L31: Microbes In Terrestrial Environment

Question 1

Soil as Microbial Habitat

Answer 1

Very dynamic habitats

Inorganic particles enmeshed with complex biological communities

Rainfall can: generate saturated soils, wash nutrients out of soil

Waterlogged soils can become anoxic

Plant and microbial activity can change soil environment e.g. consume O2 and release CO2

Structure: arrangement of solid parts of soil and pore space located between them

‘Well structured’ soil has plenty of pore spaces for movement of water, gases, nutrients, roots and vast array of organisms

Question 2

Major factors affecting soil microorganisms

Answer 2

1. Soil moisture: saturated soils stimulate anaerobic microbes. Dry soils limit all microbial activity
2. Soil temp. Tropical soils relatively stable. Mid-latitude (temp) soils very variable (summer-winter): soil microbial activity limited in winter
3. Soil aeration: Essential for gas exchange; saturated and clay soils restricted gas exchange
4. Soil pH: optimum varies among microbial groups; pH 5-8 for most bacteria, cyanobacteria and protozoans; pH4.5-6.5 for fungi
5. Available nutrients: organic matter provides carbon and energy; inorganic nutrients ‘minerals soils’ <20% organic C; ‘organic soils’ >20% organic C
6. Microbial interactions: +ve and -ve

Question 3

Soil organic matter (SOM)

Answer 3

Organic matter component of soil: critical component of soil

Retains nutrients, contributes to soil structure, holds water for plant use

Question 4

Origin of organic matter in soil

Answer 4

In situ production:

Plant growth (roots, exudates) soils animals and microbes

Exogenous inputs:

Human wastes (pollutants, sewage, refuse)

Animal bodies and wastes

Above-ground plant parts (leaf litter, stems, branches)

Question 5

SOM occurs in 3 general pools

Answer 5

1. Living biomass (microorganisms, plant roots, animals)
2. Decomposing residues of living things and added organic wastes
3. Humus

Question 6

Microbial diversity in soils

Answer 6

Is very complex and contains large variety of habitats: as result microbial diversity in soils is greater than that found in aquatic environments

All microbial groups are present in soil

Small portion have been cultured

Question 7

Metagenomics

Answer 7

Study of metagenomes

Genetic material is recovered en masse from environmental samples

Complex sequencing -> allows operational taxonomic units to be distinguished. Based on rDNAsequence analysis. %similarity thresholds set for classifying microbes within same or different OTUs (=species)

No. of OTUs provides measure of microbial diversity in soil sample

Data suggests:

1. Enormous and as-yet diversity
2. Diversity highest in pristine organic soils
3. Lowest diversity in extreme environments such as salt crystallising ponds

Question 8

Important activities of microbes in soil

Answer 8

1. Decompose (remineralise) soil organic matter
2. Play major roles in biogeochemical cycling (C, N, S, Fe and Mn cycles)
3. Support the soil food web i.e. a food source for soil protists and animals
4. Contribute to soil structure
5. Form associations with plants that determine plant survival

Question 9

Microbes contribute to soil structure

Answer 9

1. Soil stabilisation by microbes
2. Binding of soil particles to bacteria due to electrostatic charges (clay particle -vely charged + bacterium -vely charged + divalent cation -> attachment of bacterium through cation bridging
3. Humus formation by microbes. Soil organic matter (plant, animal, microbial) -> (microbial degradation, conversion and polymerisation) ->humus

Question 10

Humus

Answer 10

Sponge-like material

Retains H2O, organic and inorganic chemicals in soil

Important for soil fertility

Question 11

Humus formation

Answer 11

Easily degraded SOM is broken down by microbial activity: Half becomes CO2 (respiration) and rest biomass. Microbes become food for soil animals

Complex structural carbohydrates are degraded. Fungi and bacteria produce cellulase (degrades cellulose). Resistant material such as lignin is degraded by fungi

Question 12

Microbe associations with vascular plants

Answer 12

Some microbes are plant pathogens

Many microbe-plant interactions: commensalistic (microbes benefit without harming plant). Plant roots receive 30-60% of net photosynthesised carbon-> 40-90% of it enters soil -> creates unique environment (rhizosphere) for growth of soil microbes

Some are mutualistic

Question 13

Mutualistic microbe-plant interactions

Answer 13

Mycorrhizal (fungus-root) associations

Nitrogen fixation

Question 14

Mycorrhizal (fungus-root) associations

Answer 14

Mutualistic fungus-root associations

In most cases: fungus enters root tissues and cells (endomycorrhizae)

In some cases fungus enters root tissues but remains extracellular-> form sheath of interconnecting filaments (hyphae) around root (ectomycorrhizae)

Question 15

Mycorrhizal fungi involved in mutualistic fungus plant association

Answer 15

Involves mycorrhizal fungi that:

1. Colonise plant roots
2. Obtain photosynthetically-derived carbohydrate from host plant
3. Provide variety of benefits to host plants: enhance uptake of essential nutrients (e.g. P and N); provide plant host with protection from disease, drought, nematodes and other pests; aid in water uptake in arid environments

Question 16

Ectomycorrhizae (ECM)

Answer 16

Formed by ascomycete and basidomycete fungi

Colonise almost all trees in cooler climates

Aggregated fungal hyphae -> rhizomorphs that extend from plant root and meshwork of extracellular hyphae within root

Nutrients taken up by rhizomorphs pass through hyphal sheath -> into Hartig net filaments which have numerous contacts with root cells

Question 17

Arbuscular Mycorrhizae

Answer 17

Most common type of mycorrhizal association

Endomycorrhizal

Typically associated with crop and tropical plants

Characterised by tree-like hyphal networks: arbuscules -> develop intracellularly in host cells between cell wall and plasma membrane (intracellular)

Question 18

Nitrogen fixation

Answer 18

Occurs as result of symbiotic relationship between N-fixing bacteria and plants

N-fixing bacteria (rhizobia) invade plant roots -> nodes inside which N-fixation occurs

At least 6 genera used (Rhizobium best known)

Rhizobia enzymatically convert gaseous nitrogen (N2) to NH4+ - incorporated into AA

Important part of global nitrogen cycle

Used to enhance soil N levels (crop rotation) saving 50% of fertiliser additions aimed at preventing N limitation

Question 19

Nodule formation and N fixation

Answer 19

1. Plant flavonoids activate rhizobial nod genes
2. Resulting ‘nod factors’ induce plant root cell division (curling) and ‘uptake’ of rhizobia by plant
3. Rhizobia enter root via ‘infection thread’ and are released into plant root cells
4. Rhizobia enclosed in host cell membrane -> symbiosome
5. Bacterial cells change morphology-> N-fixing bacteroids in symbiosome
6. Assembly of bacteroids -> root enlargement -> nodules in root where N fixation occurs
7. Depends on key enzyme (nitrogenase: sensitive to O2)

O2 regulated by Fe-containing compound: leghaemoglobin