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81.
82.
Background
Improvements in high-throughput technology and its increasing use have led to the generation of many highly complex datasets that often address similar biological questions. Combining information from these studies can increase the reliability and generalizability of results and also yield new insights that guide future research. 相似文献83.
Population studies of arbuscular mycorrhizal fungi (AMF) have traditionally been achieved by indirect analyses of soil-borne spore populations. These studies are not necessarily reflective of populations of AMF within the roots. Advances in molecular biology have revolutionized the analysis of fungal populations colonizing roots and forming mycorrhizas. Initially these studies were qualitative and reported presence or absence of particular AMF species in soils or in roots for comparison between different environments. More recently, the methodology has developed for direct quantification of AMF within roots. Quantitative PCR provides the means to study spatial distribution and individual quantification of AMF in mixed communities over time. In this review, we discuss the progress and application of indirect, direct and finally quantitative methodologies for studying arbuscular mycorrhizal communities. We conclude that the molecular tools now exist to quantitatively analyse the effect of environment, management or inoculation of soils on AMF communities within roots. 相似文献
84.
Pati A Labutti K Pukall R Nolan M Glavina Del Rio T Tice H Cheng JF Lucas S Chen F Copeland A Ivanova N Mavromatis K Mikhailova N Pitluck S Bruce D Goodwin L Land M Hauser L Chang YJ Jeffries CD Chen A Palaniappan K Chain P Brettin T Sikorski J Rohde M Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Lapidus A 《Standards in genomic sciences》2010,2(1):49-56
Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022(T) is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
85.
Sikorski J Chertkov O Lapidus A Nolan M Lucas S Del Rio TG Tice H Cheng JF Tapia R Han C Goodwin L Pitluck S Liolios K Ivanova N Mavromatis K Mikhailova N Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Brambilla E Yasawong M Rohde M Pukall R Spring S Göker M Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,3(3):304-314
Ilyobacter polytropus Stieb and Schink 1984 is the type species of the genus Ilyobacter, which belongs to the fusobacterial family Fusobacteriaceae. The species is of interest because its members are able to ferment quite a number of sugars and organic acids. I. polytropus has a broad versatility in using various fermentation pathways. Also, its members do not degrade poly-β-hydroxybutyrate but only the monomeric 3-hydroxybutyrate. This is the first completed genome sequence of a member of the genus Ilyobacter and the second sequence from the family Fusobacteriaceae. The 3,132,314 bp long genome with its 2,934 protein-coding and 108 RNA genes consists of two chromosomes (2 and 1 Mbp long) and one plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
86.
Göker M Held B Lapidus A Nolan M Spring S Yasawong M Lucas S Glavina Del Rio T Tice H Cheng JF Goodwin L Tapia R Pitluck S Liolios K Ivanova N Mavromatis K Mikhailova N Pati A Chen A Palaniappan K Brambilla E Land M Hauser L Chang YJ Jeffries CD Brettin T Detter JC Han C Rohde M Sikorski J Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,3(1):66-75
Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus Ignisphaera. This archaeal species is characterized by a coccoid-shape and is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral, boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed genome sequence of the genus Ignisphaera and the fifth genome (fourth type strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
87.
Mavromatis K Abt B Brambilla E Lapidus A Copeland A Deshpande S Nolan M Lucas S Tice H Cheng JF Han C Detter JC Woyke T Goodwin L Pitluck S Held B Brettin T Tapia R Ivanova N Mikhailova N Pati A Liolios K Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Rohde M Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2010,2(3):290-299
Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium that was isolated from seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of special interest because of its phylogenetic position in a genomically under-studied area of the bacterial diversity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Puniceicoccaceae. The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
88.
Sikorski J Lapidus A Copeland A Glavina Del Rio T Nolan M Lucas S Chen F Tice H Cheng JF Saunders E Bruce D Goodwin L Pitluck S Ovchinnikova G Pati A Ivanova N Mavromatis K Chen A Palaniappan K Chain P Land M Hauser L Chang YJ Jeffries CD Brettin T Detter JC Han C Rohde M Lang E Spring S Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,2(2):149-157
Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
89.
Mavromatis K Sikorski J Pabst E Teshima H Lapidus A Lucas S Nolan M Glavina Del Rio T Cheng JF Bruce D Goodwin L Pitluck S Liolios K Ivanova N Mikhailova N Pati A Chen A Palaniappan K Land M Hauser L Chang YJ Jeffries CD Rohde M Spring S Göker M Wirth R Woyke T Bristow J Eisen JA Markowitz V Hugenholtz P Klenk HP Kyrpides NC 《Standards in genomic sciences》2010,3(2):117-125
Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteriaand Archaea project. 相似文献