Candidatus Solibacter usitatus: Difference between revisions
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Candidatus Solibacter usitatus | |||
==Description and Significance== | ==Description and Significance== | ||
Revision as of 21:11, 28 April 2014
Classification
Domain (Bacteria), Phylum (Acidobacteria), Class (Solibacteres), Order (Solibacterales), Family (Solibacteraceae), Genus (Candidatus Solibacter)
Species
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NCBI: Taxonomy |
Genus species Candidatus Solibacter usitatus
Description and Significance
Candidatus Soilbacter usitaus was initially isolated from rotationally grazed pasture of perennial ryegrass and white clover in Victoria, Australia (1). This species is common and very prevalent in its environment. It was found to be the most common organism in a study conducted in 2012 analyzing bacterial composition of Antarctic soil (2).
This species has been difficult to culture in the lab. Filaments have been observed microscopically in soils, but it was found to form clusters in liquid culture (3). In nature, this species produces a biofilm that acts as an ecosystem engineer in soil. It does this by acting as a medium between soil particles to reduce moisture and nutrient fluxuations as well as aid in resource acquisition, which serves to aid survival under environmental stress conditions (4).
This species has an exceptionally large genome and is theorized to engage in horizontal gene transfer which contributes to this species ability to persist in its environment. It is theorized to be capable breaking down plant compounds for metabolism, and to participate in respiratory denitrification which lends to the creation of heterogeneous nutrient concentrations in its environment (4).
Genome Structure
Based on the sequenced genome, Candidatus Soilbacter usitaus was found to have a genome 9.9 Mb long (5), which is about twice the size of other closely related Acidiobacteria found to inhabit soil (4). Horizontal gene transfer is hypothesized to account for how this species acquired its unusual genome size (4), and implies biological and ecological strains upon the living organism to participate in this type of gene transfer (5).
It is theorized that the amount of mobile elements encoded in a genome correlate with the historical frequency of horizontal gene transfer events. This is significant because mobile elements are theorized to contribute toward genome plasticity and evolution over time, which could provide a competitive advantage to this species and enable it to exploit various environmental resources (6). Genomic sequencing found a large number of genes encoding for carbohydrate transport and metabolism; more than “the human genome and about three times as many as Saccharomyces cerevisiae” (8). These genes were also found to have high sequence similarity with fungal homologs which further suggests an ancestral horizontal gene transfer that has been unreported among other organisms producing glycoside hydrolase enzymes (4).
Whole genome sequencing also found genes encoding for candidate cellulases of glycoside hydrolases, suggesting Candidatus Solibacter usitatus is capable of degrading cellulose substrates and implies the genome is also encoded with other enzymes capable of degrading plant compounds (4). This analysis also suggests it has the flexibility to metabolize carbon as a mixotroph because it contains genes encoding for carbon monoxide dehydrogenase (7). Since oxidation of carbon monoxide has been prevalently documented among other major groups of soil organisms (7), it is hypothesized that this along with the ability to degrade complex polymers associated with vegetation, occur as a survival mechanism in environments with low carbon concentration (4).
The genetic potential for nitrate reductase was observed though no evidence for nitrogen fixation has been demonstrated (4). The potential for respiratory denitrification is significant because it leads to heterogeneous pockets in soil causing spatial variable in nutrient concentrations across a landscape.
While Candidatus Solibacter usitatus is not thought to contain genes for iron permease, which is involved in iron uptake (9), it has sequences with domain structures similar to those used in other species. Gene sequence libraries document the 16S rRNA from iron-rich mine environments to be frequently dominated by Acidobacteria (10, 11, 12). This suggests possible involvement with iron (II) uptake and is hypothesized to be a valuable role in iron redox reactions (4).
Cell Structure, Metabolism and Life Cycle
Candidatus Solibacter usitatus is a small aerobic (4) rod shaped bacterium (1). While, it is non-motile, it is found free living in terrestrial habitats within mesophilic temperatures (1) and at a pH in the 3.5-6.5 range (4). It is chemoorganotrophic; utilizing organic carbon for growth and energy (1).
Candidatus Solibacter usitatus has a large number of anion : cation symporters(4). These transporters are thought to be advantageous to organisms living in low nutrient environments (13). When compared to other closely related species, it has a 2-4 times as many transporters than others. It also had a large number of secondary porters to transport various other substrates such as amino acids, metals, fatty acids, proteins, in a carrier-mediated process (4).
Candidatus Solibacter usitatus has a slow metabolism and is only culturable in oligotrophic media. It persists in environments with high substrate affinity and low nutrient concentration (4). It does this by producing a biofilm which functions to engineer an ecosystem for itself among soil particles.
Ecology and Pathogenesis
This species exhibits environmental dependent functional diversity in dealing with extreme variation in moisture, temperature, and nutrient cycles (6). The biofilm production exhibited by Candidatus Solibacter usitatus functions to reduce moisture and nutrient fluxuations by acting as a medium between the soil particles. This leads to heterogenous soil conditions commonly found in Antartic soil, which contain a relatively low nutrient content (2).
Cellulose production by bacteria is thought to be related to soil survival by way of lending toward biofilm production, thus increasing survivability under conditions of environmental stress by aiding in moisture retention in arid conditions by maintaining water retention capacity and soil aeration (14, 15).
Cellulase synthesis by acidobacteria has been suggested to promote the ability of a biofilm to adhere to ferric iron-rich substrates and produce “bioshrouds” to be used remedially in sulfide mine tailing environments (14). This suggests the future of characterizing cellulose production should include testing formation ability of the microfibrils to demonstrate the network formation (4).
References
1. GOLD CARD: Gc00446. Candidatus Solibacter usitatus Ellin6076. The Regents of the University of California. 2011. <http://genomesonline.org/cgi-bin/GOLD/bin/GOLDCards.cgi?goldstamp=Gc00446>.
2. Pearce D.A., Newsham K.K, Thorne M.A.S., Clavo-Bado L., Kresk M., Laskaris P., et al. "Metagenomic analysis of a southern mairitme Antartic soil". Frontiers in Microbio. 2012. 3:403.
3. Sait M., Davis, K.E., and Janssen P.H. "Effect of pH on isolation and distribution of members of subdivisions 1 of the phylum Acidobacteria occurring in soil". Appl Environ. Micorbiol. 2006. 72:1852-1857.
4. Ward N.L., Challacombe J.F., Janssen P.H., Henrissat B., Coutinho P.M., et al. "Three Acidobacteria genomes provide a first glimpse of their lifestyles in soils and sediments". Appl Environ Microbiol. 2009. 75:2046-2056.
5. Challacombe J.F., Eichorst S.A., Hauser L., Land M., Xie G., et al. "Biological consequences of ancient gene acquisition and duplication in the large genome of candidatus solibater usitatus Ellin6076". 2001. PLoS ONE 6(9): e24882.
6. Challacombe J.F., Kuske C.R. "Mobile genetic elements in the bacterial phylum Acidiobacteria". Landes Bioscience. 2012. 2:4, 179-193.
7. King G.M. and Weber C.F. "Distribution, diversity, and ecology of aerobic CO-oxidizing bacteria". Nat. Rev. Microbiol. 2007. 5:107-118.
8. Coutinho P.M., Stam M., Blanc E., Henrissat B. "Why are there so many carbohydrate-active enzyme-related genes in plants?". 2003. Trends Plant Sci. 8:563-565.
9. Stearman R.D., Yuan D.S., Yamaguchi-Iwai Y., Klausner R.D., and Dancis A. "A permease-oxidase complex involved in high-affinity iron uptake in yeast". 1996. Science 271:1552-1557.
10. Blothe M.D., Akob D.M., Kostka J.E., Goschel K., Drake H.L., and Kusel K. "pH gradient-induced heterogeneity of Fe(iii)-reducing microorganisms in coal mining-associated lake sediments". Appl. Environ. Microbiol. 2008. 74:1019-1029.
11. Kleinsteuber, S.F., Muller F.D., Chatzinotas A., Wendt-Potthoff K., and Harms H. (2008) "Diversity and in-situ quantification of Acidobacteria subdivision 1 in an acidic mining lake". FEMS Microbiol. Ecol. 63:107-117.
12. Rowe O.F., Sanchez-Espana J., Hallberg K.B., and Johnson D.B. (2007) "Microbial communities and geochemical dynamics in an extremely acidic metal-rich stream at an abandoned sulfide mine". (Huclva, Spain) underpinned by functional primary production systems. Environ. Microbiol. 9:1761-1771.
13. Paulsen L.T., Sliwinski M.K., and Saier M.H., Jr. (1998) "Microbial genome analyses :global comparisons of transport capabilities based on phylogenies, bioenergietics and substrate specifities". J. Mol. Biol. 277:573-592.
14. UDE S., Arnold D.L., Moon C.D., Timms-Wilson T., and Spiers A.J. (2006) "Biofilm formation and cellulose expression among diverse environmental Pseudomonas isolates". Environ. Microbiool. 8:1997-2011.
15. White A.T., Bigson D.L., Kim W., Kay W.W., and Surette M.G. (2006) "Thin aggregative fimbriae and cellulose enhance the long-term survival and persistence of Salmonella". J. Bacteriol. 188:3219-3227.
16. Johnson D.B., Stallwood B., Kimura S., and Hallberg K.B. (2006) "Isolation and characterization of Acidicaldus organivorus, gen. nov., sp. Nov.: a novel sulfur-oxidizing, ferric iron-reducing thermo-acidophilic heterotrophic Proteobacterium". Arch. Microbiol. 185:212-221.
Author
Page authored by Kristine Ader, student of Prof. Jay Lennon at IndianaUniversity.
