From sequences to enzymes: comparative genomics to study evolutionary conserved protein functions in marine microbes

Comparative genomics is a research field that allows comparison between genomes of different life forms providing information on the organization of the compared genomes, both in terms of structure and encoded functions. Moreover, this approach provides apowerful tool to study and understand the evolutionary changes and adaptation among organisms. Comparative genomics can be used to compare phylogenetically close marine organisms showing different vital strategies and lifestyles and obtain information regarding specific adaptations and/or their evolutionary history. Here we report a basic comparative genomics protocol to extrapolate evolutionary information about a protein of interest conserved across diverse marine microbes. The outlined approach can be used in a number of different settings and might help to gain new insight into the evolution and adaptation of marine microorganisms.

From sequences to enzymes: heterologous expression of genes from marine microbes

Heterologous expression is an easy and broadly applicable experimental approach widely used to investigate protein functions without the need to genetically manipulate the original host. The approach is used to obtain large quantities of the desired protein, which can be further analyzed from a biochemical, structural and functional perspective. The expression system consists of three main components: i) a foreign DNA sequence coding for the protein of interest; ii) a suitable expression vector; iii) a suitable host (bacterial, yeast or mammalian cells) which does not encode or express the protein of interest. Here we show how to apply an Escherichia coli-based expression system to overexpress protein encoding genes from marinemicrobes.

Exploring bioactive pigments from marine bacterial isolate from the Indonesian seas

Marine microbes offer a significant source for biodiscovery due to their rich biodiversity and genetic capacity. Particularly, microbial pigments of marine origin are getting more attention in current research due to their widely perceived application as natural food colorants, antioxidant, antimicrobial, and many more. In the past five years, our research group has successfully characterised various bioactive pigments isolated from marine bacteria, including Erythrobacter flavus strain KJ5 that produces unique sulphur-containing carotenoids, Pseudoalteromonas rubra strain PS1 and SB14 that contain antimicrobial prodiginine, and Seonamhaeicola algicola strain CCI for high content of zeaxanthin. This paper describes the challenges we encountered in conducting research in exploring bioactive pigments especially with focus on carotenoid research, reviewed critically on strategy we developed for isolation of isolate as well as identification and elucidation of the pigments, and consideration for future research.

Depth- and temperature-specific fatty acid adaptations in ctenophores from extreme habitats

Animals are known to regulate the composition of their cell membranes to maintain key biophysical properties in response to changes in temperature. For deep-sea marine organisms, high hydrostatic pressure represents an additional, yet much more poorly understood, perturbant of cell membrane structure. Previous studies in fish and marine microbes have reported correlations with temperature and depth of membrane-fluidizing lipid components, such as polyunsaturated fatty acids. Because little has been done to isolate the separate effects of temperature and pressure on the lipid pool, it is still not understood whether these two environmental factors elicit independent or overlapping biochemical adaptive responses. Here, we use the taxonomic and habitat diversity of the phylum Ctenophora to test whether distinct low-temperature and high-pressure signatures can be detected in fatty acid profiles. We measured the fatty acid composition of 105 individual ctenophores, representing twenty-one species, from deep and shallow Arctic, temperate, and tropical sampling locales (sea surface temperature -2° to 28° C). In tropical and temperate regions, remotely operated submersibles (ROVs) enabled sampling down to 4000 meters. Among specimens with body temperatures 7.5°C or colder, depth predicted fatty acid unsaturation level. In the upper 200 m of the water column, temperature predicted fatty acid chain length. Taken together, our findings suggest that lipid metabolism may be specialized with respect to multiple physical variables in diverse marine environments. Largely distinct modes of adaptation to depth and cold imply that polar marine invertebrates may not find a ready refugium from climate change in the deep.

Carbapenem Resistance among Marine Bacteria—An Emerging Threat to the Global Health Sector

The emergence of antibiotic resistance among pathogenic microorganisms is a major issue for global public health, as it results in acute or chronic infections, debilitating diseases, and mortality. Of particular concern is the rapid and common spread of carbapenem resistance in healthcare settings. Carbapenems are a class of critical antibiotics reserved for treatment against multidrug-resistant microorganisms, and resistance to this antibiotic may result in limited treatment against infections. In addition to in clinical facilities, carbapenem resistance has also been identified in aquatic niches, including marine environments. Various carbapenem-resistant genes (CRGs) have been detected in different marine settings, with the majority of the genes incorporated in mobile genetic elements, i.e., transposons or plasmids, which may contribute to efficient genetic transfer. This review highlights the potential of the marine environment as a reservoir for carbapenem resistance and provides a general overview of CRG transmission among marine microbes.

Trade-off between competition ability and invulnerability to predation in marine microbes; protist grazing versus viral lysis effects

Trade-offs between competition ability and invulnerability to predation are important mechanisms explaining how predation promotes bacterial diversity. However, existence of these trade-offs has apparently not been investigated in natural marine bacterial communities. Here, we address this question with growth-based measurements for each marine bacterial taxon by conducting on-board dilution experiments to manipulate predation pressure and using high-throughput sequencing to assess the response of bacterial communities. We determined that bacterial taxa with a higher predation-free growth rate were accompanied with higher predation-caused mortality, supporting existence of competitiveness-invulnerability trade-off. This trade-off was stronger and more consistent under viral lysis than protist grazing. In addition, predation generally flattened out the rank-abundance distribution and increased the evenness and richness of the bacterial community. These findings supported the 'Kill-the-Winner' hypothesis. All experiments supported a significant competitiveness-invulnerability trade-off, but there was substantial variation among bacterial communities in response to predation across experiments conducted in various sites and seasons. Therefore, we inferred that the Kill-the-Winner hypothesis is important but likely not the only deterministic mechanism explaining how predation shapes bacterial assemblages in natural marine systems.

Biodiversity of marine microbes is safeguarded by phenotypic heterogeneity in ecological traits

Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both phenomena by investigating a non-cooperative game that interpolates between individual-level competitions and species-level outcomes. We identified all equilibrium strategies of the game. These strategies represent the probability distribution of competitive abilities (e.g. traits) and are characterized by maximal phenotypic heterogeneity. They are also neutral towards each other in the sense that an unlimited number of species can co-exist while competing according to the equilibrium strategies. Whereas prior theory predicts that natural selection would minimize trait variation around an optimum value, here we obtained a mathematical proof that species with maximally variable traits are those that endure. This discrepancy may reflect a disparity between predictions from models developed for larger organisms in contrast to our microbe-centric model. Rigorous mathematics proves that phenotypic heterogeneity is itself a mechanistic underpinning of microbial diversity. This discovery has fundamental ramifications for microbial ecology and may represent an adaptive reservoir sheltering biodiversity in changing environmental conditions.