Microbiomes
Micromes: millions of species of archaea, bacteria, protists, and fungi that play important ecological roles worldwide.
Biomes: major types of habitat characterized by distinctive life forms.
Microbiomes: a particular assemblage of microbes and genes that occurs in a defined environment.
There are thousands of different microbial species
Diverse species of bacteria, archaea, fungi, protists, and invertebrate animals
Communicate with each other chemically and/or electrically
Difficult to identify based on size and similarity of structure
Biologists typically use genetic differences to distinguish and identify microbial species and genes present in a complex microbiome.
All living things produce proteins using ribosomes
Ribosomes contain ribosomal RNA (rRNA)
Sequences of nucleotides in rRNA are highly conserved
Changes in the sequence of rRNA can be used to evaluate evolutionary relationships
rDNA: genomes that encode rRNA
Differences in rDNA can be used to identify and classify the microbes present in a microbiome
Extract DNA from a sample
Use polymerase chain reaction to copy a particular region of rDNA
Amplicons: copied rDNA regions
16S rRNA sequences: commonly used to identify prokaryotic species
18S rRNA: used to identify and classify eukaryotic microbiome components
Subject amplicons to DNA sequencing
Compare to reference sequences in a database to identify the unknown species
Reference sequences: come from microbes whose names and metabolic functions are already known
Obtain base sequences of all the DNA present in a sample
Metagenome: the genomes of all the organisms present in a sample
Approach is known as âshotgun sequencingâ, since the process generates many tiny pieces of DNA
A computer is used to identify places where the ends of DNA fragments have the same DNA sequences
These overlapping regions are used to align the DNA fragments into contiguous sequences (or contigs)
WMS: can be used to assemble entire microbe genome sequences or even identify both prokaryotic and eukaryotic species in a microbiome.
Amplicon analysis: typically focuses on amplification of a particular gene from a selected group of species
For example, focusing on 16S rRNA amplicons will only identify prokaryotic species in a given sample
For this reason, many experts use the term microbiota to describe collections of microbial life catalogued by limited amplicon analysis
When analyzing microbiomes by WMS, another goal is to find and classify protein-encoding genes that indicate specialized microbial functions.
Nitrogen fixation: look for marker genes for enzymes essential for reduction of atmospheric nitrogen to form ammonia
Methane oxidation: the enzyme methane monooxygenase (MMO) uses oxygen gas to oxidize the greenhouse gas methane
Metabolite production: some microbes produce specific compounds as a result of metabolic pathways
Examples include certain vitamins and toxins
WMS and amplicon analysis indicate what genes are present in the microbiome.
They donât, however, reveal which genes were actually being transcribed or translated.
To get those details, biologists analyze:
Metatranscriptome: collection of all the mRNAs present in an environmental sample
Metaproteome: all the proteins produced by the members of a microbiome
Meta-metabolome: collections of information about all the types and abundances of molecules produced by metabolism of the organisms in a microbiome
Some microbiomes are found within physical systems.
Oceans
Ice
Fresh waters
Soils
Other microbiomes are associated with living organisms known as hosts
Drinking water safety and agricultural production are affected by microbiomes
Some abundant cyanobacteria produce persistent and potent toxins that harm people and wildlife
for example, Microcystis produces microcystin which interferes with many cellular processes including cell signaling
What effect will global climate change have on such microbes which grow abundantly in warmer temperatures?
Various soil microbes foster or decrease plant health
A single gram of soil contains as many as 50,000 bacterial species and diverse fungi
Holobiont: combination of host organism and its microbiome
Hologenome: The host and microbiome genomes together
Microbiomes contribute many more genomes to the hologenome than their hosts
The human genome contains approximately 22,000 protein-encoding genes
The human microbiome is estimated to have a few million genes
Microbiomes function as complex biological networks
Chemical signals produced by the host act on particular microbes that serve as information hubs, transmitting information to the broader microbial community
Host genetics and environment are important for the types of microbiomes acquired by the host
Having a functionally useful microbiome aids the survival of the young and increases fitness.
Some examples of microbiome acquisition:
Newborn bees get microbiomes from sibling worker bees
Mammals, including humans, transmit important microbes as the young transit the birth canal
Termites use specific behaviors to transfer microbes needed to break down plant materials into food
Plant seedlings acquire microbiomes from surrounding soil and air, but they also use inherited mechanisms, often secretion of particular organic compounds, to attract beneficial microbes
Certain bacterial species, such as cyanobacteria, can produce relatively large bodies that host microbiomes of ecological significance
Microcystis, for example, occurs as colonies of cells held together with mucilage that provides home to diverse heterotrophic bacteria
WMS shows that the microbiome bacteria synthesize vitamin Bââ, which the cyanobacterial host requires but cannot produce itself
Algae likewise provide a photosynthetic host for a heterotrophic microbes
Bacterial species may attach themselves to algal cell walls by secreting mucilage to form a biofilm
Photosynthetic host provides living space, oxygen, and organic materials
Some bacterial guests produce vitamins such as vitamin Bââ
Other bacteria are methane-oxidizers which perform important ecological functions
Fungi also function as hosts, most conspicuously for microbiomes known as lichens
Traditionally, lichens were regarding as symbiotic relationships between a fungus and a photosynthetic algal or cyanobacterial species
WMS revels that lichens are microbiomes that include many bacterial and fungal species
Lichens often grow on rocks, buildings, tombstones, tree bark, soil, or other surfaces that easily become dry.
Lichens acids help tp break up the surfaces of rocks, beginning to process of soil formation
Lichens with nitrogen-fixing cyanobacterial partners can increase soil fertility
Legumes and some other plants form partnerships with soil bacteria that provide fixed nitrogen
Certain fungal hyphae are important components of plant microbiomes because they absorb minerals from the soil and transport them to plant roots
Known as mycorrhizae
Plant microbiomes change with age
Plant microbiomes influence plant hormones
Plant hormones influence microbial genes in the microbiome
More than 80% of terrestrial plants form mycorrhizae
Fungal hyphae extend farther into soil than the plantâs roots
Benefits to plants:
Increased supply of water
Increased supply of minerals (phosphate, copper, zinc)
Benefit to fungi: access to photosynthetic products
Endomycorrhizae: fungal hyphae penetrate space between root cell walls and plasma membrane, forming highly branched, bushy arbuscules that the plasma membranes expand around
Known as arbuscular mycorrhizae (AM)
Fungal partners are known as AM fungi
Ectomycorrhizae: fungal hyphae coat tree-root surfaces and grow into the spaces between roots cells, but do not penetrate the cell membrane.
Fungal partners are frequently basidiomycetes
Animal microbiomes contain viruses, archaea, bacteria, fungi, protists, and microscopic animals
Affect animal health
Biofilms on teeth known as plaque are detrimental to dental health
Microbes in the digestive system of infants aid in milk digestion, aid the immune system, and reduce gut pH
Play important environmental roles
Gut bacterial species in termites allow recycling of plant biomass
Have medical applications
Bacteria in the guts of tunicates produce defensive molecules and are potential sources of antibiotics that control disease-causing microbes without harming the animal host
Microbiome engineering: manipulating the composition of a microbiome to improve host characteristics
Microbiome engineering is of particular interest for the benefits of:
Humans
Domesticated animals
Crop plants
Micromes: millions of species of archaea, bacteria, protists, and fungi that play important ecological roles worldwide.
Biomes: major types of habitat characterized by distinctive life forms.
Microbiomes: a particular assemblage of microbes and genes that occurs in a defined environment.
There are thousands of different microbial species
Diverse species of bacteria, archaea, fungi, protists, and invertebrate animals
Communicate with each other chemically and/or electrically
Difficult to identify based on size and similarity of structure
Biologists typically use genetic differences to distinguish and identify microbial species and genes present in a complex microbiome.
All living things produce proteins using ribosomes
Ribosomes contain ribosomal RNA (rRNA)
Sequences of nucleotides in rRNA are highly conserved
Changes in the sequence of rRNA can be used to evaluate evolutionary relationships
rDNA: genomes that encode rRNA
Differences in rDNA can be used to identify and classify the microbes present in a microbiome
Extract DNA from a sample
Use polymerase chain reaction to copy a particular region of rDNA
Amplicons: copied rDNA regions
16S rRNA sequences: commonly used to identify prokaryotic species
18S rRNA: used to identify and classify eukaryotic microbiome components
Subject amplicons to DNA sequencing
Compare to reference sequences in a database to identify the unknown species
Reference sequences: come from microbes whose names and metabolic functions are already known
Obtain base sequences of all the DNA present in a sample
Metagenome: the genomes of all the organisms present in a sample
Approach is known as âshotgun sequencingâ, since the process generates many tiny pieces of DNA
A computer is used to identify places where the ends of DNA fragments have the same DNA sequences
These overlapping regions are used to align the DNA fragments into contiguous sequences (or contigs)
WMS: can be used to assemble entire microbe genome sequences or even identify both prokaryotic and eukaryotic species in a microbiome.
Amplicon analysis: typically focuses on amplification of a particular gene from a selected group of species
For example, focusing on 16S rRNA amplicons will only identify prokaryotic species in a given sample
For this reason, many experts use the term microbiota to describe collections of microbial life catalogued by limited amplicon analysis
When analyzing microbiomes by WMS, another goal is to find and classify protein-encoding genes that indicate specialized microbial functions.
Nitrogen fixation: look for marker genes for enzymes essential for reduction of atmospheric nitrogen to form ammonia
Methane oxidation: the enzyme methane monooxygenase (MMO) uses oxygen gas to oxidize the greenhouse gas methane
Metabolite production: some microbes produce specific compounds as a result of metabolic pathways
Examples include certain vitamins and toxins
WMS and amplicon analysis indicate what genes are present in the microbiome.
They donât, however, reveal which genes were actually being transcribed or translated.
To get those details, biologists analyze:
Metatranscriptome: collection of all the mRNAs present in an environmental sample
Metaproteome: all the proteins produced by the members of a microbiome
Meta-metabolome: collections of information about all the types and abundances of molecules produced by metabolism of the organisms in a microbiome
Some microbiomes are found within physical systems.
Oceans
Ice
Fresh waters
Soils
Other microbiomes are associated with living organisms known as hosts
Drinking water safety and agricultural production are affected by microbiomes
Some abundant cyanobacteria produce persistent and potent toxins that harm people and wildlife
for example, Microcystis produces microcystin which interferes with many cellular processes including cell signaling
What effect will global climate change have on such microbes which grow abundantly in warmer temperatures?
Various soil microbes foster or decrease plant health
A single gram of soil contains as many as 50,000 bacterial species and diverse fungi
Holobiont: combination of host organism and its microbiome
Hologenome: The host and microbiome genomes together
Microbiomes contribute many more genomes to the hologenome than their hosts
The human genome contains approximately 22,000 protein-encoding genes
The human microbiome is estimated to have a few million genes
Microbiomes function as complex biological networks
Chemical signals produced by the host act on particular microbes that serve as information hubs, transmitting information to the broader microbial community
Host genetics and environment are important for the types of microbiomes acquired by the host
Having a functionally useful microbiome aids the survival of the young and increases fitness.
Some examples of microbiome acquisition:
Newborn bees get microbiomes from sibling worker bees
Mammals, including humans, transmit important microbes as the young transit the birth canal
Termites use specific behaviors to transfer microbes needed to break down plant materials into food
Plant seedlings acquire microbiomes from surrounding soil and air, but they also use inherited mechanisms, often secretion of particular organic compounds, to attract beneficial microbes
Certain bacterial species, such as cyanobacteria, can produce relatively large bodies that host microbiomes of ecological significance
Microcystis, for example, occurs as colonies of cells held together with mucilage that provides home to diverse heterotrophic bacteria
WMS shows that the microbiome bacteria synthesize vitamin Bââ, which the cyanobacterial host requires but cannot produce itself
Algae likewise provide a photosynthetic host for a heterotrophic microbes
Bacterial species may attach themselves to algal cell walls by secreting mucilage to form a biofilm
Photosynthetic host provides living space, oxygen, and organic materials
Some bacterial guests produce vitamins such as vitamin Bââ
Other bacteria are methane-oxidizers which perform important ecological functions
Fungi also function as hosts, most conspicuously for microbiomes known as lichens
Traditionally, lichens were regarding as symbiotic relationships between a fungus and a photosynthetic algal or cyanobacterial species
WMS revels that lichens are microbiomes that include many bacterial and fungal species
Lichens often grow on rocks, buildings, tombstones, tree bark, soil, or other surfaces that easily become dry.
Lichens acids help tp break up the surfaces of rocks, beginning to process of soil formation
Lichens with nitrogen-fixing cyanobacterial partners can increase soil fertility
Legumes and some other plants form partnerships with soil bacteria that provide fixed nitrogen
Certain fungal hyphae are important components of plant microbiomes because they absorb minerals from the soil and transport them to plant roots
Known as mycorrhizae
Plant microbiomes change with age
Plant microbiomes influence plant hormones
Plant hormones influence microbial genes in the microbiome
More than 80% of terrestrial plants form mycorrhizae
Fungal hyphae extend farther into soil than the plantâs roots
Benefits to plants:
Increased supply of water
Increased supply of minerals (phosphate, copper, zinc)
Benefit to fungi: access to photosynthetic products
Endomycorrhizae: fungal hyphae penetrate space between root cell walls and plasma membrane, forming highly branched, bushy arbuscules that the plasma membranes expand around
Known as arbuscular mycorrhizae (AM)
Fungal partners are known as AM fungi
Ectomycorrhizae: fungal hyphae coat tree-root surfaces and grow into the spaces between roots cells, but do not penetrate the cell membrane.
Fungal partners are frequently basidiomycetes
Animal microbiomes contain viruses, archaea, bacteria, fungi, protists, and microscopic animals
Affect animal health
Biofilms on teeth known as plaque are detrimental to dental health
Microbes in the digestive system of infants aid in milk digestion, aid the immune system, and reduce gut pH
Play important environmental roles
Gut bacterial species in termites allow recycling of plant biomass
Have medical applications
Bacteria in the guts of tunicates produce defensive molecules and are potential sources of antibiotics that control disease-causing microbes without harming the animal host
Microbiome engineering: manipulating the composition of a microbiome to improve host characteristics
Microbiome engineering is of particular interest for the benefits of:
Humans
Domesticated animals
Crop plants