N

nanopore- Soil pore having dimensions measured in nanometers. Materials encased in nanopores are beyond the reach of microorganisms and enzymes.

necrosis- Damage of living tissues because of infection or injury.

necrotrophic- Nutritional mechanism by which an organism produces a battery of hydrolytic enzymes to kill and break down host cells and then absorb nutritional compounds from the dead organic matter.

nematode- Multicellular eukaryote defined as an unsegmented, usually microscopic roundworm. Various species feed on plants, animals, fungi, and bacteria.

neutralism- Lack of interaction between two organisms in the same habitat.

niche- Functional role of a given organism within its habitat.

nicotinamide adenine dinucleotide (NAD+)- Important coenzyme, functioning as a hydrogen and electron carrier in a wide range of redox reactions; the oxidized form of the coenzyme is written NAD+, the reduced form as NADH.

nicotinamide adenine dinucleotide phosphate (NADP+)- Important coenzyme, functioning as a hydrogen and electron carrier in a wide range of redox reactions; the oxidized form of the coenzyme is written NADP+, the reduced form as NADPH.

nitrate reduction (biological)- Process whereby nitrate is reduced by plants and microorganisms to ammonium for cell synthesis (nitrate assimilation, assimilatory nitrate reduction) or to various lower oxidation states (N2, N2O, NO,) by bacteria using nitrate as the terminal electron acceptor in anaerobic respiration.

nitrification- Biological oxidation of ammonium to nitrite and nitrate, or a biologically induced increase in the oxidation state of nitrogen.

nitrifying bacteria- Chemolithotrophs capable of carrying out the transformations from NH3 to NO2- or NO2- to NO3-.

nitrogen cycle- Sequence of biochemical changes wherein nitrogen is used by a living organism, transformed upon the death and decomposition of the organism, and converted ultimately to its original state of oxidation.

nitrogen fixation- See dinitrogen fixation.

nitrogenase- Specific enzyme system required for biological N2 fixation.

nodule bacteria-see rhizobia.

nodule- See root nodule.

nodulins- Unique proteins produced in root hairs or nodules in response to rhizobial infection.

nomenclature- System of naming organisms.

nonpolar- Possessing hydrophobic (water repelling) characteristics and not easily dissolved in water.

northern blot- Hybridization of single-stranded nucleic acid (DNA or RNA) to RNA fragments immobilized on a filter.

nucleic acid- Polymer of nucleotides.

nucleoid- Aggregated mass of DNA that makes up the chromosome of prokaryotic cells.

nucleophilic compound- Chemical that attracks or is drawn to electron-deficient regions in other chemicals; reducing agents act as nucleophilic compounds.

nucleoside- Nucleotide without the phosphate group.

nucleotide- Monomeric unit of nucleic acid, consisting of a sugar (pentose), a phosphate, and a nitrogenous base.

nucleus- Membrane-enclosed structure containing the genetic material (DNA) organized in chromosomes.

nutrient- Substance taken by a cell from its environment and used in catabolic or anabolic reactions.

O

obligate- (i) Adjective referring to an environmental factor (for example, oxygen) that is always required for growth. (ii) Organism that can grow and reproduce only by obtaining carbon and other nutrients from a living host, such as obligate symbiont.

oligonucleotide- Short nucleic acid chain, either obtained from an organism or synthesized chemically.

oligotroph- Microorganism specifically adapted to grow under low nutrient supply. Thought to subsist on the more resistant soil organic matter and be little affected by the addition of fresh organic materials. Sometimes a synonym for autochthonous.

oogonium- Specialized sexual structure formed as a female gametangium by funguslike organisms in the phylum Oomycota.oospore- Thick-walled spore formed within an oogonium by fungus-like organisms in the phylum Oomycota.

operon- Cluster of genes whose expression is controlled by a single operator; typical in prokaryotic cells

organelle- Membrane-enclosed body specialized for carrying out certain functions; found only in eukaryotic cells.

organic soil- Soil that contains a high percentage (>200 g kg-1, or >120-180 g kg-1 if saturated with water) of organic carbon.

organotroph- Organism that obtains reducing equivalents (stored electrons) from organic substrates.

osmosis- Diffusion of water through a membrane from a region of low solute concentration to one of higher concentration.

osmotic potential- Portion of total soil water potential due to the presence of solutes in soil water.

oven-dry soil- Soil that has been dried at 105°C until it reaches constant mass.

oxic- Containing oxygen; aerobic. Usually used in reference to a microbial habitat.

oxidation- Process by which a compound gives up electrons, acting as an electron donor, and becomes oxidized.

oxidation-reduction (redox) reaction- Coupled pair of reactions, in which one compound becomes oxidized, while another becomes reduced and takes up the electrons released in the oxidation reaction.

oxidation state- Number of electrons to be added (or subtracted) from an atom in a combined state to convert it to the elemental form.

oxidative phosphorylation- Synthesis of ATP involving a membrane-associated electron-transport chain and the creation of a proton-motive force. Also called electron-transport chain phosphorylation.

oxygenic photosynthesis- Use of light energy to synthesize ATP and NADPH by noncyclic photophosphorylation with the production of oxygen from water.

P

parasitism- Feeding by one organism on the cells of a second organism, which is usually larger than the first. The parasite is, to some extent, dependent on the host at whose expense it is maintained.

parasexual cycle- Nuclear cycle in which genes of haploid nuclei recombine without meiosis.

particle density- Density of the soil particles, the dry mass of the particles being divided by the solid (not bulk) volume of the particles, in contrast with bulk density.

particle size- Effective diameter of a particle measured by sedimentation, sieving or micrometric methods.

pasteurization- Process using mild heat to reduce microbial numbers in heat-sensitive materials.

pathogen- Organism able to inflict damage on a host it infects.

pathogenicity- Ability of a parasite to inflict damage on the host.

pathogen- suppressive soil- Soil where a pathogen does not establish or persist, a pathogen establishes but causes little or no damage, or a pathogen causes disease for a while, but the disease becomes less important even though the pathogen persists in soil.

peat- Unconsolidated soil material consisting largely of undecomposed, or only slightly decomposed, organic matter accumulated under conditions of excessive moisture.

pectin- Important component of the plant cell walls containing chains of galacturonic acid that is often esterified with a methyl group.

pellicle- Relatively rigid layer of proteinaceous elements just beneath the cell membrane in many protozoa and algae.

peptidoglycan-Rigid layer of cell walls of bacteria, a thin sheet composed of N-acetylglucosamine, N-acetylmuramic acid, and a few amino acids. Also called murein.

peribacteroid membrane- Plant-derived membrane surrounding one to several rhizobia within host cells of legume nodules.

periplasmic space- Area between the cell membrane and the cell wall in Gram-negative bacteria, containing certain enzymes involved in nutrition.

perithecium- Flask-shaped ascocarp open at the tip; containing asci of fungi in the phylum Ascomycota.

peritrichous flagellation- Having flagella attached to many places on the cell surface.

permanent wilting point- Greatest water content of a soil at which indicator plants, growing in that soil wilt and fail to recover when placed in a humid chamber. Often estimated by the water content at -1.5-MPa soil matric potential.

pH- Negative logarithm of the hydrogen ion activity. The degree of acidity (or alkalinity) of a soil as determined by means of a glass or other suitable electrode or indicator at a specified moisture content or soil-water ratio, and expressed in terms of the pH scale.

phage- See bacteriophage.

phagotrophic- Form of feeding where animals, such as protozoans, engulf particulate nutrients, such as bacterial cells or detritus.

phenotype- Observable properties of an organism.

phosphobacterium- Bacterium that is especially good at solubilizing the insoluble inorganic phosphate in soil.

phosphodiester bond- Type of covalent bond linking nucleotides together in a polynucleotide.

phospholipid- Lipids containing a substituted phosphate group and two fatty acid chains on a glycerol backbone.

phosphorus cycle- sequence of transformations undergone by phosphorus where it is transformed between soluble and insoluble, and organic and inorganic forms.

photic zone- Uppermost layer of a body of water or soil that receives enough sunlight to permit the occurrence of photosynthesis.

photoautotroph- Organism able to use light as its sole source of energy and carbon dioxide as sole carbon source.

photoheterotroph- Organism able to use light as a source of energy and organic materials as carbon source.

photophosphorylation- Synthesis of high-energy phosphate bonds, as ATP, using light energy.

photosynthesis- Process of using light energy to synthesize carbohydrates from carbon dioxide.

phototaxis- Movement toward light.

phototroph- Organism that uses light as the energy source to drive the electron flow from the electron donors, such as water, hydrogen, or sulfide.

phycobilin- Water-soluble pigment that occurs in cyanobacteria and functions as the light-harvesting pigments for Photosystem II.

phylogeny- Ordering of species into higher taxa and the construction of evolutionary trees based on evolutionary (genetic) relationships.

pilus (plural pili)- Fimbria-like structure that is present on fertile cells and is involved in DNA transfer during conjugation. Sometimes called sex pilus.

plaque- Localized area of lysis or cell inhibition caused by virus infection on a lawn of cells.

plant growth-promoting rhizobacteria (PGPR)- Broad group of soil bacteria that exert beneficial effects on plant growth usually as root colonizers. Many members of the genus Pseudomonas.

plasma membrane- See cytoplasmic membrane.

plasmid- Covalently closed, circular piece of DNA which, as an extrachromosomal genetic element, is not essential for growth.

plasmogamy- Fusion of the contents of two cells, including cytoplasm and nuclei.

plastid- Specialized cell organelles containing pigments or protein materials.

plate count- Number of colonies formed on a solid culture medium when uniformly inoculated with a known amount of soil, generally as a dilute soil suspension. The technique estimates the number of certain organisms present in the soil sample.

polar- Possessing hydrophilic characteristics and generally water soluble.

popoly-beta-hydroxybutyrate (PHB)- Common storage material of prokaryotic cells consisting of beta-hydroxybutyrate or other beta-alkanoic acids.lar flagellation- Condition of having flagella attached at one end or both ends of the cell.

polyclonal antiserum- Mixture of antibodies to a variety of antigens or to a variety of determinants on a single antigen.

polymer- Large molecule formed by polymerization of monomeric units.

polymerase chain reaction (PCR)- Method for amplifying DNA in vitro, involving the use of oligonucleotide primers complementary to nucleotide sequences in target genes and the copying of the target sequences by the action of DNA polymerase.

polysaccharide- Long chain of monosaccharides (sugars) linked by glycosidic bonds.

polysome- Strings of ribosomes attached by strands of mRNA.

pore space- Portion of soil bulk volume occupied by soil pores.

porin- A protein channel in the lipopolysaccharide layer of Gram-negative bacteria.

porosity- Volume of pores in a soil sample (nonsolid volume) divided by the bulk volume of the sample.

pour plate- Method for performing a plate count of microorganisms. A known amount of a serial dilution is placed in a sterile Petri dish and then a melted agar medium is added and the inoculum mixed well by gently swirling. After growth the number of colony forming units is counted.

predation- Relationship between two organisms whereby one organism (predator) engulfs or captures and digests the second organism (prey).

primary producer- Organism that adds biomass to the ecosystem by synthesizing organic molecules from carbon dioxide and simple inorganic nutrients.

primer- Molecule (usually a polynucleotide) to which DNA polymerase can attach the first nucleotide during DNA replication.

prokaryote- Organism lacking a unit membrane-bound nucleus and other organelles, usually having its DNA in a single circular molecule.

promoter- Site on DNA where the RNA polymerase binds and begins transcription.

propagule- Cell unit capable of developing into a complete organism.

prophage- State of the genome of a temperate virus when it is replicating in synchrony with that of the host, typically integrated into the host genome.

prosthetic group- Tightly bound, nonprotein portion of an enzyme; not the same as coenzyme.

protocooperation- See synergism.

proton motive force (PMF)- Energized state of a membrane created by expulsion of protons through action of an electron transport chain.

protoplasm- Complete cellular contents, cytoplasmic membrane, cytoplasm, and nucleus; usually considered the living portion of the cell, thus excluding those layers peripheral to the cell membrane.

protoplast- Cell from which the wall has been removed.

Protista-Old taxonomic term referring to algae, fungi, and protozoa (collectively, the eukaryotic protists), and the prokaryotes.

protozoan (plural, protozoa)- Unicellular eukaryotic microorganisms that move by either protoplasmic flow (amoebae), flagella (flagellates) or, cilia (ciliates). Most species feed on bacteria, fungi, or detrital particles.

provirus- See prophage.

pseudomonad- Member of the genus Pseudomonas, a large group of Gram-negative, obligately respiratory (never fermentative) bacteria.

pseudopodium (plural, pseudopodia)- Protrusion of an amoeboid cell formed by the extrusion or streaming of the cytoplasm (but still enclosed in the membrane) for the purpose of movement or feeding.

psychrophile- Organism able to grow at low temperatures and showing a growth temperature optimum < 15 deg. C.

pure culture- Population of microorganisms composed of a single strain. Such cultures are obtained through selective laboratory procedures and are rarely found in a natural environment.

Q

Q10- Relative increase in a reaction rate with temperature. It is expressed as the increase over a 10 deg.C interval.