Promiscuous community reveals hidden values

Molecular genetic techniques are providing Antarctic scientists with novel ways of investigating global questions about ecosystem structure and function.

The techniques allow scientists to unlock previously hidden values in Antarctic ecosystems, providing information that will assist in their future protection. They could also lead to new discoveries relevant to human health, industries such as food production or cleaning, and our search for life on other planets.

A case in point is the recent work of a team led by Professor Rick Cavicchioli, from the University of New South Wales, in collaboration with other Australian and American research institutions and support from the Australian Antarctic Division.

Using ‘metagenomics’ (genome sequencing of an entire environmental sample, such as a lake or marine microbial community), Professor Cavicchioli has created a detailed ecological picture of the microbial community in the isolated and hypersaline Deep Lake in the Vestfold Hills near Davis.

Deep Lake was formed about 3500 years ago when the Antarctic continent rose, isolating a section of the ocean. The water is now so salty it remains liquid down to −20°C and almost nothing is able to grow in it.

Research by Antarctic Division scientists and others at Deep Lake in the 1980s identified halophilic (salt-loving) ‘archaea’ using culturing techniques. (Archaea represent a third ‘domain of life’ that evolved billions of years ago, which is distinct from the Bacteria and Eucarya domains). Individual genomes of these archaea species, and other species isolated more recently, were DNA sequenced. However, metagenomics enables a more rapid and expanded view of microbial diversity and the function of entire mixed communities. It also enables genome analysis of organisms that won’t grow in the laboratory.

Professor Cavicchioli’s team took water samples from Deep Lake at depths of 5, 13, 24 and 36 metres and performed metagenomics analysis of each sample, to learn about the microbial communities throughout the depth of the lake.

They found that the lake was completely and uniformly dominated by ‘haloarchaea’, with four distinct isolates comprising 72% of the microbial community. The isolates demonstrated a high rate of DNA exchange between each other, but retained genomic characteristics indicative of niche adaptation.

‘The Deep Lake community structure differs greatly from temperate and tropical hypersaline environments,’ Professor Cavicchioli said.

‘Not only are the types of haloarchaea different, but gene swapping occurs frequently between haloarchaea that are quite unrelated to each other; that is, gene exchange occurs between different genera, and not just between different species.

‘Despite this promiscuity, the dominant members of the community retain their own identity as a species and coexist with others, exploiting different niches without impinging on each other.’

Professor Cavicchioli said some of the microbes survive by consuming proteins in the water, while others consume sugars like glycerol, which is a by-product of algae living in the upper waters of the lake.

‘By choosing different food sources they can coexist and continue to reproduce and eke out a living in relative harmony,’ he said.

And the sharing of large amounts of genetic material could confer benefits such as resistance to viruses or an improved ability of the haloarchaea to respond to their environment.

Senior Australian Antarctic Division scientist Dr Martin Riddle, who leads a program that Professor Cavicchioli’s work contributes to, said the research has realised the value of Antarctic lakes as model systems for understanding ecosystem processes.

‘For decades, scientists have spoken of the potential value of Antarctic lakes as model systems for understanding global questions about biodiversity, its spread and its ubiquity or rarity, across the planet,’ Dr Riddle said.

‘Compared to penguins or mosses, the scientific value of a body of water is not obvious. But now metagenomics allows us to see how these types of ecosystems are structured and how they function. Now we can articulate the value of these lakes and how unique or common they are.

‘This information will also help us work out how to best protect these ecosystems and to select representative areas for protection.’

Dr Riddle said the work could also provide a reason for leaving some areas of Antarctica untouched.

‘The techniques Professor Cavicchioli is using were beyond our imaginings 15 years ago, so where will technology take us in another 15 or 50 years time?

‘Some areas of Antarctica may have scientific potential that we can’t access right now, but that new technologies will enable in the future. We don’t want to accidentally disturb what we can’t understand.’

Meanwhile, further research into extreme environments like Deep Lake could provide insights of relevance to astrobiology. As well as the haloarchaea in Deep Lake, which have adapted to life at low temperature, under highly saline and dehydrating conditions, another group of Archaea known as ‘methanogens’ grow in Ace Lake in the Vestfold Hills. Methanogens have been proposed as a kind of life that could live on Mars, due to their ability to grow under cold conditions, devoid of oxygen.

Professor Cavicchioli said enzymes from both haloarchaea and methanogens could be valuable for use in biosensors to assess whether biological reactions are occurring on other planets. The enzymes could also have value in industrial processes that need to occur at cold temperatures — such as food production or the clean-up of pollutants from contaminated sites in Antarctica.

‘Every time we poke an “-omics stick” into these amazing Antarctic systems we find things we never expected,’ he said.

The University of New South Wales scientific team is spending the next 12 months in Antarctica to continue research on microbial communities in three Vestfold Hills lakes — Ace Lake, Organic Lake and Deep Lake — and a nearshore marine location. The team will investigate how microbial communities change throughout a complete annual cycle.

‘Establishing what microbes do in different seasons will reveal which microbial processes change and how environmental perturbation will impact on normal ecological cycles in Antarctica,’ Professor Cavicchioli said.

‘This essential evidence-based knowledge will form the underpinnings for evaluating the effects of climate change on sensitive ecosystems in the Antarctic.’

Wendy Pyper
Corporate Communications, Australian Antarctic Division

More information

DeMaere MZ, Williams TJ et al. High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. PNAS (2013).

Sequencing secrets of whole microbial communities. Australian Antarctic Magazine 14: 8 (2008).