LEC 12 and lec 11

omics

derived from gene and chromosome and means the total number of genes in a set

Pangenome

total set of genes in a population of a species

Genome

the total set of genes in an indivual

Pangenome determines a populations

niche breath

pangenome is common among

Niche generalists and nniche specialists, diverse community interactions, large population size, limmited community interactions, small population size

Metagenome

the total set of genes in a community

Omics

technologies are accurate ways to count biological molecules like DNA/RNA, proteins, and metabolites

Omics

is every biomolecule we can count in a cel

Genomics

total set of genes

Transcriptiomics

total set of genes transcribed

Proteomics

total set of translated protein

Metabolomics

total set of biochemicals

Metagenomics

total set of genes in the community

Metatransxriptiomics

total set of genes transcribed by the community

Metaproteomics

total set of protein translated by the communtiy

Metametabolomics

The total set of biochemicals produced by the community

16S rDNA

16S metagenomics

DNA

Metagenomics

mRNA

metatranscriptomics

Proteins

Metaproteomics

Metabolites

Metametabolomics

What omics approach should we use?

step 1: Obtain inoculant genomes

isolate indiviuals

a mixture of two bacteria — sequence DNA mixture metagomics

Every soil organism contains nucleic acids which

are used in molecular biology to idenfity them

Matching sequences obtained from the environment to an organism’s genome

is used to determine if they are present in soil

There are two methods:

one PCR-based and one whole DNA extract. the former is cheaper, but cannot resolve closely related organisms

Of the two inoculants, only R. viceas preseted

in framer’s soil

DNA

metagenomics

mRNA

Metatranscriptionics

Proteins

metaprotemics

Metabolites

metametabolomics

what gene was used to construct this tree

red depicts a phylum without a single specie species grown in a lab

What is required for life?

Water, Enegry, carbon source, nutrients

Macronutrients

nitregen, phosporus, and sulfur

Micronutrients

Iron, calcium, magnesium, mangense

What fuels a cell?

Energy is the capacity to perform work or produce heat. all lifeforms require it. Cells harvest energy from chemical reactions and light.

Energy is always lost as heat.

Cells generate energy like a

battery

A battery couples two materials:

One that tends to lose electrons (donor) and one that tends to steal them (acceptor)

An electron-rich material

that tends to lose electrons

An electron-poor material that tends

to suck up electrons

Cells generate energy like a battey

The movement of electrons provides energy

Powered by redox reactions

The combined reduction and oxidation of electrons in the battery is called a redox reaction

enery yield increases with

voltage

Voltage is the difference

how strong the electron donor grips its eelctrons versus the pull exerted by the electron acceptor.

To represent this give and take, moleculaes are ranked by their tendecny to donate or accept electrons

this system is called redox tower

donate e at the top

moleculaes are more electron rich. they tend to have more hydrogen and carbon.

Accept e are at the bottom

molecules are more electron poor, they tend to contain more oxygens

Soil communities use diverse

energy-generating reactions

Glucose, NH3

Are more likely to donate

NO3-, Fe3+. O2

Greedier

Nitrate reduction

Glucose + No3 —— CO2 + N2

Nirtate reducation

Glucose + No-3 —- CO2 + N2

Iron oxidation

Fe2 + O2 —— H20 + Fe3+

Organic carbon oxidation

Glucose + 02 —- CO2 + H20 = 0.4 +0.9 = 1.3V

Ammonia oxidation

Ammonia + 02 —— N03 + H20 = 0.3 +0.9= 1.2 V

Nitrate reducation

Glucose + N03 —- CO2 + N2 =0.4 +0.6 = 1.0 V

Iron oxidation

Fe2+ + O2 —- H20 + Fe3+ = -0.7 +0.9 = 0.2V

Electron transport chain

Cells transfer electrons across proteins

embedded in their inner membrane. This

electron transport chain is the ‘wire’ of the

battery.

The movement of electrons across the ETC generates

chemical enegry that is eventually stored in the bonds of reactive molecules.

Metabolism describes how a cell acquires enegry and how it spends energy

and it divided into: Catabolic and anabolic processes

Catabolic processes

generate energy by breaking down molecules and store energy

Anabolic processes

spending the money,

consume energy to synthesize biomiocules and perform cellular functions

Cells generate energy

using redox reactions

These reactions drive electrons along a transport

chain to generate energy

greater the difference between redox pairs

the more energy the reaction can generate

Cells gain energy from catabolism and

spend energy in anabolism

Patterns in

beta-diversity mirror the depletion of electron acceptors

Energy generation in

soils follows a predictable pattern based on the availability of e-acceptors

Without an energy source a cell will conserve energy

or switch to new donor or acceptor if it can

Energy generation ____ when a cell runs out of either a donor or an acceptor

stops

A chemoheterotroph runs out

of glucose

A nitrate reducer runs out

of nitrate

the depletion of a donor or acceptor

causes a shift in community composition

Competition for e- acceptors and

e-donors has favored niche differentiation among microbes

The result is a web of dependencies, in which the by-products of one populations’s energy-

generating reactions fuel other community members

Other forms of community metabolism

are unevenly distributed among populations

Many photosynthetic microbes

fix N

Winogradshy in soil macroaggregates

similar redox gradients form in macroaggregates

all chemical sources of energy

no light

In soil microboes run out of

electron donors and acceptors quickly

Different populations within the community can regnerate donors

and acceptors due to diverse forms of energy generating metabolism.

The interdependeny of populations creates a relatively predicatable pattern in

community composotion.

The pattern manifests with time

as a form of ecologigal succession

How do the words genome and metagenome differ in meaning?

A genome refers to the total number of genes present in an organism

A metagenome refers

to the toal number of genes present in a community

What are omics technology

they are tools to quantify biomolecules in the environment

Soil carbon

is green carbon

Plant photosynthesis is

the main source of soil carbon

Plant carbon that contributes to soil formation

comes from structural and non-structural tissues

Structural sources include

leaves, stems, and roots,

On average, structural plant tissues are

45-50 carbon by mass

These tissues have thick cell walls made of a carbon-rich polymer

lignocellulose

Stuctural sources tend to be

insoluable in water

Lignocellulose is made of 3 carbon rich polymers

lignin, cellulose, and hemicellulose

Plant matter is mostly

lignocellulose

Plant carbon that contributes to soil formation

comes from structural and non-structural tisses

Non-structural sources include litter

leachate and root exudates

Like in all cells, carbon is found in plant cells,

in nucleic acids, proteins, and lipids

Non-strucutral carbon tends to be

soulable in water

The seasonal die back of leaves, roots, and other plant tissues is a

major source of dissolved organic carbon to soil