The genome of the Arctic snow alga Limnomonas spitsbergensis (Chlamydomonadales).

Snow algae are a diverse group of extremophilic microeukaryotes found on melting polar and alpine snowfields. They play an important role in the microbial ecology of the cryosphere, and their propagation on snow and ice surfaces may in part accelerate climate-induced melting of these systems. High-quality snow algae genomes are needed for studies on their unique physiology, adaptive mechanisms, and genome evolution under multiple forms of stress, including cold temperatures and intense sunlight. Here, we assembled and annotated the genome of Limnomonas spitsbergensis, a cryophilic biciliate green alga originally isolated from melting snow on Svalbard, in the Arctic. The L. spitsbergensis genome assembly is based primarily on the use of PacBio long reads and secondly Illumina short reads, with an assembly size of 260.248 Mb in 124 contigs. A combination of 3 alternative annotation strategies was used including protein homology, RNA-seq evidence, and PacBio full-length transcript isoforms. The best merged set of annotations identified 18,277 protein-coding genes, which were 95.2% complete based on Benchmarking Universal Single-Copy Orthologs analysis. We also provide the annotated mitogenome, which is a relatively large 77.942 kb circular mapping sequence containing extensive repeats. The L. spitsbergensis genome will provide a new resource for research on snow algae adaptation, behavior, and natural selection in unique, low-temperature terrestrial environments that are under threat from climate change.

Phylogeny and lipid profiles of snow-algae isolated from Norwegian red-snow microbiomes.

Snow algae blooms often form green or red coloured patches in melting alpine and polar snowfields worldwide, yet little is known about their biology, biogeography, and species diversity. We investigated eight isolates collected from red snow in northern Norway, using a combination of morphology, 18S rRNA gene and internal transcribed spacer 2 (ITS2) genetic markers. Phylogenetic and ITS2 rRNA secondary structure analyses assigned six isolates to the species Raphidonema nivale, Deuterostichococcus epilithicus, Chloromonas reticulata, and Xanthonema bristolianum. Two novel isolates belonging to the family Stichococcaceae (ARK-S05-19) and the genus Chloromonas (ARK-S08-19) were identified as potentially new species. In laboratory cultivation, differences in the growth rate and fatty acid profiles were observed between the strains. Chlorophyta were characterized by abundant C18:3n-3 fatty-acids with increases in C18:1n-9 in the stationary phase, whilst Xanthonema (Ochrophyta) was characterized by a large proportion of C20:5n-3, with increases in C16:1n-7 in the stationary phase. In a further experiment, lipid droplet formation was studied in C. reticulata at the single-cell level using imaging flow cytometry. Our study establishes new cultures of snow algae, reveals novel data on their biodiversity and biogeography, and provides an initial characterization of physiological traits that shape natural communities and their ecophysiological properties.

Microbial Community Dynamics during a Harmful Chrysochromulina leadbeateri Bloom in Northern Norway.

A harmful algal bloom occurred in late spring 2019 across multiple, interconnected fjords and bays in northern Norway. The event was caused by the haptophyte Chrysochromulina leadbeateri and led to severe fish mortality at several salmon aquaculture facilities. This study reports on the spatial and temporal succession dynamics of the holistic marine microbiome associated with this bloom by relating all detectable 18S and 16S rRNA gene amplicon sequence variants to the relative abundance of the C. leadbeateri focal taxon. A k-medoid clustering enabled inferences on how the causative focal taxon cobloomed with diverse groups of bacteria and microeukaryotes. These coblooming patterns showed high temporal variability and were distinct between two geographically separated time series stations during the regional harmful algal bloom. The distinct blooming patterns observed with respect to each station were poorly connected to environmental conditions, suggesting that other factors, such as biological interactions, may be at least as important in shaping the dynamics of this type of harmful algal bloom. A deeper understanding of microbiome succession patterns during these rare but destructive events will help guide future efforts to forecast deviations from the natural bloom cycles of the northern Norwegian coastal marine ecosystems that are home to intensive aquaculture activities. IMPORTANCE The 2019 Chrysochromulina leadbeateri bloom in northern Norway had a major impact on the local economy and society through its devastating effect on the aquaculture industry. However, many fail to remember that C. leadbeateri is, in fact, a common member of the seasonal marine microbiome and the same spring phytoplankton blooms that support the marine ecosystem. It is challenging to draw any conclusions about exact causation behind the harmful bloom of 2019, especially since the natural bloom cycles of C. leadbeateri are not well understood. This study begins to fill major knowledge gaps that may lead to future forecasting abilities, by providing a molecular-based investigation of the destructive 2019 bloom that presents new insights into a seasonal marine microbial ecosystem during one of these sporadically reoccurring events.

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae.

Haptophytes are biogeochemically and industrially important protists with underexplored genomic diversity. We present a nuclear genome assembly for the class Pavlovales, which was assembled with PacBio long-read data into highly contiguous sequences. We sequenced strain Diacronema lutheri NIVA-4/92, formerly known as Pavlova lutheri, because it has established roles in aquaculture and has been a key organism for studying microalgal lipid biosynthesis. Our data show that D. lutheri has the smallest and most streamlined haptophycean genome assembled to date, with an assembly size of 43.503 Mb and 14,446 protein-coding genes. Together with its high nuclear GC content, Diacronema is an important genus for investigating selective pressures on haptophyte genome evolution, contrasting with the much larger and more repetitive genome of the coccolithophore Emiliania huxleyi. The D. lutheri genome will be a valuable resource for resolving the genetic basis of algal lipid biosynthesis and metabolic remodeling that takes place during adaptation and stress response in natural and engineered environments.

Warming impairs trophic transfer efficiency in a long-term field experiment.

In ecosystems, the efficiency of energy transfer from resources to consumers determines the biomass structure of food webs. As a general rule, about 10% of the energy produced in one trophic level makes it up to the next1-3. Recent theory suggests that this energy transfer could be further constrained if rising temperatures increase metabolic growth costs4, although experimental confirmation in whole ecosystems is lacking. Here we quantify nitrogen transfer efficiency-a proxy for overall energy transfer-in freshwater plankton in artificial ponds that have been exposed to seven years of experimental warming. We provide direct experimental evidence that, relative to ambient conditions, 4 °C of warming can decrease trophic transfer efficiency by up to 56%. In addition, the biomass of both phytoplankton and zooplankton was lower in the warmed ponds, which indicates major shifts in energy uptake, transformation and transfer5,6. These findings reconcile observed warming-driven changes in individual-level growth costs and in carbon-use efficiency across diverse taxa4,7-10 with increases in the ratio of total respiration to gross primary production at the ecosystem level11-13. Our results imply that an increasing proportion of the carbon fixed by photosynthesis will be lost to the atmosphere as the planet warms, impairing energy flux through food chains, which will have negative implications for larger consumers and for the functioning of entire ecosystems.

Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana.

Nutrient limited conditions are common in natural phytoplankton communities and are often used to increase the yield of lipids from industrial microalgae cultivations. Here we studied the effects of bioavailable nitrogen (N) and phosphorus (P) deprivation on the proteome and transcriptome of the oleaginous marine microalga Nannochloropsis gaditana. Turbidostat cultures were used to selectively apply either N or P deprivation, controlling for variables including the light intensity. Global (cell-wide) changes in the proteome were measured using Tandem Mass Tag (TMT) and LC-MS/MS, whilst gene transcript expression of the same samples was quantified by Illumina RNA-sequencing. We detected 3423 proteins, where 1543 and 113 proteins showed significant changes in abundance in N and P treatments, respectively. The analysis includes the global correlation between proteomic and transcriptomic data, the regulation of subcellular proteomes in different compartments, gene/protein functional groups, and metabolic pathways. The results show that triacylglycerol (TAG) accumulation under nitrogen deprivation was associated with substantial downregulation of protein synthesis and photosynthetic activity. Oil accumulation was also accompanied by a diverse set of responses including the upregulation of diacylglycerol acyltransferase (DGAT), lipase, and lipid body associated proteins. Deprivation of phosphorus had comparatively fewer, weaker effects, some of which were linked to the remodeling of respiratory metabolism.

The complete mitogenome and plastome of the haptophyte Pavlova lutheri NIVA-4/92.

The complete mitochondrial and plastid genomes of the microalga Pavlova lutheri strain NIVA-4/92 are reported. The circular-mapping mitogenome is 36,202 bp in length, contains 22 protein-coding genes, 24 tRNAs, and has a GC content of 37.5%. Like other haptophytes the mitogenome contains a single large, complex repeat region of approximately 5.4 kbp. The plastome is 95,281 bp in length and has a GC content of 35.6%. It contains 111 protein-coding genes and 27 tRNAs.

Polar snow algae as a valuable source of lipids?

Microalgae offer excellent opportunities for producing food and fuel commodities, but in colder climates the low growth rates of many varieties may hamper production. In this work, extremophilic Arctic microalgae were tested to establish whether satisfactory growth and lipid production could be obtained at low water temperature. Five species of snow/soil algae originating from Svalbard (78-79°N) were cultivated at 6°C, reaching high cell densities (maximum dry weight 3.4g·L-1) in batch cultivations, and high productivity (maximum 0.63g·L-1·d-1). After 20days of cultivation total lipids ranged from 28% to 39% of the dry weight, and diverse patterns of neutral lipid (triacylglycerol; TAG) accumulation were observed. The five species largely accumulated unsaturated fatty acyl chains in neutral lipids, especially polyunsaturated C16 series fatty acids, C18:1n-9 and C18:3n-3. The results indicate that polar microalgae could provide an opportunity to increase the yields of microalgal biomass and oil products at low temperatures.

Production of Fatty Acids and Protein by Nannochloropsis in Flat-Plate Photobioreactors.

Nannochloropsis is an industrially-promising microalga that may be cultivated for alternative sources of nutrition due to its high productivity, protein content and lipid composition. We studied the growth and biochemical profile of Nannochloropsis 211/78 (CCAP) in optimized flat-plate photobioreactors. Eighteen cultivations were performed at two nutrient concentrations. The fatty acid, protein content and calorific values were analyzed after 8, 12 and 16 days. Neutral lipids were separated and the changes in fatty acids in triglycerides (TAGs) during nutrient depletion were recorded. The maximum cell density reached 4.7 g∙L-1 and the maximum productivity was 0.51 g∙L-1∙d-1. During nutrient-replete conditions, eicosapentaneoic acid (EPA) and total protein concentrations measured 4.2-4.9% and 50-55% of the dry mass, respectively. Nutrient starvation induced the accumulation of fatty acids up to 28.3% of the cell dry weight, largely due to the incorporation of C16:0 and C16:1n-7 fatty acyl chains into neutral lipids. During nutrient starvation the total EPA content did not detectibly change, but up to 37% was transferred from polar membrane lipids to the neutral lipid fraction.

Radiocarbon dating of fluvial organic matter reveals land-use impacts in boreal peatlands.

This study measured the effects of land use on organic matter released to surface waters in a boreal peat catchment using radiocarbon dating of particulate and dissolved organic carbon (POC and DOC), DOC concentration, stable carbon and nitrogen isotope composition, and optical measurements. Undisturbed sites invariably released modern DOC and POC (<20 years old), and seasonal forcing had little impact on the age distribution. Release of pre-1950 carbon was detected at peat extraction, agricultural and drained sites, and was consistently observed at agricultural and peat extraction areas throughout the seasons. Conventional mean DOC ages reached 3,100 (±122) years before collection. On average, DOC concentrations were up to 38% higher at impacted sites compared to natural areas, but there was no significant effect of land use on surface water DOC concentrations. The study indicates that the true extent of land use impacts is not necessarily detectible through changes in DOC concentration alone: Radiocarbon dating was essential to show that leaching of old soil organic matter at modified sites had replaced, rather than supplemented, the modern DOM that is usually released from pristine peatlands. Relationships between the specific fluorescence intensity of DOM and its radiocarbon age were identified, indicating that optical techniques may provide a method for the detection of changes in DOM age.

Eukaryotic and prokaryotic microbial communities during microalgal biomass production.

Eukaryotic and bacterial communities were characterized and quantified in microalgal photobioreactor cultures of freshwater Chlorella vulgaris and marine Dunaliella tertiolecta. The microalgae exhibited good growth, whilst both cultures contained diverse bacterial communities. Both cultures included Proteobacteria and Bacteroidetes, while C. vulgaris cultures also contained Actinobacteria. The bacterial genera present in the cultures were different due to different growth medium salinities and possibly different extracellular products. Bacterial community profiles were relatively stable in D. tertiolecta cultures but not in C. vulgaris cultures likely due to presence of ciliates (Colpoda sp.) in the latter. The presence of ciliates did not, however, cause decrease in total number of C. vulgaris or bacteria during 14 days of cultivation. Quantitative PCR (qPCR) reliably showed relative microalgal and bacterial cell numbers in the batch cultures with stable microbial communities, but was not effective when bacterial communities varied. Raw culture samples were successfully used as qPCR templates.

Energy efficiency of an outdoor microalgal photobioreactor sited at mid-temperate latitude.

This work examined the energetic performance of a 6-month semi-continuous cultivation of Scenedesmus obliquus in an outdoor photobioreactor at mid-temperate latitude, without temperature control. By measuring the seasonal biomass production (mean 11.31, range 1.39-23.67 g m(-2)d(-1)), higher heating value (22.94 kJ g(-1)) and solar irradiance, the mean seasonally-averaged photosynthetic efficiency (2.18%) and gross energy productivity (0.27 MJ m(-2) d(-1)) was calculated. When comparing the solar energy conversion efficiency to the energy investment for culture circulation, significant improvements in reactor energy input must be made to make the system viable. Using the data collected to model the energetic performance of a substitute photobioreactor design, we conclude that sustainable photobioreactor cultivation of microalgae in similar temperate climates requires a short light path and low power input, only reasonably obtained by flat-panel systems. However, temperature control was not necessary for effective long-term cultivation.

Productivity, carbon dioxide uptake and net energy return of microalgal bubble column photobioreactors.

This work examined the energy return of Chlorella vulgaris and Dunaliella tertiolecta cultivated in a gas-sparged photobioreactor design where the power input for sparging was manipulated (10, 20, and 50 Wm(-3)). Dry weight, organic carbon and heating values of the biomass were measured, plus a suite of variables including Fv/Fm and dissolved oxygen. A model for predicting the higher heating value of microalgal biomass was developed and used to measure the energetic performance of batch cultivations. High power inputs enhanced maximum biomass yields, but did not improve the energy return. Cultivation in 10 Wm(-3) showed up to a 39% higher cumulative net energy return than 50 Wm(-3), and increased the cumulative net energy ratio up to fourfold. The highest net energy ratio for power input was 19.3 (D. tertiolecta, 12% CO(2), 10 Wm(-3)). These systems may be a sustainable method of biomass production, but their effectiveness is sensitive to operational parameters.

Thermophilic, anaerobic co-digestion of microalgal biomass and cellulose for H2 production.

Microalgal biomass has been a focus in the sustainable energy field, especially biodiesel production. The purpose of this study was to assess the feasibility of treating microalgal biomass and cellulose by anaerobic digestion for H2 production. A microbial consortium, TC60, known to degrade cellulose and other plant polymers, was enriched on a mixture of cellulose and green microalgal biomass of Dunaliella tertiolecta, a marine species, or Chlorella vulgaris, a freshwater species. After five enrichment steps at 60°C, hydrogen yields increased at least 10% under all conditions. Anaerobic digestion of D. tertiolecta and cellulose by TC60 produced 7.7 mmol H2/g volatile solids (VS) which were higher than the levels (2.9-4.2 mmol/g VS) obtained with cellulose and C. vulgaris biomass. Both microalgal slurries contained satellite prokaryotes. The C. vulgaris slurry, without TC60 inoculation, generated H2 levels on par with that of TC60 on cellulose alone. The biomass-fed anaerobic digestion resulted in large shifts in short chain fatty acid concentrations and increased ammonium levels. Growth and H2 production increased when TC60 was grown on a combination of D. tertiolecta and cellulose due to nutrients released from algal cells via lysis. The results indicated that satellite heterotrophs from C. vulgaris produced H2 but the Chlorella biomass was not substantially degraded by TC60. To date, this is the first study to examine H2 production by anaerobic digestion of microalgal biomass. The results indicate that H2 production is feasible but higher yields could be achieved by optimization of the bioprocess conditions including biomass pretreatment.

Dissolved organic matter (DOM) in microalgal photobioreactors: a potential loss in solar energy conversion?

Microalgae are considered to be a potential alternative to terrestrial crops for bio-energy production due to their relatively high productivity per unit area of land. In this work we examined the amount of dissolved organic matter exuded by algal cells cultured in photobioreactors, to examine whether a significant fraction of the photoassimilated biomass could potentially be lost from the harvestable biomass. We found that the mean maximum amount of dissolved organic carbon (DOC) released measured 6.4% and 17.3% of the total organic carbon in cultures of Chlorellavulgaris and Dunaliella tertiolecta, respectively. This DOM in turn supported a significant growth of bacterial biomass, representing a further loss of the algal assimilated carbon. The release of these levels of DOC indicates that a significant fraction of the photosynthetically fixed organic matter could be lost into the surrounding water, suggesting that the actual biomass yield per hectare for industrial purposes could be somewhat less than expected. A simple and inexpensive optical technique, based on chromophoric dissolved organic matter (CDOM) measurements, to monitor such losses in commercial PBRs is discussed.