Wikipedia Entry by Carley Pazzi
Scientific Classification 
Species: F. agariphila
Formosa agariphila (KMM 3901) is an algal-associated, short, rod-shaped, chemo-organotrophic, and gram-negative marine bacterium . This marine microbe lines the surfaces of a wide variety of corals and algae, which are generally located in shallow coastal waters  . Similarly to other Flavobacteria, F. agariphila possess a strong ability to degrade organic matter with high molecular weight such as proteins and polysaccharides  . F. agariphila’s genome is unique because it has been found to contain more CAZymes (5% of genes), which are biodegradation enzymes involved in the breakdown and synthesis of carbohydrates, than most other bacterial species which generally only have around 2% of CAZymes genes    . This microbe is predominantly found attached to algae, which are located in nutrient-rich environments where proteins and polysaccharides are highly present . F. agariphila’s biodegradation ability is further facilitated by the gliding motility that is characteristic of the Formosa genus and of the Flavobacteria class    . This bacterium is known to be a facultative anaerobe and it is also capable of mixed acid fermentation. F. agariphila was first isolated in the Troitsa Bay in the Gulf of Peter and the Great (Sea of Japan) from the shallow water alga Acrosiphonia sonderi by Ivanova et al. in 2004 .
Genome and Genetic Adaptation
The genome of the F. agariphila strain (KMM 3901) exceeds 4M base pairs, a size that is much larger than that of other members of the Bacterioidetes phylum, which tend to have genomes of around 3M base pairs . The genome of KMM 3901 is made up of a single chromosome comprised of 4,229,450 bp with 33.5% GC content . The GC content of other Flavobacteria ranges between 30 and 41 %, indicating that F. agariphilia’s GC content is right within the range for this bacterial class  . Studies have found that F. agariphilia’s (KMM 3901) genome contains 3642 genes of which 3,528 were deemed to be protein coding . While genetic screening did not detect extrachromosomal components, four ribosomal RNA operons were found in addition to 45 transfer RNAs for all amino acids . Researchers have suggested that the genome of F. agariphilia (KMM 3901) is well adapted for an organism that lives in an algal environment rich of nutrients such as proteins and polysaccharides . F. agariphilia is adapted to algal life because it features numerous CAZymes which are able to breakdown the polysaccharides which reside on marine algae . Additionally, KMM 3901 also encodes for 129 peptidases, which are helpful to degrade proline-rich proteins, and numerous metalloproteases, especially from the M20, M24A,M23, and M28 families . Furthermore, the genome of F. agariphilia (KMM 3901) contains 18 genes that were associated to temperate phages and 17 transposases . The GenBank/EMBL/DDBJ accession number for F. agariphilia (KMM 3901) genome is AY187688 .
Formosa agariphila is a rod-shaped, gram-negative bacterium  . The short rod-shaped cells from the KMM 3901 strain are 0.5-0.6 um in diameter and 0.8-1.0 um in length . This microbe is part of the Bacteroidetes phylum, of the Flavobacteria class, and of the Formosa genus . F. agariphila has several genes for gliding motility, suggesting that it glides while colonizing algal surfaces and that it is also able to form biofilms .
Metabolism and Energy Generation
F. agariphila (KMM 3901) features a complete Embden-Meyerhof-Parnas (EMP) pathway . This pathway enables cells to metabolize the glucose based polysaccharides obtained from algal tissue with the goal of generating ATP, NADH and other metabolic components that are key to energy generation . The EMP pathway can take place both aerobically, when oxygen is present, or anaerobically, when oxygen is absent . F. agariphila is able to oxidize pyruvate to acetyl-coenzyme (CoA) using a three-component pyruvate dehydrogenase in addition to a pyruvate formate lyase . This microbe is able to complete a Krebs cycle, which is carried out without the glyoxylate shunt . F. agariphila also has a redox chain for aerobic respiration which includes different enzymes such as quinone oxidoreducase, succinate dehyodrogenase, cytochrome d oxidase, cytochrome c oxidase and an ATPase. In anaerobic conditions, the microbe can also take part in mixed acid fermentation . F. agariphila (KMM 3901)'s genetic profile suggests that the bacterium would be able to reduce nitrate to nitrite, however physiological testing has not confirmed this finding . Given that the genome F. agariphila (KMM 3901) encodes one polyphosphate kinase and one exopolypohosphatase, it is possible that the microbe collects and stores energy along with phosphorus as polyphosphates . It also believed that F. agariphila may also store energy and carbon through glycogen molecules. This hypothesis is based on the presence of a glycogen synthase and several other genes that code for glycogen breakdown enzymes such as glycogen phosphorylase and a glycogen debranching enzyme.
F. agariphila (KMM 3901) is cultured on marine agar and forms round, flat, translucent, and yellow colonies . Yellow colonies are a common feature of Flavobacteriia due to carotenoid and flexirubin production . These colonies are generally 2-3 mm in diameter and are occasionally slightly sunken in the agar . In mature cells of F. agariphila,buds become visible and threads connect multiple cells occasionally forming biofilms . The growth temperature of F. agariphila is optimal between 4-33 degree Celsius and the concentration of sodium chloride needs to be within 1-8% range for most efficient growth . This microbe was found to susceptible to oleadomycin, carbenicillin, lincomycin, and ampicillin . Furthermore, it was also found to be resistant benzylpeniccillin, gentamicin, kanamycin, neomycin, polymyxinB, streptomycin and tetracycline . Many Flavobacteriia are known to be pathogenic to humans, fish, or amphibian . Despite the widespread antiobitic resistance of F. agariphila, it is not known if this bacteria strain (KMM 3901) is pathogenic . This microbe (KMM 3901) has been found to decompose gelatin,agar, and aesculin but not casein, chitin, cellulose, Tween 80 and DNA .
The genome of F. agariphilia (KMM 3901) codes for 129 proteases and 88 glycoside hydrolases strongly supporting the protein degrading ability of this microbe . Genome analysis also found genome loci for multiple Ton-B dependent receptors, SuD-like proteins, sensors, transporters, and sulfates, which are known to help with biodegradation . These presence of these genes supports this microbe’s ability to degrade a variety of polysaccharides found in different algae .
- Ivanova EP. Formosa. Bergey’s Manual of Systematics of Archaea and Bacteria. American Cancer Society; 2015. pp. 1–7. doi:10.1002/9781118960608.gbm00313
- Mann AJ, Hahnke RL, Huang S, Werner J, Xing P, Barbeyron T, et al. The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901T Reveals a Broad Potential for Degradation of Algal Polysaccharides. Appl Environ Microbiol. 2013;79: 6813–6822. doi:10.1128/AEM.01937-13
- Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean - Gómez‐Pereira - 2012 - Environmental Microbiology - Wiley Online Library. [cited 23 Mar 2020]. Available: https://sfamjournals-onlinelibrary-wiley-com.ezproxy.haverford.edu/doi/abs/10.1111/j.1462-2920.2011.02555.x
- Eilers H, Pernthaler J, Glöckner FO, Amann R. Culturability and In Situ Abundance of Pelagic Bacteria from the North Sea. Appl Environ Microbiol. 2000;66: 3044–3051. doi:10.1128/AEM.66.7.3044-3051.2000
- Nedashkovskaya OI, Kim SB, Vancanneyt M, Snauwaert C, Lysenko AM, Rohde M, et al. Formosa agariphila sp. nov., a budding bacterium of the family Flavobacteriaceae isolated from marine environments, and emended description of the genus Formosa. International Journal of Systematic and Evolutionary Microbiology,. 2006;56: 161–167. doi:10.1099/ijs.0.63875-0.
- Bernardet J-F. Flavobacteriales ord. nov. Bergey’s Manual of Systematics of Archaea and Bacteria. American Cancer Society; 2015. pp. 1–2. doi:10.1002/9781118960608.obm00033
- Coutinho PM, Deleury E, Davies GJ, Henrissat B. An Evolving Hierarchical Family Classification for Glycosyltransferases. Journal of Molecular Biology. 2003;328: 307–317. doi:10.1016/S0022-2836(03)00307-3
- Lairson LL, Henrissat B, Davies GJ, Withers SG. Glycosyltransferases: structures, functions, and mechanisms. Annu Rev Biochem. 2008;77: 521–555. doi:10.1146/annurev.biochem.76.061005.092322
- Reilly PJ. Chapter 5 - Amylase and Cellulase Structure and Function. In: Yang S-T, editor. Bioprocessing for Value-Added Products from Renewable Resources. Amsterdam: Elsevier; 2007. pp. 119–130. doi:10.1016/B978-044452114-9/50006-2
- Peretó J. Embden-Meyerhof-Parnas Pathway. In: Gargaud M, Amils R, Quintanilla JC, Cleaves HJ (Jim), Irvine WM, Pinti DL, et al., editors. Encyclopedia of Astrobiology. Berlin, Heidelberg: Springer; 2011. pp. 485–485. doi:10.1007/978-3-642-11274-4_503