Biological and physical cycle

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Biological and physical cycle in nature (自然界の生物・物質循環)

Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

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geosphere (地圏)

domain of the earth inside

↓ lithosphere
↓ asthenosphere
↓ mesosphere
↓ outer core
↓ inner core

hydrosphere (水圏)

domain consisting of water ≈ ocean + lake + river

atmosphere (大気圏)

domain covered with air

biosphere (生物圏)

domain where natural life forms occur (s.l.) → biota (s.s.)

[biogeochemical cycle, nitrogen cycle, water cycle, biomagnification, trophic level, photosynthesis]

Material and energy cycles

Balance of energy

One of Commoner's lasting legacies is his four laws of ecology, as written in The Closing Circle in 1971. The four laws are:

Everything is connected to everything else. There is one ecosphere for all living organisms and what affects one, affects all.
Everything must go somewhere. There is no "waste" in nature and there is no "away" to which things can be thrown.
Nature knows best. Humankind has fashioned technology to improve upon nature, but such change in a natural system is, says Commoner, "likely to be detrimental to that system"
There is no such thing as a free lunch. Exploitation of nature will inevitably involve the conversion of resources from useful to useless forms.

Biogeochemical cycle (生物地球化学循環)

Circulation at global scale → material cycle observed between atmosphere-hydrosphere-geosphere-biosphere
thermal cycling
water cycle = hydrologic cycle
atmospheric circulation

thermohaline circulation
material circulation,
etc.

Classification by materials

nitrogen cycle (N)
oxygen cycle (O)

carbon cycle (C)
phosphorus cycle (P)
sulfur cycle (S)
water cycle (H2O)
hydrogen cycle (H),
etc.

Stable isotope (安定同位体)

Detecting: direct linkage between lithosphere, biosphere, atmosphere, etc.

Standard

Sample ratio as it relates to the standard is in the following form:
δX (‰) = (R_sample - R_std)/R_std × 1000
______ = (R_sample/R_std - 1) × 1000

δ: the isotopic notation
X: the element in its heavy form (e.g., ¹³C and ¹⁵N)
R: the ratio of heavy to light isotopes (e.g., ¹³C:¹²C)

Discrimination

Δ = {(δ_source - δ_sample)/(1 + δ_sample/10³)} × 10³ or
Δ = δ_source - δ_sample

International standards

A 0‰ value of the δ-scale
Internal lab standards must be corrected to international reference standards
δ¹³C = Vienna peedee belemnite (VPDB)
δ¹⁵N = atmospheric nitrogen

Fractionation (分別)

Equilibrium fractionation, e.g.,
α¹⁸O_water-vapor = (¹⁸O/¹⁶O_water/¹⁸O/¹⁶O_vapor)

occurring when substrates and products of chemical equilibrium reactions differ in their isotope ratios because the heavier isotopes create stronger bonds with either the substrate or product
Ex. CO₂ + H₂¹⁸O ↔ H⁺ + HCO₃^- ↔ C¹⁸O₂ + H₂O

Kinetic fractionations (= non-equilibrium fractionations), e.g.,
α = R_reactant/R_product

occurring when a single type of molecule changes phase (e.g., from liquid to gas) or when the chemical reaction is non-reversible
Ex. in colder temperatures evaporation of H₂O molecules from a water body is faster than D₂O ones because the intermolecular bonds for the former are weaker

Fig. Interactions between processes that influence stable isotope ratios of herbivores and carnivores, showing biochemical, physiological (underlined), and behavioral (in rectangles) processes. Solid lines represent ecological interactions; dotted lines represent factors affecting diffusion rates and enzymatic reactions (i.e., photosynthesis, nutrient routing and nutrient recycling). A single isotopic value obtained from tissue of a carnivore is the emergent property of multiple ecological, behavioral, and physiological processes of various ecosystem components. (Modified from Ben-David et al. 2001). (a) Effects of marine subsidies on wolf diets and ungulate population dynamics are described in Adams et al. (2010).
isotope

Fig. Trophic enrichment in δ¹³C and δ¹⁵N from primary producers (plants), to herbivores, to predators for terrestrial ecosystems. The panel also shows differences in δ¹³C between food webs based on C₃ (black symbols) and C₄ plants (gray symbols). Values (mean ± SE) are adapted from the following sources: willows (Salix) from Ben-David et al. (2001); moose (Alces alces) and wolves (Canis lupus) from Szepanski et al. (1999); grasses from Wang et al. (2010); zebra (Equus burchellii) and lions (Panthera leo) from Codron et al. (2007). (Ben-David & Flaherty 2012)

Plant samples

Measurement: TCEA-IRMS (isotope-ratio mass spectrometry)
Sample: dried at 60-80°C → grinded the samples at 40 μm

The smaples are stable after drying up

Nitrogen cycle (窒素循環)

Fig. δ¹⁵N in an ecosystem. The unit of numeral is ‰.

Atmospheric reservoir of 0‰
Fractionation is generally low
Nitrification and denitrification are the key sources of fractionation

Fig.1. Biogeochemical and physical-chemical (pc) processes affecting the speciation of nitrogen in aquatic systems. Highlighted are some of the major reactions considered in the current study, including nitrification, denitrification, anammox, and NH4⁺ exchange with solids
assimilation (同化), anammox (anaerobic ammonium oxidation) (嫌気性アンモニア酸化), denitrification (脱窒), mineralization (無機化), nitrification (硝化, 硝化作用), nitrogen fixation (窒素固定)
Norg: proteins of plants, animals and microbes, etc.

A. Nitrogen fixation (窒素固定)

(1) Physical or chemical nitrogen fixation
(2) Biological nitrogen fixation: nitrogen fixing bacteria (窒素固定菌)
Extracellular symbiont
azotobacter around plant roots, not developing specific organs
anabaena: fern developing specific leaves for anabaena
Intracellular symbiont
Rhizobium (根粒菌): rrhizobium = root nodule bacterium - polyphyletic

specific host = leguminous plants
nitrogenase: unstable under O₂

Infection: approximation → recognition → nodule formation

approximation, by the chemotaxis of bacteria
recognition, by contact stimuli to roots
nodule formation, developing infection thread (感染糸) -

moving to cortical cells +
dispersion into cytoplasm by peribacteroid membrane
endo-reduplication
bacteroid - intercellular nitrogen fixing bacteria

bacteroid: nif gene group = all genes related to nitrogen fixation

nif genes coded by plasmid in the bacteria
common plasmids = megaplasmid (3-5 × 10⁸ dt)

1979 Cannon FC: megaplasmid of Rhizobium leguminosarum

≈ nitrogen fixer, Klebsiella pneumoniae

nodulin: nodule-specific protein, function unknown
leghemoglobin (leguminous hemoglobin)

structure and function comparable with hemoglobin →
O₂ transportation and removal

Frankia - alder

B. Nitrogen assimilation (窒素同化)

NH₃ produced by isolated root nodulde bacteria under specific conditions

→ nitrogen fixation is conduced by the bacteria

C. Denitrification (脱窒)

Microbially facilitated process of whcih nitrate (NO₃^-) is reduced and finally produces N₂

Half reactions

NO₃⁻ + 2H+ + 2e⁻ → NO₂⁻ + H₂O (nitrate reductase)
NO₂⁻ + 2H⁺ + e⁻ → NO + H₂O (nitrite reductase)
2NO + 2H⁺ + 2e⁻ → N₂O + H₂O (nitric oxide reductase)
N₂O + 2H⁺ + 2e⁻ → N₂ + H₂O (nitrous oxide reductase)

The complete process is expressed as a net balanced redox reaction, where nitrate (NO₃^-) fully reduces to dinitrogen (N₂):

2NO₃⁻ + 10e⁻ + 12H⁺ → N₂ + 6H₂O

Nitrate reduction (硝酸還元)
Nitrite reduction (亜硝酸還元)

Carbon cycle (炭素循環)

Fig. δ¹³C in an ecosystem. The unit of numeral is ‰.

Atmospheric CO₂ (≈ -8‰)
C₃ photosynthesis ≈ -20‰ fractionation (-28‰ plant tissue)
C₄, CAM photosynthesis ≈ 5‰ (-13‰)

Biomagnification (生態濃縮)

Bioaccumulation (生体蓄積・生物蓄積・生物濃縮)

= biological accumulation
the biological sequestering of a substance at a higher concentration than that at which it occurs in the surrounding environment or medium
→ biomagnification + bioconcentration

Biomagnification (生態濃縮)

= bioamplification or biological magnification
the increase in concentration of a substance, such as a pestside, in organisms along a food chain or web as a consequence of:

persistence (not broken down by environmental processes)
food web energetics
low (or non-existent) rate of internal degradation or excretion of the substance, often due to water-insolubility

→ bioaccumulation + bioconcentration

Bioconcentration (生物濃縮)

= biological concentration
the accumulation of a chemical in the tissues of an organism as a result of direct exposure to the surrounding medium, such as water (i.e., it does not include food web transfer)

The three terms described above are often jumbled up.

Seagrass (海草)

Seagrass is recorded from two (Engler's syllabus エングラー体系) to six families with ca 60 species:
All of them are in monocotyledons
Potamogetonaceae (ヒルムシロ)

Zosteraceae (アマモ)
Cymodoceaceae (ベニアマモ)
Posidoniaceae (ポシドニア)
Ruppiaceae (カワツルモ)

Zannichelliaceae (イトクズモ)
Hydrocharitaceae (トチカガミ)

Fig. 1. Distribution of seagrass species along the Australian coast line divided into CONCOM regions.
Seagrass meadows are the shaded areas along the coast and the lists are of seagrass species found in each CONCOM region.

Ocean ecology (海洋生態学)

Research on ocean ecosystems and the interactions between chemical cycles and life

Pelagic zone (漂泳帯): water column where swimming and floating organisms live

= neritic + oceanic zones
Neritic zone (沿岸帯): coastal ocean or the sublittoral zone
Oceanic zone (海洋帯)

Photic zone (有光層)

≈ Epipelagic zone (海面表層)

Aphotic zone (無光層)

Mesopelagic (中深層)
Bathypelagic (漸深層)
Abyssolpelagic or abyssal zone (深海層)
Hadolpelagic or hadal zone (超深海層)

Light and vertical distribution

Lambert-Beer law (ランバート・ベーア則)

= Beer-Lambert law, Beer-Lambert-Bouguer law, or Beer's law
Showing the abosrbance curves of light intensity with increasing the depth of water or other materials (in particular in sea)

Application: chemical measurements

I = I₀·e^-KD

D: depth (or leaf area index above the depth)
I: light intensity at depth D
I₀: initial light indensity at depth zero
K: absorption or extinction coefficient (吸光係数), depending on the transparency, e.g., 0.15-0.3 in sea water, and 0.15-1.0 in land water, in general)
→ light intensity is decreaded with light absorbed by water molecule (the decreases differ between light wavelengths)

⇒ log(I/I₀) = -KD

K is obtained by I/I₀ and D

Photosynthetic productivity, Qx = ∫P(λ)·Ix(λ)·dλ

x: depth
λ: wavelength
P(λ): photosynthetic rate at wavelength λ
I(λ): light intensity

Sea surface temperature, SST (海面温度)

Paleothermometry (古温度測定法)
TEX86 paleothermometry
Analisysi of organic molecules by LC-MS/MS

Euphotic zone (有光層)

Layers of which photosynthesis is higher than respiration → plants can grow
= range beteween water surface and compensation depth (補償深度)

Marine: compensation depth (m)
Outer sea: 100-120
Japan Current (Black Stream): 80-100
Oyashio Current: 30-50

Littoral zone (沿岸帯)

Zonation: three zones are developmed in most littoral communities
↓ Supratidal zone (supralittoral zone)
↓ Eulittoral zone

Intertidal zone (tidal zone): occurring between the levels of low and high tides; thus, exposed at low tide; also reffered to as eulittoral

↓ Sublittoral zone Tide pool (us → en = rock pool)

developing specific ecosystems

Aquatic organisms (水生生物)

lifeform: determined mostly by the movement of water (water flow) Plankton: the community of minute organisms suspended in water

Meroplankton (meroplanktonic, adj.): refers to organisms that spend a part of their life cycle as planktonic and a part as bentic (as in a resting stage), which restricts such organisms largely to neritic conditions

Necton (or nekton): marine and freshwater organisms that swim freely and are generally independent of currents, ranging in size from microscopic organisms to whales Ex. fish, squid, octopus
Benthos: organisms which live on, in, or near the seafloor (called benthic zone). Ex. bentic algae, barnacle, sea urchin, sea cucumber
+ Seston: the organisms (bioseston) and non-living matter (abioseston or tripton) swimming or floating in a water body.

→ seeds of seagrass

Bloom (異常発生)

Red tide (赤潮)

= red water, or discolored water

Blue tide (青潮)

Ocean circulation (海洋循環)

Ocean

= the sea or the world ocean
Arctic Ocean (smallest)
Atlantic Ocean
Pacific Ocean (largest)
Indian Ocean
Southern Ocean (or Antarctic Ocean)

Surface water current

→ warm current. → cold current.
Fig. Ocean surface currents

Overfview of flow:
Northern Hemisphere = clockwise ↔
Southern Hemisphere = counter-clockwise

Kuroshio Current: north flowing warm ocean current on the west side of the North Pacific Ocean
Oyashio Current: cold subarctic ocean current in the Pacific Ocean

Deep water current

Upwelling current or upwelling flow (湧昇流)

Current due to wind (吹送流): water flow induced by sea-surface wind

→ upwelling current (from the bottom)