Winogradsky himself had already recognized the problem very early in his career
(Winogradsky 1891):
Le fait que la production de nitrites devenait de plus en plus abondante à mesure des
ferments, paraissait conduire à la conclusion que la formation d’acide nitreux serait leur
seule function. Mais l’énigme, que comportait cette conclusion, empêchait de l’accepter,
avant que l’on eût attaqué le problème de tous les côtés. Comment, en effect, s’expliquer
qu’un organisme, possédant des moyens énergiques d’oxyations, termine son action par la
production d’un corps chimique plus oxydable que celui du début. En admettant même qu’il
ne soit capable de parfaire d’emblée l’oxydation complète de l’ammoniac, comment
comprendre, qu’il paraisse totalement dépourvu d’action sur l’acide nitreux, alors que
l’oxydation de ce corps pourrait lui lui fournir un surcroît d’énergie?
[The fact that the production of nitrites became more and more abundant commensurate with
the ferments, seemed to lead to the conclusion that the formation of nitrous acid would be
their only function. But the enigma that was included in this conclusion prevents it to be
accepted before one would have attacked the problem from all sides. How, in fact, could one
explain that an organism that possesses the energetic machinery to perform oxidations
should end its action with the production of a chemical compound that is easier to oxidize
than the starting material? Even if one admits that it would not be able to finish from the
outset the complete oxidation of ammonia, how can it be understood that it seems to be
completely devoid of action on nitrous acid, while the oxidation of that substance would
supply it with additional energy.]
This is one of the few cases in which Winogradsky discussed energetics-related
considerations in his writings.
One of the possible solutions to the paradox of the division of labor is based on
the kinetic theory of optimal design of metabolic pathways, which postulates the
existence of an optimal length for a pathway that maximizes the rate of ATP
production. Shortening long pathways could result in an increased growth rate.
This is offset by a reduced growth yield if the shorter pathway has fewer
ATP-generating steps. A complete nitrifier should gain more energy per mole of
substrate but may grow at a slower rate than organisms carrying out the individual
steps of the pathway. A complete nitrifier could have advantages over the classical
two-step process when microbes grow slowly in clonal colonies (Costa et al. 2006;
Santoro 2016). It is therefore not surprising that complete ammonia oxidizers
(“comammox” bacteria) were found in biofilms in an aquaculture treatment system,
in a deep subsurface pipe, and in a bioactive filter at a drinking water treatment plant
(van Kessel et al. 2015; Daims et al. 2015).
Complete ammonia oxidation to nitrate was found in a low-oxygen bioreactor fed
with low concentrations of ammonium, nitrite, and nitrate. Nitrospira species developing in the reactor possessed genes for all the enzymes necessary for ammonia
oxidation via nitrite to nitrate, including genes for ammonia monooxygenase (AMO)
that are phylogenetically distinct from the known AMOs (van Kessel et al. 2015). A
thermophilic comammox bacterium, “Candidatus Nitrospira inopinata,” was
obtained in co-culture with a bacterium affiliated with the Hydrogenophilaceae.
Genes affiliated with the distinct ammonia monooxygenase and hydroxylamine
dehydrogenase genes of Nitrospira are present globally in many environments.
164
A. Oren
(Winogradsky 1891):
Le fait que la production de nitrites devenait de plus en plus abondante à mesure des
ferments, paraissait conduire à la conclusion que la formation d’acide nitreux serait leur
seule function. Mais l’énigme, que comportait cette conclusion, empêchait de l’accepter,
avant que l’on eût attaqué le problème de tous les côtés. Comment, en effect, s’expliquer
qu’un organisme, possédant des moyens énergiques d’oxyations, termine son action par la
production d’un corps chimique plus oxydable que celui du début. En admettant même qu’il
ne soit capable de parfaire d’emblée l’oxydation complète de l’ammoniac, comment
comprendre, qu’il paraisse totalement dépourvu d’action sur l’acide nitreux, alors que
l’oxydation de ce corps pourrait lui lui fournir un surcroît d’énergie?
[The fact that the production of nitrites became more and more abundant commensurate with
the ferments, seemed to lead to the conclusion that the formation of nitrous acid would be
their only function. But the enigma that was included in this conclusion prevents it to be
accepted before one would have attacked the problem from all sides. How, in fact, could one
explain that an organism that possesses the energetic machinery to perform oxidations
should end its action with the production of a chemical compound that is easier to oxidize
than the starting material? Even if one admits that it would not be able to finish from the
outset the complete oxidation of ammonia, how can it be understood that it seems to be
completely devoid of action on nitrous acid, while the oxidation of that substance would
supply it with additional energy.]
This is one of the few cases in which Winogradsky discussed energetics-related
considerations in his writings.
One of the possible solutions to the paradox of the division of labor is based on
the kinetic theory of optimal design of metabolic pathways, which postulates the
existence of an optimal length for a pathway that maximizes the rate of ATP
production. Shortening long pathways could result in an increased growth rate.
This is offset by a reduced growth yield if the shorter pathway has fewer
ATP-generating steps. A complete nitrifier should gain more energy per mole of
substrate but may grow at a slower rate than organisms carrying out the individual
steps of the pathway. A complete nitrifier could have advantages over the classical
two-step process when microbes grow slowly in clonal colonies (Costa et al. 2006;
Santoro 2016). It is therefore not surprising that complete ammonia oxidizers
(“comammox” bacteria) were found in biofilms in an aquaculture treatment system,
in a deep subsurface pipe, and in a bioactive filter at a drinking water treatment plant
(van Kessel et al. 2015; Daims et al. 2015).
Complete ammonia oxidation to nitrate was found in a low-oxygen bioreactor fed
with low concentrations of ammonium, nitrite, and nitrate. Nitrospira species developing in the reactor possessed genes for all the enzymes necessary for ammonia
oxidation via nitrite to nitrate, including genes for ammonia monooxygenase (AMO)
that are phylogenetically distinct from the known AMOs (van Kessel et al. 2015). A
thermophilic comammox bacterium, “Candidatus Nitrospira inopinata,” was
obtained in co-culture with a bacterium affiliated with the Hydrogenophilaceae.
Genes affiliated with the distinct ammonia monooxygenase and hydroxylamine
dehydrogenase genes of Nitrospira are present globally in many environments.
164
A. Oren