BiofilmA biofilm comprises any syntrophic consortium of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPSs). The cells within the biofilm produce the EPS components, which are typically a polymeric conglomeration of extracellular polysaccharides, proteins, lipids and DNA. Because they have three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes".
River ecosystemRiver ecosystems are flowing waters that drain the landscape, and include the biotic (living) interactions amongst plants, animals and micro-organisms, as well as abiotic (nonliving) physical and chemical interactions of its many parts. River ecosystems are part of larger watershed networks or catchments, where smaller headwater streams drain into mid-size streams, which progressively drain into larger river networks. The major zones in river ecosystems are determined by the river bed's gradient or by the velocity of the current.
EcosystemAn ecosystem (or ecological system) consists of all the organisms and the physical environment with which they interact. These biotic and abiotic components are linked together through nutrient cycles and energy flows. Energy enters the system through photosynthesis and is incorporated into plant tissue. By feeding on plants and on one another, animals play an important role in the movement of matter and energy through the system. They also influence the quantity of plant and microbial biomass present.
Biogeochemical cycleA biogeochemical cycle, or more generally a cycle of matter, is the movement and transformation of chemical elements and compounds between living organisms, the atmosphere, and the Earth's crust. Major biogeochemical cycles include the carbon cycle, the nitrogen cycle and the water cycle. In each cycle, the chemical element or molecule is transformed and cycled by living organisms and through various geological forms and reservoirs, including the atmosphere, the soil and the oceans.
Extracellular polymeric substanceExtracellular polymeric substances (EPSs) are natural polymers of high molecular weight secreted by microorganisms into their environment. EPSs establish the functional and structural integrity of biofilms, and are considered the fundamental component that determines the physicochemical properties of a biofilm. EPS in the matrix of biofilms provides compositional support and protection of microbial communities from the harsh environments. Components of EPS can be of different classes of polysaccharides, lipids, nucleic acids, proteins, lipopolysaccharides, and minerals.
Organic matterOrganic matter, organic material, or natural organic matter refers to the large source of carbon-based compounds found within natural and engineered, terrestrial, and aquatic environments. It is matter composed of organic compounds that have come from the feces and remains of organisms such as plants and animals. Organic molecules can also be made by chemical reactions that do not involve life. Basic structures are created from cellulose, tannin, cutin, and lignin, along with other various proteins, lipids, and carbohydrates.
Marine biogeochemical cyclesMarine biogeochemical cycles are biogeochemical cycles that occur within marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. These biogeochemical cycles are the pathways chemical substances and elements move through within the marine environment. In addition, substances and elements can be imported into or exported from the marine environment. These imports and exports can occur as exchanges with the atmosphere above, the ocean floor below, or as runoff from the land.
Soil organic matterSoil organic matter (SOM) is the organic matter component of soil, consisting of plant and animal detritus at various stages of decomposition, cells and tissues of soil microbes, and substances that soil microbes synthesize. SOM provides numerous benefits to the physical and chemical properties of soil and its capacity to provide regulatory ecosystem services. SOM is especially critical for soil functions and quality.
Nutrient cycleA nutrient cycle (or ecological recycling) is the movement and exchange of inorganic and organic matter back into the production of matter. Energy flow is a unidirectional and noncyclic pathway, whereas the movement of mineral nutrients is cyclic. Mineral cycles include the carbon cycle, sulfur cycle, nitrogen cycle, water cycle, phosphorus cycle, oxygen cycle, among others that continually recycle along with other mineral nutrients into productive ecological nutrition. The nutrient cycle is nature's recycling system.
Light therapyLight therapy, also called phototherapy or bright light therapy is the exposure to direct sunlight or artificial light at controlled wavelengths in order to treat a variety of medical disorders, including seasonal affective disorder (SAD), circadian rhythm sleep-wake disorders, cancers, and skin wound infections. Treating skin conditions such as neurodermatitis, psoriasis, acne vulgaris, and eczema with ultraviolet light is called ultraviolet light therapy.
Light-emitting diodeA light-emitting diode (LED) is a semiconductor device that emits light when current flows through it. Electrons in the semiconductor recombine with electron holes, releasing energy in the form of photons. The color of the light (corresponding to the energy of the photons) is determined by the energy required for electrons to cross the band gap of the semiconductor. White light is obtained by using multiple semiconductors or a layer of light-emitting phosphor on the semiconductor device.
Particulate organic matterParticulate organic matter (POM) is a fraction of total organic matter operationally defined as that which does not pass through a filter pore size that typically ranges in size from 0.053 millimeters (53 μm) to 2 millimeters. Particulate organic carbon (POC) is a closely related term often used interchangeably with POM. POC refers specifically to the mass of carbon in the particulate organic material, while POM refers to the total mass of the particulate organic matter.
PyrosequencingPyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the "sequencing by synthesis" principle, in which the sequencing is performed by detecting the nucleotide incorporated by a DNA polymerase. Pyrosequencing relies on light detection based on a chain reaction when pyrophosphate is released. Hence, the name pyrosequencing.
Aquatic ecosystemAn aquatic ecosystem is an ecosystem found in and around a body of water, in contrast to land-based terrestrial ecosystems. Aquatic ecosystems contain communities of organisms—aquatic life—that are dependent on each other and on their environment. The two main types of aquatic ecosystems are marine ecosystems and freshwater ecosystems. Freshwater ecosystems may be lentic (slow moving water, including pools, ponds, and lakes); lotic (faster moving water, for example streams and rivers); and wetlands (areas where the soil is saturated or inundated for at least part of the time).
DNA sequencingDNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. Knowledge of DNA sequences has become indispensable for basic biological research, DNA Genographic Projects and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics.
Ecosystem healthEcosystem health is a metaphor used to describe the condition of an ecosystem. Ecosystem condition can vary as a result of fire, flooding, drought, extinctions, invasive species, climate change, mining, fishing, farming or logging, chemical spills, and a host of other reasons. There is no universally accepted benchmark for a healthy ecosystem, rather the apparent health status of an ecosystem can vary depending upon which health metrics are employed in judging it and which societal aspirations are driving the assessment.
Colored dissolved organic matterColored dissolved organic matter (CDOM) is the optically measurable component of dissolved organic matter in water. Also known as chromophoric dissolved organic matter, yellow substance, and gelbstoff, CDOM occurs naturally in aquatic environments and is a complex mixture of many hundreds to thousands of individual, unique organic matter molecules, which are primarily leached from decaying detritus and organic matter. CDOM most strongly absorbs short wavelength light ranging from blue to ultraviolet, whereas pure water absorbs longer wavelength red light.
Light pollutionLight pollution is the presence of unwanted, inappropriate, or excessive artificial lighting. In a descriptive sense, the term light pollution refers to the effects of any poorly implemented lighting, during the day or night. Light pollution can be understood not only as a phenomenon resulting from a specific source or kind of pollution, but also as a contributor to the wider, collective impact of various sources of pollution. Although this type of pollution can exist throughout the day, its effects are magnified during the night with the contrast of darkness.
Bacterial taxonomyBacterial taxonomy is subfield of taxonomy devoted to the classification of bacteria specimens into taxonomic ranks. In the scientific classification established by Carl Linnaeus, each species is assigned to a genus resulting in a two-part name. This name denotes the two lowest levels in a hierarchy of ranks, increasingly larger groupings of species based on common traits. Of these ranks, domains are the most general level of categorization. Presently, scientists classify all life into just three domains, Eukaryotes, Bacteria and Archaea.
MetagenomicsMetagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample.
