An introduction to the analysis of nitrogen fixation

This article has been cited by other articles in PMC.

An introduction to the analysis of nitrogen fixation

A comprehensive aligned nifH gene database: Published by Oxford University Press. This article has been cited by other articles in PMC. Abstract We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms.

The database contains 32 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata.

An introduction to the analysis of nitrogen fixation

Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core.

Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Biological nitrogen fixation is catalyzed by nitrogenase, a complex enzyme that has two components, a heterotetrameric core encoded by nifD and nifK, and a dinitrogenase reductase subunit encoded by nifH 5.

Dinitrogenase reductase transfers reducing equivalents to the core enzyme complex where those reducing equivalents are used to convert N2 into NH3 equivalents. The nifH gene is the biomarker most widely used to study the ecology and evolution of nitrogen-fixing bacteria 6.

Surveys of nifH diversity have been conducted in a wide range of environments including various marine 7—9terrestrial 10—12 and hydrothermal sites 13 among others. The diversity of nitrogen-fixing organisms varies dramatically across habitats with different habitats selecting for different groups of nitrogen-fixing organisms 14 Homologs of the nifH gene can be divided into five main phylogenetic clusters Cluster I contains a diverse group of nifH genes primarily from aerobic and facultatively anaerobic organisms that belong to phyla including Proteobacteria, Cyanobacteria, Firmicutes and Actinobacteria.


Cluster III contains nifH genes that are almost exclusively found in obligate anaerobes including methanogenic Archaea, Treponema, Clostridium and sulfate-reducing and sulfur-reducing species of Deltaproteobacteria.

There also exist V—Fe alternative nitrogenases encoded by vnfH. The alternative nitrogenases appear to be found only in the genomes of organisms that also contain nif genes Clusters IV and V contain paralogous genes that do not participate in nitrogen fixation 618— Analyses of microbial gene sequences that serve as functional biomarkers are facilitated by the availability of annotated databases of aligned sequences.

Aligned sequences are required for phylogenetic analyses [e. Universal and group-specific PCR primers are used in quantitative real-time PCR for the quantification of gene copy numbers in the environment [e.

Hence, many contemporary techniques in molecular microbial ecology require PCR and specific primers, which must be designed and evaluated using annotated sequence databases.


There is strong demand for the creation of a centralized, well-described, aligned and vetted nifH database. In this work, we describe a comprehensive nifH database, a multipurpose tool to facilitate the work of researchers who use sequence-based techniques to study nitrogen-fixing bacteria.

The database is implemented in the ARB software package 35 that allows for the compilation and association of aligned sequence data, sequence metadata and phylogenetic trees. Phylogenetic trees can be used to navigate the sequences and to explore phylogenetic patterns found in associated metadata.

Preliminary versions of this nifH database, one containing 16 and another 23 sequences, were used to evaluate the diversity of nifH genes in different environments 15 and to evaluate PCR primers used in environmental surveys of nifH diversity An introduction to the analysis of nitrogen fixation Daimen Harland recovered, his very arrogant dump.

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Apr 29,  · Keywords: biofuel, legumes, life-cycle analysis, nitrogen fixation. 1. Introduction. Two of humanity’s major needs are food and energy.

An introduction to the analysis of nitrogen fixation

With the human population rising at an alarming rate (1 billion increase from present billion in the next 12 years (UN estimate)), food security, mainly due to increasing scarcity of land and. The plant supplies photosynthates for the bacterium and in turn, the bacterium gives assimilated nitrogen to the plant.

In these days of energy crisis, increasing the capacity of biological nitrogen fixation, is felt as an additional, if not an alternative to chemical fertilizers.

Abstract. A genome-wide association study (GWAS) was conducted to explore the genetic basis of variation for symbiotic nitrogen fixation (SNF) and related traits in the Andean Diversity Panel (ADP) comprising common bean (Phaseolus vulgaris) ADP was evaluated for SNF and related traits in both greenhouse and field experiments.

CHAPTER Nitrogen fixation and nitrogen metabolism. Introduction Living organisms need nitrogen because it is a part of the amino acids that make up proteins, and the nucleic acids that make up DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).Nitrogen(dinitrogen, N2) is highly inter gas.

fixation genes in dyrhizobiumBra, and a global census of nitrogenases and nitrogen fixation genes. Section 5 covers the genomics of selected nitrogen fixing .

The Role of Symbiotic Nitrogen Fixation in Sustainable Production of Biofuels