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Microbiomes

Introduction

  • 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.

Analyzing Genes That Encode Ribosomal RNA

  • 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

Amplicon Analysis

  • 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

Whole Metagenomic Sequencing (WMS)

  • 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 “shotgun sequencing”, 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 vs Amplicon Analysis

  • 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

Functions within Microbiome

  • 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

Analysis of mRNAs, Proteins, and Metabolites

  • WMS and amplicon analysis indicate what genes are present in the microbiome.

  • They don’t, 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

Diversity of Earth’s Microbiomes

  • Some microbiomes are found within physical systems.

    • Oceans

    • Ice

    • Fresh waters

    • Soils

  • Other microbiomes are associated with living organisms known as hosts

Microbiomes in Freshwater and Soil

  • 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

Host-Associated Microbiomes

  • 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 Extend Host Capabilities

  • 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

Hosts Acquire Microbiomes in Different Ways

  • 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

Bacterial Microbiomes

  • 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 B₁₂, which the cyanobacterial host requires but cannot produce itself

Protist Microbiomes

  • 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 B₁₂

  • Other bacteria are methane-oxidizers which perform important ecological functions

Fungal Microbiomes

  • 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

Subterranean Root Microbiomes

  • 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

Mycorrhizae

  • More than 80% of terrestrial plants form mycorrhizae

  • Fungal hyphae extend farther into soil than the plant’s roots

  • Benefits to plants:

    • Increased supply of water

    • Increased supply of minerals (phosphate, copper, zinc)

  • Benefit to fungi: access to photosynthetic products

Endomycorrhizae

  • 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

  • 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

  • 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

Engineering Plant and Animal Microbiomes

  • 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

Microbiomes

Introduction

  • 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.

Analyzing Genes That Encode Ribosomal RNA

  • 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

Amplicon Analysis

  • 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

Whole Metagenomic Sequencing (WMS)

  • 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 “shotgun sequencing”, 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 vs Amplicon Analysis

  • 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

Functions within Microbiome

  • 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

Analysis of mRNAs, Proteins, and Metabolites

  • WMS and amplicon analysis indicate what genes are present in the microbiome.

  • They don’t, 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

Diversity of Earth’s Microbiomes

  • Some microbiomes are found within physical systems.

    • Oceans

    • Ice

    • Fresh waters

    • Soils

  • Other microbiomes are associated with living organisms known as hosts

Microbiomes in Freshwater and Soil

  • 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

Host-Associated Microbiomes

  • 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 Extend Host Capabilities

  • 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

Hosts Acquire Microbiomes in Different Ways

  • 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

Bacterial Microbiomes

  • 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 B₁₂, which the cyanobacterial host requires but cannot produce itself

Protist Microbiomes

  • 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 B₁₂

  • Other bacteria are methane-oxidizers which perform important ecological functions

Fungal Microbiomes

  • 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

Subterranean Root Microbiomes

  • 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

Mycorrhizae

  • More than 80% of terrestrial plants form mycorrhizae

  • Fungal hyphae extend farther into soil than the plant’s roots

  • Benefits to plants:

    • Increased supply of water

    • Increased supply of minerals (phosphate, copper, zinc)

  • Benefit to fungi: access to photosynthetic products

Endomycorrhizae

  • 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

  • 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

  • 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

Engineering Plant and Animal Microbiomes

  • 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

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