What's in a niche? Time to rethink microbial ecology, say researchers

April 16, 2018

Scientists in Canada, the United States and Europe are looking to rewrite the textbook on microbial ecology, advocating a new approach to studying the most abundant form of life on Earth.

When it comes to microbe species, they argue, niche is much more important than names.

"Traditional ecology tells us species derive energy one way within an ecosystem--plant species convert light into chemical energy through photosynthesis, and animals burn organic carbon using oxygen to extract energy," explains University of British Columbia (UBC) scientist Stilianos Louca, who led the synthesis published in Nature Ecology and Evolution.

"But microbial systems have many more ways to get energy, and are highly redundant. Hundreds of species can co-exist and perform the same biochemical functions in one setting, and switch functions in a different setting."

The finding has major implications for interpreting changes in microbial communities or predicting their health--whether in the human gut, in engineered bio-refining processes, or during environmental perturbation or loss of diversity in the ocean.

"As researchers we need to decouple biochemical processes from taxonomic labels. And we need to refine, and update, our terminology to represent this decoupling, and we need new paradigms to interpret changes in microbial communities."

How do microbes come about this jack-of-all-trades redundancy? Based on an analysis of more than 59,000 sequenced microbial genomes, Louca and colleagues argue it's baked into the system--genes responsible for specific biochemical functions are widely and irregularly distributed across the microbial tree of life.

The researchers also ruled out another prevailing paradigm--that frequent and unpredictable fluctuations in microbial species composition are due to random birth and death events in small populations. What some researchers call 'ecological drift'.

"Our synthesis, and new computer simulations, show that view is likely wrong," says Louca. "We should be focusing on the largely unexplored biological interactions between organisms--such as predation by viruses or antibiotic warfare, that don't necessarily affect the major biogeochemical fluxes in the system."

The synthesis is based on microbial community research from the last two years, and involved researchers from UBC, the Massachusetts Institute of Technology, Simon Fraser University, the University of California, Woods Hole Oceanographic Institution, Massachusetts, and the Eidgenössische Technische Hochschule, Switzerland.

"Microbial ecosystems outside the lab can typically sustain a large number of taxa with the potential to perform the same metabolic functions, begging the question of how such apparently redundant species coexist," says Otto Cordero, an assistant professor at the Massachusetts Institute of Technology, who was not involved in the study.

"One possibility is that coexistence is maintained by neutral processes, such as demographic fluctuations. Another is that seemingly redundant taxa are differentiated in their 'micro-niches' based on fine-scale trait differences, such as attachment, motility, enzyme affinities. This research builds a strong case for the latter and presents a thoughtful discussion of its implications for the study of microbial ecosystems. An important corollary of this paper is the need to group taxa into functional units, similar to how trait-based ecology groups plants in guilds."
The work was funded by the Canadian Institute of Ecology and Evolution, which brings together top scientists in order to accelerate research on how forests, fields, lakes and oceans work, and help maintain the goods and services they supply.

Canadian Institute of Ecology and Evolution

University of British Columbia

Related Energy Articles from Brightsurf:

Energy System 2050: solutions for the energy transition
To contribute to global climate protection, Germany has to rapidly and comprehensively minimize the use of fossil energy sources and to transform the energy system accordingly.

Cellular energy audit reveals energy producers and consumers
Researchers at Gladstone Institutes have performed a massive and detailed cellular energy audit; they analyzed every gene in the human genome to identify those that drive energy production or energy consumption.

First measurement of electron energy distributions, could enable sustainable energy technologies
To answer a question crucial to technologies such as energy conversion, a team of researchers at the University of Michigan, Purdue University and the University of Liverpool in the UK have figured out a way to measure how many 'hot charge carriers' -- for example, electrons with extra energy -- are present in a metal nanostructure.

Mandatory building energy audits alone do not overcome barriers to energy efficiency
A pioneering law may be insufficient to incentivize significant energy use reductions in residential and office buildings, a new study finds.

Scientists: Estonia has the most energy efficient new nearly zero energy buildings
A recent study carried out by an international group of building scientists showed that Estonia is among the countries with the most energy efficient buildings in Europe.

Mapping the energy transport mechanism of chalcogenide perovskite for solar energy use
Researchers from Lehigh University have, for the first time, revealed first-hand knowledge about the fundamental energy carrier properties of chalcogenide perovskite CaZrSe3, important for potential solar energy use.

Harvesting energy from walking human body Lightweight smart materials-based energy harvester develop
A research team led by Professor Wei-Hsin Liao from the Department of Mechanical and Automation Engineering, The Chinese University of Hong Kong (CUHK) has developed a lightweight smart materials-based energy harvester for scavenging energy from human motion, generating inexhaustible and sustainable power supply just from walking.

How much energy do we really need?
Two fundamental goals of humanity are to eradicate poverty and reduce climate change, and it is critical that the world knows whether achieving these goals will involve trade-offs.

New discipline proposed: Macro-energy systems -- the science of the energy transition
In a perspective published in Joule on Aug. 14, a group of researchers led by Stanford University propose a new academic discipline, 'macro-energy systems,' as the science of the energy transition.

How much energy storage costs must fall to reach renewable energy's full potential
The cost of energy storage will be critical in determining how much renewable energy can contribute to the decarbonization of electricity.

Read More: Energy News and Energy Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.