CIVIL ENGINEERING 365 ALL ABOUT CIVIL ENGINEERING


  • 1.

    Amesbury MJ, Gallego-Sala A, Loisel J. Peatlands as prolific carbon sinks. Nat Geosci. 2019;12:880–1.

    CAS 
    Article 

    Google Scholar
     

  • 2.

    Rydin H, Jeglum J. The biology of peatlands. 2nd ed. New York: Oxford University Press; 2013.

  • 3.

    Kremer C, Pettolino F, Bacic A, Drinnan A. Distribution of cell wall components in Sphagnum hyaline cells and in liverwort and hornwort elaters. Planta. 2004;219:1023–35.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 4.

    Theander O. Studies on Sphagnum peat. III. A quantitative study on the carbohydrate constituents of Sphagnum mosses and Sphagnum peat. Acta Chem Scand. 1954;8:989–1000.

    CAS 
    Article 

    Google Scholar
     

  • 5.

    Ballance S, Borsheim KY, Inngjerdingen K, Paulsen BS, Christensen BE. A re-examination and partial characterisation of polysaccharides released by mild acid hydrolysis from the chlorite-treated leaves of Sphagnum papillosum. Carbohydr Polym. 2007;67:104–15.

    CAS 
    Article 

    Google Scholar
     

  • 6.

    Painter TJ. Residues of D-lyxo-5-hexosulopyranuronic acid in Sphagnum holocellulose, and their role in cross-linking. Carbohydr Res. 1983;124:C18–C21.

    CAS 
    Article 

    Google Scholar
     

  • 7.

    Bartels D, Baumann A, Maeder M, Geske T, Heise EM, von Schwartzenberg K, et al. Evolution of plant cell wall: arabinogalactan-proteins from three moss genera show structural differences compared to seed plants. Carbohydr Polym. 2017;163:227–35.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 8.

    Woodcroft BJ, Singleton CM, Boyd JA, Evans PN, Emerson JB, Zayed AAF, et al. Genome-centric view of carbon processing in thawing permafrost. Nature. 2018;560:49–54.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 9.

    Ivanova AA, Wegner C-E, Kim Y, Liesack W, Dedysh SN. Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis. Mol Ecol. 2016;25:4818–35.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 10.

    Duddleston KN, Kinney MA, Kiene RP, Hines ME. Anaerobic microbial biogeochemistry in a northern bog: acetate as a dominant metabolic end product. Glob Biogeochem Cycles. 2002;16:11–1-11–9.

    Article 
    CAS 

    Google Scholar
     

  • 11.

    Ye R, Jin Q, Bohannan B, Keller JK, McAllister SA, Bridgham SD. pH controls over anaerobic carbon mineralization, the efficiency of methane production, and methanogenic pathways in peatlands across an ombrotrophic-minerotrophic gradient. Soil Biol Biochem. 2012;54:36–47.

    CAS 
    Article 

    Google Scholar
     

  • 12.

    van Beelen P, Wouterse MJ, Masselink MJ, Spijker J, Mesman M. The application of a simplified method to map the aerobic acetate mineralization rates at the groundwater table of the Netherlands. J Contam Hydrol. 2011;122:86–95.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 13.

    Conrad R. Importance of hydrogenotrophic, aceticlastic and methylotrophic methanogenesis for methane production in terrestrial, aquatic and other anoxic environments: a mini review. Pedosphere. 2020;30:25–39.

    Article 

    Google Scholar
     

  • 14.

    Walpen N, Getzinger GJ, Schroth MH, Sander M. Electron-donating phenolic and electron-accepting quinone moieties in peat dissolved organic matter: quantities and redox transformations in the context of peat biogeochemistry. Environ Sci Technol. 2018;52:5236–45.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 15.

    Dettling MD, Yavitt J, Zinder S. Control of organic carbon mineralization by alternative electron acceptors in four peatlands, central New York State, USA. Wetlands. 2006;26:917–27.

    Article 

    Google Scholar
     

  • 16.

    Keller JK, Bridgham SD. Pathways of anaerobic carbon cycling across an ombrotrophic-minerotrophic peatland gradient. Limnol Oceanogr. 2007;52:96–107.

    CAS 
    Article 

    Google Scholar
     

  • 17.

    Keller JK, Takagi KK. Solid-phase organic matter reduction regulates anaerobic decomposition in bog soil. Ecosphere. 2013;4:1–12.

    Article 

    Google Scholar
     

  • 18.

    Keller JK, Weisenhorn PB, Megonigal JP. Humic acids as electron acceptors in wetland decomposition. Soil Biol Biochem. 2009;41:1518–22.

    CAS 
    Article 

    Google Scholar
     

  • 19.

    Yavitt JB, Seidman-Zager M. Methanogenic conditions in northern peat soils. Geomicrobiol J. 2006;23:119–27.

    CAS 
    Article 

    Google Scholar
     

  • 20.

    He S, Lau MP, Linz AM, Roden EE, McMahon KD. Extracellular electron transfer may be an overlooked contribution to pelagic respiration in humic-rich freshwater lakes. mSphere. 2019;4:1–8.

    Article 

    Google Scholar
     

  • 21.

    Lovley DR, Coates JD, Blunt-Harris EL, Phillips EJ, Woodward JC. Humic substances as electron acceptors for microbial respiration. Nature. 1996;382:445–8.

    CAS 
    Article 

    Google Scholar
     

  • 22.

    Stams AJM, De Bok FAM, Plugge CM, Van Eekert MHA, Dolfing J, Schraa G. Exocellular electron transfer in anaerobic microbial communities. Environ Microbiol. 2006;8:371–82.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 23.

    Klupfel L, Piepenbrock A, Kappler A, Sander M. Humic substances as fully regenerable electron acceptors in recurrently anoxic environments. Nat Geosci. 2014;7:195–200.

    Article 
    CAS 

    Google Scholar
     

  • 24.

    Bräuer SL, Yavitt JB, Zinder SH. Methanogenesis in McLean Bog, an acidic peat bog in upstate New York: stimulation by H2/CO2 in the presence of rifampicin, or by low concentrations of acetate. Geomicrobiol J. 2004;21:433–43.

    Article 
    CAS 

    Google Scholar
     

  • 25.

    Cadillo-Quiroz H, Brauer S, Yashiro E, Sun C, Yavitt J, Zinder S. Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. Environ Microbiol. 2006;8:1428–40.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 26.

    Kotsyurbenko O, Chin K, Glagolev M, Stubner S, Simankova M, Nozhevnikova A, et al. Acetoclastic and hydrogenotrophic methane production and methanogenic populations in an acidic West-Siberian pear bog. Environ Microbiol. 2004;6:1159–73.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 27.

    Lai DYF. Methane dynamics in northern peatlands: a review. Pedosphere. 2009;19:409–21.

    CAS 
    Article 

    Google Scholar
     

  • 28.

    Xu XF, Elias DA, Graham DE, Phelps TJ, Carroll SL, Wullschleger SD, et al. A microbial functional group-based module for simulating methane production and consumption: application to an inbucated permafrost soil. J Geophys Res Biogeosci. 2015;120:1315–33.

    CAS 
    Article 

    Google Scholar
     

  • 29.

    Chen I-MA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 2017;45:D507–16.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 30.

    Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformat. 2008;9:559.

    Article 
    CAS 

    Google Scholar
     

  • 31.

    Langfelder P, Horvath S. Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol. 2007;1:54.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 32.

    Sun CL, Brauer SL, Cadillo-Quiroz H, Zinder SH, Yavitt JB. Seasonal changes in methanogenesis and methanogenic community in three peatlands, New York State. Front Microbiol. 2012;3:81.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 33.

    Osvald H. Vegetation and stratigraphy of peatlands in North America. Uppsala: Acta Universitatis Upsaliensis; 1970.

  • 34.

    Pepe-Ranney C, Campbell AN, Koechli CN, Berthrong S, Buckley DH. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil. Front Microbiol. 2016;7:703.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 35.

    Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 36.

    Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17:132.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 37.

    Kang D, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 38.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 39.

    Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 40.

    Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun. 2013;4:2304.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 41.

    Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12:59.

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • 42.

    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 43.

    Rodriguez-R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative substractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ Microbiol. 2020;22:3394–412.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 44.

    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 45.

    Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 46.

    Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr. 2016;4:e1900v1.


    Google Scholar
     

  • 47.

    Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015;16:51.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 48.

    Zalman C, Keller JK, Tfaily M, Kolton M, Pfeifer-Meister L, Wilson RM, et al. Small differences in ombrotrophy control regional-scale variation in methane cycling among Sphagnum-dominated peatlands. Biogeochemistry. 2018;139:155–77.

    CAS 
    Article 

    Google Scholar
     

  • 49.

    Williams CJ, Yavitt JB. Botanical composition of peat and degree of peat decomposition in three temperate peatlands. Ecoscience. 2003;10:85–95.

    Article 

    Google Scholar
     

  • 50.

    Dedysh SN. Cultivating uncultured bacteria from northern wetlands: knowledge gained and remaining gaps. Front Microbiol. 2011;2:184.

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 51.

    Hattori S. Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes Environ. 2008;23:118–27.

    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 52.

    Hines ME, Duddleson KN, Kiene RP. Carbon flow to acetate and C1 compounds in northern wetlands. Geophys Res Lett. 2001;28:4251–4.

    CAS 
    Article 

    Google Scholar
     

  • 53.

    Karakashev D, Batstone DJ, Trably E, Angelidaki I. Acetate oxidation is the dominant methanogenic pathway from acetate in the absence of Methanosaetaceae. Appl Environ Microbiol. 2006;72:5138–41.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 54.

    Cervantes FJ, van der Velde S, Lettinga G, Field JA. Competition between methanogenesis and quinone respiration for ecologically important substrates in anaerobic consortia. FEMS Microbiol Ecol. 2000;34:161–71.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 55.

    Cervantes FJ, Gutierrez CH, Lopez KY, Estrada-Alvarado MI, Meza-Escalante AC, Texier AC, et al. Contribution of quinone-reducing microorganisms to the anaerobic biodegradation of organic compounds under different redox conditions. Biodegradation. 2008;19:235–46.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 56.

    Lokshina LY, Vavilin VA, Kettunen RH, Rintala JA, Holliger C, Nozhevnikova AN. Evaluation of kinetic coefficients using integrated monod and haldane models for low-temperature acetoclastic methanogenesis. Water Res. 2001;35:2913–22.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 57.

    Kotsyurbenko OR, Friedrich MW, Simankova MV, Nozhevnikova AN, Golyshin PN, Timmis KN, et al. Shift from acetoclastic to H2-dependent methanogenesis in a West Siberain peat bog at low pH values and isolation of an acidophilic Methanobacterium strain. Appl Environ Microbiol. 2007;73:2344–8.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 58.

    Schmidt O, Hink L, Horn M, Drake H. Peat: home to novel syntrophic species that feed acetate- and hydrogen-scavenging methanogens. ISME J. 2016;10:1954–66.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 59.

    Wolfe AJ. The acetate switch. Microbiol Mol Biol Rev. 2005;69:12–50.

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 60.

    Starai VJ, Escalante-Semerena JC. Acetyl-coenzyme A synthetase (AMP forming). Cell Mol Life Sci. 2004;61:2020–30.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 61.

    Pankratov TA, Dedysh SN, Zavarzin GA. The leading role of Actinobacteria in aerobic cellulose degradation in Sphagnum peat bogs. Dokl Biol Sci. 2006;410:428–30.

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 62.

    Mannisto M, Ganzert L, Tjirola M, Haggblom MM, Stark S. Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil? Soil Biol Biochem. 2016;96:216–28.

    CAS 
    Article 

    Google Scholar
     

  • 63.

    Kang H, Kwon MJ, Kim S, Lee S, Jones TG, Johncock AC, et al. Biologically driven DOC release from peatlands during recovery from acidification. Nat Commun. 2018;9:3807.

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 64.

    Dedysh SN, Dunfield PF. Beijerinckiaceae. In: Whitman WB, editor. Bergey’s manual of systematics of archaea and bacteria. Hoboken, NJ: John Wiley & Sons, Inc.; 2016. p. 1–4.



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