Marine photosynthetic microalgae are ubiquitously associated with bacteria in nature. However, the influence of these bacteria on algal cultures in artificial outdoor bioreactors is still largely unknown. In this study, a culture collection of 18 bacterial strains was obtained from cultures of Nannochloropsis sp. CCAP211/78 in two outdoor pilot-scale tubular bioreactors. The majority of isolates identified by sanger sequencing of 16S rDNAs were members from the classes Alphaproteobacteria and Flavobacteriia. To access the effect of bacteria on the growth of Nannochloropsis sp. CCAP211/78, a LED device was developed to simultaneously compare replicated micro-algal cultures with addition of individual bacterial isolates. In liquid co-cultivation, three bacteria (YP26, YP210, DMSP31) enhance growth of co-cultured microalgae while one bacterium (YP206) inhibits the growth of Nannochloropsis. Furthermore, YP26 also exhibit strong growth stimulation on the algal host as demonstrated by the double-layer agar assay. Co-cultures of algae with YP26 and YP206 were selected for transcriptomic investigation. The transcriptomic data indicate profound association between algae and bacteria. Our study suggests that in algal industry potential influence of the algal microbiome should be considered when carrying out algal production at large scale.