soil ecology
aggregate formation
structure stabilizes organic matter from plants and microbes hierarchical structure role of biology in forming aggregates: roots, mycorrihizae (AMF), earthworms (ecosystem engineers)
Carl woese: discovery of archaea and use of 165 ribosomal dna for taxonomy
Bacteria, archaea, eukarya
Primary production:products of photosynthesis
"Gross primary production": all photosynthesis in a given system But immediate losses by the producer (plant) for own metabolic need: Plant respiration (Rplant) or autotrophic respiration (RA) What is left over: "net primary production" GPP-Rplant=NPP
pore space units
%pore space= [pore volume/soil volume]x100 bulk density= soil mass/soil bulk volume (g/m3) particle density= 100-[(bulk density/particle density)x100]
secondary production: what happens
(CH20)n+nO2+nH20+energy ATP ingestion of organic carbon and associated nutrients assimilate carbohydrates, lipids, protein >40% lost as metabolic heat and CO2 c-c and c-o bonds: energy rich c-n, c-p, c-s bonds: require energy but release nutrients 1000s of compounds being decomposed 1. primary compounds: directly derived from plant, microbial, or animal material 2. secondary compounds: produced from OM mineral interactions, changes in chemical bonds or aromaticity
Free Air Enrichment ( FACE): ecosystem scale, decade long carbon cycle experiments
+200ppm CO2 above ambient atmosphere CO2 concentrations
why use pulse chase technique
1. allocation of C 2. timing (speed of cycling) 3. in situ determination, minimal disturbance method development: applied a low level C label in a small black spruce
what is NPP made up of
1. biomass increment: increase in aboveground biomass per unit time 2. litter production: dead plant material that is shed leaves, branches, bark, flowers, seeds, roots
label application
1. labeled biocarbonate solution 2. acidified to release CO2 3. circulated 14CO2 through dome enclosure 1 hour 4. produce a capital delta14C signature=100,00%
pulse change labeling: adding 14C
1. pulse single addition of an isotopically enriched label (CO2 or specific C substrates) 2. chase with time, follow the same rate of the label by measuring the amount incorporated into different C pools C pools that can be followed: respiration, storage, structural material, microbial pools, leaching and volatiles
heterotrophs in soil: range of sizes
<1um bacterial cells aardvarks, badgers, giant earthworms 2m in length large food webs develop based on secondary production
soil organisms: size determines accessibility
distribution in pore spaces in anoisol in manaus two different depths (top 2-5cm, bottom 5-10cm)
Definition of soil function
Biological, geochemical, and physical processes Decomposition, C and N cycling, regulation of plant growth/primary production
Photosynthesis: fundamental energetic process in most ecosystems
CO2+H2O+suns enerfy=(CH2O)n+O2
type of mycorrhizal association impacts response to CO2 compared to AM forests
ECM associated forests had a greater response too elevated CO2 compared to AM forests difference are particularly pronounced under low N conditions
Key factor for controlling soil function is biodiversity
Ecosystem services: tangible and intangible benefits for humans Benefits people derive from ecosystems Provisioning, regulating, supporting, cultural services
When do organisms matter
Invasion of non native earth worms: Earthworms are not native to the Great Lakes region, they were all wiped out after last glaciation The current population brought here by early Europeans, is slowly changing the face of our native forests
NPP in context: terrestrial carbon cycle
NPP is the pathway by which C enters soils litterfall, roots, root exudates, transfer of C to mutualist
Respiration
Opposite of photosynthesis, how we get energy (sugar/starch/fat) (CH2O)n+O2=CO2+H2O+suns energy
Organisms help form aggregates and pore spaces
Roots, mycorrhiza (AMF), earthworms
How to classify organisms: by their function
Size, feeding, habitat, taxonomy: problem that none of these are linked to function Concept of functional groups, organisms that carry out similar functions, ultimately determine ecosystem functions
Diversity/function: central question of soil ecology
Soil bio geochemistry perspective (hypothesis 1): who's there doesn't matter much Soil biology perspective ( hypothesis 2): who's there matters Hypothesis 1: difference in organic matter dynamics are mainly driven by the environment Physiology and metabolic activity constrained temp, water, soil type, resource availability/quality To understand C and nutrient dynamics, no need to know soil organisms identify Hypothesis 2: population dynamics explain community structure Ecosystem processes depend on population and community ecology Functional groups/composition matters for all aggregate ecosystem functioning Hypothesis 1: functional redundancy Hugh diversity, ability to adapt quickly, ubiquitous preserve Hypothesis 2: complementarity between organisms promotes ecosystem processes
measuring above ground biomass increment: annual grassland
biomass harvest with in a known area litter collected from the same area
Traditional method: enrichment culture
The paradox of non culture bacteria Microscopy 10^9 cells/ml Culturing 10^5 cells/ml
human effects
anthropogenic effects
decomposition: 2 major players
bacteria: initial breakdown of less stable compounds (sugars and lipids) immobilization of inorganic V limited individual range and physical impact fungi: breakdown of persistent molecules (lignin, cellulose, hemicellulose) uptake of dissolved organic N growing hyphae can penetrate litter and transport molecules elsewhere (back into roots system)
microbial accessibility of OM
biochemical limitations environmental limitations accessibility, O2, water etc energetic limitations
earthworms
can cover surface with castings (digested OM and soil) can burrow deep into soil feed on fresh litter and partially decomposed OM ( including microfauna and flora) mucus secretions that line the burrows of earthworms: drilosphere lumbricus terrestris can: remove 90% of autumn leaves in an apple orchid produce 4-8lbs castings per m^2 per year consume 120g dry weight/m^2/yr notoscolex can: produce individual casts weighing 3lbs
why is there so much carbon in soils
carbon sequestration
soil microbes: new horizon of biodiversity
carry out most soil function challenging to study: physically inaccessible most abundant and diverse of soil contains 10^5 species most studies: bacteria and fungi less studies: archaea and viruses
decomposition of cellulose
cellulose: up to 10,000 repeating units of D-glucose relatively easily digested in soluble form forms crystals that are much more resistant some anaerobic bacterial (clostridium) have a cellulosome= specialized extracellular complex for cellulose degradation anaerobic bacteria need many different extracellular cellulases to cope with different forms and bonds of cellulose, these act together degraded by both white and brown rot fungi
bypassing decomposition:biominerals
certain groups of plants, algae and fungi produce silicate crystals as byproducts or as supporting and protecting structures: phytoliths frustule of diatoms many contribute to composition of mineral fraction
Aggregates
clumps of soil particles glued together by moist clay and organic matter macroaggregates: >0.25mm mesoaggregates: 0.02-0.25mm microaggregates: 0.002-0.02mm
decomposition of lignin
complex polymer of phenylpropane units resistant to decomposition and to chemical analysis forms physical barriers to decomposition of other structural molecules major contribution to formation of humus (exact chem pathways not clear) only degraded by white rot fungi and some ( less efficient) actinomycetes
two types of secondary production
consumption of living plants: grazing food chain done by herbivores, parasites consumption of dead (OM): detrital food chain done by decomposers (bacteria), detrivors (earthworms, invertebrates), sporotrophs (fungi)
biological soil crusts
cover not just soils, but rocks and plants able to fix atmospheric C and N (CO2 and N2) important in arid lands contribution of cryptogamic covers to the global scales of carbon and nitrogen importance for biological biochemsitry: 3.9gC/yr, equivalent to 7% of NPP by terrestrial regulation 49TgN/yr, nearly half of all biological N fixation composed of soil cyanobacteria, lichens, moss in environments with sparse plant cover essential to providing stability and fertility to desert soils component organisms easily damaged by soil surface disturbance are very slow to recover: grazing, vehicles, development protecting biological soil crusts should be a top priority in desert regions, or we will lose the important ecosystem services they provide
secondary production processes
decomposition=breakdown of OM into smaller organic compounds and inorganic minerals incorporation is the first step of decomposition: movement of materials to places where they can be further broken down
Rhizosphere
definition: portion of the soil in which microorganisms mediated processes are under the influence of the root system extends only a few mm from root surface up to 10^11 microbial cell/gram of root
FACE carbon isotope label
delta13C carbon fixed in soil before the experiment has a different signature than carbon fixed during the experiment
measuring NPP belowground
destructive sampling: soil coring, rinse, float, sieve final product: root dry mass root ingrowth core: remove core, sieve soil, replace with 5-7mm mesh bag roots grow in, sample at various intervals assumes roots grow as they do in normal soil non destructive sampling: rhizotrons and mini rhizotrons: direct viewing of root growth rhizotrons: glass plate in observation gallery soil profile must be recreated only a small fraction of forest minirhizotrons: glass tube 5-7cm diameter small surface area, extensive replication possible may form preferential flow paths
root lifetime continuum
different kinds of roots have different life times contribution of root C to formation of soils organic matter needs to be re examined this information should provide accurate quantification of NPP and belowground C allocation
incorporating agents
earthworms and termites can drastically increase speed and depth of incorporation major contributors to formation of mulls droppings present bacteria and fungi with more fragmented OM in aggregates that decompose faster
FACE
elevated CO2 in atmosphere forests to look at ecosystem impacts use natural gas derived CO2 to fumigate forests
Vasily Dokuchaev
father of soil science soils are natural bodies that develop under the influence of climate and biological activity acting on geologic substrates (1883) first to acknowledge development of soils active role of organisms
soils at field capacity: subaqueous system
first phase of soil water evaporation: natural displacement of mites and springtails, free water RHsoil=100%, Tsoil=T0=10 degreesC second phase after evapotranspiration: capillary bound water natural displacement of mites, migration, and active fallout of springtails water vapor T0<Tsoil,<Tair, RHsoil<100% Third phase after extensive evaporation: only absorbed water remains migration and active fallout of mites RHsoil=RHair=51%, Tsoil=Tair=15 degrees C
measuring above ground biomass increment: forest
forest inventory: measure the diameters at breast height compute change in diameter to get diameter growth rate allometric equations: scale diameter to biomass for each species dendrometer bands: monitoring specific individuals, more precise than inventory litter baskets: catch litterfall, collect every month or two (depending on decomposition rate
myco=fungi
fungi heterotrophic eukaryotes: non photosynthetic, excrete extracellular enzymes to decompose mobility: growth or spores cell wall structures made of chitin, long chain polymer of N-acetylglucosamine, as opposed to cellulose, long chain polymer of beta-glucose
secondary production
groups of compounds: 1. soluble=>labile: organic acids, amino acids, simple sugars 2. insoluble=> resistant: lignin, cellulose, cutins, waxes
decomposition of hemicellulose
hemicellulose: complex branching molecules of different sugars (xylose) with various kinds of side chains forms complexes with cellulose and lignin fibers more side chains and more cross linking with other molecules make for a more resistant molecule some bacteria produce enzymes that digest components of some hemicelluloses (xylases) degraded by both white and brown rot fungi
why is there so much biodiversity in soils
heterogeneity of resources
secondary production: decomposition
heterotrophic production of biomass using primary products of autotrophs system level catabolism: breaking down NPP NPP supports a wide range of heterotrophs: food chain, energy dissipation returns CO2 fixed by photosynthesis to the atmosphere at every decomposition step, a heterotroph will dissipate 40% of NPP energy as metabolic heat and CO2
fungal structure
hyphae: main mode of fungal regulative growth mycellium: vegetative part of fungus, collection of hyphae sporocarp: fungal fruiting body
composition and properties of humus
includes humic acids, fulvic acids: complex molecules with many -COOH and-Phenol-OH groups buffers pH pH dependent cation exchange capacity chelates cu,zn,co,ni,mn main reserve of soil N and S glomalins cause formation of aggregates with other humic particles clays, etc
incorporation
incorporation=fragmentation of organic matter and mixing with soil particles sources of OM being incorporated in soil: litterfall: shed daily or seasonally by live plants, fruits, seeds, stems, roots, spores, annuals litterfall from occasional events: storms, floods, fires, droughts, forests, disease death and feces: feces of grazers and parasites, feces of predators, dead animals
two ways to use isoptopes
labeling experiments and natural abundance
habitat for soil organisms
mean soil prokaryotic density or 2.6x10^13/m3 preys, predators, parasites, saprobes soils harbor most of earths genetic diversity tremendous range of niches and habitats in soil
chase period 4 hours to 30 days
measurements of the CO2 flux and isotopic content (capital delta14C) of dark respiration 1. soil surface: moss, grass, roots, soil 2. canopy: needles, stems 3. ecosystem 4. incubations: exised roots, moss, grass 5. soil gas: multiple depths
rhizodeposition
mechanisms by which roots influence the rhizosphere community organic C (organic acids and sugars) released by roots 5-21% of photosynthate C allocated to root exudates , root turnover, and sloughing off of cells feeds microbial communities (root microbiome) many contribute to nutrient availability and disease suppression
soil organism sizes
microbes:<1005um body width microflora: 0.3-20um: bacteria, archaea, fungi microfauna:,0.2mm: protozoa, nematodes mesofauna: 1005um-1010mm:collembola, mites macrofauna:>10mm: earthworms, insects megafauna: >1cm? moles, voles
pore space
mineral soils: 35-55% pore space organic soils: 80-98% pore space varies with mineralogy, bulk density, OM content, disturbance (role of biology) conduits for gases, water, nutrients carbon habitats for microorganisms role of minerals: particle density 2.65gcm3 for silicate minerals, generally 1-1.16gcm3 for most soils, lower organic soils down to 0.02gcm3
rhizosphere organisms
mire abundant in rhizosphere resource availability is more homogenous than in bulk soil communities are less diverse than in bulk soil selected for fast growth (r selected) food web: predation on herbivores by protozoa and nematodes
differences between fungi and bacteria
mode of growth: hyphae vs unicellular colonies exploration of microhabitats vs occupy discrete patches translocation of C: nutrients vs dependence on episodic events or motility in water films for movement
other types of primary production
most primary productivity on land: photosynthesis by vascular plant (mosses, liverworts, hornworts, bryophytes) algae on soil surface: cyanobacteria and algae uptake of CO2 in agricultural soil, 5% of NPP cryptogamic crust in arid environments biological soil crusts are most often composed of fungi, lichens, cyanobacteria, bryophytes, and algae in varying proportions these organisms live in intimate association in the uppermost few mm of the soil surface and are the biological basis for the formation of soils
two types of OM profiles
mull=relatively deep and uniform mixture of OM with soil heavily mixed by incorporation activities of soil animals, OM horizons poorly defined mor= OM horizons well defined incorporation and decomposition may or may not occur in distinct phases that create distinct OM layers in the upper soil profile layer little or no mixing by soil animals, horizons well defined
rhizosphere symbioses
mutualism between roots and microbes exchange of C for nutrients: microbes exchange decomposition of organic matter and food web structure releases N exchange of C for protection from pathogens: beneficial microbes produce pathogen inhibitory compounds
mycorrhiza: symbiotic associates or roots
mycorrhiza: a symbiotic associate between a fungus and the roots of vascular host plant two major types of associates: intracellular association: arbuscular mycorrhizal fungi also ericoid mycorrhiza extracellular association: ectomycorrhizal fungi
how do we measure NPP belowground
not easy but its important: >50% in many ecosystems fine roots: high turnover rates root exudates
importance of soil for climate
physical conditions of soil determine their emissions which can affect climate: CO2, CH4, N20 soils are the largest reservoir of terrestrial carbon possible carbon cycle feedback from soils
medium for plant growth
physical support, air, water, temperature moderation, protection from toxins, nutrients
fine roots are difficult to measure
pre 1990s roots were measured manually fine roots live for 1-3 years minirhizotrons: direct observations of root growth and mortality fine roots live for 3 month to 1 yr isotopic techniques (incorporation of bomb radiocarbon or other labels)
effects of polyphenols
produced by many plants, presumably defensive against grazers and fungi why do plants growing in very poor soils produce higher amounts of polyphenolic compounds form complexes with proteins that are poorly soluble, resistant against microbial enzymes, prevent mineralization but allow uptake by mycorrhizae detoxification of Al, Fe, in acidic soils allelopathy: prevent competing seed germination and root growth increase cation exchange capacity of humus
regulator of water quality
removal of impurities kill disease agents degradation contaminants
FACE: ecosystem scale, decade long carbon cycle experiments
results: pine forest elevated CO2 increased NPP: increased tree growth, litterfall, and root growth accumulation of C in organic horizon (litter layer) due to increased litterfall and no change in decomposition rate no change in C in mineral soil horizons despite root growth elevated CO2 increases rates when N is limiting enhanced decomposition in mineral soils may have limited soil C accumulation results: seegum elevated CO2 increased NPP initially, but declined over the course of the experiment
components of belowground NPP
roots: coarse roots, fine roots, root exudate, carbohydrate transfer to mutualists challenge: root architecture (morphology and distribution of roots) varies greatly among ecosystems
soil texture
sand: 0.0625-2mm silt:2um-0.0625mm clay: >2um important for soil organisms because of the influence on distribution of water and air in soil
spatial constraints on soil biology
size: access to resources, risk of predation, competition air and water availability: determined by soil structure biological needs for air and water vary
why is there so much OM in soils
soil carbon:2300pg C plant biomass: 500PgC Atmosphere: 800PgC some microbially available, accessible, easily (quickly) decomposed, some decomposed slowly hypotheses: 1. previous view: fast vs slow turnover compounds 2. current view: driven by microbial accessibility
rhizosphere priming effect
soil organic matter decomposition rates are faster when energy rich carbon substrates (organic acids and sugars) are added to soils rhizodeposition: stimulates microbial community, microbial growth and extracellular enzyme release, soil organic matter decomposition decomposition of soil organic matter releases N, P for plant uptake
Hans Jenny soils forming factors
soil properties regional climate organisms relief: slope, very steep=no soil, steep=shallow soil, lowland valley=very thick rich soil, flat=thick soil parent material time: chrono sequence of alluvial terraces, exposed at different points of geological time, profile development driven by time
recycling system for nutrients and organic wastes
soils assimilate great quantities of OM: turning it to humus converting the nutrients to forms that can be used by plants and animals returning the C to the atmosphere
resistant compounds
some persistent molecules produced by living organisms take very long to decompose cellulose, hemicellulose, lignin, polyphenols, glomalin, biominerals
termites
some species build mounds containing 2.5t earth, with galleries and chambers extending 3ft down and 9ft away from mounds feed on different types of plant material above and belowground: bark, drygrass, freshly fallen wood, decomposing litter, dung, OM rich soils, lichens, termitiomycetes fungus cultivated on their feces nigerian savannah (all dry weight): 400-700g wood and grass litter produced/m^2/year 170g consumed by termites /m^2/yr 25g returned as feces and dead termites /m^2/yr cellulose decomposers symbiotic protozoa and protists in their guts aid with cellulose decomposition major source of atmospheric CH3 (up to 11%)
ericaceous (ericoid) mycorrhiza
some traits in common with ECM, some with AMF symbiotic with heathlant plants rhododendra, kalmia direct uptake of organic N in low pH environments decomposing ability: produce lignase and phenoloxidase enzymes to expose nutrient containing substrates
soil biodiversity arises from the many strategies to overcome life in soils
spatial/structural challenges resource availability role of aggregates in biology: inteaggregate pore space, regulates accessibility of OM and air, protection from predation/microhabitats
challenges of life in soil
spatial: pore space, air/water availability, connectivity resources: litter, root, OM, resistant to digestion, stoichiometric imbalances
ectomycorrhizal fungi (ECM)
structures between root cells presence is obvious in a root exterior matle and hartignet 10% of plant species associate with ECM bagaceae, beeches, and oaks pinaceae, conifers roses, eucalypters, orchids 160 million years of association basidiomycota, ascomycota, zygomycota able to be cultivated apart form host long hyphae extend out several meters reproductive structures (sporocarps): mushrooms aid in nutrient uptake: organic and inorganic N and P components capable of decomposition significant proportion of belowground C allocation in coniferous forest
arbuscular mycorrhizal fungi (AMF)
structures with in roots cells: vessicles and arbuscules vessicle: storage structure between cells arbuscule: structures with in cells most terrestrial plants (angiosperm) associated with AMF >400 million years of association obligate mutualist (exchange of C for nutrients) hyphae extend a few up to 6-10cm for nutrient uptake
actinorhiza
symbiotic associate with roots: actinomycetes prokaryotes: filamentous, branching, gram+ bacteria form nodules and fix N2 nitrogen fixation: conversion of atmospheric N2 to NH3 with nitrogenase enzyme symbiotic with pioneer species in N poor soils Alnus, myrica, ceanotous, casuarina not actually mycorrhiza
different kinds of roots and different ecosystems have different root lifetimes
the pine forest showed a very slow replacement of old root C, suggesting that fine root population is composed mainly semi permanent roots that survive for many years in contrast, the rapid turnover of C in roots under sweetgum forest suggest that its fine root system is composed mostly of ephemeral roots that do not survive more than one growing season
modifier of the atmosphere composition
they absorb O2 and methane they release greenhouse gases such as CO2 and N20
threats to biological crusts
trampling and compaction offroading,grazing cheatgrass invasion, climate change severe fires, land use change
FACE label
two field sites, one control one FACE per site fumigated/not over a 5yr period root cores were taken from the soil and ingrowth cores sorted and categorized by size dead/alive isotope ratio mass spectrometry determines signatures calculated the MRT (mean residence time) of root C roots incorporated labeled C in elevated CO2 plots using delta13C, can calculate % new root bigger roots tend to be older than smaller roots mean residence calculated by examining the decay of old C over time
water in soil system
unique role of water for life on earth ecosystems determined by water availability special role in soils: semi-aqueous environment, physical structure, relative humidity 98% in air dried soils (2% water by weight) enables organisms that absorb and lose water through integument
components of soil structure
vertical, soil aggregation, soil pore space, texture
soil is a complex habitat for microbial growth
very heterogenous across landscape and with depth 3 phases: liquid, gas, solid microorganisms are dependent on the movement of nutrients to them competition for nutrients, space, and moisture
microbial abundance in soils
very patchy, hot spots and hot moments, patches of fecal pellets, drilosphere, rhizosphere bacteria: 2x10^9 cells/g in top of soil 1x10^8 cells/g in 1-8m of soil double in lab every 20 min only 2-3 divisions /yr on avg in soil copiotrophs vs oligotrophs G- , fungi, protozoa G+, actinomycetes
definition of soils
weathered rock, organic material
clay minerals
weathered, secondary minerals negatively charged: good at holding on to water cation exchange capacity high surface area: kaolonite: 50-100m2/g illite: 300-500m2/g smectite: 700-800m2/g
microbial metabolism
what do soil organisms need to survive 1. raw materials to build and repair own cells 2. energy to synthesize ATP 3. means of transferring electrons between compounds (following the laws of thermodynamics) stoichiometry: redfield ratio atomic ration of C:N:P in phytoplankton is 106:16:1 elemental composition of marine OM (dead or alive) is very consistent across the globe bulk soil: 186:13:1