Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph

A variety of culture-independent techniques have been developed that can be used in conjunction with culture-dependent physiological and metabolic studies of key microbial organisms, in order to better understand how the activity of natural populations influences and regulates all major biogeochemical cycles. In this study, we combined DNA-stable isotope probing with metagenomics and metaproteomics to characterize an as yet uncultivated marine methylotroph that actively incorporated carbon from 13C-labeled methanol into biomass. By metagenomic sequencing of the heavy DNA, we retrieved virtually the whole genome of this bacterium and determined its metabolic potential. Through protein-stable isotope probing, the RuMP cycle was established as the main carbon assimilation pathway, and the classical methanol dehydrogenase-encoding gene mxaF, as well as three out of four identified xoxF homologues were found to be expressed. This proof-of-concept study is the first in which theculture-independent techniques of DNA- and protein-stable isotope probing have been used to characterize the metabolism of a naturally-ocurring Methylophaga-like bacterium in the marine environment (i.e. M. thiooxydans L4) and thus provides a powerful approach to access the genome and proteome of uncultivated microbes involved in key processes in the environment

Evolution of alternative biosynthetic pathways for vitamin C following plastid acquisition in photosynthetic eukaryotes.

Ascorbic acid (vitamin C) is an enzyme co-factor in eukaryotes that also plays a critical role in protecting photosynthetic eukaryotes against damaging reactive oxygen species derived from the chloroplast. Many animal lineages, including primates, have become ascorbate auxotrophs due to the loss of the terminal enzyme in their biosynthetic pathway, L-gulonolactone oxidase (GULO). The alternative pathways found in land plants and Euglena use a different terminal enzyme, L-galactonolactone dehydrogenase (GLDH). The evolutionary processes leading to these differing pathways and their contribution to the cellular roles of ascorbate remain unclear. Here we present molecular and biochemical evidence demonstrating that GULO was functionally replaced with GLDH in photosynthetic eukaryote lineages following plastid acquisition. GULO has therefore been lost repeatedly throughout eukaryote evolution. The formation of the alternative biosynthetic pathways in photosynthetic eukaryotes uncoupled ascorbate synthesis from hydrogen peroxide production and likely contributed to the rise of ascorbate as a major photoprotective antioxidant.

Does predation control adult sex ratios and longevities in marine pelagic copepods?

We assess the causes of adult sex ratio skew in marine pelagic copepods by examining changes in these ratios between the juveniles and adults, sexual differences in juvenile stage durations, and mortality rates of adults in the field and laboratory (when free from predators). In the field, late copepodite stages (CIV and CV) commonly have sex ratios that are either not significantly different from equity (1 : 1), or slightly male biased. By contrast, in adults, these ratios are commonly significantly biased toward female dominance. Sex ratio skews are therefore primarily attributable to processes in adults. Members of the non-Diaptomoidea have especially skewed adult ratios; in the members Oithonidae and Clausocalanidae this is not generated from differences between male and female adult physiological longevity (i.e., laboratory longevity when free of predators). In the genera Acartia, Oithona, and Pseudocalanus, we estimate that predation mortality contributed ≥ 69% of the field mortality rate in adult males, whereas in Acartia, Oithona, and Calanus adult females, this is ≥ 36%.We conclude that (1) adult sex ratio skew in pelagic copepods is primarily due to differential mortality of the sexes in the adult stage and not in juveniles, (2) mortality rates of adult Acartia, Pseudocalanus, and Oithona are dominated by predation mortality rather than physiological longevity (except under extreme food limitation), and (3) in Pseudocalanus and Oithona, elevated mortality rates in adult males to females is predominantly due to higher predation on males. Our work demonstrates that we now need to develop a more comprehensive understanding of the importance of feeding preferences in predators. Continue reading full article

Female-biased sex ratios in marine pelagic copepods: comment on Gusmao et al

Gusmão et al. (2013; Mar Ecol Prog Ser 482:279-298) review causes of sex ratio skew in pelagic copepods and in doing so repeatedly dispute the paper of Hirst et al. (2010) ‘Does predation control adult sex ratios and longevities in marine pelagic copepods?’ Here we respond to some important errors in their citation of our paper and briefly highlight where future work is needed in order to attribute the causes of strong sex ratio skew seen in some copepod families.

Quantitative pathways for Northeast Atlantic fisheries based on climate, ecological–economic and governance modelling scenarios

Here we present quantitative projections of potential futures for ecosystems in the North Atlantic basin generated from coupling a climate change-driven biophysical model (representing ecosystem and fish populations under climate change) and a scenario-driven ecological–economic model (representing fleets and industries under economic globalization). Four contrasting scenarios (Baseline, Fortress, Global Commons, Free Trade) were defined from the perspective of alternative regional management and governance of the oceanic basin, providing pathways for the future of ecosystems in the Northeast Atlantic basin by 2040. Results indicate that in the time frame considered: (1) the effects of governance and trade decisions are more significant in determining outcomes than the effects of climate change alone, (2) climate change is likely to result in a poleward latitudinal shift of species ranges and thus resources, with implications for exploitation patterns, (3) the level of fisheries regulation is the most important factor in determining the long term evolution of the fisheries system, (4) coupling climate change and governance impacts demonstrates the complex interaction between different components of this social–ecological system, (5) an important driver of change for the future of the North Atlantic and the European fishing fleets appears to be the interplay between wild fisheries and aquaculture development, and finally (6) scenarios demonstrate that the viability and profit of fisheries industries is highly volatile. This study highlights the need to explore basin-scale policy that combines medium to long-term environmental and socio-economic considerations, and the importance of defining alternative sustainable pathways.