25-26 microbial ecology

Microbial genome + environmental factors

determines the ability of microbe to fill a niche

Assimilation

process by which organisms acquire an element to build into cells

Dissimilation

Process of breaking down organic nutrients into inorganic minerals. Bringing in molecules

Biomass

Bodies of living organisms. everything added up

Primary producers

every food web depends on them for two things:

• absorbing energy from outside the ecosystem

• assimilating minerals into biomass

consumers

• grazers

• predators

Marine producers

CO₂ fixation and biomass production are performed by the phototrophic bacteria; consumers: protists and viruses

Terrestrial Producers

plants; consumers: herbivores

Symbiosis

Intimate association of microbe with another species

Mutualism

both partners benefit

Parasitism

one benefits at the expense of the other

Commensalism

one benefits while the other is unaffected

Symbiotic relationship

between a fungal partner and a photosynthetic partner. fungus provides shelter, water and minerals. cyanobacteria generate organic carbon and fix atmospheric nitrogen.

specific relationship between rhizobia and legumes

mutualism

• plants provide carbon source and shelter

• rhizobia fix atmospheric nitrogen to ammonia and provide it to the plants

• a major source of available nitrogen in the biosphere

• rhizobia enter root cortical cells through infection threads

Myxotricha paradoxa

A multiple symbiont: digestive symbiont of termites. termites need symbionts to digest wood

• a large ciliate that grows in guts of termite

• has its own bacterial endosymbionts to digest wood

• 4 kinds of bacteria attached to its surface (2 spirochetes and 2 anchor bacteria)

Plat pathogens

the most common plat pathogens are fungi

Parasitism/ plat pathogens

bacterial plasmid in a eukaryotic host and gets translated

Lichens

examples of mutualism

• fungus + (alga or cyanobacterium; sometimes both)

• rhizobium inside bean plants

• mixotricha, bacterial endosymbionts, and termines

• Mycorrhizae

Marine Microbiology

the water column in the open ocean is pelagic zone is divided

• neuston: air-water interface

• euphotic zone: receives light so phototrophs grow

• aphotic zone: below the reach of light

• benthos: ocean floor plus sediment below surface

Neuston

air-water interface

• contians the highest microbe concentration

Euphotic zone

receives light so phototrophs grow

Aphotic zone

below the reach of light

• only heterotrophs and lithotrophs can grow

Benthos

ocean floor plus sediment below surface

• thermal vent communities (benthic organisms)

Metagenomics is used for

Measuring the unculturable . you can characterize by using the sequencing of “community DNA”

Metagenomics

the analysis of total microbial community DNA

Measuring Planktonic Communities

• counting organisms

  • dna content

    • fluorescence

  • measure biomass

    • chemical assays of organic matter

  • carbon fixation

    • radiolabeled ¹⁴CO₂

  • metagenomics

    • revealed 25,00 different microbial species

Rumen

critical for digesting cellulose, largest digestive chamber in cattle

Human microbes

humans are tubes of microbes. gut is a tube inside of us

What does the microbe do?

The microbe is analogous to an organ system, some functions are:

• bitamin production

• immune system development

• digestion keeping out pathogens

whos there?

each body has its own microbial community

• the microbiome is mostly bacteria, but also has archaea, fungi, eukaryotes and viruses

Microbes produce beneficial compounds

Microbes digest complex molecules and make short-chain fatty acids

• butyrate feeds the gut epithelium

• acetate tempers the immune system

How does the body control microbes?

• low pH inhibits bacterial growth

• bile salts can kill bacteria

• the gut produces antimicrobial compounds

Why would we limit bacterial growth?

• we want to eat first

• host digestion happens before microbes’

• microbial fermentation helps break down plant polysaccharides downstream in the gut

How do we get a microbiome

• Infants are colonized by maternal vaginal and fecal microbes at birth

• babies naturally drink breast milk

  • milk contains compounds that we can’t digest

  • microbes feed on these compounds

  • milk also contains microbes