Full-text resources of PSJD and other databases are now available in the new Library of Science.
Visit https://bibliotekanauki.pl

PL EN


Preferences help
enabled [disable] Abstract
Number of results
2017 | 64 | 4 | 693-698

Article title

First insight into microbial community composition in a phosphogypsum waste heap soil

Content

Title variants

Languages of publication

EN

Abstracts

EN
The aim of this study was to investigate the soil microbial communities of a phosphogypsum waste heap. The soil microbial community structures can differ over time, as they are affected by the changing environmental conditions caused by a long-term exposure to different kinds of pollutions, like is the case of soil in the post-production waste area in Wiślinka (in the northern part of Poland) currently undergoing restoration. Our analyses indicated that the most abundant phyla were Proteobacteria, Acidobacteria, and Actinobacteria, and generally such an abundance is common for most of the studied soils. The most dominant class were Alphaproteobacteria, with their participation in 33.46% of the total reads. Among this class, the most numbered order was Sphingomonadales, whereas among this order the Sphingomonadaceae family was the most abundant one. The Sphingomonadaceae family is currently in the center of interest of many researchers, due to the ability of some of its members to utilize a wide range of naturally occurring organic compounds and many types of environmental contaminants. This kind of knowledge about microbial populations can support efforts in bioremediation and can improve monitoring changes in the contaminated environments.

Year

Volume

64

Issue

4

Pages

693-698

Physical description

Dates

published
2017
received
2017-08-10
revised
2017-11-03
accepted
2017-11-28
(unknown)
2017-12-16

Contributors

  • Department of Molecular Biology, University of Gdansk, Gdańsk, Poland
  • Center for Medical Genomics - OMICRON, Jagiellonian University Medical College Faculty of Medicine, Kraków, Poland
  • Department of Analytical Chemistry, University of Gdansk, Gdańsk, Poland
  • Center for Medical Genomics - OMICRON, Jagiellonian University Medical College Faculty of Medicine, Kraków, Poland
author
  • Department of Molecular Biology, University of Gdansk, Gdańsk, Poland
author
  • Department of Molecular Biology, University of Gdansk, Gdańsk, Poland

References

  • Andrews S (2010) FastQC a Quality Control Tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
  • Aronesty E (2011) Command-line tools for processing biological sequencing data, ea-utils. http://code.google.com/p/ea-utils: Expression Analysis, Durham, NC
  • Azarbad H, Niklińska M, Laskowski R, van Straalen NM, van Gestel CA, Zhou J, He Z, Wen C, Röling WF (2015) Microbial community composition and functions are resilient to metal pollution along two forest soil gradients. FEMS Microbiol Ecol 91: 1-11. doi: 10.1093/femsec/fiu003.
  • Balkwill DL, Fredrickson JK, Romine MF (2006) Sphingomonas and related genera. The prokaryotes, a handbook of the biology of bacteria. Vol 7: Proteobacteria: Delta and Epsilon Subclasses. Deeply Rooting Bacteria. Dworkin M, ed. Singapore.
  • Berg J, Brandt KK, Al-Soud WA, Holm PE, Hansen LH, Sørensen SJ, Nybroe O (2012) Selection for Cu-tolerant bacterial communities with altered composition, but unaltered richness, via long-term cu exposure. Appl Environ Microbiol 78: 7438-7446. doi: 10.1128/AEM.01071-12.
  • Boryłko A, Skwarzec B (2013) Biogeochemistry of uranium in the southern Baltic ecosystem. J Ecol Protec Coastline 92: 53-69
  • Boryło A, Skwarzec B (2014) Activity disequilibrium between 234U and 238U isotopes in natural environment. J Radioanal Nucl Chem 300: 719-727.
  • Campbell BJ, Polson SW, Hanson TE, Mack MC, Schuur EA (2010) The effect of nutrient deposition on bacterial communities in Arctic tundra soil. Environ Microbiol 12: 1842-1854. doi: 10.1111/j.1462-2920.2010.02189.x.
  • Caporaso JG, Bittinger K, Bushman F, DeSantis T, Andersen G, Knight R (2010) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266-267. doi: 10.1093/bioinformatics/btp636.
  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2011) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336. doi: 10.1038/nmeth.f.303.
  • Ceja-Navarro JA, Rivera-Orduña FN, Patiño-Zúñiga L, Vila-Sanjurjo A, Crossa J, Govaerts B, Dendooven L (2010) Phylogenetic and multivariate analyses to determine the effects of different tillage and residue management practices on soil bacterial communities. Appl Environ Microbiol 76: 3685-3691. doi: 10.1128/AEM.02726-09.
  • Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P (2010) Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 12: 2998-3006. doi: 10.1111/j.1462-2920.2010.02277.x.
  • Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3: 470-478. doi: 10.1038/nrmicro1160.
  • Dell'Amico E, Mazzocchi M, Cavalca L, Allievi L, Andreoni V (2008) Assessment of bacterial community structure in a long-term copper-polluted ex-vineyard soil. Microbiol Res 163: 671-683. doi: 10.1016/j.micres.2006.09.003.
  • DeSantis T, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072. doi: 10.1128/AEM.03006-05.
  • Edgar R (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
  • Ellis R, Morgan P, Weightman A, Fry JA (2003) Cultivation-dependent and -independent approaches for determining bacterial diversity in heavy-metal-contaminated soil. Appl Environ Microbiol 69: 3223-3320.
  • Felczykowska A, Krajewska A, Zielińska S, Łos JM (2015) Sampling, metadata and DNA extraction - Important steps in metagenomic studies. Acta Biochim Polon 62: 151–160. doi: 10.18388/abp.2014_916.
  • Ferrera-Rodríguez O, Greer CW, Juck D, Consaul LL, Martínez-Romero E, Whyte LG (2013) Hydrocarbon-degrading potential of microbial communities from Arctic plants. J Appl Microbiol 114: 71-83. doi: 10.1111/jam.12020.
  • Gołębiewski M, Deja-Sikora E, Cichosz M, Tretyn A, Wróbel B (2014) 16S rDNA pyrosequencing analysis of bacterial community in heavy metals polluted soils. Microb Ecol 67: 635-647. doi: 10.1007/s00248-013-0344-7.
  • Gray CM, Helmig D, Fierer N (2015) Bacteria and fungi associated with isoprene consumption in soil. Elementa: Science of the Anthropocene 3: 53. doi: 10.12952/journal.elementa.000053.t003
  • Guan X, Wang J, Zhao H, Wang J, Luo X, Liu F, Zhao F (2013) Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau. BMC Genomics 14: 820. doi: 10.1186/1471-2164-14-820.
  • Committee on Metagenomics: Challenges and Functional Applications (2007) The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington, DC: The National Academies Press.
  • Hupka J (2006) The impact of the phosphogypsum waste dump on the environment and eutrophication of the Gdańsk Gulf. Gdańsk (in Polish)
  • Janssen P (2006) Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes. Appl Environ Microbiol 72: 1719-1728. doi: 10.1128/AEM.72.3.1719-1728.2006.
  • Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M (2002) Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions acidobacteria, actinobacteria. Appl Environ Microbiol 68: 2391-2396.
  • Kim HM, Jung JY, Yergeau E, Hwang CY, Hinzman L, Nam S, Hong SG, Kim OS, Chun J, Lee YK (2014) Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska. FEMS Microbiol Ecol 89: 465-475. doi: 10.1111/1574-6941.12362.
  • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41: e1-e11. doi: 10.1093/nar/gks808.
  • Kravchenko IK, Kizilova AK, Bykova SA, Men'ko EV, Gal'chenko VF (2010) Molecular analysis of high-affinity methane-oxidizing enrichment cultures isolated from a forest biocenosis and agrocenoses. Mikrobiologiia 79: 106-114. doi: 10.1134/S0026261710010145
  • Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
  • Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17: 10-12
  • McDonald D, Clemente J, Kuczynski J, Rideout J, Stombaugh J, Wendel D, Wilke A, Huse S, Hufnagle J, Meyer F, Knight R, Caporaso JG (2012) The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 1: 7. doi: 10.1186/2047-217X-1-7.
  • Myślińska E ed (1998) Laboratory soil research. PWN, Warszawa (in Polish)
  • Neufeld JD, Mohn WW (2005) Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial Ana. Appl Environ Microbiol 71: 5710-5718. doi: 10.1128/AEM.71.10.5710-5718.2005.
  • Ramirez KS, Lauber CL, Knight R, Bradford MA, Fierer N (2010) Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology 91: 3463-3470. http://www.ncbi.nlm.nih.gov/pubmed/21302816. doi: 10.1890/10-0426.1.
  • Reith F, Brugger J, Zammit CM, Gregg AL, Goldfarb KC, Andersen GL, DeSantis TZ, Piceno YM, Brodie EL, Lu Z, He Z, Zhou J, Wakelin SA (2012) Influence of geogenic factors on microbial communities in metallogenic Australian soils. ISME J 6: 2107-2118. doi: 10.1038/ismej.2012.48.
  • Skwarzec B, Borylo A, Kosinska A, Radzajewska S (2010) Polonium (Po-210) and uranium (U-234, U-238) in water, phosphogypsum and their bioaccumulation in plants around phosphogypsum waste heap at Wislinka (northern Poland). Nukleonika 55: 187-193 (in Polish)
  • Stefanowicz AM, Niklińska M, Laskowski R (2009) Pollution-induced tolerance of soil bacterial communities in meadow and forest ecosystems polluted with heavy metals. Eur J Soil Biol 45: 363-369. doi: 10.1016/j.ejsobi.2009.05.005
  • Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R (2009) EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2: 16. doi: 10.1186/2047-217X-2-16.
  • Xu Z, Hansen MA, Hansen LH, Jacquiod S, Sørensen SJ (2014) Bioinformatic approaches reveal metagenomic characterization of soil microbial community. PLoS ONE 9. doi: 10.1371/journal.pone.0093445.
  • Zielińska S, Radkowski P, Blendowska A, Ludwig-Gałęzowska A, Łoś JM, Łoś M (2017) The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis. Microbiologyopen 6: doi: 10.1002/mbo3.453.
  • Zwolicki A, Barcikowski M, Barcikowski A, Cymerski M, Stempniewicz L, Convey P (2015) Seabird colony effects on soil properties and vegetation zonation patterns on King George Island, Maritime Antarctic. Polar Biology 38: 1645-1655. doi: 10.1007/s00300-015-1730-z

Document Type

Publication order reference

Identifiers

YADDA identifier

bwmeta1.element.bwnjournal-article-abpv64p693kz
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.