Mame terms

help

Autotrophy

the process by which organisms produce their own energy through inorganic substances often using light or chemicals

bacterial growth efficiency (BGE)

is defined as the ratio of bacterial biomass production (BP) to the total carbon assimilated (BP + BR), where BR is bacterial respiration.

copiotroph

a microorganism that thrives in nutrient rich environments and often exhibits rapid growth rates and high metabolic activity

cyanobacteria

a primary producer and prokaryote that makes up 25 percent of the oxygen on earth

Enzymes

are encoded by genes. They are important for
heterotrophic bacteria in carrying out hydrolysis of various compounds.

functional gene

A functional gene is a section of DNA that contains the genetic code for a single polypeptide and functions as a hereditary unit. It acts as an instruction to make molecules called proteins, which are needed for the body to function.

genome

is the collection of all genes within an organism’s cell, including
protein-encoding genes as well as the genes encoding the RNA molecules important for translation
(e.g. rRNA, tRNA).

genomics

1. the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes.

metagenomics

Metagenomics is the study of all genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential.

metaproteomic

Metaproteomics (also community proteomics, environmental proteomics, or community proteogenomics) is an umbrella term for experimental approaches to study all proteins in microbial communities and microbiomes from environmental sources. Metaproteomics is used to classify experiments that deal with all proteins identified and quantified from complex microbial communities.

meta transcriptomics

study of all RNA molecules study can tell us about the oceanic bacterial
community’s expression patterns of functional genes, without having to culture any of those
bacteria. NOTE - “Genomics” tells us they have the genes, BUT NOT whether or not if a gene
or set of functional genes is/are being expressed. Gene expression can be detected with
transcripts (mRNA) or with proteins.

microbial loop

is the dissolved organic material (DOM)-based
pathway consisting of:
primary production  DOM  microbes  grazers  higher trophic levels

mineralization

In seawater, detritus is mineralized by heterotrophic bacteria into CO2 and other inorganic
constituents.

oligotrophy

able to grow on very low concentrations of
dissolved compounds or low concentrations of
organic matter

oxygenic photosynthesis

Oxygenic photosynthesis is the process by which certain organisms, including plants, algae, and cyanobacteria, convert light energy into chemical energy while producing oxygen as a byproduct.6CO2​+6H2​O+light energy→C6​H12​O6​+6O

pangenome

A pangenome is defined as the entire collection of genes found across all individuals or strains within a specific group, such as a species. It encompasses the complete set of genes from all strains within a clade, acknowledging the genetic variations present in a population. This concept moves beyond a single, fixed genome, reflecting the diversity of genetic material

photoheterotroph

A photoheterotroph is an organism that uses light as its energy source and relies on organic compounds (such as carbohydrates, fatty acids, or alcohols) for carbon. Unlike photoautotrophs, which use carbon dioxide for carbon, photoheterotrophs cannot use carbon dioxide as their sole carbon source. They are typically found in various environments and play a role in the food chain by utilizing sunlight for energy while depending on organic materials for growth

Phylogenetic marker gene

is a gene whose sequence establishes the taxonomic
position of an organism and its evolutionary relationships to other organisms

Prochlorococcus

Prochlorococcus is a genus of very small (0.6 μm) marine cyanobacteria with an unusual pigmentation (chlorophyll a2 and b2). prokaryote

protorodopsin

Proteorhodopsins (PRs) are membrane-embedded, retinal-containing proteins that function as light-driven proton pumps. Since their discovery in 2000 in uncultured marine bacteria, PRs have been detected in numerous bacteria, archaea, and microbial eukarya. PRs have now been detected in diverse habitats, including marine, brackish, and freshwater environments; leaf surfaces; and soil crusts. Their widespread distribution and relatively simple single-molecule design suggests them as the earliest light-energy transducing proteins to have evolved. Currently, PRs represent the simplest biological means to convert light energy into chemical energy.

protists

single celled eukaryote

SAR11

SAR11 is a group of small, carbon-oxidizing bacteria that reach a global estimated population size of 2.4×10²⁸ cells—approximately 25% of all plankton. They are found throughout the oceans but reach their largest numbers in stratified, oligotrophic gyres,

shotgun sequencing

Shotgun sequencing is a laboratory technique that involves randomly breaking the genome of an organism into small DNA fragments, which are then sequenced individually. The resulting sequences are analyzed using computational algorithms to identify overlapping regions, allowing researchers to reconstruct the original DNA sequence. This method is particularly useful for sequencing large genomes quickly and efficiently.

transcript

In biology, transcription is the process of copying genetic information from DNA into messenger RNA (mRNA). This process is crucial for gene expression, as it allows the information stored in DNA to be translated into proteins

translation

In biology, translation is the process by which the genetic code carried by messenger RNA (mRNA) is converted into a specific sequence of amino acids, forming a polypeptide chain that eventually becomes a protein. This process occurs in three main steps: initiation, elongation, and termination, and takes place on ribosomes

amino acid

protein building blocks made up of carboxyl and amino groups

aminopepdiase

Aminopeptidase is defined as an enzyme that hydrolyzes peptides by acting on the peptide bond next to a terminal amino acid containing a free amino group. These enzymes are classified as exopeptidases and specifically cleave amino acids from the N-terminus of proteins and peptides. They play a crucial role in the final stages of protein digestion, helping to break down small peptides into individual amino acids for

biological pump

The biological pump is/are the sinking of organisms and
detritus from the surface layer to deep waters and sediments, moving carbon away from the
surface.

functional redundancy

functional redundancy is/are the presence of
several microbial taxa with the same or very similar metabolic capabilities

eukaryote

1. an organism consisting of a cell or cells in which the genetic material is DNA in the form of chromosomes contained within a distinct nucleus. Eukaryotes include all living organisms other than the eubacteria and archaea. Compare with prokaryote

FISH (Fluorescence in situ hybridization)

FISH is a powerful laboratory technique that allows researchers and clinicians to visualize and identify specific nucleic acid sequences within cells or tissue samples. It involves the use of fluorescently labeled DNA or RNA probes that bind to complementary sequences in the target DNA, enabling the detection of genetic material directly on chromosomes.

gross primary production GPP

Gross Primary Production (GPP)_______ is the production of O2 or of organic
material or the consumption of CO2 before respiration is subtracted out.

Kill the Winner

The Kill the Winner hypothesis in biology posits that host-specific predators control the population of each prey, preventing a winner from emerging and thus maintaining the coexistence of all species in the system. This hypothesis addresses the diversity paradox by suggesting that dominant species are targeted by predators and viruses, preventing any one species from taking over. This dynamic maintains biodiversity by allowing less dominant species to thrive when "winners" are controlled by predation.

microautoradiography

___________microautoradiography____________, which shows all cells stained with DAPI (a
general DNA stain that gives off fluorescence), while also showing which cells are “active.”
The “active” cells are indicated by the small black dots around the cell, resulting from uptake of
radioactively-labeled amino acids.

p v i curve

• In photosynthesis, it represents the empirical relationship between solar irradiance and photosynthesis.

phototrophy

Microorganisms capable of _________ phototrophy __________________ use at least one
type of light harvesting molecule (pigment, pigments), but do not necessarily have Rubisco.

Rubisco

RuBisCO, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is one of the most abundant proteins in the biosphere and a key enzyme in the global carbon cycle. It catalyzes the first step of carbon fixation by facilitating the reaction between carbon dioxide and ribulose bisphosphate, producing 3-phosphoglycerate, which is essential for the formation of glucose and other organic molecules

Winkler method

The Winkler Method is a technique used to measure dissolved oxygen in water, which is crucial for assessing the health of aquatic ecosystems. Developed by Hungarian chemist Lajos Winkler in 1888, this method involves filling a sample bottle completely with water to avoid air bias, followed by adding reagents that react with the dissolved oxygen to form a compound that can be titrated. The method is widely used in freshwater systems and is essential for water quality studies, as higher dissolved oxygen levels indicate better water quality and less pollution.

microscopy

use microscope

Seed bank hypothesis

Seed bank hypothesis in microbiology

The seed bank hypothesis in microbiology suggests that seed banks can stabilize coexistence among microbial species by providing a reservoir of diversity that allows them to persist under adverse conditions. This hypothesis is supported by research showing that seed banks can maintain bacterial diversity and stabilize community dynamics.

cultivation dependent

Cultivation-dependent __________ studies of aquatic bacteria communities
provide the least accurate diversity statistics and relative abundances of bacteria living in the
water column.

cultivation independent

Cultivation-independent methods refer to techniques used in microbiology and environmental studies that do not require the growth of microorganisms in culture. These methods are essential for studying microbial communities that are difficult or impossible to cultivate,

Endosymbiotic theory

The endosymbiotic theory is a scientific theory that suggests that certain organelles in eukaryotic cells, such as mitochondria and chloroplasts, originated from free-living prokaryotes (bacteria and archaea) that entered into a symbiotic relationship with a host cell. This theory explains how complex cells evolved from simpler ones and is widely accepted in the field of biology.

Growth rate hypothesis

The growth rate hypothesis in biology refers to the relationship between the rate of growth of an organism and its phosphorus (P) content. It posits that organisms with faster growth rates require more phosphorus for rapid protein synthesis, which is dependent on the abundance of phosphorus-rich ribosomes in cells.