Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures

Discovery of antimicrobial activity in chemical extracts derived from unexplored algal-bacterial culture systems and isolates

Global health is affected by viral, bacterial, and fungal infections that cause chronic and often fatal diseases. Identifying novel antimicrobials through innovative methods that are active against human pathogens will create a new, necessary pipeline for chemical discovery and therapeutic development. Our goal was to determine whether algal production systems represent fertile ground for discovery of antibiotics and antifungals. To this end, we collected high-biomass algal-bacterial samples from outdoor mass cultivation systems, 18-L outdoor algal open cultures mesocosms, and non-axenic laboratory samples. We also cultivated 33 marine bacterial isolates for chemical extraction. Ultimately, we filtered, concentrated, extracted, and screened 77 chemically-complex mixtures using a conventional agar-based microbial growth inhibition assay against three microbes: Escherichia coli, Bacillus subtilis, and Candida albicans. We discovered that 23 of our chemical extracts (almost one-third of the chemical samples tested) exhibited some degree of growth inhibition toward B. subtilis and/or C. albicans. Our work here demonstrates the feasibility and potential of isolating bioactive natural products from high-biomass algal-bacterial samples from algal mass cultivation systems.

Spectral Algal Fingerprinting and Long Sequencing in Synthetic Algal-Microbial Communities

Synthetic biology has advanced in creating artificial microbial and algal communities, but technical and evolutionary complexities still pose significant challenges. Traditional methods, like microscopy and pigment analysis, are limited in throughput and resolution. In contrast, advancements in full-spectrum cytometry enabled high-throughput, multidimensional analysis of single cells based on size, complexity, and spectral fingerprints, offering more precision and flexibility than conventional flow cytometry. This study uses full-spectrum cytometry to analyze synthetic algal-microbial communities, enabling rapid species identification and enumeration. The workflow involves recording individual spectral signatures from monocultures, using autofluorescence to capture populations of interest, and creating a spectral library for further analysis. This spectral library was used for the analysis of the synthetic phytoplankton communities, revealing differences in spectral signatures. Moreover, the synthetic consortium experiment monitored algal growth, comparing results from different instruments, highlighting the advantages of the spectral virtual filter system for precise population separation and abundance tracking. By capturing the entire emission spectrum of each cell, this method enhances understanding of algal-microbial community dynamics and responses to environmental stressors. The development of standardized spectral libraries would improve the characterization of algal communities, further advancing synthetic biology and phytoplankton ecology research.

Bacterial diversity in different outdoor pilot plant photobioreactor types during production of the microalga Nannochloropsis sp. CCAP211/78

As large-scale outdoor production cannot be done in complete containment, cultures are (more) open for bacteria, which may affect the productivity and stability of the algae production process. We investigated the bacterial diversity in two indoor reactors and four pilot-scale outdoor reactors for the production of Nannochloropsis sp. CCAP211/78 spanning four months of operation from July to October. Illumina sequencing of 16S rRNA gene amplicons demonstrated that a wide variety of bacteria were present in all reactor types, with predominance of Bacteroidetes and Alphaproteobacteria. Bacterial communities were significantly different between all reactor types (except between the horizontal tubular reactor and the vertical tubular reactor) and also between runs in each reactor. Bacteria common to the majority of samples included one member of the Saprospiraceae family and one of the NS11-12_marine group (both Bacteroidetes). Hierarchical clustering analysis revealed two phases during the cultivation period separated by a major shift in bacterial community composition in the horizontal tubular reactor, the vertical tubular reactor and the raceway pond with a strong decrease of the Saprospiraceae and NS11-12_marine group that initially dominated the bacterial communities. Furthermore, we observed a less consistent pattern of bacterial taxa appearing in different reactors and runs, most of which belonging to the classes Deltaproteobacteria and Flavobacteriia. In addition, canonical correspondence analysis showed that the bacterial community composition was significantly correlated with the nitrate concentration. This study contributes to our understanding of bacterial diversity and composition in different types of outdoor reactors exposed to a range of dynamic biotic and abiotic factors. Key points • Reactor types had significantly different bacterial communities except HT and VT • The inoculum source and physiochemical factors together affect bacterial community • The bacterial family Saprospiraceae is positively correlated to microalgal growth.

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria

Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using ¹³C and ¹⁵N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.