Eukaryotic and prokaryotic microbial communities during microalgal biomass production

Strategy for the formation of microalgae-bacteria aggregates in high-rate algal ponds

This work studied the formation of aggregates used for wastewater treatment in high-rate algal ponds (HRAP). For this, the establishment of microalgae-bacteria aggregates in these systems was evaluated, considering strategies for the inoculation and start-up. Two HRAP were operated in parallel, at first in batch mode and then in continuous flow. The wastewater treatment was efficient, with removal rates around 80% for COD and N-ammoniacal. Volatile suspended solids and chlorophyll for the culture grew continuously reached a concentration of 548 ± 11 mg L^-1 and 7.8 mg L^-1, respectively. Larger photogranules were observed when the system was placed in a continuous regime. The protein fraction of extracellular polymeric substances was identified as a determinant in photogranules formation. During the continuous regime, more than 50% of the biomass was higher than 0.2 mm, flocculation efficiency of 78 ± 6%, and the volumetric sludge index of 32 ± 5 mL g^-1. The genetic sequencing showed the growth of cyanobacteria in the aggregate and the presence of microalgae from the chlorophytes and diatoms groups in the final biomass.

Significant Effects of Associated Microorganisms on the Community of Photosynthetic Picoeukaryotes

Photosynthetic picoeukaryotes (PPEs) form associations with other microorganisms. However, whether and how the associated microbes affect PPE communities remain unknown. We used flow cytometric cell sorting combined with parallel high-throughput sequencing of the 18S and 16S rRNA genes to simultaneously investigate PPEs and their associated microbial communities in the Yangtze-connected Lake Dongting. The lake harbors a great diversity of PPEs. PPE communities exhibited significant temporal rather than spatial variations. Two distinct PPE taxa affiliated with Discostella nipponica and Poterioochromonas malhamensis were dominant during winter/spring and summer, respectively. Parallel high-throughput sequencing revealed a great diversity of associated bacteria and non-pigmented eukaryotes (NPEs) in PPEs sorts. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria among the associated bacteria and fungi among the associated NPEs were dominant. PPEs were more apparently associated with bacteria than with NPEs. The co-occurrence network of PPEs and associated microbes formed five major modules, which exhibited distinct temporal patterns, being specific to a certain period. Variations in PPEs communities were significantly correlated with both environmental factors and associated microbial communities. In variation partitioning analysis, the associated bacteria explained the greatest variations in PPE communities, and associated bacteria and NPEs co-explained a large portion of environmental effects on PPE communities. Our results highlight the significance of associated microbes in shaping PPE communities.

The Dynamics of the Bacterial Community of the Photobioreactor-Cultivated Green Microalga Haematococcus lacustris during Stress-Induced Astaxanthin Accumulation

Simple Summary

The microalga Haematococcus lacustris is a source of the natural colorant astaxanthin, a powerful antioxidant and key component of cosmetics and animal feed. Haematococcus is cultivated in photobioreactors. It can obtain energy just from a light illuminating photobioreactor and uses inorganic salts and CO₂ as sources for chemical elements. The most widespread approach for Haematococcus cultivation is the two stage scheme. At the first stage, biomass accumulation under favorable growth conditions occurs. At the second stage, the cells are subjected to stress inducing astaxanthin synthesis. Generally, the culture of Haematococcus is not axenic. It exists in the form of a community with bacteria constituting its microbiome. The information on photobioreactor-cultivated Haematococcus microbiome is scarce. We analyzed its dynamic during astaxanthin production by DNA metabarcoding and microscopic observations. The main results of the work include the characterization of the daily dynamic of this microbiome and the revealing of contact between microalgae and bacteria. These findings are of potential significance for biotechnology. On one hand, they provide an insight into possible bacterial contamination of the harvested algal biomass. On the other hand, they reveal the presence of a core microbiome or bacteria essential for the growth of the microalga existing in all Haematococcus cultures.

Abstract

Haematococcus lacustris is a natural source of a valuable ketocarotenoid astaxanthin. Under autotrophic growth conditions, it exists in the form of a community with bacteria. The close coexistence of these microorganisms raises two questions: how broad their diversity is and how they interact with the microalga. Despite the importance these issues, little is known about microorganisms existing in Haematococcus cultures. For the first time, we characterize the dynamic of the H. lacustris microbiome of the microbiome of Haematococcus (a changeover of the bacterial associated species as function of the time) cultivated autotrophically in a photobioreactor based on 16S rRNA metabarcoding data. We found that Proteobacteria and Bacteroidetes are predominant phyla in the community. The Caulobacter bacterium became abundant during astaxanthin accumulation. These data were supported by microscopy. We discuss possible roles and interactions of the community members. These findings are of potential significance for biotechnology. They provide an insight into possible bacterial contamination in algal biomass and reveal the presence of bacteria essential for the algal growth.

Influence of photobioreactor set-up on the survival of microalgae inoculum

Cultivation of specific microalgae is still difficult in an industrial setup as contamination and balancing the economic cost are not always possible. Understanding the ecology of cultivation of microalgae is therefore necessary to implement stable production. The aim of the study was to understand how different types of photobioreactors and types of culture medium influenced the survival of a specific microalgae inoculum, S. almeriensis. The bacterial and microalgae community were studied using Illumina sequencing. Only the closed configuration was able to maintain the inoculated species while all the other systems developed a different eukaryotic community due to contamination and the higher fitness of contaminants. Photobioreactor configuration was more important than medium in shaping the eukaryotes community, while the bacterial community was influenced strongly by both. Results showed that even a well-adapted strain is maintained only in the closed reactor while the open reactors are colonized by a multispecies consortium.

Comparison of the Performance and Microbial Community Structure of Two Outdoor Pilot-Scale Photobioreactors Treating Digestate

This study aimed at examining and comparing the nutrient removal efficiency, biomass productivity and microbial community structure of two outdoor pilot-scale photobioreactors, namely a bubble column and a raceway pond, treating the liquid fraction of an agricultural digestate. Bacterial and eukaryotic communities were characterized using a metabarcoding approach and quantitative PCR. The abundance, composition, diversity, and dynamics of the main microbes were then correlated to the environmental conditions and operational parameters of the reactors. Both photobioreactors were dominated either by Chlorella sp. or Scenedesmus sp. in function of temperature, irradiance and the nitrogen compounds derived by nitrification. Other species, such as Chlamydomonas and Planktochlorella, were sporadically present, demonstrating that they have more specific niche requirement. Pseudomonas sp. always dominated the bacterial community in both reactors, except in summertime, when a bloom of Calothrix occurred in the raceway pond. In autumn, the worsening of the climate conditions decreased the microalgal growth, promoting predation by Vorticella sp. The study highlights the factors influencing the structure and dynamics of the microbial consortia and which ecological mechanisms are driving the microbial shifts and the consequent reactor performance. On these bases, control strategies could be defined to optimize the management of the microalgal-based technologies.

Hydrocarbon-Degrading Bacteria Alcanivorax and Marinobacter Associated With Microalgae Pavlova lutheri and Nannochloropsis oculata

Marine hydrocarbon-degrading bacteria play an important role in natural petroleum biodegradation processes and were initially associated with man-made oil spills or natural seeps. There is no full clarity though on what, in the absence of petroleum, their natural niches are. Few studies pointed at some marine microalgae that produce oleophilic compounds (alkanes, long-chain fatty acids, and alcohols) as potential natural hosts of these bacteria. We established Dansk crude oil-based enrichment cultures with photobioreactor-grown marine microalgae cultures Pavlova lutheri and Nannochloropsis oculata and analyzed the microbial succession using cultivation and SSU (16S) rRNA amplicon sequencing. We found that petroleum enforced a strong selection for members of Alpha- and Gamma-proteobacteria in both enrichment cultures with the prevalence of Alcanivorax and Marinobacter spp., well-known hydrocarbonoclastic bacteria. In total, 48 non-redundant bacterial strains were isolated and identified to represent genera Alcanivorax, Marinobacter, Thalassospira, Hyphomonas, Halomonas, Marinovum, Roseovarius, and Oleibacter, which were abundant in sequencing reads in both crude oil enrichments. Our assessment of public databases demonstrated some overlaps of geographical sites of isolation of Nannochloropsis and Pavlova with places of molecular detection and isolation of Alcanivorax and Marinobacter spp. Our study suggests that these globally important hydrocarbon-degrading bacteria are associated with P. lutheri and N. oculata.

Characterization of Chlorella vulgaris (Trebouxiophyceae) associated microbial communities1

Microalgae exhibit extensive potential for counteracting imminent challenges in the nutraceutical, pharmaceutical, and biomaterial sectors, but lack economic viability. Biotechnological systems for contamination control could advance the economic viability of microalgal feedstock, but the selection of suitable strains that sustainably promote microalgal productivity remains challenging. In this study, total diversity in phototrophic Chlorella vulgaris cultures was assessed by amplicon sequencing comparing cultures subjected to five different cultivation conditions. Overall, 12 eukaryotic and 53 prokaryotic taxa were identified; Alphaproteobacteria (36.7%) dominated the prokaryotic and C. vulgaris (97.2%) the eukaryotic community. Despite altering cultivation conditions, 2 eukaryotic and 40 prokaryotic taxa remained stably associated with C. vulgaris; diversity between systems did not significantly differ (P > 0.05). Among those, 20 cultivable taxa were isolated and identified by 16S rDNA sequencing. Subsequently, controlled co-cultures were investigated showing stable associations of C. vulgaris with Sphingopyxis sp. and Pseudomonas sp.. Out-competition of C. vulgaris due to ammonium or phosphate limitation was not observed, despite significantly elevated growth of Sphingopyxis sp. and Tistrella sp.. (P < 0.05). Nevertheless, C. vulgaris growth was impaired by Tistrella sp.. Hence, the study provides a selection of stable indigenous prokaryotes and eukaryotes for artificially tailoring microbial biocenoses. Following a bottom-up approach, it provides a base for controlled co-cultures and thus the establishment of even more complex biocenoses using interkingdom assemblages. Such assemblages can benefit from functional richness for improved nutrient utilization, as well as bacterial load control, which can enhance microalgal feedstock production through improved culture stability and productivity.

Organic degrading bacteria and nitrifying bacteria stimulate the nutrient removal and biomass accumulation in microalgae-based system from piggery digestate

The microalgae-based system has been applied in anaerobic digestate treatment for nutrient removal and biomass production. To optimize its performance in treating piggery digestate, here, commercial bacterial agents, including organic degrading bacteria (Cb) and nitrifying bacteria (Nb), were inoculated into the microalgae-based system dominated by Desmodesmus sp. CHX1 (D). Reactor DN (inoculated with D and Nb) and DCN (inoculated with D, and Cb to Nb at a ratio of 1:2) have better performance on NH₄⁺-N removal, with a final efficiency at 40.26% and 39.87%, respectively, and no NO₃^--N or NO₂^--N accumulations. The final total chlorophyll concentration, an indicator of microalgal growth, reached 4.74 and 5.47 mg/L in DN and DCN, respectively, three times more than that in D. These results suggested that high NH₄⁺-N removal was achieved by the assimilation into high microalgal biomass after the inoculation with functional bacteria. High-throughput sequencing showed that the richness of microbial community decreased but the evenness increased by inoculating functional microorganisms. Microalgae aggregating bacteria were Cellvibrio, Sphingobacterium, Flavobacterium, Comamonas, Microbacterium, Dyadobacter, and Paenibacillus. This study revealed that the inoculation with functional bacteria reconstructed the microbial community which benefited for the microalgal growth and nutrient removal, providing a promising strategy for treating highly-concentrated digestate.

High density long-term cultivation of Chlorella vulgaris SAG 211-12 in a novel microgravity-capable membrane raceway photobioreactor for future bioregenerative life support in SPACE

Hybrid life support systems are of great interest for future far-distant space exploration missions to planetary surfaces, e.g. Mars, planned until 2050. By synergistically combining physicochemical and biotechnological algae-based subsystems, an essential step towards the closure of the carbon loop in environmental control and life support systems (ECLSS) shall be accomplished, offering a wide beneficial potential for ECLSS through the utilization of oxygenic photosynthesis: O₂ and potential human food can be formed in-situ from CO₂ and water. The wild type green alga Chlorella vulgaris strain SAG 211-12 was selected as model microorganism due to its photoautotrophic growth, high biomass yield, cultivation flexibility and long-term cultivation robustness. The current study presents for the first time a stable xenic long-term processing of microalgae in a novel microgravity capable membrane raceway photobioreactor for 188 days with the focus on algal growth kinetics and gas evolution. In particular, culture homogeneity and viability were monitored and evaluated during the whole cultivation process due to their putative crucial impact on long-term functionality and efficiency of a closed cultivation system. Based on a specially designed cyclic batch cultivation process for SAG 211-12, a successive biomass growth up to a maximum of 12.2 g l^-1 with a max. global volumetric productivity of 1.3 g l^-1 d^-1 was reached within the closed loop system. The photosynthetic capacity was assessed to a global molar photosynthetic quotient of 0.31. Furthermore, cultivation parameters for a change from batch to continuous processing at high biomass densities and proliferation rates are introduced. The presented µgPBR miniature plant and the developed high throughput cultivation process are planned to be tested under real space conditions within the PBR@LSR project (microgravity and cosmic radiation) aboard the International Space Station with an operation period of up to 180 days to investigate the impact on long-term system stability.

Analysis of growth and lipid production characteristics of Chlorella vulgaris in artificially constructed consortia with symbiotic bacteria

The aim was to study the effect of artificially constructed consortia of microalgae-bacterial symbionts on growth and lipid production by Chlorella vulgaris (C. vulgaris), as well as the inter-relationship between microalgae and bacterial in a photoautotrophic system. The results showed that compared to an axenic culture of C. vulgaris, H1 co-culture system (axenic C. vulgaris-Stenotrophomona smaltophilia) had the strongest effect on the C. vulgaris growth. The biomass, specific growth rate and maximum productivity of C. vulgaris were increased by 21.9, 20.4, and 18%, respectively. The bacteria in co-culture system had a significant effect on the accumulation of lipid and fatty acid components of C. vulgaris: the content of lipid was increased by 8.2-33.83%, and the components of the saturated fatty acids and oleic acids also had an obvious improvement. The results indicate that the microalgae-bacterial co-culture system can improve microalgal biomass and the quality of biodiesel.

Metagenomic analysis of the complex microbial consortium associated with cultures of the oil-rich alga Botryococcus braunii

Microalgae are widely viewed as a promising and sustainable source of renewable chemicals and biofuels. Botryococcus braunii synthesizes and secretes significant amounts of long-chain (C30 -C40 ) hydrocarbons that can be subsequently converted into gasoline, diesel, and aviation fuel. B. braunii cultures are not axenic and the effects of co-cultured microorganisms on B. braunii growth and hydrocarbon yield are important, but sometimes contradictory. To understand the composition of the B. braunii microbial consortium, we used high throughput Illumina sequencing of metagenomic DNA to profile the microbiota within a well established, stable B. braunii culture and characterized the demographic changes in the microcosm following modification to the culture conditions. DNA sequences attributed to B. braunii were present in equal quantities in all treatments, whereas sequences assigned to the associated microbial community were dramatically altered. Bacterial species least affected by treatments, and more robustly associated with the algal cells, included members of Rhizobiales, comprising Bradyrhizobium and Methylobacterium, and representatives of Dyadobacter, Achromobacter and Asticcacaulis. The presence of bacterial species identified by metagenomics was confirmed by additional 16S rDNA analysis of bacterial isolates. Our study demonstrates the advantages of high throughput sequencing and robust metagenomic analyses to define microcosms and further our understanding of microbial ecology.

An efficient strategy using k-mers to analyse 16S rRNA sequences

The use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k-mer size was inversely proportional to the occurrence of k-mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k-mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.

Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures

Large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.

Use of diluted urine for cultivation of Chlorella vulgaris

Our aim was to study the biomass growth of microalga Chlorella vulgaris using diluted human urine as a sole nutrient source. Batch cultivations (21 days) were conducted in five different urine dilutions (1:25-1:300), in 1:100-diluted urine as such and with added trace elements, and as a reference, in artificial growth medium. The highest biomass density was obtained in 1:100-diluted urine with and without additional trace elements (0.73 and 0.60 g L(-1), respectively). Similar biomass growth trends and densities were obtained with 1:25- and 1:300-diluted urine (0.52 vs. 0.48 gVSS L(-1)) indicating that urine at dilution 1:25 can be used to cultivate microalgal based biomass. Interestingly, even 1:300-diluted urine contained sufficiently nutrients and trace elements to support biomass growth. Biomass production was similar despite pH-variation from < 5 to 9 in different incubations indicating robustness of the biomass growth. Ammonium formation did not inhibit overall biomass growth. At the beginning of cultivation, the majority of the biomass consisted of living algal cells, while towards the end, their share decreased and the estimated share of bacteria and cell debris increased.

Ecological functions of zoosporic hyperparasites

Zoosporic parasites have received increased attention during the last years, but it is still largely unnoted that these parasites can themselves be infected by hyperparasites. Some members of the Chytridiomycota, Blastocladiomycota, Cryptomycota, Hyphochytriomycota, Labyrinthulomycota, Oomycota, and Phytomyxea are hyperparasites of zoosporic hosts. Because of sometimes complex tripartite interactions between hyperparasite, their parasite-host, and the primary host, hyperparasites can be difficult to detect and monitor. Some of these hyperparasites use similar mechanisms as their parasite-hosts to find and infect their target and to access food resources. The life cycle of zoosporic hyperparasites is usually shorter than the life cycle of their hosts, so hyperparasites may accelerate the turnaround times of nutrients within the ecosystem. Hyperparasites may increase the complexity of food webs and play significant roles in regulating population sizes and population dynamics of their hosts. We suggest that hyperparasites lengthen food chains but can also play a role in conducting or suppressing diseases of animals, plants, or algae. Hyperparasites can significantly impact ecosystems in various ways, therefore it is important to increase our understanding about these cryptic and diverse organisms.

High lipid productivity of an Ankistrodesmus-Rhizobium artificial consortium

Microalgae have great potential as alternative productive platforms for sustainable production of bioenergy, food, feed and other commodities. Process optimization to realize the claimed potential often comprises strains selection and improvement and also developing of more efficient cultivation, harvesting and downstream processing technology. In this work we show that inoculation with the bacterium Rhizobium strain 10II resulted in increments of up to 30% in chlorophyll, biomass and lipids accumulation of the oleaginous microalgae Ankistrodesmus sp. strain SP2-15. Inoculated cultures have reached a high lipid productivity of up to 112 mg L(-1) d(-1) after optimization. The resulting biomass presented significant levels of Ω3 fatty acids including stearidonic acid, suggesting potential as an alternative land-based source of essential fatty acids.

Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors

Photobioreactors (PBRs) are very attractive for sunlight-driven production of biofuels and capturing of anthropogenic CO2. One major problem associated with PBRs however, is that the bacteria usually associated with microalgae in nonaxenic cultures can lead to biofouling and thereby affect algal productivity. Here, we report on a phylogenetic, metagenome, and functional analysis of a mixed-species bacterial biofilm associated with the microalgae Chlorella vulgaris and Scenedesmus obliquus in a PBR. The biofilm diversity and population dynamics were examined through 16S rRNA phylogeny. Overall, the diversity was rather limited, with approximately 30 bacterial species associated with the algae. The majority of the observed microorganisms were affiliated with Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes. A combined approach of sequencing via GS FLX Titanium from Roche and HiSeq 2000 from Illumina resulted in the overall production of 350 Mbp of sequenced DNA, 165 Mbp of which was assembled in larger contigs with a maximum size of 0.2 Mbp. A KEGG pathway analysis suggested high metabolic diversity with respect to the use of polymers and aromatic and nonaromatic compounds. Genes associated with the biosynthesis of essential B vitamins were highly redundant and functional. Moreover, a relatively high number of predicted and functional lipase and esterase genes indicated that the alga-associated bacteria are possibly a major sink for lipids and fatty acids produced by the microalgae. This is the first metagenome study of microalga- and PBR-associated biofilm bacteria, and it gives new clues for improved biofuel production in PBRs.

Genetic engineering of multispecies microbial cell factories as an alternative for bioenergy production

There is currently much interest in developing technology to use microlgae or cyanobacteria for the production of bioenergy and biomaterials. Here, we summarize some remarkable achievements in strains improvement by traditional genetic engineering and discuss common drawbacks for further progress. We present general knowledge on natural microalgal-bacterial mutualistic interactions and discuss the potential of recent developments in genetic engineering of multispecies microbial cell factories. This synthetic biology approach would rely on the assembly of complex metabolic networks from optimized metabolic modules such as photosynthetic or nitrogen-fixing parts.

Microalgae cultivation for bioenergy production using wastewaters from a municipal WWTP as nutritional sources

In order to reduce input cost for microalgal cultivation, we investigated the feasibility of wastewater taken from a municipal WWTP in Busan, Korea as wastewater nutrients. The wastewaters used in this study were the effluent from a primary settling tank (PS), the effluent from an anaerobic digestion tank (AD), the conflux of wastewaters rejected from sludge-concentrate tanks and dewatering facilities (CR), and two combined wastewaters of AD:PS (10:90, v/v) and AD:CR (10:90, v/v). Chlorella sp. ADE5, which was isolated from the AD, was selected for the feasibility test. The highest biomass production (3.01 g-dry cell weight per liter) of the isolate was obtained with the combined wastewater ADCR, and it was 1.72 times higher than that with BG 11 medium. Interestingly, the cells cultivated with wastewater containing PS wastewater were easily separated from the culture and improved lipid content, especially oleic acid content, in their cells.