L31: Microbes In Terrestrial Environment Flashcards
Soil as Microbial Habitat
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
Major factors affecting soil microorganisms
- Soil moisture: saturated soils stimulate anaerobic microbes. Dry soils limit all microbial activity
- Soil temp. Tropical soils relatively stable. Mid-latitude (temp) soils very variable (summer-winter): soil microbial activity limited in winter
- Soil aeration: Essential for gas exchange; saturated and clay soils restricted gas exchange
- Soil pH: optimum varies among microbial groups; pH 5-8 for most bacteria, cyanobacteria and protozoans; pH4.5-6.5 for fungi
- Available nutrients: organic matter provides carbon and energy; inorganic nutrients ‘minerals soils’ <20% organic C; ‘organic soils’ >20% organic C
- Microbial interactions: +ve and -ve
Soil organic matter (SOM)
Organic matter component of soil: critical component of soil
Retains nutrients, contributes to soil structure, holds water for plant use
Origin of organic matter in soil
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)
SOM occurs in 3 general pools
- Living biomass (microorganisms, plant roots, animals)
- Decomposing residues of living things and added organic wastes
- Humus
Microbial diversity in soils
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
Metagenomics
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:
- Enormous and as-yet diversity
- Diversity highest in pristine organic soils
- Lowest diversity in extreme environments such as salt crystallising ponds
Important activities of microbes in soil
- Decompose (remineralise) soil organic matter
- Play major roles in biogeochemical cycling (C, N, S, Fe and Mn cycles)
- Support the soil food web i.e. a food source for soil protists and animals
- Contribute to soil structure
- Form associations with plants that determine plant survival
Microbes contribute to soil structure
- Soil stabilisation by microbes
- 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
- Humus formation by microbes. Soil organic matter (plant, animal, microbial) -> (microbial degradation, conversion and polymerisation) ->humus
Humus
Sponge-like material
Retains H2O, organic and inorganic chemicals in soil
Important for soil fertility
Humus formation
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
Microbe associations with vascular plants
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
Mutualistic microbe-plant interactions
Mycorrhizal (fungus-root) associations
Nitrogen fixation
Mycorrhizal (fungus-root) associations
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)
Mycorrhizal fungi involved in mutualistic fungus plant association
Involves mycorrhizal fungi that:
- Colonise plant roots
- Obtain photosynthetically-derived carbohydrate from host plant
- 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
Ectomycorrhizae (ECM)
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
Arbuscular Mycorrhizae
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)
Nitrogen fixation
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
Nodule formation and N fixation
- Plant flavonoids activate rhizobial nod genes
- Resulting ‘nod factors’ induce plant root cell division (curling) and ‘uptake’ of rhizobia by plant
- Rhizobia enter root via ‘infection thread’ and are released into plant root cells
- Rhizobia enclosed in host cell membrane -> symbiosome
- Bacterial cells change morphology-> N-fixing bacteroids in symbiosome
- Assembly of bacteroids -> root enlargement -> nodules in root where N fixation occurs
- Depends on key enzyme (nitrogenase: sensitive to O2)
O2 regulated by Fe-containing compound: leghaemoglobin
