Cellulose degradation and assimilation by the unicellular phototrophic eukaryote Chlamydomonas reinhardtii

A Study on the Effect of Various Media and the Supplementation of Organic Compounds on the Enhanced Production of Astaxanthin from Haematococcus lacustris (Girod-Chantrans) Rostafinski (Chlorophyta)

Natural astaxanthin is in high demand due to its multiple health benefits. The microalga Haematococcus lacustris has been used for the commercial production of astaxanthin. In this study, we investigated the effects of six different media with and without a nitrogen source and supplementation with nine organic compounds on the growth and astaxanthin accumulation of H. lacustris. The highest astaxanthin contents were observed in cultures of H. lacustris in Jaworski's medium (JM), with a level of 9.099 mg/L in JM with a nitrogen source supplemented with leucine (0.65 g/L) and of 20.484 mg/L in JM without a nitrogen source supplemented with sodium glutamate (0.325 g/L). Six of the nine organic compounds examined (leucine, lysine, alanine, sodium glutamate, glutamine, and cellulose) enhanced the production of astaxanthin in H. lacustris, while malic acid, benzoic acid, and maltose showed no beneficial effects.

Engineering Yarrowia lipolytica as a Cellulolytic Cell Factory for Production of p-Coumaric Acid from Cellulose and Hemicellulose

De novo biosynthesis of high-value added food additive p-coumaric acid (p-CA) direct from cellulose/hemicellulose is a more sustainable route compared to the chemical route, considering the abundant cellulose/hemicellulose resources. In this study, a novel factory was constructed for the production of p-CA in Yarrowia lipolytica using cellulose/hemicellulose as the sole carbon source. Based on multicopy integration of the TAL gene and reprogramming the shikimic acid pathway, the engineered strain produced 1035.5 ± 67.8 mg/L p-CA using glucose as a carbon source. The strains with overexpression of cellulases and hemicellulases produced 84.3 ± 2.4 and 65.3 ± 4.6 mg/L p-CA, using cellulose (carboxymethyl-cellulose) or hemicellulose (xylan from bagasse) as the carbon source, respectively. This research demonstrated the feasibility of conversion of cost-effective cellulose/hemicellulose into a value-added product and provided a sustainable cellulolytic cell factory for the utilization of cellulose/hemicellulose.

Exogenous Electroactive Microbes Regulate Soil Geochemical Properties and Microbial Communities by Enhancing the Reduction and Transformation of Fe(III) Minerals

Electroactive microbes can conduct extracellular electron transfer and have the potential to be applied as a bioresource to regulate soil geochemical properties and microbial communities. In this study, we incubated Fe-limited and Fe-enriched farmland soil together with electroactive microbes for 30 days; both soils were incubated with electroactive microbes and a common iron mineral, ferrihydrite. Our results indicated that the exogenous electroactive microbes decreased soil pH, total organic carbon (TOC), and total nitrogen (TN) but increased soil conductivity and promoted Fe(III) reduction. The addition of electroactive microbes also changed the soil microbial community from Firmicutes-dominated to Proteobacteria-dominated. Moreover, the total number of detected microbial species in the soil decreased from over 700 to less than 500. Importantly, the coexistence of N-transforming bacteria, Fe(III)-reducing bacteria and methanogens was also observed with the addition of electroactive microbes in Fe-rich soil, indicating the accelerated interspecies electron transfer of functional microflora.

Use of exogenous substrate in Chlorella cultivation: Strategy for biomass and polyhydroxybutyrate production

The aim of this study was to investigate the influence of exogenous carbon supplementation and nitrogen source reduction on Chlorella fusca LEB 111 growth, biomass composition, and polyhydroxybutyrate accumulation. First, assays were performed with 50 % and 25 % reduced nitrogen source concentrations (NaNO₃). In the second stage, the influence of culture supplementation with 10, 20, and 30 mg L^-1 D-xylose, associated with 50 and 25 % reductions in NaNO₃, was evaluated. The experiments conducted with a 25 % reduction in NaNO₃ and supplementation with 10 mg L^-1 D-xylose resulted in a positive effect on the biomass productivity of C. fusca LEB 111, with production as high as 354.4 mg L^-1 d^-1. The maximum concentration of PHB extracted from C. fusca LEB 111 was 3.7 % (w w^-1) and was obtained when the microalgae were cultivated with a 25 % of reduction in NaNO₃ and supplementation of D-xylose at 20 mg L^-1. Therefore, this study brings new perspectives regarding reducing the use of nutritional sources and using exogenous carbon sources in using microalgae to produce molecules of high biotechnological potential.

Molecular insight into cellulose degradation by the phototrophic green alga Scenedesmus

Lignocellulose is the most abundant natural biopolymer on earth and a potential raw material for the production of fuels and chemicals. However, only some organisms such as bacteria and fungi produce enzymes that metabolize this polymer. In this work we have demonstrated the presence of cellulolytic activity in the supernatant of Scenedesmus quadricauda cultures and we identified the presence of extracellular cellulases in the genome of five Scenedesmus species. Scenedesmus is a green alga which grows in both freshwater and saltwater regions as well as in soils, showing highly flexible metabolic properties. Sequence comparison of the different identified cellulases with hydrolytic enzymes from other organisms using multisequence alignments and phylogenetic trees showed that these proteins belong to the families of glycosyl hydrolases 1, 5, 9, and 10. In addition, most of the Scenedesmus cellulases showed greater sequence similarity with those from invertebrates, fungi, bacteria, and other microalgae than with the plant homologs. Furthermore, the data obtained from the three dimensional structure showed that both, their global structure and the main amino acid residues involved in catalysis and substrate binding are well conserved. Based on our results, we propose that different species of Scenedesmus could act as biocatalysts for the hydrolysis of cellulosic biomass produced from sunlight.

From Genomics to Metagenomics in the Era of Recent Sequencing Technologies

Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.

Marine Cellulases and their Biotechnological Significance from Industrial Perspectives

Marine microorganisms represent virtually unlimited sources of novel biological compounds and can survive extreme conditions. Cellulases, a group of enzymes that are able to degrade cellulosic materials, are in high demand in various industrial and biotechnological applications, such as in the medical and pharmaceutical industries, food, fuel, agriculture, and single-cell protein, and as probiotics in aquaculture. The cellulosic biopolymer is a renewable resource and is a linearly arranged polysaccharide of glucose, with repeating units of disaccharide connected via β-1,4-glycosidic bonds, which are broken down by cellulase. A great deal of biodiversity resides in the ocean, and marine systems produce a wide range of distinct, new bioactive compounds that remain available but dormant for many years. The marine environment is filled with biomass from known and unknown vertebrates and invertebrate microorganisms, with much potential for use in medicine and biotechnology. Hence, complex polysaccharides derived from marine sources are a rich resource of microorganisms equipped with enzymes for polysaccharides degradation. Marine cellulases' extracts from the isolates are tested for their functional role in degrading seaweed and modifying wastes to low molecular fragments. They purify and renew environments by eliminating possible feedstocks of pollution. This review aims to examine the various types of marine cellulase producers and assess the ability of these microorganisms to produce these enzymes and their subsequent biotechnological applications.

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

BACKGROUND

Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities.

RESULTS

To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes.

CONCLUSIONS

The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance. Video Abstract.

Redispersion of dried plant nanocellulose: A review

Nanocellulose has undergone substantial development as a high value-added cellulose product with broad applications. Dried products are advantageous to decrease transportation costs. However, dried nanocellulose has redispersion challenges when rewetting. In this work, drying techniques, factors affecting redispersibility, and strategies improving the nanocellulose redispersibility are comprehensively reviewed. Hydrogen bonds of nanocellulose are unavoidably developed during drying, leading to inferior redispersibility of dried nanocellulose, even hornification. Drying processes of nanocellulose are discussed first. Then, factors affecting redispersibility are discussed. Following that, strategies improving the nanocellulose redispersibility are analyzed and their advantages and disadvantages are highlighted. Surface charge modification and steric hindrance concept are two main pathways to overcome the redispersion challenge, which are mainly carried out by chemical modification, additive incorporation and non-cellulosic component preservation. Despite several advancements having been achieved, new approaches for enhancing the nanocellulose redispersibility are still required to promote the industrial-scale applications of nanocellulose in various domains.

Advanced pathway engineering for phototrophic putrescine production

The polyamine putrescine (1,4-diaminobutane) contributes to cellular fitness in most organisms, where it is derived from the amino acids ornithine or arginine. In the chemical industry, putrescine serves as a versatile building block for polyamide synthesis. The green microalga Chlamydomonas reinhardtii accumulates relatively high putrescine amounts, which, together with recent advances in genetic engineering, enables the generation of a powerful green cell factory to promote sustainable biotechnology for base chemical production. Here, we report a systematic investigation of the native putrescine metabolism in C. reinhardtii, leading to the first CO₂ -based bio-production of putrescine, by employing modern synthetic biology and metabolic engineering strategies. A CRISPR/Cas9-based knockout of key enzymes of the polyamine biosynthesis pathway identified ornithine decarboxylase 1 (ODC1) as a gatekeeper for putrescine accumulation and demonstrated that the arginine decarboxylase (ADC) route is likely inactive and that amine oxidase 2 (AMX2) is mainly responsible for putrescine degradation in C. reinhardtii. A 4.5-fold increase in cellular putrescine levels was achieved by engineered overexpression of potent candidate ornithine decarboxylases (ODCs). We identified unexpected substrate promiscuity in two bacterial ODCs, which exhibited co-production of cadaverine and 4-aminobutanol. Final pathway engineering included overexpression of recombinant arginases for improved substrate availability as well as functional knockout of putrescine degradation, which resulted in a 10-fold increase in cellular putrescine titres and yielded 200 mg/L in phototrophic high cell density cultivations after 10 days.

Bacterial Community under the Influence of Microplastics in Indoor Environment and the Health Hazards Associated with Antibiotic Resistance Genes

Selectively colonized microbial communities and enriched antibiotic resistance genes (ARGs) in (micro)plastics in aquatic and soil environments make the plastisphere a great health concern. Although microplastics (MPs) are distributed in indoor environments in high abundance, information on the effect of MPs on a microbial community in an indoor environment is lacking. Here, we detected polymers (containing MPs and natural polymers), bacterial communities, and 18 kinds of ARGs in collected indoor dust samples. A significant correlation by Procrustes analysis between bacterial community composition and the abundance of MPs was observed, and correlation tests and redundancy analysis identified specific associations between MP polymers and bacterial taxa, such as polyamide and Actinobacteria. In addition, the abundance of MPs showed a positive correlation with the relative abundance of the ARGs (to 16S RNA), while natural polymers, such as cellulosics, showed positive correlations with the absolute abundance of ARGs and 16S rRNA. Simulated experiments verified that significantly higher bacterial biomasses and ARGs were observed on the surface of cotton, hair, and wool than on MPs, while a higher relative abundance of ARGs was detected on MPs. However, a significantly higher amount of ARG was found on MPs of poly(lactic acid), the biodegradable plastics with the highest yield. In addition to the plastisphere in water and soil environments, MPs in an indoor environment may also affect the bacterial community and specifically enrich ARGs. Moreover, degradable MPs and nondegradable MPs may result in different health hazards due to their distinct effects on bacterial community.

Environmental Factors Associated with the Eukaryotic Microbial Community and Microalgal Groups in the Mountain Marshes of South Korea

The diversity indices of eukaryotic microalgal groups in the Jeonglyeongchi, Waegok, and Wangdeungjae marshes of Mount Jiri, Korea, were measured using Illumina MiSeq and culture-based analyses. Waegok marsh had the highest species richness, with a Chao1 value of 828.00, and the highest levels of species diversity, with Shannon and Simpson index values of 6.36 and 0.94, respectively, while Wangdeungjae marsh had the lowest values at 2.97 and 0.75, respectively. The predominant species in all communities were Phagocata sibirica (Jeonglyeongchi, 68.64%), Aedes albopictus (Waegok, 34.77%), Chaetonotus cf. (Waegok, 24.43%), Eimeria sp. (Wangdeungjae, 26.17%), and Eumonhystera cf. (Wangdeungjae, 22.27%). Relative abundances of the microalgal groups Bacillariophyta (diatoms) and Chlorophyta (green algae) in each marsh were respectively: Jeonglyeongchi 1.38% and 0.49%, Waegok 7.0% and 0.3%, and Wangdeungjae 10.41% and 4.72%. Illumina MiSeq analyses revealed 34 types of diatoms and 13 types of green algae. Only one diatom (Nitzschia dissipata) and five green algae (Neochloris sp., Chlamydomonas sp., Chlorococcum sp., Chlorella vulgaris, Scenedesmus sp.) were identified by a culture-based analysis. Thus, Illumina MiSeq analysis can be considered an efficient tool for analyzing microbial communities. Overall, our results described the environmental factors associated with geographically isolated mountain marshes and their respective microbial and microalgal communities.

The establishment of new protein expression system using N starvation inducible promoters in Chlorella

Chlorella is a unicellular green microalga that has been used in fields such as bioenergy production and food supplementation. In this study, two promoters of N (nitrogen) deficiency-inducible Chlorella vulgaris N Deficiency Inducible (CvNDI) genes were isolated from Chlorella vulgaris UTEX 395. These promoters were used for the production of a recombinant protein, human granulocyte-colony stimulating factor (hG-CSF) in Chlorella vulgaris UTEX 395 and Chlorella sp. ArM0029B. To efficiently secrete the hG-CSF, the protein expression vectors incorporated novel signal peptides obtained from a secretomics analysis of Chlorella spp. After a stable transformation of those vectors with a codon-optimized hG-CSF sequence, hG-CSF polypeptides were successfully produced in the spent media of the transgenic Chlorella. To our knowledge, this is the first report of recombinant protein expression using endogenous gene components of Chlorella.

Biocomponent-based microalgal transformations into biofuels during the pretreatment and fermentation process

Microalgal cell wall integrity and composition have a significant impact on the fermentation process and biofuel recovery. In this study, various biofuels (bioethanol, higher alcohols (C3-C5), and biodiesel) were produced by the fermentation of carbohydrates and proteins, and transesterification of lipids from three different microalgal strains (Pseudochlorella sp., Chlamydomonas mexicana, and Chlamydomonas pitschmannii), each possessing different proportions of bioconstituents (carbohydrates, proteins, and lipids). Changes in the cell wall structure and thickness were observed before and after fermentation using transmission electron microscopy. Pseudochlorella sp. showed the highest yields of bioethanol (0.45 g-ethanol/g-carbohydrates), higher alcohols (0.44 g-higher alcohols/g-proteins), and biodiesel (0.55 g-biodiesel/g-lipids), which consequently revealed a maximum energy recovery (42%) from whole constituents. This study suggests that different physiological properties, including cell wall thickness and the proportion of bioconstituents in microalgae, could have a significant impact on the pretreatment and fermentation efficiencies for biofuels production.

Toxicity, Biodegradation, and Metabolic Fate of Organophosphorus Pesticide Trichlorfon on the Freshwater Algae Chlamydomonas reinhardtii

This study investigated the toxicity of trichlorfon (TCF) to the freshwater algae Chlamydomonas reinhardtii, as well as its biodegradation and metabolic fate. The growth of C. reinhardtii decreased with increasing TCF concentration, and the maximum inhibition ratio was 51.3% at 200 mg L^-1 TCF compared to the control. Analyses of pigment content, chlorophyll fluorescence, and antioxidant enzymes indicated that C. reinhardtii can produce resistance and acclimatize to the presence of TCF. The variations in pH during cultivation suggested that photosynthetic microalgae have innate advantages over bacteria and fungi in remediating TCF. A 100% biodegradation rate was achieved at a maximum concentration of 100 mg L^-1 TCF. Ten metabolites were identified by GC-MS, and the degradation pathways of TCF by the algae were proposed. This research demonstrated that C. reinhardtii is highly tolerant to and can efficiently degrade TCF. Thus, C. reinhardtii can be used to remove traces of TCF from natural water environments and to treat TCF-contaminated wastewater.

Draft Genome Sequences of Strains TAV3 and TAV4 (Verrucomicrobia: Opitutaceae), Isolated from a Wood-Feeding Termite, and In Silico Analysis of Their Polysaccharide-Degrading Enzymes

Here, we report the high-quality draft genome sequences of Opitutaceae sp. strains TAV3 and TAV4, which were isolated from the hindgut of the wood-feeding termite Reticulitermes flavipes Using a combination of Illumina and PacBio sequencing, we constructed nearly complete assemblies totaling 5.84 and 5.91 Mbp in length for strains TAV3 and TAV4, respectively. In addition, we report an in silico analysis of potential lignocellulose-digesting enzymes present in these strains.

Green Production and Biotechnological Applications of Cell Wall Lytic Enzymes

: Energy demand is constantly growing, and, nowadays, fossil fuels still play a dominant role in global energy production, despite their negative effects on air pollution and the emission of greenhouse gases, which are the main contributors to global warming. An alternative clean source of energy is represented by the lignocellulose fraction of plant cell walls, the most abundant carbon source on Earth. To obtain biofuels, lignocellulose must be efficiently converted into fermentable sugars. In this regard, the exploitation of cell wall lytic enzymes (CWLEs) produced by lignocellulolytic fungi and bacteria may be considered as an eco-friendly alternative. These organisms evolved to produce a variety of highly specific CWLEs, even if in low amounts. For an industrial use, both the identification of novel CWLEs and the optimization of sustainable CWLE-expressing biofactories are crucial. In this review, we focus on recently reported advances in the heterologous expression of CWLEs from microbial and plant expression systems as well as some of their industrial applications, including the production of biofuels from agricultural feedstock and of value-added compounds from waste materials. Moreover, since heterologous expression of CWLEs may be toxic to plant hosts, genetic strategies aimed in converting such a deleterious effect into a beneficial trait are discussed.

Thermally coupled dark-anoxia incubation: A platform technology to induce auto-fermentation and thus cell-wall thinning in both nitrogen-replete and nitrogen-deplete Nannochloropsis slurries

Nitrogen-deprived Nannochloropsis cells invested their fixed carbon into the accumulation of triacylglycerol and cell wall cellulose (thickness of N-replete cell walls = 27.8 ± 5.8, N-deplete cell walls = 51.0 ± 10.2 nm). In this study, the effect of nitrogen depletion on the ability of the cells to weaken their own cell walls via autolysis was investigated. Autolytic cell wall thinning was achieved in both N-replete and N-deplete biomass by incubating highly concentrated slurries in darkness at 38 °C. The incubation forced cells to anaerobically ferment their intracellular cellulose and resulted in 30-40% reduction in cell wall thickness for both biomass types. This wall depletion weakened the cells and increased the extent of cell rupture by mechanical force (from 42 to 78% for N-replete biomass, from 36 to 62% for N-deplete biomass). Importantly, autolysis did not adversely impact the amino acid content of protein-rich N-replete biomass or the fatty acid content of lipid-rich N-deplete biomass.

Secretion of Acetylxylan Esterase From Chlamydomonas reinhardtii Enables Utilization of Lignocellulosic Biomass as a Carbon Source

Microalgae offer a promising biological platform for sustainable biomanufacturing of a wide range of chemicals, pharmaceuticals, and fuels. The model microalga Chlamydomonas reinhardtii is thus far the most versatile algal chassis for bioengineering and can grow using atmospheric CO2 and organic carbons (e.g., acetate and pure cellulose). Ability to utilize renewable feedstock like lignocellulosic biomass as a carbon source could significantly accelerate microalgae-based productions, but this is yet to be demonstrated. We observed that C. reinhardtii was not able to heterotrophically grow using wheat straw, a common type of lignocellulosic biomass, likely due to the recalcitrant nature of the biomass. When the biomass was pretreated with alkaline, C. reinhardtii was able to grow using acetate that was released from the biomass. To establish an eco-friendly and self-sustained growth system, we engineered C. reinhardtii to secrete a fungal acetylxylan esterase (AXE) for hydrolysis of acetylesters in the lignocellulosic biomass. Two transgenic strains (CrAXE03 and CrAXE23) secreting an active AXE into culture media were isolated. Incubation of CrAXE03 with wheat straw resulted in an eight-fold increase in the algal cell counts with a concomitant decrease of biomass acetylester contents by 96%. The transgenic lines showed minor growth defects compared to the parental strain, indicating that secretion of the AXE protein imposes limited metabolic burden. The results presented here would open new opportunities for applying low-cost renewable feedstock, available in large amounts as agricultural and manufacturing by-products, for microalgal cultivation. Furthermore, acetylesters and acetate released from them, are well-known inhibitors in lignocellulosic biofuel productions; thus, direct application of the bioengineered microalga could be exploited for improving renewable biofuel productions.

Biomass from microalgae: the potential of domestication towards sustainable biofactories

Interest in bulk biomass from microalgae, for the extraction of high-value nutraceuticals, bio-products, animal feed and as a source of renewable fuels, is high. Advantages of microalgal vs. plant biomass production include higher yield, use of non-arable land, recovery of nutrients from wastewater, efficient carbon capture and faster development of new domesticated strains. Moreover, adaptation to a wide range of environmental conditions evolved a great genetic diversity within this polyphyletic group, making microalgae a rich source of interesting and useful metabolites. Microalgae have the potential to satisfy many global demands; however, realization of this potential requires a decrease of the current production costs. Average productivity of the most common industrial strains is far lower than maximal theoretical estimations, suggesting that identification of factors limiting biomass yield and removing bottlenecks are pivotal in domestication strategies aimed to make algal-derived bio-products profitable on the industrial scale. In particular, the light-to-biomass conversion efficiency represents a major constraint to finally fill the gap between theoretical and industrial productivity. In this respect, recent results suggest that significant yield enhancement is feasible. Full realization of this potential requires further advances in cultivation techniques, together with genetic manipulation of both algal physiology and metabolic networks, to maximize the efficiency with which solar energy is converted into biomass and bio-products. In this review, we draft the molecular events of photosynthesis which regulate the conversion of light into biomass, and discuss how these can be targeted to enhance productivity through mutagenesis, strain selection or genetic engineering. We outline major successes reached, and promising strategies to achieving significant contributions to future microalgae-based biotechnology.

Features of cues and processes during chloroplast-mediated retrograde signaling in the alga Chlamydomonas

Retrograde signaling is an intracellular communication process defined by cues generated in chloroplast and mitochondria which traverse membranes to their destination in the nucleus in order to regulate nuclear gene expression and protein synthesis. The coding and decoding of such organellar message(s) involve gene medleys and metabolic components about which more is known in higher plants than the unicellular organisms such as algae. Chlamydomonas reinhardtii is an oxygenic microalgal model for genetic and physiological studies. It harbors a single chloroplast and is amenable for generating mutants. The focus of this review is on studies that delineate retrograde signaling in Chlamydomonas vis a vis higher plants. Thus, communication networks between chloroplast and nucleus involving photosynthesis- and ROS-generated signals, functional tetrapyrrole biosynthesis intermediates, and Ca²⁺-signaling that modulate nuclear gene expression in this alga are discussed. Conceptually, different signaling components converge to regulate either the same or functionally-overlapping gene products.

Novel Insights from Comparative In Silico Analysis of Green Microalgal Cellulases

The assumption that cellulose degradation and assimilation can only be carried out by heterotrophic organisms was shattered in 2012 when it was discovered that the unicellular green alga, Chlamydomonas reinhardtii (Cr), can utilize cellulose for growth under CO₂-limiting conditions. Publications of genomes/transcriptomes of the colonial microalgae, Gonium pectorale (Gp) and Volvox carteri (Vc), between 2010⁻2016 prompted us to look for cellulase genes in these algae and to compare them to cellulases from bacteria, fungi, lower/higher plants, and invertebrate metazoans. Interestingly, algal catalytic domains (CDs), belonging to the family GH9, clustered separately and showed the highest (33⁻42%) and lowest (17⁻36%) sequence identity with respect to cellulases from invertebrate metazoans and bacteria, respectively, whereas the identity with cellulases from plants was only 27⁻33%. Based on comparative multiple alignments and homology models, the domain arrangement and active-site architecture of algal cellulases are described in detail. It was found that all algal cellulases are modular, consisting of putative novel cysteine-rich carbohydrate-binding modules (CBMs) and proline/serine-(PS) rich linkers. Two genes were found to encode a protein with a putative Ig-like domain and a cellulase with an unknown domain, respectively. A feature observed in one cellulase homolog from Gp and shared by a spinach cellulase is the existence of two CDs separated by linkers and with a C-terminal CBM. Dockerin and Fn-3-like domains, typically found in bacterial cellulases, are absent in algal enzymes. The targeted gene expression analysis shows that two Gp cellulases consisting, respectively, of a single and two CDs were upregulated upon filter paper addition to the medium.

A Platform for High-Throughput Assessments of Environmental Multistressors

A platform compatible with microtiter plates to parallelize environmental treatments to test the complex impacts of multiple stressors, including parameters relevant to climate change and point source pollutants is developed. This platform leverages (1) the high rate of purely diffusive gas transport in aerogels to produce well-defined centimeter-scale gas concentration gradients, (2) spatial light control, and (3) established automated liquid handling. The parallel gaseous, aqueous, and light control provided by the platform is compatible with multiparameter experiments across the life sciences. The platform is applied to measure biological effects in over 700 treatments in a five-parameter full factorial study with the microalgae Chlamydomonas reinhardtii. Further, the CO2 response of multicellular organisms, Lemna gibba and Artemia salina under surfactant and nanomaterial stress are tested with the platform.

De novo transcriptome of the cosmopolitan dinoflagellate Amphidinium carterae to identify enzymes with biotechnological potential

Dinoflagellates are phytoplanktonic organisms found in both freshwater and marine habitats. They are often studied because related to harmful algal blooms but they are also known to produce bioactive compounds for the treatment of human pathologies. The aim of this study was to sequence the full transcriptome of the dinoflagellate Amphidinium carterae in both nitrogen-starved and -replete culturing conditions (1) to evaluate the response to nitrogen starvation at the transcriptional level, (2) to look for possible polyketide synthases (PKSs) in the studied clone (genes that may be involved in the synthesis of bioactive compounds), (3) if present, to evaluate if nutrient starvation can influence PKS expression, (4) to look for other possible enzymes of biotechnological interest and (5) to test strain cytotoxicity on human cell lines. Results showed an increase in nitrogen metabolism and stress response in nitrogen-starved cells and confirmed the presence of a type I β-ketosynthase. In addition, L-asparaginase (used for the treatment of Leukemia and for acrylamide reduction in food industries) and cellulase (useful for biofuel production and other industrial applications) have been identified for the first time in this species, giving new insights into possible biotechnological applications of dinoflagellates.

Evolutionary consequences of multidriver environmental change in an aquatic primary producer

Climate change is altering aquatic environments in a complex way, and simultaneous shifts in many properties will drive evolutionary responses in primary producers at the base of both freshwater and marine ecosystems. So far, evolutionary studies have shown how changes in environmental drivers, either alone or in pairs, affect the evolution of growth and other traits in primary producers. Here, we evolve a primary producer in 96 unique environments with different combinations of between one and eight environmental drivers to understand how evolutionary responses to environmental change depend on the identity and number of drivers. Even in multidriver environments, only a few dominant drivers explain most of the evolutionary changes in population growth rates. Most populations converge on the same growth rate by the end of the evolution experiment. However, populations adapt more when these dominant drivers occur in the presence of other drivers. This is due to an increase in the intensity of selection in environments with more drivers, which are more likely to include dominant drivers. Concurrently, many of the trait changes that occur during the initial short-term response to both single and multidriver environmental change revert after about 450 generations of evolution. In future aquatic environments, populations will encounter differing combinations of drivers and intensities of selection, which will alter the adaptive potential of primary producers. Accurately gauging the intensity of selection on key primary producers will help in predicting population size and trait evolution at the base of aquatic food webs.

In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases

The glycoside hydrolase 9 superfamily, mainly comprising the endoglucanases, is represented in all three domains of life. The current division of GH9 enzymes, into three subclasses, namely A, B, and C, is centered on parameters derived from sequence information alone. However, this classification is ambiguous, and is limited by the paralogous ancestry of classes B and C endoglucanases, and paucity of biochemical and structural data. Here, we extend this classification schema to putative GH9 endoglucanases present in green plants, with an emphasis on identifying novel members of the class C subset. These enzymes cleave the β(1 → 4) linkage between non-terminal adjacent D-glucopyranose residues, in both, amorphous and crystalline regions of cellulose. We utilized non redundant plant GH9 enzymes with characterized molecular data, as the training set to construct Hidden Markov Models (HMMs) and train an Artificial Neural Network (ANN). The parameters that were used for predicting dominant enzyme function, were derived from this training set, and subsequently refined on 147 sequences with available expression data. Our knowledge-based approach, can ascribe differential endoglucanase activity (A, B, or C) to a query sequence with high confidence, and was used to construct a local repository of class C GH9 endoglucanases (GH9C = 241) from 32 sequenced green plants.

Substrate-Independent Robust and Heparin-Mimetic Hydrogel Thin Film Coating via Combined LbL Self-Assembly and Mussel-Inspired Post-Cross-linking

In this work, we designed a robust and heparin-mimetic hydrogel thin film coating via combined layer-by-layer (LbL) self-assembly and mussel-inspired post-cross-linking. Dopamine-grafted heparin-like/-mimetic polymers (DA-g-HepLP) with abundant carboxylic and sulfonic groups were synthesized by the conjugation of adhesive molecule, DA, which exhibited substrate-independent adhesive affinity to various solid surfaces because of the formation of irreversible covalent bonds. The hydrogel thin film coated substrates were prepared by a three-step reaction: First, the substrates were coated with DA-g-HepLP to generate negatively charged surfaces. Then, multilayers were obtained via LbL coating of chitosan and the DA-g-HepLP. Finally, the noncovalent multilayers were oxidatively cross-linked by NaIO4. Surface ATR-FTIR and XPS spectra confirmed the successful fabrication of the hydrogel thin film coatings onto membrane substrates; SEM images revealed that the substrate-independent coatings owned 3D porous morphology. The soaking tests in highly alkaline, acid, and concentrated salt solutions indicated that the cross-linked hydrogel thin film coatings owned high chemical resistance. In comparison, the soaking tests in physiological solution indicated that the cross-linked hydrogel coatings owned excellent long-term stability. The live/dead cell staining and morphology observations of the adhered cells revealed that the heparin-mimetic hydrogel thin film coated substrates had low cell toxicity and high promotion ability for cell proliferation. Furthermore, systematic in vitro investigations of protein adsorption, platelet adhesion, blood clotting, and blood-related complement activation confirmed that the hydrogel film coated substrates showed excellent hemocompatibility. Both the results of inhibition zone and bactericidal activity indicated that the gentamycin sulfate loaded hydrogel thin films had significant inhibition capability toward both Escherichia coli and Staphylococcus aureus bacteria. Combined the above advantages, it is believed that the designed heparin-mimetic hydrogel thin films may show high potential for applications in various biological and clinical fields, such as long-term hemocompatible and drug-loading materials for implants.

Lignocellulose degradation mechanisms across the Tree of Life

Organisms use diverse mechanisms involving multiple complementary enzymes, particularly glycoside hydrolases (GHs), to deconstruct lignocellulose. Lytic polysaccharide monooxygenases (LPMOs) produced by bacteria and fungi facilitate deconstruction as does the Fenton chemistry of brown-rot fungi. Lignin depolymerisation is achieved by white-rot fungi and certain bacteria, using peroxidases and laccases. Meta-omics is now revealing the complexity of prokaryotic degradative activity in lignocellulose-rich environments. Protists from termite guts and some oomycetes produce multiple lignocellulolytic enzymes. Lignocellulose-consuming animals secrete some GHs, but most harbour a diverse enzyme-secreting gut microflora in a mutualism that is particularly complex in termites. Shipworms however, house GH-secreting and LPMO-secreting bacteria separate from the site of digestion and the isopod Limnoria relies on endogenous enzymes alone. The omics revolution is identifying many novel enzymes and paradigms for biomass deconstruction, but more emphasis on function is required, particularly for enzyme cocktails, in which LPMOs may play an important role.

Characterization of nutrient removal and microalgal biomass production on an industrial waste-stream by application of the deceleration-stat technique

Industrial wastewaters can serve as a nutrient and water source for microalgal production. In this study the effluent of an internal circulation (IC) reactor anaerobically treating the wastes of a biotechnology production facility were chosen as the cultivation medium for Chlorella sorokiniana in batch and continuous cultures. The aim was to evaluate the rates of nutrient removal and biomass production possible at various dilution rates. The results demonstrate that the industrial wastewater served as a highly effective microalgae culture medium and that dilution rate strongly influenced algae productivity in a short light-path photobioreactor. Batch culture on undiluted wastewater showed biomass productivity of 1.33 g L(-1)day(-1), while removing over 99% of the ammonia and phosphate from the wastewater. Deceleration-stat (D-stat) experiments performed at high and low intensities of 2100 and 200 (μmol photon m(2)s(-1)) established the optimal dilution rates to reach volumetric productivity of 5.87 and 1.67 g L(-1)day(-1) respectively. The corresponding removal rates of nitrogen were 238 and 93 mg L(-1)day(-1) and 40 and 19 mg L(-1)day(-1) for phosphorous. The yield on photons at low light intensity was as high as had been observed in any previous report indicating that the waste stream allowed the algae to grow at its full potential.

High-yield production of extracellular type-I cellulose by the cyanobacterium Synechococcus sp. PCC 7002

Cellulose synthase, encoded by the cesA gene, is responsible for the synthesis of cellulose in nature. We show that the cell wall of the cyanobacterium Synechococcus sp. PCC 7002 naturally contains cellulose. Cellulose occurs as a possibly laminated layer between the inner and outer membrane, as well as being an important component of the extracellular glycocalyx in this cyanobacterium. Overexpression of six genes, cmc–ccp–cesAB–cesC–cesD–bgl, from Gluconacetobacter xylinus in Synechococcus sp. PCC 7002 resulted in very high-yield production of extracellular type-I cellulose. High-level cellulose production only occurred when the native cesA gene was inactivated and when cells were grown at low salinity. This system provides a method for the production of lignin-free cellulose from sunlight and CO₂ for biofuel production and other biotechnological applications.

First laccase in green algae: purification and characterization of an extracellular phenol oxidase from Tetracystis aeria

A green algal phenol oxidase was firstly purified, confirmed to be a laccase, and a hetero-oligomeric quaternary structure is suggested. The operation of a laccase-mediator system is firstly described in algae. Laccases (EC 1.10.3.2) catalyze the oxidation of a multitude of aromatic substrates. They are well known in higher plants and fungi, while their presence in green algae appears uncertain. Extracellular laccase-like enzyme activity has previously been described in culture supernatants of the green soil alga Tetracystis aeria [Otto et al. in Arch Microbiol 192:759-768, (2010)]. As reported herein, the T. aeria enzyme was purified 120-fold by employing a combination of anion exchange and size exclusion chromatography. The purified enzyme was confirmed to be a laccase according to its substrate specificity. It oxidizes 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), syringaldazine, and 2,6-dimethoxyphenol (pH optima of pH ≤ 2.5, 7.0, and 6.5; K m values of 28.8, 40.5, and 1,830 µM; respectively), but not L-tyrosine or Fe(2+). ABTS is by far the most efficient substrate. Two polypeptides, A (~110 kDa) and B (71 kDa), were co-purified by the applied procedure, both being highly N-glycosylated (≥~53 and ≥ 27 %, respectively). As suggested by various gel electrophoretic analyses, the native enzyme (apparent molecular mass of ~220 kDa) most probably is a hetero-oligomer with the composition AB 2 , wherein A is the catalytic subunit and B forms a disulfide-linked homo-dimer B2. The decolorization of anthraquinone (Acid Blue 62 and Remazol Brilliant Blue R) and diazo dyes (Reactive Black 5) was studied in the presence of redox-mediating compounds (ABTS and syringaldehyde), demonstrating the operation of the laccase-mediator system in algae for the first time. Thus, laccases from green algae may participate in the biotransformation of a wide spectrum of natural and xenobiotic compounds.

Comparative transcriptome analysis of a toxin-producing dinoflagellate Alexandrium catenella and its non-toxic mutant

The dinoflagellates and cyanobacteria are two major kingdoms of life producing paralytic shellfish toxins (PSTs), a large group of neurotoxic alkaloids causing paralytic shellfish poisonings around the world. In contrast to the well elucidated PST biosynthetic genes in cyanobacteria, little is known about the dinoflagellates. This study compared transcriptome profiles of a toxin-producing dinoflagellate, Alexandrium catenella (ACHK-T), and its non-toxic mutant form (ACHK-NT) using RNA-seq. All clean reads were assembled de novo into a total of 113,674 unigenes, and 66,812 unigenes were annotated in the known databases. Out of them, 35 genes were found to express differentially between the two strains. The up-regulated genes in ACHK-NT were involved in photosynthesis, carbon fixation and amino acid metabolism processes, indicating that more carbon and energy were utilized for cell growth. Among the down-regulated genes, expression of a unigene assigned to the long isoform of sxtA, the initiator of toxin biosynthesis in cyanobacteria, was significantly depressed, suggesting that this long transcript of sxtA might be directly involved in toxin biosynthesis and its depression resulted in the loss of the ability to synthesize PSTs in ACHK-NT. In addition, 101 putative homologs of 12 cyanobacterial sxt genes were identified, and the sxtO and sxtZ genes were identified in dinoflagellates for the first time. The findings of this study should shed light on the biosynthesis of PSTs in the dinoflagellates.

Integration of carbon assimilation modes with photosynthetic light capture in the green alga Chlamydomonas reinhardtii

The unicellular green alga Chlamydomonas reinhardtii is capable of using organic and inorganic carbon sources simultaneously, which requires the adjustment of photosynthetic activity to the prevailing mode of carbon assimilation. We obtained novel insights into the regulation of light-harvesting at photosystem II (PSII) following altered carbon source availability. In C. reinhardtii, synthesis of PSII-associated light-harvesting proteins (LHCBMs) is controlled by the cytosolic RNA-binding protein NAB1, which represses translation of particular LHCBM isoform transcripts. This mechanism is fine-tuned via regulation of the nuclear NAB1 promoter, which is activated when linear photosynthetic electron flow is restricted by CO(2)-limitation in a photoheterotrophic context. In the wild-type, accumulation of NAB1 reduces the functional PSII antenna size, thus preventing a harmful overexcited state of PSII, as observed in a NAB1-less mutant. We further demonstrate that translation control as a newly identified long-term response to prolonged CO(2)-limitation replaces LHCII state transitions as a fast response to PSII over-excitation. Intriguingly, activation of the long-term response is perturbed in state transition mutant stt7, suggesting a regulatory link between the long- and short-term response. We depict a regulatory circuit operating on distinct timescales and in different cellular compartments to fine-tune light-harvesting in photoheterotrophic eukaryotes.

Optimal eukaryotic 18S and universal 16S/18S ribosomal RNA primers and their application in a study of symbiosis

Eukaryotic 18S ribosomal RNA (rRNA) gene primers that feature a wide coverage are critical in detecting the composition of eukaryotic microscopic organisms in ecosystems. Here, we predicted 18S rRNA primers based on consecutive conserved sites and evaluated their coverage efficiency and scope of application to different eukaryotic groups. After evaluation, eight of them were considered as qualified 18S primers based on coverage rate. Next, we examined common conserved regions in prokaryotic 16S and eukaryotic 18S rRNA sequences to design 16S/18S universal primers. Three 16S/18S candidate primers, U515, U1390 and U1492, were then considered to be suitable for simultaneous amplification of the rRNA sequences in three domains. Eukaryotic 18S and prokaryotic 16S rRNA genes in a sponge were amplified simultaneously using universal primers U515 and U1390, and the subsequent sorting of pyrosequenced reads revealed some distinctive communities in different parts of the sample. The real difference in biodiversity between prokaryotic and eukaryotic symbionts could be discerned as the dissimilarity between OTUs was increased from 0.005 to 0.1. A network of the communities in external and internal parts of the sponge illustrated the co-variation of some unique microbes in certain parts of the sponge, suggesting that the universal primers are useful in simultaneous detection of prokaryotic and eukaryotic microbial communities.