Flocculation dynamics of cell associated suspended particulate matter

Flocculation dynamics of cell-associated suspended particulate matter Thu Ha Nguyen School of Civil Engineering Faculty of Engineering The University of Sydney A thesis submitted to fulfil requirements for the degree of Doctor of Philosophy Supervisor: Assoc Prof Federico Maggi Auxiliary supervisors: Prof John Patterson Dr Fiona Tang 2020 Abstract Transport of suspended particulate matter (SPM) plays a vital role in controlling large-scale processes related to geophysical flows such as dispersal and sinking of organic matter and contaminants to offshore and deep waters, nutrient cycles, food web stability, morphodynamics and sedimentation in both limnetic and pelagic ecosystems Although it has been recognized that small-scale microbial processes can introduce substantial differences to the way in which SPM moves in natural waters, the extent to which the attached biological matter affects SPM dynamics is still not well characterized This thesis focuses on quantifying the attached biomass fraction on SPM aggregates and investigating its contribution to SPM flocculation dynamics, which consequently control SPM aggregate geometrical properties and transport A novel laboratory-based Optical Measurement of Cell Colonization (OMCEC) system and a microbiological-physical model (BFLOC2) are the main achievements of this thesis that allow the analyses of the correlations between environmental conditions, aggregate-attached biomass fraction, cell colonization patterns, aggregate size, fractal dimension and settling velocity OMCEC is an experimental system that can simultaneously measure the material composition, geometric properties, and motion of individual suspended aggregates in a non-invasive and nondestructive way OMCEC consists of a full-color high-resolution optical system and real-time algorithms for (i) material segmentation based on light spectra emission analysis, (ii) quantification of various geometrical properties, and (iii) motion detection with micro particle tracking velocimetry (µPTV) OMCEC was applied herein on three types of aggregates: cell-associated minerals, cellassociated microplastics, and three-phase aggregates made of minerals, microplastics, and biological matter OMCEC application on Saccharomyces cerevisiae-colonized minerals at four sucrose concentrations showed the likelihood of cell colonization to increase with increasing nutrient concentration The attached biomass fraction was found to increase nonlinearly regarding an increase of aggregate size but almost constant with fractal dimension variation Cell distribution on mineral surfaces was then analyzed and classified into three colonization patterns: (i) scattered, (ii) well-touched, and (iii) poorly-touched, with the second being predominant Cell clusters in the well-touched pattern were found to have lower fractal dimension than those in the other patterns A strong correlation of colonization patterns with aggregate biomass fraction and properties suggests dynamic colonization iv mechanisms from cell attachment to minerals, to joining of isolated cell clusters, and finally cell growth over the entire aggregate OMCEC application on microplastics (MPs) being colonized by natural biological matter from Hawkesbury River, NSW, Australia demonstrated that the biomass fraction of MP aggregates has substantial control over their size, shape and, most importantly, their settling velocity Polyurethane MP aggregates made of 80% biological matter had an average size almost double that of MP aggregates containing 5% biological matter and sank two times slower Based on our experimental data, we introduce a settling velocity equation that accounts for the shape irregularity and fractal structure of MP aggregates This equation can capture the settling velocity of both virgin MPs and cell-associated MP aggregates with 7% error and can be applied widely to predict the settling flux of MP aggregates made of different polymers and various types of biological matter To consider the complex genesis of cell-associated mineral aggregates, the BFLOC2 model was introduced to predict aggregate geometry and settling velocity under simultaneous effects of hydrodynamic and biological processes While minerals can contribute to aggregate dynamics through collision, aggregation, and breakup, living microorganisms can colonize and establish food web interactions that involve growth and grazing, and modify the aggregate structure Modeling of cell-associated mineral aggregate dynamics over a wide range of environmental conditions showed that maximum aggregate size, biomass fraction, and settling velocity could occur at different optimal environmental conditions Unlike mineral aggregates, which have maximum size when shear rates tend to zero, a relative maximum size of cell-associated mineral aggregates can be reached at intermediate shear rates as a result of microbiological processes The settling velocity was ultimately controlled by aggregate size, fractal dimension, and biomass fraction The innovative aspect of this thesis is the simultaneous quantification of composition, architecture, and settling velocity of individual aggregates Therefore, it puts forth the analysis and prediction of cell colonization impacts on dynamics and transport of suspended particulate matter in natural waters The output of this thesis can be used in natural water monitoring programs to estimate the biological content based on SPM size, capacity dimension, and settling velocity, which can be measured using in-situ methods Furthermore, the evidence and tools to quantify the sinking and floating of microplastic subjected to bio-fouling can be implemented in microplastics transport models to enable the three-dimension modeling of both low- and high-density microplastics The BFLOC2 model can be coupled to traditional sediment transport models to better describe the sediment formation dynamics, thus giving a more precise prediction of sedimentation and carbon flux to deep waters and offshore v Statement of Originality This is to certify that to the best of my knowledge, the content of this thesis is my own work This thesis has not been submitted for any degree or other purposes I certify that the intellectual content of this thesis is the product of my own work and that all the assistance received in preparing this thesis and sources have been acknowledged Name: Thu Ha Nguyen Signature: (signed) Date: 30/01/2020 viii Authorship Attribution Statement Chapter of this thesis was published in manuscripts [195, 197, 198] I developed the method, conducted the experiments, and wrote the manuscripts The settling column used in the system was designed and built by the co-authors (F Maggi and F.H.M Tang) Chapter of this thesis was published in manuscript [195] I conducted the experiments, analyzed the data, and wrote the manuscripts Chapter of this thesis was published in manuscript [198] I conducted the experiments, analyzed the data, developed the equation, and wrote the manuscripts The field sampling was done by all authors with the support of New South Wales Office of Environment and Heritage (NSW-OEH) Chapter of this thesis was published in manuscript [196] I developed the model, conducted the simulation, analyzed the data, and wrote the manuscripts The source code of the BFLOC model, which is the based of the BFLOC2 model in the thesis, was developed by the co-author (F Maggi) List of publications: [195] Nguyen, T H., Tang, F H M., and Maggi, F (2017) Optical measurement of cell colonization patterns on individual suspended sediment aggregates J Geophys Res Earth Surf., 122(10):1794-1807 https://doi.org/10.1002/2017JF004263 [196] Nguyen, T H., Tang, F H M., and Maggi, F (2018) Micro food web networks on suspended sediment Sci Total Environ., 643:1387-1399 https://doi.org/10.1016/j.scitotenv.2018.06.247 [197] Nguyen, T H., Tang, F H M., and Maggi, F (2019) OMCEC: A novel method for simultaneous detection of composition, geometry and motion of suspended particles In Proceedings 16th International Conference on Environmental Science and Technology CEST2019 [198] Nguyen, T H., Tang, F H M., and Maggi, F (2020) Sinking of microbial-associated microplastics in natural waters PLoS ONE, 15(2):e0228209 https://doi.org/10.1371/journal.pone.0228209 x Hereby, I (T H Nguyen) confirm that I am the first and the corresponding author of the publications listed above Name: Thu Ha Nguyen Signature: (signed) Date: 30/01/2020 As supervisor for the candidature upon which this thesis is based, I can confirm that the authorship attribution statements above are correct Name: Assoc Prof Federico Maggi Signature: (signed) Date: 30/01/2020 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 310.8 264.0 418.0 247.5 330.0 272.3 539.0 255.8 962.5 294.3 445.5 497.8 396.0 321.8 572.0 602.3 566.5 517.0 495.0 415.3 189.8 599.5 338.3 286.0 547.3 662.8 511.5 52.3 519.8 434.5 382.3 220.0 291.5 489.5 503.3 451.0 442.8 327.3 407.0 610.5 121.0 286.0 731.5 858.0 374.0 418.0 671.0 583.0 759.0 310.8 343.8 475.8 261.3 275.0 156.8 588.5 453.8 294.3 222.8 640.8 206.3 313.5 401.5 0.684 0.031 0.047 0.030 0.082 0.997 0.165 0.034 0.475 0.016 0.092 0.788 1.000 0.114 0.615 0.107 0.416 0.152 0.076 0.054 0.098 0.088 0.015 0.038 0.057 0.149 0.060 1.000 0.989 0.127 0.060 0.125 0.032 0.029 0.424 0.069 0.071 0.069 0.088 0.454 0.992 0.081 0.247 0.467 0.003 0.022 0.387 0.007 0.334 0.181 0.991 0.022 0.015 0.046 0.081 0.038 0.114 0.247 0.030 0.159 0.007 0.028 0.068 0.057 0.033 0.070 0.032 0.052 0.027 0.085 0.035 0.394 0.045 0.067 0.099 0.077 0.046 0.147 0.109 0.086 0.107 0.118 0.088 0.027 0.134 0.037 0.050 0.099 0.112 0.067 0.002 0.067 0.047 0.056 0.030 0.044 0.088 0.095 0.081 0.066 0.067 0.063 0.135 0.008 0.036 0.237 0.095 0.074 0.068 0.181 0.096 0.107 0.051 0.041 0.092 0.029 0.040 0.015 0.115 0.082 0.038 0.030 0.161 0.026 0.054 0.061 1.185 0.817 1.205 0.778 1.053 0.787 2.184 0.745 6.507 0.894 1.477 2.390 1.284 0.987 3.284 1.939 3.490 2.098 1.672 1.480 0.602 1.936 0.968 0.886 1.810 2.261 1.485 0.140 3.110 1.455 1.133 0.646 1.009 1.383 2.109 1.438 1.361 1.166 1.829 3.242 0.341 0.858 3.820 2.959 1.144 1.276 3.149 2.013 3.256 1.128 1.617 1.378 0.734 0.850 0.448 1.878 1.656 0.968 0.710 2.002 0.611 0.913 1.331 0.589 0.467 0.403 0.530 0.482 0.365 0.294 0.533 0.426 0.523 0.337 0.400 0.490 0.443 0.449 0.301 0.267 0.402 0.483 0.509 0.741 0.372 0.327 0.607 0.329 0.256 0.257 0.745 0.248 0.247 0.386 0.612 0.518 0.369 0.374 0.399 0.336 0.626 0.379 0.361 0.577 0.438 0.443 0.129 0.530 0.392 0.403 0.283 0.186 0.529 0.349 0.405 0.422 0.535 0.616 0.332 0.399 0.444 0.605 0.393 0.622 0.551 0.379 3.814 3.094 2.882 3.144 3.192 2.889 4.051 2.914 6.760 3.037 3.315 4.801 3.243 3.068 5.740 3.219 6.160 4.059 3.378 3.563 3.174 3.229 2.862 3.096 3.307 3.411 2.903 2.684 5.984 3.348 2.964 2.938 3.462 2.826 4.191 3.189 3.075 3.563 4.493 5.311 2.818 3.000 5.222 3.449 3.059 3.053 4.693 3.453 4.290 3.628 4.704 2.896 2.811 3.090 2.860 3.192 3.648 3.290 3.185 3.124 2.960 2.912 3.315 0.875 0.660 1.717 1.304 0.700 0.198 2.102 1.032 2.055 1.906 1.873 1.180 0.627 0.397 0.850 2.046 1.254 3.540 3.232 2.648 0.867 3.921 0.817 1.429 1.444 0.984 1.281 0.074 0.165 0.306 1.135 0.593 1.775 2.821 2.376 1.759 0.973 0.668 0.693 0.925 0.190 0.608 2.433 0.710 1.964 1.848 1.180 3.225 1.650 0.908 0.091 2.409 1.593 1.585 0.157 2.749 1.442 0.626 1.066 3.045 0.966 1.970 0.775 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 371.3 506.0 310.8 896.5 407.0 902.0 343.8 365.8 217.3 255.8 385.0 500.5 167.8 786.5 363.0 569.3 294.3 437.3 437.3 365.8 409.8 621.5 330.0 272.3 420.8 404.3 308.0 277.8 1001.0 294.3 569.3 654.5 442.8 354.8 341.0 231.0 434.5 360.3 528.0 332.8 577.5 539.0 352.0 574.8 239.3 258.5 324.5 753.5 154.0 280.5 415.3 522.5 503.3 481.3 415.3 209.0 662.8 522.5 459.3 492.3 313.5 737.0 376.8 0.013 0.183 0.102 0.989 0.080 0.491 0.119 0.128 0.155 0.167 0.477 0.081 0.140 0.138 0.025 0.045 0.038 0.139 0.275 0.041 0.052 0.047 0.086 0.032 0.049 0.061 0.988 0.015 0.612 0.142 0.090 0.334 0.071 0.411 0.179 0.027 0.157 0.083 0.079 0.251 0.090 0.108 0.027 0.067 0.039 0.115 0.050 0.550 0.914 0.044 0.077 0.031 0.050 0.089 0.044 0.020 0.040 0.410 0.114 0.667 0.018 0.882 0.049 0.063 0.083 0.045 0.277 0.057 0.114 0.045 0.087 0.023 0.042 0.048 0.101 0.016 0.242 0.076 0.093 0.044 0.091 0.090 0.050 0.062 0.145 0.030 0.037 0.056 0.080 0.052 0.059 0.282 0.047 0.110 0.140 0.065 0.048 0.056 0.029 0.097 0.065 0.080 0.043 0.134 0.103 0.059 0.104 0.030 0.038 0.049 0.160 0.012 0.047 0.070 0.121 0.089 0.078 0.081 0.027 0.090 0.081 0.067 0.077 0.043 0.165 0.085 1.144 1.606 1.150 4.837 1.205 3.905 1.007 1.227 0.888 0.754 1.540 1.735 0.506 3.355 1.174 1.768 0.905 2.082 1.394 1.004 1.273 2.109 0.987 1.048 1.304 1.438 0.949 0.924 6.210 0.853 1.801 2.956 1.645 1.290 1.257 0.674 1.713 1.898 1.722 1.334 1.964 2.329 1.042 2.167 0.748 0.745 1.040 3.209 0.564 0.943 1.298 1.598 1.576 1.936 1.392 0.605 1.900 2.558 1.482 2.219 0.954 4.837 1.161 0.455 0.326 0.467 0.345 0.343 0.141 0.379 0.654 0.492 0.639 0.321 0.404 0.576 0.391 0.574 0.287 0.510 0.475 0.470 0.377 0.370 0.375 0.274 0.499 0.315 0.493 0.547 0.760 0.281 0.542 0.339 0.327 0.332 0.383 0.480 0.551 0.512 0.498 0.287 0.391 0.401 0.353 0.479 0.314 0.532 0.571 0.468 0.281 0.525 0.596 0.406 0.445 0.350 0.336 0.469 0.608 0.204 0.296 0.315 0.316 0.439 0.304 0.600 3.081 3.174 3.699 5.396 2.959 4.329 2.928 3.353 4.089 2.946 4.000 3.467 3.016 4.266 3.235 3.106 3.075 4.761 3.189 2.744 3.107 3.394 2.992 3.848 3.098 3.558 3.080 3.327 6.203 2.897 3.164 4.517 3.714 3.636 3.685 2.917 3.943 5.267 3.260 4.008 3.400 4.321 2.961 3.770 3.126 2.883 3.203 4.259 3.661 3.363 3.126 3.058 3.131 4.023 3.351 2.895 2.867 4.895 3.228 4.508 3.044 6.563 3.080 2.228 1.386 1.585 0.710 0.660 1.453 0.429 1.485 0.381 0.671 0.505 1.787 0.264 2.045 1.916 2.014 1.684 1.114 1.497 1.396 1.404 3.194 0.231 1.188 1.279 1.784 0.082 1.708 1.065 1.435 1.975 0.917 1.535 1.601 0.924 0.835 0.841 0.840 1.032 0.289 2.748 1.783 1.204 1.926 0.669 0.512 1.049 1.549 0.215 2.137 1.643 3.106 2.016 1.463 1.424 0.868 1.314 1.644 0.578 0.759 0.916 0.479 1.831 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 385.0 357.5 242.0 552.8 528.0 473.0 382.3 506.0 313.5 335.5 415.3 665.5 448.3 495.0 492.3 365.8 407.0 569.3 580.3 242.0 451.0 456.5 613.3 217.3 429.0 393.3 687.5 324.5 379.5 431.8 533.5 159.5 497.8 299.8 434.5 492.3 250.3 409.8 418.0 709.5 280.5 522.5 338.3 253.0 269.5 764.5 539.0 459.3 277.8 275.0 385.0 550.0 178.8 167.8 239.3 173.3 539.0 943.3 464.8 668.3 431.8 316.3 407.0 0.516 0.042 0.014 0.254 0.055 0.101 0.032 0.440 0.090 0.078 0.081 0.196 0.047 0.091 0.051 0.063 0.087 0.253 0.180 0.004 0.088 0.062 0.114 0.022 0.074 0.120 0.080 0.078 0.008 0.120 0.065 0.067 0.050 0.998 0.058 0.081 0.021 0.106 0.448 0.475 0.065 0.106 0.105 0.043 0.094 0.664 0.155 0.009 0.077 1.000 0.086 0.263 0.019 0.105 0.049 0.039 0.094 0.172 0.211 0.890 0.579 0.124 0.116 0.078 0.052 0.032 0.114 0.124 0.091 0.059 0.102 0.044 0.044 0.062 0.151 0.082 0.114 0.093 0.047 0.070 0.194 0.127 0.024 0.087 0.062 0.123 0.028 0.051 0.082 0.140 0.053 0.044 0.091 0.080 0.015 0.111 0.039 0.076 0.088 0.032 0.062 0.059 0.177 0.041 0.100 0.040 0.024 0.030 0.262 0.109 0.066 0.046 0.047 0.073 0.096 0.020 0.017 0.035 0.018 0.127 0.198 0.085 0.189 0.068 0.047 0.076 1.276 1.229 0.693 2.266 1.612 1.579 1.136 2.285 0.930 0.932 1.389 2.569 1.370 2.181 1.683 1.114 1.218 2.503 1.972 0.710 1.856 1.386 2.610 0.701 1.271 1.436 2.398 1.251 1.086 1.540 1.859 0.454 1.997 1.009 1.411 1.689 0.789 1.342 1.691 3.528 0.935 1.826 1.210 0.726 0.762 2.890 1.964 1.345 0.932 0.831 1.172 2.203 0.512 0.506 0.682 0.547 2.016 4.804 1.678 2.973 1.708 1.001 1.268 0.525 0.406 0.544 0.374 0.444 0.405 0.401 0.398 0.448 0.394 0.358 0.340 0.408 0.467 0.382 0.350 0.422 0.600 0.379 0.414 0.429 0.298 0.327 0.600 0.280 0.528 0.296 0.505 0.304 0.489 0.279 0.587 0.446 0.433 0.401 0.362 0.508 0.369 0.338 0.351 0.523 0.365 0.349 0.375 0.414 0.449 0.373 0.315 0.590 0.620 0.490 0.319 0.636 0.604 0.619 0.612 0.436 0.223 0.392 0.423 0.363 0.471 0.460 3.314 3.438 2.864 4.100 3.052 3.337 2.971 4.516 2.965 2.779 3.344 3.860 3.055 4.406 3.419 3.045 2.993 4.396 3.398 2.932 4.116 3.036 4.256 3.228 2.962 3.650 3.488 3.856 2.862 3.567 3.485 2.845 4.011 3.367 3.247 3.430 3.154 3.275 4.046 4.973 3.333 3.495 3.577 2.870 2.827 3.781 3.643 2.928 3.356 3.020 3.043 4.005 2.862 3.016 2.851 3.159 3.740 5.093 3.609 4.449 3.955 3.165 3.115 0.949 0.710 1.262 1.898 3.277 2.169 1.205 2.006 0.801 0.685 0.866 2.558 1.915 3.517 1.057 0.848 1.288 2.351 2.005 0.239 1.657 1.015 1.289 0.652 0.520 1.427 2.368 0.851 1.098 1.402 0.875 0.199 3.608 0.157 0.925 1.585 0.652 0.801 0.900 0.941 0.883 1.923 0.743 0.404 0.387 1.655 1.880 1.800 2.821 0.371 0.990 1.154 0.569 0.099 0.990 0.289 1.585 1.684 1.270 1.188 0.866 0.561 0.520 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 882.8 492.3 880.0 643.5 992.8 555.5 764.5 349.3 195.3 409.8 519.8 316.3 462.0 343.8 830.5 470.3 0.572 0.111 0.093 0.924 0.761 0.051 0.999 0.810 0.027 0.123 0.117 0.039 0.023 0.017 0.128 0.215 0.245 0.075 0.213 0.134 0.144 0.088 0.159 0.069 0.029 0.089 0.135 0.053 0.052 0.040 0.329 0.086 4.263 1.678 3.482 2.494 4.485 1.603 4.004 1.284 0.671 1.334 1.966 0.957 1.482 0.979 4.925 1.617 0.315 0.311 0.275 0.324 0.146 0.286 0.273 0.565 0.754 0.533 0.501 0.529 0.245 0.341 0.477 0.387 4.829 3.408 3.956 3.876 4.518 2.886 5.237 3.677 3.437 3.255 3.783 3.026 3.208 2.848 5.930 3.439 2.277 1.091 2.103 0.644 0.661 1.577 0.380 0.833 1.007 1.633 3.904 1.632 0.355 0.930 4.175 1.855 Table B.2 Data of the cell-associated microplastic experiments described in Chapter for for the MP-only experiment Data include aggregate [1] name, [2] size L, [3] area A, [4] perimeter P, [5] area-based shape factor bs , and [6] perimeter-based shape factor cs ID [1] L (µm) [2] A (mm2 ) [3] P (mm) [4] bs (-) [5] cs (-) [6] 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 305.3 156.8 239.3 236.5 49.5 112.8 68.8 222.8 352.0 239.3 148.5 247.5 379.5 412.5 310.8 288.8 154.0 173.3 250.3 426.3 481.3 473.0 275.0 244.8 129.3 236.5 93.5 115.5 255.8 324.5 121.0 60.5 107.3 277.8 214.5 134.8 305.3 214.5 286.0 324.5 228.3 198.0 217.3 0.022 0.010 0.029 0.030 0.002 0.007 0.003 0.024 0.031 0.018 0.014 0.027 0.050 0.050 0.038 0.043 0.013 0.011 0.033 0.055 0.048 0.043 0.023 0.019 0.006 0.018 0.005 0.005 0.025 0.034 0.010 0.002 0.004 0.017 0.017 0.012 0.029 0.015 0.029 0.034 0.017 0.013 0.016 0.930 0.437 0.762 0.649 0.140 0.338 0.184 0.688 1.009 0.682 0.432 0.792 1.389 1.474 0.902 1.053 0.424 0.512 0.888 1.537 1.504 1.397 0.842 0.688 0.396 0.718 0.278 0.341 0.831 1.147 0.347 0.171 0.300 0.781 0.616 0.399 1.221 0.630 0.811 0.965 0.726 0.575 0.644 0.241 0.409 0.512 0.534 0.685 0.581 0.656 0.481 0.248 0.309 0.614 0.437 0.346 0.294 0.391 0.513 0.532 0.371 0.521 0.300 0.206 0.194 0.300 0.317 0.357 0.316 0.559 0.379 0.388 0.327 0.707 0.671 0.353 0.226 0.370 0.654 0.312 0.335 0.357 0.325 0.335 0.340 0.331 3.045 2.789 3.184 2.744 2.833 3.000 2.680 3.086 2.867 2.851 2.907 3.200 3.659 3.573 2.903 3.648 2.750 2.952 3.549 3.606 3.126 2.953 3.060 2.809 3.064 3.035 2.971 2.952 3.247 3.534 2.864 2.818 2.795 2.812 2.872 2.959 4.000 2.936 2.837 2.975 3.181 2.903 2.962 List of Symbols α αH βg δ ε ηB γ µ µs Ω ΩB ΩC ΩF Ωj φ φmax ρ ρb ρf ρi ρm ρMP ρOM ρs σo σe θB θC θF Scaling power of ambient concentrations Heaviside function parameter Integral time parameter for turbulence Primary particle fractal dimension Turbulence dissipation rate Maximum specific bacterial growth rate Fractal scaling parameter Fluid dynamic viscosity Suspension dynamic viscosity Ambient total biomass fraction Bacterial ambient biomass fraction Ciliate ambient biomass fraction Flagellate ambient biomass fraction Ambient biomass fraction of microorganism j Suspension solid volume fraction Maximum suspension solid volume fraction Aggregate density Biological density Fluid density Density of material i Mineral density Microplastic density Organic matter density Suspension density Standard deviation of observed values Standard deviation of modeled values Bacterial aging mortality rate Ciliate aging mortality rate Flagellate aging mortality rate [-] [-] [-] [-] [L2 T−3 ] [T−1 ] [-] [ML−1 T−1 ] [ML−1 T−1 ] [-] [-] [-] [-] [-] [-] [-] [ML−3 ] [ML−3 ] [ML−3 ] [ML−3 ] [ML−3 ] [ML−3 ] [ML−3 ] [ML−3 ] [-] [-] [T−1 ] [T−1 ] [T−1 ] 172 List of Symbols θj υ ϑj ϑp ξ Aging mortality rate of microorganism j Fluid kinematic viscosity Volume of microorganism j Primary particle volume Ambient nutrient concentration [T−1 ] [L2 T−1 ] [L3 ] [L3 ] [ML−3 ] ab ab,k as at bL bs bt c cg ci cj cL cb cm cj cs d db db,k ds ec ed ek fb fb,m fg fi fj fm fm,m fMP Average projected area of cell clusters Projected area of cell cluster k Estimated volume-based shape factor Parameter for material threshold line Estimated area-based shape factor Experimental area-based shape factor Parameter for material threshold line Ambient SPM concentration Grid bar shape parameter Ambient concentration of material i Ambient concentration of microorganism j Estimated perimeter-based shape factor Ambient biological concentration Ambient mineral concentration Ambient concentration of microorganism j Experimental perimeter-based shape factor Aggregate 3-D capacity dimension Biological phase 3-D capacity dimension 3-D capacity dimension of cell cluster k Surface fractal dimension Collision efficiency parameter Diffusion efficiency parameter Modeled value of point k Biological fraction Biomass fraction Oscillating frequency Fraction of material i Fraction of microorganism j Mineral fraction Mineral mass fraction Microplastic fraction [L2 ] [L2 ] [-] [-] [-] [-] [-] [ML−3 ] [-] [ML−3 ] [ML−3 ] [-] [ML−3 ] [ML−3 ] [ML−3 ] [-] [-] [-] [-] [-] [-] [-] [*] Unit varies [-] [-] [T−1 ] [-] [-] [-] [-] [-] 173 fMP,m fOM fs g g ka′ ′ ka,DB ′ ka,DC ′ ka,DF ′ ka,D j ′ ka,G kb′ ′ kb,EB ′ kb,EC ′ kb,EF ′ kb,E j ′ kb,G ℓmb mb mg mm mMP n1 n2 n3 n4 nw ok p p1b p2b p1c p2c pb pC pF pPo Microplastic mass fraction Organic fraction Shape factor Gravitational acceleration vector Gravitational acceleration magnitude Aggregation dimensionless parameter Bacterial motility-induced aggregation parameter Ciliate motility-induced aggregation parameter Flagellate motility-induced aggregation parameter Motility-induced aggregation parameter of microorganism j Shear-induced aggregation parameter Breakup dimensionless parameter Bacterial motility-induced loss parameter Ciliate motility-induced loss parameter Flagellate motility-induced loss parameter Motility-induced loss parameter of microorganism j Shear-induced breakup parameter Contact length of mineral and cell clusters Wet biomass Grid bar shape parameter Mineral mass Microplastic mass Unit vector of Fg Unit vector of Fb Unit vector of Fv Unit vector of Fi Unit vector of w Observed value of point k ANOVA test significant parameter Parameter for bL Parameter for bL Parameter for cL Parameter for cL Total perimeter of cell clusters Ciliate grazing rate Flagellate grazing rate Protozoan grazing rate [-] [-] [-] [LT−2 ] [LT−2 ] [-] [M1−α L3α−3 ] [M1−α L3α−3 ] [M1−α L3α−3 ] [M1−α L3α−3 ] [M1−α L3α−3 ] [-] [-] [-] [-] [-] [-] [L] [M] [-] [M] [M] [-] [-] [-] [-] [-] [*] Unit varies [-] [L−1 ] [-] [L−1 ] [-] [L] [L2 T−1 ] [L2 T−1 ] [L2 T−1 ] 174 List of Symbols r s t tr v vLi w w xb xe Radius of a spherical aggregate Standard deviation of cell cluster area Time Residence time Experimental settling velocity Averaged settling velocity of size range Li Modeled terminal velocity vector Modeled terminal (settling/rising) velocity magnitude Horizontal distance between Ca and Cb Horizontal distance between aggregate left vertical tangent and Ca [L] [-] [T] [T] [LT−1 ] [LT−1 ] [LT−1 ] [LT−1 ] [L] [L] A Ab Am AMP As Bp B′p Cd CLi DB DC Dcc DF Dj Dmb Dmm EB EC EF Ej Fb Fb Fd Fd Fg Fg Aggregate projected area Biological pixel area Mineral pixel area Microplastic pixel area Aggregate surface area Blue pixel intensity Normalized blue pixel intensity Drag coefficient MP concentration of size range Li Bacterial diffusion coefficient Ciliate diffusion coefficient Average distance between cell clusters Flagellate diffusion coefficient Diffusion coefficient of microorganism j Euclidean distance between biological and mineral centroids Average distance between mineral clusters Bacterial detachment rate Ciliate detachment rate Flagellate detachment rate Detachment rate of microorganism j Buoyancy force vector Buoyancy force magnitude Resistance force vector Resistance force magnitude Gravitational force vector Gravitational force magnitude [L2 ] [L2 ] [L2 ] [L2 ] [L2 ] [-] [-] [-] [ML−3 ] [L2 T−1 ] [L2 T−1 ] [L] [L2 T−1 ] [L2 T−1 ] [L] [L] [T−1 ] [T−1 ] [T−1 ] [T−1 ] [MLT−2 ] [MLT−2 ] [MLT−2 ] [MLT−2 ] [MLT−2 ] [MLT−2 ] 175 Fi Fv Fy G Gp G′p H Ib Ic IG Im Ip JB JB∗ JC JF Jj JPe JPo KI Kξ L LB LC LF Lj Lp M N N∗ Nb Nc Ncm Nm NMP NRMSD P Impact force vector Viscous force vector Aggregate strength Turbulent shear rate Green pixel intensity Normalized green pixel intensity Spacing between two grid elements Dispersion index of cell cluster area Contact index between cell and mineral clusters Shear-induced cell motility reduction parameter Dispersion index of mineral cluster area Maximum pixel intensity in an image Bacterial cell count per aggregate Threshold bacteria density for resources shortage Ciliate cell count per aggregate Flagellate cell count per aggregate Cell count per aggregate of microorganism j Cell count per aggregate of prey Cell count per aggregate of protozoans Ambient sucrose inhibition concentration Half-saturation nutrient concentration Aggregate size Bacterial cell size Ciliate cell size Flagellate cell size Size of microoganism j Primary particle size Grid mesh size Total pixel count in an image Biological pixel count on the left side Biological pixel count in an aggregate image Cell cluster count in an aggregate Mineral cluster count in an aggregate Mineral pixel count in an aggregate image Microplastic pixel count in an aggregate image Normalized root-mean-square deviation Aggregate outer perimeter [MLT−2 ] [MLT−2 ] [MLT−2 ] [T−1 ] [-] [-] [L] [-] [-] [-] [-] [-] [-] [-] [-] [-] [-] [-] [-] [ML−3 ] [ML−3 ] [L] [L] [L] [L] [L] [L] [L] [-] [-] [-] [-] [-] [-] [-] [-] [L] 176 List of Symbols PE Pr Qm,L Sh R Re Rp R′p S V Vb VB VC Ve VF Vi Vj Vm Xp YC YF Yp YPo Yt Zg Percentage error Probability of observing aggregates MP vertical max flux Sherwood number Correlation coeffition Reynolds number Red pixel intensity Normalized red pixel intensity Piston stroke Aggregate solid volume Biological volume Total bacterial volume Total ciliate volume Aggregate pore volume Total flagellate volume Total volume of material i Total volume of microorganism j Mineral volume Horizontal coordinate of a material threhold graph Ciliate growth yield Flagellate growth yield Vertical coordinate of a material threhold graph Protozoan growth yield Threshold intensity for material seperation Vertical distance away from a grid 2-D 3-D µ-CT µPTV e i j m o B C Two-dimensional Three-dimensional X-ray microcomputed tomography Micro particle tracking velocimetry Modeled values Subscript, representing representing {m, B, F,C} Subscript, representing {B, F,C} Subscript, representing minerals Observation values Subscript, representing bacteria Subscript, representing ciliates [-] [-] [MT−1 L−2 ] [-] [-] [-] [-] [-] [L] [L3 ] [L3 ] [L3 ] [L3 ] [L3 ] [L3 ] [L3 ] [L3 ] [L3 ] [-] [-] [-] [-] [-] [-] [L] 177 Ca Aggregate centroid Cb Biological phase centroid F Subscript, representing flagellates ANOVA One-way analysis of variance AO Acridine orange DAPI 4’-6-diamidio-2-phenylidole DDT Dichloro-diphenyl-trichloroethane DOM Dissolved organic matter EPS Extracellular polymeric substances FAME Fatty acid methyl esters FFT Fast Fourier transform FIB-nt Focused ion beam nanotomography HDPE High-density polyethylene INSSEV In Situ Settling Velocity LDPE Low-density polyethylene LISST Laser In Situ Scattering and Transmissometery LLDPE Linear low-density polyethylene MDPE Medium-density polyethylene MPs Microplastics OMCEC Optical Measurement Of CEll Colonization PA Polyamide PBDE Polybrominated diphenyl ethers PCBs Polychlorinated biphenyl PE Polyethylene PET Polyethylene terephthalate PLFA Phospholipid fatty acids POM Particulate organic matter PP Polypropylene PS Polystyrene PSE Expanded polystyrene PTV Particle tracking velocimetry PUR Polyurethane PVC Polyvinyl chloride SPM Suspended particulate matter TOC Total organic carbon X Material phase other than mineral Acknowledgements First, I would like to thank my supervisor, Assoc Prof Federico Maggi, for his guidance and support during my PhD journey I start my PhD journey with little research experience, and his strict and high requirement for research has urged me to develop myself However, his demands have accompanied substantial supports in all aspects of the thesis, including the idea, experimental facilities, data analyses, modeling, and especially the writing I will never forget his patience and effort in correcting my English and logical problems in each manuscript so that today I can complete writing this PhD thesis confidently His creativity and passion for research are inspiring that help me think out of the box and come up with plenty of ideas Sincere gratitude is also devoted to Fiona Tang, my mentor and co-supervisor She has not only set up a strong basement for my PhD thesis to be built up but also closely consulted its construction Together with Federico, she has given me uncountable advice and supports Fiona would be the first one I reached out for advice when I encountered a problem during my research She was the one with me in the lab trying to get the camera focused and came in many times during the experiments to check if I needed a hand I am the first PhD student that she has co-supervised, but she has shown mature and confident supervision Fiona is also a friend to me that shared my difficulties in work and life I would like to acknowledge Jaimie Potts, Angus Ferguson and their group in New South Wales Office of Environment and Heritage (NSW-OEH) for letting me join their sampling campaigns and collect samples in Hunter and Hawkesbury Rivers I would like to thank also my annual progress review panel members, Prof Chengwang Lei, Dr Kapil Chauhan, Prof Kenny Kwok, Prof Jianlei Niu, and Prof Archie Johnston for their constructive feedback and suggestion My thankfulness is also addressed to Dr Cao Hung Pham for introducing me to Federico I would like to acknowledge the technicians at the School of Civil Engineering, Mr Garry Towell, Mr Theo Gresley-Daines, Mr Ross Barker, for their supports in the experimental facilities and materials, and Tino Kausmann from the School of Chemical Engineering for chemical disposal I would like to address special thanks to the ICT officers, Andy Nguyen and Patrick Ninh, who saved me from many computer problems with instant services I fully acknowledge the Australian Government - Department of Foreign Affairs and Trade for sponsoring me the Australia Awards Scholarship (AAS), which not only makes my study in Australia possible but also makes it as smooth as I could expect, especially through mostly covering my daughter’s school fee I am very grateful to the International Sponsorships team at the University of Sydney including Amy Wan, Annie Dinh, Bojan Bozic, Susan Sullivan, and Georgina Donovan for making my university life much more comfortable I would like to thank the Ho Chi Minh City University of Technology, my employer in Vietnam, for facilitating my scholarship application and holding my lecturer position during my PhD candidature in Australia My warmly thanks to my research group colleagues Chiara Pasut, Daniele la Cecilia, Cai Li, Giovanni Michele Porta, Magda Guglielmo, Dario Zambonini, and Giulia Ceriotti for their friendship, cultural lessons, delicious cakes, lunches, dinners, and memorable moments I also thank other PhD students in postgraduate rooms 101 and 360, Chiara Pasut, Daniele la Cecilia, Noor Mohammad, Sheng Jiang, Amir Zaghloul, Thi Huynh, Van Vinh Nguyen, Khoa Phan, Song Hong Pham, An Nhien Truong, Minh Toan Huynh, Cuong Nguyen, Bac Mai, Duy Khanh Pham, Hieu Pham, Quang Duy Nguyen, and others for sharing with me the peaks and valleys of a PhD graph My gratefully thanks are devoted to my Vietnamese AAS friends, Long Hong Nguyen, Dao Tran, Khoa Dang Le, Thi Anh Duong, Minh Duc Nguyen, Huu Nghi Tran, Hoang Long Nguyen, Van Long Nguyen, and their families; we have started this Australian journey at the same time and accompanied each other through all difficulties since then Late thanks to my grandmother, who always worried about my PhD study but was not able to see the day I complete I would never thank enough my parents for their motivation, unconditional love and supports; they are the reason why I became a water resources engineer, why I want to a PhD, and why I have to finish it I would like to sincerely thank my husband, who left behind his successful career in Vietnam to come with me to Australia and started up from zero And lastly, thank you my daughter, a lovely distraction from my PhD research; raising and loving her has somehow eased me from stress and balanced my life from work ... current knowledge of cell- associated mineral aggregates dynamics may not well represent the dynamics of cell- associated MPs aggregates Recent studies have quantified the sinking rate of MPs incorporating... number of cell cluster Nc , [9] relative area of cell clusters ab /A, [10] dispersion index of cell cluster area Ib , [11] relative distance between cell clusters Dcc /L, [12] number of mineral... 99 Appendix A Data of cell- associated mineral experiments 121 Appendix B Data of cell- associated microplastic experiments 157 List of Symbols 171 Acknowledgements 179 List of figures 2.1 2.2