Recommendations for the Next Generation of Global Freshwater Biological Monitoring Tools

Advances in Ecological Research

Volumn 55, Issue , 2016, Pages 615-636

  Jackson, M C ^a,b   Weyl, O L F ^c   Altermatt, F ^d,e   Durance, I ^f   Friberg, N ^g,h   Dumbrell, A J ⁱ   Piggott, J J ^j,k   Tiegs, S D ^l   Tockner, K ^m,n   Krug, C B ^o   Leadley, P W ^o   Woodward, G ^b  

^a UNIVERSITY OF PRETORIA   (South Africa)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c SOUTH AFRICAN INSTITUTE FOR AQUATIC BIODIVERSITY   (South Africa)

^d SWISS FEDERAL INSTITUTE OF AQUATIC SCIENCE AND TECHNOLOGY   (Switzerland)

^e UNIVERSITY OF ZURICH   (Switzerland)

^f CARDIFF UNIVERSITY   (United Kingdom)

^g NORWEGIAN INSTITUTE FOR WATER RESEARCH   (Norway)

^h UNIVERSITY OF LEEDS   (United Kingdom)

ⁱ UNIVERSITY OF ESSEX   (United Kingdom)

^j UNIVERSITY OF OTAGO   (New Zealand)

^k KYOTO UNIVERSITY   (Japan)

^l OAKLAND UNIVERSITY   (United States)

^m LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES   (Germany)

ⁿ FREIE UNIVERSITÄT BERLIN   (Germany)

^o UNIVERSITÉ PARIS SUD   (France)

more..

Author keywords

Ecological networks; eDNA; Global biomonitoring; IPBES; Multiple stressors; Next generation sequencing; Remote sensing

Indexed keywords

EID: 84995616644     PISSN: 00652504     EISSN: None     Source Type: Book Series    
DOI: 10.1016/bs.aecr.2016.08.008     Document Type: Chapter

References (90)

1. Allan, J.D., Abell, R., Hogan, Z.E.B., Revenga, C., Taylor, B.W., Welcomme, R.L., Winemiller, K., Overfishing of inland waters. Bioscience 55 (2005), 1041–1051.
2. Altermatt, F., Seymour, M., Martinez, N., River network properties shape α-diversity and community similarity patterns of aquatic insect communities across major drainage basins. J. Biogeogr. 40 (2013), 2249–2260.
3. Baird, D.J., Hajibabaei, M., Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Mol. Ecol. 21 (2012), 2039–2044.
4. Bartley, D.M., De Graaf, G.J., Valbo-Jørgensen, J., Marmulla, G., Inland capture fisheries: status and data issues. Fish. Manag. Ecol. 22 (2015), 71–77.
5. Beche, L.A., McElravy, E.P., Resh, V.H., Long-term seasonal variation in the biological traits of benthic macroinvertebrates in two Mediterranean-climate streams in California, USA. Freshw. Biol. 51 (2006), 56–75.
6. Bellard, C., Bertelsmeier, C., Leadley, P., Thuiller, W., Courchamp, F., Impacts of climate change on the future of biodiversity. Ecol. Lett. 15 (2012), 365–377.
7. Boersma, K.S., Dee, L.E., Miller, S.J., Bogan, M.T., Lytle, D.A., Gitelman, A.I., Linking multidimensional functional diversity to quantitative methods: a graphical hypothesis-evaluation framework. Ecology 97 (2016), 583–593.
8. 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.
9. Brooks, E.G.E., Holland, R.A., Darwall, W.R.T., Eigenbrod, F., Global evidence of positive impacts of freshwater biodiversity on fishery yields. Glob. Ecol. Biogeogr. 25 (2016), 553–562.
10. Brummett, R.E., Beveridge, M., Cowx, I.G., Functional aquatic ecosystems, inland fisheries and the Millennium Development Goals. Fish Fish. 14 (2013), 312–324.
11. Calizza, E., Costantini, M.L., Rossi, L., Effect of multiple disturbances on food web vulnerability to biodiversity loss in detritus-based systems. Ecosphere 6 (2015), 1–20.
12. Charvet, S., Statzner, B., Usseglio-Polatera, P., Dumont, B., Traits of benthic macroinvertebrates in semi-natural French streams: an initial application to biomonitoring in Europe. Freshw. Biol. 43 (2000), 277–296.
13. Chauvet, E., Ferreira, V., Giller, P.S., Mckie, B.G., Tiegs, S.D., Woodward, G., et al. Litter decomposition as an indicator of stream ecosystem functioning at local-to-continental scales: insights from the European RivFunction Project. Adv. Ecol. Res. 55 (2016), 99–182.
14. Coll, M., Shannon, L.J., Kleisner, K.M., Juan-Jordá, M.J., Bundy, A., Akoglu, A.G., Banaru, D., Boldt, J.L., Borges, M.F., Cook, A., Diallo, I., Ecological indicators to capture the effects of fishing on biodiversity and conservation status of marine ecosystems. Ecol. Indic. 60 (2016), 947–962.
15. Costello, M.J., Claus, S., Dekeyzer, S., Vandepitte, L., Tuama, E.O., Lear, D., Tyler-Walters, H., Biological and ecological traits of marine species. PeerJ, 3, 2015, e1201, 10.7717/peerj.1201.
16. Crain, C.M., Kroeker, K., Halpern, B.S., Interactive and cumulative effects of multiple human stressors in marine systems. Ecol. Lett. 11 (2008), 1304–1315.
17. Crowl, T.A., McDowell, W.H., Covich, A.P., Johnson, S.L., Freshwater shrimp effects on detrital processing and nutrients in a tropical headwater stream. Ecology 82 (2001), 775–783.
18. Deiner, K., Altermatt, F., Transport distance of invertebrate environmental DNA in a natural river. PLoS One, 9, 2014, e88786.
19. Demars, B.O.L., Kemp, J.L., Friberg, N., Usseglio-Polatera, P., Harper, D.M., Linking biotopes to invertebrates in rivers: biological traits, taxonomic composition and diversity. Ecol. Indic. 23 (2012), 301–311.
20. Devred, E., Turpie, K., Moses, W., Klemas, V., Moisan, T., Babin, M., et al. Future retrievals of water column bio-optical properties using the hyperspectral infrared imager (HyspIRI). Remote Sens. 5 (2013), 6812–6837.
21. Dickens, C.W., Graham, P.M., The South African Scoring System (SASS) version 5 rapid bioassessment method for rivers. Afr. J. Aquat. Sci. 27 (2002), 1–10.
22. Doledec, S., Statzner, B., Bournard, M., Species traits for future biomonitoring across ecoregions: patterns along a human-impacted river. Freshw. Biol. 42 (1999), 737–758.
23. Domisch, S., Amatulli, G., Jetz, W., Near-global freshwater-specific environmental variables for biodiversity analyses in 1 km resolution. Sci. Data, 2, 2015, 150073.
24. Dudgeon, D., Arthington, A.H., Gessner, M.O., Kawabata, Z., Knowler, D.J., Lévêque, C., Naiman, R.J., et al. Freshwater biodiversity: importance, threats, status and conservation challenges. Biol. Rev. 81 (2006), 163–182.
25. Durance, I., Bruford, M.W., Chalmers, R., Chappell, N.A., Christie, M., Cosby, B.J., Noble, D., Ormerod, S.J., Prosser, H., Weightman, A., Woodward, G., The challenges of linking ecosystem services to biodiversity: lessons from a large-scale freshwater study. Adv. Ecol. Res. 54 (2016), 87–134.
26. FAO, FishStat Plus: universal software for fishery statistical time series. 2015, Data and Statistics Unit, FAO, Rome http://www.fao.org/fishery/statistics/software/fishstat/en.
27. Follett, R., Strezov, V., An analysis of citizen science based research: usage and publication patterns. PLoS One, 10, 2015, e0143687.
28. Friberg, N., Bonada, N., Bradley, D.C., Dunbar, M.J., Edwards, F.K., Grey, J., Biomonitoring of human impacts in freshwater ecosystems: the good, the bad and the ugly. Adv. Ecol. Res. 44 (2011), 1–68.
29. Garibaldi, L., The FAO global capture production database: a six-decade effort to catch the trend. Mar. Policy 36 (2012), 760–768.
30. Global Biodiversity Outlook 4, A mid-term assessment of progress towards the implementation of the strategic plan for biodiversity 2011–2020. 2014, Secretariat of the CBD, Montréal, Canada Available at https://www.cbd.int/gbo/gbo4/publication/gbo4-en.pdf.
31. Gray, C., Baird, D.J., Baumgartner, S., Jacob, U., Jenkins, G.B., O'Gorman, E.J., Lu, X., Ma, A., Pocock, M.J., Schuwirth, N., Thompson, M., FORUM: ecological networks: the missing links in biomonitoring science. J. Appl. Ecol. 51 (2014), 1444–1449.
32. Gray, C., Hildrew, A., Lu, X., Ma, A., McElroy, D., Monteith, D., et al. Recovery and nonrecovery of freshwater food webs from the effects of acidification. Adv. Ecol. Res. 55 (2016), 475–534.
33. Griffiths, N.A., Tiegs, S.D., Organic-matter decomposition along a temperature gradient in a forested headwater stream. Freshw. Sci. 35 (2016), 518–533.
34. Gurnell, A.M., Downward, S.R., Jones, R., Channel planform change on the River Dee meanders, 1876–1992. Regul. Rivers Res. Manag. 9 (1994), 187–204.
35. Hestir, E., Brando, V.E., Bresciani, M., Giardino, C., Matta, E., Villa, P., Dekker, A., Measuring freshwater aquatic ecosystems: the need for a hyperspectral global mapping satellite mission. Remote Sens. Environ. 167 (2015), 181–195.
36. Hladyz, S., Åbjörnsson, K., Giller, P.S., Woodward, G., Impacts of an aggressive riparian invader on community structure and ecosystem functioning in stream food webs. J. Appl. Ecol. 48 (2011), 443–452.
37. Hoffmann, A., Penner, J., Vohland, K., Cramer, W., Doubleday, R., Henle, K., Kõljalg, U., Kühn, I., Kunin, W., Negro, J.J., Penev, L., The need for an integrated biodiversity policy support process—building the European contribution to a global Biodiversity Observation Network (EU BON). Nat. Conserv., 6, 2014, 49.
38. Huddart, J.E., Thompson, M.S., Woodward, G., Brooks, S.J., Citizen science: from detecting pollution to evaluating ecological restoration. WIREs Water 3 (2016), 287–300.
39. Jackson, M.C., Loewen, C.J., Vinebrooke, R.D., Chimimba, C.T., Net effects of multiple stressors in freshwater ecosystems: a meta-analysis. Glob. Chang. Biol. 22 (2016), 180–189.
40. Jenkins, G.B., Woodward, G., Hildrew, A.G., Long-term amelioration of acidity accelerates decomposition in headwater streams. Glob. Chang. Biol. 19 (2013), 1100–1106.
41. Kaelin, K., Altermatt, F., Landscape-level predictions of diversity in river networks reveal opposing patterns for different groups of macroinvertebrates. Aquat. Ecol. 50 (2016), 283–295.
42. Kidwell, S.M., Biology in the anthropocene: challenges and insights from young fossil records. Proc. Natl. Acad. Sci. U.S.A. 112 (2015), 4922–4929.
43. Kokeš, J., Zahrádková, S., Němejcová, D., Hodovský, J., Jarkovský, J., Soldán, T., The PERLA system in the Czech Republic: a multivariate approach for assessing the ecological status of running waters. The Ecological Status of European Rivers: Evaluation and Intercalibration of Assessment Methods, 2006, Springer, Netherlands, 343–354.
44. Lansdown, K., McKew, B.A., Whitby, C., Heppell, C.M., Dumbrell, A.J., Binley, A., Olde, L., Trimmer, M., Importance and controls of anaerobic ammonium oxidation influenced by riverbed geology. Nat. Geosci. 9 (2016), 357–360.
45. Lee, B.S., McGwire, K.C., Fritsen, C.H., Identification and quantification of aquatic vegetation with hyperspectral remote sensing in western Nevada rivers, USA. Int. J. Remote Sens. 32 (2011), 9093–9117.
46. Legleiter, C.J., Overstreet, B.T., Retrieving river attributes from remotely sensed data: an experimental evaluation based on field spectroscopy at the outdoor stream lab. River Res. Appl. 30 (2014), 671–684.
47. 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 (AOB) not archaea (AOA) dominate N cycling in the Colne estuary, UK. Appl. Environ. Microbiol. 81 (2015), 159–165.
48. Lodge, D.M., Turner, C.R., Jerde, C.L., Barnes, M.A., Chadderton, L., Egan, S.P., Feder, J.L., Mahon, A.R., Pfrender, M.E., Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol. Ecol. 21 (2012), 2555–2558.
49. Mächler, E., Deiner, K., Spahn, F., Altermatt, F., Fishing in the water: effect of sampled water volume on environmental DNA-based detection of macroinvertebrates. Environ. Sci. Technol. 50 (2016), 305–312.
50. Matthews, M.W., A current review of empirical procedures of remote sensing in inland and near-coastal transitional waters. Int. J. Remote Sens. 32 (2011), 6855–6899.
51. Mcgill, B.J., Enquist, B.J., Weiher, E., Westoby, M., Rebuilding community ecology from functional traits. Trends Ecol. Evol. 21 (2006), 178–185.
52. Menezes, S., Baird, D.J., Soares, A., Beyond taxonomy: a review of macroinvertebrate trait-based community descriptors as tools for freshwater biomonitoring. J. Appl. Ecol. 47 (2010), 711–719.
53. Nedwell, D.B., Underwood, G.J.C., McGenity, T.J., Whitby, C., Dumbrell, A.J., The Colne Estuary: a long-term microbial ecology observatory. Adv. Ecol. Res. 55 (2016), 225–281.
54. Nicholson, E., Collen, B., Barausse, A., Blanchard, J.L., Costelloe, B.T., Sullivan, K.M., Underwood, F.M., Burn, R.W., Fritz, S., Jones, J.P., McRae, L., Making robust policy decisions using global biodiversity indicators. PLoS One, 7, 2012, e41128.
55. O'Gorman, E.J., Fitch, J.E., Crowe, T.P., Multiple anthropogenic stressors and the structural properties of food webs. Ecology 93 (2012), 441–448.
56. Pajares, G., Overview and current status of remote sensing applications based on unmanned aerial vehicles (UAVs). Photogramm. Eng. Remote. Sens. 81 (2015), 281–330.
57. 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, 2014, e94111.
58. Pauly, D., Froese, R., Comments on FAO's state of fisheries and aquaculture, or ‘SOFIA 2010’. Mar. Policy 36 (2012), 746–752.
59. Pereira, H.M., Ferrier, S., Walters, M., Geller, G.N., Jongman, R.H.G., Scholes, R.J., Bruford, M.W., Brummitt, N., Butchart, S.H.M., Cardoso, A.C., Coops, N.C., Essential biodiversity variables. Science 339 (2013), 277–278.
60. Perkins, D.M., Bailey, R.A., Dossena, M., Gamfeldt, L., Reiss, J., Trimmer, M., Woodward, G., Higher biodiversity is required to sustain multiple ecosystem processes across temperature regimes. Glob. Chang. Biol. 21 (2015), 396–406.
61. Piggott, J.J., Salis, R.K., Lear, G., Townsend, C.R., Matthaei, C.D., Climate warming and agricultural stressors interact to determine stream periphyton community composition. Glob. Chang. Biol. 21 (2015), 206–222.
62. Piggott, J.J., Townsend, C.R., Matthaei, C.D., Reconceptualizing synergism and antagonism among multiple stressors. Ecol. Evol. 5 (2015), 1538–1547.
63. QUINTESSENCE Consortium, Networking our way to better ecosystem service provision. Trends Ecol. Evol. 31 (2016), 105–115.
64. Rabeni, C.F., Doisy, K.E., Zweig, L.D., Stream invertebrate community functional responses to deposited sediment. Aquat. Sci. 67 (2005), 395–402.
65. Raffaelli, D., Bullock, J.M., Cinderby, S., Durance, I., Emmett, B., Harris, J., Hicks, K., Oliver, T.H., Patersonk, D., White, P.C., Big data and ecosystem research programmes. Adv. Ecol. Res. 51 (2014), 41–77.
66. Rawlence, N.J., Lowe, D.J., Wood, J.R., Young, J.M., Churchman, G., Huang, Y.T., Cooper, A., Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects. J. Quat. Sci. 29 (2014), 610–626.
67. Rees, H.C., Maddison, B.C., Middleditch, D.J., Patmore, J.R., Gough, K.C., REVIEW: 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.
68. Revenga, C., Campbell, I., Abell, R., De Villiers, P., Bryer, M., Prospects for monitoring freshwater ecosystems towards the 2010 targets. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360 (2005), 397–413.
69. Salzburger, W., Mack, T., Verheyen, E., Meyer, A., Out of Tanganyika: genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes. BMC Evol. Biol., 5, 2005, 17.
70. Scholes, R.J., Biggs, R., A biodiversity intactness index. Nature 434 (2005), 45–49.
71. Seymour, M., Deiner, K., Altermatt, F., Scale and scope matter when explaining varying patterns of community diversity in riverine metacommunities. Basic Appl. Ecol. 17 (2016), 134–144.
72. Silvertown, J., A new dawn for citizen science. Trends Ecol. Evol. 24 (2016), 467–471.
73. Smith, M.J., Kay, W.R., Edward, D.H.D., Papas, P.J., Richardson, K.S.J., Simpson, J.C., Pinder, A.M., Cale, D.J., Horwitz, P.H.J., Davis, J.A., Yung, F.H., AusRivAS: using macroinvertebrates to assess ecological condition of rivers in Western Australia. Freshw. Biol. 41 (1999), 269–282.
74. Smol, J.P., Cumming, B.F., Tracking long-term changes in climate using algal indicators in lake sediments. J. Phycol. 36 (2008), 986–1011.
75. Stark, J.D., A macroinvertebrates community index of water quality for stony streams. 1985, National Water and Soil Conservation Authority Wellington, Wellington, New Zealand.
76. Statzner, B., Hoppenhaus, K., Arens, M.F., Richoux, P., Reproductive traits, habitat use and templet theory: a synthesis of world-wide data on aquatic insects. Freshw. Biol. 38 (1997), 109–135.
77. Sterk, M., Gort, G., Klimkowska, A., van Ruijven, J., van Teeffelen, A.J.A., Wamelink, G.W.W., Assess ecosystem resilience: linking response and effects traits to environmental variability. Ecol. Indic. 30 (2013), 21–27.
78. Strayer, D.L., Dudgeon, D., Freshwater biodiversity conservation: recent progress and future challenges. J. N. Am. Benthol. Soc. 29 (2010), 344–358.
79. Stucki, P., 2010. Methoden zur Untersuchung und Beurteilung der Fliessgewässer: Makrozoobenthos Stufe F. Bundesamt für Umwelt, Bern. Umwelt-Vollzug, 1026, 61.
80. Thompson, M.S.A., Bankier, C., Bell, T., Dumbrell, A.J., Gray, C., Ledger, M.E., Lehmann, K., McKew, B.A., Sayer, C.D., Shelley, F., Trimmer, M., Warren, S.L., Woodward, G., Gene-to-ecosystem impacts of a catastrophic pesticide spill: testing a multilevel bioassessment approach in a river ecosystem. Freshw. Biol., 2016 in press.
81. Tiegs, S.D., Pohl, M.M., Planform channel dynamics of the lower Colorado river: 1976–1999. Geomorphology 69 (2005), 14–27.
82. Tiegs, S.D., Clapcott, J.E., Griffiths, N.A., Boulton, A.J., A standardized cotton-strip assay for measuring organic-matter decomposition in streams. Ecol. Indic. 32 (2013), 131–139.
83. Tittensor, D.P., Walpole, M., Hill, S.L., Boyce, D.G., Britten, G.L., Burgess, N.D., Butchart, S.H., Leadley, P.W., Regan, E.C., Alkemade, R., Baumung, R., A mid-term analysis of progress toward international biodiversity targets. Science 346 (2014), 241–244.
84. 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., Chapter one-learning ecological networks from next-generation sequencing data. Adv. Ecol. Res. 54 (2016), 1–39.
85. Welcomme, R.L., An overview of global catch statistics for inland fish. ICES J. Mar. Sci. 68 (2011), 1751–1756.
86. Welcomme, R.L., Cowx, I.G., Coates, D., Béné, C., Funge-Smith, S., Halls, A., Lorenzen, K., Inland capture fisheries. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365 (2010), 2881–2896.
87. Weyl, O.L., Ribbink, A.J., Tweddle, D., Lake Malawi: fishes, fisheries, biodiversity, health and habitat. Aquat. Ecosyst. Health Manag. 13:3 (2010), 241–254.
88. Woodward, G., Gessner, M.O., Giller, P.S., Gulis, V., Hladyz, S., Lecerf, A., Malmqvist, B., McKie, B.G., Tiegs, S.D., Cariss, H., Dobson, M., Elosegi, A., Ferreira, V., Graça, M.A., Fleituch, T., Lacoursière, J.O., Nistorescu, M., Pozo, J., Risnoveanu, G., Schindler, M., Vadineanu, A., Vought, L.B., Chauvet, E., Continental-scale effects of nutrient pollution on stream ecosystem functioning. Science 336:6087 (2012), 1438–1440.
89. Wright, J.F., Furse, M.T., Moss, D., River classification using invertebrates: RIVPACS applications. Aquat. Conserv. Mar. Freshwat. Ecosyst. 8 (1998), 617–631.
90. WWF, Living planet report 2014: species and spaces, people and places. McLellan, R., Iyengar, L., Jeffries, B., Oerlemans, N., (eds.), 2014, World Wide Fund for Nature, Gland, Switzerland.