Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

The ISME Journal
Wei WeiKeishi Senoo

Abstract

Denitrification is an important process in the global nitrogen cycle. The genes encoding NirK and NirS (nirK and nirS), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. However, conventional polymerase chain reaction (PCR) primers can only detect a limited range of the phylogenetically diverse nirK and nirS. Thus, we developed new PCR primers covering the diverse nirK and nirS. Clone library and qPCR analysis using the primers showed that nirK and nirS in terrestrial environments are more phylogenetically diverse and 2-6 times more abundant than those revealed with the conventional primers. RNA- and culture-based analyses using a cropland soil also suggested that microorganisms with previously unconsidered nirK or nirS are responsible for denitrification in the soil. PCR techniques still have a greater capacity for the deep analysis of target genes than PCR-independent methods including metagenome analysis, although efforts are needed to minimize the PCR biases. The methodology and the insights obtained here should allow us to achieve a more precise understanding of the ecological behavior of denitrifiers and facilitate more...Continue Reading

References

Apr 2, 1999·Applied and Environmental Microbiology·S Hallin, P E Lindgren
Feb 28, 2001·Proceedings of the National Academy of Sciences of the United States of America·F CutruzzolaM Brunori
Jan 1, 1988·Annual Review of Microbiology·L I Hochstein, G A Tomlinson
Sep 26, 2002·Journal of the American Chemical Society·Oliver EinsleFrank Neese
Oct 4, 2006·Environmental Microbiology·Kim HeylenPaul De Vos
Feb 15, 2007·Environmental Microbiology·J Jason L Cantera, Lisa Y Stein
Jul 20, 2007·Cellular and Molecular Life Sciences : CMLS·T Sakurai, K Kataoka
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Nov 29, 2007·The ISME Journal·Luiz F W RoeschEric W Triplett
Mar 6, 2009·Environmental Microbiology·Laurent PhilippotMiloslav Simek
Feb 2, 2010·Applied and Environmental Microbiology·Karin EnwallSara Hallin
Feb 6, 2010·Environmental Microbiology·Rita BartossekChrista Schleper
Feb 26, 2010·The ISME Journal·Sergio E MoralesWilliam E Holben
Oct 26, 2010·Journal of Microbiological Methods·Kazuo IsobeYuichi Suwa
Jan 1, 2009·Standards in Genomic Sciences·Matt NolanJohn C Detter
Feb 18, 2011·Molecular Plant·Sakiko Okumoto, Guillaume Pilot
Jun 17, 2011·The ISME Journal·Satoshi IshiiKeishi Senoo
Sep 14, 2012·Microbes and Environments·Megumi YoshidaKeishi Senoo

❮ Previous
Next ❯

Citations

Apr 15, 2017·Environmental Science & Technology·Xiaohui WangNan Luo
Sep 16, 2017·Environmental Microbiology Reports·Jessica A LisaBongkeun Song
Jul 29, 2017·Molecular Ecology·Md Sainur SamadSergio E Morales
Jul 1, 2018·Applied and Environmental Microbiology·Silvia PajaresJorge D Etchevers
Feb 7, 2019·Environmental Microbiology·Yanjun MaAngela D Kent
Apr 30, 2019·FEMS Microbiology Ecology·Ianina AltshulerLyle G Whyte
Dec 13, 2016·Environmental Microbiology·Sara CoyotziJosh D Neufeld
Feb 23, 2020·Archives of Microbiology·Cumhur Avşar, E Sümer Aras
Apr 13, 2017·Scientific Reports·Yong WangMasahito Hayatsu
Feb 11, 2018·Applied and Environmental Microbiology·Mamoru OshikiSatoshi Ishii
Mar 1, 2020·Microorganisms·Antonio Castellano-Hinojosa, Sarah L Strauss
Dec 12, 2019·Environmental Science & Technology·Miguel Semedo, Bongkeun Song
Mar 6, 2021·The ISME Journal·Haoyang ShenKeishi Senoo
Aug 30, 2019·Environmental Science & Technology·Yunpeng QiuShuijin Hu

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.