User:Vrondon/Formatothrops

From Latin (formica meaning "ants") and from Greek (trophy, meaning "nourishment or food").

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Formatotrophs are organism that can assimilate formate or formic acid as carbon source or reducing power. Some authors classify them as one of the the five thropic groups of methanogens: hydrogenotrophs, formatotrophs, acetotrophs, methylotrophs, and alcoholotrophs. Nonetheless, formatotrophs are not restricted a microorganism that produce methane. Formatotrophs has been gaining attention in modern applications in biotechnology due to the urge to develop of bioprocess based in formate assimilation "The formate bioeconomy", formate can be electrochemically synthesized from CO2 and renewable energy, and the genetical engineering of formatothrops that will be used for the production of high value products as biofuels. Technical limitations for the culture of formatotroph microorganisms has limited the discovery of natural formatotrophs and their formate metabolism enzymes of interest for applications and development of carbon sequestration.

Natural Formatotrophs and their ecological role

Formatotrophs perform key metabolic interactions through syntrophic relationships where formate is used as currency transfer redox in diverse environments. This reactions are the particular importance in biogeochemical process related with carbon cycling and transfer of reducing agents such as hydrogen and formate, in some environments acting as the keystone in particular with formate from abiotic source. Some methanogenic communities convert formate into hydrogen and bicarbonate forming cooperative relationships providing usually hydrogen for methanogens, in some of them formate can be just assimilated when in they form a mutualistic relationship with methanogen present during oxidation of formate due this reaction is not energetically sufficient to support growth and thermodynamically unlikely (△G= +1.3 kJ /mol), thus a least one methanogenic partner microorganism need to be present to remove de hydrogen ( Formate oxidation equation ${\ce {HCOO- + H2O -> HCO3- + H2}}$). Other microorganism as Desulfurococcus amylolyticus are able to convert formate into carbon dioxide, acetate, citrate, and ethanol.

Table 1: Examples of natural formatotrophs

Specie	Source
Methylacidiphilum sp RTK17.1	Carere et al 2021
Cupriavidus necator
Methylobacterium thicyanatum
Desulfurococcus amylolyticus	Ergal et al 2020
Thermococcus onnurineus
Methylobacterium extorquens

Recently, metagenomic studies in the Lost city hydrothermal Field, an area of alkaline hydrothermal chimneys in the Atlantic ocean where serpentinization reactions of rock water reactions form calcium carbonate structures, hydrogen, metane and other components as formate. This harsh environmental conditions limit the development of microorganism because those reactions keep a low concentrations of dissolved inorganic carbon, indicating that carbon dioxide is not the primary carbon source. Thus, initial studies hypothesized that formate was the main carbon source , due the high concentrations of formate found in the place (36 to 158 μM Formate). The metabolism of the microbial communities in the Lost city hydrothermal Field are unknow due to difficulties for isolation and culture in laboratory. Mcgonigle (et al 2020) by Chloroflexi was determined by metagenomics and genomic evidence of the assimilation of formate in the chimneys as the only carbon source. The MAGs (Metagenome Assembled Genomes) determined that the most abundant genome was the Methanosarcinales, which did not presented metabolic pathways related with formate metabolism, and the Chloroflexi's MAGs that were five time less abundant, showed cycling carbon metabolic pathways through formate and additional enzymes like carboxysomes probably implicated in the concentration of CO₂ providing carbon source for the entire biofilm formed over the chimneys, showing some evidence about how would be the carbon cycling in a place were the support of energy of the ecosystem is based on geochemical reactions and might help to explain how life in earth was sustained in early evolution. Similarly studies of carbon assimilation strategies in ultrabasic groundwater mediated as well by serpentinization explored the chemosynthesis microbial reactions in the subsurface of wells into the ultramafic Coast Range Ophiolite Microbial Observatory (CROMO) found that the microbial communities present in those aquifers use the products of serpentinization as carbon source, including formate and methane.

C. necator is one of the most known aerobic formatotrophs, d can use carbon dioxide, formate, and hydrogen as carbon and energy source and denitrification process. It is a model microorganism to produce polyhydroxyalkanoate (PHA), a compound of interest to produce bioplastics. It has been gaining particular attention to be used as a chassis for metabolic engineering for the synthesis of alcohols and other bio-based compounds. However, one remarkable limitation for further improvements with this strain is the limited cell density that can achieve in chemically defined media.

Formate assimilation metabolic pathways

There are more than four natural metabolic pathways for formate assimilation: Reductive pentose phosphate pathway, Serine pathway, reductive acetyl-CoA pathway (WL) in acetogens, Reductive acetyl-CoA pathway in methanogens, Xylulose5- phosphate pathway and the glycine pathway. Among them the less efficient pathway is the reductive pentose that necessitates 11 formate molecules (4 for NAD(P)H regeneration and 7 for ATP production) (See Table 1).

Table 1: Summary of metabolic pathways for formate assimilation

Pathway	Need of formate to sythesize Acetyl CoA
Reductive pentose phospahte Pathway. Calvin Benson pathway (CBB)	Requires 11 formate molecules (4 for NAD(P)H regeneration and 7 for ATP production)
The serine pathway	Requires 7 formate molecules (1 is assimilated, 3 provide NAD(P)H, and 3 for ATP generation
Reductive acetyl-CoA pathway (WL) in acetogens	Requires 4 formate molecules (1 is assimilated, 3 provide NAD(P)H
The reductive acetyl-coA pathway (WL) in methanogens	Requires 4 formate molecules (1 is assimliated, 3 provide NAD(P)H.

Formatotrophs for carbon sequestration (Ongoing research):

The actual trends for fermentation of formate are focused on the development of synthetic pathways or matching enzymes from different microorganism to create totally new pathways (Mao et al. 2020; Yishai et al. 2016). The most innovative research areas are in the development of synthetic pathways or matching of parts of existing ones or the improving of catalytic activities by directed evolution techniques. It has been proposed a pool of at least twelve new pathways to assimilate formate, whether by using existing formate fixing reactions or by synthesis of de novo enzymes.

DOE (Department of Energy) and the NREL (National Renewable Energy Laboratory) and ARPA-E has settled up multiple Funding opportunity Announcemets (FOAs) to improve formate assimilation via Calvin Benson Pathway (CBB) with C. necator, improving efficiency of formate assimilation with synthetic pathways.

Two strains expressing the reductive glycine pathways has been engineered to assimilate formate,

This technology in innovation terms is disruptive but it is in its early stages of development. The recent creation of the starup b.fab, their combined strengths in synthetic biology, process development and focused in green products based in formic acid provide an excellent platform and business model for a wide range of products. The company was founded in 2018 and recently received founding from BMBF (German Federal Ministry of Education and Research) and include 7 project partners Max Planck Institute, University of Stuttgart, Ertel IonStream UG, YNCORIS GmbH , KG and Dechema, their target products are polyhydroxy butyric acid (PHB) and crotonic acid.

Formatotrophs are source of enzymes for biological carbon sequestration.