Duarte K, Justino CI, Pereira R, Panteleitchouk TS, Freitas AC, Rocha-Santos TA, Duarte AC
(2013) Removal of the organic content from a bleached kraft pulp mill effluent by a treatment
with silica–alginate–fungi biocomposites. J Environ Sci Heal A Tox Hazard Subst Environ Eng
48:166–172
Edwards SJ, Kjellerup BV (2013) Applications of biofilms in bioremediation and biotransformation
of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals. Appl
Microbiol Biotechnol 97:9909–9921
Ellegaard-Jensen L, Aamand J, Kragelund BB, Johnsen AH, Rosendahl S (2013) Strains of the soil
fungus Mortierella show different degradation potentials for the phenylurea herbicide diuron.
Biodegradation 24:765–774
Ferguson SJ (1998) The Paracoccus denitrificans electron transport system: aspects of organisation,
structures and biogenesis. In: Canters GW, Vijgenboom E (eds) Biological electron transport
chains: genetics, composition and mode of operation. Kluwer Academic Publisher, Dordrecht,
pp 77–88
Ferguson SJ, Richardson DJ, van Spanning RJM (2007) Biochemistry and molecular biology of
nitrification. In: Bothe H, Ferguson SJ, Newton WE (eds) Biology of the nitrogen cycle.
Elsevier, Amsterdam, pp 209–222
Freitag A, Bock E (1990) Energy conservation in Nitrobacter. FEMS Microbiol Lett 66:157–162
Gadd GM (2010) Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 156:609–643
Gardes M, Bruns TD (1996) Community structure of ectomycorrhizal fungi in a Pinus muricata
forest: above- and below-ground views. Can J Bot 74:1572–1583
Gedalanga PB, Pornwongthong P, Mora R, Chiang SYD, Baldwin B, Ogles D, Mahendra S (2014)
Identification of biomarker genes to predict biodegradation of 1, 4-dioxane. Appl Environ
Microbiol 80(10):3209–3218
Girard JM, Roy ML, Hafsa MB, Gagnon J, Faucheux N, Heitz M, Tremblay R, Deschenes JS
(2014) Mixotrophic. cultivation of green microalgae Scenedesmus obliquus on cheese whey
permeate for biodiesel production. Algal Res 5:241–248
Grosbacher M, Eckert D, Cirpka OA, Griebler C (2018) Contaminant concentration versus flow
velocity: drivers of biodegradation and microbial growth in groundwater model systems.
Biodegradation 29(3):211–232
Guazzaroni M-E, Ferrer M (2011) Metagenomic approaches in systems biology. In: de Bruijn FJ
(ed) Handbook of molecular microbial ecology I: metagenomics and Complementary
Approaches. John Wiley & Sons, New Jersy, pp 473–489
Guieysse B, Plouviez M, Coilhac M, Cazali L (2013) Nitrous oxide (N2O) production in axenic
chlorella vulgaris microalgae cultures: evidence, putative pathways, and potential environmental impacts. Biogeosciences 10:6737–6746
Hadibarata T, Teh ZC, Zubir MM, Khudhair AB, Yusoff AR, Salim MR, Hidayat T (2013a)
Identification of naphthalene metabolism by white-rot fungus Pleurotus eryngii. Bioprocess
Biosyst Eng 24:728–732
Hadibarata T, Zubir MM, Rubiyabto TZ, Chuang TZ, Yusoff AR, Fulazzaky MA, Seng B, Nugroho
AE (2013b) Degradation and transformation of anthracene by white-rot fungus Armillaria sp.
F022. Folia Microbiol 58:385–391
Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK et al (2014) A review of biological sulfate
conversions in wastewater treatment. Water Res 65:1–21. https://doi.org/10.1016/j.watres.2014.
06.043
Harms H, Schlosser D, Wick LY (2011) Untapped potential: Exploiting fungi in bioremediation of
hazardous chemicals. Nat Rev Microbiol 9:177–192
Hartmann A, Bashan Y (2009) Ecology and application of Azospirillum and other plant growthpromoting bacteria (PGPB)—special issue. Eur J Soil Biol 45:1–2
Hatamoto M, Imachi H, Yashiro Y, Ohashi A, Harada H (2007) Diversity of anaerobic
microorganisms involved in long-chain fatty acid degradation in methanogenic sludges as
revealed by RNA-based stable isotope probing. Appl Environ Microbiol 73:4119–4127
8 Bioinformatics: A New Insight Tool to Deal with Environment Management
179
(2013) Removal of the organic content from a bleached kraft pulp mill effluent by a treatment
with silica–alginate–fungi biocomposites. J Environ Sci Heal A Tox Hazard Subst Environ Eng
48:166–172
Edwards SJ, Kjellerup BV (2013) Applications of biofilms in bioremediation and biotransformation
of persistent organic pollutants, pharmaceuticals/personal care products, and heavy metals. Appl
Microbiol Biotechnol 97:9909–9921
Ellegaard-Jensen L, Aamand J, Kragelund BB, Johnsen AH, Rosendahl S (2013) Strains of the soil
fungus Mortierella show different degradation potentials for the phenylurea herbicide diuron.
Biodegradation 24:765–774
Ferguson SJ (1998) The Paracoccus denitrificans electron transport system: aspects of organisation,
structures and biogenesis. In: Canters GW, Vijgenboom E (eds) Biological electron transport
chains: genetics, composition and mode of operation. Kluwer Academic Publisher, Dordrecht,
pp 77–88
Ferguson SJ, Richardson DJ, van Spanning RJM (2007) Biochemistry and molecular biology of
nitrification. In: Bothe H, Ferguson SJ, Newton WE (eds) Biology of the nitrogen cycle.
Elsevier, Amsterdam, pp 209–222
Freitag A, Bock E (1990) Energy conservation in Nitrobacter. FEMS Microbiol Lett 66:157–162
Gadd GM (2010) Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology 156:609–643
Gardes M, Bruns TD (1996) Community structure of ectomycorrhizal fungi in a Pinus muricata
forest: above- and below-ground views. Can J Bot 74:1572–1583
Gedalanga PB, Pornwongthong P, Mora R, Chiang SYD, Baldwin B, Ogles D, Mahendra S (2014)
Identification of biomarker genes to predict biodegradation of 1, 4-dioxane. Appl Environ
Microbiol 80(10):3209–3218
Girard JM, Roy ML, Hafsa MB, Gagnon J, Faucheux N, Heitz M, Tremblay R, Deschenes JS
(2014) Mixotrophic. cultivation of green microalgae Scenedesmus obliquus on cheese whey
permeate for biodiesel production. Algal Res 5:241–248
Grosbacher M, Eckert D, Cirpka OA, Griebler C (2018) Contaminant concentration versus flow
velocity: drivers of biodegradation and microbial growth in groundwater model systems.
Biodegradation 29(3):211–232
Guazzaroni M-E, Ferrer M (2011) Metagenomic approaches in systems biology. In: de Bruijn FJ
(ed) Handbook of molecular microbial ecology I: metagenomics and Complementary
Approaches. John Wiley & Sons, New Jersy, pp 473–489
Guieysse B, Plouviez M, Coilhac M, Cazali L (2013) Nitrous oxide (N2O) production in axenic
chlorella vulgaris microalgae cultures: evidence, putative pathways, and potential environmental impacts. Biogeosciences 10:6737–6746
Hadibarata T, Teh ZC, Zubir MM, Khudhair AB, Yusoff AR, Salim MR, Hidayat T (2013a)
Identification of naphthalene metabolism by white-rot fungus Pleurotus eryngii. Bioprocess
Biosyst Eng 24:728–732
Hadibarata T, Zubir MM, Rubiyabto TZ, Chuang TZ, Yusoff AR, Fulazzaky MA, Seng B, Nugroho
AE (2013b) Degradation and transformation of anthracene by white-rot fungus Armillaria sp.
F022. Folia Microbiol 58:385–391
Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK et al (2014) A review of biological sulfate
conversions in wastewater treatment. Water Res 65:1–21. https://doi.org/10.1016/j.watres.2014.
06.043
Harms H, Schlosser D, Wick LY (2011) Untapped potential: Exploiting fungi in bioremediation of
hazardous chemicals. Nat Rev Microbiol 9:177–192
Hartmann A, Bashan Y (2009) Ecology and application of Azospirillum and other plant growthpromoting bacteria (PGPB)—special issue. Eur J Soil Biol 45:1–2
Hatamoto M, Imachi H, Yashiro Y, Ohashi A, Harada H (2007) Diversity of anaerobic
microorganisms involved in long-chain fatty acid degradation in methanogenic sludges as
revealed by RNA-based stable isotope probing. Appl Environ Microbiol 73:4119–4127
8 Bioinformatics: A New Insight Tool to Deal with Environment Management
179