Microbial diversity-Prokaryote diversity.docx

Microbial diversity: Prokaryote diversity

Classification

Taxonomy: the science of classifying life forms, complex approaches focused on an organism’s genetics
Living things belong in 5 kingdoms:

Classification of Microbes

In 19th century, the scientist Ernst Haeckel categorised bacteria, fungi, protozoans, and algae as a third kingdom, the Protista
In 1969, Robert Whittaker proposed the five-kingdom system, based on an improved understanding of cells and molecules, in which bacteria were placed in the Monera kingdom (were considered prokaryotes)
In the 1970s, scientists grouped the Monera into three different domains (which are even larger than kingdoms)
Prokaryotic life forms are divided into the domains of archaea and bacteria
All eukaryotic organisms are classified in the Eukarya domain
The Protista kingdom broadly fits with the Eukarya domain and includes protozoans, algae, water moulds, and slime moulds

Bergey’s Manual and methods of classification

Bacteria, based on their phenotypic characteristics, are classified in the Bergey’s manual of systematic Bacteriology
These are the organism’s observable characteristics, which in bacteria it includes metabolic properties, pathogenicity, staining reactions, …
Scientists, when characterising bacteria, apply phylogenetic or genotypic classification based on DNA (they compere their ribosomal RNA to see which species are similar)

Domain: Archaea

In the 1970s, the scientist Carl Woese and his colleagues studied on 16S ribosomal RNA sequences in archaea and bacteria concluding that archaea were different from bacteria, one difference is in the composition of their plasma membranes and cell walls

General features of the Archaea

Archaeans are widespread on land an in the sea and can survive in extreme environments, including thermal vents and salt ponds
Scientists still know little about them, making them difficult to categorise
Archaeans have a variety of shapes and do not show noticeable morphological differences compared to bacteria
They can be aerobic or anaerobic and can gain autotrophic or heterotrophic nutrition
Their DNA is made of a single circular double-stranded molecule, without a nuclear membrane
They have different cell walls to bacteria; their cell walls are made of proteinaceous subunits called an S-layer, and do not contain peptidoglycan, which protects them from some antibacterial agents like penicillin (which targets peptidoglycan)

Classification of the Archaea

There are two major phyla of Archaea and three minor ones

The major ones are:

The minor ones are:

Euryarchaeota

The Euryarchaeota is the largest, most diverse group
It includes methanogenic (methane-producing) and halophilic (living in high slat concentrations)
The genera Methanococcus and Methanobacterium inhabit hot springs, marshes, and the guts of some grazing mammals, and generate methane from carbon compounds

Domain: Bacteria

Bacteria are divided into 30 different phyla

Phylum: Proteobacteria

The proteobacteria phylum includes, about a third of known bacteria
They’re morphologically and physically diverse, but may share a common ancestor
They’re subdivided into six classes based on molecular similarity
Many bacteria that share a class are morphologically and physiologically very different from one another
Photosynthetic Proteobacteria – purple sulphur/non-sulphur bacteria can photosynthesise without producing oxygen (they’re facultatively anaerobic), living in stagnant ponds they photosynthesise using light that reaches below the surface
Nitrifying proteobacteria – they’re aerobic chemolithoautotrophs that oxidise inorganic nitrogen compounds (ammonia or nitrite) to gain energy, they also gain carbon from CO2, and they live on land, or in fresh/saltwater
More examples of proteobacteria: Iron and sulphur-oxidising, Hydrogen-oxidising, Nitrogen-fixing, Methanotrophic, Enteric, the Pseudomonads, Acetic acid bacteria, Stalked proteobacteria, and Predatory proteobacteria

Other Gram-Negative phyla

Cyanobacteria (blue-green algae) – they carry out oxygenic photosynthesis (like plants/algae) instead of chloroplasts they have thylakoids (membranes) which are the location of light-gathering and electron transfer, and many of these bacteria reduce nitrogen to ammonium ions
Aquificae and Thermotogae – the world’s oldest bacteria
Chlamydiae – they parasitise birds and mammals using the host cells to generate energies
Spirochaete – they’re helical in shape and move like corkscrews, they can be aerobic or anaerobic, and live in water, soil, and the guts of some animals

The Gram-Positive Bacteria: phyla Actinobacteria, Firmicutes

Gram-positive bacteria include two large phyla Actinobacteria and Firmicutes and one small one Tenericutes
Most species are chemoheterotrophs
Several human pathogens are gram-positive
An organism’s DNA can be expressed as a percentage of cytosine and guanine residue, written as %GC content
Gram-positive bacteria are divided into groups with a GC content of over or under 50%

High GC Gram-Positive Bacteria: phylum Actinobacteria

Many Actinobacteria are aerobic species that grow in soil and resemble fungi
One genus is Streptomyces, the source of the antibiotics streptomycin and tetracycline
Coryneform bacteria are rod-shaped bacteria that resemble the letter “V” or “Y”, many of them live in soil, or animal’s mouths, such as, Corynebacterium diphtheriae, which causes diphtheria
Mycobacteria are a type of rod-shaped bacteria
Two species of the Mycobacterium genus are responsible for causing leprosy and tuberculosis in humans

Low GC Gram-Positive Bacteria: phylum Firmicutes

Many of the firmicutes are members of the genera Clostridium and Bacillus and both use endospores to reproduce
Clostridium species are aerobic bacteria, live in soil, get ATP substrate-level phosphorylation, and include the pathogens botulism, tetanus, and gastroenteritis

Bacillus species

Low GC Gram-Positive Bacteria: phylum Firmicutes-Lactic acid bacteria

These bacteria ferment and produce lactic acid
They depend on amino acids and vitamins to produce energy, as they cannot carry out electron transport phosphorylation
The Lactobacillus genus is used to produce fermented foods (yogurt, cheese, pickled vegetables)