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".
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.
Ribosomal RNARibosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA (tRNA) and messenger RNA (mRNA) to process and translate the latter into proteins.
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.
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.
Bacterial phylaBacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla. It has been estimated that ~1,300 bacterial phyla exist. As of May 2020, 41 bacterial phyla are formally accepted by the LPSN, 89 bacterial phyla are recognized on the Silva database, dozens more have been proposed, and hundreds likely remain to be discovered.
FiltrationFiltration is a physical separation process that separates solid matter and fluid from a mixture using a filter medium that has a complex structure through which only the fluid can pass. Solid particles that cannot pass through the filter medium are described as oversize and the fluid that passes through is called the filtrate. Oversize particles may form a filter cake on top of the filter and may also block the filter lattice, preventing the fluid phase from crossing the filter, known as blinding.
Trophic state indexThe Trophic State Index (TSI) is a classification system designed to rate water bodies based on the amount of biological productivity they sustain. Although the term "trophic index" is commonly applied to lakes, any surface water body may be indexed. The TSI of a water body is rated on a scale from zero to one hundred. Under the TSI scale, water bodies may be defined as: oligotrophic (TSI 0–40, having the least amount of biological productivity, "good" water quality); mesotrophic (TSI 40–60, having a moderate level of biological productivity, "fair" water quality); or eutrophic to hypereutrophic (TSI 60–100, having the highest amount of biological productivity, "poor" water quality).
Metabolic theory of ecologyThe metabolic theory of ecology (MTE) is the ecological component of the more general Metabolic Scaling Theory and Kleiber's law. It posits that the metabolic rate of organisms is the fundamental biological rate that governs most observed patterns in ecology. MTE is part of a larger set of theory known as metabolic scaling theory that attempts to provide a unified theory for the importance of metabolism in driving pattern and process in biology from the level of cells all the way to the biosphere.
Gram-positive bacteriaIn bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bacteria take up the crystal violet stain used in the test, and then appear to be purple-coloured when seen through an optical microscope. This is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test.
