Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation

BMC Microbiology

Research Article

Ricardo M. Figueiredo¹  Ana Teresa Freitas¹  Ana Tereza Ribeiro de Vasconcelos²  Sinara Carla da Silva Araújo³  Rita C. B. Silva-Portela³  Alaine de Brito Guerra³  Carolina Minnicelli³  Lucymara F. Agnez-Lima³  Aline Cardoso Carlos³  Jorge S. Oliveira⁴  Wydemberg J. Araújo⁵ 

[1] INESC-ID/IST Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol, 9, 1000-029, Lisbon, Portugal;Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil;Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil;Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil;INESC-ID/IST Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol, 9, 1000-029, Lisbon, Portugal;Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil;Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil;Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil;

关键词: Hydrocarbon degradation;    Biosurfactants;    Environmental microbiology;    Metagenomics;    Metagenomics bioinformatics pipeline;    Geographical ecology;    Microbiome data analysis;   

DOI  :  10.1186/s12866-017-1077-4

 received in 2017-02-16, accepted in 2017-07-18,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundBacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects.ResultsA metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential.ConclusionIn this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity.

【 授权许可】

CC BY   
© The Author(s). 2017