Applicability of API ZYM to capture seasonal and spatial variabilities in lake and river sediments

References

• Leach JH. Biota of Lake St. Clair: habitat evaluation and environmental assessment. Hydrobiologia. 1991;219:187–202. doi: 10.1007/BF00024755
   Web of Science ®Google Scholar
• USACE (United States Army Corps of Engineers). St. Clair River and Lake St. Clair Comprehensive Management Plan. U.S. Army Corps of Engineers. Detroit District, MI; 2004. 718 p.
   Google Scholar
• Fogarty LR. Bacteria and emerging chemical contaminants in the St. Clair River/ Lake St. Clair Basin, Michigan: U.S. Geological Survey Open-File Report 2007; 1083, 10.
   Google Scholar
• Oliver BG, Bourbonniere RA. Chlorinated contaminants in surficial sediments of Lakes Huron, St. Clair and Erie: implications regarding sources along the St. Clair and Detroit Rivers. J Great Lakes Res. 1985;11:366–372. doi: 10.1016/S0380-1330(85)71780-7
   Web of Science ®Google Scholar
• Tong Y, Lin G, Ke X, et al. Comparison of microbial community between two shallow freshwater lakes in middle Yangze basin, East China. Chemosphere. 2005;60:85–92. doi: 10.1016/j.chemosphere.2005.01.037
   PubMed Web of Science ®Google Scholar
• Jennerjahn TC. Biogeochemical response of tropical coastal systems to present and past environmental change. Earth-Sci Rev. 2012;114:19–41. doi: 10.1016/j.earscirev.2012.04.005
   Web of Science ®Google Scholar
• Allan JD. Stream ecology: structure and function of running waters. London: Chapman and Hall; 1995. 388 p.
   Google Scholar
• Tiquia SM. Metabolic diversity of the heterotrophic microorganisms and potential link to pollution of the Rouge River. Environ Pollut. 2010;158:1435–1443. doi: 10.1016/j.envpol.2009.12.035
   PubMed Web of Science ®Google Scholar
• Boivin MEY, Massieux B, Breuve AM, et al. Functional recovery of biofilm communities after copper exposure. Environ Pollut. 2006;140:239–246. doi: 10.1016/j.envpol.2005.07.014
   PubMed Web of Science ®Google Scholar
• Torsvik V, Vreas L, Thingstad TF. Prokaryotic diversity magnitude, dynamics, and controlling factors. Science. 2002;296:1064–1066. doi: 10.1126/science.1071698
   PubMed Web of Science ®Google Scholar
• Liu X, Tiquia SM, Holguin G, et al. Molecular diversity of denitrifying genes in continental margin sediments within the oxygen deficient zone of the Pacific Coast of Mexico. Appl Environ Microbiol. 2003;69:3549–3560. doi: 10.1128/AEM.69.6.3549-3560.2003
   PubMed Web of Science ®Google Scholar
• Tiquia SM, Masson SA, Devol AH. Vertical distribution of nitrite reductase (nirS) genes in continental margin sediments of the Gulf of Mexico. FEMS Microbiol Ecol. 2006;58:464–475. doi: 10.1111/j.1574-6941.2006.00173.x
   PubMed Web of Science ®Google Scholar
• Flood M, Frabutt D, Floyd D, et al. Ammonia-oxidizing bacteria and archaea in sediments of the Gulf of Mexico. Environ Technol. 2015;36:124–135. doi: 10.1080/09593330.2014.942385
   PubMed Web of Science ®Google Scholar
• Chrost RJ. Microbial enzymatic degradation and utilization of organic matter. In: Chrost R, Overbeck J, editor. Microbial ecology of Lake Plußsee. New York (NY): Springer-Verlag; 1994. p. 118–174.
   Google Scholar
• Findlay S, Hickey CW, Quinn JM. Microbial enzymatic response to catchment-scale variations in supply of dissolved organic carbon. New Zealand J Mar Freshwater Res. 1997;31:701–706. doi: 10.1080/00288330.1997.9516800
   Web of Science ®Google Scholar
• Keith SC, Arnosti C. Extracellular enzyme activity in a river-bay-shelf transect: variations in polysaccharide hydrolysis ratio with substrate and size class. Aqua Microb Ecol. 2001;24:243–253. doi: 10.3354/ame024243
   Web of Science ®Google Scholar
• Shiah FK, Chen TY, Gong C, et al. Differential coupling of bacterial and primary production in mesotrophic and oligotrophic systems of the East China Sea. Aquat Microb Ecol. 2001;23:273–282. doi: 10.3354/ame023273
   Web of Science ®Google Scholar
• Hoppe HG. Microbial extracellular enzyme activity: a new key parameter in aquatic ecology. In: Chrost RJ, editor. Microbial enzymes in aquatic environments. New York (NY): Springer-Verlag; 1991. p. 60–83.
   Google Scholar
• Meyer-Reil LA. Seasonal and spatial distribution of extracellular enzymatic activities and microbial incorporation of dissolved organic substrates in marine sediments. Appl Environ Microbiol. 1987;53:1748–1755.
   PubMed Web of Science ®Google Scholar
• Arnosti C. Microbial extracellular enzymes and their role in dissolved organic matter cycling. In: Sinsabaugh RL, editor. Aquatic ecosystems: interactivity of dissolved organic matter. San Diego (CA): Academic Press; 2003. p. 315–342.
   Google Scholar
• Weintraub SR, Wieder WR, Cleveland CC, et al. Organic matter inputs shift soil enzyme activity and allocation patterns in a wet tropical forest. Biochemistry. 2013;114:313–326.
   Google Scholar
• Bidochka MJ, Burke S, Ng L. Extracellular hydrolytic enzymes in fungal genus Verticulum: adaptation for pathogenesis. Can J Microbiol. 1999;45:856–864. doi: 10.1139/w99-085
   Web of Science ®Google Scholar
• Tiquia SM. Evolution of enzyme activities during manure composting. J Appl Microbiol. 2002;92:764–775. doi: 10.1046/j.1365-2672.2002.01582.x
   PubMed Web of Science ®Google Scholar
• Tiquia SM, Wan JHC, Tam NFY. Extracellular enzyme profiles during co-composting of poultry manure and yard trimmings. Process Biochem. 2001;36:813–820. doi: 10.1016/S0032-9592(00)00281-8
   Web of Science ®Google Scholar
• Tiquia SM, Wan HC, Tam NFY. Microbial population dynamics and enzyme activities during composting. Compost Sci Util. 2002;10:150–161. doi: 10.1080/1065657X.2002.10702075
   Web of Science ®Google Scholar
• Bonilla N, Vida C, Martínez-Alonso M, et al. Organic amendments to avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities. Appl Environ Microbiol. 2015;81:3405–3418. doi: 10.1128/AEM.03787-14
   PubMed Web of Science ®Google Scholar
• Martínez D, Molina MJ, Sánchez J, et al. API ZYM assay to evaluate enzyme fingerprinting and microbial functional diversity in relation to soil processes. Biol Fertil Soils. 2016;52:77–89. doi: 10.1007/s00374-015-1055-7
   Web of Science ®Google Scholar
• Palmisano AC, Sewab BS, Marusak DA. Hydrolytic enzyme activity in landfilled refuse. Appl Microbiol Biotechnol. 1993;38:828–832. doi: 10.1007/BF00167153
   Web of Science ®Google Scholar
• Palmisano AC, Marusak DA, Ritchie CJ, et al. A novel bioreactor simulation composting of municipal solid waste. J Microbiol Method. 1993;18:99–112. doi: 10.1016/0167-7012(93)90026-E
   Web of Science ®Google Scholar
• Tiquia SM. Extracellular hydrolytic enzyme activities of the heterotrophic microbial communities of the Rouge River: An approach to evaluate ecosystem response to urbanization. Microb Ecol. 2011;62:679–689. doi: 10.1007/s00248-011-9871-2
   PubMed Web of Science ®Google Scholar
• Zanardini E, Valle A, Gigliotti CJ, et al. Laboratory-scale trials of electrolytic treatment on industrial wastewaters: microbiological aspects. J Environ Sci Health A. 2002;37:1463–1481. doi: 10.1081/ESE-120013270
   Web of Science ®Google Scholar
• Parkinson D. Filamentous fungi. In: Weaver RW, Angle JS, Bottomley PS, editors. Methods of soil analysis Part 2. Microbiological and biochemical properties. Madison (WI): Soil Science Society of America; 1994. p. 329–350.
   Google Scholar
• Zuberer DA. Recovery and enumeration of viable bacteria. In: Weaver RW, Angle JS, Bottomley PS, editors. Methods of soil analysis Part 2. Microbiological and biochemical properties. Madison (WI): Soil Science Society of America; 1994. p. 119–144.
   Google Scholar
• Tiquia SM, Wan JHC, Tam NFY. Dynamics of yard trimmings composting as determined by dehydrogenase activity, ATP content, arginine ammonification, and nitrification potential. Process Biochem. 2002;37:1057–1065. doi: 10.1016/S0032-9592(01)00317-X
   Web of Science ®Google Scholar
• Lebart L, Morineau A, Warwick K. Multivariate descriptive statistical analysis. New York (NY): J. Wiley; 1984. 250 p.
   Google Scholar
• Tiquia SM, Schleibak M, Schlaff J, et al. Microbial community profiling and characterization of some heterotrophic bacterial isolates from river waters and shallow groundwater wells along the Rouge River, Southeast Michigan. Environ Technol. 2008;29:651–663. doi: 10.1080/09593330801986998
   PubMed Web of Science ®Google Scholar
• Burns A, Ryder DS. Potential for biofilms as biological indicators in Australian riverine systems. Ecol Man Rest. 2001;2:53–64. doi: 10.1046/j.1442-8903.2001.00069.x
   Google Scholar
• Rulík M, Spacil R. Extracellular enzyme activity within hyporheic sediments of a small lowland stream. Soil Biol Biochem. 2004;36:1653–1662. doi: 10.1016/j.soilbio.2004.07.005
   Web of Science ®Google Scholar
• Wilczek S, Fischer H, Pusch MT. Regulation and seasonal dynamics of extracellular enzyme activities in the sediments of a large lowland river. Microb Ecol. 2005;50:253–267. doi: 10.1007/s00248-004-0119-2
   PubMed Web of Science ®Google Scholar
• Munster U. Extracellular enzyme activity in eutrophic and polyhumic lakes. In: Chróst RJ, editor. Microbial enzymes in aquatic environments. New York (NY): Springer-Verlag; 1991. p. 96–122.
   Google Scholar
• Hill BH, Elonen CM, Jicha TM, et al. Sediment microbial enzyme activity as an indicator of nutrient limitation in great lakes coastal wetlands. Freshwater Biol. 2006;51:1670–1683. doi: 10.1111/j.1365-2427.2006.01606.x
   Web of Science ®Google Scholar
• Helisto P, Korpela T. Effects of detergents on activity of microbial lipases as measured by the paranitrophenyl alkanoate esters method. Enzyme Microb Technol. 1998;23:113–117. doi: 10.1016/S0141-0229(98)00024-6
   Web of Science ®Google Scholar
• Gajewski A, Kirschner AK, Velimirov B. Bacterial lipolytic activity in a hypertrophic dead arm of the river Danube in Vienna. Hydrobiologia. 1997;344:1–10. doi: 10.1023/A:1002933706785
   Web of Science ®Google Scholar
• Chróst RJ. Environmental control of the synthesis and activity of aquatic microbial ectoenzymes. In: Chróst RJ, editor. Microbial enzymes in aquatic environments. New York (NY): Springer-Verlag; 1991. p. 29–59.
   Google Scholar
• Francoeur SN, Wetzel RG. Regulation of periphytic leucine–aminopeptidase activity. Aquat Microb Ecol. 2003;31:249–258. doi: 10.3354/ame031249
   Web of Science ®Google Scholar
• Barman TE. Enzyme handbook. New York (NY): Springer-Verlag; 1969. 928 p.
   Google Scholar
• Cunha A, Almeida A, Coelho FJRC, Gomes NCM, Oliveira V, Santos AC. Bacterial extracellular enzyme activity in globally changing aquatic ecosystems. In: Mendez-Vilas A, editor. Current research, technology and education in applied microbiology and microbial biotechnology. Badajoz: Formatex Research Center; 2010. p. 124–135.
   Google Scholar
• Albers CS, Kattner G, Hagen W. The compositions of wax esters, triacylglycerols and phospholipids in Arctic and Antarctic copepods: evidence of energetic adaptations. Mar Chem. 1996;55:347–358. doi: 10.1016/S0304-4203(96)00059-X
   Web of Science ®Google Scholar
• Meyers PA, Ishiwatari R. The early diagenesis of organic matter in lacustrine sediments. In: Engel MH, Macko SA, editors. Organic geochemistry, principles and applications. New York (NY): Plenum Press; 1993. p. 185.
   Google Scholar
• Muri G, Wakeham SG, Pease TK, et al. Evaluation of lipid biomarkers as indicators of changes in organic matter delivery to sediments from Lake Planina, a remote mountain lake in NW Slovenia. Org Geochem. 2004;35:1083–1093. doi: 10.1016/j.orggeochem.2004.06.004
   Web of Science ®Google Scholar
• Rigo E, Rigoni RE, Lodea P, et al. Comparison of two lipases in the hydrolysis of oil and grease in wastewater of the swine meat industry. Ind Eng Chem Res. 2008;47:1760–1765. doi: 10.1021/ie0708834
   Web of Science ®Google Scholar
• Aluyor EO, Obahiagbon KO, Ori-jesu M. Biodegradation of vegetable oils: A review. Sci Res Essay. 2009;4:543–548.
   Web of Science ®Google Scholar
• Canuel EA, Martens CS. Seasonal variations in the sources and alteration of organic matter associated with recently deposited sediments. Org Geochem. 1993;20:563–577. doi: 10.1016/0146-6380(93)90024-6
   Web of Science ®Google Scholar
• Hernandez ME, Mead R, Peralba MC, et al. Origin and transport of n-alkane-2-ones in a subtropical estuary: potential biomarkers for seagrass-derived organic matter. Org Geochem. 2001;32:21–32. doi: 10.1016/S0146-6380(00)00157-1
   Web of Science ®Google Scholar
• Hoppe HG. Phosphatase activity in the sea. Hydrobiologia. 2003;493:187–200. doi: 10.1023/A:1025453918247
   Web of Science ®Google Scholar
• Marxsen J, Schmidt HH. Extracellular phosphatase activity in sediments of the Breitenbach, a central European mountain stream. Hydrobiologia. 1993;253:207–216. doi: 10.1007/BF00050739
   Web of Science ®Google Scholar
• Vidal M, Duarte CM, Agusti SM, et al. Alkaline phosphatase activities in the central Atlantic Ocean indicate large areas with phosphorus deficiency. Mar Ecol Progr Ser. 2003;262:43–53. doi: 10.3354/meps262043
   Web of Science ®Google Scholar
• Chróst R, Overbeck J. Kinetics of alkaline phosphatase activity and phosphorus availability for phytoplankton and bacterioplankton in Lake Pluβsee (North German eutrophic lake). Microbiol Ecol. 1987;13:229–248. doi: 10.1007/BF02025000
   Google Scholar
• Mudryk Z. Decomposition of organic and solubilization of inorganic phosphorus compounds by bacteria isolated from a marine sandy beach. Mar Biol. 2004;145:1227–1234. doi: 10.1007/s00227-004-1397-4
   Web of Science ®Google Scholar
• Zdanowski MK, Donachie SP. Bacteria in the sea-ice zone between Elephant Island and the South Orkneys during the Polish sea-ice zone expedition, (December 1988 to January 1989). Polar Biol. 1993;13:245–254. doi: 10.1007/BF00238760
   Web of Science ®Google Scholar
• Koch AL. The macroeconomics of bacterial growth. In: Fletcher M, Floodgate GD, editors. Bacteria in their natural environments. London: Academic Press; 1985. p. 1–42.
   Google Scholar
• Harder W, Dijkhuizen L. Physiological responses to nutrient limitation. Annual Rev Microbiol. 1983;37:1–23. doi: 10.1146/annurev.mi.37.100183.000245
   PubMed Web of Science ®Google Scholar
• Chróst RJ, Siuda W. Ecology of microbial enzymes in lake ecosystems. In: Burns RC, Dick RP, editors. Microbial enzymes in the environment activity, ecology, and applications. New York (NY): Marcel Dekker; 2002. p. 35–72.
   Google Scholar
• Taubea R, Ganzert L, Grossart HP, et al. Organic matter quality structures benthic fatty acid patterns and the abundance of fungi and bacteria in temperate lakes. Sci Tot Environ. 2018;610–611:469–481. doi: 10.1016/j.scitotenv.2017.07.256
   PubMed Web of Science ®Google Scholar
• Ruiz-Gonzalez C, Niño-García JP, Lapierre JF, et al. The quality of organic matter shapes the functional biogeography of bacterioplankton across boreal freshwater ecosystems. Glob Ecol Biogeogr. 2015;24:1487–1498. doi: 10.1111/geb.12356
   Web of Science ®Google Scholar
• Oest A, Alsaffar A, Fenner M, et al. Patterns of change in metabolic capabilities of sediment microbial communities in river and lake ecosystems. J Inter Microbiol. In press.
   Google Scholar