It is obvious that the bacterial composition in the reference well was relatively
stable over the whole sampling period while the treatment strongly influenced the
microbial community structure. When the physicochemical data are available, an
experienced environmental microbiologist can interpret the NGS results in a broader
context and can help to efficiently plan the next remediation strategy.
References
APHA (2005) Standard methods for the examination of water and wasterwater, 21st edn. American
Public Health Association, Washington, DC
Baldrian P, Větrovský T, Cajthaml T, Dobiášová P, Petránková M, Šnajdr J, Eichlerová I (2013)
Estimation of fungal biomass in forest litter and soil. Fungal Ecol 6(1):1–11. https://doi.org/10.
1016/j.funeco.2012.10.002
Balvočiūtė M, Huson DH (2017) SILVA, RDP, Greengenes, NCBI and OTT—how do these
taxonomies compare? BMC Genomics 18(2):114. https://doi.org/10.1186/s12864-017-3501-4
Barrero-Canosa J, Moraru C, Zeugner L, Fuchs BM, Amann R (2017) Direct-geneFISH: a
simplified protocol for the simultaneous detection and quantification of genes and rRNA in
microorganisms. Environ Microbiol 19(1):70–82. https://doi.org/10.1111/1462-2920.13432
Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem
Physiol 37(8):911–917. https://doi.org/10.1139/y59-099
Dolinová I, Czinnerová M, Dvořák L, Stejskal V, Ševců A, Černík M (2016) Dynamics of
organohalide-respiring bacteria and their genes following in-situ chemical oxidation of chlorinated ethenes and biostimulation. Chemosphere 157:276–285. https://doi.org/10.1016/j.
chemosphere.2016.05.030
Dolinová I, Štrojsová M, Černík M, Němeček J, Macháčková J, Ševců A (2017) Microbial
degradation of chloroethenes: a review. Environ Sci Pollut Res 24(15):13262–13283. https://
doi.org/10.1007/s11356-017-8867-y
Emerson D, Fleming EJ, McBeth JM (2010) Iron-oxidizing bacteria: an environmental and
genomic perspective. Annu Rev Microbiol 64:561–583. https://doi.org/10.1146/annurev.
micro.112408.134208
Kubota K (2013) CARD-FISH for environmental microorganisms: technical advancement and
future applications. Microbes Environ 28(1):3–12. https://doi.org/10.1264/jsme2.ME12107
Němeček J, Lhotský O, Cajthaml T (2014) Nanoscale zero-valent iron application for in situ
reduction of hexavalent chromium and its effects on indigenous microorganism populations.
Sci Total Environ 485–486:739–747. https://doi.org/10.1016/j.scitotenv.2013.11.105
Němeček J, Dolinová I, Macháčková J, Špánek R, Ševců A, Lederer T, Černík M (2017) Stratification of chlorinated ethenes natural attenuation in an alluvial aquifer assessed by
hydrochemical and biomolecular tools. Chemosphere 184:1157–1167. https://doi.org/10.
1016/j.chemosphere.2017.06.100
Nguyen NHA, Špánek R, Kasalický V, Ribas D, Vlková D, Řeháková H, Kejzlar P, Ševců A (2018)
Different effects of nano-scale and micro-scale zero-valent iron particles on planktonic microorganisms from natural reservoir water. Environ Sci Nano 5(5):1117–1129. https://doi.org/10.
1039/C7EN01120B
Sampedro I, Giubilei M, Cajthaml T, Federici E, Federici F, Petruccioli M, D’annibale A (2009)
Short-term impact of dry olive mill residue addition to soil on the resident microbiota. Bioresour
Technol 100(23):6098–6106. https://doi.org/10.1016/j.biortech.2009.06.026
Stella T, Covino S, Burianová E, Filipová A, Křesinová Z, Voříšková J, Větrovský T, Baldrian P,
Cajthaml T (2015) Chemical and microbiological characterization of an aged
PCB-contaminated soil. Sci Total Environ 533:177–186. https://doi.org/10.1016/j.scitotenv.
2015.06.019
656
A. Ševců et al.
stable over the whole sampling period while the treatment strongly influenced the
microbial community structure. When the physicochemical data are available, an
experienced environmental microbiologist can interpret the NGS results in a broader
context and can help to efficiently plan the next remediation strategy.
References
APHA (2005) Standard methods for the examination of water and wasterwater, 21st edn. American
Public Health Association, Washington, DC
Baldrian P, Větrovský T, Cajthaml T, Dobiášová P, Petránková M, Šnajdr J, Eichlerová I (2013)
Estimation of fungal biomass in forest litter and soil. Fungal Ecol 6(1):1–11. https://doi.org/10.
1016/j.funeco.2012.10.002
Balvočiūtė M, Huson DH (2017) SILVA, RDP, Greengenes, NCBI and OTT—how do these
taxonomies compare? BMC Genomics 18(2):114. https://doi.org/10.1186/s12864-017-3501-4
Barrero-Canosa J, Moraru C, Zeugner L, Fuchs BM, Amann R (2017) Direct-geneFISH: a
simplified protocol for the simultaneous detection and quantification of genes and rRNA in
microorganisms. Environ Microbiol 19(1):70–82. https://doi.org/10.1111/1462-2920.13432
Bligh EG, Dyer WJ (1959) A rapid method of total lipid extraction and purification. Can J Biochem
Physiol 37(8):911–917. https://doi.org/10.1139/y59-099
Dolinová I, Czinnerová M, Dvořák L, Stejskal V, Ševců A, Černík M (2016) Dynamics of
organohalide-respiring bacteria and their genes following in-situ chemical oxidation of chlorinated ethenes and biostimulation. Chemosphere 157:276–285. https://doi.org/10.1016/j.
chemosphere.2016.05.030
Dolinová I, Štrojsová M, Černík M, Němeček J, Macháčková J, Ševců A (2017) Microbial
degradation of chloroethenes: a review. Environ Sci Pollut Res 24(15):13262–13283. https://
doi.org/10.1007/s11356-017-8867-y
Emerson D, Fleming EJ, McBeth JM (2010) Iron-oxidizing bacteria: an environmental and
genomic perspective. Annu Rev Microbiol 64:561–583. https://doi.org/10.1146/annurev.
micro.112408.134208
Kubota K (2013) CARD-FISH for environmental microorganisms: technical advancement and
future applications. Microbes Environ 28(1):3–12. https://doi.org/10.1264/jsme2.ME12107
Němeček J, Lhotský O, Cajthaml T (2014) Nanoscale zero-valent iron application for in situ
reduction of hexavalent chromium and its effects on indigenous microorganism populations.
Sci Total Environ 485–486:739–747. https://doi.org/10.1016/j.scitotenv.2013.11.105
Němeček J, Dolinová I, Macháčková J, Špánek R, Ševců A, Lederer T, Černík M (2017) Stratification of chlorinated ethenes natural attenuation in an alluvial aquifer assessed by
hydrochemical and biomolecular tools. Chemosphere 184:1157–1167. https://doi.org/10.
1016/j.chemosphere.2017.06.100
Nguyen NHA, Špánek R, Kasalický V, Ribas D, Vlková D, Řeháková H, Kejzlar P, Ševců A (2018)
Different effects of nano-scale and micro-scale zero-valent iron particles on planktonic microorganisms from natural reservoir water. Environ Sci Nano 5(5):1117–1129. https://doi.org/10.
1039/C7EN01120B
Sampedro I, Giubilei M, Cajthaml T, Federici E, Federici F, Petruccioli M, D’annibale A (2009)
Short-term impact of dry olive mill residue addition to soil on the resident microbiota. Bioresour
Technol 100(23):6098–6106. https://doi.org/10.1016/j.biortech.2009.06.026
Stella T, Covino S, Burianová E, Filipová A, Křesinová Z, Voříšková J, Větrovský T, Baldrian P,
Cajthaml T (2015) Chemical and microbiological characterization of an aged
PCB-contaminated soil. Sci Total Environ 533:177–186. https://doi.org/10.1016/j.scitotenv.
2015.06.019
656
A. Ševců et al.