DE GRUYTER Physical Sciences Reviews. 2017; 20160118 Felicita Briški1 / Marija Vuković Domanovac1 Environmental microbiology 1 Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia, E-mail: [email protected] Abstract: For most people, microorganisms are out of sight and therefore out of mind but they are large, extremely di- verse group of organisms, they are everywhere and are the dominant form of life on planet Earth. Almost every surface is colonized by microorganisms, including our skin; however most of them are harmless to humans. Some microorganisms can live in boiling hot springs, whereas others form microbial communities in frozen sea ice. Among their many roles, microorganisms are necessary for biogeochemical cycling, soil fertility, decom- position of dead plants and animals and biodegradation of many complex organic compounds present in the environment. Environmental microbiology is concerned with the study of microorganisms in the soil, water and air and their application in bioremediation to reduce environmental pollution through the biological degra- dation of pollutants into non-toxic or less toxic substances. Field of environmental microbiology also covers the topics such as microbially induced biocorrosion, biodeterioration of constructing materials and microbiological quality of outdoor and indoor air. Keywords: microorganisms, environment, indicator microorganisms, biodegradation, bioremediation DOI: 10.1515/psr-2016-0118 Gentlemen, it is the microbes who will have the last word. (Louis Pasteur) 1 Evolution of microorganisms Earth is about 4.5 billion years old and scientists estimate that life first emerged at least 3.8 billion years ago after the surface of crust had cooled enough to allow liquid water to form. Early Earth was inhospitable from time to time because space rocks crushed into the Earth’s surface. Some impacts were powerful enough to vaporize oceans and create clouds of steam which sterilized the Earth’s surface. Nonetheless, some microorganisms were able to survive this period deep underground while some may have had the capacity of modern microorganism to produce survival forms called endospores. Early in the planet’s history conditions were harsh. The Earth’s surface was exposed to strong ultraviolet (UV) radiation because the ozone layer was not yet formed in the atmosphere. Nevertheless, the prokaryotic microorganisms began to develop. The first prokaryotic microor- ganisms lived in anaerobic environment because atmosphere was a mixture of CO2,N2, and H2O vapour and in traces H2.O2 gas began to appear in significant amount in the Earth’s atmosphere between 2.5 and 2 billion years ago as a result of microbial metabolic process called oxygenic photosynthesis. Oxygenic photosynthesis which started around 3 billion years ago differed from earlier forms of photosynthesis and the bacteria respon- sible for this type of photosynthesis are called cyanobacteria. Cyanobacteria brought the O2 level of the Earth’s from River Valley Technologies Ltd atmosphere up to 10 % of today’s level and due to it the formation of ozone layer started. O2 level was high enough to enable evolution of oxygen-utilizing organisms [1, 2]. An approximate timeline of the development of life on Earth is presented in Figure 1. Since many eukaryotes are O2 dependent, researchers had theorized ProofCheck that protists first appeared around 2 billion years ago but according to recent evidence the first protistsap- peared about 3 billion years ago. Although bacteria and archaea are older than protists, an early appearance of the first eukaryotes is evidenced with a high degree of diversity in this group. Algae appeared after cyanobac- teria within the last 2 billion years, because their chloroplasts were derived from cyanobacteria. Fungi appeared during the last several hundred million years. Marija Vuković Domanovac is the corresponding author. © 2017 Walter de Gruyter GmbH, Berlin/Boston. Automatically generated rough PDF by This content is free. 1 Briški and Vuković Domanovac DE GRUYTER Figure 1: Approximate timeline in the history of life on Earth [1]. 2 The microbial world: classification, metabolism and growth Microorganisms are the foundation for all life on Earth. They vary in their appearance, ability to carry out differ- ent biochemical transformations, ability to grow in wide variety of environments and in their interactions with other organisms. Due to a great variety of different organisms on Earth, a systematic approach to classifying these organisms is necessary. The science of classifying organisms is called taxonomy and the groups making up the classification hierarchy are called taxa. Nomenclature refers to the actual naming of organisms. The binominal system of nomenclature is used for microorganisms. The names are given in Latin or are Latinized. The first word in the name is the genus, with the first letter always capitalized; the second isthe species name, which is not capitalized. Both words are always italicized. Classification of well-known bacterium Escherichia coli is presented in Example 1. Example 1. Classification of bacterium Escherichia coli E. coli is a member of genus Escherichia. It was named after the person who first isolated and described it, Theodor Escherich. The species name comes from the location where it was found, in this case in human intestinal tract. Its classification is as follows: Domain: Bacteria, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae, Genus: Escherichia, Species: E. coli. Traditional classification of living organisms was based on morphological differences like shape, colouring or appendages (flagella) extending from the cells. In the 1970s, a research by Woese and others suggested that life on Earth evolved along three evolutionary lineages. Analysis of 16S rRNA (ribosomal ribonucleic acid) has led to the modern phylogenetic classification of living organisms in three domains: Archaea, Bacteria and Eukarya. Phylogenetic information along with other taxonomic information has been used to construct the phylogenetic tree (Figure 2). from River Valley Technologies Ltd ProofCheck Figure 2: Schematics of universal phylogenetic tree evolved from a common ancestor. Using the rRNA gene sequences of many different organisms resulted in formation of a tree with longer and shorter branches; the longer the branches lengths, the greater the diversity in the group. The branches lengths are shorter for newly evolved organisms such as fungi, plants and animals in comparison with the branches lengths for prokaryotic and lower eukaryotic microorganisms [1, 3]. Members of microbial world consist of two major cell types: the simple prokaryotic and the complex eu- Automatically generated rough PDF by karyotic cells. Microscopically, the cells in domains Bacteria and Archaea look similar. They do not contain 2 DE GRUYTER Briški and Vuković Domanovac a membrane-bound nucleus or other intracellular lipid-bound organelles. Their genetic information is stored in a circular strand of deoxyribonucleic acid (DNA) in the nucleotide and cytoplasm is surrounded by a rigid cell wall. Due to structural similarities bacteria and archaea are prokaryotes but they differ in their chemical composition and therefore they are in different domains. The domain Eukarya is comprised of four kingdoms: Animalia, Fungi, Plantae and Protista. All members in this domain contain eukaryotic cells and this microbial world is composed of single-celled and multicellular organisms. The cells contain a membrane-bound nucleus and other internal organelles (mitochondria, chloroplast and cytoskeleton) that make eukaryotes more com- plex than the simple prokaryotes. Term microorganism is used to describe an organism that is so small that it cannot be seen without the use of microscope. Microscopy plays an integral role in the study of microorganisms and can provide extremely useful information about them. Even today, one of the most important tools for studying microorganisms is the bright- field light microscope that can magnify images 1000×. Most living microorganisms are nearly transparent and move rapidly about the slide. Consequently, cells must be immobilised and stained with dyes. Simple staining employs one dye to stain the cells. Differential staining is used to distinguish one group of bacteria from another. One of most frequently used staining procedures is the Gram stain (Example 2). Example 2. Gram staining is the procedure (Figure 3) by which bacteria can be separated in two major groups: Gram positive and Gram negative. Difference in the staining properties of these two groups isdueto the difference in the chemical structure of their cell walls. This procedure was developed over a century agoby Dr. Hans Christian Gram. Figure 3: Staining bacteria for microscopic observation. The bacteria are the smallest prokaryotic cells and the least structurally complex unicellular microorgan- isms. They possess the greatest metabolic flexibility. Typical shapes of common bacteria are: (a) sphere (coccus), (b) rod (bacillus) and (c) spiral (spirillum). Diameter of a typical cell is 1 µm. A representative of rod-shaped bac- teria is presented in Figure 4(a). The cell wall contains chemical compound peptidoglycan, which is not found in organisms in other domains. They multiply by binary fission in which one cell divides in two cells, and many can move using flagella. The archaea are a group of ancient organisms