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201.
Juan José Pierella Karlusich Eric Pelletier Lucie Zinger Fabien Lombard Adriana Zingone Sébastien Colin Josep M. Gasol Richard G. Dorrell Nicolas Henry Eleonora Scalco Silvia G. Acinas Patrick Wincker Colomban de Vargas Chris Bowler 《Molecular ecology resources》2023,23(1):16-40
Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities. 相似文献
202.
Total DNA was isolated from 10 species of microalgae, including representatives of the Chlorophyceae (Chlorella ellipsoidea, Chlamydomonas reinhardtii, and Monoraphidium minutum), Bacillariophyceae (Cyclotella cryptica, Navicula saprophila, Nitzschia pusilla, and Phaeodactylum tricornutum), Charophyceae (Stichococcus sp.), Dinophyceae (Crypthecodinium cohnii), and Prasinophyceae (Tetraselmis suecica). Control samples of Escherichia coli and calf thymus DNA were also analyzed. The nucleoside base composition of each DNA sample was determined by reversed-phase high performance liquid chromatography. All samples contained 5-methyldeoxycytidine, although at widely varying levels. In M. minutum, about one-third of the cytidine residues were methylated. Restriction analysis supported this high degree of methylation in M. minutum and suggested that methylation is biased toward 5′-CG dinucleotides. The guanosine + cytosine (GC) contents of the green algae were, with the exception of Stichococcus sp., consistently higher than those of the diatoms. Monoraphidium minutum exhibited an extremely high GC content of 71%. Such a value is rare among eukaryotic organisms and might indicate an unusual codon usage. This work is important for developing strategies for transformation and gene cloning in these algae. 相似文献
203.
A virus infection is described within the unilocular sporangia of Feldmannia sp., a filamentous brown alga (Phaeophyceae). The alga is easily maintained in culture and vegetative growth is vigorous, but formation of icosahedral virions 150 nm in diameter completely displaces production of zoospores. The viruses, estimated at 1–5 × 106 per sporangium, are eventually released by rupture of the sporangial wall. Deoxyribonucleic acid (DNA) isolated from the viruses can be readily digested with restriction endonucleases and consists of ca. 170 kbp of double-stranded DNA. 相似文献
204.
205.
Effect of Planting Unit Size and Sediment Stabilization on Seagrass Transplants in Western Australia 总被引:2,自引:0,他引:2
Abstract The effect of increasing planting unit size and stabilizing sediment was examined for two seagrass planting methods at Carnac Island, Western Australia in 1993. The staple method (sprigs) was used to transplant Amphibolis griffithii (J. M. Black) den Hartog and the plug method was used to transplant A. griffithii and Posidonia sinuosa Cambridge and Kuo. Transplant size was varied by increasing the number of rhizomes incorporated into a staple and increasing the diameter of plugs. Planting units were transplanted into bare sand, back into the original donor seagrass bed, or into a meadow of Heterozostera tasmanica, which is an important colonizing species. Sprigs of A. griffithii were extracted from a monospecific meadow; tied into bundles of 1, 2, 5, and 10 rhizomes; and planted into unvegetated areas. Half the units were surrounded by plastic mesh and the remainder were unmeshed. All treatments were lost within 99 days after transplanting, and although larger bundles survived better than smaller ones, no significant differences could be attributed to the effects of mesh or sprig size. Plugs of P. sinuosa and A. griffithii were extracted from monospecific meadows using polyvinyl chloride pipe of three diameters, 5, 10, and 15 cm, and planted into unvegetated areas nearby. Half the units were surrounded by plastic mesh and the remainder were unmeshed. Posidonia sinuosa plugs were also placed within a meadow of H. tasmanica (Martens ex Aschers.) den Hartog. Only 60% of A. griffithii plug sizes survived 350 days after transplanting back into the donor bed; however, survival of transplants at unvegetated areas varied considerably, and analysis of variance indicated a significant two‐way interaction between treatment and plug size. Transplants survived better when meshed (90% survived) and survival improved with increasing plug size. Posidonia sinuosa transplants survived poorly (no plugs survived beyond 220 days in bare or meshed treatments) regardless of size. Survival of 10‐ and 15‐cm plugs was markedly better than the 5‐cm plugs in vegetated areas, including the H. tasmanica meadow. The use of large seagrass plugs may be appropriate for transplantation in high‐energy wave environments. 相似文献
206.
Elisabeth Grohmann Günther Muth Manuel Espinosa 《Microbiology and molecular biology reviews》2003,67(2):277-301, table of contents
Conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. Thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. While conjugation in gram-negative bacteria has been studied in great detail over the last decades, the transfer mechanisms of antibiotic resistance plasmids in gram-positive bacteria remained obscure. In the last few years, the entire nucleotide sequences of several large conjugative plasmids from gram-positive bacteria have been determined. Sequence analyses and data bank comparisons of their putative transfer (tra) regions have revealed significant similarities to tra regions of plasmids from gram-negative bacteria with regard to the respective DNA relaxases and their targets, the origins of transfer (oriT), and putative nucleoside triphosphatases NTP-ases with homologies to type IV secretion systems. In contrast, a single gene encoding a septal DNA translocator protein is involved in plasmid transfer between micelle-forming streptomycetes. Based on these clues, we propose the existence of two fundamentally different plasmid-mediated conjugative mechanisms in gram-positive microorganisms, namely, the mechanism taking place in unicellular gram-positive bacteria, which is functionally similar to that in gram-negative bacteria, and a second type that occurs in multicellular gram-positive bacteria, which seems to be characterized by double-stranded DNA transfer. 相似文献
207.
Contribution of pilA to Competitive Colonization of the Squid Euprymna scolopes by Vibrio fischeri
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Vibrio fischeri colonizes the squid Euprymna scolopes in a mutualistic symbiosis. Hatchling squid lack these bacterial symbionts, and V. fischeri strains must compete to occupy this privileged niche. We cloned a V. fischeri gene, designated pilA, that contributes to colonization competitiveness and encodes a protein similar to type IV-A pilins. Unlike its closest known relatives, Vibrio cholerae mshA and vcfA, pilA is monocistronic and not clustered with genes associated with pilin export or assembly. Using wild-type strain ES114 as the parent, we generated an in-frame pilA deletion mutant, as well as pilA mutants marked with a kanamycin resistance gene. In mixed inocula, marked mutants were repeatedly outcompeted by ES114 (P < 0.05) but not by an unmarked pilA mutant, for squid colonization. In contrast, the ratio of mutant to ES114 CFUs did not change during 70 generations of coculturing. The competitive defect of pilA mutants ranged from 1.7- to 10-fold and was more pronounced when inocula were within the range estimated for V. fischeri populations in Hawaiian seawater (200 to 2,000 cells/ml) than when higher densities were used. ES114 also outcompeted a pilA mutant by an average of twofold at lower inoculum densities, when only a fraction of the squid became infected, most by only one strain. V. fischeri strain ET101, which was isolated from Euprymna tasmanica and is outcompeted by ES114, lacks pilA; however, 11 other diverse V. fischeri isolates apparently possess pilA. The competitive defect of pilA mutants suggests that cell surface molecules may play important roles in the initiation of beneficial symbioses in which animals must acquire symbionts from a mixed community of environmental bacteria. 相似文献
208.
Tressia M. Dayton Karen A. Diefenbach Michelle L. Fuller Joshua Valtos Eric C. Niederhoffer 《Biometals》1996,9(2):131-137
Proteus mirabilis and Proteus vulgaris expressed a combination of superoxide dismutase (Sod) activities, which was assigned to FeSod1, FeSod2 and MnSod for P. mirabilis, and FeSod, MnSod and CuZnSod for P. vulgaris. Production of the Sod proteins was dependent on the availability of iron, whether cells were grown under anaerobiosis or aerobiosis and growth phase. Nalidixic acid and chloramphenicol inhibited cell growth and the iron- and dioxygen-dependent production of Sod. These results support the involvement of metal ions and redox status in the production of Proteus Sods. 相似文献
209.
Jan Oscarsson Yoshimitsu Mizunoe Bernt Eric Uhlin David J. Haydon 《Molecular microbiology》1996,20(1):191-199
The Salmonella typhimurium protein SlyAST, originally described as a cytolysin, shows sequence similarities to several known bacterial regulatory proteins. A homologue to the slyASt gene has been localised to min 37 of the Eschericia coli K-12 chromosome and has been designated slyAEC When introduced in trans on a plasmid, the slyAEC gene conferred a haemolytic phenotype on wild-type but not clyA-knockout strains of E. coli K-12. The clyA gene encodes a novel haemolysin that is not expressed by wild-type E. coli under tested laboratory conditions. Western and Northern blot analyses, and DNA-band-shift assays support a model whereby the SlyAEC protein activates clyA expression by binding to the clyA promoter region, thereby supporting the sequence similarity data in suggesting that SlyAST is a haemolysin activator rather than being a haemolysin per se. 相似文献
210.
Two species of diatoms were genetically transformed by introducing plasmid vectors containing the Escherichia coli neomycin phosphotransferase II (npt II ) gene. Expression of the bacterial npt II gene in the diatoms was achieved using the putative promoter and terminator sequences from the acetyl-CoA carboxylase gene from the centric diatom Cyclotella cryptica T13L Reimann, Lewin, and Guillard. The vectors were introduced into C. cryptica and the pennate diatom Navicula saprophila NAVIC1 Lange-Bertalot and Bonik by microprojectile bombardment. Putative transformants were selected based on their ability to grow in the presence of the antibiotic G418, and production of the neomycin phosphotransferase protein by the transformed cells was confirmed by western blotting. The foreign DNA integrated into one or more random sites within the genome of the transformed algal cells, often in the form of tandem repeats. This is the first report of reproducible, stable genetic transformation of a chlorophyll c -containing alga . 相似文献