Lecture 1 - the global impact of microbes 1 Flashcards
why are microbes bad?
When we think of microbes we tend to associate them with negative outcomes. Living in the middle of this pandemic , we are more aware that ever of the diseases they cause both to man and animals, their capacity to destroy crops, resulting in food scarcity and how they can be weaponised by man for warfare.
why are microbes good?
microbes play an essential role not only in the production of our food and drink but also in the recycling of nutrients that are essential for soil fertility and carbon capture.
They play a role in removal and destruction of man made waste products including sewage and pollutant ts such as plastic.
As out knowledge of their genetics has increased we have increasingly been able to use them for the generation of new therapies against both infectious and non –infectious disease.
how has Robert koch related specific organisms to disease?
Robert Koch, was one of the first scientists to grow microbes in pure culture but his focus was very much around isolating bacteria that were associated with disease.
what are the facts we know about microbes?
Historically, much of our knowledge about bacterial life has come from our capacity to grow and study bacteria in the laboratory and yet less than 0.1% of organisms within the biosphere can be cultured conventionally.
This means that even in a fecal sample from a newborn baby there wil be several thousand bacteria that we know very little about
what did Angelina and Walter Hesse 1880s do?
Modifications to growth media including the introduction of agar as a gelling substrate, use of different temperatures and modification of the concentration of oxygen has allowed the isolation of many more bacterial species. However, despite different approaches to enrich for specific types of bacteria we can still only routinely culture a few 100 different bacterial species from human feces.
what is the capacity to culture?
However, even in Koch’s time, several of his comtempories recognized that successful culture maybe dependent on the nutrients and conditions found within any specific environmental niche.
One such Russian scientist, Sergei Windogradsky showed that using media that contained only inorganic minerals, he could recover organisms from the soil that could fix C02 into biomass using hydrogen sulphide rather than oxygen as a source of energy.
He was first to identify bacteria that could fix carbon dioxide using inorganic minerals (lithotrophs)
To reproduce the conditions of the marshlands he built a model wetland ‘the Winogradsky column
what important role does bacteria play in nitrogen cycling?
Bacteria play a key role in soil fertility and food provision through their capacity fix nitrogen to a form that can be readily used by plants
In fact, bacteria are entirely responsible for the natural cycling of nitrogen in our environment being involved in the fixation of atmospheric nitrogen, a very energy intense activity, through its oxidation to nitrates and nitrites, forms that can be used by plants through to denitification back to atmospheric N2.
what does intensive farming cause?
However, it is the anaerobic denitrification step of the cycle …in which bacteria break down excessive nitrates and nitrites in the soil…. that is becoming a global issue. This is because during this process nitrous oxide, a potent greenhouse gas, is generated.
Mankind, in its need to feed a growing human population, have created an in-balance in this cycle by introducing artificially fixed nitrates in the form of fertilizers to the soil ….to improve crop yields. The problem is that when these excess nitrates undergo denitrification in aquatic environments, high levels of potent greenhouse gases are released that are significantly increasing global warming.
what is the Hoff symbiotic relationship?
Simple examples of such mutualistic relationships include the deep sea crab, Kiwa tyleri, which survives at the periphery of life, at the base of marine hot vents….where food is scare.
Nicknamed the HOFF, it survives by farming and eating bacteria, that are able to assimilate carbon through redction of inorganic minerals such as hydrogen sulphide, which it grows on the hairs of its claws.
This is a mutualistic relationship……whilst the crab gains from ready supply of food, the bacteria benefit as the crabs are able to move towards and away from the erupting vents
what is the leaf cutter ant symbiotic relationship?
Similarly leaf cutter ants share a mutualistic relationship with fungi. I am sure you will have seen pictures of ants cutting and carrying leaves to their nests. But did you know that these leaves are not cut to provide food for the ants but rather a food supply fungi which they farm in their nests. These fungi in turn provide a food source for the developing ant larvae of the colony.
To further protect the farmed fungi from contamination by other fungal species, the ants cultivate bacteria on their external surfaces that produce anti-fungal metabolites to which their own fungal strains are resistant.
what is the difference between a mutualistic and a symbiotic relationship?
Whilst these relationships are mutualistic with organisms being interdependent, other relationships can be synergistic…. Such relationship are ones in which the organisms involved are capable of independent life but share benefits when grown together.
symbiotic relationships are now so intertwined that many forms of life could not exist without these microbes
what is an example of a mutualistic relationship?
Examples of these include the Mycorrhizae, or fungal internet, which has recently been recognized as an important ecological system that links the roots of trees within a forest. Here, the fungal communities benefit from accessibility to carbon fixed during photosynthesis by the tress, whilst the trees benefit from the interconnecting fungal network through which nutrients can move
what is another example of a mutualistic relationship?
Another similar symbiotic relationship is the one that exists between bacterial species of Rhizobium and plants…that helps in the fixation of Nitrogen of use by the plant.
This is an energetically demanding task as it requires breakage of the triplicate bond between the two nitrogen atoms. However, combining their resources, the bacterium can fix the nitrogen essential for the plant whilst the plant provides the bacteria with a energy derived from photsynthesis and protection from predators.
One slight difference in this example is that during this process the bacteria actually become endosymbionts of the plants… being internalized within the roots themselves and undergoing a morphological changes that means that the resultant bacteroid form of the organism is no longer capable of independent life. Interesting, some species have plants have evolved to produce pheromones that attract the bacteria to the root surface
what are acellular biological entities?
viruses, viroids and prions
what are cellular biological entities?
fungi, protists, bacteria and archea
how did bacteria previously get grouped by?
been placed in different groups depending on measurable observable features. To be placed in the group they largely had to be unicellular, with no disernible nuclear membrane. Consideration was also given to features such as cell shape and whether the organisms was linked to disease, maybe of a specific niche. how its reproduced and by its action
how is bacteria grouped now?
based on molecular characterisation and small subunit ribosomal 16S/18S sequence analysis
In fact it was Carl Woese from the University of Louisania who first proposed that the DNA sequence which encodes the 16S structural protein…. one of the subnuits of the ribosomal complex used in the conversion of mRNA to protein … could be used as a molecular clock for looking at relationships between bacterial species
This is because functionally all self-sustaining organisms encode and express this protein, however, its essential role in protein synthesis means that mutations in the DNA are limited to specific relatively unimportant regions within the sequence and where there is no evolutionary advantage for changes to occur
what did the sequencing of regions allow for?
As a consequence of this and other types of molecular analysis, it became clear that 3 kingdoms of life developed independently on earth. The first includes all the eukaryotic forms of life (animals plants etc) whilst the remaining 2 reflect the independent evolution of two different types of microbial life – the prokaryotes and the archea
what are archaea?
Common Traits between bacteria and archea-
Size (1-100um3)
Circular DNA chromosome
DNA organisation – nucleoid (no nuclear membrane)
Both archea and bacteria are members of the PROKARYOTES – no nuclear membrane
Simple cell structure
Common traits between archea and eukarya-
Introns between genes common
RNA polymerase and transcription factors eukaryotic homologs
Translation initiator – methionine (bacteria – use formylmethionine)
Cell wall pseudopeptidoglycan or other polymers
Unique features of Archea-
Undertake methanogenesis
Non pathogenic
Capable of thermophilic growth (up to 120oC)
how are Archaea extremorphiles?
Most ecological diverse colonisers
Thermophiles and Barophiles
inhabit hottest environments on earth – hydrothermal vents on the seafloor
Marine organisms
Survive high pressure, cold and darkness of deep oceans
Psychrophiles
grow below sea ice in Arctic and Antarctic locations
Halobacteria
Require high concentrations of salt to grow
Methanogens
Capacity to generate methane from carbon substrates – essential for carbon recycling
Wetlands, lake sediments and digestive tracts of animals
what is the earth microbiome project?
hrough the use of 16S analysis we have begun to catalogue the organisms found in the human microbiome and more widely the earth microbiome project. This was a project initiated by Rob Knight and Jack Gilbert which seeks to provide a global map of the organisms found in the many different ecological niches on earth.
Whilst knowing who is there is one thing, gaining a greater understanding of their contribution will require a much more in depth investigation of their interactions within the community. So plenty of work for microbiologists in the future.
