.. include:: ../defs.hrst .. _Bacteria: Bacteria ^^^^^^^^ To enable heterotrophic uptake for plankton type j, set :varlink:`bactType`\ (j) to a non-zero value and set one of :varlink:`isAerobic`\ (j) and :varlink:`isDenit`\ (j) to 1. The allowed values and associated types are summarized in :numref:`tab_phys_pkg_darwin_bacteria_types`. Note that ammonia and nitrite oxidizers must be aerobic. .. csv-table:: Darwin bacteria types :delim: & :widths: auto :header: bacttype, isAerobic, isDenit, Description :name: tab_phys_pkg_darwin_bacteria_types 1 & 1 & 0 & Aerobic particle-associated: POM :math:`\to` inorganic, DOM 1 & 0 & 1 & Denitrifying particle-associated: POM :math:`\to` inorganic, DOM 2 & 1 & 0 & Aerobic free-living: DOM :math:`\to` inorganic 2 & 0 & 1 & Denitrifying free-living: DOM :math:`\to` inorganic You may also set the corresponding group parameters, :varlink:`grp_bacttype`, :varlink:`grp_aerobic` and :varlink:`grp_denit`. To disable remineralization other than by bacteria, set the parameterized remineralization rates :varlink:`KDOC`, ... to zero, see :numref:`Remineralization`. This is not done automatically. Note that bacteria have fixed elemental ratios. For now, no elemental quotas may be turned on in DARWIN_OPTIONS.h. In the future, elemental quotas will be kept at fixed ratios if turned on. Growth and energy sources ''''''''''''''''''''''''' Bacterial growth is represented by a growth rate, .. math:: \partial_t{c}_j = \mu_j {c}_j \;, which is computed from various limiting resources. Aerobic bacteria are limited by and take up oxygen, .. math:: \mu^{{\mathrm{O}}}_j = y^{\mathrm{O}_2}_j P^{\max}_{\mathrm{O}2} \mathrm{O}_2 \;, .. math:: U^{{\mathrm{O}}2}_j = \frac{1}{{y^{{\mathrm{O}}_2}_j}} \mu_j {c}_j \;, denitrifiers nitrate, .. math:: \mu^{{\mathrm{O}}}_j = y^{\op{NO}_3}_j V^{\max}_{\op{DIN}} \dfrac{\op{NO}_3}{\op{NO}_3 + k^{\op{DIN}}} f^{\op{remin}}(T) \;, .. math:: U^{\op{NO3}}_j = \frac{1}{{y^{\op{NO}_3}_j}} \mu_j {c}_j \;. The nitrogen is released as N\ :sub:`2` which is not represented in the model. Generic particle-associated ''''''''''''''''''''''''''' BactType 1 consume POC, PON, POP, POFe and produce DIN, NH\ :sub:`4`, PO\ :sub:`4` and FeT and, by hydrolysis, DOC, DON, DOP, DOFe. The growth rate is limited by the presence of particulate organic matter and oxygen or nitrate, see above, .. math:: \mu_j = \min(\mu^{\op{PON}}_j, \mu^{\op{POC}}_j, \mu^{\op{POP}}_j, \mu^{\op{POFe}}_j, \mu^{{\mathrm{O}}}_j) .. math:: \mu^{\op{PON}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{PON}}{\op{PON}+ k^{\op{PON}}_j} f^{\op{remin}}(T) .. math:: \mu^{\op{POC}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{POC}}{\op{POC}+ k^{\op{POC}}_j} f^{\op{remin}}(T) .. math:: \mu^{\op{POP}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{POP}}{\op{POP}+ k^{\op{POP}}_j} f^{\op{remin}}(T) .. math:: \mu^{\op{POFe}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{POFe}}{\op{POFe}+ {k^{\op{POFe}}}_j} f^{\op{remin}}(T) The update rates for organic matter are .. math:: U^{\op{POC}}_j = \frac{{\alpha^{\op{hydrol}}}}{y_j} \mu_j {c}_j .. math:: U^{\op{POX}}_j = U^{\op{POC}}_j R^{X{\mathrm{C}}}_j \qquad X={\mathrm{N}},{\mathrm{P}},\op{Fe} Part of POM is hydrolized to DOM: .. math:: H^{\op{POC}}_j = \frac{{\alpha^{\op{hydrol}}}- 1}{y_j} \mu_j {c}_j .. math:: H^{\op{POX}}_j = H^{\op{POC}}_j R^{X:\mathrm{C}}_j \qquad X=\mathrm{N},\mathrm{P},\op{Fe} Part is respired back to inorganics: .. math:: R^{\op{DIC}}_j = \left( \frac{1}{y_j} - 1 \right) \mu_j {c}_j .. math:: R^{\op{NH4}}_j &= R^{\op{DIC}}_j R^{\mathrm{N:C}}_j R^{\op{PO4}}_j &= R^{\op{DIC}}_j R^{\mathrm{P:C}}_j R^{\op{FeT}}_j &= R^{\op{DIC}}_j R^{\mathrm{Fe:C}}_j \;. Generic free-living ''''''''''''''''''' BactType 2 consume DOC, DON, DOP, DOFe and produce DIN, NH\ :sub:`4`, PO\ :sub:`4` and FeT. The growth rate is limited by the presence of dissolved organic matter and oxygen or nitrogen, .. math:: \mu_j = \min(\mu^{\op{DON}}_j, \mu^{\op{DOC}}_j, \mu^{\op{DOP}}_j, \mu^{\op{DOFe}}_j, \mu^{{\mathrm{O}}}_j) .. math:: \mu^{\op{DON}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{DON}}{\op{DON}+ k^{\op{DON}}_j} f^{\op{remin}}(T) .. math:: \mu^{\op{DOC}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{DOC}}{\op{DOC}+ k^{\op{DOC}}_j} f^{\op{remin}}(T) .. math:: \mu^{\op{DOP}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{DOP}}{\op{DOP}+ k^{\op{DOP}}_j} f^{\op{remin}}(T) .. math:: \mu^{\op{DOFe}}_j = y_j {P^{\op{max}}_{{\mathrm{C}},j}} \frac{\op{DOFe}}{\op{DOFe}+ {k^{\op{DOFe}}}_j} f^{\op{remin}}(T) The uptake rates for organic matter are .. math:: U^{\op{DOC}}_j = \frac{1}{y_j} \mu_j {c}_j .. math:: U^{\op{DOX}}_j = U^{\op{DOC}}_j R^{X{\mathrm{C}}}_j \qquad X={\mathrm{N}},{\mathrm{P}},\op{Fe} Part of it is respired back to inorganics: .. math:: R^{\op{DIC}}_j = \left( \frac{1}{y_j} - 1 \right) \mu_j {c}_j .. math:: R^{\op{NH4}}_j &= R^{\op{DIC}}_j R^{\mathrm{N:C}}_j R^{\op{PO4}}_j &= R^{\op{DIC}}_j R^{\mathrm{P:C}}_j R^{\op{FeT}}_j &= R^{\op{DIC}}_j R^{\mathrm{Fe:C}}_j \;. Bacteria parameters ''''''''''''''''''' .. csv-table:: Bacteria parameters :delim: & :widths: 13,17,8,15,18,29 :class: longtable :header: Trait, Param, Symbol, Default, Units, Description :varlink:`bactType` & :varlink:`grp_bacttype` & & 0 & & 1: particle associated, 2: free living bacteria, 0: not bacteria :varlink:`isAerobic` & :varlink:`grp_aerobic` & & 0 & & 1: is aerobic, 0: not :varlink:`isDenit` & :varlink:`grp_denit` & & 0 & & 1: is dentrifying, 0: not & :varlink:`pcoefO2` & :math:`P^{\max}_{\mathrm{O}2}` & 290.82 / 86400 & s\ :sup:`--1` & max O2-specific O2 uptake rate for aerobic bacteria & :varlink:`pmaxDIN` & :math:`V^{\max}_{\op{DIN}}` & 20/86400 & mmol N mmol C\ :sup:`--1` s\ :sup:`--1` & max C-specific DIN uptake rate for denitrifying bacteria & :varlink:`ksatDIN` & :math:`k^{\op{DIN}}` & 0.01 & mmol N m\ :sup:`--3` & half-saturation conc of dissolved inorganic nitrogen & :varlink:`alpha_hydrol` & :math:`\alpha^{\op{hydrol}}` & 2.0 & 1 & increase in POM needed due to hydrolysis :varlink:`PCmax` & :varlink:`a `,\ :varlink:`b_PCmax` & :math:`P^{\op{max}}_{\op{C},j}` & (1/day) ยท V\ :sup:`--0.15`, see [#pcmax]_ & s\ :sup:`--1` & maximum carbon-specific growth rate :varlink:`yield` & :varlink:`yod` (aerobic) :varlink:`ynd` (denit) & :math:`y_j` & 0.2 (aerobic) 0.16 (denit) & 1 & bacterial growth yield for all organic matter :varlink:`yieldO2` & :varlink:`yoe` & :math:`y^{{\mathrm{O}}_2}_j` & 0.2/467*4/ (1-0.2)*106 & mmol C / mmol O\ :sub:`2` & bacterial growth yield for oxygen :varlink:`yieldNO3` & :varlink:`yne` & :math:`y^{\op{NO}_3}_j` & 0.16/467*5/ (1-0.16)*106 & mmol C / mmol N & bacterial growth yield for nitrate :varlink:`ksatPON` & :varlink:`a_ksatPON` & :math:`k^{\op{PON}}_j` & 1 & mmol N m\ :sup:`--3` & half-saturation of PON for bacterial growth :varlink:`ksatPOC` & & :math:`k^{\op{POC}}_j` & see below & mmol C m\ :sup:`--3` & half-saturation of POC for bacterial growth :varlink:`ksatPOP` & & :math:`k^{\op{POP}}_j` & see below & mmol P m\ :sup:`--3` & half-saturation of POP for bacterial growth :varlink:`ksatPOFe` & & :math:`k^{\op{POFe}}_j` & see below & mmol Fe m\ :sup:`--3` & half-saturation of POFe for bacterial growth :varlink:`ksatDON` & :varlink:`a_ksatDON` & :math:`k^{\op{DON}}_j` & 1 & mmol N m\ :sup:`--3` & half-saturation of DON for bacterial growth :varlink:`ksatDOC` & & :math:`k^{\op{DOC}}_j` & see below & mmol C m\ :sup:`--3` & half-saturation of DOC for bacterial growth :varlink:`ksatDOP` & & :math:`k^{\op{DOP}}_j` & see below & mmol P m\ :sup:`--3` & half-saturation of DOP for bacterial growth :varlink:`ksatDOFe` & & :math:`k^{\op{DOFe}}_j` & see below & mmol Fe m\ :sup:`--3` & half-saturation of DOFe for bacterial growth .. [#pcmax] A more appropriate value for the maximum growth rate of bacteria is 5/day which was used in previous versions of the code. The organic nitrogen half-saturation constant, ksatPON and ksatDON, are set from trait parameters. Others are computed from nitrogen ones using elemental ratios, .. math:: k^{\op{POC}}_j &= \frac{1}{R^{\mathrm{N}:\mathrm{C}}_j} k^{\op{PON}}_j & k^{\op{DOC}}_j &= \frac{1}{R^{\mathrm{N}:\mathrm{C}}_j} k^{\op{DON}}_j k^{\op{POP}}_j &= \frac{R^{\mathrm{P}:\mathrm{C}}_j}{R^{\mathrm{N}:\mathrm{C}}_j} k^{\op{PON}}_j & k^{\op{DOP}}_j &= \frac{R^{\mathrm{P}:\mathrm{C}}_j}{R^{\mathrm{N}:\mathrm{C}}_j} k^{\op{DON}}_j k^{\op{POFe}}_j &= \frac{R^{\mathrm{Fe}:\mathrm{C}}_j}{R^{\mathrm{N}:\mathrm{C}}_j} k^{\op{PON}}_j & k^{\op{DOFe}}_j &= \frac{R^{\mathrm{Fe}:\mathrm{C}}_j}{R^{\mathrm{N}:\mathrm{C}}_j} k^{\op{DON}}_j