Algae–bacteria interactions: Evolution, ecology and emerging applications

AbstractAlgae and bacteria have coexisted ever since the early stages of evolution. This coevolution has revolutionized life on earth in many aspects. Algae and bacteria together influence ecosystems as varied as deep seas to lichens and represent all conceivable modes of interactions — from mutualism to parasitism. Several studies have shown that algae and bacteria synergistically affect each other's physiology and metabolism, a classic case being algae–roseobacter interaction. These interactions are ubiquitous and define the primary productivity in most ecosystems. In recent years, algae have received much attention for industrial exploitation but their interaction with bacteria is often considered a contamination during commercialization. A few recent studies have shown that bacteria not only enhance algal growth but also help in flocculation, both essential processes in algal biotechnology. Hence, there is a need to understand these interactions from an evolutionary and ecological standpoint, and integrate this understanding for industrial use. Here we reflect on the diversity of such relationships and their associated mechanisms, as well as the habitats that they mutually influence. This review also outlines the role of these interactions in key evolutionary events such as endosymbiosis, besides their ecological role in biogeochemical cycles. Finally, we focus on extending such studies on algal–bacterial interactions to various environmental and bio-technological applications

An Integrated Korean Biodiversity and Genetic Information Retrieval System

Background: On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results: The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion: A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims to be integral in maximizing biofrom resource utilization for conservation, management, research, education, industrial applications, and integration with other bioinformation data resources. It can be found at http://www.naris.go.krclose1

The ancient phosphatidylinositol 3-kinase signaling system is a master regulator of energy and carbon metabolism in algae

Algae undergo a complete metabolic transformation under stress by arresting cell growth, inducing autophagy and hyperaccumulating biofuel precursors such as triacylglycerols and starch. However, the regulatory mechanisms behind this stress-induced transformation are still unclear. Here, we use biochemical, mutational, and “omics” approaches to demonstrate that PI3K signaling mediates the homeostasis of energy molecules and influences carbon metabolism in algae. In Chlamydomonas reinhardtii, the inhibition and knockdown (KD) of algal class III PI3K led to significantly decreased cell growth, altered cell morphology, and higher lipid and starch contents. Lipid profiling of wild-type and PI3K KD lines showed significantly reduced membrane lipid breakdown under nitrogen starvation (-N) in the KD. RNA-seq and network analyses showed that under -N conditions, the KD line carried out lipogenesis rather than lipid hydrolysis by initiating de novo fatty acid biosynthesis, which was supported by tricarboxylic acid cycle down-regulation and via acetyl-CoA synthesis from glycolysis. Remarkably, autophagic responses did not have primacy over inositide signaling in algae, unlike in mammals and vascular plants. The mutant displayed a fundamental shift in intracellular energy flux, analogous to that in tumor cells. The high free fatty acid levels and reduced mitochondrial ATP generation led to decreased cell viability. These results indicate that the PI3K signal transduction pathway is the metabolic gatekeeper restraining biofuel yields, thus maintaining fitness and viability under stress in algae. This study demonstrates the existence of homeostasis between starch and lipid synthesis controlled by lipid signaling in algae and expands our understanding of such processes, with biotechnological and evolutionary implications.Ministry of Science, ICT and Future Planning 2015M3A6A2065697Ministry of Oceans and Fisheries 2015018

Toxicity and Toxin Composition of Microcystis aeruginosa from Wangsong Reservoir

Objective: The increasing world population, resulting in increased anthropogenic water pollution, is negatively impacting the limited available water resources. In South Korea, this similarly affects the water quality of reservoirs. As water is a basic necessity for life, water quality monitoring is essential but typically does not include toxicity testing. However, as toxic bloom event frequencies are increasing, this previously neglected aspect becomes pertinent. Therefore, in the present study, the toxin composition and toxicity of a Microcystis aeruginosa strain isolated from a persistent bloom in lake Wangsong, South Korea, was investigated. Methods: A combination of bioassays and chemical analysis was used for this purpose. The bioassay species included terrestrial and aquatic plants, an alga, a rotifer, a tubificid annelid, and crustaceans, representing various trophic levels. Results: The strain was found to produce microcystin-LR, -RR, and YR, as well as β-N-methylamino-L-alanine. The bioassays indicated that the primary producers were less sensitive to the crude extract. Conclusion: The presence or absence of a visible cyanobacterial bloom is also not an indication of the toxins that may be present in the afflicted waters, and thus does not predict exposure risk. Similarly, the presence and absence of toxins and mixtures thereof do not indicate the ecological effect. Therefore, it would be advantages to include toxicity testing into routine water testing regimes to better understand the impact of harmful algal blooms.Peer reviewe

Assembly strategies for polyethylene-degrading microbial consortia based on the combination of omics tools and the “Plastisphere”

Numerous microorganisms and other invertebrates that are able to degrade polyethylene (PE) have been reported. However, studies on PE biodegradation are still limited due to its extreme stability and the lack of explicit insights into the mechanisms and efficient enzymes involved in its metabolism by microorganisms. In this review, current studies of PE biodegradation, including the fundamental stages, important microorganisms and enzymes, and functional microbial consortia, were examined. Considering the bottlenecks in the construction of PE-degrading consortia, a combination of top-down and bottom-up approaches is proposed to identify the mechanisms and metabolites of PE degradation, related enzymes, and efficient synthetic microbial consortia. In addition, the exploration of the plastisphere based on omics tools is proposed as a future principal research direction for the construction of synthetic microbial consortia for PE degradation. Combining chemical and biological upcycling processes for PE waste could be widely applied in various fields to promote a sustainable environment

Alishewanella aestuarii sp. nov., isolated from tidal flat sediment, and emended description of the genus Alishewanella

The genus Alishewanella, proposed by Fonnesbech Strain B11 T was isolated from tidal flat sediment in Yeosu (34 u 479 260 N 127 u 349 010 E), Republic of Korea. The strain was isolated on R2A agar (Difco) followed by repeated restreaking to obtain a pure culture. The Gram reaction was determined according to the non-staining method described by T and closely related strains. Chromosomal DNA was extracted and purified using a DNA extraction kit (IntronBiotechnology). The G+C content was determined using HPLC as described by T is affiliated phylogenetically with A. fetalis; this affiliation is supported by high bootstrap values (100, 98 and 94 % by the neighbour-joining, maximum-parsimony and maximum-likelihood methods, respectively). Similarities between the 16S rRNA gene sequence of strain B11 T and those of A. fetalis CCUG 30811 T Rheinheimera aquimaris SW-353 T and Rheinheimera perlucida BA131 T were 98.3, 96.5 and 96.4 %, respectively. A DNA-DNA hybridization experiment was performed as described previously For quantitative analysis of cellular fatty acids, strain B11 T and A. fetalis CCUG 30811 T were grown under the same conditions on blood agar plates at 30 u C for 2 days. Cells were harvested and cellular fatty acids were saponified, methylated and extracted as described by the Sherlock Microbial Identification System T were C 18 : 1 v7c, C 17 : 1 v8c, summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH), C 16 : 0 and C 17 : 0 . Complete fatty acid compositions of the novel strain and A. fetalis CCUG 30811 T are shown in T and the type strain of A. fetalis are similar. In addition to 16S rRNA gene similarity, the major fatty acid components of strain B11 T and its temperature range for growth confirm affiliation of this strain with the genus Alishewanella

Deep Learning for Simulating Harmful Algal Blooms Using Ocean Numerical Model

In several countries, the public health and fishery industries have suffered from harmful algal blooms (HABs) that have escalated to become a global issue. Though computational modeling offers an effective means to understand and mitigate the adverse effects of HABs, it is challenging to design models that adequately reflect the complexity of HAB dynamics. This paper presents a method involving the application of deep learning to an ocean model for simulating blooms of Alexandrium catenella. The classification and regression convolutional neural network (CNN) models are used for simulating the blooms. The classification CNN determines the bloom initiation while the regression CNN estimates the bloom density. GoogleNet and Resnet 101 are identified as the best structures for the classification and regression CNNs, respectively. The corresponding accuracy and root means square error values are determined as 96.8% and 1.20 [log(cells L-1)], respectively. The results obtained in this study reveal the simulated distribution to follow the Alexandrium catenella bloom. Moreover, Grad-CAM identifies that the salinity and temperature contributed to the initiation of the bloom whereas NH4-N influenced the growth of the bloom.</p&gt

Simple, Rapid and Cost-Effective Method for High Quality Nucleic Acids Extraction from Different Strains of Botryococcus braunii

This study deals with an effective nucleic acids extraction method from various strains of Botryococcus braunii which possesses an extensive extracellular matrix. A method combining freeze/thaw and bead-beating with heterogeneous diameter of silica/zirconia beads was optimized to isolate DNA and RNA from microalgae, especially from B. braunii. Eukaryotic Microalgal Nucleic Acids Extraction (EMNE) method developed in this study showed at least 300 times higher DNA yield in all strains of B. braunii with high integrity and 50 times reduced working volume compared to commercially available DNA extraction kits. High quality RNA was also extracted using this method and more than two times the yield compared to existing methods. Real-time experiments confirmed the quality and quantity of the input DNA and RNA extracted using EMNE method. The method was also applied to other eukaryotic microalgae, such as diatoms, Chlamydomonas sp., Chlorella sp., and Scenedesmus sp. resulting in higher efficiencies. Cost-effectiveness analysis of DNA extraction by various methods revealed that EMNE method was superior to commercial kits and other reported methods by >15%. This method would immensely contribute to area of microalgal genomics

CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii

Genome editing is crucial for genetic engineering of organisms for improved traits, particularly in microalgae due to the urgent necessity for the next generation biofuel production. The most advanced CRISPR/Cas9 system is simple, efficient and accurate in some organisms; however, it has proven extremely difficult in microalgae including the model alga Chlamydomonas. We solved this problem by delivering Cas9 ribonucleoproteins (RNPs) comprising the Cas9 protein and sgRNAs to avoid cytotoxicity and off-targeting associated with vector-driven expression of Cas9. We obtained CRISPR/Cas9-induced mutations at three loci including MAA7, CpSRP43 and ChlM, and targeted mutagenic efficiency was improved up to 100 fold compared to the first report of transgenic Cas9-induced mutagenesis. Interestingly, we found that unrelated vectors used for the selection purpose were predominantly integrated at the Cas9 cut site, indicative of NHEJ-mediated knock-in events. As expected with Cas9 RNPs, no off-targeting was found in one of the mutagenic screens. In conclusion, we improved the knockout efficiency by using Cas9 RNPs, which opens great opportunities not only for biological research but also industrial applications in Chlamydomonas and other microalgae. Findings of the NHEJ-mediated knock-in events will allow applications of the CRISPR/Cas9 system in microalgae, including safe harboring techniques shown in other organisms.

CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii

Genome editing is crucial for genetic engineering of organisms for improved traits, particularly in microalgae due to the urgent necessity for the next generation biofuel production. The most advanced CRISPR/Cas9 system is simple, efficient and accurate in some organisms; however, it has proven extremely difficult in microalgae including the model alga Chlamydomonas. We solved this problem by delivering Cas9 ribonucleoproteins (RNPs) comprising the Cas9 protein and sgRNAs to avoid cytotoxicity and off-targeting associated with vector-driven expression of Cas9. We obtained CRISPR/Cas9-induced mutations at three loci including MAA7, CpSRP43 and ChlM, and targeted mutagenic efficiency was improved up to 100 fold compared to the first report of transgenic Cas9-induced mutagenesis. Interestingly, we found that unrelated vectors used for the selection purpose were predominantly integrated at the Cas9 cut site, indicative of NHEJ-mediated knock-in events. As expected with Cas9 RNPs, no off-targeting was found in one of the mutagenic screens. In conclusion, we improved the knockout efficiency by using Cas9 RNPs, which opens great opportunities not only for biological research but also industrial applications in Chlamydomonas and other microalgae. Findings of the NHEJ-mediated knock-in events will allow applications of the CRISPR/Cas9 system in microalgae, including "safe harboring" techniques shown in other organisms142561sciescopu