Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon

The genus Acidithiobacillus, which we covered earlier in our blog, has been subject of study by researchers all over the world for almost 100 years now. Although A. ferrooxidans is probably the best known member of the group, it is A. thiooxidans who was first described 1. Originally characterized in 1922, this sulfur-oxidizing microorganism is the type species of the group, which now comprises seven validated species, the last one formally described last year 2.

Members of the genus have been isolated all around the world in a great variety of natural and industrial settings, including acid rock drainages, sulfur springs, sulfidic caves, ore concentrates, leaching mine solutions, and so on. These sites are characterized by a varying range of physicochemical characteristics, including redox potentials, heavy metal concentrations and pH, among others. Hence, Acidithiobacillus isolates exhibit a wide set of phenotypic adaptations and distinctive genetic traits that make it really interesting to study them.

Over the years the number of strains and sequence clones that have been obtained has raised steadily, making their analysis somewhat difficult. In fact, many isolates remain unclassified at the species level and several conflicting specific assignments have been detected in public databases. This raised the necessity of further scrutiny of the current status of taxon and the evolutionary relations among its members.

In our last paper, we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). Our work acknowledges their inherent diversity of the taxon, suggests the existence of unrecognized species (and probably also a new genus), and provides a new phylogenetic framework for those fond of the acidithiobacilli.

Harold Nuñez, Ana Moya-Beltrán et. al. Molecular Systematics of the Genus Acidithiobacillus: Insights into the Phylogenetic Structure and Diversification of the Taxon. Front. Microbiol. January 2017.

 

Post by Harold Nuñez

Edited by Raquel Quatrini


References

  1. Waksman, S. A., and Joffe, J. S. Microorganisms concerned in the oxidation of sulfur in the soil: Thiobacillus thiooxidans, a new sulfur-oxidizing organism isolated from the soil. J. Bacteriol. 7, 239–256 (1922). Back to text
  2. Falagán, C., and Johnson, D. B. Acidithiobacillus ferriphilus sp. nov., a facultatively anaerobic iron- and sulfur-metabolizing extreme acidophile. Int. J. Syst. Evol. Microbiol. 66, 206 (2016). doi: 10.1099/ijsem.0. 000698. Back to text
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International Visitor

The Microbial Ecoophysiology Lab is happy to welcome Prof. Barrie Johnson. He is a well-known U.K. based researcher working on metal-microbe interactions, focusing on microorganisms from acidic environments. He will be teaching an international course this Thursday in Fundación Ciencia y Vida. The course, Techniques for isolating, cultivating and identifying extreme acidophiles, will be held on our dependencies and if you are interested, you can write us directly (microecolab@cienciavida.org) or contact our PI Raquel Quatrini for further details (rquatrini@cienciavida.org).

 

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Acidithiobacillus: a review of species and strains identification.

The most studied group of bacteria within MEL are the Acidithiobacillus. They represent an extraordinary example of adaptation to extreme environments, and as such, has been subjected to great scrutiny by several research groups. They are a bacterial genus composed of obligatory acidophilic, Gram-negative, rod-shaped bacteria, but one of their most relevant and analyzed characteristics, is their capacity to derive energy from oxidation of elemental sulfur and reduced sulfur compounds to support autotrophic growth. Thanks to this ability, they are able to live in both natural and man-made low pH environments in a great variety of geo-climatic contexts, including acidic ponds, lakes and rivers, sulfur springs, acid mine/rock drainage waters and mining areas around the world.

These characteristics have made Acidithiobacillus bacteria a highly relevant member in the processing of minerals or biomining, but also in environmental pollution due to their generation of acid mine drainages.

The detection, identification and typing of members of this group has been a mayor focus of research since their description over 50 years ago.  Several molecular typing methods are available to these effects, but their major contribution has been to provide specific insight into the diversity of acidithiobacilli present in industrial and natural environments, improving our knowledge of the inherent diversity within the Acidithiobacilli. We have recently published a review covering these topics, if you want to have a grasp of these techniques and their contributions to the advancement of the research within the Acidithiobacillus genus, you can check out our paper:

Nuñez H et al. “Detection, identification and typing of Acidithiobacillus species and strains: a review”. Research in Microbiology – 2016.

Microbial Ecology and Extremophiles.

Microbial Ecology

What kinds of bacteria are out there? What are their roles in the environment? How they do what they do? What are the rules that govern their occurrence and interactions?

To us, people who work in the field of microbial ecology, these questions are an everyday challenge. Answers to these simple, but fundamental questions, are at the heart of our work. In the long term, they will allow us to answer bigger and more important questions. For instance, what are the mechanisms by which microbial communities influence and modify their ecosystem?

As you might suspect by now, microbial ecology is the study of microbes in the environment, their interactions and effects on it. It turns out that microbes are out there in staggering numbers, from to 100 bacterial cells per gram of sediments 2.5 km beneath the sea floor to 1029 cells in the seafloor sediment 1,2. To put it in perspective, that’s around the same number of stars estimated to exist in the observable universe. Certainly, this makes this field of research one of the most challenging.

Moreover, microorganisms are not found in isolation in the environment. Instead, several groups of different bacteria usually occur in each specific habitat, ranging from a few hundreds to several thousands different species 3. We refer to these assemblages of microbes as microbial communities. Microbial ecology focuses heavily on the disentangling the structure and behavior of these communities.

Microbial communities colonize every habitable niche of our planet, from the high altitude wetlands of the Chilean altiplano to the deepest depths of the Pacific Ocean in Mexico 4,5. And those are just two examples. The list of environments in which we detect signs of life, as we know it, is extensive, and keeps growing. Thermal springs, the Arctic ice, corroding mine tailings, sulfurous volcanic vents, the hyper-salty Dead Sea in Israel, you name it. However not all microorganisms can live in these environments. While the vast majority of organisms on earth live under moderate conditions of temperature, acidity, water and oxygen availability, among other conditions, there is a large group of microbes than thrive very happily in quite harsh environmental conditions. We refer to them as Extremophiles, and they are a very useful model to tackle some of the questions exposed above.

Extremophiles

To define a extreme condition we do it in comparison to normal conditions. We do this often based on physical parameters. Temperature, acidity, salinity and so on. As continuous variables, these physical parameters allow us to determine which conditions are extreme, given that they make difficult for organisms not only survive but thrive.

Simply put, extremophiles are organisms with the capacity to live and reproduce under severe, and often, extreme environmental conditions (temperature, acidity, salinity, etc.), conditions that are, for the most of the living organisms on earth, uninhabitable. However, as researchers, we like to classify things, so we have divided extremophiles into categories, depending on how they deal with these conditions. If they barely tolerate these conditions, they are called facultative extremophiles, while obligate extremophiles are those which only live in the extremes of specific physical or chemical parameters. To complicate matters further, depending of the parameter in question, we divide extremophiles into specific categories. Just one example, based on temperature, microorganisms growing between 10ºC to 42ºC are defined as mesophiles, while psychrophiles live below 15ºC, and thermophiles grow a hot temperatures, from 40ºC to up to 100ºC 6. Like these, there are several other categories of extremophiles; halophiles, which live on high salt concentration environments, acidophiles, which thrive in acid, anaerobes, which require anoxic conditions to multiply, etc..

So, why studying the microbial ecology tries to understand the dynamics and effects of these special microbes on the environment?.

Answers, some.

Until here we have established definitions; microbial ecology and extremophiles. The method, and the subject of study. For us, the observers, key answers that can be obtained through the analysis of these microbes are:

How did life on earth begin? Due to the extreme conditions found in early earth, extremophiles could provide us with clues about evolution at the very origin of life.

How do extreme microbial communities impact their environment? Given that, usually, environments were extremophiles thrive have reduced richness, meaning less species compared to habitats with normal conditions, modeling and studying such impacts is potentially easier. These simpler systems are beginning to provide clues to attempt answering similar questions on a bigger scale. How does human activity affect biodiversity in these extreme ecosystems? Despite their characteristics, most of these are fragile environments. Having a better understanding of the biology and ecology of extremophiles could help to better evaluate the potential ecological consequences of environmental changes, at local and global scale.

Of course definitive answers to these topics will take time. Nonetheless, research on extremophiles has steadily increased since the late 60’s, when Thomas D. Brock isolated the first thermophile, Thermus aquaticus, that would lead to a revolution in the field of biotechnology 20 years later. For instance, useful applications derived from research on extremophiles that have changed the way we do biotechnology include, the polymerase chain reaction (PCR), biofuels, biomining and bioremediation 7.

By now it’s easier to understand why a great deal of microbial ecology research has focused on extremophiles. They represent a great opportunity to trace back evolution, to investigate the effects of climate change and human activity in the environment, and walk towards the modeling of bigger ecosystems.

We still have a lot to cover in the quest to answer our initial question, what do bacteria do in the environment?. In the meantime, researchers have cataloged an extraordinary amount of information regarding extremophile diversity, their amazing biological strategies, and the ecological roles they play in these harsh, yet incredibly interesting, environments.

Post by Harold Nuñez

Edited by Raquel Quatrini


References

  1. Julie A. Huber. Making methane down deep.  Science 349, 376-377 (2015).   Back to text
  2. Kallmeyer, J., Pockalny, R., Adhikari, R. R., Smith, D. C. & D’Hondt, S. Global distribution of microbial abundance and biomass in subseafloor sediment. Proc. Natl. Acad. Sci. U.S.A. 109, 16213–16216 (2012).   Back to text
  3. Schloss, P. D., Girard, R., Martin, T., Edwards, J. & Thrash, J. C. The status of the microbial census: an update. (2016).   Back to text
  4. Hasan, N. A. et al. Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species. Proc. Natl. Acad. Sci. U.S.A. 112, E2813–9 (2015).   Back to text
  5. Dorador, C., Vila, I., Imhoff, J. F. & Witzel, K.-P. Cyanobacterial diversity in Salar de Huasco, a high altitude saline wetland in northern Chile: an example of geographical dispersion? FEMS Microbiology Ecology 64, 419–432 (2008).   Back to text
  6. Rothschild, L. J. & Mancinelli, R. L. Life in extreme environments. Nature 409, 1092–1101 (2001).   Back to text
  7. Coker, J. A. Extremophiles and biotechnology: current uses and prospects. F1000Research 5, 396 (2016).   Back to text

Acidophiles: Life in Extremely Acidic Environments

We are pleased to announce the release of the first book specialized in extremophiles from acidic econiches! The book “Acidophiles: Life in Extremely Acidic Environments was co-edited in by MELs PI and  Dr. D. Barrie Johnson from Bangor University. It provides a comprehensive description of the different types of acidophilic microorganisms, the communities they form, and addresses fundamental questions on their adaption strategies to cope with these extreme environments. It also covers more applied aspects, like the technologies that are used to study them, and their uses in mining  biotechnology and astrobiology.

Acidophiles are life-forms that grow preferentially in natural or man-made environments where the pH is well below seven. Together with other categories of extremophiles, they have greatly expanded our knowledge of the diversity of life, our understanding on how microorganisms can adapt to seemingly hostile situations, and provided scenarios for the possibility that life-forms may be found outside of our solar system.

Dr.  Raquel Quatrini – Dr. D Barrie Johnson.

You can find more information directly from the publisher: Caister Academic Press, or if you are really into it, you can acquire your own copy of the book. You have the choice to order a paperback or an ebook version.

acidophiles


The MEL lab.

Welcome dear readers.

This is our blog. The Microbial Ecophysiology Lab blog, or the MEL blog for short. The place where you can get info about our lab and all the activities that we carry on.

Here you can find who we are, what we have done and, sometimes, what are we up to.

Of course we have an institutional site at Fundación Ciencia & Vida. But if you want the details you should read out our research page or the about us section. And if you are in the mood you can check our publications

You can write your questions to rquatrini@cienciavida.org, the principal investigator, at our official mail, microecolab@cienciavida.org or visit the members page to contact directly anyone of our members.