| Kocuria rhizophila | |
|---|---|
Scientific classification  | |
| Domain: | Bacteria |
| Phylum: | Actinomycetota |
| Class: | Actinomycetia |
| Order: | Micrococcales |
| Family: | Micrococcaceae |
| Genus: | Kocuria |
| Species: | K. rhizophila |
| Binomial name | |
| Kocuria rhizophila Kovács et al. 1999 | |
| Type strain | |
| ATCC BAA-50 CIP 105972 DSM 11926 IFO 16319 JCM 11653 NBRC 16319 TA68 | |
Kocuria rhizophila is a soil dwelling Gram positive bacterium in the genus Kocuria . It is used in industry for antimicrobial testing and in food preparation.
The genome has been sequenced and contains 2,697,540$ base pairs, [1] which is among the smallest for Actinomycetota, with a G+C content of 71.16%. This encodes 2357 protein coding genes, including many transporters and enzymes for the transformation of phenolic compounds, contributing to its ability to metabolize plant material.
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. The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences, and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome.
Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.
Pinus taeda, commonly known as loblolly pine, is one of several pines native to the Southeastern United States, from East Texas to Florida, and north to southern New Jersey. The wood industry classifies the species as a southern yellow pine. U.S. Forest Service surveys found that loblolly pine is the second-most common species of tree in the United States, after red maple. For its timber, the pine species is regarded as the most commercially important tree in the Southeastern U.S. The common name loblolly is given because the pine species is found mostly in lowlands and swampy areas.
Acidobacteriota is a phylum of Gram-negative bacteria. Its members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture.
The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of Genomics, The Institute for Genomic Research (TIGR), the Institute for Biological Energy Alternatives, and the J. Craig Venter Science Foundation Joint Technology Center. It has facilities in Rockville, Maryland and La Jolla, California.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.
Tombusviridae is a family of single-stranded positive sense RNA plant viruses. There are three subfamilies, 17 genera, and 95 species in this family. The name is derived from Tomato bushy stunt virus (TBSV).
Micrococcus luteus is a Gram-positive to Gram-variable, nonmotile, tetrad-arranging, pigmented, saprotrophic coccus bacterium in the family Micrococcaceae. It is urease and catalase positive. An obligate aerobe, M. luteus is found in soil, dust, water and air, and as part of the normal microbiota of the mammalian skin. The bacterium also colonizes the human mouth, mucosae, oropharynx and upper respiratory tract.
The family Micrococcaceae includes bacterial genera of Gram positive cocci that inhabit the air and skin, such as Micrococcus luteus.
In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.
Micrococcus is a genus of bacteria in the Micrococcaceae family. Micrococcus occurs in a wide range of environments, including water, dust, and soil. Micrococci have Gram-positive spherical cells ranging from about 0.5 to 3 micrometers in diameter and typically appear in tetrads. They are catalase positive, oxidase positive, indole negative and citrate negative. Micrococcus has a substantial cell wall, which may comprise as much as 50% of the cell mass. The genome of Micrococcus is rich in guanine and cytosine (GC), typically exhibiting 65 to 75% GC-content. Micrococci often carry plasmids that provide the organism with useful traits.
Populus trichocarpa, the black cottonwood, western balsam-poplar or California poplar, is a deciduous broadleaf tree species native to western North America. It is used for timber, and is notable as a model organism in plant biology.
Stenotrophomonas is a genus of Gram-negative bacteria, comprising at least ten species. The main reservoirs of Stenotrophomonas are soil and plants. Stenotrophomonas species range from common soil organisms to opportunistic human pathogens ; the molecular taxonomy of the genus is still somewhat unclear.
The Nitrososphaerota are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteota. Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes. This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum. The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.
Rothia kristinae is a Gram positive bacterium. R. kristinae is a common human skin organism, but can cause opportunistic infections in humans.
Kocuria is a genus of gram-positive bacteria. Kocuria is named after Miloslav Kocur, a Czech microbiologist. It has been found in the milk of water deer and reindeer. Cells are coccoid, resembling Staphylococcus and Micrococcus, and can group in pairs, chains, tetrads, cubical arrangements of eight, or irregular clusters. They have rigid cell walls and are either aerobic or facultative anaerobic. Kocuria can usually survive in mesophilic temperatures.
Opitutus terrae is an obligately anaerobic bacterium first isolated from rice paddy soil, hence its epithet. It is coccus-shaped and is motile by means of a flagellum. Its type strain is PB90-1T. Its genome has been sequenced.
Ensifer medicae is a species of gram-negative, nitrogen-fixing, rod-shaped bacteria. They can be free-living or symbionts of leguminous plants in root nodules. E.medicae was first isolated from root nodules on plants in the genus Medicago. Some strains of E.medicae, like WSM419, are aerobic. They are chemoorganotrophic mesophiles that prefer temperatures around 28 °C. In addition to their primary genome, these organisms also have three known plasmids, sized 1,570,951 bp, 1,245,408 bp and 219,313 bp.
Kocuria rosea is a gram-positive bacteria that is catalase-positive and oxidase-positive. It has a coccus shape that occurs in the tetrad arrangement and is a strict aerobe that grows best from 25 to 37 °C. K. rosea has also been found to cause urinary tract infections in people with weakened immune systems.
Magnaporthe rhizophila is a fungus species in the family Magnaporthaceae. These dark mycelial fungi are common pathogens of cereal and grass roots. Rice blast is one disease known to be caused by M. rhizophila and presents with vascular discoloration in the host organism. The fungus lives best in drier humid conditions, explaining why it is most often found in the soils of Australia, South Africa, and the Southeastern United States.
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