BIO 346 midterm 2

Biogeochemistry

How elements move (cycle) through living organisms and the non-living environment

The movement of elements is influenced by:

– Source (atmosphere, lithosphere, biosphere)
– Chemical form(s) – determines reactivity and which organisms can use different forms
– Biological demand for that element
– Physical and chemical conditions

Source

describes a process or compartment that releases a substance into another part of the system, increasing its concentration elsewhere

Pool

refers to a reservoir or storage compartment where a particular element or compound resides

Sink

a process or compartment that removes or absorbs a substance from circulation, decreasing its concentration elsewhere

Cycle

a system consisting of two or more pools, where some of the material is transferred back and forth between the pools over time

Closed cycle, Open cycle

1. material cycles only within the ecosystem, e.g., within a lake

2. some material flows into and out of the ecosystem, e.g.
   to and from the watershed and/or atmosphere

Essential elements for plant growth: Macronutrients (required in large amounts):

C, H, O, N, P, K, S, Mg, Ca, (Si)

• Typically used to build large structures or to support many
  physiological processes

Essential elements for plant growth: Micronutrients (required in small, or trace amounts):

Fe, Cl, Cu, Mn, Zn, Mo, Bo

• Typically used for enzyme activity or a specific biological process

Redfield ratio

106:16:1

• carbon:nitrogen:phosphorus

• As plankton grow and die, they take up and release C, N, and P in roughly the
  same proportions

Remineralization

Conversion of organic nutrients to inorganic nutrients

organic carbon → CO2

nitrogen compounds (amino acids)→ NH4, NO3

phosphorus compounds (lipids) → PO4

Processes leading to remineralization:

1. Decomposition
2. Leakage
3. Heterotrophic organisms breaking down organic matter
4. Organisms producing inorganic nutrients such as ammonium and nitrate in their waste

Why is carbon important?

• Carbon is the chemical backbone of organic molecules proteins, hydrocarbons, lipids, carbohydrates
• Currency of energy transfer
• Carbon chemistry provides a buffering system for lakes to absorb excess acid
• Exchange with the atmosphere and global climate regulation (CO2 and CH4 are green house gasses

what makes up DOC?

humic and non-humic compounds

Humic compounds – large molecular weight compounds

• By product of the breakdown of other organic compounds
• Resistant to microbial use
• Different types: humic acids, fluvic acids, humin

Non-humic compounds

sugars, carbohydrates, amino acids, urea, proteins, pigments, lipids

• These fuel microbial production

Dystrophic lakes have

a lot of DOC in the water

Particulate Organic Carbon (POC)

• All living and dead organisms. Their parts, and the feces...
• Some small POC particles broken down by bacteria, some sink out from water column leading to carbon burial (e.g. diatoms, fecal pellets, cysts, etc)
• Some POC particles (e.g. plant detritus) leach DOC over time

Dissolved inorganic carbon (DIC)

• Atmosphere (CO2)
CO2 (air) + H2O ---------------> CO2 (dissolved) + H2O

• Respiration
Organic C+ H2O ---------------> 6CO2 + 6H2O

• Weathering of rocks such as calcite
CaCO3 + CO2 + H2O ---------------> Ca++ + 2HCO3-

• CO2 “reacts” with water to produce different kinds of DIC

CO2 “reacts” with water to produce

different kinds of DIC

The form(s) of DIC depends on

pH

low pH: carbonic acid

high pH: carbonate

• concentration and form of DIC help buffer pH change

Carbon flow in lake food webs

• All autotrophs consume CO2
• All heterotrophs respire/produce CO2
• Some organic carbon is buried in the sediments
• Lakes can therefore remove or add CO2 to the atmosphere

what is this representing?

Carbon flow in lake food webs

Ecosystem respiration (RE):

total CO2 produced (or O2 consumed) by living organisms

Net ecosystem production (NEP) = GPP – RE

• IF GPP> RE, lake might be a ”sink” of CO2
• IF GPP<RE, lake might be a “source” of CO2

In a typical terrestrial ecosystem (e.g., a forest):

– ecosystem respiration < photosynthesis (PS)
– because PS provides all the organic C to be respired

in many deep lakes:

– pelagic respiration > photosynthesis

Autochthonous

From within a system
• e.g. phytoplankton or other photosynthesizes in lake convert CO2 to POC
• e.g. Fish die in lake, carbon is recycled by microorganisms

Allochthonous:

From outside a system
• e.g. Streams carry terrestrial detritus (e.g. leaves) & dissolved carbon into a lake
• This is a ”subsidy” to the lake

High autochthonous contribution:

productive lakes with high algal density

High allochthonous contribution:

lots of weathered materials from watershed catchment

As DOC increases

lakes become supersaturated with CO2

• DOC ‘subsidy’ from terrestrial ecosystems (watershed) drives much of this

less C exits the lake than enters it, the remainder is

buried in sediments

Aquatic systems have ____ burial rates compared to terrestrial ecosystems

high

Reservoirs have ____ burial rates compared to natural lakes

high

Oxygen loss at depth increases activity of anaerobic bacterial producing

methane (methanogenesis)

methanogenesis

CO2 → CH4 (anoxic)

why is methanogenesis bad?

• Methane can diffuse or bubble (ebullience) to the surface
• Methane is a potent green house gas
• 1 gram of methane warms the atmosphere ~34x more than 1 gram of CO2

Methane release increases with

eutrophication

more C is buried in freshwater sediments than in

ocean sediments

• Oceans sequester ~2 Pg/yr but only 10- 15% of this is buried in sediments most is
‘sequestered’ in deep water (below ~200m) as DOC or POC

Oxygen Sinks (where it goes)

Diffusion to the atmosphere
Respiration
• Organic Carbon + O2 + H2O = CO2 + H2O + energy
Chemical oxidation (we will not discuss in this lecture)

Oxygen Sources (where it is produced)

Atmosphere
• Amount depends on diffusion, turbulence, wind
mixing
Photosynthesis
• CO2 + sun light +H2O = Organic carbon + O2

Orthograde profile

is an upright curve where oxygen is high near the surface and decreases with depth, characteristic of oligotrophic lakes where physical factors like temperature are the main influence

Clinograde profile

is a downward-sloping curve where oxygen decreases with depth, typical of eutrophic lakes where biological respiration consumes oxygen in the deeper layers

which lake shows these seasonal patterns?

oligotrophic

which lake shows these seasonal patterns?

oligotrophic

which lake shows these seasonal patterns?

eutrophic

which lake shows these seasonal patterns?

eutrophic

Biological implications of dissolved oxygen levels

• Organisms have different oxygen requirements
• Regular hypoxic/anoxic conditions have strong negative effect on community structure
• Anoxic/hypoxic conditions in hypolimnion can restrict available habitat

Chemical implication of oxygen variation

• Oxygen is a powerful “oxidizing agent”, and likes to steal electrons from other elements

• Highly oxygenated environments tend to have high redox pressure, meaning they have fewer electrons to share around

in the presence of oxygen, the forms of other elements are likely to be oxidized, electron poor versions - how does this affect lakes?

Oxidized and reduced chemical forms can behave differently

ex. Fe3 and Fe2

Fe3 can precipitate leading to Fe loss from the system

The problem with Fe3

precipitates from the system, leading to iron loss

Dissolved inorganic N can limit

primary production

Excess N supply can contribute to

eutrophication

Nitrate (NO 3 ) can be a

health hazard
• to humans if concentrations in drinking water is too high
• to other organisms at much lower concentrations

Nitrous oxide (N 2 O) is a

powerful greenhouse gas

NO X (NO, NO 2 , NO 3 ) from fossil fuels causes

acid rain

Atmospheric nitrogen (N 2 , gaseous)

Abundant in the atmosphere (78% of total gases), but only a few
prokaryotes can utilize it for nitrogen fixation

Dissolved inorganic N (DIN)

• These forms are most available to primary production and bacteria (e.g. ammonium NH 4+*, nitrate NO 3-, nitrite NO 2-)
• Oxidized forms of DIN are often abbreviated as “NO x

Nitrogen forms in freshwater

Dissolved organic N
• e.g., urea, amino acids, etc
Particulate organic N (PON)
• Organisms and detritus

Nitrogen fixation:

Certain cyanobacteria and bacteria (e.g., Anabaena, Rhizobium) convert atmospheric N₂ into ammonium (NH₄⁺), a bioavailable form

Atmospheric deposition:

Nitrate (NO₃⁻), ammonia (NH₃), and organic nitrogen can enter lakes via rainfall

Assimilation:

Phytoplankton and aquatic plants take up NH₄⁺ or NO₃⁻ to build proteins and nucleic acids

Ammonification (Mineralization):

When organisms die or excrete waste, decomposers
convert organic nitrogen back into NH₄⁺

Nitrification:

In oxygen-rich (oxic) waters and sediments, nitrifying bacteria (e.g., Nitrosomonas, Nitrobacter) oxidize:

NH₄⁺ → NO₂⁻ → NO₃⁻

• This process requires oxygen and releases energy

Denitrification:

In oxygen-poor (anoxic) zones (e.g., hypolimnion or sediments), denitrifying
bacteria (e.g., Pseudomonas) convert NO₃⁻ → N₂ or N₂O gases, which return to the
atmosphere — a key nitrogen loss pathway

Anammox (anaerobic ammonium oxidation):

Specialized bacteria convert NH₄⁺ and NO₂⁻ directly into N₂ gas under anoxic conditions

Human impacts on N cycle

Humans have greatly altered N cycle
Anthropogenic N-fixation (industrial and agricultural) now exceeds all-natural N-
fixation
Atmosphere is loaded with NOx from fossil fuel combustion
• Can lead to eutrophication
• H 2O and NO3 react to form HNO3 (nitric acid), which can contribute to acid rain
• N 2O is greenhouse gas (stronger than CO 2)
Fertilizer runoff greatly increases NH 4 and NO3 concentrations in streams and lakes

Phosphorus in lakes

• Key component of ATP, DNA, RNA, bones, scales
• In non-vertebrates (plants, algae, bacteria, invertebrates) Ribosomal RNA and nucleic acids are the biggest pool of P in the body
• In vertebrates, bones and/or scales contain more P than RNA/ribosomes/DNA

Phosphorus availability is often the limiting nutrient for primary production in

lakes, rivers, oceans (and on land)

‘Soluble reactive P’ (SRP)

Approximately equal to orthophosphate (PO43-), the form of P most available to algae and plants

Total dissolved P (TDP, or TP)

All dissolved forms, including SRP

Particulate P

• All P in particulate form in the water column
• Living and nonliving matter, but this excludes fish

Total P:

all P, dissolved and particulate, captured from the water column with a typical limnological sampler, i.e., excluding fish

Because P is often limiting, there is very little available P (i.e., SRP) in the water column; most P is in

biomass

Watershed runoff:

The main source of phosphorus, often from weathering of rocks, soil erosion,
fertilizers, and wastewater

Atmospheric deposition:

Dust or aerosols can add small amounts of phosphorus to the lake surface

Groundwater and stream inflow:

Bring dissolved and particulate forms of phosphorus

Assimilation: (P)

Phytoplankton and plants take up PO₄³⁻ for growth and incorporate it into organic matter

Mineralizatioan (Regeneration): (P)

When organisms die or decompose, microbial activity converts organic P back to inorganic phosphate

Sediment binding (P)

In oxygenated (oxic) conditions, phosphate binds to iron (Fe³⁺) compounds and becomes trapped in sediments — effectively removing it from the water column

Internal loading: (P)

Under anoxic (oxygen-poor) conditions (e.g., in the hypolimnion during stratification),
Fe³⁺ is reduced to Fe²⁺, releasing PO₄³⁻ back into the water — a process called phosphorus release or internal loading

Phosphorus and Fe 3+ dynamics

• Fe3+ and water form ferric hydroxide, which binds P
• Insoluble Fe(OH) 3PO4 (complex iron phosphate), precipitates out
of water, onto sediments
• Fe2+ does not bind phosphates, and is soluble in freshwater

what drives NO3 depth profile?

O2 profile

why is phosphorus usually more limiting than nitrogen

mineralization of P and other processes take longer than nitrogen does

what are the optimal conditions for sediment binding?

• Fe3+

• Oxic water

Even if water overlying sediments is well-oxygenated, just a few mm deep the sediments are

anoxic

P is soluble in anoxic sediments, but when it diffuses upwards into oxic sediments, it becomes

insoluble and precipitates out (anoxic → oxic → oxic)

• unless the water above the anoxic sediment is anoxic, then the ferris wheel is broken ( anoxic → anoxic → anoxic) because there no binding and burial, instead phytoplankton assimilation of soluble compounds