Extremophiles - Research Projects

Importance of oligotrophic microbial food webs Open water systems, including lakes and the oceans, cover the majority of the surface of Earth, and provide primary forces for driving the processes essential to maintain our planet in a habitable state. The oceans, which have the highest cellular production rate of any ecosystem on the planet, are vast oligotrophic environment. Despite the low level of nutrients in oligotrophic ocean waters, microbial numbers persist on the order of 0.5 – 5 x 10^5 cells mL-1. As a result, marine microorganisms contribute a large proportion of the world’s biosphere in terms of carbon, nitrogen and phosphorous.

Furthermore, of the three largest microbial habitats (seawater, soil and sediment-soil subsurface), the rates of cellular activity and turnover are highest in the open ocean. In this oligotrophic environment, prokaryotes dominate in terms of biomass and play an essential role in regulating the accumulation, export, re-mineralisation and transformation of the world’s largest pool of organic carbon. The fixation of carbon, nitrogen and phosphorus by bacteria, and their conversion into particulate matter forms the basis of the microbial food web in the oceans. While these are critically important processes in aquatic environments, they are poorly characterised.

There are global consequences for these microbial processes since the downward flow of particles is the most efficient means of transporting CO2 fixed by primary production to marine sediments, thus sequestering it from the atmosphere. The balance between particle degradation, regenerating CO2 via respiration, and burial, is a critical factor affecting climate change, and increases in ocean oligotrophy are forcast as a consequence of global warming. It is clear that we must increase our understanding of the genetic make-up and eco/physiology of the important classes of marine bacteria. Gaining this understanding is critical for future predictive modelling studies of interdependent marine ecosystems, ranging from zoo- and phytoplankton to fish and whales.

Sphingopyxis alaskensis
Sphingopyxis alaskensis (formerly Sphingomonas alaskensis) was isolated as one of the most numerically abundant bacteria from Alaskan waters, the North Sea and the North Pacific over a period spanning ten years, indicating that it is a major contributor to microbial biomass in oligotrophic marine waters. Characteristics that promote S. alaskensis as a model oligotroph include a constant ultramicro-size (<0.1 µm³), irrespective of whether it is growing or starved, that provides it with a mechanism for avoiding predation, and a high surface to volume ratio to enhance nutrient uptake. This is coupled with the ability to utilize low concentrations of nutrients using high affinity, broad specificity uptake systems (e.g. highest rates of alanine transport for any bacterium reported to date) and the ability to simultaneously take up mixed substrates. Based on the Michaelis-Menten constants for substrate transport (Kt) and the available concentrations of mixed amino acids in the ocean, S. alaskensis is predicted to have an in situ doubling time equivalent to experimentally determined doubling times for microorganisms in oligotrophic waters.

A model for laboratory studies
As a result of its importance, studies by the international community aimed at understanding the basis of microbial oligotrophy have focused on S. alaskensis. In particular, we have shown (see publications) that its capacity to thrive in oligotrophic environments is linked to unique genetic and physiological properties. The properties of this model oligotroph are fundamentally different to those of the well studied bacteria such as Escherichia coli or marine Vibrio species. Unlike the laboratory environment, most natural environments are nutrient-limited. S. alaskensis is a rare resource for probing microbial adaptation to oligotrophy.

Minimum size limits of life
S. alaskensis is an “ultramicrobacterium” with a cell volume of less than 0.1 µm³. Cells of this size (including nanobacteria) have been reported in a range of aquatic, terrestrial and clinical samples, and in fossils; many of which are controversial. The reports have raised questions about the minimum size of a free-living cell. This has prompted, for example, a workshop by the US National Academy of Sciences to discuss the size limits of very small microorganisms. The astrobiology community has been particularly interested, as the minimum cell-size has important implications for cellular evolution and for the search for extraterrestrial life (see publications). With its well characterised physiology and genetics, S. alaskensis is an excellent model system for studying the minimum size limits for cellular life.