Environmental Microbiology of Aquatic and Waste Systems

The water molecule is composed of two hydrogen atoms attached to an oxygen atom with a V-shape formation and an angle of 105° between the hydrogen atoms. It has a slightly negative charge at the oxygen end and a slight positive charge at the hydrogen end. This makes the water molecule polar, i.e., having poles like a magnet. This property makes water molecules attract each other, thus giving it unique properties such as rising in capillary tubes, plant roots, and blood vessels against gravity. Water has a high latent heat enabling it to absorb large quantities of heat before a rise in temperature; this enables the waters of the oceans to affect the earth’s temperature in a gradual manner. Water is an important solvent. Water forms about 71% of the earth’s surface, but most of it is saline. Freshwater which is required for domestic and industrial use, and for agriculture forms only about 2.5%. Water is distributed in the atmosphere as clouds; on the earth’s surface as oceans, seas, rivers, and lakes; and underground.

As a habitat for the existence of microorganisms, water has properties not found in other natural microbial habitats such as soil, and plant and animal bodies; indigenous aquatic microorganisms are adapted to these conditions. Natural waters are generally low in nutrient content (i.e., they are oligotrophic); what nutrients there are, are homogeneously distributed in the water. The movement of water freely transports microorganisms; to counter this and offer themselves some protection, many aquatic organisms are either stalked or arranged in colonies immersed in gelatinous materials. To enable free movement in water, many aquatic microorganisms and/or their gametes have locomotory structures such as flagella. Microorganisms are often adapted to, and occupy particular habitats in the water body; some occupy the air–water interphase (neuston), while others live in the sediment of water bodies (benthic). The conditions which affect aquatic microorganisms are temperature, nutrient, light, salinity turbidity, water movement. The methods for the quantitative study of aquatic microorganisms are cultural methods (plate count and MPN), direct methods (micro­scopy and flow cytometry), and the determination of microbial mass. The microscopy methods are light (optical), epi-flourescence, confocal laser scanning microscopy, transmission electron microscopy, and scanning electron microscopy. Microbial mass may be direct (weight after oven-drying) or indirect (turbidity, CO₂ release, etc).

Our increased knowledge of living things at the molecular level has greatly ­influenced the modern approach in biology. Thus, for example, the taxonomy of microorganisms is no longer based mostly on their morphology, but also on the sequence of bases in the genes of the 16S RNA of the small subunit of the ribosomes. This chapter looks at selected basic molecular biology topics of relevance to the environment. The processes of transcription and translation in protein synthesis are discussed. The principles behind some molecular procedures such as the polymerase chain reaction and micro-arrays are discussed. Many microorganisms in environments such as water and soil are not culturable and are studied only with molecular biology. Metagenomics, or the culture-independent genomic analysis of an assemblage of microorganisms, in environments such as marine or freshwater has potential to answer fundamental questions in microbial ecology.

The principles behind the taxonomy of the microorganisms, especially the ­molecular approach (using the sequence of the 16S RNA in the small subunit of the ribosome) in the identification of bacteria, are discussed. The detailed taxonomy of bacteria, fungi, algae, protozoa, and viruses (including bacteriophages) is discussed, and emphasis is laid on those microorganisms which are aquatic. The chapter includes information on some of the smaller macroorganisms found in water such as nematodes and rotifers. The activities of aquatic microorganisms in photosynthesis, and the global cycling of nitrogen and sulfur is discussed.

Freshwaters are defined as natural waters containing less than 1,000 mg per liter of dissolved solids, most often salt. Globally, freshwaters are scarce commodities and make up only 0.009% of the earth’s total water. Although they generate only about 3% of the earth’s total primary biological productivity, they contain about 40% of the world’s known fish species. Natural freshwaters are classifiable into atmospheric, surface, and underground waters each type having a unique microbial ecology. Atmospheric waters lose their microorganisms as they fall as rain or snow. Surface freshwaters are found in rivers and lakes, and contain large and diverse groups of microorganisms. Using molecular methods such as 16S rRNA analysis, which enables the study of unculturable microorganisms, new information regarding freshwater microbial ecology has emerged in recent times: There are more phylogenetic groups of bacteria than are observed by cultural methods; there is a unique and distinct bacterial group, which can be termed “typical freshwater bacteria”; contrary to previous knowledge when aquatic bacteria were thought to be mostly Gram-negative bacteria, Gram-positive bacteria are in fact abundant in freshwaters; finally, marine-freshwater transitional populations exist in coastal waters. Ground waters suffer contamination from chemicals and less from microorganisms; the deeper the groundwater, the less likely it is to contain microorganisms, which are filtered away by soil.

The waters of the seas and oceans of the world contain large amounts of solutes; mainly, salt of about 3.5 g/L, occupy about 71% of the earth’s surface and have an average depth of 3.8 km. The photic zone of seas and oceans, about 200 m deep, is the region permeated by sunlight where photosynthesis can take place. It has the greatest biodiversity, and all food for the marine population arises from the photic zone; such food includes marine snow which consists of globules of mucopolyssacharides containing dead and living microorganisms floating downward toward the deep ocean. Marine organisms are adapted to the unique conditions found in the marine open sea (pelagic zone) environment: high salinity (3.5 g/L), low temperature (about 4°C), and high barometric pressure of up to 500 bar depending on the depth. Thermophilic organisms grow near the occasional hot thermal vents where hot magma spews out onto the ocean floor.

Using the technique of 16S rRNA, it has been found that over 70% of marine bacteria have not been cultured and hence have no counterparts among known bacteria. Microscopic cyanobacteria (picophytoplankton) make up 15% of all the bacteria. Among them, Synechoccus and Prochlorococcus, predominate and constitute the most abundant photosynthetic microbes on earth, contributing more than 50% of the total marine photosynthesis. Of the cultivated bacteria, Roseobacter spp. form about 15% of the total bacteria, while green non sulfur bacteria make up about 6%.

Natural bodies of water will purify themselves and remove added materials given sufficient time. Pollution therefore occurs when the self-purifying powers of a body of water have not had enough time to remove the pollutant and return itself to its original state. Pollutants in water include bacteria, chemicals, heat and by the addition of organic or inorganic nutrients or eutrophication. Eutrophication causes excesses growth of cyanobacteria or blooms.

Pollution by fecal matter is determined principally by the identification of E. coli in water. Water bodies are expected to meet standards of the maximum content of microbial and chemical pollutants set by governments all over the world. The Total Maximum Daily Load (TDML) is a calculation of the maximum amount of a pollutant that a water body can contain and still meet water quality standards set by the regulating authority for a particular water use. Since not all E coli is necessarily of human origin, its source is determined through methods of microbial source tracking.

Oil spills are major sources of marine pollution. They are remediated physically by skimmers which collect the oil, adsorption onto suitable materials, the use of dispersants or in-situ burning. Biological methods include addition of nutrients to stimulate the growth of oil-degrading microorganisms, the use of surfactants to emulsify the oil and increase contact between oil and microorganisms, and the introduction of organisms specially adapted to growth on oil.

Disease transmission through water can occur through drinking water contaminated with microorganisms causing disease, through inhalation of aerosols of water at swimming pools, or through air-conditioners, or finally through contact in swimming pools. Diseases transmitted through drinking water include bacterial diseases (cholera, dysentery, typhoid, gastrointestinal disorders by E. coli, Yersinia, and Campylobacter), viruses (hepatitis A and E), and protozoan and helminth parasites (Cryptosporidium, Giardia, Entamoeba). Inhalation of aerosols can lead to Legionnaires’ disease and tuberculosis, while persons with open wounds can contact infections by Aeromonas and non-tubercular mycobacteria.

Drinking water is a basic necessity for the maintenance of good health in humans, but it is also a vehicle for the introduction of harmful biological agents such as bacterial and protozoan pathogens into the body. Therefore raw waters are purified to render them safe for drinking. The processes adopted in municipal water purification include the following: pretreatment (pre-coagulation, pre-disinfection), aeration, coagulation, filtration (slow, rapid, ultrafiltration, carbon filtration), disinfection (chloramines, ozonation, ultraviolet light, chlorination) miscellaneous treatments (Fe/Mn removal, deionization, reverse osmosis, algal/odor control, softening, ion-exchange, fluoridation, radioactivity removal, plumbosolvency removal). Which of the processes is actually employed depends on the quality of the raw water, the regulations of the appropriate authorities, and the budgetary considerations of the operator. The world over, regulatory authorities decide the maximum contaminants permissible in drinking water and recreational water; thus, the US Environmental Protection Agency (USEPA), the European Union Environmental Agency (EEA), the World Health Organization (WHO), and governmental agencies around the world all set standards, which differ from one another, and which reflect the level of economic, social, and technical expectations and accomplishments of the constituencies to which the standards are addressed.

Wastes are discarded or unwanted materials resulting from the domestic and industrial activities of humans. Wastes carried in water are described as sewage. It is important to determine the quantity of carbon in sewage so as to know the most appropriate method to use for treating it. One of the most common methods is the Biochemical Oxygen Demand (BOD) which measures the oxygen consumed by microorganisms to degrade the carbon over a 5-day period. Other methods are chemical in nature and related to the potential of the microbial breakdown. These chemical methods are the Permanganate Value (PV) Test, the Chemical Oxygen Demand (COD), Total Organic Carbon (TOC), Total Suspended Solids (TSS), and Volatile Suspended Solids (VSS).

Aerobic methods for disposing of sewage are: the Activated Sludge System, the Trickling Filter, the Rotating Disks, and the Oxidation Pond. Anaerobic methods include the Septic Tank, the Imhoff Tank, and Cesspools. Advanced wastewater treatment (AWT) methods are expensive and used for producing water for specialized use. They include: Reverse Osmosis, Nanofiltration, Ultrafiltration and Microfiltration, Electrodialysis, Activated Charcoal, Ion exchange, UV Oxidation, and Precipitation.

Solid wastes management involves waste reduction, reuse and recycling, composting, incineration with or without energy recovery, and landfilling.

Modern incinerators scrub the flue gases of incineration to reduce the harmful components. Newer methods of treating wastes include plasma arc gasification, in which waste is treated at very high temperatures and pressures, melting the waste into a nontoxic dross and yielding a fuel, syngas, for generating electricity. Pyrolysis operates at about 430°C. Supercritical water oxidation (SCWO) is the destruction technology for organic compounds and toxic materials at very high temperature and pressure, converting them to carbon dioxide, hydrogen to water, and chlorine atoms to chloride ion.