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