Biogenic Phosphonate Utilization by Globally Distributed Diatom Thalassiosira pseudonana.

Phosphonates are a class of organic phosphorus (P) compounds that contribute ~25% of dissolved organic P. Recent studies reveal the important role of phosphonates mediated by prokaryotes in the marine P redox cycle. However, its bioavailability by eukaryotic phytoplankton is under debate. 2-Aminoethylphosphonic acid (2-AEP) and 2-amino-3-phosphonopropionic acid (2-AP3) are two biogenic phosphonates in the marine environment. Here, Thalassiosira pseudonana, a common diatom species in the ocean, is able to recover growth from P starvation when provided with 2-AEP and 2-AP3. Moreover, 2-AEP cultures exhibited a more similar growth rate at 12 °C than at 25 °C when compared with inorganic P cultures. The cellular stoichiometry of 2-AEP groups was further determined, the values of which are in-between the P-depleted and DIP-replete cultures. This study provides evidence that biogenic phosphonates could be adopted as alternative P sources to support diatom growth and may provide physiological adaptation.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects.

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

An ancient enzyme finds a new home: Prevalence and neofunctionalization of trypsin in marine phytoplankton.

Trypsin is an ancient protease best known as a digestive enzyme in animals, and traditionally believed to be absent in plants and protists. However, our recent studies have revealed its wide presence and important roles in marine phytoplankton. Here, to gain a better understanding on the importance of trypsin in phytoplankton, we further surveyed the distribution, diversity, evolution and potential ecological roles of trypsin in global ocean phytoplankton. Our analysis indicated that trypsin is widely distributed both taxonomically and geographically in marine phytoplankton. Furthermore, by systematic comparative analyses we found that algal trypsin could be classified into two subfamilies (trypsin I and trypsin II) and exhibited highly duplicated and diversified during evolution. We also observed markedly different domain sequences and organizations between and within the subfamilies, suggesting potential neofunctionalization. Diatoms contain both subfamilies of trypsin, with higher numbers of genes and more environment-responsive expression of trypsin than other lineages. The duplication and subsequent neofunctionalization of the trypsin family may be important in diatoms for adapting to dynamical environmental conditions, contributing to diatoms' dominance in the coastal oceans. This work advances our knowledge on the distribution and neofunctionalization of this ancient enzyme and creates a new window of research on phytoplankton biology.

Roseovarius carneus sp. nov., a novel bacterium isolated from a coastal phytoplankton bloom in Xiamen.

A Gram-stain-negative, non-motile, ovoid or short rod shaped and aerobic marine bacterium, designated as strain LXJ103T, was isolated from a coastal phytoplankton bloom in Xiamen, PR China. Cells were oxidase- and catalase-positive. Strain LXJ103T grew at 4-40 °C (optimum, 28-37 °C), at pH 6-10 (optimum, pH 8.5) and with 1-15 % (w/v) NaCl (optimum, 3 %). The major cellular fatty acids (>10 %) were iso-C18 : 1 ω7c/iso-C18 : 1 ω6c (70.2 %) and C16 : 0 (10.3 %). The following polar lipids were found to be present: phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and five unknown glycolipids. The predominant respiratory quinone was ubiquinone-10. Strain LXJ103T exhibited the highest 16S rRNA gene sequence similarity to Roseovarius litorisediminis D1-W8T (96.97 %). The phylogenetic trees based on 16S rRNA gene sequences showed that strain LXJ103T was a member of the genus Roseovarius. The draft genome size of strain LXJ103T is 3.05 Mb with a genomic G+C content of 61.22 mol%. The digital DNA-DNA genome hybridization value of strain LXJ103T compared with the most similar type strain R. litorisediminis CECT 8287T was 18.80 %. The average nucleotide identity value between strain LXJ103T and R. litorisediminis CECT 8287T was 72.60 %. On the basis of polyphasic data, strain LXJ103T represents a novel species of the genus Roseovarius, for which the name Roseovarius carneus sp. nov. is proposed. The type strain is LXJ103T (=CGMCC 1.19168T=MCCC 1K06527T=JCM 34778T).

Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton.

Trypsin is best known as a digestive enzyme in animals, but remains unexplored in phytoplankton, the major primary producers in the ocean. Here we report the prevalence of trypsin genes in global ocean phytoplankton and significant influences of environmental nitrogen (N) and phosphorus (P) on their expression. Using CRISPR/Cas9 mediated-knockout and overexpression analyses, we further reveal that a trypsin in Phaeodactylum tricornutum (PtTryp2) functions to repress N acquisition, but its expression decreases under N-deficiency to promote N acquisition. On the contrary, PtTryp2 promotes phosphate uptake per se, and its expression increases under P-deficiency to further reinforce P acquisition. Furthermore, PtTryp2 knockout led to amplitude magnification of the nitrate and phosphate uptake 'seesaw', whereas PtTryp2 overexpression dampened it, linking PtTryp2 to stabilizing N:P stoichiometry. Our data demonstrate that PtTryp2 is a coordinate regulator of N:P stoichiometric homeostasis. The study opens a window for deciphering how phytoplankton adapt to nutrient-variable marine environments.

Physiological and metabolic effects of glyphosate as the sole P source on a cosmopolitan phytoplankter and biogeochemical implications.

Nutrient conditions influence the physiology and stoichiometry of marine phytoplankton. While extensive studies have documented the effects of abundances and types of nutrients such as nitrogen (N) and phosphorus (P), the effect of phosphonates as a P source is less understood and underexplored. Here, with the cosmopolitan coccolithophorid Emiliania huxleyi as a model phytoplankter, we investigated the effect of the phosphonate type of herbicide glyphosate as the sole P source in comparison with the P-depleted and P-replete (with 36 µM dissolved inorganic phosphate [DIP]) cultures. We measured changes in cellular C (carbon):P and N:P ratios and physiological performance and documented the corresponding transcriptomic and miRNAomic responses in E. huxleyi to glyphosate treatment. We found that glyphosate supported population growth but not to the full scale relative to DIP, and this was under the concerted regulation of DNA replication and cell cycle arrest genes as well as the growth-regulating miRNA. Furthermore, our data suggest that E. huxleyi took up glyphosate directly, bypassing extracellular hydrolysis, and this involved ABC transporters. Meanwhile, glyphosate-grown cultures displayed marked increases in cellular particulate organic C (POC) and PON contents, cell size, and transcription of genes for CO2 fixation and citrate cycle, nitrate transport, and protein biosynthesis. However, compared to DIP, the maximum absorption rate of glyphosate was only 33%, and glyphosate-grown E. huxleyi cells exhibited a mild P-stress symptom and elevated cellular C:P and N:P ratios. Interestingly, glyphosate-grown cells showed an increased sinking rate, suggesting that glyphosate as the sole P source might enhance the efficiency of C export by E. huxleyi, which would compensate for the expected decline in primary productivity (and hence carbon efflux) in the future more nutrient-depleted ocean. This biogeochemical implication needs to be further studied and verified, however.

Yeosuana marina sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island.

A novel Gram-stain-negative, non-flagellated, non-motile, rod-shaped (0.4-0.6×1.8-2.5 µm), aerobic bacterial strain, designated JLT21T, was isolated from seawater of a shallow-sea hydrothermal system. Growth occurred with 0-4.0 % (w/v) NaCl (optimum, 2.0 % NaCl), at 8-45 °C (optimum, 25 °C) and at pH 3.0-10.0 (optimum, pH 7.0). Analysis of 16S rRNA gene sequences revealed that strain JLT21T showed the highest 16S rRNA gene sequence similarity to Gaetbulibacter aquiaggeris KEM-8T (97.2 %), Gaetbulibacter marinus IMCC1914T (96.9 %) and Yeosuana aromativorans GW1-1T (96.9 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JLT21T clustered with Y. aromativorans GW1-1T. The predominant respiratory quinone of strain JLT21T was menaquinone-6 (MK-6). Polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids and four unidentified lipids. The major fatty acids of strain JLT21T were iso-C15 : 0 (21.7 %), C16 : 1 ω6c/ω7c (11.5 %) and iso-C17 : 0 3-OH (10.9 %). The DNA G+C content of strain JLT21T was 32.6 %. On the basis of polyphasic analysis, strain JLT21T is considered to represent a novel species of the genus Yeosuana, for which the name Yeosuana marina sp. nov. is proposed. The type strain of Yeosuana marina is JLT21T (=CGMCC 1.15787T=JCM 31511T). The study helps us better understand the bacterial species in the shallow-sea hydrothermal system and their adaptations to the hydrothermal environment.

Draft Genome Sequence of Pelagicola sp. Strain LXJ1103, Isolated from Coastal Surface Seawater.

Pelagicola sp. strain LXJ1103, a representative of a new species in the family Rhodobacteraceae, was isolated from the coastal surface waters in Xiamen, China. Here, we announce the draft genome sequence and initial findings from a preliminary analysis of strain LXJ1103.