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Olga Muter
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Muter, O. Sources of Microorganisms for Bioaugmentation. Encyclopedia. Available online: https://encyclopedia.pub/entry/42374 (accessed on 04 July 2024).
Muter O. Sources of Microorganisms for Bioaugmentation. Encyclopedia. Available at: https://encyclopedia.pub/entry/42374. Accessed July 04, 2024.
Muter, Olga. "Sources of Microorganisms for Bioaugmentation" Encyclopedia, https://encyclopedia.pub/entry/42374 (accessed July 04, 2024).
Muter, O. (2023, March 21). Sources of Microorganisms for Bioaugmentation. In Encyclopedia. https://encyclopedia.pub/entry/42374
Muter, Olga. "Sources of Microorganisms for Bioaugmentation." Encyclopedia. Web. 21 March, 2023.
Sources of Microorganisms for Bioaugmentation
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This entry is adapted from the peer-reviewed paper 10.3390/microorganisms11030710

Bioremediation encompasses a broad range of environmental biotechnologies, which require multidisciplinary approaches through implementation of innovative tools to the natural biological processes occurring in soil, water, and air. The addition of microbial biomass (bacteria, fungi, and their secreted enzymes) to contaminated areas, i.e., the process of bioaugmentation, can be adapted to the green environment and can notably improve an area’s pollutant removal efficiency (RE), as well as reduce their removal time and costs.

bioaugmentation contamination microbial succession

1. Introduction

Bioremediation encompasses a broad range of environmental biotechnologies, which require multidisciplinary approaches through implementation of innovative tools to the natural biological processes occurring in soil, water, and air. The addition of microbial biomass (bacteria, fungi, and their secreted enzymes) to contaminated areas, i.e., the process of bioaugmentation, can be adapted to the green environment and can notably improve an area’s pollutant removal efficiency (RE), as well as reduce their removal time and costs [1]. However, bioaugmentation under controlled conditions in the field remains challenging, due to the biodiversity of a whole system, competition between microbial agents and indigenous microorganisms, substrate competition, climatic conditions, remediation cycles, and other factors. To select an optimal bioaugmentation strategy, further studies on the interactions of different functional bacteria related to their resistance to multiple stress factors, enzyme activity and system robustness are needed [2]. Rigorous research and critical analyses of available databases, as well as the incorporation of genetic engineering, nanotechnology, and systems biology can bring bioremediation to a more advanced level [3].
Bioaugmentation is a site-specific approach. Thus, recent research publications and reviews on bioaugmentation have focused on the following aspects: thermophilic reductive dechlorination [4][5]; the psychrophilic treatment of groundwaters [6]; microbially induced calcium carbonate precipitation techniques to mitigate the wind-induced erosion of calcareous desert sand [7]; hydrocarbon biodegradation in freshwater sediments from historically contaminated lakes [8]; the bacterial remediation of pesticide-polluted soils [3], emerging trends in the remediation of organic contaminated soils as a whole [9]; mechanisms of microbial activity in heavy metal removal [10]; comparisons of autochthonous and allochthonous bioaugmentation [11]; the stimulation of plant growth in bioaugmented hydroponic systems [12]; and the bioaugmentation of wastewaters (WWs) with yeast in the presence of antimicrobials [13], among others.

2. Sources of Microorganisms for Bioaugmentation

There are abundant data available on the variations and successions of microbial communities upon bioaugmentation-assisted remediation where the introduced microbial “agent” disappears during the remediation process. However, positive effects on biodegradation dynamics have been detected.
In a study of the bioremediation of hydrocarbon-contaminated lake sediments, a 32-day batch incubation in (i) biostimulated (N), (ii) biostimulated and bioaugmented (NB), and (iii) unamended (K) sets resulted in an increasing abundance of Proteobacteria from 48.8% in the raw sediments to 59.3%, 58.0%, and 61.7%, respectively, mainly due to an increase in Betaproteobacteria. The relative abundance of the Pseudomonas genus (Gammaproteobacteria) was the highest in the (N) set at 35.8%, compared to 17.5% and 21.0% for the (K) and (NB) sets, respectively. The genera that dominated in the inoculum (allochthonous) were identified as Citrobacter (29.5%), Klebsiella (24.5%), Pseudomonas (15.5%), and Aeromonas (11.3%). The concentration of hydrocarbons in the lake sediments during the 32-day incubation decreased on average from 465 mg/kg to 165 mg/kg and 117.5 mg/kg in the (N) and (NB) sets, respectively [8].
Another study focused on the effect of two allochthonous bacterial consortia on the growth of Mentha aquatica in a hydroponic system. After the 47-day hydroponic greenhouse experiment, the structure of the bacterial communities attached to expanded clay pellets was represented mostly by Proteobacteria at the phylum level (80–90%). Bioaugmentation provided significant (p < 0.05) stimulation for the growth of M. aquatica, although the metagenome analysis of the rhizosphere did not reveal any abundance of bacterial strains, which were introduced into the hydroponic media at the beginning of the experiment [12].
The bioaugmentation of municipal sewage sludge/straw substrate with an autochthonous bacterial consortium resulted in a marked shift in the microbial community structure. Particularly, the raw sewage sludge contained Firmicutes/Proteobacteria/Actinobacteria at levels of 4.4%/60.2%/26.5%, respectively, while the inoculum for bioaugmentation, which was prepared using a selective broth, contained these phyla in proportions of 92.13%/1.7%/5.1%, respectively. After 16 days of batch incubation, the proportions varied as follows: (32.7–53.8%)/(30.6–54.3%)/(5.3–13.7%). All treated samples were characterised by an increased abundance of Firmicutes. Yet, an increased abundance of ungrouped reads of Pseudomonas putida was detected in all bioaugmented sets; however, it was not detected in the inoculum. Compared with non-bioaugmented sets, the combination of a wheat straw amendment to a sewage sludge with bioaugmentation showed the highest and most stable microbial respiration intensity, the lowest ammonia emissions, and the highest stimulation effect on cress seedling growth [14]. More recent studies have also shown a positive effect of bioaugmentation on manure composting, which influenced the bacterial response, matter transformation, and metal immobilisation [15].
The effect of the bioaugmentation of activated sludge with viable brewing spent yeast biomass on microbial community structure was studied in the presence of benzalkonium chloride. The added yeast biomass remained viable during 10-day treatment and reduced an inhibitory effect of BAC on Bacilli in activated sludge. Yet, the bioaugmentation stimulated bacterial growth and microbial respiration. At the phylum level, two dominant taxa, i.e., Firmicutes and Proteobacteria, were found in the activated sludge, with their abundance in the control (non-incubated) and all incubated samples ranging between 27–35% and 22–36%, respectively [13].
Recently, Ref. [16] reported that Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria were the dominant phyla during the biodegradation of crude oil. Some key enzymes related to the biodegradation of petroleum products have been detected in Bacillus megaterium (alkane hydroxylase, catechol 1,2-dioxygenase, protocatechol 3,4-dioxygenase), Bacillus pumilus (esterases and lipase), Pseudomonas aeruginosa (catechol 1,2-dioxygenase, protocatechol 3,4-dioxygenase), and Stenotrophomonas maltophilia (catechol 2,3-dioxygenase) [17]. The use of manganese-oxidising Pseudomonas sp. QJX-1 with humic acids as the sole carbon source has been proposed for the removal of pharmaceuticals (caffeine) from drinking water via sand filtration [18]. Furthermore, Rhodococcus spp. are known to play an important role in the biodegradation of organic contaminants, as well as in the recovery of the nitrification performance in the presence of antibacterial agents in activated sludge and other processes [19][20][21]. The catabolic activity of rhodococci involves catabolizing short- and long-chain alkanes, as well as aromatic (halogenated and nitro-substituted), heterocyclic, and polycyclic aromatic compounds. The high adaptability of rhodococci with respect to substrates has previously been reviewed by [22], with an emphasis on hyperrecombination evolutionary strategies. Linear plasmids in the large Rhodococcus genomes store multiple copies of many biodegradative genes [22]. Bacteria of the genera Pseudomonas, Bacillus, and Rhodococcus can be found in a broad range of ecosystems exhibiting extraordinary activities in the breakdown of natural pollutants and xenobiotics and taking part in microbial consortia and/or endophytic cooperation.
Although the overall microbial community structure in organics-polluted sites commonly depends on the geographic location [23], some bacterial genera are often predominant.
On the one hand, Bacillus spp., Pseudomonas spp., and Rhodococcus spp. appear to be dominant because of microbial succession upon biodegradation. On the other hand, researchers frequently use these bacteria as an inoculum for bioaugmentation [1][24].

References

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  2. Chen, Y.; Wang, S.; Geng, N.; Wu, Z.; Xiong, W.; Su, H. Artificially constructing mixed bacteria system for bioaugmentation of nitrogen removal from saline wastewater at low temperature. J. Environ. Manag. 2022, 324, 116351.
  3. Bokade, P.; Gaur, V.K.; Tripathi, V.; Bobate, S.; Manickam, N.; Bajaj, A. Bacterial remediation of pesticide polluted soils: Exploring the feasibility of site restoration. J. Hazard. Mater. 2023, 441, 129906.
  4. Hudari, M.S.B.; Richnow, H.; Vogt, C.; Nijenhuis, I. Effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: A review. FEMS Microbiol. Ecol. 2022, 98, fiac081.
  5. Dutta, N.; Usman, M.; Ashraf, M.A.; Luo, G.; Zhang, S. A critical review of recent advances in the bio-remediation of chlorinated substances by microbial dechlorinators. Chem. Eng. J. Adv. 2022, 12, 100359.
  6. Demir, Ö.; Atasoy, A.D.; Çalış, B.; Çakmak, Y.; Di Capua, F.; Sahinkaya, E.; Uçar, D. Impact of temperature and biomass augmentation on biosulfur-driven autotrophic denitrification in membrane bioreactors treating real nitrate-contaminated groundwater. Sci. Total Environ. 2022, 853, 158470.
  7. Dagliya, M.; Satyam, N.; Sharma, M.; Garg, A. Experimental study on mitigating wind erosion of calcareous desert sand using spray method for microbially induced calcium carbonate precipitation. J. Rock Mech. Geotech. Eng. 2022, 14, 1556–1567.
  8. Kalneniece, K.; Gudra, D.; Lielauss, L.; Selga, T.; Fridmanis, D.; Terauds, J.; Muter, O. Batch-mode stimulation of hydrocarbons biodegradation in freshwater sediments from historically contaminated Alūksne lake. J. Contam. Hydrol. 2022, 253, 104103.
  9. Gao, D.; Zhao, H.; Wang, L.; Li, Y.; Tang, T.; Bai, Y.; Liang, H. Current and emerging trends in bioaugmentation of organic contaminated soils: A review. J. Environ. Manag. 2022, 320, 115799.
  10. Sharma, P.; Parakh, S.K.; Singh, S.P.; Parra-Saldivar, R.; Kim, S.-H.; Varjani, S.; Tong, Y.W. A critical review on microbes-based treatment strategies for mitigation of toxic pollutants. Sci. Total Environ. 2022, 834, 155444.
  11. Ntroumpogianni, G.C.; Giannoutsou, E.; Karagouni, A.D.; Savvides, A.L. Bacterial Isolates from Greek Sites and Their Efficacy in Degrading Petroleum. Sustainability 2022, 14, 9562.
  12. Kalniņš, M.; Andersone-Ozola, U.; Gudra, D.; Sierina, A.; Fridmanis, D.; Ievinsh, G.; Muter, O. Effect of bioaugmentation on the growth and rhizosphere microbiome assembly of hydroponic cultures of Mentha aquatica. Ecol. Genet. Genom. 2022, 22, 100107.
  13. Zorza, L.; Kalnins, M.; Gudra, D.; Megnis, K.; Fridmanis, D.; Rapoport, A.; Muter, O. Changes in Bacterial Community Structure in Wastewaters in the presence of Saccharomyces Cerevisiae and Benzalkonium Chloride. IOP Conf. Ser. Earth Environ. Sci. 2022, 987, 012010.
  14. Rimkus, A.; Gudrā, D.; Dubova, L.; Fridmanis, D.; Alsiņa, I.; Muter, O. Stimulation of sewage sludge treatment by carbon sources and bioaugmentation with a sludge-derived microbial consortium. Sci. Total Environ. 2021, 783, 146989.
  15. Wang, C.; Jia, Y.; Li, J.; Li, P.; Wang, Y.; Yan, F.; Wu, M.; Fang, W.; Xu, F.; Qiu, Z. Influence of microbial augmentation on contaminated manure composting: Metal immobilization, matter transformation, and bacterial response. J. Hazard. Mater. 2023, 441, 129762.
  16. Pi, Y.R.; Bao, M.T. Investigation of kinetics in bioaugmentation of crude oil via high-throughput sequencing: Enzymatic activities, bacterial community composition and functions. Pet. Sci. 2022, 19, 1905–1914.
  17. Meyer, D.D.; Beker, S.A.; Bucker, F.; Peralba, M.C.R.; Frazzon, A.P.G.; Osti, J.F.; Andreazza, R.; Camargo, F.A.O.; Bento, F.M. Bioremediation strategies for diesel and biodiesel in oxisol from southern Brazil. Int. Biodeterior. Biodegrad. 2014, 95, 356–363.
  18. Ye, T.; Liu, H.; Qi, W.; Qu, J. Removal of pharmaceutical in a biogenic/chemical manganese oxide system driven by manganese-oxidizing bacteria with humic acids as sole carbon source. J. Environ. Sci. 2023, 126, 734–741.
  19. Guo, Y.; Gao, J.; Zhao, Y.; Liu, Y.; Zhao, M.; Li, Z. Mitigating the inhibition of antibacterial agent chloroxylenol on nitrification system-The role of Rhodococcus ruber in a bioaugmentation system. J. Hazard. Mater. 2023, 447, 130758.
  20. Zhu, G.; Zhang, H.; Yuan, R.; Huang, M.; Liu, F.; Li, M.; Zhang, Y.; Rittmann, B.E. How Comamonas testosteroni and Rhodococcus ruber enhance nitrification in the presence of quinoline. Water Res. 2023, 229, 119455.
  21. Bai, F.; Tian, H.; Wang, C.; Ma, J. Treatment of nanofiltration concentrate of landfill leachate using advanced oxidation processes incorporated with bioaugmentation. Environ. Pollut. 2023, 318, 120827.
  22. Larkin, M.J.; Kulakov, L.A.; Allen, C.C.R. Biodegradation and Rhodococcus-Masters of catabolic versatility. Curr. Opin. Biotechnol. 2005, 16, 282–290.
  23. Liang, Y.; Van Nostrand, J.D.; Deng, Y.; He, Z.; Wu, L.; Zhang, X.; Li, G.; Zhou, J. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J. 2011, 5, 403–413.
  24. Lara-Moreno, A.; Morillo, E.; Merchán, F.; Madrid, F.; Villaverde, J. Bioremediation of a trifluralin contaminated soil using bioaugmentation with novel isolated bacterial strains and cyclodextrin. Sci. Total Environ. 2022, 840, 156695.
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Olga Muter
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