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Archaeal community compositions in tilapia pond systems and their influencing factors

  • Limin Fan
  • Kamira Barry
  • Leilei Shi
  • Chao Song
  • Shunlong Meng
  • Liping Qiu
  • Gengdong Hu
  • Yao Zheng
  • Fajun Li
  • Jiazhang Chen
  • Pao Xu
Original Paper

Abstract

Archaea, like the bacterial communities are gradually being realized as key players in the biogeochemical progress of water ecosystems. In this study, tilapia aquaculture ponds were used for an in-depth understanding of archaeal community compositions in water and surface sediment. Some of the main functions, as well as the communities’ response patterns, to time variations, pond differences and some physio-chemical parameters were investigated. The results revealed the dominant phylum in both the water and surface sediment, as Euryarchaeota, while, the most abundant classes were: Halobacteria and Methanomicrobia respectively. Significant differences in the archaeal community compositions in the water and surface sediment, were observed in the early stages of cultivation, which became minimal at the later stage of the GIFT tilapia cultivation. Additionally to the differences in the most abundant classes, more OTUs were observed in water samples than in surface sediment samples. The methane generation could be attributed to the large proportion of methanogens found in both pond water and in the surface sediment. Furthermore, the archaeal community compositions in water and the surface sediment were shaped mainly by temporal variations and pond differences respectively. In the pond water, the archaeal community compositions were highly co-related to the concentration changes of ammonia, sulfate and total nitrogen; while in the surface sediment, the correlation to the content changes was significant in total phosphorus. The archaeal community compositions in surface sediment should be considered as an indicator for future environmental capacity studies in aquaculture.

Keywords

Tilapia pond Archaeal community Illumina high-throughput sequencing Influencing factors 

Notes

Acknowledgements

This research was jointly supported by the China Agriculture Research System (Grant CARS-46) and the Special Fund of Fundamental Scientific Research Business Expense of the Central Public Research Institutes (Grant 2015JBFM12).

References

  1. Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M (2013) Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J 7:1344–1353CrossRefGoogle Scholar
  2. Auguet JC, Barberan A, Casamayor EO (2010) Global ecological patterns in uncultured Archaea. ISME J 4:182–190CrossRefGoogle Scholar
  3. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120CrossRefGoogle Scholar
  4. Bonnie C, Ng SYM, Jarrell KF (2006) Archaeal habitats—from the extreme to the ordinary. Can J Microbiol 52:73–116CrossRefGoogle Scholar
  5. Boström B, Persson G, Broberg B (1988) Bioavailability of different phosphorus forms in freshwater systems. Hydrobiologia 170:133–155CrossRefGoogle Scholar
  6. Brown MN, Briones A, Diana J, Raskin L (2013) Ammonia-oxidizing archaea and nitrite-oxidizing nitrospiras in the biofilter of a shrimp recirculating aquaculture system. FEMS Microbiol Ecol 83:17–25CrossRefGoogle Scholar
  7. Cavicchioli R (2006) Cold-adapted archaea. Nat Rev Microbiol 4:331–343CrossRefGoogle Scholar
  8. Christa S, German J, Melanie J (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488CrossRefGoogle Scholar
  9. Fan LM, Barry K, Hu GD, Meng SL, Song C, Wu W, Chen JZ, Xu P (2016) Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing. World J Microbiol Biotechnol 32:1–11CrossRefGoogle Scholar
  10. Fan L, Barry K, Hu G, Meng S, Song C, Qiu L, Zheng Y, Wu W, Qu J, Chen J (2017) Characterizing bacterial communities in tilapia pond surface sediment and their responses to pond differences and temporal variations. World J Microbiol Biotechnol 33:1CrossRefGoogle Scholar
  11. Guyader J, Silberberg M, Popova M, Seradj AR, Morgavi D, Martin C (2014) Dietary nitrates decrease methane emission by inhibiting rumen methanogenic archaea without influencing nitrate reducing bacteria. In: Proceedings of the 9th Joint Rowett/INRA symposium, gut microbiology: from sequence to function, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, p 13Google Scholar
  12. Hu A, Hou L, Yu CP (2015) Biogeography of planktonic and benthic archaeal communities in a subtropical eutrophic estuary of China. Microb Ecol 70:322–335CrossRefGoogle Scholar
  13. Hu A, Wang H, Li J, Liu J, Chen N, Yu CP (2016) Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes. Appl Microbiol Biotechnol 100:1–14CrossRefGoogle Scholar
  14. Llirós M, Casamayor EO, Borrego C (2008) High archaeal richness in the water column of a freshwater sulfurous karstic lake along an interannual study. FEMS Microbiol Ecol 66:331–342CrossRefGoogle Scholar
  15. Lu S, Liao M, Xie C, He X, Li D, He L, Chen J (2015a) Seasonal dynamics of ammonia-oxidizing microorganisms in freshwater aquaculture ponds. Ann Microbiol 65:651–657CrossRefGoogle Scholar
  16. Lu S, Liu X, Ma Z, Liu Q, Wu Z, Zeng X, Shi X, Gu Z (2015b) Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond. Front Microbiol 6:177–183Google Scholar
  17. Martin F, Torelli S, Le PD, Barbance A, Martin-Laurent F, Bru D, Geremia R, Blake G, Jouanneau Y (2012) Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene. Environ Pollut 162:345–353CrossRefGoogle Scholar
  18. Mendonça FZ, Volpato GL, Costa-Ferreira RS, Gonçalves-De-Freitas E (2010) Substratum choice for nesting in male Nile tilapia Oreochromis niloticus. J Fish Biol 77:1439–1445CrossRefGoogle Scholar
  19. Miroshnichenko ML (2003) Thermophilic microbial communities of deep-sea hydrothermal vents. Microbiology 73:1–13CrossRefGoogle Scholar
  20. Ochsenreiter T, Pfeifer F, Schleper C (2002) Diversity of Archaea in hypersaline environments characterized by molecular-phylogenetic and cultivation studies. Extremophiles Life Under Extreme Conditions 6:267–274CrossRefGoogle Scholar
  21. Offre P, Spang A, Schleper C (2013) Archaea in biogeochemical cycles. Annu Rev Microbiol 67:437–457CrossRefGoogle Scholar
  22. Pesce S, Bouchez A, Montuelle B (2011) Effects of organic herbicides on phototrophic microbial communities in freshwater ecosystems. Rev Environ Contam Toxicol 214:87–124Google Scholar
  23. R Development Core Team (2011) R: a language and environment for statistical computing, 2.13.1 ed. R Foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
  24. Rafael D (2008) Tilapia farming: a global review (1924–2004). Asia Life Sci 17:207–229Google Scholar
  25. Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK (2012) FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30:460–465CrossRefGoogle Scholar
  26. Robertson C, Harris J, Spear J, Nr (2005) Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol 8:638–642CrossRefGoogle Scholar
  27. Sakami T, Abo K, Takayanagi K, Toda S (2003) Effects of water mass exchange on bacterial communities in an aquaculture area during summer. Estuar Coast Shelf Sci 56:111–118CrossRefGoogle Scholar
  28. Sakami T, Andoh T, Morita T, Yamamoto Y (2012) Phylogenetic diversity of ammonia-oxidizing archaea and bacteria in biofilters of recirculating aquaculture systems. Mar Genomics 7:27–31CrossRefGoogle Scholar
  29. Salvador M, Figueras CG, De Gonzalez-Pastor JE (2011) Diversity of Archaea in Icelandic hot springs based on 16S rRNA and chaperonin genes. FEMS Microbiol Ecol 77:165–175CrossRefGoogle Scholar
  30. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541CrossRefGoogle Scholar
  31. Sims A, Horton J, Gajaraj S, Mcintosh S, Miles RJ, Mueller R, Reed R, Hu Z (2012) Temporal and spatial distributions of ammonia-oxidizing archaea and bacteria and their ratio as an indicator of oligotrophic conditions in natural wetlands. Water Res 46:4121–4129CrossRefGoogle Scholar
  32. Srithep P, Khinthong B, Chodanon T, Powtongsook S, Pungrasmi W, Limpiyakorn T (2015) Communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in shrimp ponds. Ann Microbiol 65:267–278CrossRefGoogle Scholar
  33. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849CrossRefGoogle Scholar
  34. Su Y, Bian G, Zhu Z, Smidt H, Zhu W (2014) Early methanogenic colonisation in the faeces of Meishan and Yorkshire piglets as determined by pyrosequencing analysis. Archaea 2014:547908–547908CrossRefGoogle Scholar
  35. Tomoko S, Yoshimi F, Toru S (2008) Comparison of microbial community structures in intensive and extensive shrimp culture ponds and a mangrove area in Thailand. Fish Sci 74:889–898Google Scholar
  36. Tonge DP, Pashley CH, Gant TW (2014) Amplicon–based metagenomic analysis of mixed fungal samples using proton release amplicon sequencing. PLoS ONE 9:e93849CrossRefGoogle Scholar
  37. Webster G, O’Sullivan LA, Meng Y, Williams AS, Sass AM, Watkins AJ, Parkes RJ, Weightman AJ (2014) Archaeal community diversity and abundance changes along a natural salinity gradient in estuarine sediments. FEMS Microbiol Ecol 91:1–18CrossRefGoogle Scholar
  38. Xie W, Zhang C, Zhou X, Wang P (2014) Salinity-dominated change in community structure and ecological function of Archaea from the lower Pearl River to coastal South China Sea. Appl Microbiol Biotechnol 98:7971–7982CrossRefGoogle Scholar
  39. Zhang M, Liao M, Dapeng LI, Shimin LU, Chen J, Xugang HE (2013) Effects of three kinds of antibiotic on the nitrification and the growth of ammonia-oxidizing microorganism in freshwater aquaculture pond sediment. Fish Modernization 3:25–36 (in Chinese)Google Scholar
  40. Zhang DP, Wei M, Qiu QF, Wang CL (2016) Seasonal variations of ammonia-oxidizing archaea in two kinds of ponds of Portunus trituberculatus. J Biol 1:21–26 (in Chinese)Google Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Limin Fan
    • 1
    • 2
  • Kamira Barry
    • 2
  • Leilei Shi
    • 2
  • Chao Song
    • 1
  • Shunlong Meng
    • 1
  • Liping Qiu
    • 1
  • Gengdong Hu
    • 1
  • Yao Zheng
    • 1
  • Fajun Li
    • 3
  • Jiazhang Chen
    • 1
  • Pao Xu
    • 1
    • 2
  1. 1.Freshwater Fisheries Research Center, Chinese Academy of Fishery SciencesScientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze RiverWuxiChina
  2. 2.Nanjing Agricultural University, Wuxi Fisheries CollegeWuxiChina
  3. 3.College of Agronomic SciencesWeifang University of Science and TechnologyShouguangChina

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