The Colne Estuary: A Long-Term Microbial Ecology Observatory

Advances in Ecological Research

Volumn 55, Issue , 2016, Pages 227-281

  Nedwell, D B ^a   Underwood, G J C ^a   McGenity, T J ^a   Whitby, C ^a   Dumbrell, A J ^a  

^a UNIVERSITY OF ESSEX   (United Kingdom)

Author keywords

Anammox; Biogeochemistry; Denitrification; Engineered nanoparticles; Hydrocarbon degradation; Hypernutrified; Methanogenesis; Microbial benthic communities; Microphytobenthos; Molecular microbiology; Nitrate reduction; Nitrification; Organic matter breakdown; Phytoplankton primary production; Saltmarshes; Sulphate reduction; Trace gas emissions

Indexed keywords

EID: 85010992253     PISSN: 00652504     EISSN: None     Source Type: Book Series    
DOI: 10.1016/bs.aecr.2016.08.004     Document Type: Chapter

References (136)

1. Acuña Alvarez, L., Exton, D.A., Suggett, D.J., Timmis, K.N., McGenity, T.J., Characterization of marine isoprene-degrading communities. Environ. Microbiol. 11 (2009), 3280–3291.
2. Agedah, E.C., Binalaiyifa, H.E., Ball, A.S., Nedwell, D.B., Sources, turnover and bioavailability of dissolved organic nitrogen (DON) in the Colne estuary, UK. Mar. Ecol. Prog. Ser. 382 (2009), 23–33.
3. Azni, S. bin Abd. Aziz, Nedwell, D.B., The nitrogen cycle of an East Coast, U.K., saltmarsh: I. Nitrogen assimilation during primary production; detrital mineralisation. Estuar. Coast. Shelf Sci. 22 (1986), 559–575.
4. Azni, S. bin Abd. Aziz, Nedwell, D.B., The nitrogen cycle of an East Coast, U.K. saltmarsh: II Nitrogen fixation, nitrification, tidal exchange. Estuar. Coast. Shelf Sci. 22 (1986), 689–704.
5. Balba, M.T., Nedwell, D.B., Microbial metabolism of acetate, propionate and butyrate in anoxic sediments from the Colne Point saltmarsh, Essex, U.K. J. Gen. Microbiol. 128 (1982), 1415–1422.
6. Banat, I.M., Lindström, E.B., Nedwell, D.B., Balba, M.T., Evidence for coexistence of two distinct functional groups of sulfate-reducing bacteria in salt marsh sediment. Appl. Environ. Microbiol. 42 (1981), 985–992.
7. Barnes, M.A., Turner, C.R., Jerde, C.L., Renshaw, M.A., Chadderton, W.L., Lodge, D.M., Environmental conditions influence eDNA persistence in aquatic systems. Environ. Sci. Technol. 48:2014 (2014), 1819–1827.
8. Barnett, A., Méléder, V., Blommaert, L., Lepetit, B., Gaudin, P., Vyverman, W., Sabbe, K., Dupuy, C., Lavaud, J., Growth form defines physiological photoprotective capacity in intertidal benthic diatoms. ISME J. 9 (2015), 32–45.
9. Beddow, J., Stolpe, B., Cole, P.A., Lead, J.R., Sapp, M.S., Lyons, B.P., McKew, B., Steinke, M., Benyahia, F., Colbeck, I., Whitby, C., Estuarine sediment hydrocarbon-degrading microbial communities demonstrate resilience to nanosilver. Int. J. Biodeter. Biodegr. 96 (2014), 206–215.
10. Beddow, J., Stolpe, B., Cole, P.A., Lead, J.R., Sapp, M., Lyons, B.P., Colbeck, I., Whitby, C., Nanosilver inhibits nitrification and reduces ammonia-oxidizing bacterial but not archaeal amoA gene abundance in estuarine sediments. Environ. Microbiol, 2016, 10.1111/1462-2920.13441.
11. Bellinger, B.J., Underwood, G.J.C., Ziegler, S.E., Gretz, M.R., Significance of diatom-derived polymers in carbon flow dynamics within estuarine biofilms determined through isotopic enrichment. Aquat. Microb. Ecol. 55 (2009), 169–187.
12. Benyoucef, I., Blandin, E., Lerouxel, A., Jesus, B., Rosa, P., Méléder, V., Launeau, P., Barillé, L., Microphytobenthos interannual variations in a north-European estuary (Loire estuary, France) detected by visible infrared multispectral remote sensing. Estuar. Coast. Shelf Sci. 136:2014 (2014), 43–52.
13. Bernhard, A.E., Donn, T., Giblin, A.E., Stahl, D.A., Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system. Environ. Microbiol. 7 (2005), 1289–1297.
14. Blanchard, G.F., Agion, T., Guarini, J.-M., Herlory, O., Richard, P., Analysis of the short-term dynamics of microphytobenthic biomass on intertidal mudflats. Kromkamp, J., (eds.), Functioning of Microphytobenthos in Estuaries: Proceedings of the Microphytobenthos Symposium, August 2003, 2006, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands, 85–97.
15. Bohmann, K., Evans, A., Gilbert, M.T.P., Carvalho, G.R., Creer, S., Knapp, M., Yu, D.W., de Bruyn, M., Environmental DNA for wildlife biology and biodiversity monitoring. Trends Ecol. Evol. 29 (2014), 358–367.
16. Braker, G., Fesefeldt, A., Witzel, K.P., Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl. Environ. Microbiol. 64 (1998), 3769–3775.
17. Caffrey, J.M., Bano, N., Kalanetra, K., Hollibaugh, J.T., Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with different histories of hypoxia. ISME J. 1 (2007), 660–662.
18. Casciotti, K.L., Ward, B.B., Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria. FEMS Microbiol. Ecol. 52 (2005), 197–205.
19. Charlson, R.J., Lovelock, J.E., Andreae, M.O., Warren, S.G., Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate. Nature 326 (1987), 655–661.
20. Chronoupolou, P.-M., Fahy, A., Coulon, F., Paissé, S., Goñi-Urriza, M.S., Peperzak, L., Acuña-Alvarez, L., McKew, B.A., Lawson, T., Timmis, K.N., Duran, R., Underwood, G.J.C., McGenity, T.J., Impact of a simulated oil spill on benthic phototrophs and nitrogen-fixing bacteria. Environ. Microbiol. 15 (2013), 241–252.
21. Cook, P., Veuger, B., Böer, S., Middelburg, J.J., Effect of nutrient availability on carbon and nitrogen incorporation and flows through benthic algae and bacteria in near-shore sandy sediment. Aquat. Microb. Ecol. 49 (2007), 165–180.
22. Coulon, F., Chronoupolou, P.-M., Fahy, A., Païssé, S., Goñi-Urriza, M.S., Peperzak, L., Acuña-Alvarez, L., McKew, B.A., Brussard, C., Underwood, G.J.C., Timmis, K.N., Duran, R., McGenity, T.J., Central role of dynamic tidal biofilms dominated by aerobic hydrocarbonoclastic bacteria and diatoms in the biodegradation of hydrocarbons in coastal mudflats. Appl. Environ. Microbiol. 78 (2012), 3638–3648.
23. Crombie, A.T., El Khawand, M., Rhodius, V.A., Fengler, K.A., Miller, M.C., Whited, G.M., McGenity, T.J., Murrell, J.C., Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle. Environ. Microbiol. 17 (2015), 3314–3329.
24. Deiner, K., Altermatt, F., Transport distance of invertebrate environmental DNA in a natural river. PLoS One, 9(2), 2014, e88786.
25. De Jonge, V.N., van Beusekom, J.E.E., Wind- and tide-induced resuspension of sediment microphytobenthos from the tidal flats in the Ems Estuary. Limnol. Oceanogr. 40:4 (1995), 766–778.
26. De Jonge, V.N., de Boer, W.F., de Jong, D.J., Brauer, V.S., Long-term mean annual microphytobenthos chlorophyll a variation correlates with air temperature. Mar. Ecol. Prog. Ser. 468 (2012), 43–56.
27. Dong, L.F., Thornton, D.C.O., Nedwell, D.B., Underwood, G.J.C., Denitrification in sediments of the River Colne estuary, England. Mar. Ecol. Prog. Ser. 73 (2000), 109–112.
28. Dong, L.F., Nedwell, D.B., Stott, A., Sources of nitrogen used for denitrification and nitrous oxide formation in sediments of the of the hypernutrified Colne, the nitrified Humber and the oligotrophic Conway estuaries, United Kingdom. Limnol. Oceanogr. 51 (2006), 545–557.
29. Dong, L.F., Smith, C.J., Papaspyrou, S., Stott, A., Osborn, A.M., Nedwell, D.B., Changes in benthic denitrification, nitrate ammonification, and Annamox process rates and nitrate and nitrite reductase gene abundances along an estuarine gradient (the Colne estuary, United Kingdom). Appl. Environ. Microbiol. 75 (2009), 3171–3179.
30. Eichmiller, J.J., Bajer, P.G., Sorensen, P.W., The relationship between the distribution of common carp and their environmental DNA in a small lake. PLoS One, 9, 2014, e112611.
31. Elliot, M., de Jonge, V.N., Burrell, K.L., Johnson, M.W., Phillips, G.L., Turner, T.M., Trophic status of the Ore/Ald, Deben, Stour and Colne estuaries: Report to the National Rivers Authority. 1994, University of Hull.
32. Elliott, M., McLusky, D.S., The need for definitions in understanding estuaries. Estuar. Coast. Shelf Sci. 55 (2002), 815–827.
33. Elliott, M., Whitfield, A.K., Potter, I.C., Blaber, S.J., Cyrus, D.P., Nordlie, N.G., Harrison, T.D., The guild approach to categorizing estuarine fish assemblages: a global review. Fish Fish. 8 (2007), 241–268.
34. Exton, D.A., Suggett, D.J., Steinke, M., McGenity, T.J., Spatial and temporal variability of biogenic isoprene emissions from a temperate estuary. Global Biogeochem. Cycles, 26, 2012, GB2012.
35. Exton, D.A., Suggett, D.J., McGenity, T.J., Steinke, M., Chlorophyll-normalized isoprene production in laboratory cultures of marine microalgae and implications for global models. Limnol. Oceanogr. 58 (2013), 1301–1311.
36. Exton, D.A., McGenity, T.J., Steinke, M., Smith, D.J., Suggett, D.J., Uncovering the volatile nature of tropical coastal marine ecosystems in a changing world. Glob. Chang. Biol. 21 (2015), 1383–1394.
37. Flindt, M.R., Pardal, M.A., Lillebo, A.I., Martins, I., Marques, J.C., Nutrient cycling and plant dynamics in estuaries: a brief review. Acta Oecol. 20 (1999), 237–248.
38. Foote, A.D., Thomsen, P.F., Sveegaard, S., Wahlberg, M., Kielgast, J., et al. Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS One, 7(8), 2012, e41781.
39. Forster, R.M., Creach, V., Sabbe, K., Vyverman, W., Stal, L.J., Biodiversity-ecosystem function relationship in microphytobenthic diatoms of the Westerschelde estuary. Mar. Ecol. Prog. Ser. 311 (2006), 192–201.
40. Gillanders, B.M., Using elemental chemistry of fish otoliths to determine connectivity between estuarine and coastal habitats. Estuar. Coast. Shelf Sci. 64 (2005), 45–67.
41. Goldberg, C.S., Sepulveda, A., Ray, A., Baumgardt, J., Waits, L.P., Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshw. Sci., 2013, 792–800.
42. Grangeré, K., Lefebvre, S., Blin, J.-L., Spatial and temporal dynamics of biotic and abiotic features of temperate coastal ecosystems as revealed by a combination of ecological indicators. Estuar. Coast. Shelf Sci. 108 (2012), 109–118.
43. Green, B.C., Smith, D.J., Grey, J., Underwood, G.J.C., High site fidelity and low site connectivity in temperate salt marsh fish populations: a stable isotope approach. Oecologia 168 (2012), 245–255.
44. Grobbellar, J.U., Modelling algal productivity in large outdoor cultures and waste treatment systems. Biomass 21 (1990), 279–314.
45. Guenther, A.B., Jiang, X., Heald, C.L., Sakulyanontvittaya, T., Duhl, T., Emmons, L.K., Wang, X., The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions. Geosci. Model Dev. 5 (2012), 1471–1492.
46. Hanlon, A.R.M., Bellinger, B., Haynes, K., Xiao, G., Hofmann, T.A., Gretz, M.R., Ball, A.S., Osborn, A.M., Underwood, G.J.C., Dynamics of EPS production and loss in an estuarine, diatom-dominated, microalgal biofilm over a tidal emersion immersion period. Limnol. Oceanogr. 51 (2006), 79–93.
47. Haynes, K., Hofmann, T.A., Smith, C.J., Ball, A.S., Underwood, G.J.C., Osborn, A.M., Diatom-derived carbohydrates as factors affecting bacterial community composition in estuarine sediments. Appl. Environ. Microbiol. 73 (2007), 6112–6124.
48. Hofmann, T., Hanlon, A.R.M., Taylor, J.D., Ball, A.S., Osborn, A.M., Underwood, G.J.C., Dynamics and compositional changes in extracellular carbohydrates in estuarine sediments during degradation. Mar. Ecol. Prog. Ser. 379 (2009), 45–58.
49. Howarth, R., Chan, F., Conley, D.J., Garnier, J., Doney, S.C., Marino, R., Billen, G., Coupled biogeochemical cycles: eutrophication and hypoxia in temperate estuaries and coastal marine ecosystems. Front. Ecol. Environ. 9 (2011), 18–26.
50. Humborg, C., Ittekkot, V., Coclasu, A., Bodunges, B.V., Effect of Danube River dam on Black Sea biogeochemistry and ecosystem structure. Nature 386 (1997), 385–388.
51. Hussey, A., The net primary production of an Essex saltmarsh, with particular reference to Puccinellia maritima. PhD thesis, 1980, University of Essex.
52. Hussey, A., Long, S.P., Seasonal changes in weight of above- and below-ground vegetation and dead plant material in a salt marsh at Colne Point, Essex. J. Ecol. 70 (1982), 757–771.
53. Jackson, M.C., Weyl, O.L.F., Altermatt, F., Durance, I., Friberg, N., Dumbrell, A.J., Piggott, J.J., Tiegs, S.D., Tockner, K., Lehmann, A., Narwani, A.J., Krug, C.B., Leadley, P.W., Woodward, G., Recommendations for the next generation of global freshwater biological monitoring tools. Adv. Ecol. Res. 55 (2016), 607–630.
54. Jørgensen, B.B., Mineralisation of organic matter in the sea bed: the role of sulphate reduction. Nature 296 (1982), 643–645.
55. Jørgensen, B.B., Okholm-Hansen, B., Emissions of biogenic sulphur gases from a Danish estuary. Atmos. Environ. 19 (1985), 1737–1749.
56. Juneau, P., Barnett, A., Meleder, V., Dupuy, C., Lavaud, J., Combined effect of high light and high salinity on the regulation of photosynthesis in three diatom species belonging to the main growth forms of intertidal flat inhabiting microphytobenthos. J. Exp. Mar. Biol. Ecol. 463 (2015), 95–104.
57. Justic, D., Rabelais, N.N., Turner, R.E., Dortch, Q., Changes in nutrient structure of river-dominated coastal waters: stoichiometric nutrient balance and its consequences. Estuar. Coast. Shelf Sci. 40 (1995), 339–356.
58. King, D., Nedwell, D.B., The influence of nitrate concentration upon the end-products of nitrate dissimilation by bacteria in anaerobic saltmarsh sediment. FEMS Microbiol. Ecol. 31 (1985), 23–28.
59. Kocum, E., Underwood, G.J.C., Nedwell, D.B., Simultaneous measurement of phytoplanktonic primary production, nutrient and light availability along a turbid, eutrophic UK east coast estuary (the Colne estuary). Mar. Ecol. Prog. Ser. 231 (2002), 1–12.
60. Kocum, E., Nedwell, D.B., Underwood, G.J.C., Regulation of phytoplankton primary production along a hypernutrified estuary. Mar. Ecol. Prog. Ser. 231 (2002), 13–22.
61. Konneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., Stahl, D.A., Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437 (2005), 543–546.
62. Kuenen, J.G., Robertson, L.A., Ecology of nitrification and denitrification. Cole, J.A., Ferguson, S.J., (eds.) The Nitrogen and Sulphur Cycles, 1987, Cambridge University Press, Cambridge, 162–218.
63. Li, J., Nedwell, D.B., Beddow, J., Dumbrell, A.J., McKew, B.A., Thorpe, E.L., Whitby, C., amoA gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not archaea dominate N cycling in the Colne estuary, United Kingdom. Appl. Environ. Microbiol. 81 (2015), 159–165.
64. Luisetti, T., Turner, R.K., Jickells, T., Andrews, J., Elliott, M., Schaafsma, M., et al. Coastal Zone Ecosystem Services: from science to values and decision making; a case study. Sci. Total Environ. 493 (2014), 682–693.
65. Maček, I., Vodnik, D., Pfanz, H., Low-Décarie, E., Dumbrell, A.J., Locally extreme environments as natural long-term experiments in ecology. Adv. Ecol. Res. 55 (2016), 283–324.
66. Mächler, E., Deiner, K., Steinmann, P., Altermatt, F., Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species. Freshw. Sci. 33 (2014), 1174–1183.
67. Martens-Habbena, W., Berube, P.M., Urakawa, H., de la Torre, J.R., Stahl, D.A., Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 46:1 (2009), 976–979.
68. McGenity, T.J., Hydrocarbon biodegradation in intertidal wetland sediments. Curr. Opin. Biotechnol. 27 (2014), 46–54.
69. McGenity, T.J., Oren, A., Hypersaline environments. Bell, E.M., (eds.) Life at Extremes: Environments, Organisms and Strategies for Survival, 2012, CAB International, Wallingford, UK, 402–437.
70. McKew, B.A., Taylor, J.D., McGenity, T.J., Underwood, G.J.C., Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting. ISME J. 5 (2011), 30–41.
71. McKew, B.A., Dumbrell, A., Taylor, J.D., McGenity, T.J., Underwood, G.J.C., Differences between aerobic and anaerobic degradation of microphytobenthic biofilm-derived organic matter within intertidal sediments. FEMS Microbiol. Ecol. 84 (2013), 495–509.
72. McMellor, S., Underwood, G.J.C., Water policy effectiveness: 30 years of change in the hypernutrified Colne estuary, England. Mar. Pollut. Bull. 81 (2014), 200–209.
73. Miles, A., Sundbäck, K., Diel variation in microphytobenthic productivity in areas of different tidal amplitude. Mar. Ecol. Prog. Ser. 205 (2000), 11–22.
74. Munson, M.A., Nedwell, D.B., Embley, T.M., Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl. Environ. Microbiol. 63 (1997), 4729–4733.
75. Nedwell, D.B., Distribution and pool sizes of microbially available carbon in sediment measured by a microbiological assay. FEMS Microbiol. Ecol. 45 (1987), 47–52.
76. Nedwell, D.B., Abram, J.W., Relative influence of temperature and electron donor and electron acceptor concentrations on bacterial sulphate reduction in saltmarsh sediment. Microb. Ecol. 5 (1979), 67–72.
77. Nedwell, D.B., Takii, S., Bacterial sulphate reduction in sediments of a European salt marsh: acid-volatile and tin-reducible products. Estuar. Coast. Shelf Sci. 26 (1988), 599–606.
78. Nedwell, D.B., Shabbeer, M.T., Harrison, R.M., Dimethyl sulphide in North Sea waters and sediments. Estuar. Coast. Shelf Sci. 39 (1994), 209–217.
79. Nedwell, D.B., Dong, L.F., Sage, A.S., Underwood, G.J.C., Variations of the nutrient loads to the mainland U.K. estuaries: correlation with catchment areas, urbanisation and coastal eutrophication. Estuar. Coast. Shelf Sci. 54 (2002), 951–970.
80. Nedwell, D.B., Embley, T.M., Purdy, K.J., Sulphate reduction, methanogenesis and phylogenetics of the sulphate reducing bacterial communities along an estuarine gradient. Aquat. Microb. Ecol. 37 (2004), 209–217.
81. Nielsen, L.P., Denitrification in sediment determined from nitrogen isotope pairing. FEMS Microbiol. Ecol. 86 (1992), 357–362.
82. Nixon, S.W., Coastal marine eutrophication: a definition, social causes and future concerns. Ophelia 41 (1995), 199–219.
83. Nogales, B., Timmis, K.N., Nedwell, D.B., Osborn, A.M., Detection and diversity of expressed denitrification genes in estuarine sediments after reverse-transcription-PCR amplification from mRNA. Appl. Environ. Microbiol. 68 (2002), 5017–5025.
84. Oakes, J.M., Eyre, B.D., Middelburg, J.J., Boschker, H.T.S., Composition, production, and loss of carbohydrates in subtropical shallow subtidal sandy sediments: rapid processing and long-term retention revealed by 13C-labeling. Limnol. Oceanogr. 55 (2010), 2126–2138.
85. Oakes, J.M., Eyre, B.D., Middelburg, J.J., Transformation and fate of microphytobenthos carbon in subtropical shallow subtidal sands: a 13C-labeling study. Limnol. Oceanogr. 57 (2012), 1846–1856.
86. Oakley, B.B., Carbonero, F., Dowd, S.E., Hawkins, R.J., Purdy, K.J., Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter. ISME J 6 (2012), 905–914.
87. Ogilvie, B., Nedwell, D.B., Harrison, R.M., Robinson, A., Sage, A., High nitrate, muddy estuaries as nitrogen sinks: the nitrogen budget of the River Colne estuary (United Kingdom). Mar. Ecol. Prog. Ser. 150 (1997), 217–228.
88. Orvain, F., Sauriau, P.-G., Sygut, A., Joassard, L., Le Hir, P., Interacting effects of Hydrobia ulvae bioturbation and microphytobenthos on the erodibility of mudflat sediments. Mar. Ecol. Prog. Ser. 278 (2004), 205–223.
89. O'Sullivan, L.A., Sass, A.M., Webster, G., Fry, J.C., Parkes, R.J., Weightman, A.J., Contrasting relationships between biogeochemistry and prokaryotic diversity depth profiles along an estuarine sediment gradient. FEMS Microbiol. Ecol. 85 (2013), 143–157.
90. Pacifico, F., Harrison, S.P., Jones, C.D., Sitch, S., Isoprene emissions and climate. Atmos. Environ. 43 (2009), 6121–6135.
91. Papaspyrou, S., Smith, C.J., Dong, L.F., Whitby, C., Dumbrell, A.J., Nedwell, D.B., Nitrate reduction functional genes and nitrate reduction potentials persist in deeper estuarine sediments. Why?. PLoS One 9:4 (2014), 1–13.
92. Peletier, H., Long-term changes in intertidal estuarine diatom assemblages related to reduced input of organic waste. Mar. Ecol. Prog. Ser. 137 (1996), 265–271.
93. Platell, M.E., Orr, P.A., Potter, I.C., Inter- and intraspecific partitioning of food resources by six large and abundant fish species in a seasonally open estuary. J. Fish Biol. 69 (2006), 243–262.
94. Pollard, D.A., Estuaries are valuable contributors to fisheries production. Aust. Fish. 40 (1981), 7–9.
95. Poole, J., Impact of engineered nanoparticles on aquatic microbial processes. PhD thesis, 2013, University of Essex, United Kingdom.
96. Prastka, K.E., Sanders, R., Jickells, T., Has the role of estuaries as sources or sinks of dissolved inorganic phosphate changed over time? Results of a Ks study. Mar. Pollut. Bull. 36 (1998), 718–728.
97. Purdy, K.J., Cresswell-Maynard, T.D., Nedwell, D.B., McGenity, T.J., Grant, W.D., Timmis, K.N., Embley, T.M., Isolation of haloarchaea that grow at low salinities. Environ. Microbiol. 6 (2004), 591–595.
98. Purdy, K.J., Munson, M.A., Embley, T.M., Nedwell, D.B., Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary. FEMS Microbiol. Ecol. 44 (2003), 361–371.
99. Raffaelli, D.G., Bullock, J.M., Cinderby, S., Durance, I., Emmett, B., Harris, J., Hicks, K., Oliver, T.H., Paterson, D., White, P.C.L., Big data and ecosystem research programmes. Adv. Ecol. Res. 51 (2014), 41–77.
100. Rees, H.C., Maddison, B.C., Middleditch, D.J., Patmore, K.J., Gough, R.M.C., The detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J. Appl. Ecol. 51 (2014), 1450–1459.
101. Richardson, D.J., Bacterial respiration: a flexible process for a changing environment. Microbiology 146 (2000), 551–571.
102. 2O and NOx gases to the atmosphere. PhD thesis, 1996, University of Essex.
103. 2O emission to the atmosphere: the estuary of the River Colne, Essex, UK. Mar. Ecol. Prog. Ser. 164 (1998), 59–71.
104. Rotthauwe, J.-H., Witzel, K.P., Liesack, W., The ammonia-monoxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidising populations. Appl. Environ. Microbiol. 63 (1997), 4704–4712.
105. Sanni, G.O., Coulon, F., McGenity, T.J., Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms. Environ. Sci. Pollut. Res. Int. 22 (2015), 15230–15247.
106. Scranton, M.I., Gaseous nitrogen compounds in the marine environment. Carpenter, E.J., Capone, D.G., (eds.) Nitrogen in the Marine Environment, 1983, Academic Press, New York, 37–64.
107. Senior, E., Linström, E.B., Banat, I.M., Nedwell, D.B., Sulfate reduction and methanogenesis in the sediment of a saltmarsh on the East Coast of the United Kingdom. Appl. Environ. Microbiol. 43 (1982), 987–996.
108. Skiba, U., Smith, K.A., Fowler, D., Nitrification and denitrification as sources of nitric oxide and nitrous oxide in a sandy loam soil. Soil Biol. Biochem. 25 (1993), 1527–1536.
109. Smith, C.J., Nedwell, D.B., Dong, L.F., Osborn, A.M., Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirs and nrefA), and their transcripts in estuarine sediments. Appl. Environ. Microbiol. 73 (2007), 3612–3622.
110. Smith, C.J., Dong, L.F., Wilson, J., Stott, A., Osborn, A.M., Nedwell, D.B., Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia, process rates and corresponding key functional genes along an estuarine nitrate gradient. Front. Microbiol. 5 (2015), 1–11, 10.3389/fmicb.2015.00542.
111. Spilmont, N., Seuront, L., Meziane, T., Welsh, D.T., There's more to the picture than meets the eye: sampling microphytobenthos in a heterogeneous environment. Estuar. Coast. Shelf Sci. 95 (2011), 470–476.
112. Steele, D., Franklin, D.J., Underwood, G.J.C., Protection of cells from salinity stress by extracellular polymeric substances (EPS) in diatom biofilms. Biofouling 30 (2014), 987–998.
113. Sutka, R.L., Ostrom, N.E., Ostrom, P.H., Breznak, J.A., Gandhi, H., Pitt, A.J., Li, F., Distinguishing nitrous oxide production from nitrification from denitrification on the basis of isotopomer abundances. Appl. Environ. Microbiol. 72 (2006), 638–644.
114. Taylor, J.D., McKew, B.A., Kuhl, A., McGenity, T.J., Underwood, G.J.C., Microphytobenthic extracellular polymeric substances (EPS) in intertidal sediments fuel both generalist and specialist EPS-degrading bacteria. Limnol. Oceanogr. 58 (2013), 1463–1480.
115. Thomsen, P.F., Kielgast, J., Iversen, L.L., et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21 (2012), 2565–2573.
116. Thornton, D.C.O., Underwood, G.J.C., Nedwell, D.B., Effect of illumination and emersion period on the exchange of ammonium across the sediment-water interface. Mar. Ecol. Prog. Ser. 184 (1999), 11–20.
117. Thornton, D.C.O., Dong, L.F., Underwood, G.J.C., Nedwell, D.B., Factors affecting microphytobenthic biomass, species composition and production in the Colne estuary (UK). Aquat. Microb. Ecol. 27 (2002), 285–300.
118. Thornton, D.C.O., Dong, L.F., Underwood, G.J.C., Nedwell, D.B., Sediment-water inorganic nutrient exchange and nitrogen budgets in the Colne estuary (UK). Mar. Ecol. Prog. Ser. 337 (2007), 63–77.
119. Throbäck, I.N., Enwall, K., Jarvis, A., Hallin, S., Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol. Ecol. 49 (2004), 401–417.
120. Trimmer, M., Nedwell, D.B., Sivyer, D.B., Malcolm, S.J., Seasonal benthic organic matter mineralisation measured by oxygen uptake and denitrification along a transect of the inner and outer River Thames estuary, UK. Mar. Ecol. Prog. Ser. 197 (2000), 103–119.
121. Ubertini, M., Lefebvre, S., Gangnery, A., Grangeré, K., Le Gendre, R., et al. Spatial variability of benthic-pelagic coupling in an estuary ecosystem: consequences for microphytobenthos resuspension phenomenon. PLoS One, 7(8), 2012, e44155, 10.1371/journal.pone.0044155.
122. Underwood, G.J.C., Kromkamp, J., Primary production by phytoplankton and microphytobenthos in estuaries. Adv. Ecol. Res. 29 (1999), 93–153.
123. Underwood, G.J.C., Paterson, D.M., Seasonal changes in diatom biomass, sediment stability and biogenic stabilisation in the Severn Estuary, UK. J. Mar. Biol. Assoc. U. K. 73 (1993), 871–887.
124. Underwood, G.J.C., Paterson, D.M., The importance of extracellular carbohydrate production by marine epipelic diatoms. Adv. Botan. Res. 40 (2003), 184–240.
125. Underwood, G.J.C., Provot, L., Determining the environmental preferences of four estuarine epipelic diatom taxa—growth across a range of salinity, nitrate and ammonium conditions. Eur. J. Phycol. 35 (2000), 173–182.
126. Underwood, G.J.C., Phillips, M., Saunders, K., Distribution of estuarine benthic diatom species along salinity and nutrient gradients. Eur. J. Phycol. 33 (1998), 173–183.
127. Underwood, G.J.C., Perkins, R.G., Consalvey, M., Hanlon, A.R.M., Oxborough, K., Baker, N.R., Paterson, D.M., Patterns in microphytobenthic primary productivity: species-specific variation in migratory rhythms and photosynthetic efficiency in mixed-species biofilms. Limnol. Oceanogr. 50 (2005), 755–767.
128. Vacher, C., Tamaddoni-Nezhad, A., Kamenova, S., Peyrard, N., Moalic, Y., Sabbadin, R., Schwaller, L., Chiquet, J., Smith, M.A., Vallance, J., Fievet, V., Jakuschkin, B., Bohan, D.A., Learning ecological networks from next-generation sequencing data. Adv. Ecol. Res. 54 (2016), 1–39.
129. Van Colen, C., Underwood, G.J.C., Serôdio, J., Paterson, D.M., Ecology of intertidal microbial biofilms: mechanisms, patterns and future research needs. J. Sea Res. 92 (2014), 2–5.
130. Van de Graaf, A.A., Mulder, A., de Bruijn, P., Jetten, M.S., Robertson, L.A., Kuenen, J.G., Anaerobic oxidation of ammonium is a biologically mediated process. Appl. Environ. Microbiol. 61 (1995), 1246–1251.
131. van der Wal, D., Wielemaker-van den Dool, A., Peter, M.J., Herman, P.M.J., Spatial synchrony in intertidal benthic algal biomass in temperate coastal and estuarine ecosystems. Ecosystems 13 (2010), 338–351.
132. 2 removal and the role of plant roots. Soil Biol. Biochem. 29 (1997), 1257–1267.
133. Webster, G., Sullivan, L.A., Meng, Y., Williams, A.S., Sass, A.M., Watkins, A.J., Parkes, R.J., Weightman, A.J., Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments. FEMS Microbiol. Ecol. 91 (2015), 1–18.
134. Weerman, E.J.P., Herman, P.M.J., van de Koppel, J., Top-down control inhibits spatial self-organization of a patterned landscape. Ecology 92 (2011), 487–495.
135. Woodward, G., Speirs, D.C., Hildrew, A.G., Quantification and resolution of a complex, size-structured food web. Adv. Ecol. Res. 46 (2005), 85–135.
136. Zumft, W.G., Cell biology and molecular basis of denitrification. Microbiol. Mol. Rev. 61 (1997), 533–616.