Microbial diversity and microbiology of extreme environments

Description

The group of microbial diversity and microbiology of extreme environments is devoted to investigate the functional role of microbial diversity in a variety of environments, and different microorganisms, their genes and biomolecules with a special, but not exclusive, focus on extremophiles. A wide range of techniques and procedures are generally applied in our research which includes basic and applied initiatives and a high interest in biotechnology. http://www.microextreme.net

Research Background

The great majority of life on Earth is microscopic in size, and it is only visible through the microscope. Microbes are everywhere and they inhabit any environment, from very cold (below 0°C) to very hot (above 100°C) places, from very acidic to very alkaline sites, or high saline concentration, high pressure, or any other environment that might not look normal to humans. Microorganisms thriving under extreme conditions are the extremophiles.
This variable selection of systems is reflected by the huge diversity exiting in the microbial world. Currently, the level of microbial diversity on Earth is a topic of debate. While many microorganisms can easily be dispersed across the planet, the so called extreme environments present a selective factor for the living beings to develop in them. Thus, extreme environments can be considered as ideal model systems for studying ecological properties of microorganisms, their physiology, adaptative properties and many other characteristics related to microbial communities and specific microbial cells.
Due to the small size of microbes, working with them is not an easy task. Microscopic examination is required to see them. Classical microbiological studies required the ability to growth the microorganisms in the laboratory to be able to study their properties, such as growth conditions, nutrient sources, metabolic products, and so on. We now know that most microorganisms in the environment can not be brought into cultivation. So we have to design novel strategies to investigate their diversity, function, and potential applications. In order to understand our Planet, we are interested in the who, what, when, where, why and how questions about microbial life. The way to do it brings up an exciting experience to discover step by step the diverse microbial world.
It is too difficult (just to avoid to say impossible) to duplicate an organism’s host environment/ecosystem in a laboratory. However, some microbial processes or properties can be analyzed in the laboratory using isolated microorganisms. This apparent contradiction suggests a need for a variety of methodologies to be applied either in the laboratory or in the field.
With the advent of modern molecular techniques, we can understand the microbial environment in much greater detail. It is possible to use the information hold in the nucelic acids of microorganisms to detect those present in an environment. Thus, molecular methods based on DNA and RNA represent a very useful set of techniques to analyze microbial communities in situ. But nucleic acids can be used to both detect a microorganism and to look at its functional genes, and we can do similar research on microbial communities through metagenomic approaches. Of course, the amount of data to be processed increases exponentially with the number of different microorganisms in a sample and bioinformatic tools become an essential part of the research process. Detection of microorganisms and their functional genes are also complemented with an evaluation and analysis of the processes being carried out by those microbial communities in the environment.
Microorganisms are never alone. They work in communities, often composed by a large number of different types of cells. The study of microbial communities and their interaction with the environment are key aspects to understand the role and function of microorganisms in nature, and consequently the implications of microbial life at local and global scales in our planet.
Microorganisms thriving under extreme conditions generally present specific adaptations which allow them to develop in unique environments. The properties of their biomolecules are of interest in biotechnology due to their high stability which can be used in potential applications to industry or processes of commercial interest. The search for unique microorganisms and molecules also require the use of a variety of techniques.
Our group is keen in searching for novel methodologies and the application of a wide variety of strategies to answer specific questions. Methods involving a wide range of molecular techniques, the cultivation of microorganisms, biochemistry, physiology, ecology, biotechnology, genomics, bioinformatics, among others are some of the procedures commonly applied in our research. We pretend to further study microbial life from a multidisciplinary perspective and we will be glad to collaborate with other groups and individuals interested in related topics. For a list of our publications and projects, please, visit the corresponding page.

Projects

Comparative Microbial Genomics. MICROGEN. Ministry of Science and Innovation, project CSD2009-00006.
Microorganisms are still the main cause of death in the world, they are the main source of genetic biodiversity and the main players in ecosystem functioning. However, the way bacterial populations are structured, the way they evolve or interact with other biotic components or the way they adapt to the environment and evolve are still poorly known. This is partly due to the need for pure culture in order to perform experiments and to the application of an evolutionary model imported from eukaryotic systems. With the advent of genomics and the new high-throughput sequencing techniques of low cost, a new era has emerged in which bacteria can be studied through their genomes, obviating the need for culturing the microorganisms and allowing a holistic study of ecosystems. In addition, the study of this vast genetic reservoir may provide access to a wealth of new bioactive compounds previously unreachable by standard techniques. Some important changes in our way of understanding microbes are starting to emerge, a crucial one being the existence of a gigantic pool of genes within each bacterial species, in such a way that this gene pool (the “pan-genome”) is much larger than the genome of each individual strain. This is vital to understand bacterial biology and has important consequences from an applied point of view.

The present project aims to study microorganisms by a combination of genomics, bioinformatics, molecular biology, metagenomics and next generation sequencing. This will be achieved by the creation of a multidisciplinary team combining all those skills in an ambitious proposal that would not be possible by standard funding. The consortium will use many different bacterial species as models of pathogenicity and symbiosis in human, animal and plant hosts, as well as studying different natural and human-related ecosystems to unravel the population genomics and genome fluidity of bacteria. This will shed light on the species concept, the structure of bacterial populations, its interaction with viruses and the environment, their adaptation and their evolution, as well as opening new avenues for treating infectious diseases. In addition, a web-based server will be created to study, annotate and analyze bacterial genomes, and new scripts and computer programs will be developed that will be of great use for the scientific community. It is anticipated that the group will serve as a nucleating agent that will permit Spanish Microbiology to remain in the mainstream of international Microbiology and to continue being a support to the future of Spanish Biotechnology and Biomedicine.

The presence and role of low abundance microorganisms could explain the huge microbial diversity of natural systems. A case study in the Doñana National Park. Ministry of Science and Innovation, project CGL2009-12328/BOS.
Microbial diversity in natural environments is huge and difficult to determine. These microbial communities can be considered as formed by a low number of highly abundant microorganisms and a very high number of rare, low abundant, microorganisms. We present the hypothesis that the microorganisms representing that minority are important in natural ecosystems. The study of the rare microorganisms is essential for understanding the functional role of microbial communities in an spatial and temporal environment, as well as to comprehend why exist a so large microbial diversity. The selection of microorganisms adapted to thrive under extreme conditions (high temperature, low or high pH) from moderate environments is proposed. The selected environment is the sediment from the natural ponds at Doñana National Park. Environmental variables will be determined and changes in the microbial communities will be monitored during the selecting process. Molecular methods will be used for the detection of microorganisms based on both fingerprinting techniques and sequencing, and in situ detection methods. Cultures of selected microorganisms will be approached. Microorganisms, Bacteria and Archaea, will be identified and their physiological properties evaluated. Also, their spatial distribution will be analyzed and will contribute to decipher the potential function within their ecosystem. The possibility that those extreme conditions could represent natural situations will be studied. The analyzed processes will represent a model of the dynamic of microbial communities as a consecuence of environmental changes and their potential response both in the ecosystem and global biogeochemical cycles.

Microbial diversity and microbiology of extreme environments. Andalusian Government, BIO288.
Microbial diversity is a broad term that can be approached from very different perspectives. This includes not only the phylogenetic diversity but also includes molecular, functional, and mechanistics points of view. To achieve this broad assessment of the whole microbial world we use a wide and radically different methodologies which point towards a common objective, decipher the functioning of the microbial world. The focus on extremophiles allows to center on a specific type of microorganisms and communities which are of great interest for their potential biotechnological applications as well as model systesms for the study of natural communities.

Components:

Juan Miguel Gonzalez Grau. Principal Investigator

Maximino Piñeiro Vidal. Doctor. Ph.D. Hired through a research project.

Alba Cuecas Morano. Ph.D. student.

Collaborators and recent members of the group

María Carmen Portillo Guisado. Current position: Researcher at Abengoa Research

Francesca Stomeo. Current position: Researcher at the International Livestock Research Institute, Kenya