Functional and molecular approaches for studying and controlling microbial communities in anaerobic digestion of organic waste: a review

Aguiar-Pulido V, Huang W, Suarez-Ulloa V, Cickovski T, Mathee K, Narasimhan G (2016) Metagenomics, metatranscriptomics, and metabolomics approaches for microbiome analysis: supplementary issue: bioinformatics methods and applications for big metagenomics data. Evol Bioinform. https://doi.org/10.4137/EBO.S36436

Article  Google Scholar 

Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D (2018) A next-generation sequencing primer—How does it work and what can it do? Acad Pathol. https://doi.org/10.1177/2374289518766521

Article  Google Scholar 

Amann RI, Stromley J, Devereux R, Key R, Stahl DA (1992) Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl Environ Microbiol. https://doi.org/10.1128/aem.58.2.614-623.1992

Article  Google Scholar 

Andreef M, Pinkel D (1999) Introduction to fluorescence in situ hybridization: principles and clinical applications. Wiley-Liss

Google Scholar 

Aschar-Sobbi R, Abramov AY, Diao C, Kargacin ME, Kargacin GJ, French RJ, Pavlov E (2008) High sensitivity, quantitative measurements of polyphosphate using a new DAPI-based approach. J Fluoresc. https://doi.org/10.1007/s10895-008-0315-4

Article  Google Scholar 

Barati rashvanlou R, Rezaee A, Farzadkia M, Gholami M, Kermani M (2020) Effect of micro-aerobic process on improvement of anaerobic digestion sewage sludge treatment: flow cytometry and ATP assessment. RSC Adv. https://doi.org/10.1039/D0RA05540A

Article  Google Scholar 

Bedoya K, Coltell O, Cabarcas F, Alzate JF (2019) Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia. Sci Total Environ. https://doi.org/10.1016/j.scitotenv.2018.08.119

Article  Google Scholar 

Belouhova M (2015) Management of the water treatment by biofilm communities in innovative detoxifying technologies

Bi S, Westerholm M, Hu W, Mahdy A, Dong T, Sun Y, Qiao W, Dong R (2021) The metabolic performance and microbial communities of anaerobic digestion of chicken manure under stressed ammonia condition: A case study of a 10-year successful biogas plant. Renew Energy. https://doi.org/10.1016/j.renene.2020.11.133

Article  Google Scholar 

Bitton G (2005) Wastewater microbiology, 3rd edn. John, Hoboken, New Jersey

Book  Google Scholar 

Burns RG, Dick RP (eds) (2002) Enzymes in the environment. CRC Press, Boca Raton. https://doi.org/10.1201/9780203904039

Cabezas A, de Araujo JC, Callejas C, Galès A, Hamelin J, Marone A, Sousa DZ, Trably E, Etchebehere C (2015) How to use molecular biology tools for the study of the anaerobic digestion process? Rev Environ Sci Bio/technol. https://doi.org/10.1007/s11157-015-9380-8

Article  Google Scholar 

Callaghan AV (2013) Metabolomic investigations of anaerobic hydrocarbon-impacted environments. Curr Opin Biotechnol. https://doi.org/10.1016/j.copbio.2012.08.012

Article  Google Scholar 

Calusinska M, Goux X, Fossépré M, Muller EEL, Wilmes P, Delfosse P (2018) A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems. Biotechnol Biofuels. https://doi.org/10.1186/s13068-018-1195-8

Article  Google Scholar 

Campanaro S, Treu L, Kougias PG, de Francisci D, Valle G, Angelidaki I (2016) Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. Biotechnol Biofuels. https://doi.org/10.1186/s13068-016-0441-1

Article  Google Scholar 

Campanaro S, Treu L, Kougias PG, Zhu X, Angelidaki I (2018) Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies. Sci Rep. https://doi.org/10.1038/s41598-018-20414-0

Article  Google Scholar 

Carabeo-Pérez A, Guerra-Rivera G, Ramos-Leal M, Jiménez-Hernández J (2019) Correction to: metagenomic approaches: effective tools for monitoring the structure and functionality of microbiomes in anaerobic digestion systems. Appl Microbiol Biotechnol. https://doi.org/10.1007/s00253-019-10137-1

Article  Google Scholar 

Cauchi M, Fowler DP, Walton C, Turner C, Waring RH, Ramsden DB, Hunter JO, Teale P, Cole JA, Bessant C (2015) Comparison of GC-MS, HPLC-MS and SIFT-MS in conjunction with multivariate classification for the diagnosis of Crohn’s disease in urine. Anal Methods. https://doi.org/10.1039/C5AY01322D

Article  Google Scholar 

Chen JL, Ortiz R, Steele TWJ, Stuckey DC (2014) Toxicants inhibiting anaerobic digestion: a review. Biotechnol Adv 32(8):1523–1534. https://doi.org/10.1016/j.biotechadv.2014.10.005

Article  CAS  Google Scholar 

Chung Y-C, Neethling JB (1988) ATP as a measure of anaerobic sludge digester activity. Water Pollut Control Federation 60(1):107–112

CAS  Google Scholar 

Crocetti G, Murto M, Björnsson L (2006) An update and optimisation of oligonucleotide probes targeting methanogenic Archaea for use in fluorescence in situ hybridisation (FISH). J Microbiol Methods. https://doi.org/10.1016/j.mimet.2005.07.007

Article  Google Scholar 

Daims H, Lücker S, Wagner M (2006) daime, a novel image analysis program for microbial ecology and biofilm research. Environ Microbiol. https://doi.org/10.1111/j.1462-2920.2005.00880.x

Article  Google Scholar 

Dar SA, Kleerebezem R, Stams AJM, Kuenen JG, Muyzer G (2008) Competition and coexistence of sulfate-reducing bacteria, acetogens and methanogens in a lab-scale anaerobic bioreactor as affected by changing substrate to sulfate ratio. Appl Microbiol Biotechnol. https://doi.org/10.1007/s00253-008-1391-8

Article  Google Scholar 

de Jonge N, Davidsson Å, la Cour Jansen J, Nielsen JL (2020) Characterisation of microbial communities for improved management of anaerobic digestion of food waste. Waste Manag. https://doi.org/10.1016/j.wasman.2020.07.047

Article  Google Scholar 

Delafontaine MJ, Naveau HP, Nyns EJ (1979) Fluorimetric monitoring of methanogenesis in anaerobic digestors. Biotechnol Lett. https://doi.org/10.1007/BF01398311

Article  Google Scholar 

DeVree BT, Steiner LM, Głazowska S, Ruhnow F, Herburger K, Persson S, Mravec J (2021) Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries. Biotechnol Biofuels. https://doi.org/10.1186/s13068-021-01922-0

Article  Google Scholar 

de Vrieze J, Ijaz UZ, Saunders AM, Theuerl S (2018) Terminal restriction fragment length polymorphism is an “old school” reliable technique for swift microbial community screening in anaerobic digestion. Sci Rep. https://doi.org/10.1038/s41598-018-34921-7

Article  Google Scholar 

de Vrieze J, Saunders AM, He Y, Fang J, Nielsen PH, Verstraete W, Boon N (2015) Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome. Water Res. https://doi.org/10.1016/j.watres.2015.02.025

Article  Google Scholar 

Dimkov R, Topalova Y, Schneider I (2017) Environmental biotechnology. PublishSciSet-Eco

Dinova N (2019) Strategies for functional control of the methanogenesis in key technologies for biogas production

Dinova N, Belouhova M, Schneider I, Rangelov J, Topalova Y (2018a) Control of biogas production process by enzymatic and fluorescent image analysis. Biotechnol Biotechnol Equip 32(2):366–375. https://doi.org/10.1080/13102818.2018.1425637

Article  CAS  Google Scholar 

Dinova N, Belouhova M, Schneider I, Topalova Y (2016) Functional control of the technologies for biogas production. Ecol Eng Environ Protect 1:52–64

Google Scholar 

Dinova N, Peneva K, Belouhova M, Rangelov J, Schneider I, Topalova Y (2018b) FISH analysis of microbial communities in a full-scale technology for biogas production. Eng Life Sci 18(12):914–923. https://doi.org/10.1002/elsc.201800041

Article  CAS  Google Scholar 

Dolinšek J, Lagkouvardos I, Wanek W, Wagner M, Daims H (2013) Interactions of nitrifying bacteria and heterotrophs: identification of a micavibrio-like putative predator of Nitrospira spp. Appl Environ Microbiol. https://doi.org/10.1128/AEM.03408-12

Article  Google Scholar 

Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI (2020) PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 38(6):685–688

Article  CAS  Google Scholar 

Duan H, He P, Shao L, Lü F (2021) Functional genome-centric view of the CO-driven anaerobic microbiome. ISME J. https://doi.org/10.1038/s41396-021-00983-1

Article  Google Scholar 

Dumont MG, Murrell JC (2005) Stable isotope probing — linking microbial identity to function. Nature Rev Microbiol. https://doi.org/10.1038/nrmicro1162

Article  Google Scholar 

Dumont MG, Pommerenke B, Casper P (2013) Using stable isotope probing to obtain a targeted metatranscriptome of aerobic methanotrophs in lake sediment. Environ Microbiol Rep. https://doi.org/10.1111/1758-2229.12078

Article  Google Scholar 

Dumont MG, Pommerenke B, Casper P, Conrad R (2011) DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ Microbiol. https://doi.org/10.1111/j.1462-2920.2010.02415.x

Article  Google Scholar 

European Commission (2021) Fit for 55 - Delivering the EU’s 2030 climate target on the way to climate neutrality. European Commission

Feng Q, Xiao Y, Li X, Xue Z, Fang F, Cao J, Oleyiblo JO, Hu Z (2016) Using the dehydrogenase activity for alert of activated sludge system under different copper concentrations. Desalin Water Treat. https://doi.org/10.1080/19443994.2015.1087339

Article  Google Scholar 

Fischer MA, Güllert S, Refai S, Künzel S, Deppenmeier U, Streit WR, Schmitz RA (2019) Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. Microb Biotechnol. https://doi.org/10.1111/1751-7915.13313

Article  Google Scholar 

Fischer SG, Lerman LS (1983) DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci. https://doi.org/10.1073/pnas.80.6.1579

Article  Google Scholar 

Fontana A, Patrone V, Puglisi E, Morelli L, Bassi D, Garuti M, Rossi L, Cappa F (2016) Effects of geographic area, feedstock, temperature, and operating time on microbial communities of six full-scale biogas plants. Bioresour Technol. https://doi.org/10.1016/j.biortech.2016.07.058

Article  Google Scholar 

Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S (2017) Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol. https://doi.org/10.3109/1040841X.2016.1169990

Article  Google Scholar 

Gabbita KV, Huang JYC (1984) Dehydrogenases activity of activated sludge. Toxicol Environ Chem 8:2–3. https://doi.org/10.1080/02772248409357048

Article  Google Scholar 

García-Timermans C, Props R, Zacchetti B, Sakarika M, Delvigne F, Boon N (2020) Raman spectroscopy-based measurements of single-cell phenotypic diversity in microbial populations. Msphere. https://doi.org/10.1128/mSphere.00806-20

Article  Google Scholar 

Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A (2021) Next generation sequencing approaches to evaluate water and wastewater quality. Water Res 194:116907

Article  CAS  Google Scholar 

Gasch C, Hildebrandt I, Rebbe F, Röske I (2013) Enzymatic monitoring and control of a two-phase batch digester leaching system with integrated anaerobic filter. Energy Sustain Soc. https://doi.org/10.1186/2192-0567-3-10

Article  Google Scholar 

Gerardi MH (2003) The microbiology of anaerobic digesters. Wiley, Hoboken. https://doi.org/10.1002/0471468967

Article  Google Scholar 

Gomes FM, Ramos IB, Wendt C, Girard-Dias W, de Souza W, Machado EA, Miranda K (2013) New insights into the in situ microscopic visualization and quantification of inorganic polyphosphate stores by 4’,6-diamidino-2-phenylindole (DAPI)-staining. Eur J Histochem. https://doi.org/10.4081/ejh.2013.e34

Article 

留言 (0)

沒有登入
gif