Global patterns and predictions of seafloor biomass using random forests

PLoS ONE

Volumn 5, Issue 12, 2010, Pages

  Wei, Chih Lin ^a   Rowe, Gilbert T ^b   Briones, Elva Escobar ^c   Boetius, Antje ^d   Soltwedel, Thomas ^d   Caley, M Julian ^e   Soliman, Yousria ^f   Huettmann, Falk ^g   Qu, Fangyuan ^a,h   Yu, Zishan ^h   Pitcher, C Roland ⁱ   Haedrich, Richard L ^j   Wicksten, Mary K ^a   Rex, Michael A ^k   Baguley, Jeffrey G ^l   Sharma, Jyotsna ^m   Danovaro, Roberto ⁿ   MacDonald, Ian R ^o   Nunnally, Clifton C ^a   Deming, Jody W ^p   Montagna, Paul ^q   Lévesque, Mélanie ^r   Weslawski, Jan Marcin ^s   Wlodarska Kowalczuk, Maria ^s   Ingole, Baban S ^t   Bett, Brian J ^u   Billett, David S M ^u   Yool, Andrew ^u   Bluhm, Bodil A ^g   Iken, Katrin ^g   Narayanaswamy, Bhavani E ^v   more..

^a TEXAS A AND M UNIVERSITY   (United States)

^b TEXAS A AND M UNIVERSITY AT GALVESTON   (United States)

^c UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^d ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^e AUSTRALIAN INSTITUTE OF MARINE SCIENCE   (Australia)

^f QATAR UNIVERSITY   (Qatar)

^g UNIVERSITY OF ALASKA FAIRBANKS   (United States)

^h OCEAN UNIVERSITY OF CHINA   (China)

ⁱ CSIRO   (Australia)

^j MEMORIAL UNIVERSITY OF NEWFOUNDLAND   (Canada)

^k UNIVERSITY OF MASSACHUSETTS BOSTON   (United States)

^l UNIVERSITY OF NEVADA   (United States)

^m UNIVERSITY OF TEXAS AT SAN ANTONIO   (United States)

ⁿ UNIVERSITÀ POLITECNICA DELLE MARCHE   (Italy)

^o FLORIDA STATE UNIVERSITY   (United States)

^p UNIVERSITY OF WASHINGTON   (United States)

^q TEXAS A AND M UNIVERSITY CORPUS CHRISTI   (United States)

^r INSTITUT DES SCIENCES DE LA MER DE RIMOUSKI   (Canada)

^s INSTITUTE OF OCEANOLOGY   (Poland)

^t NATIONAL INSTITUTE OF OCEANOGRAPHY   (India)

^u NATIONAL OCEANOGRAPHY CENTRE   (United Kingdom)

^v SCOTTISH MARINE INSTITUTE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ORGANIC MATTER; CARBON;

ACCURACY; ARTICLE; BENTHOS; BIOMASS DISTRIBUTION; BODY SIZE; GEOGRAPHICAL VARIATION (SPECIES); MACROFAUNA; MEIOFAUNA; PARTICULATE MATTER; PHYTOPLANKTON; PREDICTION; RANDOM FOREST; SEA; SEAFLOOR; SEASONAL VARIATION; ZOOPLANKTON; ALGORITHM; ANIMAL; ARTIFICIAL INTELLIGENCE; BIODIVERSITY; BIOLOGICAL MODEL; BIOLOGY; BIOMASS; CHEMISTRY; ECOSYSTEM; MARINE BIOLOGY; METHODOLOGY; REGRESSION ANALYSIS;

INVERTEBRATA; PISCES;

ALGORITHMS; ANIMALS; ARTIFICIAL INTELLIGENCE; BIODIVERSITY; BIOMASS; CARBON; COMPUTATIONAL BIOLOGY; ECOSYSTEM; MARINE BIOLOGY; MODELS, BIOLOGICAL; OCEANS AND SEAS; REGRESSION ANALYSIS;

EID: 78651254769     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015323     Document Type: Article

References (91)

1. Rowe GT, Wei C-L. Biodiversity of Deep-Sea Macrofauna as a Function of Food Supply. In preparation.
2. Rex M, Etter R (2010) Deep-sea biodiversity: pattern and scale. Cambridge MA: Harvard University Press. 354 p.
3. Petersen CGJ (1918) The sea-bottom and its production of fish-food. Report of the Danish Biological Station 25: 1-62.
4. Petersen CGJ (1913) Valuation of the sea, Part 2. The animal communities of the sea-bottom and their importance for marine zoogeography. Report of the Danish Biological Station 21: 1-43.
5. Holme N, McIntyre A (1971) Methods for the study of marine benthos. IBP Handbook No. 16 Oxford, UK: Blackwell.
6. Vinogradov M, Tseitlin V (1983) Deep-sea pelagic domain (aspects of bioenergetics). In: Rowe GT, ed. Deep-sea biology. New York: Wilyinterscience. pp 123-165.
7. Rowe GT (1983) Biomass and production of deep-sea macrobenthos. In: Rowe GT, ed. Deep-Sea Biology. New York: Wily-interscience. pp 97-121.
8. Rex MA, Etter RJ, Morris JS, Crouse J, McClain CR, et al. (2006) Global bathymetric patterns of standing stock and body size in the deep-sea benthos. Marine Ecology Progress Series 317: 1-8.
9. Soltwedel T (2000) Metazoan meiobenthos along continental margins: a review. Progress In Oceanography 46: 59-84.
10. Deming J, Yager P (1992) Natural bacterial assemblages in deep-sea sediments: towards a global view. In: Rowe GT, Pariente V, eds. Deep-sea food chains and the global carbon cycle. Dordrecht, The Netherlands: Kluwer. pp 11-27.
11. Breiman L (2001) Random forests. Machine Learning 45: 5-32.
12. Cutler A, Stevens JR (2006) Random Forests for Microarrays. In: Alan K, Brian O, eds. Methods in Enzymology: Academic Press. pp 422-432.
13. Xu P, Jelinek F (2004) Random forests in language modeling. Proceedings of EMNLP 2004. Brcelona, Spain: Association for Computational Linguistics. pp 325-332.
14. Svetnik V, Liaw A, Tong C, Culberson JC, Sheridan RP, et al. (2003) Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling. Journal of Chemical Information and Computer Sciences 43: 1947-1958.
15. Cutler DR, Edwards TC, Beard KH, Cutler A, Hess KT, et al. (2007) Random forests for classification in ecology. Ecology 88: 2783-2792.
16. Prasad A, Iverson L, Liaw A (2006) Newer Classification and Regression Tree Techniques: Bagging and Random Forests for Ecological Prediction. Ecosystems 9: 181-199.
17. De'ath G (2007) Boosted trees for ecological modeling and prediction. Ecology 88: 243-251.
18. Oppel S, Huettmann F (2010) Using a Random Forest Model and Public Data to Predict the Distribution of Prey for Marine Wildlife Management. In: Cushman SA, Huettmann F, eds. Spatial Complexity, Informatics, and Wildlife Conservation. pp 151-163.
19. Pitcher CR, Lawton P, Ellis N, Smith SJ, Incze LS, et al. Exploring the role of environmental variables in shaping patterns of biodiversity composition in seabed assemblages. In preparation.
20. Bett B, Vanreusel A, Vincx M, Soltwedel T, Pfannkuche O, et al. (1994) Sampler bias in the quantitative study of deep-sea meiobenthos. Marine Ecology Progress Series 104: 197-197.
21. Gage JD, Hughes DJ, Vecino JLG (2002) Sieve size influence in estimating biomass, abundance and diversity in samples of deep-sea macrobenthos. Marine Ecology Progress Series 225: 97-107.
22. Gage J, Bett B (2005) Deep-sea benthic sampling. In: Eleftheriou A, McIntyre A, eds. Methods for the Study of the Marine Benthos. Oxford, UK: Blackwell. pp 273-325.
23. Behrenfeld MJ, Falkowski PG (1997) Photosynthetic rates derived from satellitebased chlorophyll concentration. Limnology and Oceanography 42: 1-20.
24. Westberry T, Behrenfeld M, Siegel D, Boss E (2008) Carbon-based primary productivity modeling with vertically resolved photoacclimation. Global Biogeochemical Cycles 22: GB2024.
25. Yool A, Shepherd JG, Bryden HL, Oschlies A (2009) Low efficiency of nutrient translocation for enhancing oceanic uptake of carbon dioxide. J Geophys Res 114: C08009.
26. Amante C, Eakins BW (2009) ETOPO1 1 Arc-Minute Global Relief Model: Procedures, Data Sources and Analysis. NOAA Technical Memorandum NESDIS NGDC-24. 19 p.
27. Breiman L, Freidman J, Olshen R, Stone C (1984) Classification and regression trees. Belmont CA: Wadsworth.
28. R Development Core Team (2010) R: A Language and Environment for Statistical Computing Vienna, Austria: R Foundation for Statistical Computing.
29. Liaw A, Wiener M (2002) Classification and Regression by randomForest. R News 2: 18-22.
30. Bivand RS, Pebesma EJ, Gomez-Rubio V (2008) Applied spatial data analysis with R. New York: Springer.
31. Grebmeier JM, Cooper LW, Feder HM, Sirenko BI (2006) Ecosystem dynamics of the Pacific-influenced Northern Bering and Chukchi Seas in the Amerasian Arctic. Progress In Oceanography 71: 331-361.
32. Williams RG, Follows MJ (2003) Physical transport of nutrients and the maintenance of biological production. In: Fasham M, ed. Ocean Biogeochemistry: The role of the ocean carbon cycle in global change: Springer. pp 19-51.
33. Dunne J, Sarmiento J, Gnanadesikan A (2007) A synthesis of global particle export from the surface ocean and cycling through the ocean interior and on the seafloor. Global Biogeochem Cycles 21: GB4006.
34. Rowe GT, Sibuet M, Deming JW, Khripounoff A, Tietjen J, et al. (1991) "Total" sediment biomass and preliminary estimates of organic carbon residence time in deep-sea benthos. Marine Ecology Progress Series 79: 99-114.
35. Rowe GT, Wei C-L, Nunnally C, Haedrich R, Montagna P, et al. (2008) Comparative biomass structure and estimated carbon flow in food webs in the deep Gulf of Mexico. Deep Sea Research Part II: Topical Studies in Oceanography 55: 2699-2711.
36. Pfannkuche O, Lochte K (2000) The biogeochemistry of the deep Arabian Sea: overview. Deep Sea Research Part II: Topical Studies in Oceanography 47: 2615-2628.
37. Gage JD, Tyler PA (1991) Deep-sea biology: A natural history of organisms at the deep-sea floor. Cambridge: Cambridge University Press. 504 p.
38. Heip CHR, Duineveld G, Flach E, Graf G, Helder W, et al. (2001) The role of the benthic biota in sedimentary metabolism and sediment-water exchange processes in the Goban Spur area (NE Atlantic). Deep Sea Research Part II: Topical Studies in Oceanography 48: 3223-3243.
39. Thiel H (1975) The size structure of the deep-sea benthos. Internationale Revue der gesamten Hydrobiologie und Hydrographie 60: 575-606.
40. Ho CK, Pennings SC, Carefoot TH (2010) Is Diet Quality an Overlooked Mechanism for Bergmann's Rule? The American Naturalist 175: 269-276.
41. Sweetman A, Witte U (2008) Response of an abyssal macrofaunal community to a phytodetrital pulse. Marine Ecology Progress Series 355: 73-84.
42. van Nugteren P, Herman P, Moodley L, Middelburg J, Vos M, et al. (2009) Spatial distribution of detrital resources determines the outcome of competition between bacteria and a facultative detritivorous worm. Limnol Oceanogr 54: 1413-1419.
43. Witte U, Wenzhofer F, Sommer S, Boetius A, Heinz P, et al. (2003) In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor. Nature 424: 763-766.
44. Rowe GT, Deming JW. An Alternative View of the Role of Bacteria in the Cycling of Organic Matter in Deep-sea Sediments. Marine Biology Research: Submitted.
45. Ingels J, Van den Driessche P, De Mesel I, Vanhove S, Moens T, et al. (2010) Preferred use of bacteria over phytoplankton by deep-sea nematodes in polar regions. Mar Ecol Prog Ser 406: 121-133.
46. Clough L, Renaud P, Ambrose Jr. W (2005) Impacts of water depth, sediment pigment concentration, and benthic macrofaunal biomass on sediment oxygen demand in the western Arctic Ocean. Canadian Journal of Fisheries and Aquatic Sciences 62: 1756-1765.
47. Rowe GT, Boland GS, Escobar Briones EG, Cruz-Kaegi ME, Newton A, et al. (1997) Sediment community biomass and respiration in the Northeast water polynya, Greenland: a numerical simulation of benthic lander and spade core data. Journal of Marine Systems 10: 497-515.
48. Kirchman DL, Moran XAG, Ducklow H (2009) Microbial growth in the polar oceans - role of temperature and potential impact of climate change. Nature Reviews Microbiology 7: 451-459.
49. Grebmeier JM, Barry JP (2007) Chapter 11 Benthic Processes in Polynyas. In: Smith WO, Barber DG, eds. Elsevier Oceanography Series: Elsevier. pp 363-390.
50. Deming J, Baross J (1993) The early diagenesis of organic matter: bacterial activity. In: Engel MH, Macko SA, eds. Organic geochemistry. New York: Plenum Press. pp 119-144.
51. Dixon JL, Turley CM (2000) The effect of water depth on bacterial numbers, thymidine incorporation rates and C:N ratios in northeast Atlantic surficial sediments. Hydrobiologia 440: 217-225.
52. Deming JW, Carpenter SD (2008) Factors influencing benthic bacterial abundance, biomass, and activity on the northern continental margin and deep basin of the Gulf of Mexico. Deep Sea Research Part II: Topical Studies in Oceanography 55: 2597-2606.
53. Lochte K (1992) Bacterial standing stock and consumption of organic carbon in the benthic boundary layer of the abyssal North Atlantic. In: Rowe GT, Pariente V, eds. Deep-sea food chains and the global carbon cycle. Dordrecht, The Netherlands: Kluwer. pp 1-10.
54. Deming JW, Colwell RR (1985) Observations of Barophilic Microbial Activity in Samples of Sediment and Intercepted Particulates from the Demerara Abyssal Plain. Appl Environ Microbiol 50: 1002-1006.
55. Patching JW, Eardly D (1997) Bacterial biomass and activity in the deep waters of the eastern Atlantic-evidence of a barophilic community. Deep Sea Research Part I: Oceanographic Research Papers 44: 1655-1670.
56. Lochte K, Turley CM (1988) Bacteria and cyanobacteria associated with phytodetritus in the deep sea. Nature 333: 67-69.
57. Deming J, Baross J (2000) Survival, dormancy, and nonculturable cells in extreme deep-sea environments. In: Colwell RR, Grimes DJ, eds. Nonculturable Microorganisms in the Environments. Washington, DC: American Society for Microbiology Press. pp 147-197.
58. Quéric N-V, Soltwedel T, Arntz WE (2004) Application of a rapid direct viable count method to deep-sea sediment bacteria. Journal of Microbiological Methods 57: 351-367.
59. Danovaro R, Dell'Anno A, Corinaldesi C, Magagnini M, Noble R, et al. (2008) Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 454: 1084-1087.
60. Boetius A, Lochte K (1994) Regulation of microbial enzymatic degradation of organic matter in deep-sea sediments. Marine Ecology-Progress Series 104: 299-299.
61. Vetter Y, Deming J, Jumars P, Krieger-Brockett B (1998) A predictive model of bacterial foraging by means of freely released extracellular enzymes. Microbial ecology 36: 75-92.
62. Flach E, Muthumbi A, Heip C (2002) Meiofauna and macrofauna community structure in relation to sediment composition at the Iberian margin compared to the Goban Spur (NE Atlantic). Progress In Oceanography 52: 433-457.
63. Danovaro R, Croce ND, Eleftheriou A, Fabiano M, Papadopoulou N, et al. (1995) Meiofauna of the deep Eastern Mediterranean Sea: distribution and abundance in relation to bacterial biomass, organic matter composition and other environmental factors. Progress In Oceanography 36: 329-341.
64. Clough L, Ambrose W (1997) Infaunal density, biomass and bioturbation in the sediments of the Arctic Ocean. Deep Sea Research Part II: Topical Studies in Oceanography 44: 1683-1704.
65. Smith C (1992) Factors controlling bioturbation in deep-sea sediments and their relation to models of carbon diagenesis. In: Rowe GT, Pariente V, eds. Deep-sea food chains and the global carbon cycle. Dordrecht, The Netherlands: Kluwer. pp 375-393.
66. Rowe GT, Morse J, Nunnally C, Boland GS (2008) Sediment community oxygen consumption in the deep Gulf of Mexico. Deep Sea Research Part II: Topical Studies in Oceanography 55: 2686-2691.
67. Smith K, Hinga K (1983) Sediment community respiration in the deep sea. In: GTR, ed. Deep Sea Biology. New York: Wily-interscience. pp 331-370.
68. Levin L, Gage J, Martin C, Lamont P (2000) Macrobenthic community structure within and beneath the oxygen minimum zone, NW Arabian Sea. Deep Sea Research Part II: Topical Studies in Oceanography 47: 189-226.
69. Quiroga E, Quiñones R, Palma M, Sellanes J, Gallardo VA, et al. (2005) Biomass size-spectra of macrobenthic communities in the oxygen minimum zone off Chile. Estuarine, Coastal and Shelf Science 62: 217-231.
70. Narayanaswamy BE, Bett BJ, Hughes DJ (2010) Deep-water macrofaunal diversity in the Faroe-Shetland region (NE Atlantic): a margin subject to an unusual thermal regime. Marine Ecology 31: 237-246.
71. Smith KL, Ruhl HA, Bett BJ, Billett DSM, Lampitt RS, et al. (2009) Climate, carbon cycling, and deep-ocean ecosystems. Proceedings of the National Academy of Sciences 106: 19211-19218.
72. Billett DSM, Bett BJ, Reid WDK, Boorman B, Priede IG (2010) Long-term change in the abyssal NE Atlantic: The 'Amperima Event' revisited. Deep Sea Research Part II: Topical Studies in Oceanography 57: 1406-1417.
73. Rowe GT, Staresinic N (1979) Sources of organic matter to the deep-sea benthos. Ambio Special Report. pp 19-23.
74. Smith CR, Maybaum HL, Baco AR, Pope RH, Carpenter SD, et al. (1998) Sediment community structure around a whale skeleton in the deep Northeast Pacific: Macrofaunal, microbial and bioturbation effects. Deep Sea Research Part II: Topical Studies in Oceanography 45: 335-364.
75. Brooks J, Kennicutt M (1987) Deep-sea hydrocarbon seep communities: evidence for energy and nutritional carbon sources. Science 238: 1138.
76. Van Dover C (2000) The ecology of deep-sea hydrothermal vents. Princeton NJ: Princeton University Press.
77. Rowe GT, Boland GS, Phoel WC, Anderson RF, Biscaye PE (1994) Deep-sea floor respiration as an indication of lateral input of biogenic detritus from continental margins. Deep Sea Research Part II: Topical Studies in Oceanography 41: 657-668.
78. Rowe GT, Polloni PT, Haedrich RL (1982) The deep-sea macrobenthos on the continental margin of the northwest Atlantic Ocean. Deep Sea Research Part A Oceanographic Research Papers 29: 257-278.
79. Danovaro R, Gambi C, Della Croce N (2002) Meiofauna hotspot in the Atacama Trench, eastern South Pacific Ocean. Deep Sea Research Part I: Oceanographic Research Papers 49: 843-857.
80. Boehlert G, Genin A (1987) A review of the effects of seamounts on biological processes. In: Keating BH, ed. Seamounts, islands and atolls: American Geophysical Union. pp 319-334.
81. Gooday A, Levin L, Linke P, Heeger T (1992) The role of benthic foraminifera in deep-sea food webs and carbon cycling. In: Rowe G, Pariente V, eds. Deepsea food chains and the global carbon cycle. Dordrecht, The Netherlands: Kluwer. pp 63-91.
82. De Leo FC, Smith CR, Rowden AA, Bowden DA, Clark MR (2010) Submarine canyons: hotspots of benthic biomass and productivity in the deep sea. Proceedings of the Royal Society B: Biological Sciences: In press.
83. Soliman Y, Wicksten M (2007) Ampelisca mississippiana: a new species (Crustacea: Amphipoda: Gammaridea) from the Mississippi Canyon (Northern Gulf of Mexico). Zootaxa 1389: 45-54.
84. Smith CR, Berelson W, Demaster DJ, Dobbs FC, Hammond D, et al. (1997) Latitudinal variations in benthic processes in the abyssal equatorial Pacific: control by biogenic particle flux. Deep Sea Research Part II: Topical Studies in Oceanography 44: 2295-2317.
85. Wei C-L, Rowe G, Hubbard G, Scheltema A, Wilson G, et al. (2010) Bathymetric zonation of deep-sea macrofauna in relation to export of surface phytoplankton production. Marine Ecology Progress Series 399: 1-14.
86. Strobl C, Boulesteix A-L, Kneib T, Augustin T, Zeileis A (2008) Conditional variable importance for random forests. BMC Bioinformatics 9: 307.
87. Pace ML, Knauer GA, Karl DM, Martin JH (1987) Primary production, new production and vertical flux in the eastern Pacific Ocean. Nature 325: 803-804.
88. Johnson NA, Campbell JW, Moore TS, Rex MA, Etter RJ, et al. (2007) The relationship between the standing stock of deep-sea macrobenthos and surface production in the western North Atlantic. Deep Sea Research Part I: Oceanographic Research Papers 54: 1350-1360.
89. Rowe GT, Pariente V, eds (1992) Deep-sea food chains and the global carbon cycle. Dordrecht, The Netherlands: Kluwer. 412 p.
90. Pikitch EK, Santora C, Babcock EA, Bakun A, Bonfil R, et al. (2004) ECOLOGY: Ecosystem-Based Fishery Management. Science 305: 346-347.
91. IPCC 2007 Climate Change, editor (2007) The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change Cambridge, UK and New York, USA: Cambridge University Press.