Aggregates in aquatic ecosystems and implications for aquacultures


  • Yustian Rovi Alfiansah Center for Aquaculture Research (ZAF), Alfred Wegener Institute (AWI), Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven Germany



bacteria, food web, microbiome, particulate organic matter, shrimp


Agglomerations of suspended particulate matter serve various roles in aquatic ecosystems. They participate in nutrient and energy fluxes and are involved in important food web processes. While comprehensive studies on aggregates are available from natural freshwater and marine ecosystems, little is known about the roles of aggregates in aquacultures, particularly in shrimp pond farming. As particle-rich systems, shrimp ponds and marine aquaculture (mariculture) areas constitute interesting objects for aggregate studies, particularly as a source of natural feed, particle fluxes, microbial communities, including pathogenic bacteria, and possible vector of disease widespread. The aims of this review are i) to compile the current knowledge on the role of aggregates in aquatic ecosystems, particularly in aquaculture areas covering advantages and negative side effects of aggregates in aquacultures, ii) to explore the role of aggregates in disease ecology, and iii) perspective of aquaculture management in the context of aggregate utilization and management. Since Southeast Asia, especially Indonesia, is among the most important regions for aquaculture activities, this review focuses on Indonesian aquacultures. Although aquacultures produce important amounts of aggregates, including its associated microbial communities, they are rarely investigated in Indonesian aquacultures, particularly in shrimp pond farming. In contrast, most of the studies focused on bacterial cultivation and utilization of isolates for aquacultures. Thus, understanding the ecological roles of aggregates in aquacultures may support the improvement of aquaculture management and yields.


Download data is not yet available.


Alfiansah, Y. R., & Gärdes, A. (2019). Water quality and bacterial community management in shrimp ponds in Rembang , Indonesia : Towards sustainable shrimp aquaculture. Policy Brief 2019 / 2, 2, 1–5.

Alfiansah, Yustian Rovi, Hassenrück, C., Kunzmann, A., Taslihan, A., Harder, J., & Gärdes, A. (2018). Bacterial abundance and community composition in pond water from shrimp aquaculture systems with different stocking densities. Frontiers in Microbiology, 9, 2457.

Alfiansah, Yustian Rovi, Peters, S., Harder, J., Hassenrück, C., & Gärdes, A. (2020). Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture. Scientific Reports, 10(1), 11980.

Alldredge, A. L., Passow, U., & Haddock, S. H. D. (1998). The characteristics and transparent exopolymer particle (TEP) content of marine snow formed from thecate dinoflagellates. Journal of Plankton Research, 20(3), 393–406.

Alldredge, A. L., & Silver, M. W. (1988). Characteristics, dynamics and significance of marine snow. Progress in Oceanography, 20(1), 41–82.

Alonso-Rodrıguez, R., & Paez-Osuna, F. (2003). Nutrients, phytoplankton and harmful algal blooms in shrimp ponds: a review with special reference to the situation in the Gulf of California. Aquaculture, 219, 317–336.

Amin, S.A., Parker, M.S., Armbrust, E.V. (2012). Interactions between diatom and bacteria. Microbiol Mol Biol Rev. 76(3): 667–684. doi: 10.1128/MMBR.00007-12.

Anderson, D. M. (2009). Approaches to monitoring, control, and management of harmful algal blooms (HABs). Ocean & Coastal Management, 52(7), 1–13.

Astriana, B. H. (2012). Evaluation of the Potential of Integrated Multi-trophic Aquaculture (IMTA) using oyster (Crassostrea sp.) and seaweed (Gracilaria sp.) for shrimp (Penaeus monodon) farms to reduce negative impacts on environment and to improve coastal economy in Nusa Tenggara Barat. Marine Resource Management Program, Oregon State University.

Avnimelech, Y. (2015). Biofloc technology- a practical guide book, 3rd edition. In The World Aquaculture Society, Baton Rouge, Louisiana, United State (Issue March).

Avnimelech, Y., & Ritvo, G. (2003). Shrimp and fish pond soils: processes and management. Aquaculture, 220(1–4), 549–567.

Azizah, R., Riniatsih, I., Pringgenis, D., Suryono, C. A., & Suryono. (2017). Isolasi dan identifikasi bakteri pembentuk biofilm dari tambak udang Balai Besar Pengembangan Budidaya Air Payau Jepara untuk menghilangkan amoniak. Jurnal Kelautan Tropis, 20(2), 154–160. 1742

Biddanda, B. (1988). Microbial aggregation and degradation of phytoplankton-derived detritus in seawater. II. Microbial metabolism. Marine Ecology Progress Series, 42(1985), 89–95.

Boyd, C.E., and Tucker, C. S. (2014). Handbook for aquaculture water quality. In Handbook for aquaculture water quality (p. 439). Craftmaster Printers.

Buschmann, A. H., Troell, M., Chopin, T., Fang, J.-G., Joyce, A., & Neori, A. (2009). Ecological engineering in aquaculture — Potential for integrated multi-trophic aquaculture (IMTA) in marine offshore systems. Aquaculture, 297(1–4), 1–9.

Cabello FC (2006). Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment. Environ Microbiol 8:1137-1144.

Colwell, R.R., Huq, A., Islam, M.S., Aziz, K.M.A., Yunus, M., Khan, N.H., Mahmud, A., Sack, R.B., Nair, G.B., Cakraborty, J., Sack, D.A., Rusek-Cohen, E. (2003). Reduction of cholera in Bangladeshi villages by simple filtration. Proceedings of the National Academy of Sciences, 100(3), 1051–1055. doi:10.1073/pnas.0237386100

Crab, R., Avnimelech, Y., Defoirdt, T., Bossier, P., & Verstraete, W. (2007). Nitrogen removal techniques in aquaculture for a sustainable production. Aquaculture, 270(1–4), 1–14.

Crab, R., Defoirdt, T., Bossier, P., & Verstraete, W. (2012). Biofloc technology in aquaculture: beneficial effects and future challenges. Aquaculture, 356–357, 351–356. 10.1016/j.aquaculture.2012.04.046

Danovaro, R., Umani, S. F., & Pusceddu, A. (2009). Climate change and the potential spreading of marine mucilage and microbial pathogens in the mediterranean sea. PLoS ONE, 4(9).

Davies, C. M., Long, J. A. H., Donald, M., & Ashbolt, N. J. (1995). Survival of fecal microorganisms in marine and freshwater sediments. Applied and Environmental Microbiology, 61(5), 1888–1896.

Davoll, P., & Silver, M. (1986). Marine snow aggregates: life history sequence and microbial community of abandoned larvacean houses from Monterey Bay, California. Marine Ecology Progress Series, 33, 111–120. 10.3354/meps033111

De Schryver P.D., Crab, R., Defoirdt, T., Boon, N., Verstraete, W. (2008). The basics of bio-flocs technology: The added value for aquaculture. Aquaculture 277:125-137. 10.1016/j.aquaculture.2008.02.019.

Decho, A.W. (2000). Microbial biofilms in intertidal systems: an overview. Cont Shelf Res 20:1257-1273. 10.1016/s0278-4343(00)00022-4.

Di Cesare A, Luna MG, Vignaroli C, Pasquaroli S, Tota S, Paroncini P (2013) Aquaculture can promote the presence and spread of antibiotic-resistant Enterococci in marine sediment. PLOS One 8 issue 4:1-8.

Emerenciano, M., Gaxiola, G., & Cuzon, G. (2013). Biofloc Technology (BFT): A Review for Aquaculture Application and Animal Food Industry. Biomass Now - Cultivation and Utilization. doi:10.5772/53902

Froelich, B., Ayrapetyan, M., & Oliver, J. D. (2013). Integration of vibrio vulnificus into marine aggregates and its subsequent uptake by crassostrea virginica oysters. Applied and Environmental Microbiology, 75(5), 1454–1458.

Gärdes, A., Iversen, M. H., Grossart, H. P., Passow, U., & Ullrich, M. S. (2011). Diatom-associated bacteria are required for aggregation of Thalassiosira weissflogii. ISME Journal, 5(3), 436–445.

Grossart, H. P., Kiørboe, T., Tang, K. W., Allgaier, M., Yam, E. M., & Ploug, H. (2006). Interactions between marine snow and heterotrophic bacteria: aggregate formation and microbial dynamics. Aquatic Microbial Ecology, 42(1), 19–26.

Grossart, H., Ploug, H., & Mar, N. (2007). Microbial degradation of organic carbon and nitrogen on diatom aggregates. Limnology and Oceanography, 46(2), 267–277. doi:10.4319/lo.2001.46.2.0267

Grossart, Hans Peter, & Simon, M. (1998). Bacterial colonization and microbial decomposition of limnetic organic aggregates (lake snow). Aquatic Microbial Ecology, 15(2), 127–140.

Grossart, Hans Peter, & Simon, M. (2007). Interactions of planktonic algae and bacteria: Effects on algal growth and organic matter dynamics. Aquatic Microbial Ecology, 47(2), 163–176.

Hansen, J. L. S., Kiørboe, T., & Alldredge, A. L. (1996). Marine snow derived from abandoned larvacean houses: sinking rates, particle content and mechanisms of aggregate formation. Marine Ecology Progress Series, 141, 205–215.

Hargreaves, J. A. (2013). Biofloc production systems for aquaculture. SRAC Publ. 4503, 1–12. Available at:

Hatmanti, A., Nuchsin, R., & Darmayanti, Y. (2008). Studi penyakit bakterial pada budidaya ikan kerapu dan bakteri penghambatnya di Perairan Teluk Lampung. Jurnal Akuakultur Indonesia, 7(1), 51–58. 10.19027/jai.7.51-58.

Hennersdorf, P., Kleinertz, S., Theisen, S., Abdul-Aziz, M. A., Mrotzek, G., Palm, H. W., & Saluz, H. P. (2016). Microbial diversity and parasitic load in tropical fish of different environmental conditions. PLoS ONE, 11(3), 1–18.

Hennersdorf, P., Mrotzek, G., Abdul-Aziz, M. A., & Saluz, H. P. (2016). Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus under different environmental conditions in Indonesian waters. Marine Pollution Bulletin, 110(2), 726–734. marpolbul.2016.05.009

Herbeck, L. S., Unger, D., Wu, Y., & Jennerjahn, T. C. (2013). Effluent, nutrient and organic matter export from shrimp and fish ponds causing eutrophication in coastal and back-reef waters of NE hainan, tropical China. Continental Shelf Research.

Herfiani, Rantetondok, A., & Anshary, H. (2010). Diagnosis penyakit bakterial pada ikan kerapu macan (Epinephelus fuscoguttatus) pada keramba jaring apung Boneatiro di Kabupaten Buton (Vol. 50).

Holmer, M., Duarte, C. M., Heilskov, A., Olesen, B., & Terrados, J. (2003). Biogeochemical conditions in sediments enriched by organic matter from net-pen fish farms in the Bolinao area, Philippines. Marine Pollution Bulletin, 46(11), 1470–1479.

Hsieh, J. L., Fries, J. S., & Noble, R. T. (2007). Vibrio and phytoplankton dynamics during the summer of 2004 in a eutrophying estuary. Ecological Applications, 17(5), 102–109.

Jackson, G. A., & Burd, A. B. (1998). Aggregation in the marine environment. Environmental Science & Technology, 32(19), 2805–2814.

Kautsky, N., Rönnbäck, P., Tedengren, M., Troell, M. (2000). Ecosystem perspectives on management of disease in shrimp pond farming. Aquaculture 191:145-161.

Kementerian Kelautan dan Perikanan/KKP. 2015. Laporan Kinerja Kementerian Kelautan dan Perikanan tahun 2014. 177pp.

Kementerian PPN/Bappenas. 2014. Kajian strategis pengelolaan perikanan berkelanjutan. Bappenas. Report. 120pp.

Kiørboe, T. (2001). Formation and fate of marine snow: small-scale processes with large- scale implications. Scientia Marina, 65(S2), 57–71. 65s257

Kiørboe, T., Grossart, H.-P., Ploug, H., & Tang. (2002). Mechanisms and Rates of Bacterial Colonization of Sinking Aggregates. Applied and Environmental Microbiology, 68(8), 3996–4006. doi:10.1128/aem.68.8.3996-4006.2002

Kiørboe, T., Tang, K., Grossart, H.-P., & Ploug, H. (2003). Dynamics of microbial communities on marine snow aggregates: colonization, growth, detachment , and grazing mortality of attached bacteria. Applied and Environmental Microbiology, 69(6), 3036–3047.

Kramer, A. M., Lyons, M. M., Dobbs, F. C., & Drake, J. M. (2013). Bacterial colonization and extinction on marine aggregates: stochastic model of species presence and abundance. Ecology and Evolution, 3(13), 4300–4309. ece3.789

Leyva-Flores, J. A., Zavala-Leal, O. I., Cadena-Roa, M. A., Pérez-Bravo, E., Pacheco-Vega, J. M., & Ruiz-Velazco, J. M. J. (2018). Effect of isolated bacteria and microalgae on the biofloc characteristics in the Pacific white shrimp culture. Aquaculture Reports, 11(June), 24–30. 10.1016/j.aqrep.2018.05.003

Liu, P., Xu, B., Hua, Y., Cheng, M., Aitola, K., Sveinbjörnsson, K., Zhang, J., Boschloo, G., Sun, L., & Kloo, L. (2017). Design, synthesis and application of a Π-conjugated, non-spiro molecular alternative as hole-transport material for highly efficient dye-sensitized solar cells and perovskite solar cells. Journal of Power Sources, 344(3), 11–14. 10.1016/j.jpowsour.2017.01.092

Liu, Y., De Schryver, P., Van Delsen, B., Maignien, L., Boon, N., Sorgeloos, P., Verstraete, W., Bossier, P., & Defoirdt, T. (2010). PHB-degrading bacteria isolated from the gastrointestinal tract of aquatic animals as protective actors against luminescent vibriosis. FEMS Microbiology Ecology, 74, 196–204.

Lyons, M. M., Ward, J. E., Gaff, H., Hicks, R. E., Drake, J. M., & Dobbs, F. C. (2010). Theory of island biogeography on a microscopic scale: organic aggregates as islands for aquatic pathogens. Aquatic Microbial Ecology, 60, 1–13. ame01417

Lyons, M Maille, Ward, J. E., Smolowitz, R., Uhlinger, K. R., & Gast, R. J. (2005). Lethal marine snow: pathogen of bivalve mollusc concealed in marine aggregates. Limnol. Oceanogr, 50(6), 1983–1988.

Martin, J. L. M., Veran, Y., Guelorget, O., & Pham, D. (1998). Shrimp rearing: Stocking density, growth, impact on sediment, waste output and their relationships studied through the nitrogen budget in rearing ponds. Aquaculture. 10.1016/S0044-8486(98)00182-3

Mecozzi, M., Pietrantonio, E., Di Noto, V., & Pápai, Z. (2005). The humin structure of mucilage aggregates in the Adriatic and Tyrrhenian seas: Hypothesis about the reasonable causes of mucilage formation. Marine Chemistry, 95(3–4), 255–269.

Oetama, V. S. P., Hennersdorf, P., Abdul-Aziz, M. A., Mrotzek, G., Haryanti, H., & Saluz, H. P. (2016). Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali. Marine Pollution Bulletin, 110(2), 718–725.

Panjaitan, P. (2010). Shrimp culture of Penaeus monodon with zero water exchange model (ZWEM) using molasses. Journal of Coastal Development, 14(1), 35–44.

Passow, U., Ziervogel, K., Asper, V., & Diercks, A. (2012). Marine snow formation in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico. Environmental Research Letters, 7(3).

Piedrahita, R. H. (2003). Reducing the potential environmental impact of tank aquaculture effluents through intensification and recirculation. Aquaculture, 226(1–4), 35–44.

Precali, R., Giani, M., Marini, M., Grilli, F., Ferrari, C. R., Pečar, O., & Paschini, E. (2005). Mucilaginous aggregates in the northern Adriatic in the period 1999-2002: Typology and distribution. Science of the Total Environment, 353(1–3), 10–23.

Ray, A. J., Seaborn, G., Leffler, J. W., Wilde, S. B., Lawson, A., & Browdy, C. L. (2010). Characterization of microbial communities in minimal-exchange, intensive aquaculture systems and the effects of suspended solids management. Aquaculture, 310(1–2), 130–138. j.aquaculture.2010.10.019

Reichardt, W. T., Reyes, J. M., Pueblos, M. J., & Lluisma, A. O. (2013). Impact of milk fish farming in the tropics on potentially pathogenic vibrios. Marine Pollution Bulletin, 77(1–2), 325–332.

Seyfried, E.E., Newton, R.J., Rubert, K.F. IV, Pedersen, J.A., McMahon, K.D. (2010). Occurrence of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline. Microbial Ecology, 59:799-807.

Shanks, A. L., & Del Carmen, K. A. (1997). Larval polychaetes are strongly associated with marine snow. Marine Ecology Progress Series, 154 (January 1997), 211–221. /10.3354/meps154211

Sidabutar, T. (2016). Mass mortality of fish in lampung Bay, Indonesia. OmniAkuatika, 12(1), 31–40.

Simon, M., Grossart, H., Schweitzer, B., & Ploug, H. (2002). Microbial ecology of organic aggregates in aquatic ecosystems. Aquatic Microbial Ecology, 28, 175–211.

Sinha, A.K., Baruah, K., and Bossier, P. (2008). Horizon scanning: the potential use of biofloc as an anti-infective strategy in aquaculture-an overview. Aquac Health Int 13:8-10.

Steinberg, D. K., Pilskaln, C. H., & Silver, M. W. (1998). Contribution of zooplankton associated with detritus to sediment trap “swimmer” carbon in Monterey Bay, California, USA. Marine Ecology Progress Series, 164, 157–166.

Suantika, G., Aditiawati, P., Astuti, D. I., & Khotimah, Z. F. (2013). The use of indigenous probiotic Halomonas aquamarina and Shewanella algae for white shrimp (Litopenaeus vannamei Boone) hatchery productivity in zero water discharge system. Journal of Aquaculture Research & Development, 04(05), 1000194.

Tamminen, M., Karkman, A., Löhmus, A., Muziasari, W.I., Takasu, H. (2011). Tetracycline resistance genes persist at aquaculture farms in the absence of selection pressure. Environ Sci Technol 45:386-391.

Ward, J. E., & Kach, D. J. (2009). Marine aggregates facilitate ingestion of nanoparticles by suspension-feeding bivalves. Marine Environmental Research, 68(3), 137–142.

Wu, Y., Li, T., & Yang, L. (2012). Mechanisms of removing pollutants from aqueous solutions by microorganisms and their aggregates: A review. Bioresource Technology, 107, 10–18.

Zhang, D., Wang, X., Xiong, J., Zhu, J., Wang, Y., Zhao, Q., Chen, H., Guo, A., Wu, J., & Dai, H. (2014). Bacterioplankton assemblages as biological indicators of shrimp health status. Ecological Indicators, 38, 218–224. 2013.11.002




How to Cite

Alfiansah, Y. R. (2020). Aggregates in aquatic ecosystems and implications for aquacultures. Marine Research in Indonesia, 45(2), 87–96.



Review Articles

Most read articles by the same author(s)