Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas. Environmental microbiology also includes the study of microorganisms that exist in artificial environments such as bioreactors.
Microbial life is amazingly diverse and microorganisms literally cover the planet.
An average gram of soil contains approximately one billion (1,000,000,000) microbes representing probably several thousand species. Microorganisms have special impact on the whole biosphere. They are the backbone of ecosystems of the zones where light cannot approach. In such zones, chemosynthetic bacteria are present which provide energy and carbon to the other organisms there. Some microbes are decomposers which have ability to recycle the nutrients. Microbes have a special role in biogeochemical cycles. Microbes, especially bacteria, are of great importance because their symbiotic relationship (either positive, neutral, or negative) have special effects on the ecosystem.
Microorganisms are used for in-situ microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since most sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial species and strains, each specific to the biodegradation of one or more types of contaminants. It is vital to monitor the composition of the indigenous and added bacteria in order to evaluate the activity level and to permit modifications of the nutrients and other conditions for optimizing the bioremediation process.
Microbial biodegradation of pollutants plays a pivotal role in the bioremediation of contaminated soil and groundwater sites. Such pollutants include chloroethenes, steroids, organophosphorus compounds, alkanes, PAHs and PCBs.[1] moisture effect in microbes
Petroleum oil is toxic, and pollution of the environment by oil causes major ecological concern. Oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult; much of the oil can, however, be eliminated by the hydrocarbon-degrading activities of microbial communities, in particular the hydrocarbonoclastic bacteria (HCB). These organisms can help remedy the ecological damage caused by oil pollution of marine habitats. HCB also have potential biotechnological applications in the areas of bioplastics and biocatalysis.[1]
Biotreatment, the processing of wastes using living organisms, is an environmentally friendly alternative to other options for treating waste material. Bioreactors have been designed to overcome the various limiting factors of biotreatment processes in highly controlled systems. This versatility in the design of bioreactors allows the treatment of a wide range of wastes under optimized conditions. It is vital to consider various microorganisms and a great number of analyses are often required.[2]
Wastewater treatment processes are geared towards one purpose: cleaning up water. Recent application of molecular techniques is unveiling the microbial composition and architecture of the complex communities involved in the treatment processes. It is now recognized that wastewater processes harbor a vast variety of microorganisms most of which are yet-to-be cultured, hence uncharacterized. Metagenomic technology is being used to study the diversity, structure and functions of microbial communities in nitrifying processes, anaerobic ammonia oxidation processes and methane fermenting processes.[3][4][5]
The application of molecular biology and genomics to environmental microbiology has led to the discovery of a huge complexity in natural communities of microbes. Diversity surveying, community fingerprinting and functional interrogation of natural populations have become common, enabled by a range of molecular and bioinformatics techniques. Recent studies on the ecology of cyanobacteria have covered many habitats and have demonstrated that cyanobacterial communities tend to be habitat-specific and that much genetic diversity is concealed among morphologically simple types. Molecular, bioinformatics, physiological and geochemical techniques have combined in the study of natural communities of these bacteria.[6]
Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage, skin, and cheese smear. Some, such as Corynebacterium diphtheriae, are important pathogens while others, such as Corynebacterium glutamicum, are of immense industrial importance. C. glutamicum is one of the biotechnologically most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine.[7]
Legionella is common in many environments, with at least 50 species and 70 serogroups identified. Legionella is commonly found in aquatic habitats where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans.[8]
Originally, Archaea were once thought of as extremophiles existing only in hostile environments but have since been found in all habitats and may contribute up to 20% of total biomass. Archaea are particularly common in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are subdivided into four phyla of which two, the Crenarchaeota and the Euryarchaeota, are most intensively studied.[9]
Lactobacillus species are found in the environment mainly associated with plant material. They are also found in the gastrointestinal tract of humans, where they are symbiotic and make up a portion of the gut flora.[10][11]
Aspergillus spores are common components of aerosols where they drift on air currents, dispersing themselves both short and long distances depending on environmental conditions. When the spores come in contact with a solid or liquid surface, they are deposited and if conditions of moisture are right, they germinate. The ability to disperse globally in air currents and to grow almost anywhere when appropriate food and water are available means that ubiquitous is among the most common adjectives used to describe these moulds.[12]
Microorganisms that convert gaseous nitrogen (N2) to a form suitable for use by living organisms are pivotal for life on earth. This process is called nitrogen fixation. Another set of microbial reactions utilise the bioavailable nitrogen creating N2 and completing the cycle in a process called denitrification. This crucial nutrient cycle has long been the subject of extensive research.[13]
Symbiotic nitrogen fixation is a mutualistic process in which bacteria reside inside plants and reduce atmospheric nitrogen to ammonia. This ammonia can then be used by the plant for the synthesis of proteins and other nitrogen-containing compounds such as nucleic acids. The Gram-negative soil bacteria that carry out this process are collectively referred to as rhizobia (from the Greek words Riza = Root and Bios = Life). The process of symbiotic nitrogen fixation is of agricultural and ecological significance because plants capable of nitrogen fixation do not need to compete for limited quantities of soil nitrogen, nor do they require expensive nitrogenous fertilizers that can be harmful to the environment.[13][14]
Algae are a highly diverse group of protists, ranging from simple, unicellular organisms to complex, multicellular entities with a range of differentiated tissues and distinct organs. They are found among diverse aquatic ecosystems and play important roles by supplying carbon and energy as well as providing habitat to other members of the biological communities. Some algae cause significant environmental and health problems. There are three algal groups: the dinoflagellates, the diatoms and the haptophytes.[15] their 3 main phylla are chlorophyta,rhodophyta and phaeophyta.
Diplomonads are a group of mitochondrion-lacking, binucleated flagellates found in anaerobic or micro-aerophilic environments. Most research on diplomonads has focused on Giardia, which is a major cause of water-borne enteric disease in humans and other animals. The first diplomonad to have its genome sequenced was a Giardia isolate (WB) and the 11.7 million basepair genome is compact in structure and content with simplified basic cellular machineries and metabolism.[16]
An adequate supply of safe drinking water is one of the major prerequisites for a healthy life, but waterborne diseases are still a major cause of death in many parts of the world, particularly in young children, the elderly, or those with compromised immune systems. As the epidemiology of waterborne diseases is changing, there is a growing global public health concern about new and reemerging infectious diseases that are occurring through a complex interaction of social, economic, evolutionary, and ecological factors. An important challenge is therefore the rapid, specific and sensitive detection of waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. However, newer enzymatic, immunological and genetic methods are being developed to replace and/or support classical approaches to microbial detection. Moreover, innovations in nanotechnology and nanosciences are having a significant impact in biodiagnostics, where a number of nanoparticle-based assays and nanodevices have been introduced for biomolecular detection.[17][18]
Molecular techniques based on genomics, proteomics and transcriptomics are rapidly growing as complete microbial genome sequences are becoming available, and advances are made in sequencing technology, analytical biochemistry, microfluidics and data analysis. While the clinical and food industries are increasingly adapting these techniques, there appear to be major challenges in detecting health-related microbes in source and treated drinking waters. This is due in part to the low density of pathogens in water, necessitating significant processing of large volume samples. From the vast panorama of available molecular techniques, some are finding a place in the water industry: Quantitative PCR, protein detection and immunological approaches, loop-mediated isothermal amplification (LAMP), microarrays.[18]
Bacteria have evolved abilities to regulate aspects of their behaviour (such as gene expression) in response to signals in the intracellular and extracellular environment. The interaction of a signal with its receptor (usually a protein or RNA molecule) triggers a series of events that lead to reprogramming of cellular physiology, typically as a consequence of altered patterns of gene expression. In this way, the bacterial cell is able to mount appropriate and effective responses to changing physical and/or chemical environments. The versatility with which many bacteria adapt to environmental change underlies many important aspects of microbiology. For example, pathogens encounter multiple environments as they invade a host from the outside, and then progress through different sites within host tissues. There is growing evidence that pathogenic bacteria make use of physical and chemical cues to signal their presence in a suitable host, and need to adapt to the host environment in order to mount a successful infection. On the other hand, it should not be assumed that all signals to which bacteria must respond originate in the extracellular environment. For many species, even the cosseted life in a laboratory shake flask is 'stressful', in the sense that there is often a need to avoid or reverse the effects of harmful intermediates or by-products of metabolism. For example, all organisms that use dioxygen as a terminal electron acceptor have to deal with the reactive oxygen species that arise as adventitious by-products of aerobic metabolism. In bacteria, multiple protein receptors for oxygen radicals have been described, which control the expression of genes encoding enzymes that detoxify oxygen radicals or repair the damage that they cause.[19]
The bacterial stress response ensures that bacteria can survive adverse and fluctuating conditions in their immediate surroundings. Various mechanisms recognise different environmental changes and mount an appropriate response. A bacterial cell can react simultaneously to a wide variety of stresses.[20]
The stress response in bacteria involves a number of systems that act against the external stimulus. A complex network of global regulatory systems in bacteria ensures that the various stress response systems interact with each other and leads to a coordinated and effective response.[21]
Metagenomics is the cultivation-independent analysis of the collective genomes of microbes within a given environment, using sequence- and function-based approaches. Metagenomic studies have revealed the vast size and richness of the microbial and viral world and demonstrated the phylogenetic diversity of various environments. Access to huge volume genomic sequence data from uncultured organisms has opened up many new avenues of research. Advances in the throughput of sequencing and screening technologies have greatly facilitated metagenomics research.[5]