Philippa Kaur

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All the materials followed relevant institutional and national guidelines and legislation.MitesWe used a T. kanzawai population collected from trifoliate orange trees (Poncirus trifoliata [L.] Raf.) in 2018 in Kyoto, Japan, and a T. urticae population collected from chrysanthemum plants (Chrysanthemum morifolium Ramat.) in 1998 in Nara, Japan. These populations were reared on adaxial surfaces of kidney bean (Phaseolus vulgaris L.) primary leaves, which were pressed onto water-saturated cotton in Petri dishes (90 mm diameter, 14 mm depth). The water-saturated cotton served as a barrier to prevent mites from escaping. The dishes were maintained at 25 °C, 50% relative humidity, and a 16L:8D photoperiod. All experiments were conducted under these conditions. We only used mated adult females (i.e., the dispersal stage) of T. kanzawai or T. urticae mites.CaterpillarsWe used caterpillars of four lepidopteran species: Bombyx mori L., P. Xuthus, Spodoptera litura Fabricius and T. oldenlandiae. We collected eggs and larvae of T. oldenlandiae from C. japonica in 2021 in Kyoto, Japan, and reared them on C. japonica leaves until pupation. Theretra oldenlandiae shares Vitaceae host plants with T. kanzawai and T. urticae8,15. We collected eggs and larvae of P. xuthus from Ptelea trifoliata in 2021 in Kyoto, Japan, and reared them on Citrus unshiu Markov. leaves until pupation. Papilio. xuthus and T. kanzawai share P. trifoliata as a host plant in Kyoto (Kinto, personal observation).We obtained commercial populations of the B. mori Kinshu × Showa strain (Ueda-sanshu Co., Ltd, Nagano, Japan) or the w1-pnd strain. We reared B. mori larvae on an artificial diet produced at the Kyoto Institute of Technology. Although T. kanzawai use Morus alba, a food plant for the B. mori strain, the mite and the strain never encounter one another in the wild, because the B. mori strain has been domesticated for hundreds of years.We obtained a sub-cultured population of S. litura from the Kyoto Institute of Technology. We reared first to fourth instars of S. litura on an artificial diet (Insecta LFM, Nosan Insect Materials, Kanagawa, Japan), while final instars were fed P. vulgaris leaves. Because S. litura feeds on various wild and cultivated plants22,23, it may share some host plants with T. kanzawai and T. urticae, both of which also feed on many host plant species8,9,10.We reared caterpillars of T. oldenlandiae, P. xuthus, and S. litura in 900 mL transparent plastic cups and caterpillars of B. mori in transparent plastic containers (140 × 220 × 35 mm). All caterpillars were maintained under the same laboratory conditions described above.PlantsWe used several parts of P. vulgaris plants in the following experiments. This species is a preferred food for both mite species16,17 and S. litura24, but the other three caterpillar species do not feed on it (Kinto, personal observation). We thus used P. vulgaris rather than shared host plants, because some caterpillars and mites (T. urticae and P. xuthus, for example) do not share any host plant.Avoidance of caterpillar traces on leaf surfaces by spider mitesTo examine whether spider mites avoid settling on host plant surfaces bearing caterpillar traces, we conducted dual-choice tests using paired adjacent leaf squares with and without caterpillar traces. We did not use whole plants because, in practice, it was difficult to induce caterpillar traces on whole plants. We used two spider mite species (T. kanzawai and T. urticae) and four caterpillar species (T. oldenlandiae, P. xuthus, B. mori, and S. litura). We cut a 10 × 20 mm leaf piece from a fully expanded primary kidney bean leaf and then cut the piece into two equal squares (10 × 10 mm). To introduce caterpillar traces to one square, we arranged them on a separate piece of paper towel on water-saturated cotton. This procedure was necessary because the caterpillars used were larger than individual leaf squares. Then we placed a fourth or final instar caterpillar on the squares and induced the caterpillar to walk across every leaf square three times (Fig. 1a). We carefully removed all caterpillar-produced silk threads from the squares. Within 30 min, we arranged the square (trace +) to touch against the other square (trace −) on water-saturated cotton in a Petri dish. Subsequently, a 2- to 4-day-old mated adult female of T. kanzawai or T. urticae was introduced onto a pointed piece of Parafilm in contact with both leaf edges using a fine brush (Fig. 1a). We recorded the leaf square onto which the mite had settled at 2 h after its introduction, as preliminary observations confirmed that all females would settle on a particular leaf within that period. Each female mite and pair of leaf squares were used only once. All tests described below were conducted between 13:00 and 17:00 h, when adult female spider mites actively disperse by walking. There were 14 replicates using traces of T. oldenlandiae, 48 of P. xuthus, 20 of B. mori, and 26 of S. litura for T. kanzawai, as well as 18, 32, 16, and 47, respectively, for T. urticae. Data were subjected to two-tailed binomial tests with the common null hypothesis that a spider mite would settle on the two squares with equal probability (i.e., 0.5).Figure 1(a) Procedure used to observe avoidance of caterpillar traces by spider mites. (b) Experimental setup used to observe avoidance of B. mori traces on plant stems by T. kanzawai. (c) Experimental setup used to observe avoidance of B. mori trace extracts by T. kanzawai.Full size imageDuration of B. mori trace avoidance by T. kanzawai
To examine whether the effects of caterpillar traces on spider mite avoidance decline over time, we used T. kanzawai mites and B. mori caterpillars. We used B. mori because populations can be easily maintained over many generations. We prepared bean leaf squares with B. mori traces in the same manner descried above and preserved the traced square on water-saturated cotton for 0 h (n = 30), 24 h (n = 29), 48 h (n = 28), or 72 h (n = 28). Then we arranged the square (trace +) to lie in close proximity to the control square (trace −) that had been preserved for the same periods of time. Then we compared the avoidance response of T. kanzawai females in the same manner described above.Avoidance of B. mori traces on plant stems by T. kanzawai
To examine whether T. kanzawai females avoid walking along plant stems bearing caterpillar traces, we used Y-shaped kidney bean stems (Fig. 1b). We cut symmetric bean plants ca. 15 days after sowing from their base and inserted them perpendicularly into a 5 mL glass bottle filled with water and wet cotton. To induce caterpillar traces on one branch of the stem, we allowed a silkworm to crawl from the branching point to the far end of one branch three times for each stem (n = 20). Then we introduced a T. kanzawai adult female at a release point 35 mm below the branch point (Fig. 1b). We recorded the branch along which the female walked to the far end. Each female mite and each Y-shaped stem were used only once. The numbers of females were compared using binomial tests in the same manner described above.Avoidance of B. mori trace extracts by T. kanzawai
To extract chemical traces of caterpillar, we introduced 10 third instar B. mori to a glass Petri dish (120 mm diameter, 60 mm depth). After 1 h, we removed all caterpillars and washed the inside bottom of the dish with 1.0 mL acetone. We replicated the procedure twice using different individuals to combine all extracts and to acquire enough extract for the following experiment.To examine avoidance of B. mori trace extracts by T. kanzawai females, we conducted dual-choice experiments using T-shaped pathways of filter paper (35 × 35 mm; width, 2 mm; Fig. 1c). Using disposable micropipettes (Drummond Scientific Co., PA, USA), 1.75 caterpillar equivalents (i.e., 60 µL) of acetone extract were applied to an alternately selected branch (17.5 mm long) of each pathway (i.e., 0.10 caterpillar equivalent/mm), with control acetone applied to the other branch. We applied each solution dropwise at the junction point to minimize mixing. After evaporating the solvent from those pathways, we perpendicularly suspended them (Fig. 1c) and introduced an adult female mite at 2 days post-maturation onto the bottom of each pathway using a fine brush and recorded the branch along which the female first walked to the far end. Each female mite and each T-shaped filter paper were used only once, with 19 replicates. Each female mite made a choice within 10 min. The avoidance response of T. kanzawai was analysed in the same manner described above.Indirect effects of B. mori traces on T. kanzawai via plantsTo determine whether B. mori traces on plants indirectly affect the performance of T. kanzawai on plants, we introduced 70–80 randomly selected quiescent female deutonymphs of T. kanzawai onto kidney bean leaf disks. Immediately after synchronized adult emergence, we introduced the same number of adult males to allow mating; the detailed procedure is described elsewhere25. After 24 h, we transferred the females singly onto 10 × 10 mm bean leaf squares with or without B. mori traces prepared as described above. Because the number of eggs laid within a certain period is considered the most sensitive performance index of spider mite females26,27, any plant-mediated indirect interaction, such as defence induction in response to caterpillar traces, should result in lower egg numbers laid by the test females. We counted the eggs laid on the leaf squares 24 h after their introduction. One female that laid no eggs during the 24 h period (n = 1, trace +) was excluded from the analysis. We obtained 33 and 36 replicates for the trail+ and trail– conditions, respectively. We compared the numbers of eggs laid on leaves with and without B. mori traces using a generalized linear model with a Poisson error distribution using the SAS 9.22 software (SAS Institute Inc., Cary, NC, USA).EthicsThis article does not contain any studies with human participants or animals. More

During the COVID-19 pandemic, behavioral restrictions were imposed, after which various health problems were reported in many countries45,46. The pandemic has also increased food insecurity worldwide; consequently, panic buying has been observed in many countries, including Japan47. However, even in such situations, we found that diversity in local food access, ranging from self-cultivation to direct-to-consumer sales, was significantly associated with health and food security variables. Specifically, our results revealed the following five key discussion points.Urban agriculture in walkable neighborhoods bore fruit for health and food system resilience. However, the magnitude of its contribution differed depending on the type of urban agricultureThe results of this study showed that those who grew food by themselves at allotment farms and home gardens had significantly better subjective well-being and physical activity levels than those who did not. This result is in line with previous studies conducted during times free from the impact of infectious disease pandemics38,39,40. The use of direct sales was not related to subjective well-being but was significantly associated with physical activity. The reason might be that farm stand users tend to live in areas with farmland and travel to purchase fruits and vegetables at farm stands on foot or by bicycle. This result is consistent with that of a previous study demonstrating that the food environment in neighborhoods is an important component in promoting physical activity17.Our results also showed that those who grew food by themselves at allotment farms and those who purchased local foods at farm stands were significantly less anxious about the availability of fresh food both during the state of emergency and in the future than their counterparts. In contrast, home garden users showed significant differences only for the state of emergency. This result might be due to the differences in the size and yield of cultivation at allotment farms and home gardens. One lot in allotment farms in Tokyo can produce as much as or more than the average annual vegetable consumption per household in Japan48. However, home gardens are generally smaller and produce limited fresh foods for consumption, which may have influenced food security concerns.As in other countries, Japan imports much food from overseas and is deeply integrated into the large-scale global food system. However, as shown in this study, urban agriculture in Japanese suburbs forms small-scale, decentralized, and community-based local food systems. This multilayered food system can complement the disruptions and shortages of the global system when various problems occur for climatic, sociopolitical, or other reasons, such as pandemics. In fact, our empirical evidence suggests that urban agriculture in walkable neighborhoods, particularly allotment farms and direct-to-consumer sales at farm stands, contributed to the mitigation of food security concerns in neighborhood communities. This means that urban agriculture could enhance the resilience of the urban food system at a time when the global food system has been disrupted due to a pandemic. This validates recent discussions about the potential of urban agriculture to facilitate food system resilience10. Furthermore, our findings imply that the types of urban agriculture employed matter in determining the degree of contribution to food system resilience.To summarize the overall results, urban agriculture in walkable neighborhoods bore fruit for health and food system resilience during the COVID-19 pandemic. However, different types of urban agriculture exhibited varying associations with health and resilience. Allotment farms were positively related to all of the following: subjective well-being, physical activity, and food security concerns, both during the state of emergency and in the future. Home gardens were positively related to subjective well-being, physical activity, and food security concerns only during the state of emergency. Farm stands were positively related to physical activity and food security concerns both during the state of emergency and in the future.These differences may be due to the characteristics of the respective spaces. It is suggested that this diversity of urban agriculture has led to different types of people benefiting from various kinds of urban agriculture. Allotment farms were found to be associated with high subjective well-being, physical activity, and food security, but they may not be feasible for those who do not have enough physical strength because users are responsible for cultivating their lots, which measure 10–30 square meters40. In contrast, home gardens can be created even by those who are not confident in their physical strength. In fact, our study showed that women and older people engaged in home gardening more than men and younger people. In addition, direct-to-consumer sales at farm stands are the easiest way to obtain local fresh foods for those who do not have the time and space for allotment farms and home gardens. The need for urban agriculture has been argued in many countries2,3. However, little attention has been paid to its scale, accessibility, and diversity. Our study suggests that it is worthwhile to create diverse food production spaces within walkable neighborhoods while considering the diversity of people who access these spaces.Compared to other urban greenery and food retailers, the benefits of urban agriculture on subjective well-being and food security could be greaterCompared to the use of other urban green spaces, including urban parks, our results indicated that self-cultivation at allotment farms and home gardens was more strongly associated with subjective well-being. Previous studies have offered limited perspectives on the differences among various types of urban green spaces33. Our study further suggests that urban parks, allotment farms, and home gardens are differently associated with human health. However, as the reason was not determined, further research is needed.Furthermore, compared to other food retailers, such as supermarkets, convenience stores, and co-op deliveries, allotment farms and farm stands were more strongly associated with less anxiety about fresh food availability in the future. The availability of local fresh foods within walkable neighborhoods might have mitigated food security concerns because residents could grow food by themselves or directly observe farmers’ production processes, which may have made the difference from purchasing at places where the food systems were not visible.Flexibility in work style might promote urban agriculture in walkable neighborhoodsThere was an association between work style—working from home—and access to local food. According to the Ministry of Health, Labor and Welfare (https://www.mhlw.go.jp/english), 52% of Tokyo office workers worked from home during the first emergency declaration. Long commute times and high train congestion rates have been a problem in Tokyo suburbs, but remote workers have gained more time at and around their homes by reducing their commute times, increasing their opportunities to access local food in their walkable neighborhoods. Those who worked from home sought outdoor activities for refreshment and exercise and used a variety of urban green spaces during the pandemic49. Allotment farms and home gardens might be used as such urban green spaces. This result is consistent with previous studies assessing the characteristics of Canadian gardeners during the COVID-19 pandemic28,30.Until now, urban planners and policymakers have rarely taken work style into account. However, the flexibility of work styles and work hours may bring new insights; for example, those who work from home may become important players in urban agriculture. It has been pointed out that cities have a large hidden potential for urban agriculture by cultivating underused lands50. Our study suggests that such underused lands could be converted into productive urban landscapes for remote workers to engage in farming or gardening in between jobs as a hobby or as a side business.Food equity might be improved by urban agriculture in walkable neighborhoodsLocal fresh food is generally considered more expensive than junk food in high-income countries, creating social issues of food inequity. Therefore, past discussions on urban agriculture and food security have focused primarily on low-income households in socioeconomically disadvantaged areas24,25,26.In contrast, our study covered people from all income groups and found no statistically significant relationship between access to local food and income. This finding might be due to two urban cultural backgrounds regarding local food in Tokyo, that is, accessibility and affordability. First, residential segregation by income levels is not noteworthy in Tokyo and people from various income brackets live mixed in the same neighborhoods51. Therefore, most urban residents living in the suburbs have geographically equitable opportunities to access local foods. Second, local foods sold at farm stands are affordable. Prices are almost the same or cheaper than buying food at food retailers. While prices increase because of middleman margins related to shipping in the wholesale market, such increases are unnecessary when selling directly to consumers at farm stands. In addition, the allotment farm lots are not expensive to rent, particularly those operated by local municipalities (Supplementary Note 1).These two backgrounds make local fresh food physically and economically accessible to consumers of all income levels, resulting in food equity. This is particularly important because the concept of food system resilience includes the equitability perspective27.The integration of urban agriculture into walkable neighborhoods is a fruitful wayWhile the current discussion on walkable neighborhoods does not emphasize urban agriculture, our evidence indicated its effectiveness. The concept of walkable neighborhoods (e.g., the 15-min city model) stresses the decarbonization benefit of limiting vehicle travel, as well as the health benefits of promoting walking and cycling13,14,15,16. In addition, our research indicated that urban agriculture in walkable neighborhoods benefited health and well-being by increasing recreational outdoor opportunities to neighborhood communities, including remote workers. It also contributed to food system resilience by providing local foods to all people, including low-income households, when the global food system was disrupted due to the pandemic. Furthermore, recent studies on urban agriculture reported the decarbonization benefit of reducing carbon footprints in food production and distribution7,8. Small-scale and community-based urban agriculture in walkable neighborhoods might especially bring this benefit because neighborhood communities travel to farms on foot or by bicycle, which means almost no emission by distribution. While urban green spaces have various health benefits32,33,34,35, urban agriculture also contributes to food system resilience as well as carbon emission reduction, which makes it unique.Urban agriculture was once considered a failure of urban planning in Japan because it symbolized uncontrolled sprawl. This is analogous to the Western view, as urban agriculture was once considered the ultimate oxymoron1. However, our empirical evidence suggests that the urban‒rural mixture at neighborhood scales is a reasonable urban form that contributes to the resilience of the urban food system and to the health and well-being of neighborhood communities. It is no longer a failure of urban planning but a legacy of urban sprawl in the current urban context.Our study showed that integrating urban agriculture into walkable neighborhoods is a fruitful way of creating healthier cities and developing more resilient urban food systems during times of uncertainty. In cities where there is no farmland in intraurban areas, it would be considered effective to utilize underused spaces such as vacant lots and rooftops as productive urban landscapes. In growing cities where urban areas are still expanding, it would be advantageous to conserve agricultural landscapes within their urban fabrics. Our study could provide referential insights and robust evidence for urban policy to integrate urban agriculture into walkable neighborhoods.This study has potential limitations, including the timing of the survey and the measurement method that was utilized. We conducted the survey between June 4 and 8, 2020, just after the end of the first declaration of a state of emergency by the Japanese government. During this period, the main cultivation activities were planting and growing, and the harvest was just beginning. This seasonal constraint may have influenced the results. Because the survey was conducted during the pandemic, we used subjective methods to measure health and well-being status. However, the results might be different using objective methods52, thus further research is necessary. In addition, a longitudinal study is needed to determine whether the trends observed in this study were specific to the emergency period or whether they will persist after the COVID-19 pandemic. More

Analytical method validationThe results of the precision study with relative standard deviation (RSD), and accuracy are shown in Table 1. Through the precision study we found the value of RSD as less than 5%. Moreover, accuracy was done with percent recovery experiments. The results showed that the percentage recoveries for spiked samples were in the range of 95.7–103.7%.Table 1 Shows percent (%) recovery and relative standard deviation.Full size tablePhysicochemical properties and water quality indexThe investigations of the water quality properties of the Narora channel are shown in Table 2. The temperature, TDS, turbidity, and alkalinity were within the standards of the country18 and WHO19 (taken from UNEPGEMS). While pH and dissolved oxygen (D.O) were above the recommended standards indicating poor water quality. Moreover, the detected heavy metals were in the following order Ni  > Fe  > Cd  > Zn  > Cr  > Cu  > Mn. Among these heavy metals Mn, Cu, and Zn were within the recommended limits whereas Cr, Fe, Ni, and Cd were crossing the limits18 contributing to the poor quality. Furthermore, the WQI calculation will give more insights into the overall quality of water as it explains the combined effect of several physicochemical properties12. Its calculation is done simply by converting numerous variables of water quality into a single number12,20. In addition to this, WQI simplifies all the data and helps in clarifying water quality issues by combining the complex data and producing a score that shows the status of water quality2,12,21. The WQI classifies water quality status into five groups such as if WQI  Cu  > Zn  > Fe  > Zn  > Ni  > Cr from root to stalk; and Mn  > Cd  > Zn  > Cu  > Fe  > Ni  > Cr from stalk to leaves.Table 5 Heavy metal concentrations in Eichhornia crassipes (mg/kg.dw).Full size tableFigure 3MPI values in E. crassipes.Full size imageTable 6 Bioaccumulation factor (BAF), transfer factor (TF), and mobility factor (MF) in plant E. crassipes.Full size tableThese factors BAF, TF, and MF are utilized to monitor the level of anthropogenic pollution in plants and their surrounding medium2,15,32,34,35. BAF shows the concentrations of heavy metals bioaccumulated by plants from the water. If the BAF  > 1 it indicates hyperaccumulation36. So, in the present study, all the concerned heavy metals were hyperaccumulated in the plant. The TF elucidates the capability of the plant to translocate the accumulated metals to its other parts. The roots of E. crassipes showed the highest translocation capacity for Ni (1.57) as well as Zn (1.30) to other parts. If the value of TF exceeds 1, then it represents the high accumulation efficiency37,38, therefore, plants will be considered as the hyperaccumulators for the Ni and Zn. Although the Cd was the highest accumulated metal in the plant, it could have been because of its may be because of its low TF. Whereas, TF values lower than 1 for Cr, Mn, Fe, Cu, and Cd pointed out that this plant’s roots act as a non-hyperaccumulator for these heavy metals. Furthermore, the highest MF values were depicted for Mn in both cases which reflects that E. crassipes can suitably be used for phytoextraction of Mn as well as for Cd, Zn, Fe, Ni, and Cu. The BAF, TF, and MF of Cr are low in the present study, which implies that roots are limiting the Cr. Moreover, if the BAF ≤ 1.00 then it shows the capability of absorption only rather than accumulation36,37. In addition, if the values of BAF, TF, and MF exceed 1, plants can also work for phytoextraction. Furthermore, if the BAF  > 1 and TF  More

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Methods for data analysis in figuresAll analyses in figures were performed using Mathematica 12.3 (Wolfram Research, Inc., Champaign, IL, USA).Analysis in Fig. 1
C&D. To calculate integrated abundances of E. huxleyi cells and EhV, we first selected days for which all the bags had a non-null value. Values were then summed up to obtain the integrated abundance.E&J. We computed a standard linear fit between the E. huxleyi total abundances and total EhV abundances for covered and uncovered bags separately. We followed the same procedure for the correlations in panel J and provide a comparison between different models in Supplementary Fig. 5.Analysis in Fig. 2
A. The ASVs that were selected appeared at a relative abundance of at least 2% in at least 4 samples for the 0.2–2 µm 16S sequences and at least in 8 samples for the 2–20 µm 18S sequences. Abundances were concatenated for each time point and normalized by row, to have maximum relative abundance of 1 across all samples. ASVs were sorted by the position of their individual center of mass ({t}_{{CM}}) defined by$${t}_{{CM}}=,frac{mathop{sum}limits_{i}{t}_{i}f({t}_{i})}{mathop{sum}limits_{i}f({t}_{i})}$$
(1)
with i representing the different time points and f(({t}_{i})) the relative abundance of the ASV. The same figure for the individual bags in shown in Supplementary Fig. 14 and Supplementary Fig. 15.B. We selected 18S ASVs with a maximum relative abundance of at least 2% and observed in at least five samples. We averaged relative abundance across bags and then smoothed the time series with a moving average filter (width 2). Then, we grouped all ASVs into clusters based on their cosine distance using Mathematica’s FindClusters function and the KMeans method. The number of possible clusters ranged from 2 to 12, and the final number of clusters was decided using the silhouette method71. Only silhouette scores for 2 and 6 clusters were positive (between-cluster distance minus within-cluster distance).D. We subset reads that map to either Flavobacteriales or Fhodobacterales, then renormalized within each class, taking the mean over bags. Results per bag are shown in Supplementary Fig. 9.F. The turnover time was defined by the exponential rate k at which the Bray-Curtis similarity ({BC}(t)) declined over time. To this end, for a given bag, we computed the Bray–Curtis similarity between the composition vector at a starting day t’ with all following days t, giving a curve that declined roughly exponentially. For earlier starting days (for which the similarity curves declined the furthest), we found that the Bray–Curtis similarity never reached 0 but instead leveled out around ({{BC}}_{infty }=0.05) (due to ASVs that are constantly present in all the samples and maintain a minimal level of similarity between bags). Thus, we imposed an offset at(,{{BC}}_{infty }) for all fits (using Mathematica’s FindFit function) with the function:$${BC}(t)=(1-{{BC}}_{{{infty }}}) times {e}^{-kleft({t}^{{prime} }-tright)}+{{BC}}_{{{infty }}}$$
(2)
The turnover is averaged over bags, showing the standard deviation as error bars in the figure.G. To find differentially abundant ASVs, we first selected a subset of ASVs that had a maximum abundance of at least 10%, and performed Mann–Whitney U-Tests between the relative abundance values of a given ASV in the focal bag and all the other bags over all timepoints of the bloom’s demise. Correcting for multiple testing, we found four 16S ASVs that were differentially abundant in any of the bags, three of which were specific to bag 7, shown in Fig. 2g; and five 18S ASVs, two specific to bags 5 and 6 (Rhizosolenia delicatula and Aplanochytrium), one specific to bag 4 (Pterosperma), and two specific to bag 7 (MAST-1C and Woloszynskia halophila, shown in Fig. 2g).H. The divergence between bags was calculated as follows: we first measured, for each bag, the Bray–Curtis distance between this given bag and all the other bags at the end of the experiment (Supplementary Fig. 13). In order to control for the existing differences between bags at the beginning of the bloom, Bray–Curtis distances were normalized according to the differences between bags at the starting day of the E. huxleyi bloom. As the exact starting days of the bloom is not clear, we normalized for starting days 11, 12, or 13. The plot shows averages with the standard deviation as error bars. For the 18S microbiome, we first removed reads that map to E. huxleyi to reduce bias toward bag 7 (which had by far the lowest E. huxleyi abundance, Fig. 1c).Analysis in Fig. 3
A. Functional annotation of dominant 18S ASVs was based on manual literature search for the 100 most abundant 18S ASVs. Automatic annotation using the functional database created by72 gave qualitatively identical results but contained fewer organisms (covering about 50% of reads). The relative abundance of each trait was obtained by summing up the relative abundance of all the species harboring a specific trait. We used the annotations from72 to further subdivide heterotrophs into osmotrophs, saprotrophs, and other types of heterotrophy (e.g., grazing), ignoring ASVs with missing annotations.D. Growth rates were computed by fitting a linear model to the log-transformed absolute abundances. For thraustochytrids, we measured growth rates until the abundances reached their maximum, i.e., for days indicated by solid lines in Fig. 3b. For bacteria in the 0.2–2 micron fraction, we measured growth rates during the bloom and demise of E. huxleyi, i.e., for the time period after day 15 until the final day, except for bag 4 (until day 22) and bag 7 (until day 18) to account for their different bloom and demise dynamics. For bacteria in the 2–20 micron fraction, we measured growth rates similarly, starting after day 10 until the final day, except bags 4 and 7 (until day 22).E. To quantify the rate of change k of the biomass ratio of thraustochytrids to bacteria we fit a linear function to the log of biomass ratio from day 10 to the time point t where the ratio was maximal; for bag 7, this was day 18, for all others, day 23. We thus have:$$,{{log }},{BR},(t)={kt},+,{{log }},{BR},(0)$$
(3)
Analysis in Fig. 4
C&D. Since TEP accumulates over time, it cannot be expressed as a weighted sum of phytoplankton abundances. Instead, we formulate the model as a recursive relation where TEP can be produced by E. huxleyi, naked nanophytoplankton, and picophytoplankton, and degraded or lost through sinking:$${TEP}left(tright)=left(1-dright){TEP}left(t-1right)+{a}_{E}Eleft(tright)+{a}_{N}Nleft(tright)+{a}_{P}Pleft(tright),$$
(4)
The amount of TEP at time t is given by the fraction (1-d) of TEP at time t-1, where d corresponds to the fraction of TEP that is degraded between time points, plus the amount of TEP produced by the phytoplankton cells present at time t (or time t-1, which gives equivalent results). E, N, and P correspond to E. huxleyi, naked nanophytoplankton, and picophytoplankton, respectively. The parameter ({a}_{E}) corresponds to the amount of TEP produced per E. huxleyi cell, reported in panel D. ({a}_{E}) is set to be fixed through time, and different for each bag. This recursion can be solved to give an explicit expression for TEP(t):$${TEP}left(tright)=mathop{sum }limits_{{t}^{{prime} }=0}^{t}{left(1-dright)}^{t-{t}^{{prime} }}[{a}_{E}Eleft({t}^{{prime} }right)+{a}_{N}Nleft({t}^{{prime} }right)+{a}_{P}Pleft({t}^{{prime} }right)].$$
(5)
This functional form was then used to perform a linear model fitting with the constraint ({a}_{i}ge 0) for various values of the parameter d. The best fit, defined by maximum ({R}^{2}) over the resulting linear model, was used to fix d = 0.12. Our model considers that the fraction of non-calcified E. huxleyi cells in the nanophytoplankton counts is small.Larger phytoplankton cells ( >40 μm) filtered out from flow-cytometry measurements can also be a major source of TEP, despite low cell density. In order to verify this, FlowCam data was analyzed. None of the identified classes of larger phytoplankton (such as Phaeocystis or Dinobryon) increased in a systematic manner toward later stages of the bloom, explaining why larger phytoplankton were not included in the TEP model (Supplementary Fig. 24 and Supplementary Fig. 25).E. Using the smFISH method that reports the proportion of infected E. huxleyi cells, we estimated the amount of TEP produced from infected cells. We first used the least infected uncovered bags (bags 1 and 3) as a baseline to fix model parameters such as how much TEP does a non-infected cell produce. We then split the E. huxleyi abundance into an uninfected subpopulation producing T TEP/cell as in the uninfected bags, and an infected subpopulation producing I×T TEP/cells. To define I, we combined the fixed model parameters (i.e., amount of TEP produced per cell from Fig. 4d for bags 1 and 3) with the measured fraction of infected cells. We adjusted the factor I = 4 to minimize deviation of the measure total TEP concentration from the model prediction including the two subpopulations. The same procedure was used for panel H, using the corresponding model for PIC.F&G. To model the amount of PIC produced per cell we assume that the measured PIC only increases via new E. huxleyi coccoliths. The equivalent model for PIC reads$${PIC}left(tright)=left(1-dright){PIC}left(t-1right)+{a}_{E}{{max }}left(Eleft(tright)-Eleft(t-1right)right).$$
(6)
Where ({a}_{E}) is the amount of PIC produced per cell, and displayed in panel G. Using the same procedure as for TEP, we obtain the best fit for d = 0.0075. Our PIC model assumes that all PIC production comes from E. huxleyi, supported by large occurrence of E. huxleyi cells observed in scanning electron microscopy (Supplementary Fig. 1).Methods for data collectionMesocosm core setupThe mesocosm experiment AQUACOSM VIMS-Ehux was carried out for 24 days between 24th May (day 0) and 16th June (day 23) 2018 in Raunefjorden at the University of Bergen’s Marine Biological Station Espegrend, Norway (60°16′11 N; 5°13′07E). The experiment consisted of seven enclosure bags made of transparent polyethylene (11 m3, 4 m deep and 2 m wide, permeable to 90% photosynthetically active radiation) mounted on floating frames and moored to a raft in the middle of the fjord. The bags were filled with surrounding fjord water (day −1; pumped from 5 m depth) and continuously mixed by aeration (from day 0 onwards). Each bag was supplemented with nutrients at a nitrogen to phosphorus ratio of 16:1 according to the optimal Redfield Ratio (1.6 µM NaNO3 and 0.1 µM KH2PO4 final concentration) on days 0–5 and 14–17, whereas on days 6, 7 and 13 only nitrogen was added to limit the growth of pico-eukaryotes and favor the growth of E. huxleyi that is more resistant to phosphate limited conditions. Silica was not added as a nutrient source in order to suppress the growth of diatoms and to enhance E. huxleyi proliferation. Bags 5, 6, 7 were covered to collect aerosols and guarantee minimal contamination while sampling for core variables. Bags 1, 2, 3, 4 were sampled for additional assays such as metabolomics, polysaccharides profiling, and vesicles, which increase sampling time and potential for contamination.Measurement of dissolved inorganic nutrientsUnfiltered seawater aliquots (10 mL) were collected from each bag and the surrounding fjord water in 12 mL polypropylene tubes and stored frozen at −20 °C. Dissolved inorganic nutrients were measured with standard segmented flow analysis with colorimetric detection73, using a Bran & Luebe autoanalyser. Data are available in ref. 74 and values for individual bags are plotted in Supplementary Fig. 26.Measurement of water temperature and salinityWater temperature and salinity were measured in each bag and the surrounding fjord water using a SD204 CTD/STD (SAIV A/S, Laksevag, Norway). Data points were averaged for 1–3 m depth (descending only). When this depth was not available, the available data points were taken. Data are missing for the fjord in days 0–1. Outliers were removed for the following samples: bag 1 at days 0, 4, 15; bag 7 at day 15. Data are available in ref. 74.Flow cytometry measurementsSamples for flow cytometric counts were collected twice a day, in the morning (7:00 a.m.) and evening (8:00–9:00 p.m.) from each bag and the surrounding fjord, which served as an environmental reference. Water samples were collected in 50 mL centrifugal tubes from 1 m depth, pre-filtered using 40 µm cell strainers, and immediately analyzed with an Eclipse iCyt (Sony Biotechology, Champaign, IL, USA) flow cytometer. A total volume of 300 µL with a flow rate of 150 µL/min was analyzed with the machine’s software ec800 v1.3.7. A threshold was applied based on the forward scatter signal to reduce the background noise.Phytoplankton populations were identified by plotting the autofluorescence of chlorophyll versus phycoerythrin and side scatter: calcified E. huxleyi (high side scatter and high chlorophyll), Synechococcus (high phycoerythrin and low chlorophyll), nano- and picophytoplankton (high and low chlorophyll, respectively). Chlorophyll fluorescence was detected by FL4 (excitation (ex): 488 nm and emission (em): 663–737 nm). Phycoerythrin was detected by FL3 (ex: 488 nm and em: 570–620 nm). Raw.fcs files were extracted and analyzed in R using ‘flowCore’ and ‘ggcyto’ packages and all data are available on Dryad74. In particular, the gating strategy was adapted to each day and each bag and individual plots for each days and each bag can be found in the Dryad link.For bacteria and viral counts, 200 µL of sample were fixed with 4 µL of 20% glutaraldehyde (final concentration of 0.5%) for 1 h at 4 °C and flash frozen. They were thawed and stained with SYBR gold (Invitrogen) that was diluted 1:10,000 in Tris-EDTA buffer, incubated for 20 min at 80 °C and cooled to room temperature. Bacteria and viruses were counted and analyzed using a Cytoflex and identified based on the Violet SSC-A versus FITC-A by comparing to reference samples containing fixed bacteria and viruses from lab cultures. A total volume of 60 µL with a flow rate of 10 µL/min was analyzed. A threshold was applied based on the forward scatter signal to reduce the background noise. For plotting bacteria (Fig. 1h), a moving average of three successive days was used.Enumeration of extracellular EhV abundance by qPCRDNA extracts from filters from the core sampling (see above) were diluted 100 times, and 1 µL was then used for qPCR analysis. EhV abundance was determined by qPCR for the major capsid protein (mcp) gene: 5′-acgcaccctcaatgtatggaagg-3′ (mcp1F) and 5′-rtscrgccaactcagcagtcgt -3′ (mcp94Rv). All reactions were carried out in technical triplicates using water as a negative control. For all reactions, Platinum SYBER Green qPCR SuperMix-UDG with ROX (Invitrogen, Carlsbad, CA, USA) was used as described by the manufacturer. Reactions were performed on a QuantStudio 5 Real-Time PCR System equipped with the QuantStudio Design and Analysis Software version 1.5.1 (Applied Biosystems, Foster City, CA, USA) as follows: 50 °C for 2 min, 95 °C for 5 min, 40 cycles of 95 °C for 15 s, and 60 °C for 30 s. Results were calibrated against serial dilutions of EhV201 DNA at known concentrations, enabling exact enumeration of viruses. Samples showing multiple peaks in melting curve analysis or peaks that were not corresponding to the standard curves were omitted. Data are available in ref. 74. A comparison of viral counts based on flow-cytometry and qPCR is shown in Supplementary Fig. 2.FlowCam analysisSamples for automated flow imaging microcopy were collected once a day in the morning (7:00 a.m.) from each bag and the surrounding fjord, which served as an environmental reference. Water samples were collected in 50 mL centrifugal tubes from 1 m depth, kept at 12 °C in darkness, and analyzed within 2 h of sampling, using a FlowCAM II (Fluid Imaging Technologies Inc., Scarborough, ME, USA) fitted with a 300 µm path length flow cell and a 4× microscope objective. Images were collected using auto-image mode at a rate of 7 frames/second. A sample volume of 10 mL was processed at a flow rate of 0.7 mL/min. Individual objects within each sample were clustered and annotated using the Ecotaxa platform75. Absolute counts for major groups, including the most abundant ciliate category Ciliophora U04, were then exported and normalized by the individual amount of water volume processed for each sample.Data are available under “Flowcam Composite Aquacosm_2018_VIMS-Ehux” project on Ecotaxa.Scanning electron microscopy50 ml of water samples from bags or fjord were collected on polycarbonate filters (0.2 µm pore size, 47 mm diameter, Millipore). The filters were air dried and stored on petri-slides (Millipore) at room temperature. Prior to observation, a small fraction of the filter was cut and coated with 2 nm of iridium using a Safematic CCU-010 coater (Safematic GMBH, Switzerland). Samples were observed on a Zeiss Ultra SEM that was set at a working distance of 6.2 ± 0.1 mm, an acceleration voltage of 3.0 kV and an aperture size of 30 mm. The secondary electron detector was used for image acquisition.Paired dilution experimentPhytoplankton growth and microzooplankton grazing rates were estimated using the dilution method76,77. A slightly modified version of the method was used with only one low dilution level (20%) and an undiluted treatment used78. Rates calculated using this method are considered conservative but accurate when compared with those using multiple dilution levels and a linear regression. Water from bags 1–4 was collected using a peristaltic pump at ~1 m depth and mixed into a 20 L clean carboy. Water was screened through a 200 µm mesh to remove larger mesozooplankton. The collected water was shaded with black plastic and returned to shore. Dilution experiments were set-up in a temperature-controlled room, set to ambient water temperature (±2 °C). Particle-free diluent (FSW) was prepared by gravity filtering whole seawater (WSW) through a 0.45 µm inline filter (PALL Acropak™ Membrane capsule) into a clean carboy. To the FSW, WSW was gently siphoned at a proportion of 20%. The 20% dilution and 100% WSW treatments were prepared in single carboys and then siphoned into triplicate 1.2 L Nalgene™ incubation bottles. To control for nutrient limitation, additional triplicate bottles of 100% WSW were incubated without added nutrients (10 µM nitrate and 1 µM phosphate). The incubation bottles were incubated for 24 h in an outdoor tank maintained at in-situ water temperatures by a flow-through system of ambient seawater. Bottles could float freely, and the seawater inflow caused gentle agitation throughout the 24 h period. A screen was used to mimic light conditions experienced within the mesocosm bags.To quantify viral mortality, we used the paired dilution method79 which involves setting up an extra low dilution level (20%) containing water filtered through a tangential flow filter (TFF) of 100 kDå to remove viral particles. During this experiment, TFF water was produced 1–2 days prior to the dilution experiment, to ensure the chemical composition of the water was as similar as possible, and experiments could be set up in a timely manner.At T0 hours and T24 hours from all dilution experiments, sub-samples were taken for the determination of chlorophyll-a and flow cytometry. For chlorophyll-a, 100–150 mL of seawater was filtered under low vacuum pressure through a 47 mm Whatman GF/F filters (effective pore size 0.7 µm), and then extracted in 7 mL of 97% methanol at 4 °C in the dark for 12 h. All chlorophyll readings were conducted on a Turner TD700 fluorometer80. Methanol blanks were included, and all samples were corrected for phaeophytin using a drop of 10% hydrochloric acid and then reading the sample again81.Water samples (2 × 1 mL) for flow cytometry were taken at T0 and T24 of dilution experiments for the determination of phytoplankton abundances. Water samples were taken in triplicate from T0, and from each bottle at T24. Samples were immediately fixed in 20 µL of glutaraldehyde (final concentration More

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