taxonomy

Taxonomy notes 

Taxonomy of bacteria 

Nomenclature 

• Binomial system created by Carl Linnaeus 

  • Used to name all cellular organisms 

• Each organism given 2 names 

  • Genus 

  • Species 

• DKPCOFGS

Classification 

• Overall similarities (phenetic) 

• Evolutionary relationships (Phylogenetic) 

• Most microorganisms reproduce asexually 

Evolution 

• Earth = 4.5 byo 

• First evidence of microbial life 

  • Found in rocks 

  • 3.5 byo 

  • Microfossil bacteria in rock 

• Stromatolites 

  • Microbial pats 

  • Layers of filamentous prokaryotes 

  • Sediments and extracellular matrix 

  • Ancient and modern types 

    • Ancient 

      • Anoxygenic phototrophic filamentous 

    • Modern 

      • Oxygenic phototrophic cyanobacteria 

• Origin of cellular life 

  • Earth earth: anoxic and hot 

    • First biochemical compounds made by abiotic systems 

  • 2 hypotheses for the origin of life 

  • 1: Surface origin hypothesis 

    • First membrane enclosed self replicating cell arose out of primordial soup rich in organic and inorganic compounds in ponds on earth's surface 

    • Problem: dramatic temperature changes 

  • 2: subsurface origin hypothesis 

    • Life originated in hydrothermal springs on ocean floor 

    • More stable conditions 

    • Abundant supply of energy 

  • Horizontal gene transfer 

    • Exchange of genetic material between cells 

  • Prebiotic chemistry of earth earth 

    • Set the stage for self replicating systems 

    • First self replicating systems 

      • RNA based since RNA can: 

        • Bind small molecules, has catalytic activity, can be copied like DNA 

          • DNA is more stable so eventually became the genetic repository 

        • 3 part system 

          • DNA, RNA, protein 

          • Universal among cells 

  • Important steps in the emergence of cellular life: 

    • Buildup of lipids 

    • Synthesis of phospholipid membrane vesicles 

    • Assembly of vesicles catalyzed by the clay of the mound to produce cytoplasmic membrane  

  • LUCA - last universal common ancestor in which cellular life mey cave diverged into modern day bacteria and archaea 

• Since earth earth was anoxic, energy generating metabolism of primitive cells was exclusively anaerobic and likely chemoautotrophic 

• Carbon source: CO2 

• Electron and energy source: H2 

  • Likely generated hy H2S reacting with FeS 

Phenetic numerical taxonomy 

• Traditional method for classification introduced by Michael Adanson 

• Incorporated categories: 

  • Morphology

  • Motility

  • Metabolism 

  • Physiology 

  • Cell lipid 

  • Cell wall 

  • Other traits 

• Large number of characteristics were determined for each organism and then calculated and expressed by S or S_J

• Then construction of dendrogram illustrated the relationship between species 

• Phenon: 

  • Group of organisms that have characters in common 

Evolutionary process 

• Mutation is a change in the genome of an organisms 

• Gene duplication, gene loss, horizontal gene transfer, silent, deleterious, beneficial, neutral 

Phylogenetic sequencing rRNA 

• Carl Woese 

  • Sequencing of ssu rRNA 

  • Established the 3 domains of life 

  • Provided a unified phylogenetic framework for bacteria 

• Comparative rRNA sequencing is routine procedure that involves the following: 

  • Amplification of the gene encoding ssu rRNA 

  • Sequencing of the amplified gene 

  • Analysis of sequence in reference to other sequences 

• rRNA sequencing is used to infer the phylogeny of prokaryotes and other microorganisms 

• SSU rRNA 

  • Conserved and variable region 

  • Accumulation of neutral mutations - genetic drift 

  • Evolutionary relationship between 2 organisms is correlated to the number of mutations that have accumulated in each one 

• Sequencing rRNA 

  • Sequence 16S rRNA and align sequences to take into account insertion and deletion 

• Phylogenetic trees

  • Illustrate relationship among sequences 

  • Length - number of changes 

  • Branches - ogre of descent of notes 

  • Nodes - putative common ancestor 

Endosymbiotic origin of eukaryotes 

• Well supported hypothesis 

• Implied mitochondria and chloroplasts arose from symbiotic association 

• Eukaryotic cell is chimeric: 

  • Similar lipids and energy metabolism to bacteria 

  • Transcription and translation similar to archaea 

  • Phylogeny closer to archaea 

• 2 hypotheses exist to explain the formation of the eukaryotic cell 

• 1: 

  • Began as nucleus bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis 

• 2: 

  • Arose form intracellular association between H2 producing bacterium which have rise to mitochondria and H2 consuming archaeal host 

    • Archaeal host later developed a nucleus 

Filamentous actinobacteria: streptomyces 

• Hyphal growth 

• Filament of cytoplasm usually not separated by cross-walls 

• Produce desiccation resistant spores at the tip of an elevated structure called sporophore 

Predatory bacteria: Bdellovibrio 

• Infect other bacterial cells 

• Acquire nutrients from host cells 

• Does not grow on agar 

• Gram positive bacteria are not infected

Stalked bacteria: caulobacter 

• Found in aquatic environment 

• Unique cell cycle 

• Differentiation: sedentary stalked mother cell and a motile flagellated daughter cell 

• Tip of stalk secretes stickiest substance known 

Obligate intracellular bacteria: chlamydia 

• Grow inside host cells 

• Elementary bodies 

  • Infectious release form host cells 

• Reticulate bodies 

  • Intracellular active growth 

Bacterial and archaeal taxonomy 

• Different strains of the same species 

  • Phylogenetic analysis 

  • Phenotypic analysis 

  • Genotypic analysis 

• MLST 

  • Method which several different housekeeping genes from a species are sequenced and aligned to the respective sequences of other individuals of the same species 

  • Has sufficient resolving power to distinguish between very closely related strains 

Identification 

• Dichotomous key 

  • yes/no 

• Serotyping 

  • Based on binding of specific antibodies 

  • Agglutination - positive reaction 

  • Antibodies will react with the microorganisms 

Taxonomy of eukaryotes 

Phylogeny of the eukarya

• Sequencing 18S rRNA genes is used to infer the phylogenies of the eukaryotes 

• The relationship between 18S is weaker for eukaryotes than the 16S for prokaryotes 

• Phylogenies have been constructed by taking into account other genes 

•  New insights have arisen because of these new phylogenies like fungi and animals being closely related as well as to amoebas 

Red Algae 

• Rhodophytes 

• Marine and freshwater and terrestrial 

• Red = phycoerythrin 

• Deeper = more phycoerythrin 

• Most are multicellular 

• Unicellular: Galdieria = acidic hot spring habitat 

Green Algae 

• Chlorophytes 

• Related to plants 

• Freshwater marine terrestrial 

• Unicellular with flagella or multicellular 

• Sexual and asexual reproduction 

• Endolithic algae grow inside porous rock 

Amitochondriate

• Lack mitochondria 

• Have mitosomes instead 

  • Reduced mitochondria 

  • Does not have enzymes for TCA or respiratory chain 

  • Involved in the maturation of FeS clusters 

• Hydrogenosomes 

  • Metabolism is strictly fermentative 

  • Carries out the oxidation of pyruvate to H2, CO2, and acetate 

  • Sometimes H2 consuming endosymbiotic bacteria also present secondary endosymbiosis 

Cysts 

• Some species of protists are able to differentiate into cyst and become encysted 

• They are similar to endospores 

Diplomonads and parabasalids 

• Unicellular 

• Flagellated 

• No chloroplasts 

• Anoxic habitats 

• Diplomonads 

  • 2 nuclei 

  • Mitosomes 

• Parabasalids 

  • Parabasal body 

  • No mitochondria 

  • Hydrogenosomes 

  • Intestinal tract 

  • Parasites 

  • STD and don't survive well outside the host 

Euglenozoans 

• Unicellular flagellated 

• Kinetoplastids 

  • Contain a kinetoplast which is a mass of DNA present in their single large mitochondria 

  • Live in aquatic habitats 

  • Feed on bacteria 

  • Cause diseases 

  • African sleeping sickness 

• Euglenids 

  • Nonpathogenic and phototrophic 

  • Contain chloroplasts 

  • Heterotrophs 

  • Lose chloroplasts if incubated 

  • Feed on bacteria by phagocytosis 

Alveolates 

• Have an alveoli 

  • Sac for osmotic balance 

• Ciliates 

  • Possess cilia 

  • Paramecium 

  • Motility and food - cilia function 

  • 2 nuclei 

  • During sexual reproduction - conjugation - sharing of micronuclei occurs 

  • Some are parasites or symbionts 

• Dinoflagellates 

  • Diverse marine phototrophic 

  • Free living 

  • Or living with corals 

  • 2 flagella 

    • Transverse and longitudinal 

  • Some secrete neurotoxins 

    • Red tides 

• Apicomplexans 

  • Parasites 

  • Complex life cycle 

  • Lack pigment but contain a chloroplast 

  • Anabolic pathways 

  • Cause malaria 

Stramenopiles 

• Flagella with short hairlike extensions 

• Chemoheterotrophs and phototrophs 

• Oomycetes, diatoms, golden and brown algae

• Oomecetes 

  • Chemoheterotrophs 

  • Water Molds 

  • Cellulose cell wall but similar to fungi - which is why they are not in fungi group since no chitin 

  • Potato famine 

• Golden algae

  • Phototrophs 

  • Unicellular 

  • Called chrysophytes 

  • Some are colonial 

  • Chloroplast pigments dominated by the carotenoid fucoxanthin 

• Diatoms 

  • Unicellular 

  • Phototrophic 

  • Freshwater 

  • Marine 

  • Frustules 

    • Cell walls made of silica with proteins and polysaccharides attached to protect against prediction 

Cercozoans and radiolarians 

• Threadlike pseudopodia 

• Cercozoans 

  • Foraminifera 

  • Marine 

  • Shell structure 

  • Tests made of organic materials reinforced with calcium carbonate 

• Radiolarians 

  • Marine 

  • Heterotrophic 

  • Tests made of silica 

  • Name derived from radial symmetry 

Amoeba 

• Terrestrial and aquatic 

• Protists 

• Pseudopodia 

• Phagocytosis 

• Gymnamoebas 

  • Free living 

• Entamoeba 

  • Parasites of vertebrates and invertebrates 

• Slime mold 

  • Previously grouped with fungi 

  • Fruiting bodies 

  • Spore for dispersal 

  • Motile 

  • Vegetative forms are masses of protoplasm if indefinite size and shape that contain multiple nuclei 

• Cellular slime mold

  • Vegetative forms composed of single amoebae (haploid) 

  • Aggregate as a pseudoplasmodium that can move as a single unit 

  • Fruiting body formed cells differentiate into spores 

  • May form diploid macrocystis that undergo meiosis to form new amoebae 

    • Sexual reproduction 

Fungi 

• Most fungi are multicellular 

• Hyphae - mycelium 

  • Coenocytic 

    • Not subdivided nuclei and cytoplasm 

  • Septate 

    • Nuclei are separated by cross wall 

Symbiosis and pathogenesis 

• Symbiotic association 

  • Some species of fungi form close relationships with plant roots - mycorrhizae 

  • Glomeromycetes 

• Ectomycorrhizal 

  • Form a sheath around the plant root but doesn't penetrate it 

• Endomycorrhizae 

  • Fungal and hyphae is embedded in the plant root 

• Fungi can cause disease in plants and animals 

• Specialized hyphae - haustoria - to penetrate the plant cells and consume cytoplasm 

• Mycoses 

  • Humans range in severity from athlete’s foot to histoplasmosis 

Fungal reproduction 

• Most fungi reproduce by asexual means 

  • Growth and spread 

  • Asexual production of spores 

  • Cell division 

• Some fungi produce spores as a result of sexual reproduction 

Saccharomyces cerevisiae 

• Cells are spherical to oval cell division through budding 

• Sexual reproduction 

  • Mating types in saccharomyces cerevisiae 

Infectious particles notes  

Viruses 

• Obligate intracellular parasites 

• Can only replicate inside a host cell 

• Outside a host cell, viruses are virions 

• Each virus is a piece of nucleic acid enclosed within a protein coat called a capsid 

• Only one type of nucleic acid is found in the virion of a given virus 

Examples of viruses 

• Simple viruses have 3 proteins 

• Complex viruses have more than 100 proteins 

Structure of a virion 

• Capsid 

  • Protein coat around the nucleic acid 

• Nucleocapsid 

  • Nucleic acid and protein coat 

• Capsomere 

  • Protein subunit that makes up the capsid 

• Envelope 

  • Lipid containing layer with embedded proteins

  • Can be taken from the membrane of host cells 

  • Proteins in envelope are virus specific and are encoded in the viral genome 

• Shapes of virions 

  • Helical 

  • Polyhedral 

    • Several shapes are possible 

    • Icosahedron is most common 

    • Only some capsomere numbers are possible due to geometry 

  • Complex 

    • Composed of several parts 

    • Most complicated virus in terms of structure 

    • Not necessary genome organization 

    • Viruses of bacteria - bacteriophages (phage) 

Viroids 

• Enclosed circles of single stranded RNA containing 240-380 nucleotides 

• Replication is dependent on host machinery, disease is caused by the overtaking of this machinery by the viroid 

• Cause of: 

  • Cadang-cadang disease and potato spindle tuber 

Prions 

• Consist solely one one protein 

• Causes neurological degenerative disorder 

  • Mad cow disease 

• Misfolding of proteins 

  • Misfolding of specific proteins causes the misfolding of other proteins which will cause the cell to not replicate and die which is primarily found in neurons 

Taxonomy of viruses 

• Family - viridae 

• Genus - virus 

• Given species name in english 

• Classification is based on characteristics 

  • Nature of the host 

  • Type of disease caused 

  • Life cycle 

  • Naked or enveloped 

  • Nucleic acids and strandedness 

• Baltimore classification scheme 

  • Based on type of genome 

  • Useful because the kind of genome will dictate the replication mechanism 

  • RNA genomes 

    • Plus configuration 

      • Same mRNA strand is translated 

    • Minus configuration 

      • mRNA must be transcribed before translation 

Life cycle of viruses 

• Absorption 

  • Attachment of the virus to specific receptors on the surface of the cell

  • Plant viruses are usually introduced into the host by insect vectors or following mechanical damage 

• Penetration 

  • Virus genome enters the cell 

    • In  enveloped and naked virus the entire virion enters the cell 

    • Enveloped: envelope may be left at the cell surface such that only the nucleocapsid enters  

      • Most enveloped viruses of eukaryotes use endocytosis (viropexis) 

        • Viruses are then delivered to lysosomes which degrade the capsid and the nucleic acid is released into the cytoplasm 

    • Naked: capsid may be left at the surface 

• Uncoating 

  • Removal of the envelope and/or capsid by host enzymes sometimes with lysosomes 

• Replication 

  • Of the nucleic acid 

  • Transcription and protein synthesis 

• Maturation 

  • Assembly of virus components 

  • Nucleic acid

  • Nucleocapsid 

  • Accessory proteins 

    • Form new virion 

      • Spontaneous 

• Release 

  • Mature virions exit the host cell by means of budding or by causing lysis of the cell 

  • Plant viruses exit and are transmitted by means of vectors 

Virus replication 

• Latent period 

  • Eclipse and maturation 

• Eclipse 

  • Time necessary for the host cells to replicate the viral genome and to synthesize the viral components 

• Maturation 

  • Time needed for the different components to be assembled 

• Release 

  • Rise period 

  • Virions are detectable outside the cell 

  • Lysis 

    • Virus encoded proteins damage the membrane and bacteria peptidoglycan layer gets destroyed 

  • Budding 

    • Enveloped virus 

• Burst size 

  • Number of virions released 

Phages 

• Best studied phages infect e. Coli (gram - ) 

• Most phages contain linear dsDNA genomes 

• Most are naked but some possess lipid envelopes 

• 2 types of phages 

  • Virulent 

    • Infection of host leads to replication resulting in host cell lysis 

  • Temperate 

    • Lytic 

    • Lysogenic 

      • Genome becomes incorporated into the bacterial host genome 

Bacteriophage T4

• Absorption 

  • T4 attaches to the core region of LPS by tail fibers 

• Following attachment, tail sheath contracts and forces the central core through the outer membrane 

  • Tail lysosomes digest the peptidoglycan layer and forms a small pore 

• Phage DNA is injected into the cytoplasm of the host cell 

• Replication (temperate phage) 

  • Infection by temperate phage results in a prolonged latent state of infection 

    • Lysogeny 

  • Phage is carried on the chromosome 

  • Prophage 

    • Genome within the host cell chromosome 

  • Lysogen 

    • Bacteria that contains a prophage 

  • Sometimes the prophage can exit the chromosome in a process called excision and continue along the lytic pathway resulting in the production of new virus particles and host cell lysis 

  • Lambda genome is linear and dsDNA with cohesive ends which are ss complementary DNA which will come together and form a circular dsDNA 

• Lambda genome is integrated at a specific site in the bacterial chromosome at the att region in the phage genome which is homologous to eh att(lambda)  site 

  • The enzyme lambda integrase catalyzes integration of the phage genome at this site and is encoded on the phage genome 

Animal viruses 

• In eukaryotic cells, DNA replication occurs in the nucleus 

• Genomes of DNA virus will usually be replicated in the nucleus of the cell 

• Genomes of RNA viruses will be replicated in the cytoplasm of the cell

DNA genome 

• Herpes is an example 

• Penetration 

  • Fusion with the cell cytoplasm with viral envelope and nucleocapsid is transported to nucleus where viral DNA is uncoated 

• transcription/translation apparatus synthesize 

  • Immediate early proteins 

  • Delayed early proteins 

  • Late proteins: nucleocapsid 

• Assembly occurs in the nucleus 

• Envelope is added via budding process through the inner membrane of the nucleus 

• Complete virions are then excreted out of the cell by the ER golgi pathway 

• ssDNA genome 

  • First converted to a dsDNA replicative form 

RNA genome: plus strand RNA 

• Polio and hep A 

• Genome can be translated directly 

• In polio - plus strand RNA serves as template for synthesis of a large polyprotein that is cleaved into proteins 

RNA genome: minus strand RNA 

• Measles and rabies and the flu 

• Genome cannot be translated directly 

• Rna genome is transcribed into plus strand by RNA-dependent RNA polymerase and carried inside the virions 

RNA genome: dsRNA 

• Rotavirus 

• dsRNA genome cannot be translated 

• Plus strand RNA must be synthesized by viral-encoded RNA dependent RNA polymerase using the minus strand as the template 

• Plus strand is then translated into proteins and is used as a template to synthesize the minus strand to yield dsRNA genomes 

RNA genome - retrovirus 

• HIV 

• Cancer causing 

• The virion carries 2 identical copies of the genome 

• Reverse transcriptase 

  • RNA dependent DNA polymerase 

  • Reverse transcribed the RNA genome into DNA 

• DNA genome travels to the nucleus and integrated into host DNA 

• LTR - long terminal repeats 

  • Contain promoters for transcription and participate in the integration process 

• Provirus

  • Integrated viral DNA 

  • Contrary to the lambda prophage, cannot excise from the host genome 

Cell fusion 

• Enveloped viruses that fuse with the host cell cytoplasmic membrane carries viral proteins that fuse biological membranes 

• Cell fusion results in hybrid cells that have chromosomal aberrations and are usually short lived 

oncogenetic/tumor producing viruses 

• Some viral infection are implicated in the conversion of a normal cell to a tumor cell

• Both DNA and RNA viruses can cause tumors 

• 4 different mechanisms

  • Transduction 

  • Insertion of a strong promoter 

  • Inactivation of a tumor suppressor gene 

  • Expression of a viral protein that induces transformation 

4 expressions of a viral protein 

• DNA virus 

• Viral protein does not have a cell counterpart 

• Integration of the viral genome into the host genome 

• Viral genome may persist in the cell as extrachromosomal episome 

• Some DNA viruses cause tumors do so because they have infected a non permissive host 

  • Cannot complete their infection cycle 

  • Cell is infected and undergoes controlled replication 

  • Because the virus cannot complete replication the cell will never die 

Antiviral drugs 

• Most target host structures and result in toxicity 

• Risk to host may not justify the use of antiviral 

• Antibiotics are ineffective 

• Most successful and commonly used antivirals are the nucleoside analogs 

  • Block reverse transcriptase and production of viral DNA (RNA viruses) 

• Protease inhibitors 

  • Inhibit the processing of large viral proteins into individual components 

• Fusion inhibitors 

  • Prevent virus from successfully fusing with the host cell 

Microorganisms in natural environments 

Ecosystems

• Defined as the sum of all organisms and abiotic factors in a particular environment 

• Is dynamic and complex of plants, animals and microbial communities as well as the nonliving surroundings which interact as a functional unit 

• Contains many habitats 

Habitat

• This is defined as a portion of an ecosystem where a community could reside 

• Many habitats are unsuitable for plants and animals and some are exclusively microbial 

Population 

• A group of microorganisms of the same species residing in the same place at the same time 

Community 

• A group of populations 

Ecological concepts 

• Diversity of microbial species in an ecosystem is expressed in two ways 

  • Species richness

    • Total number of different species present 

  • Species abundance 

    • The proportion of species in an ecosystem 

• Microbial species richness and abundance are a function of the kinds and amounts of nutrients available in a given habitat 

• Guilds

  • Metabolically related microbial populations 

  • Sets of guilds form microbial communities that interact with microorganisms and abiotic factors in the ecosystem 

• Niche 

  • Habitat shared by a guild 

  • Supplies nutrients as well as conditions for growth 

• Energy inputs 

  • Sun 

  • Carbon 

  • Reduced substances 

Microenvironments 

• The growth of microbes depends on resources and growth conditions

• Difference in type and quantity of resources and the physicochemical conditions of a habitat will define the nice for each microbe 

• For each organism there exists at least one niche in which that organism is most successful 

  • This is called the prime niche 

• A microenvironment is: 

  • The immediate environmental surroundings of a microbial cell or group of cells 

  • Soil particles contain many microenvironments 

• Physiochemical conditions in a microenvironment are subject to rapid change 

  • Spatially and temporally 

• Resources in natural environments are highly favorable 

  • Many microbes in nature face a feast-or-famine existence 

    • Storage is important 

• Growth rate of microbes 

  • Usually well below maximum growth rates defined in a lab 

• Many microbes establish relationships with other organisms 

  • Parasitism 

    • One is harmed the other benefits 

  • Mutualism 

    • Both benefit 

  • Commensalism 

    • Neither nor 

Biogeochemistry 

• Study of biologically mediated chemical transformations 

  • A biogeochemical cycle defines the transformations of a key elements by biological and chemical agents 

• Typically proceed by oxidation-reduction reactions 

• Microbes play critical roles in energy transformation and biogeochemical processes that result in the recycling of elements to living systems 

  • Carbon cycle 

  • Nitrogen cycle 

  • Sulfur cycle 

Microbiology of soil 

Soil 

• Loose outer material or earth’s surface 

  • Distinct from bedrock 

• Can be divided into two groups 

  • Mineral soils 

    • Derived from weathering and other inorganic materials 

  • Organic soils

    • Derived from sedimentation in bogs and marshes 

• Composed of 

  • Inorganic, organic, air, water, living organisms 

• Layers 

  • O horizon 

    • Layer of undecomposed plant materials 

  • A horizon 

    • Surface soil 

    • High in organic matter, dark in color, for agriculture, many microorganisms and microbes 

  • B horizon 

    • Subsoil 

    • Minerals 

    • Little organic matter 

    • Less microbial activity 

  • C horizon 

    • Low activity 

    • Soil base 

• Most microbial growth takes place on the surface of soil particles 

• Availability of water is most important factor influencing microbial activity 

  • Sand

    • Water drains quickly 

  • Silt

    • Retails water to the right extent 

  • Clay 

    • Water retained too well soil becomes anoxic 

• Nutrient availability is the most important factor in the subsurface environments 

Microorganisms in soil 

• Top few centimeters 

  • Mostly bacteria and archaea 

    • Responsible for the production of humus, release of minerals and the production of acid from organic compounds, solubilize minerals, cycle nutrients, nitrogen fixation 

  • Fungi 

  • Protozoa

  • Algae 

Nitrogen fixation 

• Only certain prokaryotes can fix nitrogen N2

• A lot of energy is required 

  • Needs to break a triple bond between nitrogens 

• One of the most important microbial processes on earth 

• Absence of fertilizer 

  • Other organisms depend on nitrogen fixers 

    • Some are free living and other are symbiotic 

• Reaction is catalyzed by nitrogenase complex 

  • Metal cofactors 

  • 8 electrons from pyruvate are required, 2 are lost as H2 

  • Ammonia is the final product and is used to produce amino acids 

• Dinitrogenase reductase is inhibited by the presence of oxygen 

Free living nitrogen fixers 

• Azotobacter 

• Widespread in soil 

• Require soil rich in organic matter to provide energy for nitrogen fixation 

• Produce ammonia for plants 

• Clostridium 

  • Strict anaerobe 

• Strict aerobe 

• Enzyme is protected by very high rate of O2 which keeps the intracellular environment anaerobic 

• Cyanobacteria 

  • Only some species are capable of fixation 

  • Major nitrogen fixing organisms in nature 

  • Produce energy by oxygenic photosynthesis 

  • Oxygen is produced in the cell 

  • Occurs in specialized anaerobic cells called heterocysts

    • Lacks photosystems II 

    • No O2 produced 

    • Heterocysts have a thick cell wall to slow O2 diffusion 

    • Regular cells provide the heterocysts with carbohydrate - pyruvate 

Symbiotic nitrogen fixers 

• The mutualistic relationship between leguminous plants and nitrogen fixing bacteria is one of the most important symbioses known 

• Colonization of legume roots by nitrogen fixing bacteria leads to the formation of root nodules that fix nitrogen 

Nodule formation 

• Oxygen levels are controlled by O2 binding 

Protein leghemoglobin produced by plant cells

• Bacteroides are a terminal state 

  • Cannot shed in the environment 

  • Nodules contain regular rhizobium cells 

    • Best known N2 fixing bacteria 

  • Inoculate the environment 

Implication for agriculture 

• Most plants will use nitrogen produced by free-living nitrogen fixers or by other organisms during ammonification 

• Nitrate 

  • More soluble than ammonium 

  • More readily available for plants 

• Nitrifying bacteria 

  • NH3 → NO2- → NO3- 

• If the soul is poorly drained and becomes waterlogged, the soul becomes anaerobic which promoted denitrification 

  • NO3- → N2

• Anaerobic conditions promote sulfur and sulfate reaction 

  • Which produce H2S 

  • Toxic for plants 

Microbiology of water 

Aquatic systems 

• Biological activity of an aquatic ecosystem depends on the activities of the primary producers 

  • Algae 

  • Cyanobacteria 

    • Fix nitrogen 

  • Oxygenic photoautotrophs, phytoplankton

• These organisms serve as a food source for chemoheterotrophs 

  • Bacteria, protozoa, fish, aquatic organisms 

• The activities and net numbers of phytoplankton depend on 

  • Temperature 

  • Light 

  • Availability of specific limiting nutrients 

    • Nitrogen 

    • Phosphorus 

Photic zone 

• In clear water 

  • Max depth of light is 300m 

  • Microorganisms must be able to harvest light that reaches them 

Marine environment 

• High salinity 

  • 3% 

  • Halotolerant organisms 

• 75% of the ocean is deeper than 1000m 

  • Deep sea

  • Pelagic zone 

  • 11km delow the surface is deepest with about 1100 atm 

• Below the 100m the temp is constant at 2-3C 

Open ocean 

• Pelagic zone - oligotrophic 

  • Primary productivity is very low due to the lack of inorganic nutrients that are required by phytoplankton 

    • Like nitrogen phosphorus and iron 

  • Temp are cooler and more constant than in areas closer to shore 

  • Some regions 

    • Wind and ocean currents cause an upwelling of water from the ocean floor to bring nutrients to the surface to promote productivity 

• Bulk of primary productivity comes from prochlorophytes 

  • Tiny phototrophs phylogenetically related to cyanobacteria (Prochlorococcus)  

• General adaptations seen in pelagic microorganisms 

  • Reduced size 

  • High affinity transport system 

• Trichodesmium 

  • Filamentous cyanobacteria 

  • Contains phycobilins 

  • Nitrogen fixation 

Costal water 

• Primary producer 

  • Algae 

  • Cyanobacteria 

• Productivity 

  • High due to influx of nutrients from rivers and other polluted sources 

    • Agriculture 

      • Runoff = excess nitrogen and phosphorus 

      • Eutrophic 

  • Can cause red tides 

    • Nitrogen is a limiting nutrient 

• At high levels of primary productivity it supports a high concentration of zooplankton and aquatic animals 

Deep sea 

• Between 300 and 1000 m 

  • Chemoheterotrophs degrade organic metter that falls from the photic zones 

  • 2-3C 

  • Psychrophiles 

• Below 1000 m 

  • Organic carbon is scarce 

  • Oligotrophic 

  • No light 

  • Few microorganisms 

    • Psychrophilic 

    • Barophilic 

    • Barotolerant 

Hydrothermal vents 

• Source of heat 

• Source of nutrients 

• Electron donors and acceptors 

• Community of microorganisms and animals 

• Tube worm 

  • Symbiosis with sulfur oxidizing chemoautotrophs 

  • Trap and transport nutrients to the bacterial symbionts 

Freshwater environments 

• Highly variable 

  • Isolated compared to ocean 

• Microbial populations will depend on the availability of nutrients and availability of light and oxygen 

• Limited by the availability of nitrogen and phosphorus 

• Lakes - poor mixing and aeration 

• Rivers - good mixing and aeration 

Oligotrophic lakes 

• N and P are limiting 

• Primary production low 

  • Availability of organic matter is low 

• Growth of aerobic chemoheterotrophs 

  • Limited by nutrient supply 

  • O2 remains high 

  • Rate of O2 dissolution is higher than consumption rate 

• Lake remains aerobic even at depth and organic matter is degraded completely 

  • Oxygen saturation 

• Clear water - deep light penetration 

Eutrophic lake - nutrient rich 

• Primary production 

  • High 

  • Algal blood 

  • Availability of organic matter is high 

• Rapid growth of chemoheterotrophs 

• Rapid depletion of dissolved oxygen 

• Low O2 concentration 

  • Anaerobic zones are created 

• Poor light penetration 

• Health risk 

  • Pathogens 

  • Blooms of algae and cyanobacteria secrete toxins 

• Bottom sediments 

  • Anaerobic and contain organic matter 

    • Dead primary producers 

      • Support the growth of denitrifiers, methanogens, and sulfate producers 

  • Anaerobic photosynthesis uses H2S as an electron donor and produces sulfate 

    • Used by sulfate reducers 

  • Excessive production of H2S and the production of organic acids from fermentation can give bad odor to water 

  • Lack of oxygen and or presence of H2S may kill fish and other aerobic organisms 

Lakes in temperate climates 

• Anaerobic zones may develop 

  • As a result of stratification 

  • Lakes become thermally stratified 

• As the air temperature increases, surface water is warmed resulting in formation of upper and low layer 

• Warmer layer - upper layer 

  • Epilimnion 

    • Less dense - aerobic 

  • The color bottom layer 

    • Hypolimnion 

      • Denser - anaerobic 

  • Separated from the epi by the zone of rapid temp 

  • Change - thermocline 

  • Mixing in the spring and fall only which brings nutrients back to the top 

Rivers 

• Good mixing and aeration 

• Ensures that organic material - within limits - is degraded effectively 

  • No fermentation or sulfur

• Excess organic matter may still result in anaerobiosis with consequences similar to those seen in eutrophic lakes 

Pollution 

• Pollution of freshwater

• - deliberate discharge of effluents into a waterway 

• Is a major source of sewage 

  • Sewage is rich in organic matter and contains a large number of organisms and some pathogens 

• Aerobic and facultative organisms oxidize organic matter using the dissolved oxygen 

• Biochemical oxygen demand is high 

  • BOD 

  • Used to measure the extent of pollution by organic matter 

  • Water tends to become anaerobic 

  • Microbial metabolisms

    • Fermentation, sulfate, reduction, nitrate reduction 

Biofilms

• Microbial cells embedded inside an extracellular matrix 

• Usually produced by a mixed population of species 

• Extracellular matrix composed of proteins, polysaccharides, DNA

• Cells inside the biofilm are more resistant to stress than planktonic (free-living) cells 

• Found in water systems, on wet surfaces, growing on medical devices, etc. 

Water-borne pathogens 

• Most of these pathogens grow in the intestinal tract and transmission of water supplies 

• Can be a source of infection 

  • Potable water 

    • Drinking and food preparation 

  • Recreational water 

    • Swimming 

• Examples of pathogens 

  • Salmonella typhi 

    • Typhoid fever, systemic infection, health carriers 

  • Vibrio cholerae 

    • Cholera, severe diarrhea, enterotoxin 

  • Shigella spp

    • Shigellosis, bacterial dysentery 

  • Salmonella spp

    • Salmonellosis, gastroenteritis 

  • Campylobacter spp

    • Gastroenteritis 

  • Enterovirus 

    • Polio, norovirus, rotavirus 

  • Hep A 

  • E. Histolytica 

    • Amoebic dysentery 

  • Giardia lamblia 

    • giardiasis , chronic diarrhea, drinking water, bevers carry it 

  • Cryptosporidium parvum

    • Chronic and acute diarrhea, self limiting in healthy individuals, major problem in immunocompromised individuals, di treatment 

      • Cysts of G Lamblia and C parvum 

        • For cysts resistant to disinfectants and chlorine 

        • Not easily or effectively removed by the filtration process in water plants since they are too small 

Water quality control 

• Impossible to check for all pathogens 

  • Most are associated with feces 

• Test water for organisms present in large number of feces 

  • Use the organisms are an indicator of fecal pollution 

  • If these organisms are present, there is a chance the water may also contain pathogens 

• 2 indicators 

  • Coliforms 

    • Facultative aerobe 

    • Gram negative 

    • Non-spore forming 

    • Rod shaped bacteria that can ferment lactose with gas formation 

    • Not all of intestinal origin 

  • Fecal coliforms 

    • Derived from intestines of warm blooded animals 

      • Presence can indicate E. Coli and water is unsafe for consumption 

      • Absence does not ensure good drinking water 

  • Membrane filtration

    • used to test large volume of water faster and easier than MPN 

  • Most probable number

    • Test for coliforms 

    • Samples are added to lactose broth 

      • Gas = positive 

      • Use statistical tables to estimate MPN 

      • Presumptive tests need further tests for confirmation

Water treatment 

• Aims 

  • Remove pathogens 

  • Improve clarity of water 

  • Remove compounds that give bad smell or taste 

  • Soften the water 

• Extent of treatment 

  • Depends on the quality and source of the water 

Steps in water treatment 

• Sedimentation 

  • Water left to stand 

  • Sediments settle 

• Flocculation - chemical coagulation 

  • Coagulant is added 

  • Water is transferred to flocculation basin 

  • Settles 

  • Flocs form, trap particles 

  • Some organic chemicals are also absorbed 

  • About 80% of bacteria, color and particles removed 

• Filtration 

  • Water is filtered 

  • Removes remaining particles 

  • Like G lamblia cysts 

  • 98-99.5% bacteria removed 

  • Filter is backflushed regularly to prevent clogging 

• Disinfection 

  • Chlorination 

    • Very reactive with water 

    • Forms oxidizing agents 

    • Kills remaining microorganisms 

      • Some are resistant 

    • Neutralizes most chemicals and bad smell/taste 

  • Residual chlorine 

    • Amount that remains in the water 

    • Desired and required for protection in distribution 

  • Ozone 

    • More effective than chlorine 

Wastewater (Sewage) treatment 

• Aims 

  • Reduce BOD 

  • Destroy pathogens 

Primary treatment 

• Sedimentation tanks 

  • 40%-70% of suspended solids settle 

  • Flocculating chemical can be added 

  • Produced primary sludge 

  • Reduces BOD and bacteria 

  • Wastewaters discharged into waterways of go through secondary treatment 

    • Use microorganisms to reduce the BOD and the concentration of bacteria further 

Secondary treatment

• Liquid  

• Trickling filter 

  • Liquid from primary treatment is sprayed over a bed of rock or plastic honeycomb, microorganisms form biofilms and coat the sidace and oxidize the organic matter present in sewage and reduce BOD and bacteria 

• Activated slide 

  • Air is blown through the liquid from primary treatment 

  • Slime forming bacteria grow in clumps together to form flocs - activated sludge 

  • Oxidize organic matter then the material passes into a settling tank and sludge is removed for disposal or secondary treatment 

  • Bod and bacteria reduced 

• Sludge 

  • Primary and secondary sludge 

    • Containing cellulose and other organic compounds 

    • Subjected to microbial digestion under anaerobic conditions 

  • Ch4 produced and can be used to power the treatment plant 

  • Bod reduced 

  • Material remaining present is incinerated or buried 

Tertiary treatment 

• Liquid 

  • Further reduced the BOD, bacteria and N and P 

  • May involve 

    • Biological treatment 

    • Flocculation 

    • Filtration 

    • Chlorination 

    • Ozonation 

  • Final liquid effluent 

    • Comes from wastewater treatment plant that uses primary secondary and tertiary treatments and may be suited for drinking 

Septictanks 

• Minimal treatment of sewage 

• Within the tank 

  • Settling of material and minimal sludge digestion required periodic emptying 

  • Effluent flows to a leaking field 

  • BOD effluent reduced by 60%