''Ensifer meliloti'' (formerly ''Rhizobium meliloti'' and ''Sinorhizobium meliloti'') are an aerobic,

Gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wa ...

, and

diazotroph Diazotrophs are bacteria and archaea that fix gaseous nitrogen in the atmosphere into a more usable form such as ammonia. A diazotroph is a microorganism that is able to grow without external sources of fixed nitrogen. Examples of organisms that ...

ic species of bacteria. ''S. meliloti'' are

motile Motility is the ability of an organism to move independently, using metabolic energy. Definitions Motility, the ability of an organism to move independently, using metabolic energy, can be contrasted with sessility, the state of organisms th ...

and possess a cluster of peritrichous

flagella A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have f ...

. ''S. meliloti'' fix atmospheric nitrogen into ammonia for their legume symbionts, such as alfalfa. ''S. meliloti'' forms a symbiotic relationship with

legume A legume () is a plant in the family Fabaceae (or Leguminosae), or the fruit or seed of such a plant. When used as a dry grain, the seed is also called a pulse. Legumes are grown agriculturally, primarily for human consumption, for livestock fo ...

s from the genera ''

Medicago ''Medicago'' is a genus of flowering plants, commonly known as medick or burclover, in the legume family ( Fabaceae). It contains at least 87 species and is distributed mainly around the Mediterranean basin. The best-known member of the genus is ...

'', ''

Melilotus ''Melilotus'', known as melilot, sweet clover, and kumoniga (from the Cumans),Bulgarian Folk Customs, Mercia MacDermott, pg 27 is a genus in the family Fabaceae (the same family that also includes the ''Trifolium'' clovers). Members are known ...

'' and '' Trigonella'', including the model legume ''

Medicago truncatula ''Medicago truncatula'', the barrelclover, strong-spined medick, barrel medic, or barrel medick, is a small annual legume native to the Mediterranean region that is used in genomic research. It is a low-growing, clover-like plant tall with trifol ...

''. This symbiosis promotes the development of a plant organ, termed a

root nodule Root nodules are found on the roots of plants, primarily legumes, that form a symbiosis with nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of bacteria know ...

. Because soil often contains a limited amount of nitrogen for plant use, the symbiotic relationship between ''S. meliloti'' and their legume hosts has agricultural applications. These techniques reduce the need for inorganic nitrogenous

fertilizer A fertilizer (American English) or fertiliser (British English; see spelling differences) is any material of natural or synthetic origin that is applied to soil or to plant tissues to supply plant nutrients. Fertilizers may be distinct from ...

Symbiosis

Symbiosis between ''S. meliloti'' and its legume hosts begins when the plant secretes an array of betaines and

flavonoid Flavonoids (or bioflavonoids; from the Latin word ''flavus'', meaning yellow, their color in nature) are a class of polyphenolic secondary metabolites found in plants, and thus commonly consumed in the diets of humans. Chemically, flavonoids ...

s into the rhizosphere: 4,4′-dihydroxy-2′-methoxy

chalcone Chalcone is the organic compound C6H5C(O)CH=CHC6H5. It is an α,β-unsaturated ketone. A variety of important biological compounds are known collectively as chalcones or chalconoids. Chemical properties Chalcones have two absorption maxima at ...

, chrysoeriol, cynaroside,

4′,7-dihydroxyflavone 4′,7-Dihydroxyflavone is a flavone. It is found in ''Medicago truncatula'' in relation with the root nodulation symbiont ''Sinorhizobium meliloti'' or in seeds of '' Sophora viciifolia''. Like many other flavonoids, 4′,7-dihydroxyflavone has ...

, 6′′-O-malonylononin, liquiritigenin,

luteolin Luteolin is a flavone, a type of flavonoid, with a yellow crystalline appearance. Luteolin is the principal yellow dye compound that is obtained from the plant ''Reseda luteola'', which has been used as a source of the dye since at least the firs ...

, 3′,5-dimethoxyluteolin, 5-methoxyluteolin, medicarpin, stachydrine, and

trigonelline Trigonelline is an alkaloid with chemical formula . It is a zwitterion formed by the methylation of the nitrogen atom of niacin (vitamin B3). Trigonelline is a product of niacin metabolism that is excreted in urine of mammals. Trigonelline occurs ...

. These compounds attract ''S. meliloti'' to the surface of the root hairs of the plant where the bacteria begin secreting

nod factor Nod factors (nodulation factors or NF), are signaling molecules produced by soil bacteria known as rhizobia in response to flavonoid exudation from plants under nitrogen limited conditions. Nod factors initiate the establishment of a symbiotic r ...

s. This initiates root hair curling. The rhizobia then penetrate the root hairs and proliferate to form an infection thread. Through the infection thread, the bacteria move toward the main root. The bacteria develop into bacteroids within newly formed root nodules and perform nitrogen fixation for the plant. A ''S. meliloti'' bacterium does not perform nitrogen fixation until it differentiates into a endosymbiotic bacteroid. A bacteroid depends on the plant for survival.

Leghemoglobin 3rd Leghemoglobin (also leghaemoglobin or legoglobin) is an oxygen-carrying phytoglobin found in the nitrogen-fixing root nodules of leguminous plants. It is produced by these plants in response to the roots being colonized by nitrogen-fixing ...

, produced by leguminous plants after colonization of ''S. meliloti,'' interacts with the free oxygen in the root nodule where the rhizobia reside. Rhizobia are contained within symbiosomes in the root nodules of leguminous plants. The leghemoglobin reduces the amount of free oxygen present. Oxygen disrupts the function of the

nitrogenase Nitrogenases are enzymes () that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria. These enzymes are responsible for the reduction of nitrogen (N2) to ammonia (NH3). Nitrogenases are the only fam ...

enzyme in the rhizobia, which is responsible for nitrogen fixation.

Genome

The ''S. meliloti''

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

contains four genes coding for flagellin. These include ''fliC1C2–fliC3C4''. The genome contains three replicons: a

chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins ar ...

(~3.7 megabases), a

chromid Secondary chromosomes (recently renamed chromids) are a class of bacterial replicons (replicating DNA molecules). These replicons are called "chromids" because they have characteristic features of both ''chrom''osomes and plasm''id''s. Early on, ...

(pSymB; ~1.7 megabases), and a

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; howev ...

(pSymA; ~1.4 megabases). Individual strains may possess additional, accessory plasmids. Five ''S. meliloti'' genomes have been sequenced to date: Rm1021, AK83, BL225C, Rm41, and SM11 with 1021 considered to be the

wild type The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, "m ...

. Indeterminate nodule symbiosis by ''S. meliloti'' is conferred by genes residing on pSymA.

DNA repair

The proteins encoded by ''E. meliloti'' genes ''uvrA'', ''uvrB'' and ''uvrC'' are employed in the repair of

DNA damage DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA da ...

s by the process of

nucleotide excision repair Nucleotide excision repair is a DNA repair mechanism. DNA damage occurs constantly because of chemicals (e.g. intercalating agents), radiation and other mutagens. Three excision repair pathways exist to repair single stranded DNA damage: Nucle ...

. ''E. meliloti'' is a desiccation tolerant bacterium. However, ''E. meliloti'' mutants defective in either genes ''uvrA'', ''uvrB'' or ''uvrC'' are sensitive to

desiccation Desiccation () is the state of extreme dryness, or the process of extreme drying. A desiccant is a hygroscopic (attracts and holds water) substance that induces or sustains such a state in its local vicinity in a moderately sealed container. ...

, as well as to

UV light Ultraviolet (UV) is a form of electromagnetic radiation with wavelength from 10 nm (with a corresponding frequency around 30 PHz) to 400 nm (750 THz), shorter than that of visible light, but longer than X-rays. UV radiation i ...

. This finding indicates that the desiccation tolerance of wild-type ''E. meliloti'' depends on the repair of DNA damages that can be caused by desiccation.

Bacteriophage

Several

bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bact ...

s that infect ''Sinorhizobium meliloti'' have been described:Systematic naming of bacteriophages is rarely followed in the scientific literature, and a variety of phages can share the same name. While there exists an RNA phage called ΦM12, which infects enterobacteria, it is not synonymous with the DNA phage ΦM12 listed here. The same may be true for other phages in this list. Within this list, two phages have independently been named ΦM5. Φ1, Φ1A, Φ2A, Φ3A, Φ4 (=ΦNM8), Φ5^t (=ΦNM3), Φ6 (=ΦNM4), Φ7 (=ΦNM9), Φ7a, Φ9 (=ΦCM2), and Φ11 (=ΦCM9), Φ12 (=ΦCM6), Φ13, Φ16, Φ16-3,
The full genome of this phage is available a
NCBI
/ref> Φ16a, Φ16B, Φ27, Φ32, Φ36, Φ38, Φ43, Φ70, Φ72, Φ111, Φ143, Φ145, Φ147, Φ151, Φ152, Φ160, Φ161, Φ166, Φ2011, ΦA3, ΦA8, ΦA161, ΦAL1, ΦCM1, ΦCM3, ΦCM4, ΦCM5, ΦCM7, ΦCM8, ΦCM20, ΦCM21, ΦDF2, Φf2D, ΦF4, ΦFAR, ΦFM1, ΦK1, ΦL1, Note that this article was reprinted in ''Plant and Soil'' (1971) 35 (1): 63—66, which is where the URL and doi direct to. ΦL3, ΦL5, ΦL7, ΦL10, ΦL20, ΦL21, ΦL29, ΦL31, ΦL32, ΦL53, ΦL54, ΦL55, ΦL56, ΦL57, ΦL60, ΦL61, ΦL62, ΦLO0, ΦLS5B, ΦM1, ΦM1, ΦM1-5, ΦM2, ΦM3, ΦM4, ΦM5, ΦM5 (=ΦF20), ΦM5N1, ΦM6, ΦM7, ΦM8, ΦM9, ΦM10, ΦM11, ΦM11S, ΦM12, ΦM14, ΦM14S, ΦM19, ΦM20S, ΦM23S, ΦM26S, ΦM27S, ΦMl, ΦMM1C, ΦMM1H, ΦMP1, ΦMP2, ΦMP3, ΦMP4, ΦN2, ΦN3, ΦN4, ΦN9, ΦNM1, ΦNM2, ΦNM6, ΦNM7, ΦP6, ΦP10, ΦP33, ΦP45, ΦPBC5,This phage has never been formally reported in the scientific literature. However, the full genomic sequence has been uploaded to NCBI, availabl
here
ΦRm108, ΦRmp26, ΦRmp36, ΦRmp38, ΦRmp46, ΦRmp50, ΦRmp52, ΦRmp61, ΦRmp64, ΦRmp67, ΦRmp79, ΦRmp80, ΦRmp85, ΦRmp86, ΦRmp88, ΦRmp90, ΦRmp145, ΦSP, ΦSSSS304, ΦSSSS305, ΦSSSS307, ΦSSSS308, and ΦT1. Of these, ΦM5, ΦM12, Φ16-3Φ16-3 Complete Genome
/ref> and ΦPBC5 have been sequenced. As of March 2020 the

International Committee on Taxonomy of Viruses The International Committee on Taxonomy of Viruses (ICTV) authorizes and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to ap ...

(ICTV) has accepted the following species in its Master Species List 2019.v1 (#35): * Realm: ''

Duplodnaviria ''Duplodnaviria'' is a realm of viruses that includes all double-stranded DNA viruses that encode the HK97 fold major capsid protein. The HK97 fold major capsid protein (HK97 MCP) is the primary component of the viral capsid, which stores the ...

'', Kingdom: ''

Heunggongvirae ''Duplodnaviria'' is a realm of viruses that includes all double-stranded DNA viruses that encode the HK97 fold major capsid protein. The HK97 fold major capsid protein (HK97 MCP) is the primary component of the viral capsid, which stores the vi ...

'', Phylum: '' Uroviricota'' :* Order: ''

Caudovirales ''Caudovirales'' is an order of viruses known as the tailed bacteriophages (''cauda'' is Latin for "tail"). Under the Baltimore classification scheme, the ''Caudovirales'' are group I viruses as they have double stranded DNA (dsDNA) genomes, ...

'', Family: '' Myoviridae'', Genus: '' Emdodecavirus'' (formerly ''M12virus'') ::* Species: ''Sinorhizobium virus M7'' (alias ΦM7) ::* Species: ''Sinorhizobium virus M12'' (alias DNA phage ΦM12, type species) ::* Species: ''Sinorhizobium virus N3'' (alias ΦN3)

References

External links