacteria/POM CO2, N, P
and
minerals
Protozoa

Zooplankton

MICROBIAL
Top consumers LOOP
 Principal ecological functions of
microorganisms in fresh water environments:

Decompose dead organic matter

Assimilate and reintroduce DOM
Perform mineral cycling activities
Contribute to primary production
Serve as a food source for grazers
Streams and Rivers
- Sufficient water movement minimize
vertical stratification
- Most microbial biomass is attached to surfaces
- Source of nutrient:
a) In-stream production
b) Outside the stream
- Limited capacity to process added organic matter
E.g. point source of pollution cause
nonpoint source of pollution depletion of O2
Streams and Rivers
- Sufficient water movement minimize
vertical stratification
- Most microbial biomass is attached to surfaces
- Source of nutrient:
a) In-stream production
b) Outside the stream
- Limited capacity to process added organic matter
E.g. point source of pollution cause
nonpoint source of pollution depletion of O2
Marine environments
- 97 % of earths water
- High pressure refrigerator
- Pressure 1 atm/10 meters depth Barophiles
- Salinity: approx. 35%
- pH 8.3-8.5
 Horizontal Stratification of Marine Habitats
Neretic
Intertidal Oceanic
1 Euphotic zone
Continental
shelf Aphotic zone
3 Continental
slope
Depth (km)

Continental
5 rise

Abyssal plain

7
Ocean trench
a.) Intertidal zone
- interface between marine ecosphere and litosphere
- at seashore
- with alternate periods of flooding and drying
b.) Neritic zone
- nearshore zone
- from low tide mark to edge of continental shelf
- average depth is less than 200 m
c.) Continental slope (or bathyl region)
- Sloping from edge of continental shelf and drops down to the
sea floor (abyssal plain) about 6,000 m
d.) Ocean trench (or hadal region)
- Extend down to 11,000 m in depth

** Euphotic zone
- Area with effective light penetration
- Below euphotic zone is aphotic zone
 Vertical Stratification of Marine Habitats

Land Pelagic zone

200 Epipelagic
zone

Littoral
1000 zone

Sublittoral
Depth (m)

zone Bathypelagic
zone

6000

Benthic zone
a.) Pelagic zone
- Can be divided into
i) Epipelagic zone
0 to 200 m
euphotic and warm
ii) Mesopelagic
200-1000m
iii) Bathypelagic zone
1000 - 4000 m
aphotic and cold with extreme
pressure
 Factors affecting growth of m/os in
marine environment:
a. Hydrostatic pressure (barophiles)
b. Light
- Different wavelengths at different depths.
Light absorbed Depth
Red

Orange Increase

Yellow 25 30 m

- Only euphotic zone (top 100 m) primary productivity

Green

Blue
c.) Temperature
d.) Nutrient
- Usually low at surface water
- Increase beneath the euphotic zone
- Surface nutrient improve only during upwelling
process

Land
Wind-driven surface
current

Continental slope
Upwelling to replace
surface water
Nutrient recycling in marine environment
- Recycling of mineral nutrients extremely slow
- Dead organisms from euphotic epipelagic zone
bathypelagic benthic zone liberated in the
process.
- Nutrients returned to surface by upwelling currents
(usually at continental slope)
- Primary production in euphotic zone limited by
nutrients
Nutrient-rich deep waters lack light energy for
photosynthetic primary production
Features of autochthonous m/os of the
marine environment
a) Growth at high salinity. Adaptations??
b) Growth at low-nutrient concentrations.
Adaptations: absorb to algal surfaces or increase
surface area
c) Growth at low temperature. Adaptations??
d) Withstand great hydrostatic pressure barotolerant
bacteria
Composition of Marine Microbial Communities
- Pelagic marine habitat macro- and m/os but lack
higher plants.
- All primary production by microscopic algae and
bacteria
- Microbial numbers relatively high in nearshore and
upwelling waters
- Heterotrophic bacteria associate with algal surfaces
Composition of Marine Microbial Communities
- Pelagic marine habitat macro- and m/os but lack
higher plants.
- All primary production by microscopic algae and
bacteria
- Microbial numbers relatively high in nearshore and
upwelling waters
- Heterotrophic bacteria associate with algal surfaces
Marine microbial community
Mostly gram negative bacteria e.g. Pseudomonas,
Vibrio, Flavobacterium
Gram positive e.g. Bacillus in marine sediments
Desulfovibrio in sediments (reduce sulfate to H2S)
Methanogens in sediments
Chemolithotropic bacteria e.g. Nitrosococcus,
Nitrosomonas, Nitrospina, Notrococcus, Nitrobacter (N
cycling)
Marine algae of various divisions
Phaeophyta (brown algae) upper littoral zone to
sublittoral zone (at a depth of 220 m in clear tropical
water)
Marine plankton (Chlorophyta and Chrysophyta) at
upper region of ocean (0-50 m)
Green algae (above 30 m)
Marine protozoa
Lithosphere
- Land masses (rocks and soil)
- Most important terrestrial habitat soil
- Different inorganic and organic components. Influence
by:
a.) weathering of rocks
b.) decomposition of plants
c.) redistribution of materials by water
movement.
Soil
- Form from weathering of rocks
- Classified by relative proportions of clay, silt, and sand
particles.
- A good soil
able to hold sufficient water
sufficient drainage
sufficient gas-filled pores
Physicochemical conditions which affect the
microbial populations:
A.) Surfaces
- Smooth difficult for adherence
- With enough nutrients (organic or minerals) and
moisture e.g. clay
- Clay particles
contain minerals e.g. kaolinite, montmorillonite
and illite
coated with metal hydroxides and sesquioxides
carry polarized but electronegative charges m/os
can absorb
B.) Water ( Moisture)
- Thin water films O2 at high level and easily
replenish
- Soil particle as small as 2 mm can be aerobic outside
and anaerobic inside
- Dependent on rainfall
particle size
drainage
- Affects movement of m/os between pores and
particles.
c.) Temperature
- Determine the composition of soil microflora
- Varies depending on
latitude and altitude
depth
d.) Acidity and Alkalinity
- Usually pH 4-8.5 (bacteria pH 6-8; molds any
pH/acidic)
- Influenced by
a) microbial metabolic activity
b) time of the year Rain leaches bases soil
c) climate acidic
d) previous cropping history e.g. type of litter and
fertilizer
e.) Soil atmosphere
- Well-drained soil well aerated
- Influenced by
soil particle size
Small particles more sealed voids microbial
respiration occur O2 decline, CO2 and other
gaseous metabolites increase
depth
Population of the soil:
Microorganisms Highest in
number
Roots of plant
Invertebrate animals (nematodes,
earthworks, snails, insects and etc.)
Soil Population - Bacteria
- Bacteria most numerous (106-109 viable cells per cm-3)
- Aerobic bacteria - 70%
Anaerobic bacteria - 14%
Filamentous bacteria - 13%
- Location: surfaces of soil particle (soil pore), water & nutrients
- Role: cycling and transformation of C, N, P, iron and
sulfur of soil
- Photoautotrophic bacterial population e.g. cyanobacteria found
on soil bare of plants.
- M/os converting atm N2 to fixed forms of N e.g. Azobacter,
anaerobic Clostridium, Rhizobium, Bradyrhizobium
A ton of microscopic bacteria may be active in each acre of soil.

Credit: Michael T. Holmes, Oregon State University, Corvallis

Bacteria dot the surface of strands of fungal hyphae.

Credit: R. Campbell. In R. Campbell. 1985. Plant Microbiology. Edward Arnold; London. P. 149.
Reprinted with the permission of Cambridge University Press.
Actinomycetes, such as this Streptomyces, give soil its "earthy" smell.
Credit: No. 14 from Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al., eds. SSSA , Madison, WI
Nodules formed where Rhizobium bacteria infected soybean roots.
Credit: Stephen Temple, New Mexico State University
Soil Population - Fungi
- Fungi 3 %
- Tolerate wide pH range
- Abundant in well aerated soil.
- Fungi: bridge open areas between soil particles
- As free-living or associate with plant root
- e.g Aspergillus, Geotrichum, Penicillium, Trichoderma
- Mostly are opportunistic.
- Role: Plant/animal residue decomposition
Tree roots (brown) are connected to the symbiotic mycorrhizal structure
(bright white) and fungal hyphae (thin white strands) radiating into the soil.

Credit: Randy Molina, Oregon State University, Corvallis

Fungus beginning to decompose leaf veins in grass clippings.
Ectomycorrhizae are important for nutrient absorption by tree and grape roots.
The dark, round masses inside the cells of this clover root are vesicules
for the arbuscular mycorrhizal fungus (AM).
Soil Population - Protozoa
- Minority
- Role: Predators of soil bacteria
- Protozoa: exposed outer surface of surface
particle (top 15 cm)
Notice the size of the speck-like bacteria next to the oval
protozoa and large, angular sand particle.
Credit: Elaine R. Ingham
Bacteria ingested by an amoeba.
Credit: No. 35 from Soil Microbiology and Biochemistry Slide Set. 1976. J.P. Martin, et al., eds.
SSSA, Madison, WI
Flagellates have one or two flagella which they use to propel or pull their way
through soil. A flagellum can be seen extending from the protozoan on the left.
The tiny specks are bacteria.
Credit: Elaine R. Ingham
Soil Population - Others
- Cyanobacteria, algae
- Viruses
- Allochthonous m/os from water, wind, dust,
plants, animal sources
Sources of substrates for microbial growth
a) Inorganic sources
- Obtained from mineralization of plant or
animal residue by microbial population
- Fertilizers
b) Organic matter
- CO2
- Crop residues - cellulose, lignins, pectins,
proteins and etc.
- Animal residues - glycogen, proteins, fats
- Plant root exudates simple sugar, a.a,
organic acids
Energy flow in soil
Crop and animal residues

Degradation to produce Mineralization

simpler molecules

Source of nutrient for

m/os and plants
Animal as a habitat
- Potential microbial colonization surfaces: skin, oral
cavity, gastrointestinal, respiratory, urinogenital
- Access via contact, ingestion or inhalation
Factors affecting the composition of the flora
a.) Anatomical and physical characteristics
- Each location with different environmental
conditions
- Oral cavity: food mixed with saliva
- Alimentary tract: reduced particle size, presence of
proteolytic enzymes, bile salt, secretions from
intestinal cells
- Privilege if m/os can adhere to surfaces
e.g. lactobacilli adhere to squamous epithelium of
stomach, yeasts to secretory epithelium of stomach
and etc.
 Advantages of adherence
a) prevent being wash out from the gut
b) formation of biofilm optimum nutrient benefit

- Skin:
Low water availability
Stratum corneum is regularly shedded
Permanent sites hair follicles and sweat
or sebaceous glands
 Advantages of adherence
a) prevent being wash out from the gut
b) formation of biofilm optimum nutrient benefit

- Skin:
Low water availability
Stratum corneum is regularly shedded
Permanent sites hair follicles and sweat
or sebaceous glands
b.) Anaerobiosis
- Alimentary tract O2 tension varies
- Skin high O2 tension aerobic m/os
- Lumen of hair follicles, sweat and sebaceous glands
anoxic environment facultative and strictly
anaerobic bacteria
c.) Temperature
- Warm blooded animal not much influence on
microbial population
- Poikilothermal animals changes of microbial
population depending on environmental
temperature
d.) Acidity
- Oral cavity: pH 7-7.5 (regulate by saliva)
- Stomach hydrochloric acid pH to 2-3
- Skin pH 5.0-6.5
- Also influenced by diet
e.) Osmotic pressure
- Osmolality varies with type of food eaten
- High volume of water, osmotic pressure falls

f.) Water availability

- Growth limiting factor for skin m/os
- Preferably high humidity areas
Microbial Contributions to Animal Nutrition
a) Predation of M/os by Animals
- Grazing on fecal pellet by coprophagous
animals
- Digestion during 1st passage incomplete.
- Excreted fecal material decomposed by
remnants of intestinal m/os and m/os from
environment
- Reingestion of fecal material more
complete utilization of the food resource.
- Snails slime trails bacterial, fungal, and algal
populations colonize
- Animals retrace their tracks graze on the
microbial populations
b) Cultivation of M/os by Animals for Food and
Nutrition
- Herbivorous animals m/os to degrade plant
materials and produce substances that they can
assimilate
- Rumen m/os convert cellulose, starch into CO2, H2,
methane, organic acids
- Contribution of rumen microbial:
i. Digest plant materials
ii. Source of nutrient for animals

- Contribution of host animal

i. Continuous supply of substrate
ii. Rumination provides increased surface area
iii. Movement of ruminant stomach
sufficient mixing
iv. Continuous removal of low
mw acids from rumen facilitate microbial
growth