Biota Flashcards
The conectedness food web
displays diet, who eats whom
not quantitative
the energy flow food web
additionally supplies information about the flux rates along the links in the web
how do you make a food web?
- stomach content analysis
- feeding trials (what eats what)(only cultured representatives)
- direct observation
- label with C13 or N15
What is biomass?
a pool (kg or mJ)
what is productivity?
a flux (in time units; kg/year)
interactions not included in food webs
mutualists, ecosystem engineers (earthworms) and litter decomposers
what is the problem with trophic levels
consumers often feed on multiple trophic levels
cannabalism
dont show energy flow
Architectural root traits
determine the spatial configuration of the entire root system of an individual plant.
commonly used traits include rooting depth, root length, density and root branching
influence carbon cycling (mainly inputs),
nutrient cycle plant uptake,
structural stability (erosion resistance and porosity, sometimes aggregation)
Morphological root traits
features of individual roots such as root diameter, specific root length, root tissue density and root dry mater content
mainly influences carbon cycling (inputs), nutrient cycling (plant uptake), structural stability (erosion resistance, porosity, aggregation)
Physiological root traits
characterise roots in terms of nutrient uptake, kinetics, root respiration, and release of root exudates
carbon cycling (inputs and decomposition (although unknown if exudates influence decomp.)) nutrient cycling (root n content affects inputs and mineralisation, exudates just inputs) structural stability (only exudates have influence on erosion resistance and aggregation)
Biotic root traits
involve direct interactions betweeen roots and soil biota that affect nutrient capture such as associations with Mycorrhizal fungi and rhizobia (in legumes) but also interactions with pathogens
carbon cycling (path. no influence on inputs, otherwise influence on inputs and decomp.) nutrient cycling (myco. no influencee on inputs and neutral on mineralisation, path negative influence on plant uptake. Otherwise others positive on inputs, mineralisation and plant uptake) structural stability (path no influence, myco no influence on porosity)
General properties of roots
high degree of plasticity
localised response to increased nutrient supply
e.g. increased root hairs when low P in soil; increasedd root hairs in localised places with high N
Lateral root initiation
lateral roots start growing out of casparian zone (under epidermis) this releases alot of exudates
Rhizodeposition consists of …
- Low molecular weight exudates
- Secretions
- Mucilages, sloughed off cells
percentage of allocated carbon lost by roots
respiration: 16-76%
Rhizodeposition: 4-70%
Low molecular weight exudates
- Compounds of low molecular weight which leak from all cells into the soil either directly or via intercellular spaces
- Examples are sugars, amino acids
- Exudation amount and composition can vary with a lot of factors (defoliation, water stress,…)
Secretions
- Includes both low and high molecular weight compounds released by metabolic processes
- Example: organic acids
chemical warfare
root - bacteria
positive interaction
PGPRs; symbionts
chemical warfare
root - fungi
positive interaction
->Biocontrol, VAM, endophytes
chemical warfare
root - root
positive interaction
growth facilitators
chemical warfare
root - nematode
positive interaction
chemical warfare
root - root
negative interaction
allelopathy
chemical warfare
root - nematodes (herbivors)
negative interaction
nematicidal/ insecticidal compounds
chemical warfare
root - fungi
negative interaction
->antifungal compounds
chemical warfare
root - bacteria
negative interaction
->antibacterial compounds, QS mimics
How can exudates even work?
theory 1. time lag in excretion of root exudates and arrival of microorganisms who “eat”/ decompose exudates (this also leads to spatial separation of initial excretion of exudates and microorganisms)
theory 2. transport of substances via a mycorrhizal fast lane
border cells role in defence (example)
“lure of the sirens”
one root tip “loses” boarder cells. Nematods swarm to root tip with boarder cells leaving tip without boarder cells nematode free
The rhizosphere
Among other factors, the release of Mucilages, mucigels, sloughed cells and tissues (plus dead roots) leads to the establishment of an important soil hot spot, the rhizosphere.
The rhizosphere
definition by Hiltner 1904
Soil region under immediate influence of plant roots and in which there is a microbial population distinct from the rest of the (bulk) soil.
Mycorrhizal fungi
Mycorrhizae (singular: mycorrhiza) are highly evolved, generally mutualistic associations between soil fungi and plant roots (literally: fungus-root).
Mycorrhizal associations involve 3-way interactions between host plants, fungi (communities) and soil factors
Arbuscular-mycorrhizal fungi (AMF)
All fungi that form this association are in the phylum Glomeromycota (Schüßler et al. 2011). There are currently about 210 morphologically described species. The sequence data base is steadily increasing with environmental sequences (MaarjAM)
it is estimated that 2/3 of all plant species on earth form associations with AMF
AMF structures
Arbuscules- in cells, dont alter cell structure (look like trees), responsible for nutrient exchange
Vesicles- only some AMF’s produce vesicles, used for storage
Spores- asexual reproduction
Hyphae
plant level function of AMF
Nutrient uptake (P, also N; micronutrients)
pathogen protection
Effects on biomass, to some extent nutrient content, very well documented
Less well known: early life history stage effects!
community level function of AMF
Influence on community structure (influence on rare or dominant plant species)
ecosystem level function of AMF
Soil aggregation, soil C storage
Nutrient cycling processes
Leaching, nutrient losses
Ectomycorrhiza ECM
Mostly Basidiomycota, a few Ascomycota; fairly large diversity (about 5,000 described)
evolutionarily much younger than Glomeromycota. Communities often species-rich (>200 morphotypes)
An estimated 2,000 plant species (Gymnosperms and Angiosperms) form this association, including Pinaceae, Fagaceae, Betulaceae. Few tropical trees.
ECM structures
mantle- covers the root, substantial modification of root morphology
Harting net- characteristic for ECM. hyphae do not grom intracellularly. (Grow in root but not in cell)
Rhizomorphs- thread or cord like structure made up of multiple hyphae in soil
fruiting bodies- can be formed above and below ground, not 1:1 relationship between fruiting bodies and ECM on roots.
Pathogenic root inhabiting fungi
a pathogent is an agent, biotic or abiotic, that causes disease by interfering with one or more of the essential functions of the plant
Parasitic root inhabiting fungi
important destinction between obligate and facultative parasites.
Facultative can use food (nutrients) from other sources when they do not parasitize. They are sacrotrophic.
Plant disease
disease triangle
what is “needed” for plants to get diseased
Pathogen - presence, virulence, abundance etc.
Environment - conditions favouring disease
Host - presence and degree of susceptibility
Amount of crops lost to fungi
Rice blast - 10-35%
Stem rust (wheat) - 10-70%
Corn smut - 2-20%
Late blight (potato) - 5-78%
soybean rust - 10-80%
Fusarium
genus with mostly harmless species but some extreme plant pathogens
e.g. fusarium wilt
Pythium
damping off disease of seedlings ( rotten apearance at soil interface)
can also be of importance without catastrophic epidemics.
e.g. black cherry seedlings are “killed” close to mother tree when in high density to avoid competition
Phytophthora infestans
cause of the potato blight and irish potato famine!
AM fungi and fungal root parasites can interact
experiment: when “no fungi”, “just AM” and “AM and parasite” present then root length and shoot biomass stay the same. when “just parasite” present both root length and shoot biomass decrease. This means that AM fungi either stops parasite from colonising root or helps plant counter act effects of the parasite
Sebacinales
Also root colonising fungi
found everywhere, very difficult to isolate
Piriformospora indica
one representative of sebacinales
similar properties to AM fungi
e.g. stress tolerance (salinity)
pathogen protection (fusarium)
3 nutritional modes of Heterotrophs
Biotrophs
sacrotrophs
necrotrophs
Symbiotic nitrogen-fixing bacteria
only prokaryotic cells can fix nitrogen
N2 + 8H^+ +16ATP -> 2NH3 + H2 + 16ADP
Nitrogenase (Fe-S, FeMoCo) -> The required enzym!!!
Limited by Molybdenum and P (for ATP, very expensive to fixate N!!!)
N- fixing organisms that form symbiosis
e.g. Rhizobium, actinomycetes
Energy source (organic carbon): sucrose and its metabolites from host plant
Legumes fix most (50-400 kg N ha^-1 yr^-1)
nodulated non legumes (20-300 kg N ha^-1 yr^-1)
N- fixing organisms that form associations
e.g. Azospirillum, Azobacter
Energy source (organic carbon): Root exudates from host plant
(10-200 kg N ha^-1 yr^-1)
free living N- fixers
e.g. Azobacter, Klebsiella, Rhodospirillium
Heterotrophs get energy from plant residues
Autotrophs from photosynthesis
Heterotrophs only fix 1-2 kg N ha^-1 yr^-1
Autotrophs 10-80 kg N ha^-1 yr^-1
Frankia
- Frankia are actinobacteria; i.e. filamentous bacteria
* Frankia also forms nodules, but on (often pioneer) woody plants (shrubs, trees), e.g. alder (Alnus, Betulaceae)
Top down control of N-fixing bacteria
Symbiosis partner very yummy!!!
Viable but non-culturables (VCN)
many bacteria cant be cultivated in labs because they are dependent on the metabolites of other bacteria (microorganisms).
Kaeberlein et al. (2002): designed diffusion growth chambers to cultivate normally uncultarable organisms. chambers were separated by a wascher with 0.03µm pores so that metabolites from other microorganisms could diffuse without contaminating the wanted bacteria.
Phototrophs
use light as ENERGY source
Chemotrophs
use chemical compounds as ENERGY source
Autotrophs
use CO2 as CARBON source
heterotrophs
need organic CARBON
Lithotrophs
use inorganic substances as ELECTRON DONOR
organitrophs
use organic substances as ELECTRON DONOR
Oligiotrophs
can grow in environments with extremely low organic C (1-15 mg soluble C l^-1)
copiotrophs
require high levels of organic C (1,000 mg soluble C l^-1)
Bacterial motility
some have flagella for movement (life at low reynolds number, even air is viscous)
endospores
only for survival not reproduction
Actinobacteria
filamentous gram-positive bacteria
- Responsible for the earthy, musky smell of soil (geosmins)
- Originally called “ray fungi” because of their filamentous growth habit.
- Most are saprobes (there are also pathogens)
- Tolerant of alkaline conditions (in alkaline soils 95% of the microbial isolates may be actinobacteria), and generally acid intolerant
- One of the most common genera in soil: Streptomyces; there are now over 80 described genera (in 1940 only five were known, before development of antibiotics)
- About 75% of all antibiotics are isolated from actinomycetes
Archea
Phylogenetically and structurally different from bacteria, for example:
o Membrane: lipids are hydrocarbons not fatty acids, and linked to glycerol by ether bonds (ester linked in bacterial & eukaryotes)
o Transcription: more complex than bacteria (polymerase is more closely related to eukaryotic polymerases)
tolerant of extremely harsh environments
also occur in soils and might be very important as ammonia oxidizers!!!
Definition of Fungi
Fungi are defined as organisms that are:
eukaryotes, heterotrophic and have absorptive nutrition;
that reproduce by means of spores and typically produce a hyphal body (mycelium).
Saprobic
Ecological function: decomposer, using dead or decaying organic material
Biotrophic
requiring a living host cell for nutrition
Necrotrophic
fungus kills tissue as it grows through them such that it always colonizes dead substrate
Haustorium
only hostile structure (mutualistic structure= arbuscule)
exoenzymes
operate outside of cell, breaks down macropieces and makes them soluble. Gets there by diffusion.
Enzymes very long living, only produced when substrate present. Produce antibiotics to kill everything else so no competition for substrate
Definition of absorptive nutrition
A process where exoenzymes are secreted from hyphal tips into the surrounding medium, breaking down polymers into soluble compounds; the soluble products are then absorbed into the hypha.
Hyphae as “tunneling machines”
filament grows from the tip, otherwise it would have to be very rigid to avoid buckling.
Exerts hydrostatic pressure
Produces hydrophobins which are protiens that attach to surrounding so that force can be exacted (bracing)
Spores
microscopic propagules that lack an embryo and are specialized for dispersal or dormant survival.
- Survival in dormant condition (dispersal in time)
- Dispersal to a different site
Many fungi produce more than one kind of spore (tight environmental control). can be sexual or asexual
How are Fungi phylogenetically defined?
They are not! they are a way of life!
Unitary organisms
form is highly determinate; there is a predictable succession of life history phases (e.g. infant, sexual maturity, senescence). Many evolutionary and ecological generalizations are based on this.
Modular organisms
Zygote develops into a unit of construction (a module), which then produces further, similar modules. Developmental program is less predictable and strongly dependent on interaction with environment. There are many groups of modular organisms (sponges, corals, fungi, many plants).
difficult to define individual: either genetic individual or module (ramet; shoot; tiller; hyphal growth unit)
heterokaryosis
Fungi exist with mixtures of genetically different nuclear types in the cytoplasm of a hypha
Arise by mutation or hyphal fusion (anastomosis)
Fungi and a kind of “subcellular population biology”
the individual is the nucleus, not the mycelium? (e.g. Wildman 1992).
…and then, of course, also mitochondria (contain DNA), and viruses can be exchanged, as well as cytoplasm….
fungal community
Any grouping of populations of different organisms found living together in a particular environment. The organisms interact and give the community a structure.
fungal assemblage
phylogenetically and geographically delineated community
fungal functional groups
always defined with respect to function of interest, e.g. decomposition
different types of fungi present at different times
example decomposers
First: pathogens/ weak parasites and pioneer saprotrophic fungi
second: polymer degrading fungi
third: degraders of recalcitrant compounds and secondary oportunistic invaders
recalcitrant compounds
complex polymeres like ligin
Protists
“…recommend to use ‘protist’ as a term for all single celled phototrophic, mixotrophic and heterotrophic eukaryotes, with the exception of fungi.”
can be phototrophs, parasites, omnivores and fungivores
Ciliates
10-150 micrometer diameter
• Motility is by means of few to many whip-like organelles
• Sexual reproduction is by conjugation and exchange of protoplasm, no gametes are formed
• Most cilitates feed by grazing and predation, primarily on bacteria, particulate organic matter, but also other protozoa and algae
• Food is ingested through a cell mouth (cytosome) and passed into a vacuole for digestion
Flagellates
2-50 micrometer diameter (i.e. generally among the smaller protozoa)
• Possess one to many flagella and a single nucleus
• Bacteria are principal prey items
• Sexual reproduction by syngamy (fusion of two cells)
Amoebae
5-200 micrometer diameter (up to 6mm for giant naked amoeba)
• Amoebas produce cytoplasmic flows into temporary extensions called pseudopodia; these are used for locomotion and feeding
• There are naked and shelled Amoebas
Ecological roles of soil protozoa
- Mineralization of N, P and S immobilized in bacterial (and fungal biomass)
- Protozoa produce ammonium as a waste product- Dominant effect!
- Release of C from soil via respiration
- Food source for predators such as nematodes
- potential supression of pathogens (bacteria, fungi) by reducing their numbers, diversity
The microbial loop
- Roots produce exudates
- This attracts bacteria
- this attracts protozoa
- protozoa excrete ammonia
- protozoa selectively do not feed on nitrifiers and IAA producing bacteria
- NO3 and IAA induce lateral root growth
- This leads to more exudates…
IAA
indol acidid acid
a plant hormone that induces lateral root growth. Some bacteria can also produce this hormone
Nematodes
Nematodes are unsegmented roundworms
- Size: Most species in soil are between 0.25 to 5.5 mm long
- Reproduction: All nematodes lay eggs.
- Abundance: Nematodes may constitute as much as 90% of all multi-cellular animals in soil and often exceed several million m-2. Nematodes are probably the most numerous multicellular animals on earth!
- Diet: Nematodes eat bacteria, fungi, algae, yeasts, and may be predators of small invertebrate animals, including other nematodes; they are also parasites. Exact feeding habits of most nematodes are unknown, but they are frequently divided into five trophic categories
Plant feeding nematodes
posses a stylet (with which they poke into plant cells)
most extensively studied because they can cause plant disease and crop loss
Fungal feeding nematodes
have slender stylets
difficult to destinguish from plant feeders
bacterial feeding nematodes
Wischmop
no stylet, mop up everything that gets in their path
Ecosystem function
important pest for agricultural crops
In native ecosystems plant consumption by nematodes can be substantial, exceeding that of other herbivores
Nutrient cycling by feeding on bacteria and fungi
Position in the food web between plant and microbe and higher trophic levels
Microarthropods
The collembolans, mites, and a variety of small insects are collectively known as microarthropods
Collembola
Primitive wingless insects (Hexapoda) (subclass Apterygota)
• Common name springtails
• Many species are able to jump by means of a lever (the furcula) attached to the bottom of the abdomen
• Collembola are ubiquitous members of the soil fauna, occurring throughout the world (even Antarctica)
• Many species in soil unnamed; there are about 6,000 known species (in general), but some researchers estimate that there could be over 50,000
• Many species are bisexual, some common species (e.g. Folsomia candida) are parthenogenetic
• Collembola can have rapid population growth rates
mites (ascari)
Mites are related to the spiders (not insects)
• A 100-g sample from a rich forest soil may contain as many as 500 mites, representing almost 100 genera!
• Four suborders occur frequently in soil
oribatei
Characteristic soil mites; an ancient group (there are fossils from Devonian)
• They are often the most numerous of the microarthropods; many species
• Juvenile polymorphism (immatures morphologically extremely dissimilar from adults)
• Reproduce relatively slowly (one or two generations per year, females do not lay many eggs); low grazing rates
• Usually fungivores or detritivores (although details of feeding habits and nutrition remain elusive in soil)
microarthropods functions
- foodweb (grazing)
- Respiration (contribution to soil is typically very low <10%); i.e. they have small contribution to total soil metabolic activity
- Transport, dispersal of microbial inoculum (they eat it and poop it out further away)
-Decomposition
o Comminution
o Mixing
o Fragmentation
- Microbial community composition: selective grazing
- soil structure
- microbial production (compensatory growth)
Tullgren (or Berlese) funnel
funnel with mesh with litter on top. Collecting pot underneath, lightbulb on top.
arthropods etc. go away from light and fall into pot
Oligochaeta (earhtworms)
Earthworms
Diversity: estimated at 6-7 thousand species
in Germany about 35 (23 common)
• Body size ranges from a few centimeters to 2-3 meters
• Earthworm species are stratified vertically based on their ecological strategy:
o Anecic (Gr. up from, out of): litter and soil, live in burrows
o Epigeic (Gr. on top): eat and live in litter
o Endogeic (Gr. in): live within soil
Physiology of an earthworm
- Aristotle: “the intestines of the earth”
- Gut conditions are significantly different from that of the soil, with massive production of intestinal mucus (5-38% of the dry weight of soil ingested); change in pH (usually more basic), association with gut microbiota, etc.
- Endogeic earthworms (geophagous) ingest daily from 5-30 times their own weight of organic and mineral particles
Biogeography of earthworms
The earthworms are invading north america!!!!
dissapeared after last ice age
Enchytraeids (also oligiocheata)
Smaller than earthworms (up to 50 mm long)
about 200-300 species in Central Europe ~600 spp total;
typically about 20-30 species per ecosystem
not geophagous (like earthworms), but rely on pore spaces to move in the soil consume bacteria, fungi and soil organic material
functional roles of enchytraeids
decomposition (communition [but no gizzard], inoculation, selective grazing)
soil structure (burrowing capacity, production of fecal pellets, transport of mineral particles); enchytraeids affect soil porosity, but effects are generally assumed to be minimal
