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Grazing and parasitism in algal production systems are significant causes of crop loss. Biological control of algal ponds, such as application of protective bacteria, represents a promising alternative to current mitigation strategies. The major barriers to probiotic methods are the lack of identified protective bacteria and uncertainty of scale-up effects, including potential negative interactions with the resident algal microbiome. Here, we report that application of Janthinobacter lividum affords robust protection against rotifer (Brachionus plicatilis) grazing on Microchloropsis salina. Protection was observed at laboratory scale from live bacteria and solvent extract additions as well as in biologically complex communities from bacterial additions to outdoor mesocosms. J. lividum persisted in outdoor communities for at least 3 days following addition, and did not lead to selective exclusion of specific taxa in the resident microbiome. These results demonstrate that J. lividum can provide protection against grazers in these diverse communities, without severe effects on the resident microbiome. Our results suggest that J. lividum is a promising treatment to mitigate algal crop losses due to pests. Additionally, the study highlights the importance of an ecologically-informed approach to algal crop management that will aid future applications in the biological control of algal ponds.

Microalgae have major functions in global biogeochemical cycles and are promising sources of renewable energy, yet the relationships between algal hosts and their associated microbiomes remain relatively underexplored. Understanding community organization of microalgal microbiomes, such as how algal species identity influences bacterial community structure, will aid in efforts to engineer more efficient phototrophic ecosystems. Here, we examined the community assembly of phycosphere-associated (attached) and free-living bacterial taxa associated with two marine microalgae: the diatom Phaeodactylum tricornutum and eustigmatophyte Microchloropsis salina. Samples were collected from outdoor mesocosms, raceway ponds, and laboratory enrichments, and bacterial taxa identified by 16S rRNA gene sequences. In outdoor mesocosms, we found distinct bacterial taxa associated with each algal species, including the Cytophagaceae and Rhodobacteraceae families with P. tricornutum, and Rhodobacteraceae, Hyphomonadaceae, and Saprospiraceae with M. salina. Additionally, there were host-specific differences in the bacterial genera associated with the phycosphere, including Novosphingobium and Rhodopirellula with P. tricornutum, and Methylophaga and Dyadobacter with M. salina. Bacterial communities from outdoor monoalgal P. tricornutum and polyalgal P. tricornutum/M. salina samples were used as inocula for laboratory enrichments with axenic P. tricornutum. Here, similar bacterial communities emerged, suggesting that the algal host exerts substantial influence over bacterial community assembly. Further enrichments for phycosphere-association revealed differing outcomes of community assembly processes contingent on the initial community composition. Phycosphere-associated communities from monoalgal P. tricornutum mesocosms were highly similar to one another, suggesting deterministic processes, whereas cultures from mixed M. salina/P. tricornutum raceways followed two apparent paths differentiated by the stochastic loss of specific community members and convergence towards or further deviation from the monoalgal samples. These results demonstrate that algal-associated bacterial communities are controlled by algal host, culture conditions, and the initial inoculum composition of the algal microbiome, and this knowledge can inform the engineering of more productive algal systems.

Open algal ponds are likely to succumb to unpredictable, devastating crashes by one or several deleterious species. Developing methodology to mitigate or prevent pond crashes will increase algal biomass production, drive down costs for algae farmers, and reduce the risk involved with algae cultivation, making it more favorable for investment by entrepreneurs and biotechnology companies. Here, we show that specific algal-bacterial co-cultures grown with the green alga Microchloropsis salina prevented grazing by the marine rotifer, Brachionus plicatilis. We obtained seven algal-bacterial co-cultures from crashed rotifer cultures, maintained them in co-culture with Microchloropsis salina, and used a microalgal survival assay to determine that algae present in each co-culture were protected from rotifer grazing and culture crash. After months of routinely diluting and maintaining these seven algal-bacterial co-cultures, we repeated the assay and found the opposite result: none of the seven bacterial communities protected the microalgae from rotifer grazing. We performed 16S rRNA gene amplicon sequencing on the protective and nonprotective co-culture samples and identified substantial differences in the makeup of the bacterial communities. Protective bacterial communities consisted primarily of Alphaproteobacteria (Rhodobacteraceae) and Gammaproteobacteria (Marinobacter, Pseudomonas, Methylophaga) while nonprotective bacterial communities were less diverse and missing many putatively crucial members. We compared the seven protective communities with the seven nonprotective communities and we correlated specific bacterial amplicon sequence variants with algal protection. With these data, our future work will aim to define and develop an engineered-microbiome that can stabilize industrial Microchloropsis salina cultures by protecting against grazer-induced pond crashes.