F 1 and 2

Explain the principles involved in the generation of methane from biomass, including the conditions needed, organisms involved and the basic chemical reaction that occurs

A variety of types of organic matter may serve as a source of biomass - including manure, seaweed, agricultural materials and sewage Several groups of bacteria are combined in a digester (a vessel where the chemical reactions will occur) Bacteria first convert the organic matter into organic acids and alcohol Other bacteria convert these organic acids and alcohol into acetate, carbon dioxide and hydrogen Finally, methanogenic bacteria create methane, either through a reaction between carbon dioxide and hydrogen or via the breakdown of acetate The digester needs to be maintained at a neutral pH (~7), a constant temperature (~35ºC) and kept under anaerobic conditions

F.1.8 Outline the diversity of structure in viruses including: naked capsid vs enveloped capsid; DNA vs RNA and single vs double-stranded DNA or RNA

A virus is a non-cellular agent consisting of a protein coat (capsid) and genetic material The genetic material may be DNA (adenovirus) or RNA (retrovirus) and may be single-stranded or double-stranded For some viruses the protein coat may be exposed (naked capsid) while others may be covered in a membranous bilayer (enveloped capsid) Retroviruses have a reverse transcriptase component to allow for production of viral DNA

F.1.9 Outline the diversity of microscopic eukaryotes, as illustrated by Saccharomyces, Amoeba, Plasmodium, Paramecium, Euglena and Chlorella

Amoeba - single-celled organism that inhabits freshwater ponds and moves and captures food via cell extensions called pseudopodia Plasmodium - a genus of parasitic protozoa that causes malaria as part of a complex life cycle involving two hosts (humans and mosquitoes) Paramecium - a protozoan that inhabits freshwater environments and moves via the coordinated beating of tiny cilia Saccharomyces - a genus of single-celled fungus known as yeasts and employed extensively in the fermentation process Chlorella - a genus of unicellular green algae that possesses a singular cup-shaped chloroplast within its cytoplasm Euglena - a flagellated protozoan that contains chloroplast and is commonly present in pond water

F.1.6 State, with one example, that some bacteria form aggregates that show characteristics not seen in individual bacteria

Bacteria may form aggregates and by interacting are capable of completing functions that individual cells could not undertake (emergent properties) The photobacterium Vibrio fischeri is able to emit light (biolouminescence) when they become part of a population with high density V. fischeri releases a regulatory substance into its surroundings which in dense populations becomes concentrated enough to trigger bioluminescence

State that biomass can be used as raw material for the production of fuels such as methane and ethanol

Biomass (organic matter) can be used as raw material for the production of biofuels such as methane and ethanol Ethanol can be produced via fermentation of starch or cellulose by bacteria and enzymes Methane can be produced from manure, which provides an organic source for anaerobic bacteria to convert the matter into methane gas and CO2

F.1.5 Outline the diversity of Eubacteria, including shape and cell wall structure

Eubacteria can be sub-classified according to a number of diverse features, including: Shape: Round (coccus), rod-shaped (bacillus), comma-shaped (vibrio) or spiral (spirilla / spirochete) Cell wall composition: Gram positive (thick peptidoglycan layer) or Gram negative (lipopolysaccharide layer) Gaseous requirements: Anaerobic (obligate vs facultative) or aerobic Nutritional patterns: Autotrophic (photosynthetic vs chemosynthetic) or heterotrophic Additional structures: Flagella, slime capsules, hyphae, endospores, etc

F.1.1 Outline the classification of living organisms into three domains

Living organisms were originally divided into five kingdoms based on the presence of certain structural features In 1978 this system was refined to account for clear biochemical differences between living organisms (specifically, differences in rRNA sequence) According to the three domain classification scheme, there are three distinct types of cellular organisms to which all living things may belong: Eukarya: Contain a membrane-bound nucleus (includes plants, animals, protists and fungi) Eubacteria: Lack a nucleus and consist of the traditional or 'true' bacteria (e.g. most pathogenic forms, E.coli, S. aureus, etc.) Archaea: Lack a nucleus and consist of the extremophiles or 'ancient' bacteria (e.g. methanogens, thermophiles, halophiles)

F.1.4 Outline the wide diversity of habitat in the Archaea as exemplified by methanogens, thermophiles and halophiles

Methanogens Obligate anaerobes (cannot survive in the presence of oxygen) Produce methane as a waste product and are found in marshes, the guts of animals and oxygen depleted soils (e.g. landfills) Thermophiles Can survive abnormally high temperatures and live at temperatures close to boiling (60 - 100ºC) Are found in hot springs and near geothermal lava flows (e.g. deep sea vents and volcanic calderas) Halophiles Live in saline habitats with very high salt concentrations Found in regions of the Great Salt Lake and the Dead Sea

F.2.4 Outline the conditions that favour denitrification and nitrification

Nitrification is the biological oxidation of ammonia to produce nitrate ions (via the intermediate production of nitrites) Denitrification is the biological process of nitrate reduction to produce molecular nitrogen (N2) Nitrification: aerated soils warm, moist, soils neutral pH Nitrosomonas and Nitrobacter Denitrification Anaerobic soils high nitrogen input Psuedomonas denitrificans

F.2.3 State the roles of Rhizobium, Azotobacter, Nitrosomonas, Nitrobacter and Pseudomonas denitrificans in the nitrogen cycle

Nitrogen fixation: Rhizobium is found in the root nodules of certain leguminous plants and fixes nitrogen gas into ammonia for its host (mutualistic nitrogen fixation) Azotobacter is found living freely in the soil and also fixes nitrogen, but without the need of a host (free-living nitrogen fixation) Nitrification: Nitrosomonas is able to convert ammonium (NH4+) into nitrites (NO2-) Nitrobacter is able to convert the nitrites (NO2-) into nitrates (NO3-), which can then be absorbed by plant roots via active transport Denitrification: Pseudomonas denitrificans is able to convert nitrites (NO2-) and nitrates (NO3-) into nitrogen gas (N2), which can return to the atmosphere

F.2.1 List the roles of microbes in ecosystems, including producers, nitrogen fixers and decomposers

Producers: Change inorganic molecules into organic molecules that can be used as food by all other organisms in the environment Nitrogen fixers: Remove nitrogen from the atmosphere and converts it into nitrates which can be used by the producers Decomposers: Break down organic material, then release inorganic components from the organic matter into the environmen

Explain the consequences of releasing raw sewage and nitrate fertiliser into rivers

Raw sewage contains organic matter, and together with nitrate fertilisers will increase the levels of nitrates and phosphates in rivers Eutrophication is the ecosystem response to the addition of such substances to an aquatic system and will include: Algal blooms (in response to increased nutrient levels) and a subsequent spike in numbers of bacteria and microbes that feed on dead algae An increase in biochemical oxygen demand (BOD) by the saprotrophic bacteria results in deoxygenation of the water supply (reduced dissolved O2) The death or emigration of oxygen sensitive organisms and the proliferation of pollution tolerant organisms reduces biodiversity Increasing levels of toxins and heavy metals, along with greater numbers of pathogens, contaminating bathing and drinking water Decreasing water transparency (increased turbidity) may stress photosynthetic organisms, affecting food chains

cell walls of Gram-positive and Gram-negative Eubacteria

Similarities: Both have walls made of a murein net Both contain peptidoglycan Differences: Peptidogycan layer- single-layer in negative multi-layered in positive Outer Coating- lipopolysaccharide layer in negative no outer coating in positive Other Components- no additional components in negative, proteins and carbohydrates in positive Periplasmic space- present in negative absent in positive

F.1.2 Explain the reasons for the reclassification of living organisms into three domains

Traditional classification schemes separated organisms into two groups: prokaryotes and eukaryotes The large diversity of the group categorised as prokaryotes prompted further division into two separate domains Differences in the genes that transcribed rRNA as well as certain structural features (e.g. cell wall composition) formed the basis for this separation The archaebacteria have been found to have certain features that share more in common with eukaryotes that eubacteria The reclassification of organisms into three domains has helped scientists to better study and understand the origin and evolution of eukaryotes

Outline the role of saprotrophic bacteria in the treatment of sewage using trickling filter beds and reed bed systems

Trickling Filter Beds Trickling filter systems utilise beds of stone 1 - 2 metres wide, through which sewage is drained A biofilm of saprotrophic bacteria are situated on the rocks and feed on the organic matter within the sewage Cleaner water filters out the bottom into another tank, whereby bacteria can be removed and water further treated (e.g. chlorinated) Reed Bed Systems Reed bed systems involve the use of artificial wetlands to treat waste water As sewage passes through the red bed system it is broken down by saprotrophic bacteria living on the root system and in the litter These microbes utilise the sewage for growth nutrient, resulting in cleaner runoff