Evolutionary relationships of superoxide dismutases and glutamine synthetases from marine species of Alteromonas, Oceanospirillum, Pseudomonas and Deleya

Genome-enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats

As a young bacteriologist just launching my career during the early days of the 'microbial revolution' in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross-disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize 'wild' bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited 'How we did it' perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene- and genome-enabled surveys, and application of genome-guided, cultivation-independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!

Effect of Na + Concentration and Nutritional Factors on the Lag Phase and Exponential Growth Rates of the Marine Bacterium Deleya aesta and of Other Marine Species

Growth of the marine bacterium Deleya aesta in a succinate minimal medium showed increasingly long lag phases as Na + was decreased below the optimum (200 to 500 mM). The minimum Na + concentration permitting growth consistently was 15 mM. Supplementation of the medium with KHCO 3 (as a source of CO 2 ) or yeast extract, especially in combination, reduced the lag phase, increased the rate of exponential growth, and allowed growth at 8 mM Na + . KHCO 3 did not reduce the lag period but did increase the rate of exponential growth of Deleya venusta, Deleya pacifica , and Alteromonas haloplanktis 214. Yeast extract was active for all three. The effect of yeast extract on D. aesta could be reproduced by a mixture of amino acids approximating its amino acid composition. l -Alanine, l -aspartate, and l -methionine, in combination, were the most effective in reducing the lag phase, although not as effective as the complete mixture. Succinate, l -aspartate, and l -alanine were transported into the cells by largely independent pathways and oxidized at rates which were much lower at 10 than at 200 mM Na + . l -Methionine was transported at a low rate in the absence of Na + and at a higher rate at 10 mM but was not oxidized. Above 25 mM Na + , the rate of transport of the carbon source was not the rate-limiting step for growth. It is concluded that a combination of transportable carbon sources reduced the lag period and increased the rate of exponential growth because they can be taken up independently and at low Na + utilized simultaneously.

Bacteriocuprein superoxide dismutases in pseudomonads

Two new instances of the rare bacteriocuprein form of superoxide dismutase have been discovered in Pseudomonas diminuta and P. maltophilia. Each species contains a manganese superoxide dismutase as well. Eight other strains of Pseudomonas and Xanthomonas spp. lacked bacteriocupreins and contained either a manganese or an iron superoxide dismutase. Native molecular weights and isoelectric points were determined for all these bacterial dismutases. A monospecific polyclonal antibody was prepared against the bacteriocuprein from Photobacterium leiognathi; it was not cross-reactive with the bacteriocuprein from either Pseudomonas strain. Bacteriocupreins have previously been identified in only two procaryotes, P. leiognathi and Caulobacter crescentus. The discovery of the Pseudomonas bacteriocupreins reveals a broader distribution, raising the possibility that bacteriocupreins are a continuous line of descent among procaryotes and not isolated evolutionary occurrences, as previous data suggested.