Microbial Ecology

, Volume 66, Issue 3, pp 500–511 | Cite as

Microbial Community Assembly and Succession on Lake Sturgeon Egg Surfaces as a Function of Simulated Spawning Stream Flow Rate

  • Masanori Fujimoto
  • James A. Crossman
  • Kim T. Scribner
  • Terence L. MarshEmail author
Microbiology of Aquatic Systems


We investigated microbial succession on lake sturgeon (Acipenser fulvescens) egg surfaces over the course of their incubation period as a function of simulated stream flow rate. The primary objective was to characterize the microbial community assembly during succession and to examine how simulated stream flow rate affect the successional process. Sturgeon eggs were reared under three flow regimes; high (0.55 m/s), low (0.18 m/s), and variable (0.35 and 0.11 m/s alternating 12 h intervals). Eggs were collected from each flow regime at different egg developmental stages. Microbial community DNA was extracted from egg surface and the communities were examined using 16S rRNA gene-based terminal restriction fragment length polymorphism and 454 pyrosequencing. Analysis of these datasets using principal component analysis revealed that microbial communities were clustered by egg developmental stages (early, middle, and late) regardless of flow regimes. 454 pyrosequencing data suggested that 90–98 % of the microbial communities were composed of the phyla Proteobacteria and Bacteroidetes throughout succession. β-Protebacteria was more dominant in the early stage, Bacteroidetes became more dominant in the middle stage, and α-Proteobacteria became dominant in the late stage. A total of 360 genera and 5,826 OTUs at 97 % similarity cutoff were associated with the eggs. Midway through egg development, the egg-associated communities of the low flow regime had a higher diversity than those communities developed under high or variable flow regimes. Results show that microbial community turnover occurred during embryogenesis, and stream flow rate influenced the microbial succession processes on the sturgeon egg surfaces.


Microbial Community Flow Regime Terminal Restriction Fragment Length Polymorphism Microbial Community Composition Lake Sturgeon 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We gratefully acknowledge the hard work and dedication of our field crew and colleagues: Christin Davis, Patrick Forsythe, and Edward Baker contributed to experimental setup and implementation. We thank the Michigan Department of Natural Resources, the Great Lakes Fishery Trust, Michigan Agricultural Experiment Station, the Center for Water Sciences, Sustainable Michigan Environmental Program, and a USGS grant to TLM for providing funding for this project.

Supplementary material

248_2013_256_MOESM1_ESM.pdf (135 kb)
Online Resource 1 Bray–Curtis dissimilarity table that summarized time and flow effect on the egg surface microbial communities (PDF 135 kb)
248_2013_256_MOESM2_ESM.pdf (170 kb)
Online Resource 2 Examples of the association of certain microbial phylotypes with certain egg developmental stages. The dotted line (linear coefficient = −1.89, R 2 = 0.44), solid line (quadratic coefficient = −2.83, R 2 = 0.23), and breaking line (linear coefficient = 1.61, R 2 = 0.55) represent regression lines for PT3, PT7, and PT16, respectively. HhaI data were used for the analysis (PDF 169 kb)
248_2013_256_MOESM3_ESM.pdf (114 kb)
Online Resource 3 Principle component loading plots displaying temporal distributions of 25 major microbial phylotypes (PT) associated with the egg surface. PC1 and PC2 account for 27.9 % and 13.6 % of the data variation, respectively. HhaI-digested TRFLP data were used for the analysis (PDF 114 kb)
248_2013_256_MOESM4_ESM.pdf (91 kb)
Online Resource 4 Jaccard index tree constructed using OTUs at 97 % similarity cutoff (PDF 90 kb)
248_2013_256_MOESM5_ESM.pdf (469 kb)
Online Resource 5 Complete listings of detected genera (PDF 469 kb)
248_2013_256_MOESM6_ESM.pdf (99 kb)
Online Resource 6 Rarefaction analysis for pyrosequencing data (PDF 99 kb)
248_2013_256_MOESM7_ESM.pdf (21 kb)
Online Resource 7 Water microbial community collected in a different year from the same stream (PDF 20.6 kb)
248_2013_256_MOESM8_ESM.pdf (10 kb)
Online Resource 8 Ambient water temperature throughout the egg incubation periods. Solid line is a linear regression line for daily mean temperature (PDF 10 kb)


  1. 1.
    Connell JH, Slatyer RO (1977) Mechanisms of succession in natural communities and their role in community stability and organization. Am Nat 111:1119–1144CrossRefGoogle Scholar
  2. 2.
    Favier CF, Vaughan EE, De Vos WM, Akkermans ADL (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68:219–226PubMedCentralCrossRefPubMedGoogle Scholar
  3. 3.
    Fierer N, Hamady M, Lauber CL, Knight R (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 105:17994–17999PubMedCentralCrossRefPubMedGoogle Scholar
  4. 4.
    Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5:e177PubMedCentralCrossRefPubMedGoogle Scholar
  5. 5.
    Redford A, Fierer N (2009) Bacterial succession on the leaf surface: a novel system for studying successional dynamics. Microb Ecol 58:189–198CrossRefPubMedGoogle Scholar
  6. 6.
    Jackson CR, Churchill PF, Roden EE (2001) Successional changes in bacterial assemblage structure during epilithic biofilm development. Ecology 82:555–566CrossRefGoogle Scholar
  7. 7.
    Lyautey E, Jackson C, Cayrou J, Rols JL, Garabétian F (2005) Bacterial community succession in natural river biofilm assemblages. Microb Ecol 50:589–601CrossRefPubMedGoogle Scholar
  8. 8.
    Martiny AC, Jorgensen TM, Albrechtsen H-J, Arvin E, Molin S (2003) Long-term succession of structure and diversity of a biofilm formed in a model drinking water distribution system. Appl Environ Microbiol 69:6899–6907PubMedCentralCrossRefPubMedGoogle Scholar
  9. 9.
    Okabe S, Odagiri M, Ito T, Satoh H (2007) Succession of sulfur-oxidizing bacteria in the microbial community on corroding concrete in sewer systems. Appl Environ Microbiol 73:971–980PubMedCentralCrossRefPubMedGoogle Scholar
  10. 10.
    Székely A, Sipos R, Berta B, Vajna B, Hajdú C, Márialigeti K (2009) DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost. Microb Ecol 57:522–533CrossRefPubMedGoogle Scholar
  11. 11.
    Fierer N, Nemergut D, Knight R, Craine JM (2010) Changes through time: integrating microorganisms into the study of succession. Res Microbiol 161:635–642CrossRefPubMedGoogle Scholar
  12. 12.
    Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103:626–631PubMedCentralCrossRefPubMedGoogle Scholar
  13. 13.
    Harris RN, Brucker RM, Walke JB, Becker MH, Schwantes CR, Flaherty DC, Lam BA, Woodhams DC, Briggs CJ, Vredenburg VT, Minbiole KPC (2009) Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus. ISME J 3:818–824CrossRefPubMedGoogle Scholar
  14. 14.
    Dethlefsen L, McFall-Ngai M, Relman DA (2007) An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature 449:811–818CrossRefPubMedGoogle Scholar
  15. 15.
    Besemer K, Singer G, Hodl I, Battin TJ (2009) Bacterial community composition of stream biofilms in spatially variable-flow environments. Appl Environ Microbiol 75:7189–7195PubMedCentralCrossRefPubMedGoogle Scholar
  16. 16.
    Besemer K, Singer G, Limberger R, Chlup A-K, Hochedlinger G, Hödl I, Baranyi C, Battin TJ (2007) Biophysical controls on community succession in stream biofilms. Appl Environ Microbiol 73:4966–4974PubMedCentralCrossRefPubMedGoogle Scholar
  17. 17.
    Al-Holy MA, Rasco BA (2006) Characterization of salmon (Oncorhynchus keta) and sturgeon (Acipenser transmontanus) caviar proteins. J Food Biochem 30:422–428CrossRefGoogle Scholar
  18. 18.
    Chadwick T, Wright P (1999) Nitrogen excretion and expression of urea cycle enzymes in the atlantic cod (Gadus morhua l.): a comparison of early life stages with adults. J Exp Biol 202:2653–2662PubMedGoogle Scholar
  19. 19.
    Steele SL, Chadwick TD, Wright PA (2001) Ammonia detoxification and localization of urea cycle enzyme activity in embryos of the rainbow trout (Oncorhynchus mykiss) in relation to early tolerance to high environmental ammonia levels. J Exp Biol 204:2145–2154PubMedGoogle Scholar
  20. 20.
    Kudo S (2000) Enzymes responsible for the bactericidal effect in extracts of vitelline and fertilisation envelopes of rainbow trout eggs. Zygote 8:257–265CrossRefPubMedGoogle Scholar
  21. 21.
    Saurabh S, Sahoo PK (2008) Lysozyme: an important defence molecule of fish innate immune system. Aquacult Res 39:223–239CrossRefGoogle Scholar
  22. 22.
    Adams PB, Grimes C, Hightower JE, Lindley ST, Moser ML, Parsley MJ (2007) Population status of North American green sturgeon, Acipenser medirostris. Environ Biol Fish 79:339–356CrossRefGoogle Scholar
  23. 23.
    Baker EA, Borgeson DJ (1999) Lake sturgeon abundance and harvest in Black Lake, Michigan, 1975–1999. N Am J Fish Manage 19:1080–1088CrossRefGoogle Scholar
  24. 24.
    Smith KM, Baker EA (2005) Characteristics of spawning lake sturgeon in the Upper Black River, Michigan. N Am J Fish Manage 25:301–307CrossRefGoogle Scholar
  25. 25.
    Forsythe PS (2010) Exogenous correlates of migration, spawning, egg deposition and egg mortality in the lake sturgeon (Acipenser fulvescens). Ph.D. Dissertation. Department of Fisheries and Wildlife. Michigan State University. #3417681. pp191Google Scholar
  26. 26.
    Auer NA (1996) Response of spawning lake sturgeons to change in hydroelectric facility operation. T Am Fish Soc 125:66–77CrossRefGoogle Scholar
  27. 27.
    Haxton TJ (2006) Characteristics of a lake sturgeon spawning population sampled a half century apart. J Great Lakes Res 32:124–130CrossRefGoogle Scholar
  28. 28.
    Jager HI, Chandler JA, Lepla KB, Van Winkle W (2001) A theoretical study of river fragmentation by dams and its effects on white sturgeon populations. Environ Biol Fish 60:347–361CrossRefGoogle Scholar
  29. 29.
    Paragamian VL, Kruse G, Wakkinen V (2001) Spawning habitat of Kootenai River white sturgeon, post-Libby Dam. N Am J Fish Manage 21:22–33CrossRefGoogle Scholar
  30. 30.
    Crossman JA (2008) Evaluating collection, rearing, and stocking methods for lake sturgeon (Acipenser fulvescens) restoration programs in the great lakes. Ph.D. Dissertation. Department of Fisheries and Wildlife. Michigan State University. #3331889. pp.192Google Scholar
  31. 31.
    Liu W, Marsh T, Cheng H, Forney L (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63:4516–4522PubMedCentralPubMedGoogle Scholar
  32. 32.
    Marsh TL (1999) Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 2:323–327CrossRefPubMedGoogle Scholar
  33. 33.
    Konstantinidis KT, Isaacs N, Fett J, Simpson S, Long DT, Marsh TL (2003) Microbial diversity and resistance to copper in metal-contaminated lake sediment. Microb Ecol 45:191–202CrossRefPubMedGoogle Scholar
  34. 34.
    Tom-Petersen A, Leser TD, Marsh TL, Nybroe O (2003) Effects of copper amendment on the bacterial community in agricultural soil analyzed by the T-RFLP technique. FEMS Microbiol Ecol 46:53–62CrossRefPubMedGoogle Scholar
  35. 35.
    Dunbar J, Ticknor LO, Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of Terminal Restriction Fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67:190–197PubMedCentralCrossRefPubMedGoogle Scholar
  36. 36.
    Hackl E, Zechmeister-Boltenstern S, Bodrossy L, Sessitsch A (2004) Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl Environ Microbiol 70:5057–5065PubMedCentralCrossRefPubMedGoogle Scholar
  37. 37.
    Anderson-Glenna MJ, Bakkestuen V, Clipson NJW (2008) Spatial and temporal variability in epilithic biofilm bacterial communities along an upland river gradient. FEMS Microbiol Ecol 64:407–418CrossRefPubMedGoogle Scholar
  38. 38.
    Aburto A, Fahy A, Coulon F, Lethbridge G, Timmis KN, Ball AS, McGenity TJ (2009) Mixed aerobic and anaerobic microbial communities in benzene-contaminated groundwater. J Appl Microbiol 106:317–328CrossRefPubMedGoogle Scholar
  39. 39.
    Quaak FCA, Kuiper I (2011) Statistical data analysis of bacterial t-RFLP profiles in forensic soil comparisons. Forensic Sci Int 210:96–101CrossRefPubMedGoogle Scholar
  40. 40.
    Bray JR, Curtis JT (1957) An ordination of the upland forest communities of Southern Wisconsin. Ecol Monogr 27:325–349CrossRefGoogle Scholar
  41. 41.
    R Development Core Team (2009) R: A language and environment for statistical computing. R foundation for Statistical Computing, Vienna, AustriaGoogle Scholar
  42. 42.
    Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Consortium THM, Petrosino JF, Knight R, Birren BW (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504PubMedCentralCrossRefPubMedGoogle Scholar
  43. 43.
    Brinkman BM, Hildebrand F, Kubica M, Goosens D, Del Favero J, Declercq W, Raes J, Vandenabeele P (2011) Caspase deficiency alters the murine gut microbiome. Cell Death Dis 2:e220PubMedCentralCrossRefPubMedGoogle Scholar
  44. 44.
    Preidis GA, Saulnier DM, Blutt SE, Mistretta T-A, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, Versalovic J (2012) Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. FASEB J 26:1960–1969PubMedCentralCrossRefPubMedGoogle Scholar
  45. 45.
    Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145PubMedCentralCrossRefPubMedGoogle Scholar
  46. 46.
    Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267PubMedCentralCrossRefPubMedGoogle Scholar
  47. 47.
    Legendre P, Gallagher ED (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129:271–280CrossRefGoogle Scholar
  48. 48.
    Fraune S, Augustin R, Anton-Erxleben F, Wittlieb J, Gelhaus C, Klimovich VB, Samoilovich MP, Bosch TCG (2010) In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides. Proc Natl Acad Sci USA 107:18067–18072PubMedCentralCrossRefPubMedGoogle Scholar
  49. 49.
    Fraune S, Augustin R, Bosch TCG (2011) Embryo protection in contemporary immunology: why bacteria matter. Commun Integr Biol 4:369–372PubMedCentralCrossRefPubMedGoogle Scholar
  50. 50.
    Callewaert L, Michiels C (2010) Lysozymes in the animal kingdom. J Biosci 35:127–160CrossRefPubMedGoogle Scholar
  51. 51.
    Besemer K, Peter H, Logue JB, Langenheder S, Lindstrom ES, Tranvik LJ, Battin TJ (2012) Unraveling assembly of stream biofilm communities. ISME J 6:1459–1468PubMedCentralCrossRefPubMedGoogle Scholar
  52. 52.
    Lamy D, Obernosterer I, Laghdass M, Artigas LF, Breton E, Grattepanche JD, Lecuyer E, Degros N, Lebaron P, Christaki U (2009) Temporal changes of major bacterial groups and bacterial heterotrophic activity during a Phaeocystis globosa bloom in the eastern English Channel. Aquat Microb Ecol 58:95–107CrossRefGoogle Scholar
  53. 53.
    Finlay BJ, Clarke KJ (1999) Ubiquitous dispersal of microbial species. Nature 400:828–828CrossRefGoogle Scholar
  54. 54.
    Dumbrell AJ, Nelson M, Helgason T, Dytham C, Fitter AH (2009) Relative roles of niche and neutral processes in structuring a soil microbial community. ISME J 4:337–345CrossRefPubMedGoogle Scholar
  55. 55.
    Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S (2011) A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol R 75:14–49CrossRefGoogle Scholar
  56. 56.
    Rickard AH, McBain AJ, Stead AT, Gilbert P (2004) Shear rate moderates community diversity in freshwater biofilms. Appl Environ Microbiol 70:7426–7435PubMedCentralCrossRefPubMedGoogle Scholar
  57. 57.
    Møller JD, Larsen JL, Madsen L, Dalsgaard I (2003) Involvement of a sialic acid-binding lectin with hemagglutination and hydrophobicity of Flavobacterium psychrophilum. Appl Environ Microbiol 69:5275–5280PubMedCentralCrossRefPubMedGoogle Scholar
  58. 58.
    Basson A, Flemming LA, Chenia HY (2008) Evaluation of adherence, hydrophobicity, aggregation, and biofilm development of Flavobacterium johnsoniae-like isolates. Microb Ecol 55:1–14CrossRefPubMedGoogle Scholar
  59. 59.
    Schneck JL, Caslake LF (2006) Genetic diversity of Flavobacterium columnare isolated from fish collected from warm and cold water. J Fish Dis 29:245–248CrossRefPubMedGoogle Scholar
  60. 60.
    Nematollahi A, Decostere A, Pasmans F, Haesebrouck F (2003) Flavobacterium psychrophilum infections in salmonid fish. J Fish Dis 26:563–574CrossRefPubMedGoogle Scholar
  61. 61.
    Ostland VE, Lumsden JS, Macphee DD, Ferguson HW (1994) Characteristics of Flavobacterium branchiophilum, the cause of salmonid bacterial gill disease in Ontario. J Aquat Anim Health 6:13–26CrossRefGoogle Scholar
  62. 62.
    M-l H, Oivanen P, Hirvelä-koski V (1997) Aeromonas species in fish, fish-eggs, shrimp and freshwater. Int J Food Microbiol 34:17–26CrossRefGoogle Scholar
  63. 63.
    Carling PA (1992) The nature of the fluid boundary layer and the selection of parameters for benthic ecology. Freshwater Biol 28:273–284CrossRefGoogle Scholar
  64. 64.
    Yannarell AC, Triplett EW (2005) Geographic and environmental sources of variation in lake bacterial community composition. Appl Environ Microbiol 71:227–239PubMedCentralCrossRefPubMedGoogle Scholar
  65. 65.
    Sekiguchi H, Watanabe M, Nakahara T, Xu B, Uchiyama H (2002) Succession of bacterial community structure along the Changjiang river determined by denaturing gradient gel electrophoresis and clone library analysis. Appl Environ Microbiol 68:5142–5150PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Masanori Fujimoto
    • 1
    • 2
  • James A. Crossman
    • 3
    • 4
  • Kim T. Scribner
    • 3
    • 5
  • Terence L. Marsh
    • 1
    • 2
    Email author
  1. 1.Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingUSA
  2. 2.The Center for Microbial EcologyMichigan State UniversityEast LansingUSA
  3. 3.Department of Fisheries and WildlifeMichigan State UniversityEast LansingUSA
  4. 4.B.C. HydroCastlegarCanada
  5. 5.Department of ZoologyMichigan State UniversityEast LansingUSA

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