scholarly journals Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers

mSphere ◽  
2021 ◽  
Author(s):  
Kazumori Mise ◽  
Yoko Masuda ◽  
Keishi Senoo ◽  
Hideomi Itoh
Keyword(s):  
Agricultural Productivity ◽  
Biogeochemical Cycling ◽  
Metagenomic Sequencing ◽  
Nitrogen Fixing ◽  
Nitrogen Fixers ◽  
Microbial Ecosystems ◽  
Nitrogenase Genes ◽  
Biological Nitrogen

Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases.

scholarly journals New Nitrogen-Fixing Microorganisms Detected in Oligotrophic Oceans by Amplification of Nitrogenase (nifH) Genes

1998 ◽  
Vol 64 (9) ◽  
pp. 3444-3450 ◽  
Author(s):  
Jonathan P. Zehr ◽  
Mark T. Mellon ◽  
Sabino Zani
Keyword(s):  
Inorganic Nitrogen ◽  
Size Fraction ◽  
Nitrogen Fixing ◽  
Nitrogen Fixers ◽  
Nitrogenase Genes ◽  
Microbiological Techniques ◽  
Nitrogen Concentrations ◽  
Ocean Gyres ◽  
Planktonic Crustaceans ◽  
Sequence Types

ABSTRACT Oligotrophic oceanic waters of the central ocean gyres typically have extremely low dissolved fixed inorganic nitrogen concentrations, but few nitrogen-fixing microorganisms from the oceanic environment have been cultivated. Nitrogenase gene (nifH) sequences amplified directly from oceanic waters showed that the open ocean contains more diverse diazotrophic microbial populations and more diverse habitats for nitrogen fixers than previously observed by classical microbiological techniques. Nitrogenase genes derived from unicellular and filamentous cyanobacteria, as well as from the α and γ subdivisions of the class Proteobacteria, were found in both the Atlantic and Pacific oceans. nifH sequences that cluster phylogenetically with sequences from sulfate reducers or clostridia were found associated with planktonic crustaceans. Nitrogenase sequence types obtained from invertebrates represented phylotypes distinct from the phylotypes detected in the picoplankton size fraction. The results indicate that there are in the oceanic environment several distinct potentially nitrogen-fixing microbial assemblages that include representatives of diverse phylotypes.

scholarly journals Inoculation with Different Nitrogen-Fixing Bacteria and Arbuscular Mycorrhiza Affects Grain Protein Content and Nodule Bacterial Communities of a Fava Bean Crop

Agronomy ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 768
Author(s):  
Virginia Sánchez-Navarro ◽  
Raúl Zornoza ◽  
Ángel Faz ◽  
Catalina Egea-Gilabert ◽  
Margarita Ros ◽  
...  
Keyword(s):  
Protein Content ◽  
Crop Yield ◽  
Rhizobium Leguminosarum ◽  
Grain Protein Content ◽  
Grain Protein ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Yield And Quality ◽  
Biological Nitrogen ◽  
Bean Crop

The introduction of nitrogen fixing bacteria (NFB) and arbuscular mycorrhizal fungi (AMF) into the soil is an advisable agricultural practice for the crop, since it enhances nutrient and water uptake and tolerance to biotic and abiotic stresses. The aim of this work was to study plant nutrition, biological nitrogen fixation (BNF) and crop yield and quality, after inoculating seeds with NFBs ((Rhizobium leguminosarum, Burkholderia cenocepacia, Burkholderia vietnamiensis)) and/or AMFs (Rhizophagus irregularis, Claroideoglomus etunicatum, Claroideoglomus claroideum and Funneliformis mosseae) in a fava bean crop in two seasons. The composition of the nodule bacterial community was evaluated by the high-throughput sequencing analysis of bacterial 16 S rRNA genes. It was found that microbial inoculation accompanied by a 20% decrease in mineral fertilization had no significant effect on crop yield or the nutritional characteristics compared with a non-inoculated crop, except for an increase in the grain protein content in inoculated plants. None of the inoculation treatments increased biological nitrogen fixation over a non-inoculated level. The bacterial rRNA analysis demonstrated that the genus Rhizobium predominated in all nodules, both in inoculated and non-inoculated treatments, suggesting the previous presence of these bacteria in the soil. In our study, inoculation with Rhizobium leguminosarum was the most effective treatment for increasing protein content in seeds, while Burkholderia sp. was not able to colonise the plant nodules. Inoculation techniques used in fava beans can be considered an environmentally friendly alternative, reducing the input of fertilizers, while maintaining crop yield and quality, with the additional benefit of increasing the grain protein content. However, further research is required on the selection and detection of efficient rhizobial strains under local field conditions, above all those related to pH and soil type, in order to achieve superior nitrogen-fixing bacteria.

Nitrogen-fixing and non-fixing trees differ in leaf chemistry and defence but not herbivory in a lowland Costa Rican rain forest

2019 ◽  
Vol 35 (6) ◽  
pp. 270-279
Author(s):  
Benton N. Taylor ◽  
Laura R. Ostrowsky
Keyword(s):  
Nitrogen Content ◽  
Rain Forest ◽  
Chemical Defence ◽  
Leaf Nitrogen ◽  
Leaf Nitrogen Content ◽  
Nitrogen Fixing ◽  
Leaf Toughness ◽  
High Productivity ◽  
Nitrogen Fixers ◽  
Nitrogen Inputs

AbstractNitrogen-fixing plants provide critical nitrogen inputs that support the high productivity of tropical forests, but our understanding of the ecology of nitrogen fixers – and especially their interactions with herbivores – remains incomplete. Herbivores may interact differently with nitrogen fixers vs. non-fixers due to differences in leaf nitrogen content and herbivore defence strategies. To examine these potential differences, our study compared leaf carbon, nitrogen, toughness, chemical defence and herbivory for four nitrogen-fixing tree species (Inga oerstediana, Inga sapindoides, Inga thibaudiana and Pentaclethra macroloba) and three non-fixing species (Anaxagorea crassipetala, Casearia arborea and Dipteryx panamensis) in a lowland tropical rain forest. Leaf chemical defence, not nutritional content, was the primary driver of herbivore damage among our species. Even though nitrogen fixers exhibited 21.1% higher leaf nitrogen content, 20.1% lower C:N ratios and 15.4% lower leaf toughness than non-fixers, we found no differences in herbivory or chemical defence between these two plant groups. Our results do not support the common hypotheses that nitrogen fixers experience preferential herbivory or that they produce more nitrogen-rich defensive compounds than non-fixers. Rather, these findings suggest strong species-specific differences in plant–herbivore relationships among both nitrogen-fixing and non-fixing tropical trees.

scholarly journals The Nodule Microbiome: N2-Fixing Rhizobia Do Not Live Alone

2017 ◽  
Vol 1 (2) ◽  
pp. 70-82 ◽  
Author(s):  
Pilar Martínez-Hidalgo ◽  
Ann M. Hirsch
Keyword(s):  
Nitrogen Fixation ◽  
Environmental Stress ◽  
Host Plant ◽  
Diverse Population ◽  
Nitrogen Fixing ◽  
Chemical Fertilizers ◽  
Associated Bacteria ◽  
Culture Techniques ◽  
Nitrogen Fixers

For decades, rhizobia were thought to be the only nitrogen-fixing inhabitants of legume nodules, and biases in culture techniques prolonged this belief. However, other bacteria, which are not typical rhizobia, are often detected within nodules obtained from soil, thus revealing the existence of a phytomicrobiome where the interaction among the individuals is not only complex, but also likely to affect the behavior and fitness of the host plant. Many of these nonrhizobial bacteria are nitrogen fixers, and some also induce nitrogen-fixing nodules on legume roots. Even more striking is the incredibly diverse population of bacteria residing within nodules that elicit neither nodulation nor nitrogen fixation. Yet, this community exists within the nodule, albeit clearly out-numbered by nitrogen-fixing rhizobia. Few studies of the function of these nodule-associated bacteria in nodules have been performed, and to date, it is not known whether their presence in nodules is biologically important or not. Do they confer any benefits to the Rhizobium-legume nitrogen-fixing symbiosis, or are they parasites/saprophytes, contaminants, or commensals? In this review, we highlight the lesser-known bacteria that dwell within nitrogen-fixing nodules and discuss their possible role in this enclosed community as well as any likely benefits to the host plant or to the rhizobial inhabitants of the nodule. Although many of these nodule inhabitants are not capable of nitrogen fixation, they have the potential to enhance legume survival especially under conditions of environmental stress. This knowledge will be useful in defining strategies to employ these bacteria as bioinoculants by themselves or combined with rhizobia. Such an approach will enhance rhizobial performance or persistence as well as decrease the usage of chemical fertilizers and pesticides.

The Leeuwenhoek Lecture, 1992 Bacterial evolution and the nitrogen-fixing plant

1992 ◽  
Vol 338 (1286) ◽  
pp. 409-416 ◽  
Keyword(s):  
Nitrogen Fixation ◽  
Biological Nitrogen Fixation ◽  
Bacterial Species ◽  
Nitrogen Fixing ◽  
Bacterial Evolution ◽  
Late Emergence ◽  
Biological Nitrogen

Biological nitrogen fixation is fundamental to the economy of the biosphere, yet it is restricted to a few dozen bacterial species. Why have plants not acquired it during evolution? No serious physiological or genetic obstacles seem to exist. Has a relatively late emergence, among genomically flexible prokaryotes, effectively precluded appropriate seletion pressure?

Evolution of nitrogen-fixing symbioses

1985 ◽  
Vol 85 (3-4) ◽  
pp. 215-237 ◽  
Author(s):  
J. I. Sprent ◽  
J. A. Raven
Keyword(s):  
Root Nodules ◽  
Land Plants ◽  
Oxygenic Photosynthesis ◽  
Ecological Niches ◽  
Energy Costs ◽  
Nitrogen Fixing ◽  
Infection Structure ◽  
Combined Nitrogen ◽  
High Level ◽  
Biological Nitrogen

SynopsisBecause of both the energy costs and the slowness of the reactions of the nitrogenase complex compared with those involving some form of combined nitrogen (oxidised or reduced), we argue that the evolution of nitrogen-fixing organisms required an environment which was very limited in combined nitrogen. This is thought to have occurred after phototrophy evolved, but before water was used as a hydrogen donor (and therefore oxygen was present in the atmosphere). After oxygenic photosynthesis evolved, the need for a high level of biological nitrogen-fixation remained, since abiotic inputs were insufficient to keep pace with the rapidly evolving biomass (flora and fauna). Symbiotic fixation probably first evolved in the form of casual associations between cyanobacteria and most other groups of plants. By inhabiting the sporophytic generation of evolving land plants (cycads in particular), protection against nitrogenase-inactivating oxygen and a more desiccating environment was achieved simultaneously.We envisage nodulated plants arising by the transfer ofnifgenes into tumour-forming bacteria. In the case of legumes, these would be ancestors of extant agrobacteria, which gain entry into their hostsviawounds. Co-evolution of symbionts from nitrogen-fixing tumours has taken several routes, leading to extant nodules differing in mode of infection, structure and physiology. Evolution towards optimisation of oxygen usage is continuing.Nitrogen-fixing symbiosis in animal systems is only advantageous in specialised ecological niches in which wood is the sole dietary intake. In the case of shipworms, the symbiosis has many of the advanced features associated with nitrogen fixing root nodules.

scholarly journals Biological Nitrogen Fixation in the Context of Global Change

2013 ◽  
Vol 26 (5) ◽  
pp. 486-494 ◽  
Author(s):  
José Olivares ◽  
Eulogio J. Bedmar ◽  
Juan Sanjuán
Keyword(s):  
Nitrogen Fixation ◽  
Biological Nitrogen Fixation ◽  
Food Production ◽  
Agricultural Practices ◽  
N Fertilization ◽  
Agricultural Crops ◽  
Nitrogen Fixing ◽  
Sustainable Technologies ◽  
Use Efficiency ◽  
Biological Nitrogen

The intensive application of fertilizers during agricultural practices has led to an unprecedented perturbation of the nitrogen cycle, illustrated by the growing accumulation of nitrates in soils and waters and of nitrogen oxides in the atmosphere. Besides increasing use efficiency of current N fertilizers, priority should be given to value the process of biological nitrogen fixation (BNF) through more sustainable technologies that reduce the undesired effects of chemical N fertilization of agricultural crops. Wider legume adoption, supported by coordinated legume breeding and inoculation programs are approaches at hand. Also available are biofertilizers based on microbes that help to reduce the needs of N fertilization in important crops like cereals. Engineering the capacity to fix nitrogen in cereals, either by themselves or in symbiosis with nitrogen-fixing microbes, are attractive future options that, nevertheless, require more intensive and internationally coordinated research efforts. Although nitrogen-fixing plants may be less productive, at some point, agriculture must significantly reduce the use of warming (chemically synthesized) N and give priority to BNF if it is to sustain both food production and environmental health for a continuously growing human population.

NON-SYMBIOTIC NITROGEN FIXATION IN SOME QUEBEC SOILS

1965 ◽  
Vol 11 (1) ◽  
pp. 29-38 ◽  
Author(s):  
P-C. Chang ◽  
R. Knowles
Keyword(s):  
Nitrogen Fixation ◽  
Symbiotic Nitrogen Fixation ◽  
Soil Types ◽  
Anaerobic Incubation ◽  
Nitrogen Fixing ◽  
Free Living ◽  
Aerobic Conditions ◽  
Bacterial Counts ◽  
Facultatively Anaerobic ◽  
Nitrogen Fixers

The occurrence of free-living nitrogen fixers, the potential for nitrogen fixation, and the correlation between the nitrogen-fixing capacities of the soils and bacterial counts were studied using representative Quebec soils.Clostridium occurred more frequently than did Azotobacter. Studies with N15showed that nitrogen fixation was more frequent under anaerobic than under aerobic conditions in all the soil types studied in their unamended state. The addition of glucose stimulated nitrogen fixation. During anaerobic incubation, nitrogen fixation was found to be correlated significantly with the increase in numbers of both total aerobes and Clostridia. The results suggested that facultatively anaerobic nitrogen fixers, and aerobic nitrogen fixers other than Azotobacter, were present.

scholarly journals Effect of bio-fertilizers on foliage and floral traits of chrysanthemum cv Little Pink

2021 ◽  
Vol 17 (2) ◽  
pp. 162-166
Author(s):  
Shashank Dixit ◽  
A.K. Panday ◽  
Anurag Bajpay
Keyword(s):  
Growth Habit ◽  
Floral Traits ◽  
Live Cells ◽  
Dendranthema Grandiflora ◽  
Nitrogen Fixers ◽  
Phosphate Solubilizing ◽  
Biological Nitrogen ◽  
Asteraceae Family ◽  
Vast Range ◽  
Pot Plant

Chrysanthemum (Dendranthema grandiflora) is a leading commercial flower crop from asteraceae family grown for cut and loose flowers and also as a pot plant. It is preferred practically due to vast range of shapes and size of flowers, brilliance of colour tones, long lasting floret life, diversity of height and growth habit of the plant, especially hardy nature, relative ease to grow all the year round and versatility of use. Biofertilizers are the multiplied live cells of beneficial strains of micro-organism, are used as biological nitrogen fixers, Phosphate solubilizing, and also used for mineralization of nitrogen and transformation of several elements like sulphur and iron etc. into available forms. The present investigation was conducted at the Horticulture experimental field of Janta College, Bakewar in Complete Randomize Design with 4 treatments and 4 replications. Observations were recorded for vegetative and floral traits upon various biofertilizers treatments viz., T1: Control, T2: (FYM 50% + Soil 50% + 2gm PSB @Per pot), T3 : (FYM 50% + Soil 50% + 2gm Azotobacter @Per pot) and T4: (FYM 50% + Soil 50% + 1gm PSB + 1g Azotobacter@Per pot).

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