Veterinary Research Forum
Vet Res Forum

Using a combination of phospholipid fatty acids profiles and DNA-based sequencing analyses to detect shifts in the biofloc microbial community in different carbon sources and carbon/nitrogen ratios

Document Type : Original Article

Authors

Ebrahim Hossein Najdegerami 1
Ramin Manaffar 2

1 Department of Biology, Faculty of Science, Urmia University, Urmia, Iran

2 Department of Fisheries, Faculty of Natural Resources, Urmia University, Urmia, Iran

https://doi.org/10.30466/vrf.2024.2015189.4060
Abstract
A 35-day study investigated the impact of carbon sources and carbon/nitrogen (C/N) ratios on the microbial community of biofloc. For this purpose, we utilized a combination of phospho-lipid fatty acids (PLFAs) profiles and DNA-based sequencing methods to investigate changes in the microbial community composition and structure. The experiment involved three carbon sources including Dextrin (DEX), corn starch (CS) and wheat bran (WB) at two C/N ratios (19 and 30). The results indicated that WB and CS were found to decrease nitrogen metabolite concentration while increasing total suspended solids and bacterial density compared to DEX. The treatments exhibited variations in microbial communities and the use of polymerase chain reaction/ denaturing gradient gel electrophoresis analysis revealed distinct dominant bacterial species linked to carbon sources and C/N ratios. Furthermore, the highest levels of bacteria and protozoa PLFAs biomarkers were observed in the C/N30 ratio and WB treatment while the ratio for poly-β-hydroxybutyrate/PLFAs and fungi biomarkers displayed a decrease. Also, by incorporating the results of PLFAs profile and conducting a principal component analysis, the treatments were categorized into distinct groups based on both the carbon source and C/N ratios. Overall, both methods yield consistent results. PLFAs offered additional insights into the microbial composition beyond bacterial structure while DNA-based analysis provided finer taxonomic resolution.

Keywords

Biofloc
C/N ratio
Microbial community
Organic carbon
Phospholipid fatty acids

Subjects

  1. The State of World Fisheries and Aquaculture 2020. Sustainability in action. Rome. Available at: https://doi.org/10.4060/ca9229en. Accessed May 16, 2024.
  2. Avnimelech Y. Bio-filters: the need for a new comprehensive approach. Aquac Eng 2006; 34(3): 172-178.
  3. Ray AJ, Lewis BL, Browdy CL, et al. Suspended solids removal to improve shrimp (Litopenaeus vannamei) production and an evaluation of a plant-based feed in minimal-exchange, superintensive culture systems. Aquaculture 2010; 299(1-4): 89-98.
  4. van Kessel MA, Harhangi HR, van de Pas-Schoonen K, et al. Biodiversity of N-cycle bacteria in nitrogen removing moving bed biofilters for freshwater recirculating aquaculture systems. Aquaculture 2010; 306(1-4): 177-184.
  5. Panigrahi A, Saranya C, Sundaram M, et al. Carbon: Nitrogen (C: N) ratio level variation influences microbial community of the system and growth as well as immunity of shrimp (Litopenaeus vannamei) in biofloc based culture system. Fish Shellfish Immunol 2018; 81: 329-337.
  6. Wei YF, Wang AL, Liao SA. Effect of different carbon sources on microbial community structure and composition of ex-situ biofloc formation. Aquaculture 2020; 515: 734492.doi: 10.1016/j.aquaculture. 2019.734492.
  7. Deng M, Chen J, Gou J, et al. The effect of different carbon sources on water quality, microbial community and structure of biofloc systems. Aquaculture 2018; 482: 103-110.
  8. Loreau M, Naeem S, Inchausti P, et al. Biodiversity and ecosystem functioning: current knowledge and future challenges. Science 2001; 294(5543): 804-808.
  9. Qin Y, Hou J, Deng M, et al. Bacterial abundance and diversity in pond water supplied with different feeds. Sci Rep 2016; 6: 35232. doi: 10.1038/srep35232.
  10. Cardona E, Lorgeoux B, Chim L, et al. Biofloc contribution to antioxidant defence status, lipid nutrition and reproductive performance of broodstock of the shrimp Litopenaeus stylirostris: consequences for the quality of eggs and larvae. Aquaculture 2016; 452: 252-262.
  11. Torsvik V, Salte K, Sørheim R, et al. Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 1990; 56(3): 776-781.
  12. Øvreås L, Torsvik VV. Microbial diversity and community structure in two different agricultural soil communities. Microb Ecol 1998; 36(3): 303-315.
  13. Frostegård Å, Tunlid A, Bååth, E. Use and misuse of PLFA measurements in soils. Soil Biol Biochem 2011; 43(8): 1621-1625.
  14. McKinley VL, Peacock AD, White DC. Microbial community PLFA and PHB responses to ecosystem restoration in tallgrass prairie soils. Soil Biol Biochem 2005; 37(10):1946-1958.
  15. Zhao C, Miao Y, Yu C, et al. Soil microbial community composition and respiration along an experimental precipitation gradient in a semiarid steppe. Sci Rep 2016; 6: 24317. doi: 10.1038/srep24317.
  16. Chen H, Zhao X, Lin Q, et al. Using a combination of PLFA and DNA-based sequencing analyses to detect shifts in the soil microbial community composition after a simulated spring precipitation in a semi-arid grassland in China. Sci Total Environ 2019; 657: 1237-1245.
  17. Fanin N, Kardol P, Farrell M, et al. The ratio of Gram-positive to Gram-negative bacterial PLFA markers as an indicator of carbon availability in organic soils. Soil Biol Biochem 2019; 128: 111-114.
  18. Lepage G, Roy CC. Improved recovery of fatty acid through direct transesterification without prior extraction or purification. J Lipid Res 1984; 25(12): 1391-1396.
  19. Hinojosa M.B, García-Ruiz R, Carreira JA. Utilizing microbial community structure and function to evaluate the health of heavy metal polluted soils. In: Soil heavy metals. soil biology, vol 19. Berlin, Geremany: Springer 2010; 185-224.
  20. Laranja JL, Ludevese-Pascual GL, Amar EC, et al. Poly-β-hydroxybutyrate (PHB) accumulating Bacillus spp. improve the survival, growth, and robustness of Penaeus monodon (Fabricius, 1798) postlarvae. Vet Microbiol 2014; 17(3-4)3: 310-317.
  21. Standard methods for examination of water and waste‐water. Washington DC, USA: American Public Health Association 1992; 465-478.
  22. Boon N, Windt W, Verstraete W, et al. Evaluation of nested PCR–DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol Ecol 2002; 39(2): 101-112.
  23. Ferreira LM, Lara G, Wasielesky W Jr, et al. Biofilm versus biofloc: are artificial substrates for biofilm production necessary in the BFT system? Aquac Int 2016; 24(4): 921-930.
  24. Chasoy GR, Chairez I, Durán-Páramo E. Carbon/ nitrogen ratio and initial pH effects on the optimization of lactic acid production by Lactobacillus casei subsp casei NRRL-441. Carbon 2020; 27(10): 37-59.
  25. Wang Y, Zou YL, Chen H, et al. Nitrate removal performances of a new aerobic denitrifier, Acinetobacter haemolyticus ZYL, isolated from domestic wastewater. Bioprocess Biosyst Eng 2021; 44(2): 391-401.
  26. Li W, Shi C, Yu Y, et al. Interrelationships between tetracyclines and nitrogen cycling processes mediated by microorganisms: a review. Bioresour Technol 2021; 319: 124036. doi: 10.1016/j.biortech.2020.124036.
  27. Zhao C, Wang Y, Wang Y, et al. Insights into the role of earthworms on the optimization of microbial community structure during vermicomposting of sewage sludge by PLFA analysis. Waste Manag 2018; 79: 700-708.
  28. Drenovsky RE, Elliott GN, Graham KJ, et al. Comparison of phospholipid fatty acid (PLFA) and total soil fatty acid methyl esters (TSFAME) for characterizing soil microbial communities. Soil Biol Biochem 2004; 36: 1793-1800.
  29. Ertefai TF, Fisher MC, Fredricks HF, et al. Vertical distribution of microbial lipids and functional genes in chemically distinct layers of a highly polluted meromictic lake. Org Geochem 2008; 39(11): 1572-1588.
  30. Carr SA, Vogel SW, Dunbar RB, et al. Bacterial abundance and composition in marine sediments beneath the Ross Ice Shelf, Antarctica. Geobiology 2013; 11(4): 377-395.
  31. Kunihiro T, Veuger B, Vasquez-Cardenas D, et al. Phospholipid-derived fatty acids and quinones as markers for bacterial biomass and community structure in marine sediments. PLoS One 2014; 9: e96219. doi: 10.1371/journal.pone.0096219.
  32. Lagerlöf J, Adolfsson L, Börjesson G, et al. Land-use intensification and agroforestry in the Kenyan highland: impacts on soil microbial community composition and functional capacity. Appl Soil Ecol 2014; 82: 93-99.
  33. Bossio DA, Scow KM. Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilization patterns. Microb Ecol 1998; 35(3): 265-278.
  34. Wang M, Wu Y, Zhu J, et al. The new developments made in the autotrophic and heterotrophic ammonia oxidation. IOP Con Ser Earth Environ Sci 2018; 178(1): 012016. doi: 10.1088/1755-1315/178/1/012016.
  35. Barak Y, van Rijn J. Atypical polyphosphate accumulation by the denitrifying bacterium Paracoccus denitrificans, Appl Environ Microbiol 2000; 66(3): 1209-1212.
  36. Gómez-Brandón M, Aira M, Lores M, et al. Changes in microbial community structure and function during vermicomposting of pig slurry. Bioresour. Technol 2011; 102(5): 4171-4178.
  37. Lange M, Habekost M, Eisenhauer N, et al. Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland, PloS One 2014; 9(5): e96182. doi: 10.1371/journal.pone.0096182.
  38. Shoda M, Ishikawa Y. Heterotrophic nitrification and aerobic denitrification of high-strength ammonium in anaerobically digested sludge by Alcaligenes faecalis strain No. 4. J Biosci Bioeng 2014; 117(6): 737-741.
  39. Kowalchuk GA, Stephen JR. Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 2001; 55: 485-529.
  40. Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol 2018; 16(5): 263-276.
  41. Thomas KL, Lloyd D, Boddy L. Effects of oxygen, pH and nitrate concentration on denitrification by Pseudomonas species. FEMS Microbiol Lett 1994; 118(1-2): 181-186.
  42. Kong Q, Wang ZB, Niu PF, et al. Greenhouse gas emission and microbial community dynamics during simultaneous nitrification and denitrification process. Bioresour Technol 2016; 210: 94-100.
  43. Zhao C, Xing M, Yang J, et al. Microbial community structure and metabolic property of biofilms in vermifiltration for liquid-state sludge stabilization using PLFA profiles. Bioresour Technol 2014; 151: 340-346.
Veterinary Research Forum
Volume 15, Issue 8
August 2024
Pages 425-434

  • Receive Date 11 November 2023
  • Revise Date 13 January 2024
  • Accept Date 04 March 2024

Home

Guide for Authors

Submit Manuscript

Reviewers

Contact Us