Ecology & Laboratory Instrumentation BBO6T13

Syllabus topics (RTMNU)

• Ecology: Definition, Branches and significance of ecology
• Climatic factors: Atmospheric (Gaseous composition), Effect of light and temperature on vegetation
• Edaphic factors: Pedogenesis, soil profile, physical and chemical properties of soil
• Biogeochemical cycles: Carbon cycle, Nitrogen cycle and Phosphorous cycle

Ecology: Definition, Branches and Significance

Definition: Ecology is the study of the relationships of living organisms with each other and with their environment. The term "Oekologie" was coined by Ernst Haeckel (1866) — from Greek oikos (house) + logos (study). Indian ecology owes much to Prof. R. Misra, the "father of Indian ecology".

Branches:

• Autecology: ecology of a single species or individual in relation to its environment.
• Synecology: ecology of groups — communities and ecosystems.
• Habitat-based: freshwater, marine, terrestrial, forest, grassland ecology.
• Applied: population ecology, community ecology, ecosystem ecology, conservation ecology, pollution ecology, human ecology, palaeoecology.

Significance: helps in conservation of biodiversity and natural resources; pollution control; forest, grassland and wildlife management; agriculture (crop–weed–pest relations); understanding climate change; environmental impact assessment; land-use planning.

Climatic Factors: Atmosphere (Gaseous Composition)

The atmosphere is the gaseous layer around the earth. Composition of dry air by volume: nitrogen about 78%, oxygen about 21%, argon about 0.93%, carbon dioxide about 0.04%, and traces of neon, helium, methane, ozone, hydrogen; plus variable water vapour and dust.

• O₂ — for respiration of all organisms.
• CO₂ — raw material of photosynthesis; greenhouse gas that keeps earth warm; its rise causes global warming.
• N₂ — fixed by microbes into usable nitrogen.
• Ozone in the stratosphere absorbs harmful UV rays.
• Water vapour — humidity, rainfall, affects transpiration.

Effect of Light and Temperature on Vegetation

Light (intensity, quality, duration):

1. Photosynthesis depends on light intensity and red/blue wavelengths.
2. Heliophytes (sun plants) vs sciophytes (shade plants) — differ in leaf thickness, chlorophyll and stomata.
3. Photoperiodism: day length controls flowering (SDP, LDP).
4. Phototropism and germination (some seeds need light, e.g. lettuce).
5. Very high light causes solarisation (destruction of chlorophyll) and higher transpiration.
6. Layering (stratification) of forest vegetation depends on light.

Temperature:

1. Controls rates of enzyme activity, photosynthesis, respiration and transpiration.
2. Each plant has cardinal temperatures — minimum, optimum, maximum.
3. Determines distribution of vegetation — tropical, temperate, alpine zones (Raunkiaer's and Köppen's classifications use it).
4. Vernalisation: low temperature promotes flowering in some plants (e.g. winter wheat).
5. Extremes cause injury — frost injury, chilling, heat injury and desiccation.
6. Plants classed as megatherms, mesotherms, microtherms, hekistotherms by temperature need.

Edaphic Factors: Pedogenesis and Soil Profile

Edaphic factors are soil-related factors affecting plants.

Pedogenesis (soil formation): (1) Weathering of parent rock — physical (temperature change, frost, wind, water), chemical (hydration, oxidation, carbonation, solution) and biological (lichens, roots, microbes) — forms regolith. (2) Humification — decomposition of dead organic matter into humus. (3) Mineralisation — release of inorganic nutrients. (4) Eluviation (washing down of materials) and illuviation (deposition in lower layers) produce horizons. Factors: climate, parent material, organisms, topography and time.

Soil profile: a vertical section of soil showing layers (horizons).

Physical and Chemical Properties of Soil

Physical: (1) Texture — proportion of sand (2–0.02 mm), silt and clay (< 0.002 mm); loam is best for plants. (2) Structure — arrangement of particles into crumbs/aggregates. (3) Porosity — pore space for air and water. (4) Water holding capacity — high in clay, low in sand; forms of soil water: gravitational, capillary (available to plants), hygroscopic. (5) Soil air and temperature. (6) Colour — black soils of Vidarbha (regur) are rich in clay and good for cotton.

Chemical: (1) Soil pH — acidic, neutral, alkaline; most crops prefer 6–7.5. (2) Mineral nutrients — macro (N, P, K, Ca, Mg, S) and micro (Fe, Zn, Cu, Mn, B, Mo). (3) Cation exchange capacity — ability of clay–humus to hold cations. (4) Organic matter/humus — improves fertility. (5) Salinity and alkalinity.

Biogeochemical Cycles: Carbon, Nitrogen and Phosphorus Cycles

Biogeochemical cycle: circulation of elements between living organisms and the non-living environment (air, water, rocks).

Carbon cycle (gaseous): CO₂ of air → fixed by photosynthesis into organic matter → passes along food chains → returned as CO₂ by respiration of plants, animals and decomposers. Some carbon gets locked as fossil fuels and limestone; returned by burning and weathering. Oceans dissolve large amounts of CO₂. Human activities (fossil fuels, deforestation) increase atmospheric CO₂.

Nitrogen cycle (gaseous):

1. Nitrogen fixation: N₂ → NH₃ by Rhizobium (in legume nodules), Azotobacter, Nostoc, Anabaena; also by lightning and industry (Haber process).
2. Assimilation: plants absorb NH₄⁺/NO₃⁻ and form proteins.
3. Ammonification: decomposers convert dead protein to NH₃.
4. Nitrification: NH₃ → NO₂⁻ (Nitrosomonas) → NO₃⁻ (Nitrobacter).
5. Denitrification: NO₃⁻ → N₂ (Pseudomonas, Thiobacillus denitrificans).

Phosphorus cycle (sedimentary — no gaseous phase): phosphate rocks weather → phosphate in soil and water → absorbed by plants → animals → returned by decomposition of dead bodies and excreta; some lost to ocean sediments and returns only over geological time (uplift); guano and fertilisers add phosphate. Phosphate is often a limiting nutrient; runoff causes eutrophication.

Likely exam questions

1. (Long, 8 marks) Define ecology. Describe the effect of light and temperature on vegetation.
2. (Long, 8 marks) What are edaphic factors? Explain pedogenesis, soil profile and the physical and chemical properties of soil.
3. (Short, 4 marks) Explain the nitrogen cycle.
4. (Short, 4 marks) Write the gaseous composition of the atmosphere.
5. (Short, 4 marks) Why is the phosphorus cycle called a sedimentary cycle?

Syllabus topics (RTMNU)

• Ecosystem: Definition, types, Components - Biotic and abiotic components, food chain, food web, Ecological pyramids
• Autecology: Definition, Importance, Ecads, Ecotypes: Characteristics and importance
• Synecology: Definition, study of community
• Quantitative characteristics - Frequency, Density, Abundance
• Qualitative characteristics - Life forms, Raunkiaer's biological spectrum
• Plant succession: Definition, causes of succession, Hydrosere and Xerosere

Ecosystem: Definition, Types and Components

Definition: An ecosystem is a functional unit of nature in which living organisms interact with each other and with their physical environment, with flow of energy and cycling of materials. The term was given by A.G. Tansley (1935).

Types: (1) Natural — terrestrial (forest, grassland, desert) and aquatic (pond, lake, river, marine, estuary); (2) Artificial/man-made — crop field, garden, aquarium, dam.

Components:

• Abiotic: inorganic substances (C, N, P, water, CO₂, O₂), organic compounds (proteins, carbohydrates, humus), and climatic factors (light, temperature, rainfall, humidity).
• Biotic: (a) Producers — green plants, algae (autotrophs); (b) Consumers — primary (herbivores), secondary (carnivores), tertiary (top carnivores); (c) Decomposers — bacteria and fungi that break dead matter into simple substances.

Food Chain, Food Web and Ecological Pyramids

Food chain: a series of organisms through which energy passes by eating and being eaten. Example (grassland): grass → grasshopper → frog → snake → hawk. Types: grazing food chain (starts with green plants) and detritus food chain (starts with dead organic matter). Each step is a trophic level. Only about 10% of energy passes to the next level (Lindeman's 10% law).

Food web: a network of interconnected food chains in an ecosystem. It gives stability — if one food source fails, consumers use another.

Ecological pyramids (Charles Elton, 1927): graphic representation of trophic levels, producers at the base.

Autecology: Definition, Importance, Ecads and Ecotypes

Autecology: the study of an individual species in relation to its environment — its life history, distribution, adaptations and responses to factors. Importance: helps in crop improvement, conservation of rare species, weed control and understanding species distribution.

Ecads (ecophenes): plants of the same species showing different forms in different habitats due to environmental effect only; the changes are not genetic and disappear when grown in the same habitat. Example: plants grown in sun and shade have different leaf sizes.

Ecotypes: genetically distinct populations of a species adapted to particular habitats; the differences are genetic and permanent, and they remain interfertile with other ecotypes. Example: ecotypes of Euphorbia hirta or Potentilla glandulosa (Clausen, Keck and Hiesey's transplant experiments).

Synecology: Quantitative Characteristics — Frequency, Density, Abundance

Synecology is the study of plant communities. Quantitative features are measured by the quadrat method (square plots, e.g. 1 m × 1 m, laid at random).

Worked example: 10 quadrats were laid.

Raunkiaer's frequency classes: A (1–20%), B (21–40%), C (41–60%), D (61–80%), E (81–100%). Law of frequency: A > B > C ≥ or ≤ D < E. If E > D, the community is homogeneous.

Qualitative Characteristics: Life Forms and Raunkiaer's Biological Spectrum

Life forms (Raunkiaer, 1934) are based on the position of perennating buds during the unfavourable season:

1. Phanerophytes — buds high above ground (trees, shrubs); tropical climate.
2. Chamaephytes — buds near soil surface (up to about 25 cm); cold climates.
3. Hemicryptophytes — buds at soil surface; temperate.
4. Cryptophytes — buds below soil or water (geophytes, helophytes, hydrophytes).
5. Therophytes — annuals surviving as seeds; deserts.

Biological spectrum: the percentage of each life form in the flora of a region. Percentage = (number of species of a life form ÷ total species) × 100. Comparison with Raunkiaer's normal spectrum shows the phytoclimate — e.g. high phanerophytes = phanerophytic (tropical) climate; high therophytes = arid climate.

Plant Succession: Definition, Causes, Hydrosere and Xerosere

Definition: the gradual and orderly replacement of one plant community by another in an area until a stable climax community is formed (Clements). The series of communities is a sere; each stage is a seral stage.

Causes: (1) Initiating — bare area formed by erosion, fire, volcano, flood; (2) Continuing — migration, ecesis (establishment), aggregation, competition, reaction (modification of habitat); (3) Stabilising — climate brings the climax.

Hydrosere (starts in water — pond): phytoplankton stage → submerged stage (Hydrilla, Vallisneria) → floating stage (Nymphaea, Trapa, Pistia) → reed-swamp stage (Typha, Phragmites) → sedge-meadow stage (Cyperus, Carex) → woodland stage (shrubs, Salix) → forest climax. Each stage adds silt and humus, making the pond shallower.

Xerosere (starts on bare rock): crustose lichens (Rhizocarpon) → foliose lichens (Parmelia) → mosses (Funaria, Polytrichum) → herbs and grasses → shrubs → forest climax. Lichens secrete acids that weather rock and start soil formation.

Likely exam questions

1. (Long, 8 marks) Define ecosystem. Describe its components and explain food chain, food web and ecological pyramids.
2. (Long, 8 marks) What is plant succession? Give its causes and describe hydrosere in detail.
3. (Short, 4 marks) Distinguish between ecads and ecotypes.
4. (Short, 4 marks) In 10 quadrats a species occurred in 5 quadrats with 30 individuals. Calculate its frequency, density and abundance.
5. (Short, 4 marks) Explain Raunkiaer's biological spectrum.

Syllabus topics (RTMNU)

• Plant Adaptations: Morphological, anatomical and physiological adaptations of Hydrophyte (Hydrilla, Eichhornia)
• Xerophyte (Nerium, Casuarina)
• Halophyte (Rhizophora)
• Epiphyte (Vanda)
• Environmental Pollution: Causes and control measures of Water pollution, Air pollution, Noise pollution
• Concept of Green Belt development
• Natural Resource: Renewable and Non-renewable resources, factors for their depletion
• Conservation strategies: Definition and Concept of Biodiversity, Biodiversity conservation and conservation of water resources

Plant Adaptations: Hydrophytes (Hydrilla, Eichhornia)

Hydrophytes are plants that grow in water or very wet places. Hydrilla is submerged; Eichhornia (water hyacinth) is free-floating.

Morphological: roots poorly developed or absent (Hydrilla), or fibrous with root pockets (Eichhornia); stem long, slender, flexible (Hydrilla) or a short stolon (Eichhornia); leaves thin, narrow, ribbon-like or dissected in submerged forms; Eichhornia has swollen spongy petioles for floating; fast vegetative propagation by fragmentation and offsets.

Anatomical: cuticle absent or very thin; epidermis has chloroplasts and absorbs water and gases; stomata absent in submerged parts (present on upper surface of floating leaves); aerenchyma (large air chambers) gives buoyancy and stores gases; mechanical tissue and xylem poorly developed; phloem relatively better.

Physiological: absorption through the whole surface; low osmotic pressure; can use dissolved CO₂/bicarbonate; tolerant to low oxygen.

Xerophytes (Nerium, Casuarina)

Xerophytes grow in dry habitats with little water.

Morphological: deep, well-branched root system; Casuarina has green photosynthetic branches (cladodes/phylloclade-like) and leaves reduced to tiny scales; Nerium has thick, leathery, narrow leaves; surface often shiny or hairy.

Anatomical: thick cuticle; multiple epidermis (Nerium leaf has a 2–3 layered epidermis); sunken stomata in hairy pits (Nerium has stomatal crypts with hairs on the lower surface); Casuarina stem has stomata in grooves between ridges; well-developed sclerenchyma and vascular tissue; compact palisade.

Physiological: high osmotic pressure; low transpiration; stomata close in hot hours; some store water (succulents) or show CAM.

Halophytes (Rhizophora)

Halophytes grow in saline soils (sea coasts, estuaries). Rhizophora is a mangrove.

• Stilt (prop) roots from the stem give support in soft mud.
• Pneumatophores (negatively geotropic breathing roots with lenticels) in many mangroves take in air from the oxygen-poor soil.
• Vivipary: seed germinates while the fruit is still on the tree; the seedling drops and fixes in mud.
• Thick, succulent, leathery leaves with thick cuticle and sunken stomata; water-storage tissue.
• High osmotic pressure of cell sap to absorb water from salty soil; salt exclusion by roots and salt secretion/storage.

Epiphytes (Vanda)

Epiphytes grow on other plants only for support, not food. Vanda is an epiphytic orchid.

• Clinging roots fix the plant on the bark.
• Aerial hanging roots with velamen — a spongy, multi-layered dead tissue that absorbs moisture from air and rain.
• Aerial roots are green and photosynthetic.
• Thick leaves with cuticle, some water storage; pseudobulbs in some orchids.
• Tiny light seeds dispersed by wind; mycorrhizal fungi help germination.

Environmental Pollution: Water, Air and Noise Pollution

Pollution is an undesirable change in physical, chemical or biological properties of air, water or soil that harms living beings.

Effects in brief: water-borne diseases and fish death; respiratory diseases, acid rain and leaf injury; hearing loss, stress and sleep problems.

Concept of Green Belt Development

A green belt is a strip of trees and shrubs planted around industries, cities, highways or mines to act as a barrier against pollution. Functions: absorb dust and gaseous pollutants, reduce noise, lower temperature, check soil erosion, provide habitat to birds, improve the look of the area. Plant choice: fast-growing, evergreen, pollution-tolerant species with dense canopy — e.g. neem, peepal, Ficus, Pongamia (karanj), Cassia, Casuarina, bamboo; planted in several rows of tall trees, small trees and shrubs.

Natural Resources: Renewable and Non-renewable, and Factors of Depletion

Renewable resources are replaced naturally within a short time — forests, water, wildlife, soil, solar and wind energy. Non-renewable resources take millions of years to form and are limited — coal, petroleum, natural gas, minerals.

Factors of depletion: population growth; over-use and wasteful consumption; deforestation for agriculture, roads and mining; over-grazing; over-exploitation of groundwater; urbanisation and industrialisation; pollution; poor management and lack of awareness.

Conservation Strategies: Biodiversity and its Conservation, Water Conservation

Biodiversity (term made popular by E.O. Wilson) is the variety of life on earth at three levels — genetic, species and ecosystem diversity. India is a mega-diverse country with four biodiversity hotspots (Himalaya, Indo-Burma, Western Ghats & Sri Lanka, Sundaland — Nicobar).

Biodiversity conservation:

• In-situ (in natural habitat): national parks, wildlife sanctuaries, biosphere reserves, sacred groves, community reserves.
• Ex-situ (outside habitat): botanical gardens, seed banks, gene banks, zoos, tissue culture, cryopreservation.
• Laws: Wildlife (Protection) Act, 1972; Forest (Conservation) Act, 1980; Biological Diversity Act, 2002.

Conservation of water resources: rainwater harvesting (rooftop, recharge pits), watershed management, check dams and farm ponds (e.g. Jalyukta Shivar in Maharashtra), drip and sprinkler irrigation, recycling of wastewater, afforestation, reducing leakage and wastage, protecting wetlands.

Likely exam questions

1. (Long, 8 marks) Describe the morphological, anatomical and physiological adaptations of hydrophytes and xerophytes with suitable examples.
2. (Long, 8 marks) Give the causes and control measures of water, air and noise pollution. Add a note on green belt development.
3. (Short, 4 marks) Write the adaptations of Rhizophora.
4. (Short, 4 marks) What is velamen? Give its function in Vanda.
5. (Short, 4 marks) Distinguish between renewable and non-renewable resources.

Syllabus topics (RTMNU)

• Microscopy: Principle, and applications of Microscope (Light and Fluorescent)
• Chromatography: Principle and application of Paper Chromatography and thin layer chromatography (TLC)
• Spectroscopy: Principle and applications of UV, visible spectrophotometer
• Electrophoresis: Principle and applications of SDS-PAGE and Agarose gel electrophoresis
• Principle and applications of Soxhlet extraction unit, Turbidity meter, Double distillation unit, Centrifuge

Microscopy: Principle and Applications of Light and Fluorescence Microscopes

Light (compound) microscope — principle: visible light passes through a thin specimen; the objective lens forms a magnified, real, inverted image, which the eyepiece magnifies again into a virtual image. Total magnification = objective × eyepiece (e.g. 40× × 10× = 400×). Resolving power (ability to show two close points separately) depends on wavelength and numerical aperture (NA): resolution d = 0.61 λ ÷ NA; best limit about 0.2 µm. Oil immersion (100×) increases NA.

Parts: light source/mirror, condenser, diaphragm, stage, objective lenses (10×, 40×, 100×), eyepiece, coarse and fine adjustment.

Applications: study of cells, tissues, pollen, microbes, stained sections; anatomy and histology; identification of algae, fungi; pathology.

Fluorescence microscope — principle: certain substances (fluorochromes) absorb light of a shorter wavelength (UV/blue) and emit light of a longer wavelength (green/red) — fluorescence. A mercury/xenon lamp or LED gives excitation light; an excitation filter selects the wavelength; a dichroic mirror reflects it on the specimen; an emission (barrier) filter passes only emitted light, so bright fluorescent structures are seen on a dark background.

Applications: locating specific proteins and DNA (DAPI stains nuclei; FITC-labelled antibodies — immunofluorescence); GFP-tagged proteins in living cells; detection of microbes; chlorophyll autofluorescence; chromosome studies (FISH).

Chromatography: Paper Chromatography and Thin Layer Chromatography (TLC)

Chromatography (Tswett, 1906 — separated plant pigments) separates components of a mixture by their different distribution between a stationary phase and a mobile phase.

Paper chromatography — principle: partition. Water held in cellulose of Whatman filter paper is the stationary phase; the solvent moving up by capillary action is the mobile phase. Components more soluble in the mobile phase move faster.

Method: spot the sample on a pencil line near one end, dip the end in solvent (ascending), let solvent rise, dry, and detect spots (colour, ninhydrin spray for amino acids, iodine vapour, UV).

TLC — principle: mainly adsorption. A glass/aluminium plate coated with a thin layer of silica gel or alumina is the stationary phase. Faster, sharper separation, needs small sample, can use corrosive sprays.

Applications of both: separation of chlorophyll pigments, amino acids and sugars; checking purity of compounds; identifying active compounds in herbal drugs (e.g. curcumin); detecting adulterants; monitoring reactions.

Spectroscopy: Principle and Applications of UV–Visible Spectrophotometer

Principle: molecules absorb light of specific wavelengths in UV (200–400 nm) and visible (400–800 nm) regions. The amount absorbed is related to concentration by the Beer–Lambert law: A = ε c l, where A = absorbance, ε = molar absorptivity, c = concentration, l = path length (usually 1 cm). Absorbance A = log (I₀/I).

Parts: light source (deuterium lamp for UV, tungsten lamp for visible) → monochromator (prism/grating) → sample cuvette (quartz for UV, glass/plastic for visible) → detector (photocell/photomultiplier) → display/recorder.

Applications: estimating concentration of proteins (280 nm), DNA (260 nm; purity by A₂₆₀/A₂₈₀), chlorophyll (645 and 663 nm — Arnon's method), sugars and enzymes (enzyme kinetics); absorption spectrum of pigments; quality control of drugs.

Electrophoresis: SDS-PAGE and Agarose Gel Electrophoresis

Principle: charged molecules move in an electric field towards the opposite electrode; the speed depends on charge, size and shape, and on the gel's pore size.

SDS-PAGE (sodium dodecyl sulphate–polyacrylamide gel electrophoresis): proteins are boiled with SDS (detergent) and a reducing agent; SDS unfolds them and gives a uniform negative charge, so they separate only by molecular weight through polyacrylamide gel (stacking gel + resolving gel). Smaller proteins move faster. Bands are stained with Coomassie Brilliant Blue; sizes found using a protein marker (ladder). Applications: protein molecular weight, purity, protein profiling of seeds/varieties, Western blotting.

Agarose gel electrophoresis: used for DNA and RNA. Nucleic acids are negative (phosphate groups), move towards the anode (+); smaller fragments move faster through the agarose gel (0.7–2%). Stained with ethidium bromide or safer dyes and seen under UV. Applications: checking DNA isolation and PCR products, size of DNA fragments with a DNA ladder, restriction analysis, DNA fingerprinting.

Soxhlet Extraction Unit, Turbidity Meter, Double Distillation Unit and Centrifuge

1. Soxhlet extraction unit — principle: continuous hot solvent extraction. Solvent in a flask is heated; vapour rises, condenses in the condenser and drips on powdered sample in a thimble; when the chamber fills, the extract siphons back to the flask. The cycle repeats, so fresh solvent extracts the sample many times. Applications: extraction of oils and fats from seeds, plant active compounds, lipid estimation.

2. Turbidity meter (nephelometer/turbidimeter) — principle: suspended particles in a liquid scatter light; the meter measures scattered light (nephelometry, at 90°) or reduction of transmitted light (turbidimetry). Result in NTU (nephelometric turbidity units). Applications: water quality testing, effluent monitoring, bacterial growth in culture, beverages.

3. Double distillation unit — principle: water is boiled, the steam is condensed (first distillation), and the distillate is distilled again in a second boiler (usually of borosilicate glass/quartz). This removes dissolved salts, organic matter and microbes, giving highly pure double-distilled water. Applications: preparing reagents, media, buffers, tissue culture, analytical work.

4. Centrifuge — principle: spinning produces a centrifugal force that makes heavier particles settle (sediment) faster than lighter ones. Force is expressed as relative centrifugal force (RCF, × g) = 1.118 × 10⁻⁵ × r × (rpm)², r in cm. Types: clinical/table-top, high-speed, refrigerated and ultracentrifuge. Methods: differential centrifugation and density-gradient centrifugation. Applications: separation of cell organelles (nuclei, mitochondria, ribosomes), harvesting cells, DNA isolation, separating serum from blood.

Likely exam questions

1. (Long, 8 marks) Explain the principle and applications of light and fluorescence microscopes.
2. (Long, 8 marks) Describe the principle and applications of SDS-PAGE and agarose gel electrophoresis.
3. (Short, 4 marks) What is Rf value? Explain paper chromatography.
4. (Short, 4 marks) State Beer–Lambert law and give applications of a UV–visible spectrophotometer.
5. (Short, 4 marks) Write the principle and uses of a centrifuge.