Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina

Synergy between microalgae and microbiome in polluted waters

Microalga-microbiome interactions are central to both health and disease of aquatic environments. Despite impressive advances in deciphering how microorganisms participate in and impact aquatic ecosystems, the evolution and ecological involvement of microalgae and the microbiome in polluted waters are typically studied independently. Here, the phycosphere (i.e., the consortia of microalgae and the related microbiome) is regarded as an independent and integrated life form, and we summarize the survival strategies exhibited by this symbiont when exposed to anthropogenic pollution. We highlight the cellular strategies and discuss the modulation at the transcriptional and population levels, which reciprocally alters community structure or genome composition for medium-term acclimation or long-term adaptation. We propose a 'PollutantBiome' concept to help the understanding of microalga-microbiome interactions and development of beneficial microbial synthetic communities for pollutant remediation.

Advances in engineering algae for biofuel production

While algae demonstrate potential as a sustainable fuel source, low productivities limit the economic realization of algal biofuels. High-throughput strain engineering, omics-informed genome-scale modeling, and microbiome engineering are key technologies for enabling algal biofuels. High-throughput strain engineering efforts generate improved traits, including high biomass productivity and lipid content, in diverse algal species. Genome-scale models, constructed with the aid of omics data, provide insight into metabolic limitations and guide rational algal strain engineering efforts. As outdoor cultivation systems introduce exogenous organisms, microbiome engineering seeks to eliminate harmful organisms and introduce beneficial species. Optimizing algal biomass production and lipid content using these technologies may overcome the productivity barrier for the commercialization of algal biofuels.

Effective removal of the rotifer Brachionus calyciflorus from a Chlorella vulgaris microalgal culture by homogeneous solar photo-Fenton at neutral pH

In this study, a citrate-modified photo-Fenton process was successfully applied to decontaminate a Chlorella vulgaris microalgae culture spiked with the rotifer Brachionus calyciflorus (5 individuals mL^-1). The applied treatment (1 mg L^-1 Fe²⁺, 20 mg L^-1 H₂O₂, 17.5 mg L^-1 citric acid) had only moderate effects on viability and regrowth of the microalgae since, after a short post-treatment delay of a few days, they reached final cell densities similar to that obtained for microalgae cultures that were not spiked. The decontamination was effective as no regrowth of rotifers was observed in the microalgae cultures after treatment. The efficacy of the citrate-modified photo-Fenton treatment was also studied with a higher starting concentration of 20 rotifers mL^-1 and was compared with a solar light/H₂O₂ treatment. Results show that both treatments had similar efficacies on the rotifer elimination, but that the citrate-modified photo-Fenton treatment had a lower negative impact on the regrowth of microalgae than the solar light/H₂O₂ treatment. However, when microalgae cultures were spiked with 20 rotifers mL^-1, rotifers were only partially inactivated and post-treatment regrowth occurred, which highlights the importance to apply the photo-Fenton process at an early stage of a contamination to achieve full rotifer elimination. In any case, a contamination with 5 rotifers mL^-1 is already a significant threat as numbers above 1000 rotifers mL^-1 were reached after 14 days and caused the microalgae culture to fail. Overall, our treatment suggests that the citrate-modified solar photo-Fenton process is an environmentally friendly solution to support the maintenance of contaminant-free microalgal cultures.

Kinopus chlorellivorus gen. nov., sp. nov. (Vampyrellida, Rhizaria), a New Algivorous Protist Predator Isolated from Large-Scale Outdoor Cultures of Chlorella sorokiniana

The vampyrellids (Vampyrellida, Rhizaria) are a major group of predatory amoebae that have attracted significant attention because of their diversity of feeding strategies. The crucial roles they play in important processes such as suppressing soil disease and controlling aquatic algae, and as microbial contaminants in outdoor large-scale algal cultures, have also received increasing attention.

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.

Pathogens and predators impacting commercial production of microalgae and cyanobacteria

Production of phytoplankton (microalgae and cyanobacteria) in commercial raceway ponds and other systems is adversely impacted by phytoplankton pathogens, including bacteria, fungi and viruses. In addition, cultures are susceptible to productivity loss, or crash, through grazing by contaminating zooplankton such as protozoa, rotifers and copepods. Productivity loss and product contamination are also caused by otherwise innocuous invading phytoplankton that consume resources in competition with the species being cultured. This review is focused on phytoplankton competitors, pathogens and grazers of significance in commercial culture of microalgae and cyanobacteria. Detection and identification of these biological contaminants are discussed. Operational protocols for minimizing contamination, and methods of managing it, are discussed.

Phosphite Reduces the Predation Impact of Poterioochromonasmalhamensis on Cyanobacterial Culture

Contamination by the predatory zooplankton Poterioochromonas malhamensis is one of the major threats that causes catastrophic damage to commercial-scale microalgal cultivation. However, knowledge of how to manage predator contamination is limited. Previously, we established a phosphite (Pt)-based culture system by engineering Synechococcus elongatus, which exerted a competitive growth advantage against microbial contaminants that compete with phosphate source. Here, we examined whether Pt is effective in suppressing predator-type contamination. Co-culture experiment of Synechococcus with isolated P. malhamensis revealed that, although an addition of Pt at low concentrations up to 2.0 mM was not effective, increased dosage of Pt (~20 mM) resulted in the reduced grazing impact of P. malhamensis. By using unsterilized raw environmental water collected from rivers or ponds, we found that the suppression effect of Pt was dependent on the type of environmental water used. Eukaryotic microbial community analysis of the cultures using environmental water samples revealed that Paraphysomonas, a colorless Chrysophyceae, emerged and dominated under high-Pt conditions, suggesting that Paraphysomonas is insensitive to Pt compared to P. malhamensis. These findings may provide a clue for developing a strategy to reduce the impact of grazer contamination in commercial-scale microalgal cultivation.

Keeping Track of Phaeodactylum tricornutum (Bacillariophyta) Culture Contamination by Potentiometric E-Tongue

The large-scale cultivation of microalgae provides a wide spectrum of marketable bioproducts, profitably used in many fields, from the preparation of functional health products and feed supplement in aquaculture and animal husbandry to biofuels and green chemistry agents. The commercially successful algal biomass production requires effective strategies to maintain the process at desired productivity and stability levels. Hence, the development of effective early warning methods to timely indicate remedial actions and to undertake countermeasures is extremely important to avoid culture collapse and consequent economic losses. With the aim to develop an early warning method of algal contamination, the potentiometric E-tongue was applied to record the variations in the culture environments, over the whole growth process, of two unialgal cultures, Phaeodactylum tricornutum and a microalgal contaminant, along with those of their mixed culture. The E-tongue system ability to distinguish the cultures and to predict their growth stage, through the application of multivariate data analysis, was shown. A PLS regression method applied to the E-tongue output data allowed a good prediction of culture growth time, expressed as growth days, with R² values in a range from 0.913 to 0.960 and RMSEP of 1.97–2.38 days. Moreover, the SIMCA and PLS-DA techniques were useful for cultures contamination monitoring. The constructed PLS-DA model properly discriminated 67% of cultures through the analysis of their growth media, i.e., environments, thus proving the potential of the E-tongue system for a real time monitoring of contamination in microalgal intensive cultivation.

Study on the isoprene-producing co-culture system of Synechococcus elongates-Escherichia coli through omics analysis

BACKGROUND

The majority of microbial fermentations are currently performed in the batch or fed-batch manner with the high process complexity and huge water consumption. The continuous microbial production can contribute to the green sustainable development of the fermentation industry. The co-culture systems of photo-autotrophic and heterotrophic species can play important roles in establishing the continuous fermentation mode for the bio-based chemicals production.

RESULTS

In the present paper, the co-culture system of Synechococcus elongates-Escherichia coli was established and put into operation stably for isoprene production. Compared with the axenic culture, the fermentation period of time was extended from 100 to 400 h in the co-culture and the isoprene production was increased to eightfold. For in depth understanding this novel system, the differential omics profiles were analyzed. The responses of BL21(DE3) to S. elongatus PCC 7942 were triggered by the oxidative pressure through the Fenton reaction and all these changes were linked with one another at different spatial and temporal scales. The oxidative stress mitigation pathways might contribute to the long-lasting fermentation process. The performance of this co-culture system can be further improved according to the fundamental rules discovered by the omics analysis.

CONCLUSIONS

The isoprene-producing co-culture system of S. elongates-E. coli was established and then analyzed by the omics methods. This study on the co-culture system of the model S. elongates-E. coli is of significance to reveal the common interactions between photo-autotrophic and heterotrophic species without natural symbiotic relation, which could provide the scientific basis for rational design of microbial community.

Isolation and identification of herbivorous ciliates from contaminated microalgal cultures

Ciliates are a common but understudied group of grazers that can invade microalgal cultures. To estimate the potential impact of ciliates on microalgal culture productivity, the identification of species that can invade these cultures is essential. Furthermore, isolation of these herbivorous ciliates allows to use them in experiments that investigate the impact of ciliate grazing on the productivity of microalgal cultures. The main aims of this study were to isolate and identify ciliates that invade cultures of the freshwater microalgae Chlorella and Chlamydomonas, and to establish a live collection of these ciliates for usage in future experiments. To this end, we optimized a method for isolating ciliates from contaminated microalgal cultures and we developed a new PCR primer set for amplifying the partial 18S rDNA of ciliates belonging to the classes Spirotrichea, Oligohymenophorea and Colpodea. As a result, we isolated 11 ciliates from microalgal enrichment cultures inoculated with non-sterile dust and various freshwater sources. Of these 11 species, 7 were found to be feeding on Chlamydomonas. Ciliate species that fed on Chlorella could not be isolated in this study. Ciliate species feeding on Chlamydomonas were identified based on a combination of morphological observations and molecular analyses of partial 18S rDNA sequences.

Enhanced Scenedesmus sp. growth in response to gibberellin secretion by symbiotic bacteria

Microalgae usually co-exist with bacteria, which may influence the microalgal growth, in aquatic environment. In this study, thirteen strains that can promote microalgal growth were isolated from Scenedesmus sp. LX1 culture. Additional results showed that these strains could secrete gibberellin (GA), which is a phytohormones, promoting the growth and metabolism of the Scenedesmus sp. LX1. Low concentration (0.1 mg L^-1) of GA can increase the microalgae biomass by 51% after 4 days. GA could enhance the photosynthetic activity by increasing the photosynthetic pigment content, such as culture after 2 h with low GA concentration (0.1 mg L^-1), chlorophyll a and β-carotene increased from 0.59 μg per 10⁶ cells to 0.72 μg per 10⁶ cells and from 0.20 μg per 10⁶ cells to 0.38 μg per 10⁶ cells, respectively. In addition, GA could also stimulate the dehydrogenase activity, ATP accumulation, and carbonic anhydrase activity to increase the metabolic activity of the microalgae. Interestingly, the microalgae can selectively enhance the bacterial GA secretion in turn, indicating that there was a specific feedback regulation mechanism between the microalgae and the bacteria. The results of this study show a new mechanism of symbiotic-bacteria that enhances microalgal growth. It's a great significance to understand the microalgal growth and water bloom in aquatic environment.

Chemical Profiling of Volatile Organic Compounds in the Headspace of Algal Cultures as Early Biomarkers of Algal Pond Crashes

Algae ponds used in industrial biomass production are susceptible to pathogen or grazer infestation, resulting in pond crashes with high economic costs. Current methods to monitor and mitigate unhealthy ponds are hindered by a lack of early indicators that precede culture crash. We used solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS) to identify volatiles emitted from healthy and rotifer infested cultures of Microchloropsis salina. After 48 hours of algal growth, marine rotifers, Brachionus plicatilis, were added to the algae cultures and volatile organic compounds (VOC) were sampled from the headspace using SPME fibers. A GC-MS approach was used in an untargeted analysis of VOCs, followed by preliminary identification. The addition of B. plicatilis to healthy cultures of M. salina resulted in decreased algal cell numbers, relative to uninfected controls, and generated trans-β-ionone and β-cyclocitral, which were attributed to carotenoid degradation. The abundances of the carotenoid-derived VOCs increased with rotifer consumption of algae. Our results indicate that specific VOCs released by infected algae cultures may be early indicators for impending pond crashes, providing a useful tool to monitor algal biomass production and pond crash prevention.

Investigation and modelling of high rate algal ponds utilising secondary effluent at Western Water, Bacchus Marsh Recycled Water Plant

There is growing interest in the ability of high rate algal ponds (HRAP) to treat wastewater. This method reduces the costs of algal production while treating the wastewater quicker and more efficiently than standard lagoon practices. Two parallel HRAPs were used in this study to treat secondary effluent. Nitrogen levels were significantly reduced with a mean reduction of 71% for ammonia and 64% for total nitrogen. The use of the HRAPs significantly increased the algal biomass levels compared to the algal growth in the storage lagoons, with a mean increase of 274%. Beneficial use of algae can be used to reduce treatment costs; so being able to predict and optimise the amount of algal biomass produced in HRAPs is vital. However, most models are complicated and require specific, detailed information. In this study, a predictive microalgal growth model was developed for HRAP by adapting two previously established models: the Steele and Monod models. The model could predict algal growth based on temperatures and solar radiation and account for limiting ammonia concentrations in an elevated pH environment with natural variations in the algal community. This model used experimental data that would be readily available to any established HRAP study.

The effect of the algal microbiome on industrial production of microalgae

Microbes are ubiquitously distributed, and they are also present in algae production systems. The algal microbiome is a pivotal part of the alga holobiont and has a key role in modulating algal populations in nature. However, there is a lack of knowledge on the role of bacteria in artificial systems ranging from laboratory flasks to industrial ponds. Coexisting microorganisms, and predominantly bacteria, are often regarded as contaminants in algal research, but recent studies manifested that many algal symbionts not only promote algal growth but also offer advantages in downstream processing. Because of the high expectations for microalgae in a bio‐based economy, better understanding of benefits and risks of algal–microbial associations is important for the algae industry. Reducing production cost may be through applying specific bacteria to enhance algae growth at large scale as well as through preventing the growth of a broad spectrum of algal pathogens. In this review, we highlight the latest studies of algae–microbial interactions and their underlying mechanisms, discuss advantages of large‐scale algal–bacterial cocultivation and extend such knowledge to a broad range of biotechnological applications.

Volatile Metabolites Emission by In Vivo Microalgae-An Overlooked Opportunity?

Fragrances and malodors are ubiquitous in the environment, arising from natural and artificial processes, by the generation of volatile organic compounds (VOCs). Although VOCs constitute only a fraction of the metabolites produced by an organism, the detection of VOCs has a broad range of civilian, industrial, military, medical, and national security applications. The VOC metabolic profile of an organism has been referred to as its 'volatilome' (or 'volatome') and the study of volatilome/volatome is characterized as 'volatilomics', a relatively new category in the 'omics' arena. There is considerable literature on VOCs extracted destructively from microalgae for applications such as food, natural products chemistry, and biofuels. VOC emissions from living (in vivo) microalgae too are being increasingly appreciated as potential real-time indicators of the organism's state of health (SoH) along with their contributions to the environment and ecology. This review summarizes VOC emissions from in vivo microalgae; tools and techniques for the collection, storage, transport, detection, and pattern analysis of VOC emissions; linking certain VOCs to biosynthetic/metabolic pathways; and the role of VOCs in microalgae growth, infochemical activities, predator-prey interactions, and general SoH.