Abstract

  Soil is a complex ecosystem whose homeostasis is affected by the presence of contaminants such as mercury. Knowing the effects of this heavy metal on edaphic microbial communities can help to establish soil quality bioindicators. For the present study, rhizospheric soils have been selected from three indigenous plants of the Almadén mining district (Spain): R. induratus (A), R. bucephalophorus (B) and Avena sativa (C), as well as bulk soil samples in plots subject to different mercury concentrations. Rhizospheres contain a huge heterogeneity of scarce microorganisms that are difficult to identify, whose functional and regulator role in their communities, is unknown. Metagenomic techniques allow to know the structure, diversity and abundance of microorganisms that make up these communities, as well as the effects that contaminants may have on their bacterial members, and the natural role played by the native plants that harbor them. The results on how mercury and the plant effect affect the taxonomic composition and microbial diversity, show a reduction in soil heterogeneity in the presence of mercury, and a partial shield of this effect by Avena sativa (C) in soils with high mercury concentration. This finding opens expectations to the selection of PGPR strains for future phytoremediation trials.

Keywords: Metagenomics, soil microbiome, BBH, LCA, Shannon index (H´), Simpson index (DSi).

References

1. Lloret Quirante J., et al. “Distrito minero de Almadén. Sostenibilidad del cierre de una actividad milenaria”. Journal of Experimental Botany 65 (2015): 1399-1409.
2. Martínez A., et al. “Sampling high to extremely high Hg concentrations at the Cerco de Almadenejos, Almadén mining district (Spain): The old metallurgical precinct (1794 to 1861 AD) and surrounding areas”. Journal of Geochemical Exploration 109 (2011): 70-77.
3. Higueras P., et al. “Intraplate mafic magmatism, degasification, and deposition of mercury: The giant Almadén mercury deposit (Spain) revisited”. Ore Geology Reviews 51 (2013): 93-102.
4. Das S., et al. “Genetic basis and importance of metal resistant genes in bacteria for bioremediation of contaminated environments with toxic metal pollutants”. Applied Microbiology and Biotechnology 100 (2016): 2967-2984.
5. Fernández-Naranjo N., et al. “Sediment characterization of an artificial reservoir impacted by mining activity in the Almadén mercury district (Spain)”. Conference: IX Congreso Geológico de España 16.1 (2016): 137-140.
6. Goberna M., et al. “Opposing phylogenetic diversity gradients of plant and soil bacterial communities”. Proceeding Biology Sciences 283.1825 (2016): 2015-3003.
7. Jiao M., et al. “Resilience associated with mental health problems among methadone maintenance treatment patients in Guangzhou, China”. AIDS Care 29.5 (2017): 660-665.
8. Patel V., et al. “Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates”. BMC Microbiology 22.16 (2016): 50.
9. Schloter M., et al. “Microbial indicators for soil quality”. Biology and Fertility of Soils 54.1 (2018): 1-10.
10. Nacke H., et al. “Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories”. FEMS Microbiology Ecology 78.1 (2011): 188-201.
11. Gołębiewski M., et al. “16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils”. Microbial Ecology 67.3 (2014): 635-647.
12. Guo W., et al. “Nonparametric regularized regression for phenotype- associated taxa selection and network construction with metagenomic count data”. Journal of Computational Biology 23.11 (2016): 877-890.
13. Baldrian P. “The known and the unknown in soil microbial ecology”. FEMS Microbiology Ecology 95.2 (2019).
14. Jansson JK and Hofmockel KS. “The soil microbiome — from metagenomics tometaphenomics”. Current Opinion in Microbiology 43 (2018): 162-168.
15. Moreno-Jiménez E., et al. “Using Mediterranean shrubs for the phytoremediation of a soil impacted by pyritic wastes in Southern Spain. A field experiment”. Journal of Environmental Management 92 (2011): 1584-1590.
16. Ashelford KE., et al. “New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras”. Applied and Environmental Microbiology 72.9 (2006): 5734-5741.
17. Arndt D., et al. “METAGENassist: A comprehensive web server for comparative metagenomics”. Nucleic Acids Research 40 (2012): 80-95.
18. Simpson EH. “Measurement of Diversity”. Nature 163 (1949): 688-688.
19. Shannon CE. “A mathematical theory of communication”. The Bell System Technical Journal (1948): 623-656.
20. Germida JJ and Siciliano SD. “Taxonomic diversity of bacteria associated with the roots of modern, recent and ancient wheat cultivars”. Biology and Fertility of Soils 33 (2001): 410-415.
21. Dybvig K. “DNA rearrangements and phenotypic switching in prokaryotes”. Molecular Microbiology 10.3 (1993): 465-471.
22. Woese CR. “Bacterial evolution”. Clinical Microbiology Reviews 51.2 (1987): 221-271.
23. Pace NR., et al. “The analysis of natural microbial populations by ribosomal RNA sequences”. Advances in Microbial Ecology 9 (1986): 1-55.
24. Janssen PH. “Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and rRNA genes”. Applied and Environmental Microbiology 72.3 (2006): 1719-1728.
25. Buckley DH and Schmidt TM. “Diversity and dynamics of microbial communities in soils from agro-ecosystems”. Environmental Microbiology 5 (2003): 441-452.
26. Felske A., et al. “Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes”. Applied and Environmental Microbiology 66 (2000): 3998-4003.
27. Da Rocha UN., et al. “Exploration of hitherto-uncultured bacteria from the rhizosphere”. FEMS Microbiology Ecology 69.3 (2009): 313-328.
28. Garrity GM., et al. “Taxonomic outline of the prokaryotes, release 5.0”. (2004).
29. Zul D., et al. “Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinantsof bacterial diversity”. Applied and Environmental Microbiology 73 (2007): 6916-6929.
30. Janssen PH., et al. “Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, ctinobacteria, Proteobacteria, and Verrucomicrobia”. Applied and Environmental Microbiology 68 (2002): 2391-2396.
31. Sait M., et al. “Cultivation of globallydistributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys”. Environmental Microbiology 4 (2002): 654-666.
32. Davis KER., et al. “Effects of growth medium, inoculum size, and incubation time on the culturability and isolation of soil bacteria”. Applied and Environmental Microbiology 1 (2005): 826-834.
33. Alexander M. “Introduction to soil microbiology”. 2^nd ed. John Wiley and Sons, New York NY (1977). 
34. Berg G and Smalla K. “Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere”. FEMS Microbiology Ecology 68.1 (2009): 1-13.
35. Xie L., et al. “The low TN:TP ratio, a cause or a result of Microcystis blooms?”. Water Research 37.9 (2003): 2073-2080.
36. Le T. “Mictocystis: Toxic Blue-Green Algae. Office of Environmental Health Hazard Assessment”. USA (2009).
37. Gademann K., et al. “Multiple toxin production in the cyanobacterium microcystis: isolation of the toxic protease inhibitor cyanopeptolin 1020”. Journal of Natural Products 73.5 (2010): 980-984.
38. Zelles L., et al. “Discrimination of microbial diversity by fatty acid profiles of phospholipids and lipopolysaccharides in differently cultivated soils”. Microbial Population Dynamic Plant and Soil 170.1 (1992): 115-122.
39. Singh BK., et al. “Influence of grass species in soil type on rhizosphere microbial community structure in grassland soils”. Applied Soil Ecology 36 (2009): 147-155.
40. Lau SCK., et al. “Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009PT), a representative of the Roseobacter group”. Standards in Genomic Sciences 10 (2015): 51.
41. Lauber LC., et al. “The influence of soil properties on the structure of bacterial and fungal communities across land-use types”. Soil Biology and Biochemistry 9.40 (2008): 2407-2415.
42. Zhang HB., et al. “Bacterial diversity at different depths in lead-zinc mine tailings as revealed by 16S rRNA gene libraries”. Journal of Microbiology 45.6 (2007): 479-484.
43. Van Elsas JD., et al. “A procedure for the metagenomics exploration of disease-suppressive soils”. Journal of Microbiology Methods 75.3 (2008): 515-522.
44. Carini P., et al. “Relic DNA is abundant in soil and obscures estimates of soil microbial diversity”. Nature Microbiology 19 (2016):16242.
45. Emerson JB., et al. “Schrödinger's microbes: tools for distinguishing the living from the dead in microbial ecosystems”. Microbiome 5 (2017): 86.
46. Flemming HC and Wingender J. “The biofilm matrix”. Nature Reviews Microbiology 8 (2010): 623-633.
47. Green ST and Rubin EM. “Metagenomics: DNA sequencing of environmental samples”. Nature Reviews Genetics 6 (2005): 805-814.
48. Falkowski PG and Colomban V. “Shotgun Sequencing in the Sea: A Blast from the Past?”. Science 304.5667 (2004): 58-60.
49. Robas Mora M., et al. “Effect of the Type of Vitis vinifera Cultivation in the Cenophenoresistome and Metabolic Profiling (CLPP) of Edaphic Bacterial Communities”. Journal of Agriculture, Science and Technology 7.8 (2018).
50. Haichar FZ., et al. “Plant host habitat and root exudates shape soil bacterial community structure”. The ISME Journal 2.12 (2008): 1221-1230.
51. Gause GF. “The struggle for existence.a classic in mathematical biology and ecology”. Georgiĭ Frantsevich) 1910-1986 Baltimore, The Williams and Wilkins company (1934).
52. Hardin G. “The competitive exclusion principle”. Science 131.3409 (1960): 1292-1297.
53. García-Salamanca A., et al. “Bacterial diversity in the rhizosphere of maize and the surrounding carbonate-rich bulk soil”. Microbial Biotechnology 6.1 (2013): 36-44.
54. Lorenz N., et al. “Response of microbial activity and microbial community composition in soils to long-term arsenic and cadmium exposure”. Soil Biology and Biochemistry 38.6 (2006): 1430-1437.
55. Ellis RJ., et al. “Cultivation-dependent and independent approaches for determining bacterial diversity in heavy-metal-contaminated soil”. Applied and Environmental Microbiology 69 (2003): 3223-3230.
56. Tenenhaus M. “Component-based structural equation modelling”. Total Quality Managementand Business Excellence 19.7 (2008): 8.
57. Hurlbert SH. “The nonconcept of Species Diversity: A Critique and Alternative Parameters”. Ecology 52 (1971): 577-586.
58. Rappé MS and Giovannoni SJ. “The uncultured microbial majority”. Annual Review of Microbiology 57 (2003): 369-394.
59. Tilman D. “Causes, consequences and ethics of biodiversity”. Nature 405 (2000): 208-211.
60. Bardgett RD. “Causes and consequences of biological diversity in soil”. Zoology 105.4 (2002): 367-374.
61. Daniel R. “The metagenomics of soil”. Nature Review Microbiology 3 (2005): 470-478.
62. Lozupone CA and Knight R. “Species divergence and the measurement of microbial diversity”. FEMS Microbiology Reviews 32.4 (2008): 557-578.
63. Woese CR and Fox GE. “Evolution Phylogenetic structure of the prokaryotic domain: The primary kingdoms”. Proceedings of the National Academy of Sciences of the United States of America 74.11 (1977): 5088-5090.
64. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
65. https://era7bioinformatics.com/en/page.cfm?id=464 and title=microbiomes:-Mg7 
66. http://rnacentral.org/expert-database

Citation

Citation: Marina Robas Mora., et al. “Metagenomic Study of the Taxonomic Profile of Rhizobacterial Communities in Soils Contaminated with Mercury". Acta Scientific Microbiology 3.3 (2020): 01-13.

Copyright

Copyright: © 2020 Marina Robas Mora., et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.