Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils
- PMID: 19201974
- PMCID: PMC2663196
- DOI: 10.1128/AEM.02294-08
Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils
Abstract
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N(2) fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
Figures
![FIG. 1.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/2663196/bin/zam0070997740001.gif)
![FIG. 2.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/2663196/bin/zam0070997740002.gif)
![FIG. 3.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/2663196/bin/zam0070997740003.gif)
Similar articles
-
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats.Appl Environ Microbiol. 2021 Aug 11;87(17):e0094721. doi: 10.1128/AEM.00947-21. Epub 2021 Aug 11. Appl Environ Microbiol. 2021. PMID: 34160232 Free PMC article.
-
Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments.Environ Microbiol. 2018 Mar;20(3):1041-1063. doi: 10.1111/1462-2920.14043. Epub 2018 Mar 12. Environ Microbiol. 2018. PMID: 29327410 Free PMC article.
-
The Ecology of Acidobacteria: Moving beyond Genes and Genomes.Front Microbiol. 2016 May 31;7:744. doi: 10.3389/fmicb.2016.00744. eCollection 2016. Front Microbiol. 2016. PMID: 27303369 Free PMC article. Review.
-
Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils.FEMS Microbiol Ecol. 2012 Nov;82(2):341-55. doi: 10.1111/j.1574-6941.2012.01381.x. Epub 2012 Apr 30. FEMS Microbiol Ecol. 2012. PMID: 22486608
-
Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria.Appl Environ Microbiol. 2011 Jan;77(2):586-96. doi: 10.1128/AEM.01080-10. Epub 2010 Nov 19. Appl Environ Microbiol. 2011. PMID: 21097594 Free PMC article.
Cited by
-
Analysis of microbial community composition and diversity in the rhizosphere of Salvia miltiorrhiza at different growth stages.Int Microbiol. 2024 Jun 4. doi: 10.1007/s10123-024-00542-6. Online ahead of print. Int Microbiol. 2024. PMID: 38833100
-
Modifying soil bacterial communities in saline mudflats with organic acids and substrates.Front Microbiol. 2024 Apr 19;15:1392441. doi: 10.3389/fmicb.2024.1392441. eCollection 2024. Front Microbiol. 2024. PMID: 38706968 Free PMC article.
-
Acidification induce chemical and microbial variation in tea plantation soils and bacterial degradation of the key acidifying phenolic acids.Arch Microbiol. 2024 Apr 30;206(5):239. doi: 10.1007/s00203-024-03858-z. Arch Microbiol. 2024. PMID: 38689148
-
Deep groundwater irrigation altered microbial community and increased anammox and methane oxidation in paddy wetlands of Sanjiang Plain, China.Front Microbiol. 2024 Feb 21;15:1354279. doi: 10.3389/fmicb.2024.1354279. eCollection 2024. Front Microbiol. 2024. PMID: 38450168 Free PMC article.
-
Reforestation of Cunninghamia lanceolata changes the relative abundances of important prokaryotic families in soil.Front Microbiol. 2024 Feb 13;15:1312286. doi: 10.3389/fmicb.2024.1312286. eCollection 2024. Front Microbiol. 2024. PMID: 38414777 Free PMC article.
References
-
- Branco, R., A. P. Chung, A. Verissimo, and P. V. Morais. 2005. Impact of chromium-contaminated wastewaters on the microbial community of a river. FEMS Microbiol. Ecol. 54:35-46. - PubMed
Publication types
MeSH terms
Substances
Associated data
- Actions
- Actions
- Actions
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases