the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 06 Jan 2026
Suspended sediment transport modulated by microbial activities in estuarine waters: Insights from molecular and structural perspectives
Abstract. Suspended sediment transport in coastal estuaries is profoundly shaped by microbial activities, yet the underlying molecular mechanisms remain poorly constrained during their flocculation. Here, we demonstrate that the estuarine bacterium Stutzerimonas decontaminans acts as a key mediator of sediment flocculation. Compared to purely physical aggregation, microbially-induced flocculation developed more slowly but yielded flocs fourfold larger, with looser fractal structures and higher organic carbon content, indicating strong microbial-mineral coupling. Bacteria modulated flocculation both physically via flagella-driven adhesion and biochemically through extracellular polymeric substances, which enhanced particulate organic carbon accumulation. Transcriptomic analyses revealed an early upregulation of flagellar genes initiating particle adhesion, followed by the activation of polysaccharide biosynthesis pathways to stabilize aggregates. This sequential regulation highlights a genetic trade-off between motility and biofilm-like stickiness in controlling floc growth. Our findings provide direct molecular and structural evidence that microbial activities fundamentally reshape sediment aggregation dynamics, thereby regulating suspended sediment transport and carbon cycling in coastal systems.
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Status: open (until 28 Mar 2026)
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RC1: 'Comment on egusphere-2025-6516', Anonymous Referee #1, 24 Feb 2026
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AC1: 'Reply on RC1', Leiping Ye, 04 Mar 2026
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Thanks a lot for the valuable and very helpful comments and we do really appreciate.
We totally agree with the reviewer that most living microorganisms can participate in estuarine flocculation processes through the secretion of TEP or EPS which needs to be added and combined in the comparison and discussions. Here in our this work, we originally and primarily focused on microbial EPS which used to be more difficult to quantified and an extension from the living microorganisms function on flucculation. We very much appreciate your suggestion to broaden the perspective. Following your advice, we have now carefully reviewed the relevant literature and have cited the following works to support this point in the References section (Page 17, 18, 19, 21, 23, 25 in the revision):
Deng, Z., He, Q., Chassagne, C., & Wang, Z. B. (2021). Seasonal variation of floc population influenced by the presence of algae in the changjiang (yangtze river) estuary. Marine Geology, 440, 106600. https://doi.org/10.1016/j.margeo.2021.106600
Deng, Z., He, Q., Safar, Z., & Chassagne, C. (2019). The role of algae in fine sediment flocculation: In-situ and laboratory measurements. Marine Geology, 413, 71～84. https://doi.org/10.1016/j.margeo.2019.02.003
Bar-Zeev, E., & Rahav, E. (2015). Microbial metabolism of transparent exopolymer particles during the summer months along a eutrophic estuary system. Frontiers in Microbiology, 6, 403. https://doi.org/10.3389/fmicb.2015.00403
Lin, Y., Ye, L., Li, C., Cui, Y., & Wu, J. (2024). Morphology and distribution of suspended particles during typhoon-induced algal bloom in the pearl river estuary. (11), 1499002. https://doi.org/10.3389/fmars.2024.1499002
Salehizadeh, H., & Yan, N. (2014). Recent advances in extracellular biopolymer flocculants. Biotechnology Advances, 32(8), 1506-1522. https://doi.org/10.1016/j.biotechadv.2014.10.004
Sheng, G.-P., Yu, H.-Q., & Li, X.-Y. (2010). Extracellular polymeric substances (EPS) of microbial aggregates in biological wastewater treatment systems: A review. Biotechnology Advances, 28(6), 882-894. https://doi.org/10.1016/j.biotechadv.2010.08.001
Ye, F., Ye, Y., & Li, Y. (2011). Effect of C/N ratio on extracellular polymeric substances (EPS) and physicochemical properties of activated sludge flocs. Journal of Hazardous Materials, 188(1-3), 37-43. https://doi.org/10.1016/j.jhazmat.2011.01.043
Zhang, Y., Ren, Jie, & Zhang, Wenyan. (2020). Flocculation under the control of shear, concentration and stratification during tidal cycles. (586), 124908. https://doi.org/10.1016/j.jhydrol.2020.124908
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Also, in the manuscript, we have added in a specific explanation for this issue in the 2nd paragraph of the Discussion section (Page 13, Line 374), i.e. ‘Microbial flocculation is strongly modulated by bacterial growth phase, hydrodynamic shear, and nutrient availability (Sheng et al., 2010; Ye et al., 2011; Salehizadeh & Yan, 2014; Tang & Maggi, 2016). For instance, Maalej et al. (2017) reported that in Pseudomonas stutzeri (now reclassified as Stutzerimonas stutzeri), EPS production and viscosity increased concurrently during exponential growth, followed by a decline upon starch depletion’.
We also have incorporated the relevant studies from both field in situ and laboratory research to support this point in the 3rd paragraph the Discussion section (Page 13, Line 386). The current logic of the Discussion section is as following: "However, the extremely swift (a few minutes) biologically-induced flocculation in estuarine waters as a result of Transparent Exopolymer Particles (mucus) secreted not just by microbes, but also bacteria and plankton and other biota (Droppo, 2001; Passow, 2002; Labille et al., 2005; Morelle et al., 2017; Mari et al., 2017). In eutrophic estuarine environments, high phytoplankton biomass drives TEP production, which fuels microbial growth and accelerates the transformation of TEP into biologically-induced aggregates (Bar-Zeev & Rahav, 2015). Eukaryotic microorganisms, especially diatoms, often bloom in estuarine waters and flocculate rapidly (within minutes), forming visible macroaggregates (Deng et al., 2019, 2021, 2023; Ho et al., 2022). Our previous work in the Pearl River Estuary showed that tidally modulated floc sizes typically range from 20 to 200 μm (Zhang et al., 2020). In contrast, typhoon-induced algal blooms enhanced bioflocculation by a factor of 1 to 8 compared to this study, yielding flocs as large as 118–920 μm (Lin et al., 2024). In addition, the composition and quantity of EPS secreted by microorganisms differ among species (Flemming & Wingender, 2010), which in turn modulate flocculation efficiency."
Specifically, we acknowledge that our controlled laboratory conditions cannot fully replicate the complexity of natural estuarine environments. We also explicitly recommend that future research should integrate field observations with laboratory experiments to more comprehensively evaluate the real-world implications of bio-flocculation (Page 16, Line 474). The current logic of the Discussion section is as following: "Given that the bioflocculation observed in laboratory settings may not fully capture those occurring in natural environments, future studies should aim to bridge this gap through in situ validation experiments or by incorporating more complex, multi-species communities into mesocosm designs. Specifically, combining controlled experiments with field measurements of TEP/EPS concentrations, floc size distributions, and settling velocities across estuarine gradients would help validate the conceptual framework proposed here."
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We hope the revision and improvement will strengthen the manuscript and satisfactory. A full revision will be formally uploaded after all the other potential reviewers' comments been addressed. Thank you again for your constructive feedback.
Â
Citation: https://doi.org/10.5194/egusphere-2025-6516-AC1 -
AC2: 'Reply on RC1', Leiping Ye, 04 Mar 2026
reply
Thanks a lot for the valuable and very helpful comments and we do really appreciate.
We totally agree with the reviewer that most living microorganisms can participate in estuarine flocculation processes through the secretion of TEP or EPS which needs to be added and combined in the comparison and discussions. Here in our this work, we originally and primarily focused on microbial EPS which used to be more difficult to quantified and an extension from the living microorganisms function on flucculation. We very much appreciate your suggestion to broaden the perspective. Following your advice, we have now carefully reviewed the relevant literature and have cited the following works to support this point in the References section (Page 17, 18, 19, 21, 23, 25 in the revision):
Deng, Z., He, Q., Chassagne, C., & Wang, Z. B. (2021). Seasonal variation of floc population influenced by the presence of algae in the changjiang (yangtze river) estuary. Marine Geology, 440, 106600. https://doi.org/10.1016/j.margeo.2021.106600
Deng, Z., He, Q., Safar, Z., & Chassagne, C. (2019). The role of algae in fine sediment flocculation: In-situ and laboratory measurements. Marine Geology, 413, 71～84. https://doi.org/10.1016/j.margeo.2019.02.003
Bar-Zeev, E., & Rahav, E. (2015). Microbial metabolism of transparent exopolymer particles during the summer months along a eutrophic estuary system. Frontiers in Microbiology, 6, 403. https://doi.org/10.3389/fmicb.2015.00403
Lin, Y., Ye, L., Li, C., Cui, Y., & Wu, J. (2024). Morphology and distribution of suspended particles during typhoon-induced algal bloom in the pearl river estuary. (11), 1499002. https://doi.org/10.3389/fmars.2024.1499002
Salehizadeh, H., & Yan, N. (2014). Recent advances in extracellular biopolymer flocculants. Biotechnology Advances, 32(8), 1506-1522. https://doi.org/10.1016/j.biotechadv.2014.10.004
Sheng, G.-P., Yu, H.-Q., & Li, X.-Y. (2010). Extracellular polymeric substances (EPS) of microbial aggregates in biological wastewater treatment systems: A review. Biotechnology Advances, 28(6), 882-894. https://doi.org/10.1016/j.biotechadv.2010.08.001
Ye, F., Ye, Y., & Li, Y. (2011). Effect of C/N ratio on extracellular polymeric substances (EPS) and physicochemical properties of activated sludge flocs. Journal of Hazardous Materials, 188(1-3), 37-43. https://doi.org/10.1016/j.jhazmat.2011.01.043
Zhang, Y., Ren, Jie, & Zhang, Wenyan. (2020). Flocculation under the control of shear, concentration and stratification during tidal cycles. (586), 124908. https://doi.org/10.1016/j.jhydrol.2020.124908
Â
Also, in the manuscript, we have added in a specific explanation for this issue in the 2nd paragraph of the Discussion section (Page 13, Line 374), i.e. ‘Microbial flocculation is strongly modulated by bacterial growth phase, hydrodynamic shear, and nutrient availability (Sheng et al., 2010; Ye et al., 2011; Salehizadeh & Yan, 2014; Tang & Maggi, 2016). For instance, Maalej et al. (2017) reported that in Pseudomonas stutzeri (now reclassified as Stutzerimonas stutzeri), EPS production and viscosity increased concurrently during exponential growth, followed by a decline upon starch depletion’.
We also have incorporated the relevant studies from both field in situ and laboratory research to support this point in the 3rd paragraph the Discussion section (Page 13, Line 386). The current logic of the Discussion section is as following: "However, the extremely swift (a few minutes) biologically-induced flocculation in estuarine waters as a result of Transparent Exopolymer Particles (mucus) secreted not just by microbes, but also bacteria and plankton and other biota (Droppo, 2001; Passow, 2002; Labille et al., 2005; Morelle et al., 2017; Mari et al., 2017). In eutrophic estuarine environments, high phytoplankton biomass drives TEP production, which fuels microbial growth and accelerates the transformation of TEP into biologically-induced aggregates (Bar-Zeev & Rahav, 2015). Eukaryotic microorganisms, especially diatoms, often bloom in estuarine waters and flocculate rapidly (within minutes), forming visible macroaggregates (Deng et al., 2019, 2021, 2023; Ho et al., 2022). Our previous work in the Pearl River Estuary showed that tidally modulated floc sizes typically range from 20 to 200 μm (Zhang et al., 2020). In contrast, typhoon-induced algal blooms enhanced bioflocculation by a factor of 1 to 8 compared to this study, yielding flocs as large as 118–920 μm (Lin et al., 2024). In addition, the composition and quantity of EPS secreted by microorganisms differ among species (Flemming & Wingender, 2010), which in turn modulate flocculation efficiency."
Specifically, we acknowledge that our controlled laboratory conditions cannot fully replicate the complexity of natural estuarine environments. We also explicitly recommend that future research should integrate field observations with laboratory experiments to more comprehensively evaluate the real-world implications of bio-flocculation (Page 16, Line 474). The current logic of the Discussion section is as following: "Given that the bioflocculation observed in laboratory settings may not fully capture those occurring in natural environments, future studies should aim to bridge this gap through in situ validation experiments or by incorporating more complex, multi-species communities into mesocosm designs. Specifically, combining controlled experiments with field measurements of TEP/EPS concentrations, floc size distributions, and settling velocities across estuarine gradients would help validate the conceptual framework proposed here."
Â
We hope the revision and improvement will strengthen the manuscript and satisfactory. A full revision will be formally uploaded after all the other potential reviewers' comments been addressed. Thank you again for your constructive feedback.
Â
Citation: https://doi.org/10.5194/egusphere-2025-6516-AC2
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AC1: 'Reply on RC1', Leiping Ye, 04 Mar 2026
reply
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There are publications in the literature that show the extremely swift (a few minutes) biologically-induced flocculation in estuarine waters as a result of Transparent Exopolymer Particles (mucus) secreted not just by microbes, but also bacteria and plankton and other biota. None of them are cited. There are also other publications that show that experimental studies in the laboratory with selected microbes to start the biological flocculation underestimate by an order of magnitude the biologically-induced flocculation. These are not cited.
This manuscript fails to address these pitfalls.Â