Marine sedimentMarine sediment, or ocean sediment, or seafloor sediment, are deposits of insoluble particles that have accumulated on the seafloor. These particles have their origins in soil and rocks and have been transported from the land to the sea, mainly by rivers but also by dust carried by wind and by the flow of glaciers into the sea. Additional deposits come from marine organisms and chemical precipitation in seawater, as well as from underwater volcanoes and meteorite debris.
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.
SedimentSediment is a naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of wind, water, or ice or by the force of gravity acting on the particles. For example, sand and silt can be carried in suspension in river water and on reaching the sea bed deposited by sedimentation; if buried, they may eventually become sandstone and siltstone (sedimentary rocks) through lithification.
DNA extractionThe first isolation of deoxyribonucleic acid (DNA) was done in 1869 by Friedrich Miescher. DNA extraction is the process of isolating DNA from the cells of an organism isolated from a sample, typically a biological sample such as blood, saliva, or tissue . It involves breaking open the cells, removing proteins and other contaminants, and purifying the DNA so that it is free of other cellular components. The purified DNA can then be used for downstream applications such as PCR, sequencing, or cloning.
Deep-sea communityA deep-sea community is any community of organisms associated by a shared habitat in the deep sea. Deep sea communities remain largely unexplored, due to the technological and logistical challenges and expense involved in visiting this remote biome. Because of the unique challenges (particularly the high barometric pressure, extremes of temperature and absence of light), it was long believed that little life existed in this hostile environment. Since the 19th century however, research has demonstrated that significant biodiversity exists in the deep sea.
Sanger sequencingSanger sequencing is a method of DNA sequencing that involves electrophoresis and is based on the random incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication. After first being developed by Frederick Sanger and colleagues in 1977, it became the most widely used sequencing method for approximately 40 years. It was first commercialized by Applied Biosystems in 1986. More recently, higher volume Sanger sequencing has been replaced by next generation sequencing methods, especially for large-scale, automated genome analyses.
Third-generation sequencingThird-generation sequencing (also known as long-read sequencing) is a class of DNA sequencing methods currently under active development. Third generation sequencing technologies have the capability to produce substantially longer reads than second generation sequencing, also known as next-generation sequencing. Such an advantage has critical implications for both genome science and the study of biology in general. However, third generation sequencing data have much higher error rates than previous technologies, which can complicate downstream genome assembly and analysis of the resulting data.
Deep seaThe deep sea is broadly defined as the ocean depth where light begins to fade, at an approximate depth of 200 metres (656 feet) or the point of transition from continental shelves to continental slopes. Conditions within the deep sea are a combination of low temperatures, darkness and high pressure. The deep sea is considered the least explored Earth biome as the extreme conditions make the environment difficult to access and explore. Organisms living within the deep sea have a variety of adaptations to survive in these conditions.
Shotgun sequencingIn genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are assembled to give the overall sequence.
Exome sequencingExome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the subset of DNA that encodes proteins. These regions are known as exons—humans have about 180,000 exons, constituting about 1% of the human genome, or approximately 30 million base pairs. The second step is to sequence the exonic DNA using any high-throughput DNA sequencing technology.
Pelagic sedimentPelagic sediment or pelagite is a fine-grained sediment that accumulates as the result of the settling of particles to the floor of the open ocean, far from land. These particles consist primarily of either the microscopic, calcareous or siliceous shells of phytoplankton or zooplankton; clay-size siliciclastic sediment; or some mixture of these. Trace amounts of meteoric dust and variable amounts of volcanic ash also occur within pelagic sediments.
Montane ecosystemsMontane ecosystems are found on the slopes of mountains. The alpine climate in these regions strongly affects the ecosystem because temperatures fall as elevation increases, causing the ecosystem to stratify. This stratification is a crucial factor in shaping plant community, biodiversity, metabolic processes and ecosystem dynamics for montane ecosystems. Dense montane forests are common at moderate elevations, due to moderate temperatures and high rainfall.
Transcriptomics technologiesTranscriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell.
Ecosystem serviceEcosystem services are the many and varied benefits to humans provided by the natural environment and healthy ecosystems. Such ecosystems include, for example, agroecosystems, forest ecosystem, grassland ecosystems, and aquatic ecosystems. These ecosystems, functioning in healthy relationships, offer such things as natural pollination of crops, clean air, extreme weather mitigation, and human mental and physical well-being.
Disturbance (ecology)In ecology, a disturbance is a temporary change in environmental conditions that causes a pronounced change in an ecosystem. Disturbances often act quickly and with great effect, to alter the physical structure or arrangement of biotic and abiotic elements. A disturbance can also occur over a long period of time and can impact the biodiversity within an ecosystem. Major ecological disturbances may include fires, flooding, storms, insect outbreaks and trampling.
Microbial loopThe microbial loop describes a trophic pathway where, in aquatic systems, dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. In soil systems, the microbial loop refers to soil carbon. The term microbial loop was coined by Farooq Azam, Tom Fenchel et al. in 1983 to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.
Restoration ecologyRestoration ecology is the scientific study supporting the practice of ecological restoration, which is the practice of renewing and restoring degraded, damaged, or destroyed ecosystems and habitats in the environment by active human interruption and action. Ecological restoration can reverse biodiversity loss, combat climate change and support local and global economies.
DNA microarrayA DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles (10−12 moles) of a specific DNA sequence, known as probes (or reporters or oligos). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target) under high-stringency conditions.
Dissolved organic carbonDissolved organic carbon (DOC) is the fraction of organic carbon operationally defined as that which can pass through a filter with a pore size typically between 0.22 and 0.7 micrometers. The fraction remaining on the filter is called particulate organic carbon (POC). Dissolved organic matter (DOM) is a closely related term often used interchangeably with DOC. While DOC refers specifically to the mass of carbon in the dissolved organic material, DOM refers to the total mass of the dissolved organic matter.
DNADeoxyribonucleic acid (diːˈɒksᵻˌraɪboʊnjuːˌkliːᵻk,_-ˌkleɪ-; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.
