Lecture 18: Root Nodules

from the time of the Roman Empire farmers knew to _____ because legumes would improve growth on non-legumes in the next growing season

rotate crops

in 1888, pure cultured bacteria from a _____showed that the pure culture could inoculate plants from _____ seeds to form nodules and spare need for fertilizer

nodule; sterile

What is the name of the bacteria that Beijerinck isolated from the root nodule?

rhizobium

what function are nif genes responsible for?

nitrogen fixation

what function are nod genes responsible for?

nodule formation

what is the primary nodule forming bacterial species that a majority of the first studies were done on?

S. japonicum

in S. japonicum, the nif and nod genes are on a _____ called the _____

plasmid; Sym plasmid

why were most of the initial studies of root nodules done with S. japonicum?

grows fast in the lab and has a plasmid

what are the 3 main systems of N2 fixation?

symbiosis, association, free living

symbiosis N2 fixation involves the formation of _____ and is the _____ efficient system

root nodules; most

what is the energy source for the symbiosis root system?

sucrose from host plant

Rhizobium is an example of a _____ N2 system?

symbiosis

how does association differ from symbiosis?

microbes live with plant and fix nitrogen for them, but don’t form nodules

what is the energy source for bacteria in an association N2 fixation system?

root exudates from plant

Axopirillum is an example of an _____ N2 fixation system

association

Free-living N2 fixation is the _____ efficient fixation system

least

how does “free living” fixation differ from Symbisosis and association?

microbes live in soil, don’t directly benefit from plants

human industrial production amounts to some 80×109 kg of _____ yearly

ammonia

what is the process of industrial nitrogen fixation called?

Haber-Bosh process

The Haber-bosh process uses an _____ catalyst to dissociate molecules of N2 to atomic nitrogen, followed by reaction with _____ to form ammonia. This reaction typically runs at _____ temperatures and _____ pressure

Fe; H2; HIGH; HIGH (massive energy input!)

True or False: nitrogen fixers are pretty broad and can match up with many different types of plants

FALSE: high specificity in host-microbe match

what is the major class of bacteria that can fix N2 free living?

alphaproteobacteria

free living nitrogen fixation increase _____ for plants

nitrogen availability

what are the 2 groups of symbiotic rhizobia?

Rhizobium and Bradyrhizobium

which group of rhizobia are FAST-growing

Rhizobium

which group of rhizobia are SLOW growing?

Bradyrhizobia

Rhizobia spp. nodulation functions are encoded on their _____

symbiotic megaplasms

Bradyrhizobium spp. nitrogen fixation and nodulation functions are encoded on their _____

chromosome

nodABC, located on the SYM plasmid encodes the _____ and is required for _____

nod factor; root hair curling

the nodF, gene encoded on the SYM plasmid, is required for the synthesis of the _____ of the nod factor

acyl side chain

nodM, located on the SYM plasmid, encodes for a _____ protein

glucosamine biosynthesis

nodD, on the SYM plasmid is encodes for a _____ response transcription factor that _____ expression of the other _____ genes

flavonoid; activates; nod

in addition to the nod genes, the _____ gene is encoded on the sim plasmid

hup

what does the hup gene encode for?

uptake hydrogenase (utilize hydrogen as an energy source)

Rhizobium is a general term referring to several _____ that fix nitrogen in specific root nodules of _____

genera; legumes

what are 4 examples of legumes that rhizobium form root nodules on?

peas, beans, clover, alfalfa

what are the 5 types of rhizobium genera?

rhizobium, Brady-, Sino-, Meso-, Azo-

most rhizobacterium are _____ that live in soil or _____ (class)

alpha-proteobacteria; beta-proteobacteria

rhizobium first bind to the _____ of the plant, causing it to _____ and _____ the bacteria

root hair; curl; entrap

After the plant curls around the rhizobium, the cell travels down the _____ into the plant’s _____ cells

infection threat; cortical

once the rhizobium reaches the plant’s cortical cells, the bacteria will _____ the cell and _____ into _____

penetrated; differentiate; bacteroids

in order for the rhizobium to bind and the plant curl in on itself, certain _____ must be produced by both the bacteria and the plant

specificity determinants

what are the two main specificity elements produced by plants?

lectins and flavenoids

what are the two main specificity elements produced by bacteria?

polar EPS and Rhicadhesin (Ca2+)

how does Lectin act as a specificity element?

binds to bacterial surface sugar residues

how does flavenoids act as a specificity element?

in induces migration of bacteria towards root hair (like gradient)

how does polar EPS act as a specificity element?

binds to plant surface

how does Rhicadhesin (Ca2+) act as a specificity element?

involved in interaction w/ specific plant (forms specific plant/microbe pair)

flavenoids are like a _____ and are made by _____ and excreted into the environment, forming a _____ towards the plant

steroid; legumes; gradient

Flavonoids are plant signals that initiate _____

the symbiosis

Flavonoids can being either an attractant or repellent for _____

motility

Flavonoids can promote or inhibit _____ gene expression in bacteria

nod

what is the “inducer” form of the flavonoids?

Luteolin

what is the “inhibitor” form of the flavonoid?

genistein

why would the plant want to have a flavonoid that inhibits motility?

prevents wrong partner from infecting (uphold the specific pairing)

Nod factors are another example of a _____

specificity element

nod factors are similar to _____ and is a modified oligosaccharide with a _____ backbone

chitin; NAG (also like PG)

who releases the nod factor? plant or bacteria?

bacteria!

nod factors are detected by the plant _____ and will stimulate _____ and _____ in the plant upon recognition. It will also help stimulate more _____ production (like a positive feedback loop)

receptors; curling; cell division; flavonoid

NOD factors induce the _____ pathway in plants

SYM (symbiosis)

the SYM pathway in plants causes the _____ of bacteria in a codex by plant-derived vesicles called _____. This leads to the formation of _____

entrapment; SNARES; bacteroids

Zone ONE of the root nodule is called the _____ and it is full of _____

meristem; actively dividing plant cells

Zone TWO of the root nodule is where bacterial cells begin to form _____

bacteroids (differentiation)

Zone THREE is where the majority of _____ are

bacteroids

Zone FOUR is where the _____ of bacteroids occurs

dying off

Which zone of the root nodule is where the majority of nitrogen fixation is occurring?

3

the _____ of the root hair forms the infection pocket and allows the bacteria to travel down into the _____

curling; cortical cells

the infection tube is a _____-like tube made by the _____

cellulose; plant

True or False; the infection tube is created by the bacteria as the burrow deep into the root hair

FALSE: made by the plant (bacteria don’t actually enter the cell!)

as bacteria makes it’s way through the infection tube, the cortical cells of the plant undergo rapid _____

proliferation

what are the two main ways that plants prevent pathogenic bacteria from utilizing the infection tube?

high oxidative stress and antimicrobials

ho does the Rhizobium avoid the innate immune system?

resistant to the antimicrobials produced

infection threat penetrates through several _____ of _____ cells

layers; cortical

plant cells in _____ of the thread will divide and organize themselves into a _____

front; nodule primordium

the branched infection thread enters the nodule _____ and _____ individual primordium cells

primordium zone; penetrates

bacteria are released from the infection thread into the _____ of the host cells but remain surrounded by the _____

cytoplasm; symbiosome membrane

bacteroid cells have no _____ and cannot do _____

cell wall; differentiation (division)

what are the two main signals for establishing the Bacteroid?

anaerobic conditions (low O2) and NCR

what are NCRs?

nodule specific cysteine-rich peptides

are bacteroids anaerobic or aerobic?

aerobic!

how are bacteroid cells able to avoid O2 damage to nitrogen fixation proteins? (despite being aerobic)

Leghemoglobin sucks up all the O2 and directly delivers it to the ETC

Bacteroids have a function central metabolic pathway because of _____ provided by the _____; why is this necessary?

sugars; plant; nitrogen fixation needs lots of ATP!

what is the main benefit of nitrogen fixation for the bacteroid?

gets amino acids

what two main amino acids get sent to the plant?

glutamine and asparagine (nitrogen rich)

what are the three main organic components that the bacteroid uses (from the plant)?

succinate, malate, fumarate

why are root nodules typically a reddish-orange?

Leghemoglobin (same as blood)

_____ are plant genes specific required for successful nodule formation

nodulins

different nodulins are expressed at different times in the _____, this shows that the _____ has an important role in regulating this process

nodule development; plant

are nodulins produced by the plant or the bacteria?

PLANT!

Stem-nodulating bacteria are primarily observed with _____

tropical legumes

nitrogen fixing fern called _____ is the only fern that can fix nitrogen and it does so by virtue of a symbiotic _____ with a _____

Azolla; association; cyanobacterium

nitrogen fixing fern (azolla) has a _____ in the center which is colonized with a symbiotic _____ bacteria. This bacteria will fix nitrogen in exchange for _____ made by the plant

hollow cavity; cyanobacterium; organic compounds

Anabaena azollae, the cyanobacterium that lives with the Azolla fern has undergone lots of _____ which has caused it to heavily rely on the plant cell, almost like an _____

genome reduction; organelle

a different _____ bacteria lives on the plan Welfia regia in an _____relationship

cyanobacterium; epiphyllic

it is believed that the cyanobacteria of Welfia regina transfer some % of fixed nitrogen to the plants through the _____. This it more of an example of _____ versus a symbiotic relationship

leaf surfaces; association