The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

https://pubs.rsc.org/en/content/articlepdf/2019/NP/C8NP00092A

Marine natural products.

If stretched end to end, the estimated 1030viruses in the oceans would span farther than the nearest 60 galaxies. This reservoir of genetic and biological diversity continues to yield exciting discoveries and, in this Review, Curtis A. Suttle highlights the areas that are likely to be of greatest interest in the next few years. Viruses are by far the most abundant 'lifeforms' in the oceans and are the reservoir of most of the genetic diversity in the sea. The estimated 1030 viruses in the ocean, if stretched end to end, would span farther than the nearest 60 galaxies. Every second, approximately 1023 viral infections occur in the ocean. These infections are a major source of mortality, and cause disease in a range of organisms, from shrimp to whales. As a result, viruses influence the composition of marine communities and are a major force behind biogeochemical cycles. Each infection has the potential to introduce new genetic information into an organism or progeny virus, thereby driving the evolution of both host and viral assemblages. Probing this vast reservoir of genetic and biological diversity continues to yield exciting discoveries.

Marine viruses — major players in the global ecosystem

http://aerg.canberra.edu.au/library/sex_general/2002_Devlin_Nagahama_sex_determination_in_fish_review.pdf

Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences

There is an urgent need in aquaculture to develop microbial control strategies, since disease outbreaks are recognized as important constraints to aquaculture production and trade and since the development of antibiotic resistance has become a matter of growing concern. One of the alternatives to antimicrobials in disease control could be the use of probiotic bacteria as microbial control agents. This review describes the state of the art of probiotic research in the culture of fish, crustaceans, mollusks, and live food, with an evaluation of the results obtained so far. A new definition of probiotics, also applicable to aquatic environments, is proposed, and a detailed description is given of their possible modes of action, i.e., production of compounds that are inhibitory toward pathogens, competition with harmful microorganisms for nutrients and energy, competition with deleterious species for adhesion sites, enhancement of the immune response of the animal, improvement of water quality, and interaction with phytoplankton. A rationale is proposed for the multistep and multidisciplinary process required for the development of effective and safe probiotics for commercial application in aquaculture. Finally, directions for further research are discussed.

/pdf/probiotic-bacteria-as-biological-control-agents-in-4778jdx241.pdf

Probiotic Bacteria as Biological Control Agents in Aquaculture

A survey of antibiotic-producing bacteria from the microbial flora attached to seaweeds and the study of their antibiotic capacities were carried out From 5 species of green and brown marine algae, 224 bacterial strains were isolated and tested for antibiotic production A total of 38 strains displayed antibiotic activity, withEnteromorpha intestinalis being the source of the highest number of producer strains All epiphytic bacteria with antibiotic activity were assigned to thePseudomonas-Alteromonas group Antagonism assays among the isolates demonstrated that each producer strain inhibits the growth of the other producers, as well as of some nonproducer strains also isolated from seaweeds Likewise, an autoinhibitory effect was observed in all antibiotic-producing strains Antibacterial spectra of all the strains include activity againstStaphylococcus, Alcaligenes, Pseudomonas, Vibrio, Pasteurella, andAchromobacter A preliminary characterization of the antibiotic substances produced by these epiphytic bacteria demonstrated that they are low molecular weight compounds, thermolabile, and anionic and are not affected by proteolytic enzymes The role that these inhibitory substances can play in the natural environment is discussed

Antibiotic activity of epiphytic bacteria isolated from intertidal seaweeds

The activity of antibiotic-producing marine bacteria was assayed against bacterial fish pathogens belonging to the genera Vibrio, Aeromonas, Pasteurella, Edwardsiella, Yersinia and Pseudomonas with the aim of evaluating the possible use of these marine strains for controlling epizootics in aquaculture. Inhibition tests on solid medium showed that, in general, the majority of fish bacteria were strongly sensitive to the marine bacteria. Only two strains (Edwardsiella tarda and Pseudomonas aeruginosa), were resistant to all the antibiotic-producing strains. The results of antagonism assays in sea water, however, varied according to the fish pathogens examined. Experiments conducted using cell-free supernatant fluids of marine bacteria demonstrated the involvement of antibiotic substances in the inhibition of fish pathogens.

Inhibitory activity of antibiotic‐producing marine bacteria against fish pathogens

Pasteurellosis in cultured gilthead seabream (Sparus aurata): first report in Spain.

A review of the literature shows that although the number of serotypes of Vibrio anguillarum reported from different countries varies, most of the vibriosis outbreaks throughout the world are caused by only 2 serotypes: 01 and 0 2 (European serotype designation). The remaining serotypes, associated mainly with environmental samples such as water, sediment, phytoand zooplankton, are generally non-pathogenic to fish. This raises the question as to whether the 2 major pathogenic serotypes of V. anguillarum (isolated only from diseased or carrier fish) should be considered opportunistic or obligate fish pathogens. In addition, information useful in epizootiological and vaccination studies is presented about the antigenic heterogeneity detected within serotype 0 2 . In this review, emphasis is placed on the presence in the marine environment of vibrios (presumptively assigned to the V. splendidus and V. pelagius) species that are taxonomically and serologically related with V. anguillarum and some of which have been associated with disease in fish cultured on the Atlantic coast of Spain and Norway. The precise phylogenetic position of these V. anguillarum-like organisms are well as their actual threat to marine aquaculture remains to be clarified.

/pdf/a-review-of-the-taxonomy-and-seroepizootiology-of-vibrio-49rw68g6bo.pdf

A review of the taxonomy and seroepizootiology of Vibrio anguillarum, with special reference to aquaculture in the northwest of Spain

The biological activities in vivo and in vitro of 59 motile Aeromonas spp. isolated from fish and water tanks were simultaneously analyzed in poikilothermic and homoiothermic systems. A total of 64.3% of the isolates tested were pathogenic for fish, and 62% of Aeromonas hydrophila and A. sobria isolates either virulent or nonvirulent for fish were enterotoxigenic. Although the majority of the strains were proteolytic and amylolytic and produced DNase, other activities, such as elastase and staphylolysis, were only present in A. hydrophila. Most of the strains (96%) produced hemolysins, and 68% had agglutinating capacity, but neither isolates pathogenic for fish nor enterotoxigenic isolates showed specificity for trout or human erythrocytes, respectively. The production of siderophores, agglutination in acriflavine, and precipitation after boiling were found not to be useful tests for screening virulent strains. Although statistical analysis revealed a significant relationship between virulence for fish and positive results for arabinose and sucrose fermentations, elastase, and hemolysis of human erythrocytes, only lysine decarboxylase showed a significant positive relationship with enterotoxigenicity. Using extracellular products from representative Aeromonas strains with different virulence markers and belonging to distinct O serogroups, we demonstrated a lack of correlation between cytotoxicity for fish and homoiothermic cell lines and pathogenicity. The extracellular products from selected pathogenic A. hydrophila strains were lethal for rainbow trout and displayed proteolytic, hemolytic, and cytotoxic activities which were simultaneously lost after heat treatment. The findings reported here indicate that it is not possible to establish a common and single mechanism involved in the invasion of Aeromonas spp. in poikilothermic and homoiothermic hosts. Images

Juan L. Barja

Papers

Antibiotic activity of epiphytic bacteria isolated from intertidal seaweeds

Inhibitory activity of antibiotic‐producing marine bacteria against fish pathogens

Pasteurellosis in cultured gilthead seabream (Sparus aurata): first report in Spain.

A review of the taxonomy and seroepizootiology of Vibrio anguillarum, with special reference to aquaculture in the northwest of Spain

Virulence properties and enterotoxin production of Aeromonas strains isolated from fish.