Topic 5 - Microbial Habitat 1b4j3t

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  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 (L) - 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 - Eutrophic  nutrient-rich  Nutrient-rich  Sediments of organic matter  Epilimnion: aerobic  Hypolimnion: anaerobic

Lake Vostok

Oligotrophic

Eutrophic

-Water is clear

-Water is not clear

- Deep

- Shallow (sediments)

- Free of weeds

- Weeds

- No algae blooms

- Algae blooms

- Low nutrients

- High nutrients

- Do not big fishes

- 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.

s nt ie f tr nof Nu ru in

Effects of eutrophication

Nutrients fertilize small floating aquatic plants Light penetration is reduced Reduced submerged aquatic vegetation

Plants die off  decompose  depletion of O2 in water

Lack of O2  animals die

Composition and Activity of Microbial Communities in Lakes/Ponds 0

O2 Cyanobacteria

Depth (m)

Epilimnion Chlorobiaceae and Chromatiaceae 10 Hypolimnion Colorless sulfur bacteria and sulfatereducing organisms 20

Heterotrophic bacteria

H2S

- Surface with full light penetration  autochthonous photoautotrophic bacteria e.g. cyanobacteria - Photoautotrophic 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

N, P

Phytoplankton DOM Heterotrophic bacteria/POM Protozoa

CO2, N, P and minerals

Zooplankton Top consumers

MICROBIAL 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 earth’s water - High pressure refrigerator - Pressure 1 atm/10 meters depth – Barophiles - Salinity: approx. 35% - pH 8.3-8.5

Horizontal Stratification of Marine Habitats Intertidal

Neretic

Oceanic

1

Depth (km)

3

5

Euphotic zone Continental shelf Continental slope

Aphotic zone

Continental 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 200

Depth (m)

1000

Land

Pelagic zone

Epipelagic zone

Littoral zone Sublittoral 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 Wind-driven surface current Upwelling to replace surface water

Continental slope

Land

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 Rain leaches bases  soil b) time of the year acidic c) climate 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 • Roots of plant

Highest in number

• 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 simpler molecules

Source of nutrient for m/os and plants

Mineralization

Animal as a habitat - Potential microbial colonization surfaces: skin, oral cavity, gastrointestinal, respiratory, urinogenital - Access via , 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 age  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