Nitrogen-fixing bacteria in Mediterranean seagrass (Posidonia oceanica) roots

KAUST Repository

Garcias Bonet, Neus

2016-03-09

Biological nitrogen fixation by diazotrophic bacteria in seagrass rhizosphere and leaf epiphytic community is an important source of nitrogen required for plant growth. However, the presence of endophytic diazotrophs remains unclear in seagrass tissues. Here, we assess the presence, diversity and taxonomy of nitrogen-fixing bacteria within surface-sterilized roots of Posidonia oceanica. Moreover, we analyze the nitrogen isotopic signature of seagrass tissues in order to notice atmospheric nitrogen fixation. We detected nitrogen-fixing bacteria by nifH gene amplification in 13 out of the 78 roots sampled, corresponding to 9 locations out of 26 meadows. We detected two different types of bacterial nifH sequences associated with P. oceanica roots, which were closely related to sequences previously isolated from the rhizosphere of a salt marsh cord grass and a putative anaerobe. Nitrogen content of seagrass tissues showed low isotopic signatures in all the sampled meadows, pointing out the atmospheric origin of the assimilated nitrogen by seagrasses. However, this was not related with the presence of endophytic nitrogen fixers, suggesting the nitrogen fixation occurring in rhizosphere and in the epiphytic community could be an important source of nitrogen for P. oceanica. The low diversity of nitrogen-fixing bacteria reported here suggests species-specific relationships between diazotrophs and P. oceanica, revealing possible symbiotic interactions that could play a major role in nitrogen acquisition by seagrasses in oligotrophic environments where they form lush meadows.

Dissecting hormonal pathways in nitrogen-fixing rhizobium symbioses

NARCIS (Netherlands)

Zeijl, van Arjan

2017-01-01

Nitrogen is a key element for plant growth. To meet nitrogen demands, some plants establish an endosymbiotic relationship with nitrogen-fixing rhizobium or Frankia bacteria. This involves formation of specialized root lateral organs, named nodules. These nodules are colonized

High-quality forage production under salinity by using a salt-tolerant AtNXH1-expressing transgenic alfalfa combined with a natural stress-resistant nitrogen-fixing bacterium.

Science.gov (United States)

Stritzler, Margarita; Elba, Pagano; Berini, Carolina; Gomez, Cristina; Ayub, Nicolás; Soto, Gabriela

2018-06-20

Alfalfa, usually known as the "Queen of Forages", is the main source of vegetable protein to meat and milk production systems worldwide. This legume is extremely rich in proteins due to its highly efficient symbiotic association with nitrogen-fixing strains. In the last years, alfalfa culture has been displaced to saline environments by other important crops, including major cereals, a fact that has reduced its biomass production and symbiotic nitrogen fixation. In this short communication, we report the high forage production and nutrient quality of alfalfa under saline conditions by alfalfa transformation with the AtNHX1 Na + /H + antiporter and inoculation with the stress-resistant nitrogen-fixing strain Sinorhizobium meliloti B401. Therefore, the incorporation of transgenic traits into salt-sensitive legumes in association with the inoculation with natural stress-resistant isolates could be a robust approach to improve the productivity and quality of these important nitrogen-fixing crops. Copyright © 2018. Published by Elsevier B.V.

What Does It Take to Evolve A Nitrogen-Fixing Endosymbiosis?

NARCIS (Netherlands)

Geurts, Rene; Xiao, Ting Ting; Reinhold-Hurek, Barbara

2016-01-01

Plant rhizo- and phyllospheres are exposed to a plethora of nitrogen-fixing bacteria, providing opportunities for the establishment of symbiotic associations. Nitrogen-fixing endosymbioses are most profitable and have evolved more than ten times in the angiosperms. This suggests that the

Endophytic colonization of plant roots by nitrogen-fixing bacteria

International Nuclear Information System (INIS)

Cocking, Edward C.

2001-01-01

Nitrogen-fixing bacteria are able to enter into roots from the rhizosphere, particularly at the base of emerging lateral roots, between epidermal cells and through root hairs. In the rhizosphere growing root hairs play an important role in symbiotic recognition in legume crops. Nodulated legumes in endosymbiosis with rhizobia are amongst the most prominent nitrogen-fixing systems in agriculture. The inoculation of non-legumes, especially cereals, with various non-rhizobial diazotrophic bacteria has been undertaken with the expectation that they would establish themselves intercellularly within the root system, fixing nitrogen endophytic ally and providing combined nitrogen for enhanced crop production. However, in most instances bacteria colonize only the surface of the roots and remain vulnerable to competition from other rhizosphere micro-organisms, even when the nitrogen-fixing bacteria are endophytic, benefits to the plant may result from better uptake of soil nutrients rather than from endophytic nitrogen fixation. Azorhizobium caulinodans is known to enter the root system of cereals, other nonlegume crops and Arabidopsis, by intercellular invasion between epidermal cells and to internally colonize the plant intercellularly, including the xylem. This raises the possibility that xylem colonization might provide a nonnodular niche for endosymbiotic nitrogen fixation in rice, wheat, maize, sorghum and other non-legume crops. A particularly interesting, naturally occurring, non-qodular xylem colonising endophytic diazotrophic interaction with evidence for endophytic nitrogen fixation is that of Gluconacetobacter diazotrophicus in sugarcane. Could this beneficial endophytic colonization of sugarcane by G. diazotrophicus be extended to other members of the Gramineae, including the major cereals, and to other major non-legume crops of the World? (author)

Nitrogen-fixing bacteria in Mediterranean seagrass (Posidonia oceanica) roots

KAUST Repository

Garcias Bonet, Neus; Arrieta, J M; Duarte, Carlos M.; Marbà , Nú ria

2016-01-01

of nitrogen for P. oceanica. The low diversity of nitrogen-fixing bacteria reported here suggests species-specific relationships between diazotrophs and P. oceanica, revealing possible symbiotic interactions that could play a major role in nitrogen acquisition

(Methyl)ammonium Transport in the Nitrogen-Fixing Bacterium Azospirillum brasilense

Science.gov (United States)

Van Dommelen, Anne; Keijers, Veerle; Vanderleyden, Jos; de Zamaroczy, Miklos

1998-01-01

An ammonium transporter of Azospirillum brasilense was characterized. In contrast to most previously reported putative prokaryotic NH4+ transporter genes, A. brasilense amtB is not part of an operon with glnB or glnZ which, in A. brasilense, encode nitrogen regulatory proteins PII and PZ, respectively. Sequence analysis predicts the presence of 12 transmembrane domains in the deduced AmtB protein and classifies AmtB as an integral membrane protein. Nitrogen regulates the transcription of the amtB gene in A. brasilense by the Ntr system. amtB is the first gene identified in A. brasilense whose expression is regulated by NtrC. The observation that ammonium uptake is still possible in mutants lacking the AmtB protein suggests the presence of a second NH4+ transport mechanism. Growth of amtB mutants at low ammonium concentrations is reduced compared to that of the wild type. This suggests that AmtB has a role in scavenging ammonium at low concentrations. PMID:9573149

Actinorhizal nitrogen fixing nodules: infection process, molecular ...

African Journals Online (AJOL)

Actinorhizal nitrogen fixing nodules: infection process, molecular biology and genomics. Mariana Obertello, Mame Oureye SY, Laurent Laplaze, Carole Santi, Sergio Svistoonoff, Florence Auguy, Didier Bogusz, Claudine Franche ...

Assessment of free-living nitrogen fixing microorganisms for commercial nitrogen fixation. [economic analysis of ammonia production

Science.gov (United States)

Stokes, B. O.; Wallace, C. J.

1978-01-01

Ammonia production by Klebsiella pneumoniae is not economical with present strains and improving nitrogen fixation to its theoretical limits in this organism is not sufficient to achieve economic viability. Because the value of both the hydrogen produced by this organism and the methane value of the carbon source required greatly exceed the value of the ammonia formed, ammonia (fixed nitrogen) should be considered the by-product. The production of hydrogen by KLEBSIELLA or other anaerobic nitrogen fixers should receive additional study, because the activity of nitrogenase offers a significant improvement in hydrogen production. The production of fixed nitrogen in the form of cell mass by Azotobacter is also uneconomical and the methane value of the carbon substrate exceeds the value of the nitrogen fixed. Parametric studies indicate that as efficiencies approach the theoretical limits the economics may become competitive. The use of nif-derepressed microorganisms, particularly blue-green algae, may have significant potential for in situ fertilization in the environment.

Visualization of channels connecting cells in filamentous nitrogen-fixing cyanobacteria.

Science.gov (United States)

Omairi-Nasser, Amin; Haselkorn, Robert; Austin, Jotham

2014-07-01

Cyanobacteria, formerly called blue-green algae, are abundant bacteria that carry out green plant photosynthesis, fixing CO2 and generating O2. Many species can also fix N2 when reduced nitrogen sources are scarce. Many studies imply the existence of intracellular communicating channels in filamentous cyanobacteria, in particular, the nitrogen-fixing species. In a species such as Anabaena, growth in nitrogen-depleted medium, in which ∼10% of the cells differentiate into anaerobic factories for nitrogen fixation (heterocysts), requires the transport of amino acids from heterocysts to vegetative cells, and reciprocally, the transport of sugar from vegetative cells to heterocysts. Convincing physical evidence for such channels has been slim. Using improved preservation of structure by high-pressure rapid freezing of samples for electron microscopy, coupled with high-resolution 3D tomography, it has been possible to visualize and measure the dimensions of channels that breach the peptidoglycan between vegetative cells and between heterocysts and vegetative cells. The channels appear to be straight tubes, 21 nm long and 14 nm in diameter for the latter and 12 nm long and 12 nm in diameter for the former.-Omairi-Nasser, A., Haselkorn, R., Austin, J. II. Visualization of channels connecting cells in filamentous nitrogen-fixing cyanobacteria. © FASEB.

The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the BISCUIT study.

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Richard Hansen

Full Text Available Children presenting for the first time with inflammatory bowel disease (IBD offer a unique opportunity to study aetiological agents before the confounders of treatment. Microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; Helicobacter and Campylobacter are previously implicated in IBD pathogenesis. We set out to study these and other microaerophilic bacteria in de-novo paediatric IBD.100 children undergoing colonoscopy were recruited including 44 treatment naïve de-novo IBD patients and 42 with normal colons. Colonic biopsies were subjected to microaerophilic culture with Gram-negative isolates then identified by sequencing. Biopsies were also PCR screened for the specific microaerophilic bacterial groups: Helicobacteraceae, Campylobacteraceae and Sutterella wadsworthensis.129 Gram-negative microaerophilic bacterial isolates were identified from 10 genera. The most frequently cultured was S. wadsworthensis (32 distinct isolates. Unusual Campylobacter were isolated from 8 subjects (including 3 C. concisus, 1 C. curvus, 1 C. lari, 1 C. rectus, 3 C. showae. No Helicobacter were cultured. When comparing IBD vs. normal colon control by PCR the prevalence figures were not significantly different (Helicobacter 11% vs. 12%, p = 1.00; Campylobacter 75% vs. 76%, p = 1.00; S. wadsworthensis 82% vs. 71%, p = 0.312.This study offers a comprehensive overview of the microaerophilic microbiota of the paediatric colon including at IBD onset. Campylobacter appear to be surprisingly common, are not more strongly associated with IBD and can be isolated from around 8% of paediatric colonic biopsies. S. wadsworthensis appears to be a common commensal. Helicobacter species are relatively rare in the paediatric colon.This study is publically registered on the United Kingdom Clinical Research Network Portfolio (9633.

Symbiosis between nitrogen-fixing bacteria and Medicago truncatula is not significantly affected by silver and silver sulfide nanomaterials.

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Judy, Jonathan D; Kirby, Jason K; McLaughlin, Mike J; McNear, David; Bertsch, Paul M

2016-07-01

Silver (Ag) engineered nanomaterials (ENMs) are being released into waste streams and are being discharged, largely as Ag2S aged-ENMs (a-ENMs), into agroecosystems receiving biosolids amendments. Recent research has demonstrated that biosolids containing an environmentally relevant mixture of ZnO, TiO2, and Ag ENMs and their transformation products, including Ag2S a-ENMs, disrupted the symbiosis between nitrogen-fixing bacteria and legumes. However, this study was unable to unequivocally determine which ENM or combination of ENMs and a-ENMs was responsible for the observed inhibition. Here, we examined further the effects of polyvinylpyrollidone (PVP) coated pristine Ag ENMs (PVP-Ag), Ag2S a-ENMs, and soluble Ag (as AgSO4) at 1, 10, and 100 mg Ag kg(-1) on the symbiosis between the legume Medicago truncatula and the nitrogen-fixing bacterium, Sinorhizobium melliloti in biosolids-amended soil. Nodulation frequency, nodule function, glutathione reductase production, and biomass were not significantly affected by any of the Ag treatments, even at 100 mg kg(-1), a concentration analogous to a worst-case scenario resulting from long-term, repeated biosolids amendments. Our results provide additional evidence that the disruption of the symbiosis between nitrogen-fixing bacteria and legumes in response to a mixture of ENMs in biosolids-amended soil reported previously may not be attributable to Ag ENMs or their transformation end-products. We anticipate these findings will provide clarity to regulators and industry regarding potential unintended consequences to terrestrial ecosystems resulting from of the use of Ag ENMs in consumer products. Copyright © 2016 Elsevier Ltd. All rights reserved.

Gene Deletions Resulting in Increased Nitrogen Release by Azotobacter vinelandii: Application of a Novel Nitrogen Biosensor

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Eberhart, Lauren J.; Ohlert, Janet M.; Knutson, Carolann M.; Plunkett, Mary H.

2015-01-01

Azotobacter vinelandii is a widely studied model diazotrophic (nitrogen-fixing) bacterium and also an obligate aerobe, differentiating it from many other diazotrophs that require environments low in oxygen for the function of the nitrogenase. As a free-living bacterium, A. vinelandii has evolved enzymes and transporters to minimize the loss of fixed nitrogen to the surrounding environment. In this study, we pursued efforts to target specific enzymes and further developed screens to identify individual colonies of A. vinelandii producing elevated levels of extracellular nitrogen. Targeted deletions were done to convert urea into a terminal product by disrupting the urease genes that influence the ability of A. vinelandii to recycle the urea nitrogen within the cell. Construction of a nitrogen biosensor strain was done to rapidly screen several thousand colonies disrupted by transposon insertional mutagenesis to identify strains with increased extracellular nitrogen production. Several disruptions were identified in the ammonium transporter gene amtB that resulted in the production of sufficient levels of extracellular nitrogen to support the growth of the biosensor strain. Further studies substituting the biosensor strain with the green alga Chlorella sorokiniana confirmed that levels of nitrogen produced were sufficient to support the growth of this organism when the medium was supplemented with sufficient sucrose to support the growth of the A. vinelandii in coculture. The nature and quantities of nitrogen released by urease and amtB disruptions were further compared to strains reported in previous efforts that altered the nifLA regulatory system to produce elevated levels of ammonium. These results reveal alternative approaches that can be used in various combinations to yield new strains that might have further application in biofertilizer schemes. PMID:25888177

Differential Sensitivity of Nitrogen-Fixing, Azolla Microphylla to ...

African Journals Online (AJOL)

Michael Horsfall

photosynthesizing and nitrogen fixing micro-organisms contributing significantly ... Pesticide treatment with increasing doses accelerated the formation of reactive ... increased amount of proline in all the insecticide treated concentrations was .... monitoring the nitrite formation from ... centrifuged for 10 minutes in high speed.

Stress tolerant crops from nitrogen fixing trees

Energy Technology Data Exchange (ETDEWEB)

Becker, R.; Saunders, R.M.

1983-01-01

Notes are given on the nutritional quality and uses of: pods of Geoffroea decorticans, a species tolerant of saline and limed soils and saline water; seeds of Olneya tesota which nodulates readily and fixes nitrogen and photosynthesizes at low water potential; and pods of Prosopis chilensis and P. tamarugo which tolerate long periods without rain. 3 references.

Indigenous Fixed Nitrogen on Mars: Implications for Habitability

Science.gov (United States)

Stern, J. C.; Sutter, B.; Navarro-Gonzalez, R.; McKay, C. P.; Freissinet, C.; Archer, D., Jr.; Eigenbrode, J. L.; Mahaffy, P. R.; Conrad, P. G.

2015-12-01

Nitrate has been detected in Mars surface sediments and aeolian deposits by the Sample Analysis at Mars (SAM) instrument on the Mars Science Laboratory Curiosity rover (Stern et al., 2015). This detection is significant because fixed nitrogen is necessary for life, a requirement that drove the evolution of N-fixing metabolism in life on Earth. The question remains as to the extent to which a primitive N cycle ever developed on Mars, and whether N is currently being deposited on the martian surface at a non-negligible rate. It is also necessary to consider processes that could recycle oxidized N back into the atmosphere, and how these processes may have changed the soil inventory of N over time. The abundance of fixed nitrogen detected as NO from thermal decomposition of nitrate is consistent with both delivery of nitrate via impact generated thermal shock early in martian history and dry deposition from photochemistry of thermospheric NO, occurring in the present. Processes that could recycle N back into the atmosphere may include nitrate reduction by Fe(II) in aqueous environments on early Mars, impact decomposition, and/or UV photolysis. In order to better understand the history of nitrogen fixation on Mars, we look to cycling of N in Mars analog environments on Earth such as the Atacama Desert and the Dry Valleys of Antarctica. In particular, we examine the ratio of nitrate to perchlorate (NO3-/ClO4-) in these areas compared to those calculated from data acquired on Mars.

An oceanic fixed nitrogen sink exceeding 400 Tg N a−1 vs the concept of homeostasis in the fixed-nitrogen inventory

Directory of Open Access Journals (Sweden)

L. A. Codispoti

2007-01-01

Full Text Available Measurements of the N2 produced by denitrification, a better understanding of non-canonical pathways for N2 production such as the anammox reaction, better appreciation of the multiple environments in which denitrification can occur (e.g. brine pockets in ice, within particles outside of suboxic water, etc. suggest that it is unlikely that the oceanic denitrification rate is less than 400 Tg N a−1. Because this sink term far exceeds present estimates for nitrogen fixation, the main source for oceanic fixed-N, there is a large apparent deficit (~200 Tg N a−1 in the oceanic fixed-N budget. The size of the deficit appears to conflict with apparent constraints of the atmospheric carbon dioxide and sedimentary δ15N records that suggest homeostasis during the Holocene. In addition, the oceanic nitrate/phosphate ratio tends to be close to the canonical Redfield biological uptake ratio of 16 (by N and P atoms which can be interpreted to indicate the existence of a powerful feed-back mechanism that forces the system towards a balance. The main point of this paper is that one cannot solve this conundrum by reducing the oceanic sink term. To do so would violate an avalanche of recent data on oceanic denitrification. A solution to this problem may be as simple as an upwards revision of the oceanic nitrogen fixation rate, and it is noted that most direct estimates for this term have concentrated on nitrogen fixation by autotrophs in the photic zone, even though nitrogen fixing genes are widespread. Another simple explanation may be that we are simply no longer in the Holocene and one might expect to see temporary imbalances in the oceanic fixed-N budget as we transition from the Holocene to the Anthropocene in line with an apparent denitrification maximum during the Glacial-Holocene transition. Other possible full or partial explanations involve plausible changes in the oceanic nitrate/phosphate and N/C ratios, an oceanic phosphorus budget that may also

The optimum energy harvest efficiency of nitrogen fixing hydrophyte: Azolla pinnata

Energy Technology Data Exchange (ETDEWEB)

Tennakone, K. (Institute of Fundamental Studies, Kandy (LK) Ruhuna Univ., Matara (LK). Dept. of Physics); Punchihewa, S.; Jayasuriya, A.C. (Institute of Fundamental Studies, Kandy (LK))

1989-01-01

Azolla is a nitrogen fixing hydrophyte that can be cultivated in absence of nitrogenous fertilizer. It is found that when biomass is continuously harvested from a culture of Azolla, solar energy can be converted at an optimum efficiency of 1.1%. (author).

Isolation and characterization of Sulfurospirillum carboxydovorans sp. nov., a new microaerophilic carbon monoxide oxidizing epsilon Proteobacterium.

Science.gov (United States)

Jensen, Anders; Finster, Kai

2005-05-01

A new microaerophilic, Gram-negative, motile, 2-3 microm long and 0.3 microm wide, vibrioid to spirillum-shaped, CO oxidizing bacterium, designated strain MV, isolated from marine sediment (The North Sea) is described. Strain MV was able to couple the oxidation of CO to the reduction of elemental sulphur, DMSO and thiosulphate. Growth occurred with up to 100% (v/v) CO in the headspace. Acetate was needed as carbon source. No growth on CO was observed with nitrate and selenate as electron acceptor. Sulphite, elemental sulphur, DMSO, thiosulphate, nitrate, nitrite, perchloroethylene, arsenate and selenate were used as electron acceptors with pyruvate as energy and carbon source. Microaerophilic growth was observed. In non-agitated cultures growth occurred at atmospheric oxygen concentrations in the headspace. Hydrogen (with acetate as carbon source), formate (with acetate as carbon source), pyruvate, lactate, succinate, fumarate, malate alpha-ketoglutaric acid, aspartate and yeast extract (1% (w/v)) supported growth with nitrate as electron acceptor. Fumarate and malate were fermented. Vitamins were not required for growth. The strain was cytochrome C oxidase and catalase positive. The DNA mol G+C content was 30.5%. 16S rRNA gene sequence comparison showed that strain MV grouped within the genus Sulfurospirillum with Sulfurospirillum arcachonense (sequence similarity 98.3%) as closest relative. The relative DNA-DNA relatedness between strain MV and S. arcachonense was 33.1%. Based on a detailed phenotypic and phylogenetic analysis, inclusion of strain MV in the genus Sulfurospirillum as a well separated new species is proposed. As species name we propose Sulfurospirillum carboxydovorans. The type strain is strain MV (ATCC BAA-937 = DSM 16295, GenBank accession number: AY740528).

[Rice endogenous nitrogen fixing and growth promoting bacterium Herbaspirillum seropedicae DX35].

Science.gov (United States)

Wang, Xiucheng; Cao, Yanhua; Tang, Xue; Ma, Xiaotong; Gao, Jusheng; Zhang, Xiaoxia

2014-03-04

To screen efficient nitrogen fixation endophytes from rice and to analyze their growth-promoting properties. We isolated strains from the roots of rice in the field where it has a rice-rice-green manure rotation system for 30 years. Efficient strains were screened by acetylene reduction assay. Phylogenetic analysis is based on 16S rRNA gene, nifH gene and the composition of fatty acid. In addition, we also detected the ability of indole acetic acid secretion through the Salkowski colorimetric method, measured the production of siderophore through the blue plate assay and detected phosphate solubilization, to analyze the growth-promoting properties. A total of 48 strains were isolated, in which DX35 has the highest nitrogenase activity. It belongs to Herbaspirillum seropedicae after identification. Its nitrogenase activity (181.21 nmol C2H4/(mg protein x h)) was 10 times as much as the reference strain Azotobacter chroococcum ACCC10006. In addition, it also can secrete siderophore and solubilize phosphorus. Strain DX35, belonging to Herbaspirillum seropedicae, is an efficient nitrogen fixation endophytes.

High diversity of nitrogen-fixing bacteria in upper reaches of Heihe River, Northwestern China

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Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.

2013-03-01

Vegetation plays a key role to water conservation in southern Qilian Mountains (Northwestern China), the upper reaches of Heihe River. Nitrogen-fixing bacteria are crucial for vegetation protection because they can supply plants with nitrogen source. Nevertheless, little is known about nitrogen-fixing bacteria in this region. In present study, nifH gene clone libraries were established for detecting the difference of nitrogen-fixing bacterial communities between Potentilla parvifolia shrub and Carex alrofusca meadow in the southern Qilian Mountains. All the identified nitrogen-fixing bacterial clones belonged to Proteobacteria. At the genus level, the Azospirillum sp. was only detected in shrub soil while Thiocapsa sp., Derxiasp., Ectothiorhodospira sp., Mesorhizobium sp., Klebsiella sp., Ensifer sp., Methylocella sp. and Peseudomonas sp. were just detected in meadow soil. Shannon-Wiener index of nifH gene ranged from 1.5 to 2.8 and was higher in meadow soil than shrub soil. Contrarily, the nifH gene copies and CFUs of cultured nitrogen-fixing bacteria ranged from 0.4 × 107 to 6.9 × 107 copies g-1 soil and 0.97 × 106 to 12.78 × 106 g-1 soil, respectively. Furthermore, both of them were lower in meadow soil than shrub soil. Statistical analysis revealed that diversity and copies of nifH gene mostly correlated with aboveground biomass in shrub soil. In meadow soil, nifH gene diversity was principally affected by altitude while copies did by soil available K.

Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

Energy Technology Data Exchange (ETDEWEB)

Moulin, Lionel [UMR, France; Klonowska, Agnieszka [UMR, France; Caroline, Bournaud [UMR, France; Booth, Kristina [University of Massachusetts; Vriezen, Jan A.C. [University of Massachusetts; Melkonian, Remy [UMR, France; James, Euan [James Hutton Institute, Dundee, United Kingdom; Young, Peter W. [University of York, United Kingdom; Bena, Gilles [UMR, France; Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lizotte-Waniewski, Michelle [University of Massachusetts; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Riley, Monica [Woods Hole Oceanographic Institution (WHOI), Woods Hole

2014-01-01

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).

Estimate of symbiotically fixed nitrogen in field grown soybeans using variations in 15N natural abundance

International Nuclear Information System (INIS)

Amarger, N.; Durr, J.C.; Bourguignon, C.; Lagacherie, B.; Mariotti, A.; Mariotti, F.

1979-01-01

The use of variations in natural abundance of 15 N between nitrogen fixing and non nitrogen fixing soybeans was investigated for quantitative estimate of symbiotic nitrogen fixation. Isotopic analysis of 4 varieties of inoculated and non-inoculated soybeans growing under field conditions, with and without N-fertilizer was determined. It was found that inoculated soybeans had a significantly lower 15 N content than non-inoculated ones. Estimates of the participation of fixed N to the total nitrogen content of inoculated soybeans were calculated from these differences. They were compared to estimates calculated from differences in N yield between inoculated and non-inoculated plants and to the nitrogenase activity, measured by the C 2 H 2 reduction assay over the growing season. Estimates given by the 15 N measurements were correlated with the C 2 H 2 reducing activity but not with the differences in the N yield. This shows that the isotopic composition was dependent on the amount of fixed nitrogen and consequently that the estimates of fixed nitrogen based on natural 15 N abundance should be reliable. The absence of correlation between estimates based on 15 N content and estimates based on N yield was explained by differences in the uptake of soil nitrogen between inoculated and non inoculated soybeans. (Auth.)

Evaluation of the influence of nitrogen fixing, phosphate solubilizing ...

African Journals Online (AJOL)

Three biofertilizers nitrobein, phosphorein, and potash, containing nitrogen fixing, phosphate solubilizing, and potash mobilizing microorganisms, respectively were studied in peanut (Arachis hypogea L.) and sunflower (Helianthus annuus L.). Amendment with each of these biofertilizers enhanced different growth ...

Novel nitrogen-fixing Acetobacter nitrogenifigens sp. nov., isolated from Kombucha tea.

Science.gov (United States)

Dutta, Debasree; Gachhui, Ratan

2006-08-01

The four nitrogen-fixing bacteria so far described in the family Acetobacteraceae belong to the genera Gluconacetobacter and Acetobacter. Nitrogen-fixing bacterial strain RG1(T) was isolated from Kombucha tea and, based on the phylogenetic analysis of 16S rRNA gene sequence which is supported by a high bootstrap value, was found to belong to the genus Acetobacter. Strain RG1(T) differed from Acetobacter aceti, the nearest member with a 16S rRNA gene sequence similarity of 98.2 %, and type strains of other Acetobacter species with regard to several characteristics of growth features in culture media, growth in nitrogen-free medium, production of gamma-pyrone from glucose and dihydroxyacetone from glycerol. Strain RG1(T) utilized maltose, glycerol, sorbitol, fructose, galactose, arabinose and ethanol, but not methanol as a carbon source. These results, along with electrophoretic mobility patterns of nine metabolic enzymes, suggest that strain RG1(T) represents a novel nitrogen-fixing species. The ubiquinone present was Q-9 and DNA G+C content was 64.1 mol%. Strain RG1(T) exhibited a low value of 2-24 % DNA-DNA relatedness to the type strains of related acetobacters, which placed it as a separate taxon. On the basis of this data, the name Acetobacter nitrogenifigens sp. nov. is proposed, with the type strain RG1(T) (=MTCC 6912(T)=LMG 23498(T)).

[Development of a liquid fermentation system and encystment for a nitrogen-fixing bacterium strain having biofertilizer potential].

Science.gov (United States)

Camelo-Rusinque, Mauricio; Moreno-Galván, Andrés; Romero-Perdomo, Felipe; Bonilla-Buitrago, Ruth

The indiscriminate use of chemical fertilizers has contributed to the deterioration of the biological, physical and chemical properties of the soil, resulting in the loss of its productive capacity. For this reason, the use of biofertilizers has emerged as a technological alternative. The objective of this research was to develop a suitable liquid fermentation system and encystment for the multiplication of Azotobacter chroococcum AC1 strain, a bacterium employed in a biofertilizer formulation produced at present by CARPOICA, Colombia. Sequential statistical designs were used to determine the conditions in the fermentation system. The interaction between agitation, aeration and pH was evaluated on the viable biomass (CFU/ml) of AC1. In addition, the encystment ability of the strain was evaluated using two encystment agents and the potential plant growth-promoting rhizobacteria (PGPR) activity was assessed by different techniques, such as nitrogen fixation by ARA, phosphate solubilization by the phospho-molybdenum-blue reaction and indolic compound production by colorimetric reaction using the Salkowski reagent. Results showed significant effects (p<0.05) on the viable biomass in the three conditions (pH, aeration and agitation) tested individually, in one dual interaction and one tripartite interaction, were demonstrated to have a positive effect on the response variable aeration and agitation. The addition of the two encystment agents evaluated, AE01 and AE02, demonstrated the ability of AC1 to form cysts under stress conditions. Likewise, fermentation and encystment conditions did not affect the biological activities tested. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Beneficial effects of aluminum enrichment on nitrogen-fixing cyanobacteria in the South China Sea.

Science.gov (United States)

Liu, Jiaxing; Zhou, Linbin; Ke, Zhixin; Li, Gang; Shi, Rongjun; Tan, Yehui

2018-04-01

Few studies focus on the effects of aluminum (Al) on marine nitrogen-fixing cyanobacteria, which play important roles in the ocean nitrogen cycling. To examine the effects of Al on the nitrogen-fixing cyanobacteria, bioassay experiments in the oligotrophic South China Sea (SCS) and culture of Crocosphaera watsonii in the laboratory were conducted. Field data showed that 200 nM Al stimulated the growth and the nitrogenase gene expression of Trichodesmium and unicellular diazotrophic cyanobacterium group A, and the nitrogen fixation rates of the whole community. Laboratory experiments demonstrated that Al stimulated the growth and nitrogen fixation of C. watsonii under phosphorus limited conditions. Both field and laboratory results indicated that Al could stimulate the growth of diazotrophs and nitrogen fixation in oligotrophic oceans such as the SCS, which is likely related to the utilization of phosphorus, implying that Al plays an important role in the ocean nitrogen and carbon cycles by influencing nitrogen fixation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Study On Ammonia Accumulation of Cellulose-Utilizing and Nitrogen-Fixing Bacteria Isolated from Various Soils

International Nuclear Information System (INIS)

Soe Myat Thandar; Aung Ko Ko Oo; Weine Nway Nway Oo

2011-12-01

Cellulose-utilizing and nitrogen-fixing bacteria were isolated from various soil. 42 bacterial strains were obtained. Among those stains, 13 strains were screened for nitrogen-fixing activity. Among them, 4 strains coded as CPB1, CMB1, GPB2 and 3LC4 showed the high nitrogen-fixing activity. Different strains produced different amount of ammonium compounds at various incubation periods. CMB1 produced the maximum amount of ammonium 1.2 mg/L NH4+ at 6th day culture but 3LC4, GPB2 and CPB1 produced more amount of NH4+ with 2, 2.5 and 3 mg/L NH4+ respectively at 5th day culture.

Cowpea symbiotic efficiency, pH and aluminum tolerance in nitrogen-fixing bacteria

Directory of Open Access Journals (Sweden)

Bruno Lima Soares

2014-06-01

Full Text Available Cowpea (Vigna unguiculata cultivation in northern and northeastern Brazil provides an excellent source of nutrients and carbohydrates for the poor and underprivileged. Production surplus leads to its consumption in other regions of Brazil and also as an export commodity. Its capacity to establish relationships with atmospheric nitrogen-fixing bacteria is crucial to the reduction of production costs and the environmental impact of nitrogen fertilizers. This study assessed the symbiotic efficiency of new strains of symbiotic nitrogen-fixing bacteria with cowpea and their tolerance to pH and aluminum. Twenty-seven strains of bacteria from different soils were evaluated under axenic conditions. These strains were compared to the following inoculant strains: INPA03-11B, UFLA03-84 and BR3267 and two controls that were not inoculated (with and without mineral nitrogen. Six strains and the three strains approved as inoculants were selected to increase the dry weight production of the aerial part (DWAP and were tested in pots with soil that had a high-density of nitrogen-fixing native rhizobia. In this experiment, three strains (UFLA03-164, UFLA03-153, and UFLA03-154 yielded higher DWAP values. These strains grow at pH levels of 5.0, 6.0, 6.8 and at high aluminum concentration levels, reaching 10(9 CFU mL-1. In particular UFLA03-84, UFLA03-153, and UFLA03-164 tolerate up to 20 mmol c dm-3 of Al+3. Inoculation with rhizobial strains, that had been carefully selected according to their ability to nodulate and fix N2, combined with their ability to compete in soils that are acidic and contain high levels of Al, is a cheaper and more sustainable alternative that can be made available to farmers than mineral fertilizers.

Phosphate enhances levan production in the endophytic bacterium Gluconacetobacter diazotrophicus Pal5

Science.gov (United States)

Idogawa, Nao; Amamoto, Ryuta; Murata, Kousaku; Kawai, Shigeyuki

2014-01-01

Gluconacetobacter diazotrophicus is a gram-negative and endophytic nitrogen-fixing bacterium that has several beneficial effects in host plants; thus, utilization of this bacterium as a biofertilizer in agriculture may be possible. G. diazotrophicus synthesizes levan, a D-fructofuranosyl polymer with β-(2→6) linkages, as an exopolysaccharide and the synthesized levan improves the stress tolerance of the bacterium. In this study, we found that phosphate enhances levan production by G. diazotrophicus Pal5, a wild type strain that showed a stronger mucous phenotype on solid medium containing 28 mM phosphate than on solid medium containing 7 mM phosphate. A G. diazotrophicus Pal5 levansucrase disruptant showed only a weak mucous phenotype regardless of the phosphate concentration, indicating that the mucous phenotype observed on 28 mM phosphate medium was caused by levan. To our knowledge, this is the first report of the effect of a high concentration of phosphate on exopolysaccharide production. PMID:24717418

Estimate of symbiotically fixed nitrogen in field grown soybeans using variations in /sup 15/N natural abundance

Energy Technology Data Exchange (ETDEWEB)

Amarger, N; Durr, J C; Bourguignon, C; Lagacherie, B [INRA Centre de Recherches de Dijon, 21 (France). Lab. de Microbiologie des Sols; Mariotti, A; Mariotti, F [Paris-6 Univ., 75 (France). Lab. de Geologie Dynamique

1979-07-01

The use of variations in natural abundance of /sup 15/N between nitrogen fixing and non nitrogen fixing soybeans was investigated for quantitative estimate of symbiotic nitrogen fixation. Isotopic analysis of 4 varieties of inoculated and non-inoculated soybeans growing under field conditions, with and without N-fertilizer was determined. It was found that inoculated soybeans had a significantly lower /sup 15/N content than non-inoculated ones. Estimates of the participation of fixed N to the total nitrogen content of inoculated soybeans were calculated from these differences. They were compared to estimates calculated from differences in N yield between inoculated and non-inoculated plants and to the nitrogenase activity, measured by the C/sub 2/H/sub 2/ reduction assay over the growing season. Estimates given by the /sup 15/N measurements were correlated with the C/sub 2/H/sub 2/ reducing activity but not with the differences in the N yield. This shows that the isotopic composition was dependent on the amount of fixed nitrogen and consequently that the estimates of fixed nitrogen based on natural /sup 15/N abundance should be reliable. The absence of correlation between estimates based on /sup 15/N content and estimates based on N yield was explained by differences in the uptake of soil nitrogen between inoculated and non inoculated soybeans.

EFFECT OF NITROGEN-FIXING BACTERIA ON GRAIN YIELD AND DEVELOPMENT OF FLOODED IRRIGATED RICE

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AMAURI NELSON BEUTLER

2016-01-01

Full Text Available This study aimed at evaluating the effect of Azospirillum brasilense , a nitrogen - fixing bacterium, on flooded irrigated rice yield. Evaluations were carried out in a shaded nursery, with seedlings grown on an Alfisol. Were performed two sets of experiments. In the first, were carried out four experiments using the flooded rice cultivars INIA Olimar, Puitá Inta - CL, Br Irga 409 and Irga 424; these trials were set up as completely randomized design in a 5x4 factorial scheme, with four replications. Treatments consisted of five nitrogen rates (0, 40, 80, 120 and 160 kg ha - 1 and four levels of liquid inoculant Ab - V5 and Ab - V6 - A. brasilense (0, 1, 2 and 4 times the manufacturer's recommendation without seed treatment. In second set, were performed two experiments using the cultivars Puitá Inta - CL and Br Irga 409, arranged in the same design, but using a 4x2 factorial. In this set, treatments were composed of four levels of Ab - V5 and Ab - V6 - A. brasilense liquid inoculant (0, 1, 2 and 4 times the recommendation of 100 mL ha - 1 , using rice seeds with and without insecticide and fungicide treatment. Shoot dry matter, number of panicles, and rice grain yield per pot were the assessed variables. The results showed that rice seed inoculation with A. brasilense had no effects on rice grain yield of the cultivars INIA Olimar, Puitá Inta - CL, Br Irga 409 and Irga 424.

High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

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X. S. Tai

2013-08-01

Full Text Available Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China, located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon–Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g−1 soil and 0.97 × 106 to 12.78 × 106 g−1 soil, respectively. Redundancy analysis (RDA revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial

High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

Science.gov (United States)

Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.; Zhang, Y.

2013-08-01

Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China), located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon-Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs) of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g-1 soil and 0.97 × 106 to 12.78 × 106 g-1 soil, respectively. Redundancy analysis (RDA) revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial communities beneath Potentilla

Nitrogen-fixing trees inhibit growth of regenerating Costa Rican rainforests.

Science.gov (United States)

Taylor, Benton N; Chazdon, Robin L; Bachelot, Benedicte; Menge, Duncan N L

2017-08-15

More than half of the world's tropical forests are currently recovering from human land use, and this regenerating biomass now represents the largest carbon (C)-capturing potential on Earth. How quickly these forests regenerate is now a central concern for both conservation and global climate-modeling efforts. Symbiotic nitrogen-fixing trees are thought to provide much of the nitrogen (N) required to fuel tropical secondary regrowth and therefore to drive the rate of forest regeneration, yet we have a poor understanding of how these N fixers influence the trees around them. Do they promote forest growth, as expected if the new N they fix facilitates neighboring trees? Or do they suppress growth, as expected if competitive inhibition of their neighbors is strong? Using 17 consecutive years of data from tropical rainforest plots in Costa Rica that range from 10 y since abandonment to old-growth forest, we assessed how N fixers influenced the growth of forest stands and the demographic rates of neighboring trees. Surprisingly, we found no evidence that N fixers facilitate biomass regeneration in these forests. At the hectare scale, plots with more N-fixing trees grew slower. At the individual scale, N fixers inhibited their neighbors even more strongly than did nonfixing trees. These results provide strong evidence that N-fixing trees do not always serve the facilitative role to neighboring trees during tropical forest regeneration that is expected given their N inputs into these systems.

Sterol Compositions of the Filamentous Nitrogen-Fixing Terrestrial Cyanobacterium Scytonema sp

Czech Academy of Sciences Publication Activity Database

Řezanka, Tomáš; Dembitsky, V. M.; Go, J. V.; Dor, I.; Prell, Aleš; Hanuš, L.

2003-01-01

Roč. 48, č. 3 (2003), s. 357-360 ISSN 0015-5632 Institutional research plan: CEZ:AV0Z5020903 Keywords : nitrogen-fixing * cyanobacterium * scytonema Subject RIV: EE - Microbiology, Virology Impact factor: 0.857, year: 2003

Effects of oxytetracycline on the abundance and community structure of nitrogen-fixing bacteria during cattle manure composting.

Science.gov (United States)

Sun, Jiajun; Qian, Xun; Gu, Jie; Wang, Xiaojuan; Gao, Hua

2016-09-01

The effects of oxytetracycline (OTC) on nitrogen-fixing bacterial communities were investigated during cattle manure composting. The abundance and community structure of nitrogen-fixing bacteria were determined by qPCR and denaturing gradient gel electrophoresis (DGGE), respectively. The matrix was spiked with OTC at four levels: no OTC, 10mg/kg dry weight (DW) OTC (L), 60mg/kg DW OTC (M), and 200mg/kg DW OTC (H). The high temperature period of composting was shorter with M and H, and the decline in temperature during the cooling stage was accelerated by OTC. OTC had a concentration-dependent inhibitory effect on the nitrogenase activity during early composting, and the nifH gene abundance declined significantly during the later composting stage. The DGGE profile and statistical analysis showed that OTC changed the nitrogen-fixing bacterial community succession and reduced the community richness and dominance. The nitrogen-fixing bacterial community structure was affected greatly by the high level of OTC. Copyright © 2016. Published by Elsevier Ltd.

Paenibacillus sonchi sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sonchus oleraceus.

Science.gov (United States)

Hong, Yuan-Yuan; Ma, Yu-Chao; Zhou, Yu-Guang; Gao, Fei; Liu, Hong-Can; Chen, San-Feng

2009-11-01

A nitrogen-fixing bacterium, designated strain X19-5(T), was isolated from rhizosphere soil of Sonchus oleraceus. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain X19-5(T) was a member of the genus Paenibacillus. Strain X19-5(T) showed the highest 16S rRNA gene sequence similarity (98.8 %) with Paenibacillus graminis RSA19(T) and below 97 % similarity with other recognized members of the genus. The level of DNA-DNA relatedness between strain X19-5(T) and P. graminis RSA19(T) was 45.7 %. The DNA G+C content of strain X19-5(T) was 46.8 mol%. The major fatty acids were anteiso-C(15 : 0), C(16 : 0) and iso-C(16 : 0). On the basis of its phenotypic characteristics and the level of DNA-DNA hybridization, strain X19-5(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sonchi sp. nov. is proposed. The type strain is X19-5(T) (=CCBAU 83901(T)=LMG 24727(T)).

Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach

DEFF Research Database (Denmark)

Tribelli, Paula Maria; Rossi, Leticia; Ricardi, Martiniano M

2018-01-01

 days was observed under low oxygen conditions but not in aerobiosis. In-silico analysis of the alkB promoter zone showed a putative binding sequence for the anaerobic global regulator, Anr. Our results indicate that some diesel fuel components can be utilized as sole carbon source under microaerophilic...

Studies on utilization of nitrogen-fixing bacteria for saving energy; Chisso koteikin no katsuyo ni yoru sho energy no kenkyu

Energy Technology Data Exchange (ETDEWEB)

Uozumi, T; Koyama, R; Horiuchi, M; Hidaka, M; Masaki, H [The University of Tokyo, Tokyo (Japan); Shigematsu, T; Inoue, A [New Energy and Industrial Technology Development Organization, Tokyo, (Japan)

1997-02-01

This paper describes analysis and enhancement of nitrogen-fixing gene of rice root bacteria, such as Klebsiella oxytoca, Azospirillum lipoferumn and Sphingomonas paucimobilis, for realizing energy saving through conservation of nitrogenous fertilizers. For K. oxytoca, modified strain R-16 was developed, which can fix nitrogen effectively even in the presence of NH4{sup +}. Nitrogen-fixing ability of A. lipoferumn depends on the activity control by the modification of nitrogen-fixing enzyme as well as on the adjustment of transcription level by the transcription activating gene, nifA. The control gene relating to the above was analyzed by making clones. As a result, a modified strain TAl without the control by NH4{sup +} was developed. The R-16 and TAl strains were inoculated into rice sterile-cultured without nitrogen. Consequently, inoculated strains were settled in the root, which resulted in the increased vegetation weight of plant to two times heavier than that without inoculation. 9 refs.

RESISTANCE OF KARST CAVERNS NITROGEN-FIXING BACTERIA TO EXTREME FACTORS

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Tashyrev O. B.

2014-10-01

Full Text Available To determine the studied bacteria resistance quantitative parameters of extreme factors such as toxic metals (Cu2+, organic xenobiotics (p-nitrochlorobenzene and UV-irradiation were the aim of the research. Six strains of nitrogen-fixing bacteria isolated from clays of two caverns Mushkarova Yama (Podolia, Ukraine and Kuybyshevskaya (Western Caucasus, Abkhazia and Azotobacter vinelandii УКМ В-6017 as a reference strain have been tested. For this purpose the maximum permissible concentration of Cu2+ and p-nitrochlorobenzene in the concentration gradient and lethal doses of UV by the survival caverns have been determined. Maximum permissible concentrations for strains were as 10 ppm Cu2+, 70–120 ppm of p-nitrochlorobenzene. The maximum doses of UV-irradiation varied in the range of 55–85 J/m2 (LD99.99. It is shown that three classes of extreme factors resistance parameters of karst caverns strains are similar to the strain of terrestrial soil ecosystems. The most active studied strains reduce the concentration of p-nitrochlorobenzene in the medium in 13 times. The ability of nitrogen-fixing bacteria to degrade p-nitrochlorobenzene could be used in creation new environmental biotechnology for industrial wastewater treatment from nitrochloroaromatic xenobiotics. Isolated strains could be used as destructors for soils bioremediation in agrobiotechnologies and to optimize plants nitrogen nutrition in terrestrial ecosystems.

Recent developments in the structural organization and regulation of nitrogen fixation genes in Herbaspirillum seropedicae.

Science.gov (United States)

Pedrosa, F O; Benelli, E M; Yates, M G; Wassem, R; Monteiro, R A; Klassen, G; Steffens, M B; Souza, E M; Chubatsu, L S; Rigo, L U

2001-10-04

Herbaspirillum seropedicae is a nitrogen-fixing bacterium found in association with economically important gramineae. Regulation of nitrogen fixation involves the transcriptional activator NifA protein. The regulation of NifA protein and its truncated mutant proteins is described and compared with that of other nitrogen fixation bacteria. Nitrogen fixation control in H. seropedicae, of the beta-subgroup of Proteobacteria, has regulatory features in common with Klebsiella pneumoniae, of the gamma-subgroup, at the level of nifA expression and with rhizobia and Azospirillum brasilense, of the alpha-subgroup, at the level of control of NifA by oxygen.

Aerobic and anaerobic nitrogen transformation processes in N2-fixing cyanobacterial aggregates.

Science.gov (United States)

Klawonn, Isabell; Bonaglia, Stefano; Brüchert, Volker; Ploug, Helle

2015-06-01

Colonies of N(2)-fixing cyanobacteria are key players in supplying new nitrogen to the ocean, but the biological fate of this fixed nitrogen remains poorly constrained. Here, we report on aerobic and anaerobic microbial nitrogen transformation processes that co-occur within millimetre-sized cyanobacterial aggregates (Nodularia spumigena) collected in aerated surface waters in the Baltic Sea. Microelectrode profiles showed steep oxygen gradients inside the aggregates and the potential for nitrous oxide production in the aggregates' anoxic centres. (15)N-isotope labelling experiments and nutrient analyses revealed that N(2) fixation, ammonification, nitrification, nitrate reduction to ammonium, denitrification and possibly anaerobic ammonium oxidation (anammox) can co-occur within these consortia. Thus, N. spumigena aggregates are potential sites of nitrogen gain, recycling and loss. Rates of nitrate reduction to ammonium and N(2) were limited by low internal nitrification rates and low concentrations of nitrate in the ambient water. Presumably, patterns of N-transformation processes similar to those observed in this study arise also in other phytoplankton colonies, marine snow and fecal pellets. Anoxic microniches, as a pre-condition for anaerobic nitrogen transformations, may occur within large aggregates (⩾1 mm) even when suspended in fully oxygenated waters, whereas anoxia in small aggregates (1.5 μM), O(2)-depleted water layers, for example, in the chemocline of the Baltic Sea or the oceanic mesopelagic zone, aggregates may promote N-recycling and -loss processes.

Novel Metabolic Attributes of the Genus Cyanothece, Comprising a Group of Unicellular Nitrogen-Fixing Cyanobacteria

Science.gov (United States)

Bandyopadhyay, Anindita; Elvitigala, Thanura; Welsh, Eric; Stöckel, Jana; Liberton, Michelle; Min, Hongtao; Sherman, Louis A.; Pakrasi, Himadri B.

2011-01-01

ABSTRACT The genus Cyanothece comprises unicellular cyanobacteria that are morphologically diverse and ecologically versatile. Studies over the last decade have established members of this genus to be important components of the marine ecosystem, contributing significantly to the nitrogen and carbon cycle. System-level studies of Cyanothece sp. ATCC 51142, a prototypic member of this group, revealed many interesting metabolic attributes. To identify the metabolic traits that define this class of cyanobacteria, five additional Cyanothece strains were sequenced to completion. The presence of a large, contiguous nitrogenase gene cluster and the ability to carry out aerobic nitrogen fixation distinguish Cyanothece as a genus of unicellular, aerobic nitrogen-fixing cyanobacteria. Cyanothece cells can create an anoxic intracellular environment at night, allowing oxygen-sensitive processes to take place in these oxygenic organisms. Large carbohydrate reserves accumulate in the cells during the day, ensuring sufficient energy for the processes that require the anoxic phase of the cells. Our study indicates that this genus maintains a plastic genome, incorporating new metabolic capabilities while simultaneously retaining archaic metabolic traits, a unique combination which provides the flexibility to adapt to various ecological and environmental conditions. Rearrangement of the nitrogenase cluster in Cyanothece sp. strain 7425 and the concomitant loss of its aerobic nitrogen-fixing ability suggest that a similar mechanism might have been at play in cyanobacterial strains that eventually lost their nitrogen-fixing ability. PMID:21972240

Competition and facilitation between the marine nitrogen-fixing cyanobacterium Cyanothece and its associated bacterial community

NARCIS (Netherlands)

Brauer, Verena S; Stomp, Maayke; Bouvier, Thierry; Fouilland, Eric; Leboulanger, Christophe; Confurius-Guns, Veronique; Weissing, Franz J; Stal, Lucas J; Huisman, Jef

2015-01-01

N2-fixing cyanobacteria represent a major source of new nitrogen and carbon for marine microbial communities, but little is known about their ecological interactions with associated microbiota. In this study we investigated the interactions between the unicellular N2-fixing cyanobacterium Cyanothece

Compatibility between Legumes and Rhizobia for the Establishment of a Successful Nitrogen-Fixing Symbiosis.

Science.gov (United States)

Clúa, Joaquín; Roda, Carla; Zanetti, María Eugenia; Blanco, Flavio A

2018-02-27

The root nodule symbiosis established between legumes and rhizobia is an exquisite biological interaction responsible for fixing a significant amount of nitrogen in terrestrial ecosystems. The success of this interaction depends on the recognition of the right partner by the plant within the richest microbial ecosystems on Earth, the soil. Recent metagenomic studies of the soil biome have revealed its complexity, which includes microorganisms that affect plant fitness and growth in a beneficial, harmful, or neutral manner. In this complex scenario, understanding the molecular mechanisms by which legumes recognize and discriminate rhizobia from pathogens, but also between distinct rhizobia species and strains that differ in their symbiotic performance, is a considerable challenge. In this work, we will review how plants are able to recognize and select symbiotic partners from a vast diversity of surrounding bacteria. We will also analyze recent advances that contribute to understand changes in plant gene expression associated with the outcome of the symbiotic interaction. These aspects of nitrogen-fixing symbiosis should contribute to translate the knowledge generated in basic laboratory research into biotechnological advances to improve the efficiency of the nitrogen-fixing symbiosis in agronomic systems.

Low nitrogen stress stimulating the indole-3-acetic acid biosynthesis of Serratia sp. ZM is vital for the survival of the bacterium and its plant growth-promoting characteristic.

Science.gov (United States)

Ouyang, Liming; Pei, Haiyan; Xu, Zhaohui

2017-04-01

Serratia sp. ZM is a plant growth-promoting (PGP) bacterial strain isolated from the rhizospheric soil of Populus euphratica in northwestern China. In this study, low nitrogen supply significantly stimulated the production of indole-3-acetic acid (IAA) in Serratia sp.ZM. The inoculation of the bacterium to wheat seedlings improved plant growth compared with the uninoculated group, and the stimulating effect was more prominent under low nitrogen stress. Inactivation of the predicted key gene in the IAA biosynthesis pathway impaired IAA production and significantly hampered mutant growth in poor medium. Furthermore, the IAA-deficient mutant lost the PGP effect under either normal or low nitrogen conditions in plant experiments. This study revealed the significant impact of environmental nitrogen levels on IAA production in the PGP strain and the vital effect of IAA on resistance physiology of both the bacterium and host plant. The characteristics of Serratia sp. ZM also indicated its application potential as a biofertilizer for plants, especially those suffering from poor nitrogen soil.

Aggregation of the rhizospheric bacterium Azospirillum brasilense in response to oxygen

Science.gov (United States)

Abdoun, Hamid; McMillan, Mary; Pereg, Lily

2016-04-01

Azospirillum brasilense spp. have ecological, scientific and agricultural importance. As model plant growth promoting rhizobacteria they interact with a large variety of plants, including important food and cash crops. Azospirillum strains are known for their production of plant growth hormones that enhance root systems and for their ability to fix nitrogen. Azospirillum cells transform in response to environmental cues. The production of exopolysaccharides and cell aggregation during cellular transformation are important steps in the attachment of Azospirillum to roots. We investigate signals that induce cellular transformation and aggregation in the Azospirillum and report on the importance of oxygen to the process of aggregation in this rhizospheric bacterium.

Response of nitrogen-fixing water fern Azolla biofertilization to rice crop.

Science.gov (United States)

Bhuvaneshwari, K; Singh, Pawan Kumar

2015-08-01

The water fern Azolla harbors nitrogen-fixing cyanobacterium Anabaena azollae as symbiont in its dorsal leaves and is known as potent N 2 fixer. Present investigation was carried out to study the influence of fresh Azolla when used as basal incorporation in soil and as dual cropped with rice variety Mahsoori separately and together with and without chemical nitrogen fertilizer in pots kept under net house conditions. Results showed that use of Azolla as basal or dual or basal plus dual influenced the rice crop positively where use of fern as basal plus dual was superior and served the nitrogen requirement of rice. There was marked increase in plant height, number of effective tillers, dry mass and nitrogen content of rice plants with the use of Azolla and N-fertilizers alone and other combinations. The use of Azolla also increased organic matter and potassium contents of the soil.

Novel heterotrophic nitrogen removal and assimilation characteristic of the newly isolated bacterium Pseudomonas stutzeri AD-1.

Science.gov (United States)

Qing, Hui; Donde, Oscar Omondi; Tian, Cuicui; Wang, Chunbo; Wu, Xingqiang; Feng, Shanshan; Liu, Yao; Xiao, Bangding

2018-04-18

AD-1, an aerobic denitrifier, was isolated from activated sludge and identified as Pseudomonas stutzeri. AD-1 completely removed NO 3 - or NO 2 - and removed 99.5% of NH 4 + during individual culturing in a broth medium with an initial nitrogen concentration of approximately 50 mg L -1 . Results showed that larger amounts of nitrogen were removed through assimilation by the bacteria. And when NH 4 + was used as the sole nitrogen source in the culture medium, neither NO 2 - nor NO 3 - was detected, thus indicating that AD-1 may not be a heterotrophic nitrifier. Only trace amount of N 2 O was detected during the denitrification process. Single factor experiments indicated that the optimal culture conditions for AD-1 were: a carbon-nitrogen ratio (C/N) of 15, a temperature of 25°C and sodium succinate or glucose as a carbon source. In conclusion, due to the ability of AD-1 to utilize nitrogen of different forms with high efficiencies for its growth while producing only trace emissions of N 2 O, the bacterium had outstanding potential to use in the bioremediation of high-nitrogen-containing wastewaters. Meanwhile, it may also be a proper candidate for biotreatment of high concentration organic wastewater. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Nitrogen-fixing cyanobacterium with a high phycoerythrin content.

Science.gov (United States)

Rodriguez, H; Rivas, J; Guerrero, M G; Losada, M

1989-03-01

The elemental and molecular composition, pigment content, and productivity of a phycoerythrin-rich nitrogen-fixing cyanobacterium-an Anabaena strain isolated from the coastal lagoon Albufera de Valencia, Spain-has been investigated. When compared with other heterocystous species, this strain exhibits similar chlorophyll a, carotene, and total phycobiliprotein contents but differs remarkably in the relative proportion of specific phycobiliproteins; the content of C-phycoerythrin amounts to 8.3% (versus about 1% in the other species) of cell dry weight. Absorption and fluorescence spectra of intact phycobilisomes isolated from this Anabaena sp. corroborate the marked contribution of phycoerythrin as an antenna pigment, a circumstance that is unusual for cyanobacteria capable of fixing N(2). The pigment content of cells is affected by variations in irradiance and cell density, these adaptive changes being more patent for C-phycoerythrin than for phycocyanins. The Anabaena strain is clumpy and capable of rapid flocculation. It exhibits outdoor productivities higher than 20 g (dry weight) m day during summer.

Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling.

Science.gov (United States)

Lidbury, Ian D E A; Murrell, J Colin; Chen, Yin

2015-03-01

Bacteria of the marine Roseobacter clade are characterised by their ability to utilise a wide range of organic and inorganic compounds to support growth. Trimethylamine (TMA) and trimethylamine N-oxide (TMAO) are methylated amines (MA) and form part of the dissolved organic nitrogen pool, the second largest source of nitrogen after N2 gas, in the oceans. We investigated if the marine heterotrophic bacterium, Ruegeria pomeroyi DSS-3, could utilise TMA and TMAO as a supplementary energy source and whether this trait had any beneficial effect on growth. In R. pomeroyi, catabolism of TMA and TMAO resulted in the production of intracellular ATP which in turn helped to enhance growth rate and growth yield as well as enhancing cell survival during prolonged energy starvation. Furthermore, the simultaneous use of two different exogenous energy sources led to a greater enhancement of chemoorganoheterotrophic growth. The use of TMA and TMAO primarily as an energy source resulted in the remineralisation of nitrogen in the form of ammonium, which could cross feed into another bacterium. This study provides greater insight into the microbial metabolism of MAs in the marine environment and how it may affect both nutrient flow within marine surface waters and the flux of these climatically important compounds into the atmosphere.

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia.

Science.gov (United States)

Lardi, Martina; Pessi, Gabriella

2018-05-18

Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).

Vertical zonation and seed germination indices of chromium resistant cellulolytic and nitrogen fixing bacteria from a chronically metal exposed land area

International Nuclear Information System (INIS)

Aslam, S.; Qazi, J.I.

2014-01-01

Twenty eight cellulolytic and 25 nitrogen fixing bacteria were isolated from 20, 40 and 60 cm depths of the chromium contaminated land area. The cellulolytic as well as nitrogen fixing microbial communities in soil profiles were dominated by genus Bacillus. More diverse nitrogen fixing bacterial isolates belonging to different genera Paenibacillus, Corynebacterium and Pseudomonas were observed as compared to cellulolytic bacterial community. Majority of the cellulolytic bacteria were found inhabitants of 20 cm soil layer while 40 cm depth was the preferred zone for the nitrogen fixing bacteria. Screening of the bacterial isolates for chromium resistance showed that isolates designated as ASK15 and ASK16 were able to resist up to 1800 mg/l of chromium while the nitrogen fixing isolates which offered a maximum resistant level up to 1650 mg/l of chromium were ASNt10 and ASNS13. Nitrogen fixing isolates enhanced seed germination by 33% and expressed efficient nitrogenase activity up to 0.80 (C/sub 2/H/sub 2/ nmol/ml/hr). Growth promoting assay proved ASNt10 a potential isolate which produced 90 meu g/ml of indoleacetic acid (IAA). Though cellulolytic isolates did not affect seed germination, a significant influence on root length similar to that of ASNt10 and ASNS13 with nearly 5-fold increase in comparison with uninoculated control was observed. The isolates ASK15, ASK16 were identified as Bacillus cereus while ASNt10 and ASNS13 as Paenibacillus barcinonensis and Bacillus megaterium, respectively. (author)

Characterization of free nitrogen fixing bacteria of the genus Azotobacter in organic vegetable-grown Colombian soils

NARCIS (Netherlands)

Jiménez Avella, Diego; Montaña, José Salvador; Martínez, María Mercedes

With the purpose of isolating and characterizing free nitrogen fixing bacteria (FNFB) of the genus Azotobacter, soil samples were collected randomly from different vegetable organic cultures with neutral pH in different zones of Boyacá-Colombia. Isolations were done in selective free nitrogen

Quantitative analysis of O-2 and Fe2+ profiles in gradient tubes for cultivation of microaerophilic Iron(II)-oxidizing bacteria

DEFF Research Database (Denmark)

Lueder, U.; Druschel, G.; Emerson, D.

2018-01-01

The classical approach for the cultivation of neutrophilic microaerophilic Fe(II)-oxidizing bacteria is agar-based gradient tubes where these bacteria find optimal growth conditions in opposing gradients of oxygen (O-2) and dissolved Fe(II) (Fe2+). The goals of this study were to quantify...... imply that transfer of cultures to fresh tubes within 48-72 h is crucial to provide optimal growth conditions for microaerophilic Fe(II)-oxidizers, particularly for the isolation of new strains....

Novel metabolic attributes of the genus cyanothece, comprising a group of unicellular nitrogen-fixing Cyanothece.

Science.gov (United States)

Bandyopadhyay, Anindita; Elvitigala, Thanura; Welsh, Eric; Stöckel, Jana; Liberton, Michelle; Min, Hongtao; Sherman, Louis A; Pakrasi, Himadri B

2011-01-01

The genus Cyanothece comprises unicellular cyanobacteria that are morphologically diverse and ecologically versatile. Studies over the last decade have established members of this genus to be important components of the marine ecosystem, contributing significantly to the nitrogen and carbon cycle. System-level studies of Cyanothece sp. ATCC 51142, a prototypic member of this group, revealed many interesting metabolic attributes. To identify the metabolic traits that define this class of cyanobacteria, five additional Cyanothece strains were sequenced to completion. The presence of a large, contiguous nitrogenase gene cluster and the ability to carry out aerobic nitrogen fixation distinguish Cyanothece as a genus of unicellular, aerobic nitrogen-fixing cyanobacteria. Cyanothece cells can create an anoxic intracellular environment at night, allowing oxygen-sensitive processes to take place in these oxygenic organisms. Large carbohydrate reserves accumulate in the cells during the day, ensuring sufficient energy for the processes that require the anoxic phase of the cells. Our study indicates that this genus maintains a plastic genome, incorporating new metabolic capabilities while simultaneously retaining archaic metabolic traits, a unique combination which provides the flexibility to adapt to various ecological and environmental conditions. Rearrangement of the nitrogenase cluster in Cyanothece sp. strain 7425 and the concomitant loss of its aerobic nitrogen-fixing ability suggest that a similar mechanism might have been at play in cyanobacterial strains that eventually lost their nitrogen-fixing ability. The unicellular cyanobacterial genus Cyanothece has significant roles in the nitrogen cycle in aquatic and terrestrial environments. Cyanothece sp. ATCC 51142 was extensively studied over the last decade and has emerged as an important model photosynthetic microbe for bioenergy production. To expand our understanding of the distinctive metabolic capabilities of

Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

Directory of Open Access Journals (Sweden)

Zhimin Dai

Full Text Available Biological nitrogen fixation is an essential function of acid mine drainage (AMD microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.

Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

Science.gov (United States)

Dai, Zhimin; Guo, Xue; Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

2014-01-01

Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.

Identification of Nitrogen-Fixing Genes and Gene Clusters from Metagenomic Library of Acid Mine Drainage

Science.gov (United States)

Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

2014-01-01

Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community. PMID:24498417

Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

NARCIS (Netherlands)

Velzen, van R.; Holmer, R.; Bu, F.; Rutten, L.J.J.; Zeijl, van A.L.; Liu, W.; Santuari, L.; Cao, Q.; Sharma, Trupti; Shen, D.; Purwana Roswanjaya, Yuda; Wardhani, T.; Seifi Kalhor, M.; Jansen, Joelle; Hoogen, van den D.J.; Gungor, Berivan; Hartog, M.V.; Hontelez, J.; Verver, J.W.G.; Yang, W.C.; Schijlen, E.G.W.M.; Repin, Rimi; Schilthuizen, M.; Schranz, M.E.; Heidstra, R.; Miyata, Kana; Fedorova, E.; Kohlen, W.; Bisseling, A.H.J.; Smit, S.; Geurts, R.

2017-01-01

Rhizobium nitrogen-fixing nodules are a well-known trait of legumes, but nodules also occur in other plant lineages either with rhizobium or the actinomycete Frankia as microsymbiont. The widely accepted hypothesis is that nodulation evolved independently multiple times, with only a few losses.

Inhibition of nitrogen-fixing activity of the cyanobiont affects the localization of glutamine synthetase in hair cells of Azolla.

Science.gov (United States)

Uheda, Eiji; Maejima, Kazuhiro

2009-10-15

In the Azolla-Anabaena association, the host plant Azolla efficiently incorporates and assimilates ammonium ions that are released from the nitrogen-fixing cyanobiont, probably via glutamine synthetase (GS; EC 6.3.1.2) in hair cells, which are specialized cells protruding into the leaf cavity. In order to clarify the regulatory mechanism underlying ammonium assimilation in the Azolla-Anabaena association, Azolla plants were grown under an argon environment (Ar), in which the nitrogen-fixing activity of the cyanobiont was inhibited specifically and completely. The localization of GS in hair cells was determined by immunoelectron microscopy and quantitative analysis of immunogold labeling. Azolla plants grew healthily under Ar when nitrogen sources, such as NO(3)(-) and NH(4)(+), were provided in the growth medium. Both the number of cyanobacterial cells per leaf and the heterocyst frequency of the plants under Ar were similar to those of plants in a nitrogen environment (N(2)). In hair cells of plants grown under Ar, regardless of the type of nitrogen source provided, only weak labeling of GS was observed in the cytoplasm and in chloroplasts. In contrast, in hair cells of plants grown under N(2), abundant labeling of GS was observed in both sites. These findings indicate that specific inhibition of the nitrogen-fixing activity of the cyanobiont affects the localization of GS isoenzymes. Ammonium fixed and released by the cyanobiont could stimulate GS synthesis in hair cells. Simultaneously, the abundant GS, probably GS1, in these cells, could assimilate ammonium rapidly.

Corals Form Characteristic Associations with Symbiotic Nitrogen-Fixing Bacteria

Science.gov (United States)

Lema, Kimberley A.; Willis, Bette L.

2012-01-01

The complex symbiotic relationship between corals and their dinoflagellate partner Symbiodinium is believed to be sustained through close associations with mutualistic bacterial communities, though little is known about coral associations with bacterial groups able to fix nitrogen (diazotrophs). In this study, we investigated the diversity of diazotrophic bacterial communities associated with three common coral species (Acropora millepora, Acropora muricata, and Pocillopora damicormis) from three midshelf locations of the Great Barrier Reef (GBR) by profiling the conserved subunit of the nifH gene, which encodes the dinitrogenase iron protein. Comparisons of diazotrophic community diversity among coral tissue and mucus microenvironments and the surrounding seawater revealed that corals harbor diverse nifH phylotypes that differ between tissue and mucus microhabitats. Coral mucus nifH sequences displayed high heterogeneity, and many bacterial groups overlapped with those found in seawater. Moreover, coral mucus diazotrophs were specific neither to coral species nor to reef location, reflecting the ephemeral nature of coral mucus. In contrast, the dominant diazotrophic bacteria in tissue samples differed among coral species, with differences remaining consistent at all three reefs, indicating that coral-diazotroph associations are species specific. Notably, dominant diazotrophs for all coral species were closely related to the bacterial group rhizobia, which represented 71% of the total sequences retrieved from tissue samples. The species specificity of coral-diazotroph associations further supports the coral holobiont model that bacterial groups associated with corals are conserved. Our results suggest that, as in terrestrial plants, rhizobia have developed a mutualistic relationship with corals and may contribute fixed nitrogen to Symbiodinium. PMID:22344646

Nitrogen fixed by wheat plants as affected by nitrogen fertilizer levels and Non-symbiotic bacteria

Energy Technology Data Exchange (ETDEWEB)

Soliman, S; Aly, S S.M.; Gadalla, A M [Soils and Water Dept., Atomic Energy Authority, Cairo (Egypt); Abou Seeda, M [Soils and Water Dept., National Res. Centre, Cairo (Egypt)

1995-10-01

Inorganic nitrogen is required for all egyptian soils for wheat. Free living and N 2-fixing microorganisms are able associate closely related with the roots of geraminacae. Pot experiment studies were carried out to examine the response of wheat plants to inoculation with Azospirillum Brasilense and Azotobacter Chroococcum, single or in combination, under various levels of ammonium sulfate interaction between both the inoculants increased straw or grain yield as well as N-uptake by wheat plants with increasing N levels. Results showed that grains of wheat plants derived over 19,24 and 15% of its N content from the atmospheric - N 2 (Ndfa) with application of 25,50 and 75 mg N kg-1 soil in the presence of + Azospirillum + azotobacter. The final amount of N 2-fixers. The highest values of N 2-fixed were observed with mixed inoculants followed by inoculation with Azospirillum and then azotobacter. The recovery of applied ammonium sulfate-N was markedly increased by inoculation with combined inoculants, but less in uninoculated treatments. Seeds inoculated with non-symbiotic fixing bacteria could be saved about 25 kg N without much affecting the grain yield. i fig., 4 tabs.

Nitrogen fixed by wheat plants as affected by nitrogen fertilizer levels and Non-symbiotic bacteria

International Nuclear Information System (INIS)

Soliman, S.; Aly, S.S.M.; Gadalla, A.M.; Abou Seeda, M.

1995-01-01

Inorganic nitrogen is required for all egyptian soils for wheat. Free living and N 2-fixing microorganisms are able associate closely related with the roots of geraminacae. Pot experiment studies were carried out to examine the response of wheat plants to inoculation with Azospirillum Brasilense and Azotobacter Chroococcum, single or in combination, under various levels of ammonium sulfate interaction between both the inoculants increased straw or grain yield as well as N-uptake by wheat plants with increasing N levels. Results showed that grains of wheat plants derived over 19,24 and 15% of its N content from the atmospheric - N 2 (Ndfa) with application of 25,50 and 75 mg N kg-1 soil in the presence of + Azospirillum + azotobacter. The final amount of N 2-fixers. The highest values of N 2-fixed were observed with mixed inoculants followed by inoculation with Azospirillum and then azotobacter. The recovery of applied ammonium sulfate-N was markedly increased by inoculation with combined inoculants, but less in uninoculated treatments. Seeds inoculated with non-symbiotic fixing bacteria could be saved about 25 kg N without much affecting the grain yield. i fig., 4 tabs

Nitrogen fixed by cyanobacteria is utilized by deposit-feeders.

Science.gov (United States)

Karlson, Agnes M L; Gorokhova, Elena; Elmgren, Ragnar

2014-01-01

Benthic communities below the photic zone depend for food on allochthonous organic matter derived from seasonal phytoplankton blooms. In the Baltic Sea, the spring diatom bloom is considered the most important input of organic matter, whereas the contribution of the summer bloom dominated by diazotrophic cyanobacteria is less understood. The possible increase in cyanobacteria blooms as a consequence of eutrophication and climate change calls for evaluation of cyanobacteria effects on benthic community functioning and productivity. Here, we examine utilization of cyanobacterial nitrogen by deposit-feeding benthic macrofauna following a cyanobacteria bloom at three stations during two consecutive years and link these changes to isotopic niche and variations in body condition (assayed as C:N ratio) of the animals. Since nitrogen-fixing cyanobacteria have δ(15)N close to -2‰, we expected the δ(15)N in the deposit-feeders to decrease after the bloom if their assimilation of cyanobacteria-derived nitrogen was substantial. We also expected the settled cyanobacteria with their associated microheterotrophic community and relatively high nitrogen content to increase the isotopic niche area, trophic diversity and dietary divergence between individuals (estimated as the nearest neighbour distance) in the benthic fauna after the bloom. The three surface-feeding species (Monoporeia affinis, Macoma balthica and Marenzelleria arctia) showed significantly lower δ(15)N values after the bloom, while the sub-surface feeder Pontoporeia femorata did not. The effect of the bloom on isotopic niche varied greatly between stations; populations which increased niche area after the bloom had better body condition than populations with reduced niche, regardless of species. Thus, cyanobacterial nitrogen is efficiently integrated into the benthic food webs in the Baltic, with likely consequences for their functioning, secondary production, transfer efficiency, trophic interactions, and

Nitrogen fixed by cyanobacteria is utilized by deposit-feeders.

Directory of Open Access Journals (Sweden)

Agnes M L Karlson

Full Text Available Benthic communities below the photic zone depend for food on allochthonous organic matter derived from seasonal phytoplankton blooms. In the Baltic Sea, the spring diatom bloom is considered the most important input of organic matter, whereas the contribution of the summer bloom dominated by diazotrophic cyanobacteria is less understood. The possible increase in cyanobacteria blooms as a consequence of eutrophication and climate change calls for evaluation of cyanobacteria effects on benthic community functioning and productivity. Here, we examine utilization of cyanobacterial nitrogen by deposit-feeding benthic macrofauna following a cyanobacteria bloom at three stations during two consecutive years and link these changes to isotopic niche and variations in body condition (assayed as C:N ratio of the animals. Since nitrogen-fixing cyanobacteria have δ(15N close to -2‰, we expected the δ(15N in the deposit-feeders to decrease after the bloom if their assimilation of cyanobacteria-derived nitrogen was substantial. We also expected the settled cyanobacteria with their associated microheterotrophic community and relatively high nitrogen content to increase the isotopic niche area, trophic diversity and dietary divergence between individuals (estimated as the nearest neighbour distance in the benthic fauna after the bloom. The three surface-feeding species (Monoporeia affinis, Macoma balthica and Marenzelleria arctia showed significantly lower δ(15N values after the bloom, while the sub-surface feeder Pontoporeia femorata did not. The effect of the bloom on isotopic niche varied greatly between stations; populations which increased niche area after the bloom had better body condition than populations with reduced niche, regardless of species. Thus, cyanobacterial nitrogen is efficiently integrated into the benthic food webs in the Baltic, with likely consequences for their functioning, secondary production, transfer efficiency, trophic

Regime shift by an exotic nitrogen-fixing shrub mediates plant facilitation in primary succession.

Directory of Open Access Journals (Sweden)

Adriano Stinca

Full Text Available Ecosystem invasion by non-native, nitrogen-fixing species is a global phenomenon with serious ecological consequences. However, in the Mediterranean basin few studies addressed the impact of invasion by nitrogen-fixing shrubs on soil quality and hydrological properties at local scale, and the possible effects on succession dynamics and ecosystem invasibility by further species. In this multidisciplinary study we investigated the impact of Genista aetnensis (Biv. DC., an exotic nitrogen-fixing shrub, on the Vesuvius Grand Cone (Southern Italy. Specifically, we tested the hypotheses that the invasion of G. aetnensis has a significant impact on soil quality, soil hydrological regime, local microclimate and plant community structure, and that its impact increases during the plant ontogenetic cycle. We showed that G. aetnensis, in a relatively short time-span (i.e. ~ 40 years, has been able to build-up an island of fertility under its canopy, by accumulating considerable stocks of C, N, and P in the soil, and by also improving the soil hydrological properties. Moreover, G. aetnensis mitigates the daily range of soil temperature, reducing the exposure of coexisting plants to extremely high temperatures and water loss by soil evaporation, particularly during the growing season. Such amelioration of soil quality, coupled with the mitigation of below-canopy microclimatic conditions, has enhanced plant colonization of the barren Grand Cone slopes, by both herbaceous and woody species. These results suggest that the invasion of G. aetnensis could eventually drive to the spread of other, more resource-demanding exotic species, promoting alternative successional trajectories that may dramatically affect the local landscape. Our study is the first record of the invasion of G. aetnensis, an additional example of the regime shifts driven by N-fixing shrubs in Mediterranean region. Further studies are needed to identity specific management practices that can

Differences in Plant Traits among N-fixing Trees in Hawaii Affect Understory Nitrogen Cycling

Science.gov (United States)

August-Schmidt, E.; D'Antonio, C. M.

2016-12-01

Nitrogen (N) fixing trees are frequently used to restore soil functions to degraded ecosystems because they can increase soil organic matter and N availability. Although N-fixers are lumped into a single functional group, the quality and quantity of the plant material they produce and the rate at which they accrete and add N to the cycling pool likely vary. This talk will focus on the questions: (1) How does N-cycling differ among N-fixing tree species? And (2) Which plant traits are most important in distinguishing the soil N environment? To address these questions, we investigated planted stands of two Hawaiian native N-fixing trees (Acacia koa and Sophora chrysophylla) and `natural' stands of an invasive N-fixing tree (Morella faya) in burned seasonal submontane woodlands in Hawaii Volcanoes National Park. We measured the relative availability of nitrogen in the soil pool and understory plant community as well as characterizing the rate and amount of N cycling in these stands both in the field and using long term soil incubations in the laboratory. We found that N is cycled very differently under these three N-fixers and that this correlates with differences in their leaf traits. S. chrysophylla had the highest foliar %N and highest specific leaf area, and stands of these trees are associated with faster N-cycling, resulting in greater N availability compared to all other site types. Incubated S. chrysophylla soils mineralized almost twice as much N as any other soil type over the course of the experiment. The comparatively high-N environment under S. chrysophylla suggests that litter quality may be more important than litter quantity in determining nitrogen availability to the understory community.

Bacteroidales ectosymbionts of gut flagellates shape the nitrogen-fixing community in dry-wood termites

Science.gov (United States)

Desai, Mahesh S; Brune, Andreas

2012-01-01

Although it is well documented that the lack of nitrogen in the diet of wood-feeding termites is compensated by the nitrogen-fixing capacity of their gut microbiota, the bacteria responsible for this activity are largely unknown. Here, we analyzed the diversity and expression of nitrogenase genes (homologs of nifH) in four species of dry-wood termites (Kalotermitidae), which thrive on a particularly nitrogen-poor resource. Although each species harbored a highly diverse suite of termite-specific homologs in their microliter-sized hindgut, only a core set related to nifH genes of Treponema and Azoarcus spp., ‘Azobacteroides pseudotrichonymphae', the first member of the Bacteroidales identified as a diazotroph, and termite-gut-specific anfH genes of hitherto unknown origin were preferentially expressed. Transcription patterns corroborated that the populations of active diazotrophs differ fundamentally between termite genera. Capillary-picked suspensions of the flagellates Devescovina arta and Snyderella tabogae revealed that their bacterial ectosymbionts each possess two paralogs of nifH, which apparently have been acquired consecutively during evolution of Bacteroidales, but only one of them (anfH) is actively expressed. Transcription patterns correlated neither with the molybdenum content of the diet nor with intestinal hydrogen concentrations, measured with microsensors. We propose that the nitrogen-fixing community in different dry-wood termites is shaped by the symbionts of their specific flagellate populations. Our findings suggest that the diazotrophic nature of ‘Armantifilum devescovinae' has an important role in the nitrogen metabolism of dry-wood termites and is the driving force of co-evolution with its flagellate host. PMID:22189498

Improved Alkane Production in Nitrogen-Fixing and Halotolerant Cyanobacteria via Abiotic Stresses and Genetic Manipulation of Alkane Synthetic Genes.

Science.gov (United States)

Kageyama, Hakuto; Waditee-Sirisattha, Rungaroon; Sirisattha, Sophon; Tanaka, Yoshito; Mahakhant, Aparat; Takabe, Teruhiro

2015-07-01

Cyanobacteria possess the unique capacity to produce alkane. In this study, effects of nitrogen deficiency and salt stress on biosynthesis of alkanes were investigated in three kinds of cyanobacteria. Intracellular alkane accumulation was increased in nitrogen-fixing cyanobacterium Anabaena sp. PCC7120, but decreased in non-diazotrophic cyanobacterium Synechococcus elongatus PCC7942 and constant in a halotolerant cyanobacterium Aphanothece halophytica under nitrogen-deficient condition. We also found that salt stress increased alkane accumulation in Anabaena sp. PCC7120 and A. halophytica. The expression levels of two alkane synthetic genes were not upregulated significantly under nitrogen deficiency or salt stress in Anabaena sp. PCC7120. The transformant Anabaena sp. PCC7120 cells with additional alkane synthetic gene set from A. halophytica increased intracellular alkane accumulation level compared to control cells. These results provide a prospect to improve bioproduction of alkanes in nitrogen-fixing halotolerant cyanobacteria via abiotic stresses and genetic engineering.

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts.

Science.gov (United States)

Remigi, Philippe; Zhu, Jun; Young, J Peter W; Masson-Boivin, Catherine

2016-01-01

Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betaproteobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nitrogen fertilization has a stronger effect on soil nitrogen-fixing bacterial communities than elevated atmospheric CO2.

Science.gov (United States)

Berthrong, Sean T; Yeager, Chris M; Gallegos-Graves, Laverne; Steven, Blaire; Eichorst, Stephanie A; Jackson, Robert B; Kuske, Cheryl R

2014-05-01

Biological nitrogen fixation is the primary supply of N to most ecosystems, yet there is considerable uncertainty about how N-fixing bacteria will respond to global change factors such as increasing atmospheric CO2 and N deposition. Using the nifH gene as a molecular marker, we studied how the community structure of N-fixing soil bacteria from temperate pine, aspen, and sweet gum stands and a brackish tidal marsh responded to multiyear elevated CO2 conditions. We also examined how N availability, specifically, N fertilization, interacted with elevated CO2 to affect these communities in the temperate pine forest. Based on data from Sanger sequencing and quantitative PCR, the soil nifH composition in the three forest systems was dominated by species in the Geobacteraceae and, to a lesser extent, Alphaproteobacteria. The N-fixing-bacterial-community structure was subtly altered after 10 or more years of elevated atmospheric CO2, and the observed shifts differed in each biome. In the pine forest, N fertilization had a stronger effect on nifH community structure than elevated CO2 and suppressed the diversity and abundance of N-fixing bacteria under elevated atmospheric CO2 conditions. These results indicate that N-fixing bacteria have complex, interacting responses that will be important for understanding ecosystem productivity in a changing climate.

Rhizospheric fungi and their link with the nitrogen-fixing Frankia harbored in host plant Hippophae rhamnoides L.

Science.gov (United States)

Zhou, Xue; Tian, Lei; Zhang, Jianfeng; Ma, Lina; Li, Xiujun; Tian, Chunjie

2017-12-01

Sea buckthorn (Hippophae rhamnoides L.) is a pioneer plant used for land reclamation and an appropriate material for studying the interactions of symbiotic microorganisms because of its nitrogen-fixing root nodules and mycorrhiza. We used high-throughput sequencing to reveal the diversities and community structures of rhizospheric fungi and their link with nitrogen-fixing Frankia harbored in sea buckthorn collected along an altitude gradient from the Qinghai Tibet Plateau to interior areas. We found that the fungal diversities and compositions varied between different sites. Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla. The distribution of sea buckthorn rhizospheric fungi was driven by both environmental factors and the geographic distance. Among all examined soil characteristics, altitude, AP, and pH were found to have significant (p < 0.05) effect on the rhizospheric fungal community. The rhizospheric fungal communities became more distinct as the distance increased. Moreover, co-inertia analysis identified significant co-structures between Frankia and AMF communities in the rhizosphere of sea buckthorn. We conclude that at the large scale, there are certain linkages between nitrogen-fixing bacteria and the AMF expressed in the distributional pattern. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methylocapsa acidiphila gen. nov., sp. nov., a novel methane-oxidizing and dinitrogen-fixing acidophilic bacterium from Sphagnum bog.

Science.gov (United States)

Dedysh, Svetlana N; Khmelenina, Valentina N; Suzina, Natalia E; Trotsenko, Yuri A; Semrau, Jeremy D; Liesack, Werner; Tiedje, James M

2002-01-01

A novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov., are proposed for a methane-oxidizing bacterium isolated from an acidic Sphagnum peat bog. This bacterium, designated strain B2T, represents aerobic, gram-negative, colourless, non-motile, curved coccoids that form conglomerates covered by an extracellular polysaccharide matrix. The cells use methane and methanol as sole sources of carbon and energy and utilize the serine pathway for carbon assimilation. Strain B2T is a moderately acidophilic organism with growth between pH 4.2 and 7.2 and at temperatures from 10 to 30 degrees C. The cells possess a well-developed system of intracytoplasmic membranes (ICM) packed in parallel on only one side of the cell membrane. This type of ICM structure represents a novel arrangement, which was termed type III. The resting cells are Azotobacter-type cysts. Strain B2T is capable of atmospheric nitrogen fixation; it possesses particulate methane monooxygenase and does not express soluble methane monooxygenase. The major phospholipid fatty acid is 18:1omega7c and the major phospholipids are phosphatidylglycerols. The G+C content of the DNA is 63.1 mol%. This bacterium belongs to the alpha-subclass of the Proteobacteria and is most closely related to the acidophilic methanotroph Methylocella palustris KT (97.3% 16S rDNA sequence similarity). However, the DNA-DNA hybridization value between strain B2T and Methylocella palustris K(T) is only 7%. Thus, strain B2T is proposed to comprise a novel genus and species, Methylocapsa acidiphila gen. nov., sp. nov. Strain B2T (= DSM 13967T = NCIMB 13765T) is the type strain.

Global Transcriptomic and Proteomic Responses of Dehalococcoides ethenogenes Strain 195 to Fixed Nitrogen Limitation

Energy Technology Data Exchange (ETDEWEB)

Lee, Patrick K. H. [University of California, Berkeley; Dill, Brian [ORNL; Louie, Tiffany S. [University of California, Berkeley; Shah, Manesh B [ORNL; Verberkmoes, Nathan C [ORNL; Andersen, Gary L. [Lawrence Berkeley National Laboratory (LBNL); Zinder, Stephen H. [Cornell University; Alvarez-Cohen, Lisa [Lawrence Berkeley National Laboratory (LBNL)

2012-01-01

Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing D. ethenogenes strain 195 to fixed nitrogen limitation (FNL) as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially up-regulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly up-regulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally down regulated in response to FNL and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and post-translational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.

Spectroscopic characterization of a truncated hemoglobin from the nitrogen-fixing bacterium Herbaspirillum seropedicae.

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Razzera, Guilherme; Vernal, Javier; Baruh, Debora; Serpa, Viviane I; Tavares, Carolina; Lara, Flávio; Souza, Emanuel M; Pedrosa, Fábio O; Almeida, Fábio C L; Terenzi, Hernán; Valente, Ana Paula

2008-09-01

The Herbaspirillum seropedicae genome sequence encodes a truncated hemoglobin typical of group II (Hs-trHb1) members of this family. We show that His-tagged recombinant Hs-trHb1 is monomeric in solution, and its optical spectrum resembles those of previously reported globins. NMR analysis allowed us to assign heme substituents. All data suggest that Hs-trHb1 undergoes a transition from an aquomet form in the ferric state to a hexacoordinate low-spin form in the ferrous state. The close positions of Ser-E7, Lys-E10, Tyr-B10, and His-CD1 in the distal pocket place them as candidates for heme coordination and ligand regulation. Peroxide degradation kinetics suggests an easy access to the heme pocket, as the protein offered no protection against peroxide degradation when compared with free heme. The high solvent exposure of the heme may be due to the presence of a flexible loop in the access pocket, as suggested by a structural model obtained by using homologous globins as templates. The truncated hemoglobin described here has unique features among truncated hemoglobins and may function in the facilitation of O(2) transfer and scavenging, playing an important role in the nitrogen-fixation mechanism.

Identification of symbiotic nitrogen-fixing bacteria from three African leguminous trees in Gorongosa National Park.

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Teixeira, Helena; Rodríguez-Echeverría, Susana

2016-07-01

The symbiosis between leguminous plants and symbiotic nitrogen-fixing bacteria is a key component of terrestrial ecosystems. Woody legumes are well represented in tropical African forests but despite their ecological and socio-economic importance, they have been little studied for this symbiosis. In this study, we examined the identity and diversity of symbiotic-nitrogen fixing bacteria associated with Acacia xanthophloea, Faidherbia albida and Albizia versicolor in the Gorongosa National Park (GNP) in Mozambique. To the best of our knowledge, this is the first report on the identity of symbiotic-nitrogen fixing bacteria in this region. 166 isolates were obtained and subjected to molecular identification. BOX-A1R PCR was used to discriminate different bacterial isolates and PCR-sequencing of 16S rDNA, and two housekeeping genes, glnII and recA, was used to identify the obtained bacteria. The gene nifH was also analyzed to assess the symbiotic capacity of the obtained bacteria. All isolates from F. albida and Al. versicolor belonged to the Bradyrhizobium genus whereas isolates from Ac. xanthophloea clustered with Mesorhizobium, Rhizobium or Ensifer strains. Soil chemical analysis revealed significant differences between the soils occupied by the three studied species. Thus, we found a clear delimitation in the rhizobial communities and soils associated with Ac. xanthophloea, F. albida and Al. versicolor, and higher rhizobial diversity for Ac. xanthophloea than previously reported. Copyright © 2016 Elsevier GmbH. All rights reserved.

Root-to-seed transport and metabolism of fixed nitrogen in soybean

International Nuclear Information System (INIS)

McClure, P.R.

1983-01-01

The great energetic demand of nitrogen fixation to support growth of the exceptionally high-N seeds is certainly a major yield barrier for soybeans. Transport of carbohydrate energy supplies to the root and of fixed nitrogen (N) from the root appear to contribute to the yield barrier, also. N is loaded into the soybean xylem stream principally as allantoin (ALL), and allantonic acid (ALLA), but xylem carries only dilute N and cannot reach the seeds at sufficient rate to support their N needs. Explants consisting of stem and a few leaves and pods were allowed to take up 14 C- and/or 15 N-ALL/ALLA in synthetic xylem sap. The 14 C label was found to become fairly quantitatively immobilized in leaves. The N (and 15 N label) almost certainly is separated from the C( 14 C label) at this time

THE STUDY OF THE BIOLOGICAL PROPERTIES OF PROBIOTIC LACTOBACILLUS SPP. STRAINS UNDER AEROBIC AND MICROAEROPHILIC CULTIVATION CONDITIONS

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Babych E.M.

2014-01-01

Full Text Available The biological properties (growth characteristics, adhesive activity and sensitivity to antimicrobial of probiotic Lactobacillus strains were studied under different gas composition of incubation atmosphere. It was found that the number of viable lactobacilli cells in the one dose of investigated probiotic preparations was lower than it was claimed by the manufacturer. Gas composition of incubation atmosphere affects cell viability of probiotic strains. The number of colony forming units of lactobacilli under microaerophilic conditions increased in 1,19-1,33 times as compared with aerobic conditions. It was proved that adhesive activity of probiotic Lactobacillus strains and sensitivity to 2th, 3th, 4th generations of cephalosporins (cefuroxime, cefotaxime, cefepime and tetracyclines (doxycycline also increased under microaerophilic conditions. The changes of the biological properties of lactobacilli under different cultivation conditions require further study for optimization of correction of dysbiotic disorders.

Determination of isotopic identity of nitrogen fixed by Frankia associated with the genus Alnus

International Nuclear Information System (INIS)

Kurdali, F.; Domenach, A.M.; Daniere, C.; Bardin, R.

1988-01-01

To use the 15 N natural abundance method to evaluate the symbiotic nitrogen fixation by actinorhizal trees, it is necessary to determine the isotopic identity of assimilated nitrogen from two sources: the soil and the air. This study reports an isotopic value of fixed nitrogen by two alder species (Alnus Incana(L.) Moench and Alnus glutinosa(L.) Gaertn.) growing on nitrogen-free medium in greenhouse experiments. The δ 15 N value of the aerial parts was -2. This value was stable with time and did not depend on the Frankia strains used. This value could be used to estimate the nitrogen fixation in the natural ecosystem. Other parameters such as the mobilization of nitrogen reserves and the choice of the reference plant must be investigated to apply this method. The nodules of these two alder species were enriched in 15 N relative to the rest of the plant but there was no relationship between symbiotic effectiveness of Frankia strains and 15 N enrichment of nodules. On the other hand, for naturally growing trees, an enrichment in 15 N was found primarily in the vesicles of nodules that are the sites of nitrogen fixation. 37 refs., 4 figs., 3 tabs. (author)

Response of the nitrogen-fixing lichen Lobaria pulmonaria to phosphorus, molybdenum, and vanadium

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Marks, Jade A; Pett-Ridge, Julie; Perakis, Steven S.; Allen, Jessica L; McCune, Bruce

2015-01-01

Nitrogen-fixing lichens (cyanolichens) are an important source of nitrogen (N) in Pacific Northwest forests, but limitation of lichen growth by elements essential for N fixation is poorly understood. To investigate how nutrient limitation may affect cyanolichen growth rates, we fertilized a tripartite cyanobacterial lichen (Lobaria pulmonaria) and a green algal non-nitrogen fixing lichen (Usnea longissima) with the micronutrients molybdenum (Mo) and vanadium (V), both known cofactors for enzymes involved in N fixation, and the macronutrient phosphorus (P). We then grew treated lichens in the field for one year in western Oregon, USA. Lichen growth was very rapid for both species and did not differ across treatments, despite a previous demonstration of P-limitation in L. pulmonaria at a nearby location. To reconcile these disparate findings, we analyzed P, Mo, and V concentrations, natural abundance δ15N isotopes, %N and change in thallus N in Lobaria pulmonaria from both growth experiments. Nitrogen levels in deposition and in lichens could not explain the large difference in growth or P limitation observed between the two studies. Instead, we provide evidence that local differences in P availability may have caused site-specific responses of Lobaria to P fertilization. In the previous experiment, Lobaria had low background levels of P, and treatment with P more than doubled growth. In contrast, Lobaria from the current experiment had much higher background P concentrations, similar to P-treated lichens in the previous experiment, consistent with the idea that ambient variation in P availability influences the degree of P limitation in cyanolichens. We conclude that insufficient P, Mo, and V did not limit the growth of either cyanolichens or chlorolichens at the site of the current experiment. Our findings point to the need to understand landscape-scale variation in P availability to cyanolichens, and its effect on spatial patterns of cyanolichen nutrient

Genomics and ecophysiology of heterotrophic nitrogen fixing bacteria isolated from estuarine surface water

DEFF Research Database (Denmark)

Bentzon-Tilia, Mikkel; Severin, Ina; Hansen, Lars H.

2015-01-01

The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing heterotrop......The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing...... heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N2 fixation by three environmentally relevant heterotrophic bacteria isolated from Baltic Sea surface water: Pseudomonas...... liter-1, presumably accommodated through aggregate formation. Glucose stimulated N2 fixation in general, and reactive N repressed N2 fixation, except that ammonium (NH4 ) stimulated N2 fixation in R. palustris BAL398, indicating the use of nitrogenase as an electron sink. The lack of correlations...

Transfer of biologically fixed nitrogen to the non-legume component of mixed pastures

International Nuclear Information System (INIS)

Haystead, A.

1983-01-01

Pasture ecosystems are extremely diverse, as are the management procedures imposed upon them by the pastoralist. In low input pasture enterprises in marginal areas, legume nitrogen fixation is frequently (but not invariably) crucial to continued productivity. Legumes usually do not dominate a pasture and their role in transferring fixed nitrogen to a non-legume, frequently graminaceous, species is important. Methods for measuring this transfer are critically assessed in terms of their usefulness in realistic pasture environments. Existing techniques all have serious disadvantages in this respect. Isotopic studies of individual processes within the transfer system are described and some new lines of investigation are proposed. The value of isotopic studies in improving pasture management is discussed. (author)

Transcriptional Activities of the Microbial Consortium Living with the Marine Nitrogen-Fixing Cyanobacterium Trichodesmium Reveal Potential Roles in Community-Level Nitrogen Cycling.

Science.gov (United States)

Lee, Michael D; Webb, Eric A; Walworth, Nathan G; Fu, Fei-Xue; Held, Noelle A; Saito, Mak A; Hutchins, David A

2018-01-01

Trichodesmium is a globally distributed cyanobacterium whose nitrogen-fixing capability fuels primary production in warm oligotrophic oceans. Like many photoautotrophs, Trichodesmium serves as a host to various other microorganisms, yet little is known about how this associated community modulates fluxes of environmentally relevant chemical species into and out of the supraorganismal structure. Here, we utilized metatranscriptomics to examine gene expression activities of microbial communities associated with Trichodesmium erythraeum (strain IMS101) using laboratory-maintained enrichment cultures that have previously been shown to harbor microbial communities similar to those of natural populations. In enrichments maintained under two distinct CO 2 concentrations for ∼8 years, the community transcriptional profiles were found to be specific to the treatment, demonstrating a restructuring of overall gene expression had occurred. Some of this restructuring involved significant increases in community respiration-related transcripts under elevated CO 2 , potentially facilitating the corresponding measured increases in host nitrogen fixation rates. Particularly of note, in both treatments, community transcripts involved in the reduction of nitrate, nitrite, and nitrous oxide were detected, suggesting the associated organisms may play a role in colony-level nitrogen cycling. Lastly, a taxon-specific analysis revealed distinct ecological niches of consistently cooccurring major taxa that may enable, or even encourage, the stable cohabitation of a diverse community within Trichodesmium consortia. IMPORTANCE Trichodesmium is a genus of globally distributed, nitrogen-fixing marine cyanobacteria. As a source of new nitrogen in otherwise nitrogen-deficient systems, these organisms help fuel carbon fixation carried out by other more abundant photoautotrophs and thereby have significant roles in global nitrogen and carbon cycling. Members of the Trichodesmium genus tend to

Is the distribution of nitrogen-fixing cyanobacteria in the oceans related to temperature?

Science.gov (United States)

Stal, Lucas J

2009-07-01

Approximately 50% of the global natural fixation of nitrogen occurs in the oceans supporting a considerable part of the new primary production. Virtually all nitrogen fixation in the ocean occurs in the tropics and subtropics where the surface water temperature is 25°C or higher. It is attributed almost exclusively to cyanobacteria. This is remarkable firstly because diazotrophic cyanobacteria are found in other environments irrespective of temperature and secondly because primary production in temperate and cold oceans is generally limited by nitrogen. Cyanobacteria are oxygenic phototrophic organisms that evolved a variety of strategies protecting nitrogenase from oxygen inactivation. Free-living diazotrophic cyanobacteria in the ocean are of the non-heterocystous type, namely the filamentous Trichodesmium and the unicellular groups A-C. I will argue that warm water is a prerequisite for these diazotrophic organisms because of the low-oxygen solubility and high rates of respiration allowing the organism to maintain anoxic conditions in the nitrogen-fixing cell. Heterocystous cyanobacteria are abundant in freshwater and brackish environments in all climatic zones. The heterocyst cell envelope is a tuneable gas diffusion barrier that optimizes the influx of both oxygen and nitrogen, while maintaining anoxic conditions inside the cell. It is not known why heterocystous cyanobacteria are absent from the temperate and cold oceans and seas.

Paenibacillus brasilensis sp nov., a novel nitrogen-fixing species isolated from the maize rhizosphere in Brazil

NARCIS (Netherlands)

Weid, von der I.; Duarte, G.F.; Elsas, van J.D.; Seldin, L.

2002-01-01

Sixteen nitrogen-fixing strains isolated from the rhizosphere of maize planted in Cerrado soil, Brazil, which showed morphological and biochemical characteristics similar to the gas-forming Paenibacillus spp., were phenotypically and genetically characterized. Their identification as members of the

Is nitrogen the next carbon?

Science.gov (United States)

Battye, William; Aneja, Viney P.; Schlesinger, William H.

2017-09-01

Just as carbon fueled the Industrial Revolution, nitrogen has fueled an Agricultural Revolution. The use of synthetic nitrogen fertilizers and the cultivation of nitrogen-fixing crops both expanded exponentially during the last century, with most of the increase occurring after 1960. As a result, the current flux of reactive, or fixed, nitrogen compounds to the biosphere due to human activities is roughly equivalent to the total flux of fixed nitrogen from all natural sources, both on land masses and in the world's oceans. Natural fluxes of fixed nitrogen are subject to very large uncertainties, but anthropogenic production of reactive nitrogen has increased almost fivefold in the last 60 years, and this rapid increase in anthropogenic fixed nitrogen has removed any uncertainty on the relative importance of anthropogenic fluxes to the natural budget. The increased use of nitrogen has been critical for increased crop yields and protein production needed to keep pace with the growing world population. However, similar to carbon, the release of fixed nitrogen into the natural environment is linked to adverse consequences at local, regional, and global scales. Anthropogenic contributions of fixed nitrogen continue to grow relative to the natural budget, with uncertain consequences.

Stable symbiotic nitrogen fixation under water-deficit field conditions by a stress-tolerant alfalfa microsymbiont and its complete genome sequence.

Science.gov (United States)

Jozefkowicz, Cintia; Brambilla, Silvina; Frare, Romina; Stritzler, Margarita; Piccinetti, Carlos; Puente, Mariana; Berini, Carolina Andrea; Pérez, Pedro Reyes; Soto, Gabriela; Ayub, Nicolás

2017-12-10

We here characterized the stress-tolerant alfalfa microsymbiont Sinorhizobium meliloti B401. B401-treated plants showed high nitrogen fixation rates under humid and semiarid environments. The production of glycine betaine in isolated bacteroids positively correlated with low precipitation levels, suggesting that this compound acts as a critical osmoprotectant under field conditions. Genome analysis revealed that strain B401 contains alternative pathways for the biosynthesis and uptake of glycine betaine and its precursors. Such genomic information will offer substantial insight into the environmental physiology of this biotechnologically valuable nitrogen-fixing bacterium. Copyright © 2017 Elsevier B.V. All rights reserved.

Ecological occurrence of Gluconacetobacter diazotrophicus and nitrogen-fixing Acetobacteraceae members: their possible role in plant growth promotion.

Science.gov (United States)

Saravanan, V S; Madhaiyan, M; Osborne, Jabez; Thangaraju, M; Sa, T M

2008-01-01

Gluconacetobacter diazotrophicus has a long-standing history of bacterial-plant interrelationship as a symbiotic endophyte capable of fixing atmospheric nitrogen. In low nitrogen fertilized sugarcane fields it plays a significant role and its occurrence was realised in most of the sugarcane growing countries. In this mini review, the association of G. diazotrophicus with sugarcane, other crop plants and with various hosts is discussed. The factors affecting survival in the rhizosphere and the putative soil mode of transmission are emphasized. In addition, other N(2)-fixing Acetobacteraceae members, including Gluconacetobacter azotocaptans, Gluconacetobacter johannae and Swaminathania salitolerans, occurring in coffee, corn and rice plants are also covered. Lastly, the plant-growth-promoting traits identified in this group of bacteria, including N(2) fixation, phytohormone synthesis, P and Zn solubilization and biocontrol, are analysed.

Biological nitrogen (N) fixation - The source of N nutrient to increase yield

International Nuclear Information System (INIS)

Heiling, M.; Hardarson, G.

2006-01-01

Nitrogen is an essential plant nutrient. It is the nutrient that is most commonly deficient, contributing to reduced agricultural yields throughout the world. Developing countries used more than 85 million metric tones of nitrogenous fertilizer in 2003, worth billions of US dollars. Such fertilizer expenditure can be significantly reduced by incorporating biological nitrogen fixed leguminous crops into a growing rotation. In leguminous crops, a symbiotic relationship between a bacterium called Rhizobium and legumes can provide large amounts of nitrogen to the plant and subsequently to soils where they are grown. In this process the bacteria form nodules on the root system and convert the nitrogen coming from air into molecules that can be absorbed by the plants. Beside their fertilizing properties, legumes are rich in protein and constitute a very important role in the human and animal nutrition. In the Soil Science Unit (SSU) of the FAO/IAEA Agriculture and Biotechnology Laboratory fellows from all over the world receive training in the use of 15 N stable isotope techniques to optimise the nitrogen fixation. Several parameters such as the placement of the nodules on the legume root system, the amount of soil mineral nitrogen and phosphorus fertilizer applied and the temperature have an impact on the amount of nitrogen fixed by the plant. It is therefore important to identify relative importance of these parameters on biological N fixation. The 15 N isotope dilution method is an appropriate technique to test the biological nitrogen fixation in the laboratory first. This useful knowledge can then be communicated to the farmers and can be tested under field conditions

Adhesive properties of a symbolic bacterium from a wood-boreing marine shipworm

International Nuclear Information System (INIS)

Imam, S.H.; Greene, R.V.; Griffin, H.L.

1990-01-01

Adhesive properties of cellulolytic, nitrogen-fixing bacterium isolated from a marine shipworm are described. 35 S-labeled cells of the shipworm bacterium bound preferentially Whatman no.1 cellulose filter paper, compared with its binding to other cellulose substrata or substrata lacking cellulose. The ability of the bacteria to bind to Whatman no. 1 filter paper was significantly reduced by glutaraldehyde or heat treatment of cells. Pretreatment of cells with azide, valinomycin, gramicidin-D, bis-hexafluoroacetylacetone (1799), or carbonyl cyanide-p-trifluoromethoxyphenylhydrazone inhibited adhesion activity. Cells pretreated with pronase or trypsin also exhibited reduced binding activity, but chymotrypsin and peptidase had no effect on adhesion activity. Cellodextrins and methyl cellulose 15 inhibited the adhesion of the shipworm bacteria to filter paper, whereas glucose, cellobiose, and soluble carboxymethyl cellulose had no significant effect. The divalent cation chelators EDTA and EGTA [ethylene hlycol-bis(β-aminoethyl ether)-N,N,N'N'-tetraacetic acid] had little or no effect on adhesive properties of shipworm bacteria. Also, preabsorbing the substratum with extracellular endoglucanase isolated from the ship worm bacterium or 1% bovine serum albumin had no apparent effect on bacterial binding. Low concentration (0.01%) of sodium dodecyl sulfate solubilized a fraction from whole cells, which appeared to be involved in cellular binding activity. After removal of sodium dodecyl, sulfate, several proteins in this fraction associated with intact cells. These cells exhibited up to 50% enhanced binding to filter paper in comparison to cells which had not been exposed to the sodium dodecyl sulfate-solubilized fraction

Nitrogen-Fixing Nodules Are an Important Source of Reduced Sulfur, Which Triggers Global Changes in Sulfur Metabolism in Lotus japonicus.

Science.gov (United States)

Kalloniati, Chrysanthi; Krompas, Panagiotis; Karalias, Georgios; Udvardi, Michael K; Rennenberg, Heinz; Herschbach, Cornelia; Flemetakis, Emmanouil

2015-09-01

We combined transcriptomic and biochemical approaches to study rhizobial and plant sulfur (S) metabolism in nitrogen (N) fixing nodules (Fix(+)) of Lotus japonicus, as well as the link of S-metabolism to symbiotic nitrogen fixation and the effect of nodules on whole-plant S-partitioning and metabolism. Our data reveal that N-fixing nodules are thiol-rich organs. Their high adenosine 5'-phosphosulfate reductase activity and strong (35)S-flux into cysteine and its metabolites, in combination with the transcriptional upregulation of several rhizobial and plant genes involved in S-assimilation, highlight the function of nodules as an important site of S-assimilation. The higher thiol content observed in nonsymbiotic organs of N-fixing plants in comparison to uninoculated plants could not be attributed to local biosynthesis, indicating that nodules are an important source of reduced S for the plant, which triggers whole-plant reprogramming of S-metabolism. Enhanced thiol biosynthesis in nodules and their impact on the whole-plant S-economy are dampened in plants nodulated by Fix(-) mutant rhizobia, which in most respects metabolically resemble uninoculated plants, indicating a strong interdependency between N-fixation and S-assimilation. © 2015 American Society of Plant Biologists. All rights reserved.

Microbial removal of fixed nitrogen in an oceanic oxygen minimum zone

DEFF Research Database (Denmark)

Dalsgaard, Tage; Thamdrup, Bo; Revsbech, Niels Peter

We quantified the removal of fixed nitrogen as N2 production by anammox and N2 and N2O production by denitrification over a distance of 1900 km along the coast of Chile and Peru, using short-term incubations with 15N-labeled substrates. The eastern tropical South Pacific (ETSP) holds an oxygen...... and that denitrification is needed for the mineralization of organic matter and production of NH4+ for anammox. Our data from frequent sampling along a 1900 km cruise track parallel to the coast of Chile and Peru show that denitrification does indeed occur, but less frequent and at higher rates than anammox...

Temporal dynamics of abundance and composition of nitrogen-fixing communities across agricultural soils.

Directory of Open Access Journals (Sweden)

Michele C Pereira E Silva

Full Text Available BACKGROUND: Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. METHODOLOGY/PRINCIPAL FINDINGS: In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K, indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. CONCLUSIONS: Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.

Nitrogen-fixing and cellulose-producing Gluconacetobacter kombuchae sp. nov., isolated from Kombucha tea.

Science.gov (United States)

Dutta, Debasree; Gachhui, Ratan

2007-02-01

A few members of the family Acetobacteraceae are cellulose-producers, while only six members fix nitrogen. Bacterial strain RG3T, isolated from Kombucha tea, displays both of these characteristics. A high bootstrap value in the 16S rRNA gene sequence-based phylogenetic analysis supported the position of this strain within the genus Gluconacetobacter, with Gluconacetobacter hansenii LMG 1527T as its nearest neighbour (99.1 % sequence similarity). It could utilize ethanol, fructose, arabinose, glycerol, sorbitol and mannitol, but not galactose or xylose, as sole sources of carbon. Single amino acids such as L-alanine, L-cysteine and L-threonine served as carbon and nitrogen sources for growth of strain RG3T. Strain RG3T produced cellulose in both nitrogen-free broth and enriched medium. The ubiquinone present was Q-10 and the DNA base composition was 55.8 mol% G+C. It exhibited low values of 5.2-27.77 % DNA-DNA relatedness to the type strains of related gluconacetobacters, which placed it within a separate taxon, for which the name Gluconacetobacter kombuchae sp. nov. is proposed, with the type strain RG3T (=LMG 23726T=MTCC 6913T).

Simulating changes in ecosystem structure and composition in response to climate change: a case study focused on tropical nitrogen-fixing trees (Invited)

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Medvigy, D.; Levy, J.; Xu, X.; Batterman, S. A.; Hedin, L.

2013-12-01

Ecosystems, by definition, involve a community of organisms. These communities generally exhibit heterogeneity in their structure and composition as a result of local variations in climate, soil, topography, disturbance history, and other factors. Climate-driven shifts in ecosystems will likely include an internal re-organization of community structure and composition and as well as the introduction of novel species. In terms of vegetation, this ecosystem heterogeneity can occur at relatively small scales, sometimes of the order of tens of meters or even less. Because this heterogeneous landscape generally has a variable and nonlinear response to environmental perturbations, it is necessary to carefully aggregate the local competitive dynamics between individual plants to the large scales of tens or hundreds of kilometers represented in climate models. Accomplishing this aggregation in a computationally efficient way has proven to be an extremely challenging task. To meet this challenge, the Ecosystem Demography 2 (ED2) model statistically characterizes a distribution of local resource environments, and then simulates the competition between individuals of different sizes and species (or functional groupings). Within this framework, it is possible to explicitly simulate the impacts of climate change on ecosystem structure and composition, including both internal re-organization and the introduction of novel species or functional groups. This presentation will include several illustrative applications of the evolution of ecosystem structure and composition under climate change. One application pertains to the role of nitrogen-fixing species in tropical forests. Will increasing CO2 concentrations increase the demand for nutrients and perhaps give a competitive edge to nitrogen-fixing species? Will potentially warmer and drier conditions make some tropical forests more water-limited, reducing the demand for nitrogen, thereby giving a competitive advantage to non-nitrogen-fixing

Controlling cyanobacterial blooms in hypertrophic Lake Taihu, China: will nitrogen reductions cause replacement of non-N2 fixing by N2 fixing taxa?

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Hans W Paerl

Full Text Available Excessive anthropogenic nitrogen (N and phosphorus (P inputs have caused an alarming increase in harmful cyanobacterial blooms, threatening sustainability of lakes and reservoirs worldwide. Hypertrophic Lake Taihu, China's third largest freshwater lake, typifies this predicament, with toxic blooms of the non-N2 fixing cyanobacteria Microcystis spp. dominating from spring through fall. Previous studies indicate N and P reductions are needed to reduce bloom magnitude and duration. However, N reductions may encourage replacement of non-N2 fixing with N2 fixing cyanobacteria. This potentially counterproductive scenario was evaluated using replicate, large (1000 L, in-lake mesocosms during summer bloom periods. N+P additions led to maximum phytoplankton production. Phosphorus enrichment, which promoted N limitation, resulted in increases in N2 fixing taxa (Anabaena spp., but it did not lead to significant replacement of non-N2 fixing with N2 fixing cyanobacteria, and N2 fixation rates remained ecologically insignificant. Furthermore, P enrichment failed to increase phytoplankton production relative to controls, indicating that N was the most limiting nutrient throughout this period. We propose that Microcystis spp. and other non-N2 fixing genera can maintain dominance in this shallow, highly turbid, nutrient-enriched lake by outcompeting N2 fixing taxa for existing sources of N and P stored and cycled in the lake. To bring Taihu and other hypertrophic systems below the bloom threshold, both N and P reductions will be needed until the legacy of high N and P loading and sediment nutrient storage in these systems is depleted. At that point, a more exclusive focus on P reductions may be feasible.

Draft Genome Sequence of the Nitrogen-Fixing Rhizobium sullae Type Strain IS123T Focusing on the Key Genes for Symbiosis with its Host Hedysarum coronarium L.

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Gaurav Sablok

2017-07-01

Full Text Available The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the Rhizobium sullae type strain IS123T nodulating the legume Hedysarum coronarium, was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp. Its features were compared with those of genomes from rhizobia representing an increasing gradient of taxonomical distance, from a conspecific isolate (Rhizobium sullae WSM1592, to two congeneric cases (Rhizobium leguminosarum bv. viciae and Rhizobium etli and up to different genera within the legume-nodulating taxa. The host plant is of agricultural importance, but, unlike the majority of other domesticated plant species, it is able to survive quite well in the wild. Data showed that that the type strain of R. sullae, isolated from a wild host specimen, is endowed with a richer array of symbiotic genes in comparison to other strains, species or genera of rhizobia that were rescued from domesticated plant ecotypes. The analysis revealed that the bacterium by itself is incapable of surviving in the extreme conditions that its host plant can tolerate. When exposed to drought or alkaline condition, the bacterium depends on its host to survive. Data are consistent with the view of the plant phenotype as the primary factor enabling symbiotic nitrogen fixing bacteria to survive in otherwise limiting environments.

Comparison of biomass productivity and nitrogen fixing potential of Azolla SPP

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Arora, A.; Singh, P.K. [Indian Agricultural Research Inst., New Delhi (India)

2003-03-01

Study was conducted on six different Azolla species, available in the germplasm collection of NCCUBGA, IARI, New Delhi namely A. filiculoides, A. mexicana, A. microphylla, A. pinnata, A. rubra and A. caroliniana in a polyhouse to assess their growth potential by determining their maximal biomass productivity, doubling time and relative growth rates. Their nitrogen fixing potential was assessed by acetylene reduction assay. Among them Azolla microphylla gave highest biomass production and relative growth rate followed by Azolla caroliniana. Both these had high nitrogenase activity also. Peak nitrogenase activity of these strains was found on 14th day of growth and it declined on further incubation. Azolla microphylla and Azolla rubra were more tolerant to salinity than others. On the other hand Azolla pinnata, which is endemic species found in India, exhibited low biomass production, relative growth rate and lower nitrogenase activity compared to other species. It was unable to sustain growth in saline medium. Under polyhouse conditions, A. microphylla was found to perform better than other cultures in terms of biomass productivity, N fixing ability and salt tolerance. Hence it is taken up for mass production.(author)

Halomonas maura is a physiologically versatile bacterium of both ecological and biotechnological interest.

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Llamas, Inmaculada; del Moral, Ana; Martínez-Checa, Fernando; Arco, Yolanda; Arias, Soledad; Quesada, Emilia

2006-01-01

Halomonas maura is a bacterium of great metabolic versatility. We summarise in this work some of the properties that make it a very interesting microorganism both from an ecological and biotechnological point of view. It plays an active role in the nitrogen cycle, is capable of anaerobic respiration in the presence of nitrate and has recently been identified as a diazotrophic bacterium. Of equal interest is mauran, the exopolysaccharide produced by H. maura, which contributes to the formation of biofilms and thus affords the bacterium advantages in the colonisation of its saline niches. Mauran is highly viscous, shows thixotropic and pseudoplastic behaviour, has the capacity to capture heavy metals and exerts a certain immunomodulator effect in medicine. All these attributes have prompted us to make further investigations into its molecular characteristics. To date we have described 15 open reading frames (ORF's) related to exopolysaccharide production, nitrogen fixation and nitrate reductase activity among others.

Nitrogen-fixing bacteria and arbuscular mycorrhizal fungi in Piptadenia gonoacantha (Mart. Macbr.

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Joel Quintino de Oliveira Júnior

Full Text Available Abstract The family Leguminosae comprises approximately 20,000 species that mostly form symbioses with arbuscular mycorrhizal fungi (AMF and nitrogen-fixing bacteria (NFB. This study is aimed at investigating and confirming the dependence on nodulation and biological nitrogen fixation in the specie Piptadenia gonoacantha (Mart. Macbr., which belongs to the Piptadenia group. Two consecutive experiments were performed in a greenhouse. The experiments were fully randomized with six replicates and a factorial scheme. For the treatments, the two AMF species and three NFB strains were combined to nodulate P. gonoacantha in addition to the control treatments. The results indicate this species’ capacity for nodulation without the AMF; however, the AMF + NFB combinations yielded a considerable gain in P. gonoacantha shoot weight compared with the treatments that only included inoculating with bacteria or AMF. The results also confirm that the treatment effects among the AMF + NFB combinations produced different shoot dry weight/root dry weight ratios. We conclude that AMF is not necessary for nodulation and that this dependence improves species development because plant growth increases upon co-inoculation.

Oxidative Stress Resulting From Helicobacter pylori Infection Contributes to Gastric CarcinogenesisSummary

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Lindsay D. Butcher

2017-05-01

Full Text Available Helicobacter pylori is a gram-negative, microaerophilic bacterium that infects the stomach and can lead to, among other disorders, the development of gastric cancer. The inability of the host to clear the infection results in a chronic inflammatory state with continued oxidative stress within the tissue. Reactive oxygen species and reactive nitrogen species produced by the immune and epithelial cells damage the host cells and can result in DNA damage. H pylori has evolved to evoke this damaging response while blunting the host’s efforts to kill the bacteria. This long-lasting state with inflammation and oxidative stress can result in gastric carcinogenesis. Continued efforts to better understand the bacterium and the host response will serve to prevent or provide improved early diagnosis and treatment of gastric cancer. Keywords: AP Endonuclease, DNA Damage, H pylori, Gastric Cancer, Oxidative Stress

Phylogenetic constraints do not explain the rarity of nitrogen-fixing trees in late-successional temperate forests.

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Menge, Duncan N L; DeNoyer, Jeanne L; Lichstein, Jeremy W

2010-08-06

Symbiotic nitrogen (N)-fixing trees are rare in late-successional temperate forests, even though these forests are often N limited. Two hypotheses could explain this paradox. The 'phylogenetic constraints hypothesis' states that no late-successional tree taxa in temperate forests belong to clades that are predisposed to N fixation. Conversely, the 'selective constraints hypothesis' states that such taxa are present, but N-fixing symbioses would lower their fitness. Here we test the phylogenetic constraints hypothesis. Using U.S. forest inventory data, we derived successional indices related to shade tolerance and stand age for N-fixing trees, non-fixing trees in the 'potentially N-fixing clade' (smallest angiosperm clade that includes all N fixers), and non-fixing trees outside this clade. We then used phylogenetically independent contrasts (PICs) to test for associations between these successional indices and N fixation. Four results stand out from our analysis of U.S. trees. First, N fixers are less shade-tolerant than non-fixers both inside and outside of the potentially N-fixing clade. Second, N fixers tend to occur in younger stands in a given geographical region than non-fixers both inside and outside of the potentially N-fixing clade. Third, the potentially N-fixing clade contains numerous late-successional non-fixers. Fourth, although the N fixation trait is evolutionarily conserved, the successional traits are relatively labile. These results suggest that selective constraints, not phylogenetic constraints, explain the rarity of late-successional N-fixing trees in temperate forests. Because N-fixing trees could overcome N limitation to net primary production if they were abundant, this study helps to understand the maintenance of N limitation in temperate forests, and therefore the capacity of this biome to sequester carbon.

NAD1 Controls Defense-Like Responses in Medicago truncatula Symbiotic Nitrogen Fixing Nodules Following Rhizobial Colonization in a BacA-Independent Manner

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Domonkos, Ágota; Kovács, Szilárd; Gombár, Anikó; Kiss, Ernő; Horváth, Beatrix; Kováts, Gyöngyi Z.; Farkas, Attila; Tóth, Mónika T.; Ayaydin, Ferhan; Bóka, Károly; Fodor, Lili; Endre, Gabriella; Kaló, Péter

2017-01-01

Legumes form endosymbiotic interaction with host compatible rhizobia, resulting in the development of nitrogen-fixing root nodules. Within symbiotic nodules, rhizobia are intracellularly accommodated in plant-derived membrane compartments, termed symbiosomes. In mature nodule, the massively colonized cells tolerate the existence of rhizobia without manifestation of visible defense responses, indicating the suppression of plant immunity in the nodule in the favur of the symbiotic partner. Medicago truncatula DNF2 (defective in nitrogen fixation 2) and NAD1 (nodules with activated defense 1) genes are essential for the control of plant defense during the colonization of the nitrogen-fixing nodule and are required for bacteroid persistence. The previously identified nodule-specific NAD1 gene encodes a protein of unknown function. Herein, we present the analysis of novel NAD1 mutant alleles to better understand the function of NAD1 in the repression of immune responses in symbiotic nodules. By exploiting the advantage of plant double and rhizobial mutants defective in establishing nitrogen-fixing symbiotic interaction, we show that NAD1 functions following the release of rhizobia from the infection threads and colonization of nodule cells. The suppression of plant defense is self-dependent of the differentiation status of the rhizobia. The corresponding phenotype of nad1 and dnf2 mutants and the similarity in the induction of defense-associated genes in both mutants suggest that NAD1 and DNF2 operate close together in the same pathway controlling defense responses in symbiotic nodules. PMID:29240711

NAD1 Controls Defense-Like Responses in Medicago truncatula Symbiotic Nitrogen Fixing Nodules Following Rhizobial Colonization in a BacA-Independent Manner

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Ágota Domonkos

2017-12-01

Full Text Available Legumes form endosymbiotic interaction with host compatible rhizobia, resulting in the development of nitrogen-fixing root nodules. Within symbiotic nodules, rhizobia are intracellularly accommodated in plant-derived membrane compartments, termed symbiosomes. In mature nodule, the massively colonized cells tolerate the existence of rhizobia without manifestation of visible defense responses, indicating the suppression of plant immunity in the nodule in the favur of the symbiotic partner. Medicago truncatula DNF2 (defective in nitrogen fixation 2 and NAD1 (nodules with activated defense 1 genes are essential for the control of plant defense during the colonization of the nitrogen-fixing nodule and are required for bacteroid persistence. The previously identified nodule-specific NAD1 gene encodes a protein of unknown function. Herein, we present the analysis of novel NAD1 mutant alleles to better understand the function of NAD1 in the repression of immune responses in symbiotic nodules. By exploiting the advantage of plant double and rhizobial mutants defective in establishing nitrogen-fixing symbiotic interaction, we show that NAD1 functions following the release of rhizobia from the infection threads and colonization of nodule cells. The suppression of plant defense is self-dependent of the differentiation status of the rhizobia. The corresponding phenotype of nad1 and dnf2 mutants and the similarity in the induction of defense-associated genes in both mutants suggest that NAD1 and DNF2 operate close together in the same pathway controlling defense responses in symbiotic nodules.

NAD1 Controls Defense-Like Responses in Medicago truncatula Symbiotic Nitrogen Fixing Nodules Following Rhizobial Colonization in a BacA-Independent Manner.

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Domonkos, Ágota; Kovács, Szilárd; Gombár, Anikó; Kiss, Ernő; Horváth, Beatrix; Kováts, Gyöngyi Z; Farkas, Attila; Tóth, Mónika T; Ayaydin, Ferhan; Bóka, Károly; Fodor, Lili; Ratet, Pascal; Kereszt, Attila; Endre, Gabriella; Kaló, Péter

2017-12-14

Legumes form endosymbiotic interaction with host compatible rhizobia, resulting in the development of nitrogen-fixing root nodules. Within symbiotic nodules, rhizobia are intracellularly accommodated in plant-derived membrane compartments, termed symbiosomes. In mature nodule, the massively colonized cells tolerate the existence of rhizobia without manifestation of visible defense responses, indicating the suppression of plant immunity in the nodule in the favur of the symbiotic partner. Medicago truncatula DNF2 (defective in nitrogen fixation 2) and NAD1 (nodules with activated defense 1) genes are essential for the control of plant defense during the colonization of the nitrogen-fixing nodule and are required for bacteroid persistence. The previously identified nodule-specific NAD1 gene encodes a protein of unknown function. Herein, we present the analysis of novel NAD1 mutant alleles to better understand the function of NAD1 in the repression of immune responses in symbiotic nodules. By exploiting the advantage of plant double and rhizobial mutants defective in establishing nitrogen-fixing symbiotic interaction, we show that NAD1 functions following the release of rhizobia from the infection threads and colonization of nodule cells. The suppression of plant defense is self-dependent of the differentiation status of the rhizobia. The corresponding phenotype of nad1 and dnf2 mutants and the similarity in the induction of defense-associated genes in both mutants suggest that NAD1 and DNF2 operate close together in the same pathway controlling defense responses in symbiotic nodules.

Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium.

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Liang Ran

can thus be considered at the initial phase of a transition from free-living organism to a nitrogen-fixing plant entity, a transition process which may mimic what drove the evolution of chloroplasts from a cyanobacterial ancestor.

Exploiting an ancient signalling machinery to enjoy a nitrogen fixing symbiosis.

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Geurts, Rene; Lillo, Alessandra; Bisseling, Ton

2012-08-01

For almost a century now it has been speculated that a transfer of the largely legume-specific symbiosis with nitrogen fixing rhizobium would be profitable in agriculture [1,2]. Up to now such a step has not been achieved, despite intensive research in this era. Novel insights in the underlying signalling networks leading to intracellular accommodation of rhizobium as well as mycorrhizal fungi of the Glomeromycota order show extensive commonalities between both interactions. As mycorrhizae symbiosis can be established basically with most higher plant species it raises questions why is it only in a few taxonomic lineages that the underlying signalling network could be hijacked by rhizobium. Unravelling this will lead to insights that are essential to achieve an old dream. Copyright © 2012. Published by Elsevier Ltd.

Prone to fix: Resilience of the active nitrogen-fixing rice root microbiome

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Hurek, Thomas; Sabale, Mugdha; Sarkar, Abhijit; Pees, Tobias; Reinhold-Hurek, Barbara

2016-04-01

Due to water consumption, many lowland rice areas in Asia are undergoing a transition that involves adoption of new management strategies, with crop rotations encompassing a non-flooded crop, including maize. Shifting from flooded to non-flooded cropping is likely to affect microbial nitrogen cycling. For analysis of the root-associated microbiome of rice and maize in response to flooding or nitrogen fertilizer, we combine methods of microbial ecology (Next-Generation sequencing of amplicons), and a reductionist approach with pure cultures of the endophytic diazotroph Azoarus sp.. Field plots of the ICON project (Introducing non-flooded crops in rice-dominated landscapes: Impact on Carbon, nitrogen and water budgets) at the International Rice Research Institute in the Philippines were analyzed. Root-associated activity of nitrogenase gene expression was assessed by quantitative RT-PCR of nifH. For rice, expression levels were surprisingly stable, in response to non-flooded versus flooded conditions, or in response to conventional nitrogen fertilizer applications versus lack of N-fertilizer. In contrast, the active diazotrophic population of maize roots was not resistant to N-fertilization, nifH expression strongly decreased. Concordant changes in the diazotrophic resident or active communities were detected by nifH amplicon sequence analysis, based on bacterial DNA or mRNA, respectively. For high-resolution analyses of the endobiome in gnotobiotic culture, we developed a dual fluorescence reporter system for Azoarcus sp. BH72 which allows to quantify and visualize epi- and endophytic gene expression by concfocal microscopy (CLSM). This allowed us to demonstrate sites of active nitrogen fixation (gene expression) in association with rice roots. We confirmed that at low nitrogen fertilizer levels, endophytic nifH gene expression persisted in rice roots, while it was repressed in maize roots. This supports our observation of remarkable stability of nitrogen fixation

Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N2 Labeling.

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Cui, Li; Yang, Kai; Li, Hong-Zhe; Zhang, Han; Su, Jian-Qiang; Paraskevaidi, Maria; Martin, Francis L; Ren, Bin; Zhu, Yong-Guan

2018-04-17

Nitrogen (N) fixation is the conversion of inert nitrogen gas (N 2 ) to bioavailable N essential for all forms of life. N 2 -fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with 15 N 2 stable isotope probing (SIP) was developed to discern N 2 -fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N 2 -fixing bacteria), along with a marked 15 N 2 -induced Cyt c band shift, generated a highly distinguishable biomarker for N 2 fixation. 15 N 2 -induced shift was consistent well with 15 N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N 2 -fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus 15 N 2 percentage allowed quantification of N 2 fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.

Ammonium inhibition of nitrogenase activity in Herbaspirillum seropedicae

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Fu, H.; Burris, R.H. (Univ. of Wisconsin, Madison (USA))

1989-06-01

The effect of oxygen, ammonium ion, and amino acids on nitrogenase activity in the root-associated N{sub 2}-fixing bacterium Herbaspirillum seropedicae was investigated in comparison with Azospirillum spp. and Rhodospirillum rubrum. H. seropedicae is microaerophilic, and its optimal dissolved oxygen level is from 0.04 to 0.2 kPa for dinitrogen fixation but higher when it is supplied with fixed nitrogen. No nitrogenase activity was detected when the dissolved O{sub 2} level corresponded to 4.0 kPa. Ammonium, a product of the nitrogenase reaction, reversible inhibited nitrogenase activity when added to derepressed cell cultures. However, the inhibition of nitrogenase activity was only partial even with concentrations of ammonium chloride as high as 20 mM. Amides such as glutamine and asparagine partially inhibited nitrogenase activity, but glutamate did not. Nitrogenase in crude extracts prepared from ammonium-inhibited cells showed activity as high as in extracts from N{sub 2}-fixing cells. The pattern of the dinitrogenase and the dinitrogenase reductase revealed by the immunoblotting technique did not change upon ammonium chloride treatment of cells in vivo. No homologous sequences were detected with the draT-draG probe from Azospirillum lipoferum. There is no clear evidence that ADP-ribosylation of the dinitrogenase reductase is involved in the ammonium inhibition of H. seropedicae. The uncoupler carbonyl cyanide m-chlorophenylhydrazone decreased the intracellular ATP concentration and inhibited the nitrogenase activity of whole cells. The ATP pool was significantly disturbed when cultures were treated with ammonium in vivo.

Relationship between sodium influx and salt tolerance of nitrogen-fixing cyanobacteria

Energy Technology Data Exchange (ETDEWEB)

Apte, S.K.; Reddy, B.R.; Thomas, J.

1987-08-01

The relationship between sodium uptake and cyanobacterial salt (NaCl) tolerance has been examined in two filamentous, heterocystous, nitrogen-fixing species of Anabaena. During diazotrophic growth at neutral pH of the growth medium, Anabaena sp. strain L-31, a freshwater strain, showed threefold higher uptake of Na+ than Anabaena torulosa, a brackish-water strain, and was considerably less salt tolerant (50% lethal dose of NaCl, 55 mM) than the latter (50% lethal dose of NaCl, 170 mM). Alkaline pH or excess K+ (more than 25 mM) in the medium causes membrane depolarization and inhibits Na+ influx in both cyanobacteria (S.K. Apte and J. Thomas, Eur. J. Biochem. 154:395-401, 1986). The presence of nitrate or ammonium in the medium caused inhibition of Na+ influx accompanied by membrane depolarization. These experimental manipulations affecting Na+ uptake demonstrated a good negative correlation between Na+ influx and salt tolerance. All treatments which inhibited Na+ influx (such as alkaline pH, K+ above 25 mM, NO3-, and NH4+), enhanced salt tolerance of not only the brackish-water but also the freshwater cyanobacterium. The results indicate that curtailment of Na+ influx, whether inherent or effected by certain environmental factors (e.g., combined nitrogen, alkaline pH), is a major mechanism of salt tolerance in cyanobacteria. (Refs. 27)

Effect of combined N applied at low level on the nitrogen fixation by grasses and contribution to nitrogen fertility in soil

International Nuclear Information System (INIS)

Yao Yunyin; Chen Ming; Ma Changlin

1990-01-01

This paper reports the study on the effect of combined N applied at low level on teh nitrogen fixation by alfalfa in monoculture and mixed culture with meadow fescue, and the effect on the absorption and utilization of indigenous soil nitrogen and nitrogen fertilizer. Amount of nitrogen fixed by alfalfa could be raised and duration of high peak of symbiotic nitrogen fixation activity could be extended when nitrogen fertilizer was applied reasonably. It was especially important for the early pastures or pastures with low supporting nitrogen capacity. Transfer of nitrogen fixed by alfalfa to meadow fescue occured in mixed culture. Nitrogen fixed from alfalfa was uptaken more easily than indigenous nitrogen in soil. Planting alfalfa could raise soil fertility significantly. Meadow fescue may be able to fix nitrogen from the air in some way. When combined N was appropriately applied to soil, on which alfalfa and meadow fescue had been planted, it could promote increasing nitrogen fertility in soil

PGPRs and nitrogen-fixing legumes: a perfect team for efficient Cd phytoremediation?

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María Teresa eGómez-Sagasti

2015-02-01

Full Text Available Cadmium (Cd is a toxic, biologically non-essential and highly mobile metal that has become an increasingly important environmental hazard to both wildlife and humans. In contrast to conventional remediation technologies, phytoremediation based on rhizobia-legume symbiosis has emerged as an inexpensive decontamination alternative which also revitalize contaminated soils due to the role of legumes in nitrogen cycling. In recent years, there is growing interest in understanding symbiotic rhizobia-legume relationship and its interactions with Cd. The aim of the present review is to provide a comprehensive picture of the main effects of Cd in N2-fixing leguminous plants and the benefits of exploiting this symbiosis together with plant growth promoting rhizobacteria (PGPRs to boost an efficient reclamation of Cd-contaminated soils.

Metabolic adaptations of Azospirillum brasilense to oxygen stress by cell-to-cell clumping and flocculation.

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Bible, Amber N; Khalsa-Moyers, Gurusahai K; Mukherjee, Tanmoy; Green, Calvin S; Mishra, Priyanka; Purcell, Alicia; Aksenova, Anastasia; Hurst, Gregory B; Alexandre, Gladys

2015-12-01

The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms

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Villahermosa, Desirée; Corzo, Alfonso; Garcia-Robledo, Emilio; González, Juan M.; Papaspyrou, Sokratis

2016-01-01

Nitrate decreases sulfide release in wastewater treatment plants (WWTP), but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm) showed low sulfide production (0.31 μmol cm-3 h-1) and oxygen consumption rates (0.01 μmol cm-3 h-1). The anoxic lower layer showed high sulfide production (2.7 μmol cm-3 h-1). Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR) in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB). This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB) were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1) an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2) a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm-3 h-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR-SOB syntrophic

Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms.

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Desirée Villahermosa

Full Text Available Nitrate decreases sulfide release in wastewater treatment plants (WWTP, but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm showed low sulfide production (0.31 μmol cm-3 h-1 and oxygen consumption rates (0.01 μmol cm-3 h-1. The anoxic lower layer showed high sulfide production (2.7 μmol cm-3 h-1. Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB. This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1 an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2 a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm-3 h-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR

Can mushrooms fix atmospheric nitrogen?

Indian Academy of Sciences (India)

Unknown

Introduction. Rhizobium is a genus of symbiotic N2-fixing soil bacteria that induce ... To produce biofilm cultures, a 2 × 2 cm yeast manitol agar. (YMA) slab was .... determination of antibiotic susceptibilities of bacterial biofilms;. J. Clin. Microbiol.

Can mushrooms fix atmospheric nitrogen?

Indian Academy of Sciences (India)

Unknown

culation was maintained as a control. At maximum mycelial colonization by the ... cant increase in nitrogen concentration were observed in the inoculated cultures compared to the controls. The mycelial weight reduction could be .... ing of Belgian Administration for Development Corpora- tion (BADC) during that period were ...

Responses of the nitrogen-fixing aquatic fern Azolla to water contaminated with ciprofloxacin: Impacts on biofertilization.

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Gomes, Marcelo Pedrosa; de Brito, Júlio César Moreira; Carvalho Carneiro, Marília Mércia Lima; Ribeiro da Cunha, Mariem Rodrigues; Garcia, Queila Souza; Figueredo, Cleber Cunha

2018-01-01

We investigated the ability of the aquatic fern Azolla to take up ciprofloxacin (Cipro), as well as the effects of that antibiotic on the N-fixing process in plants grown in medium deprived (-N) or provided (+N) with nitrogen (N). Azolla was seen to accumulate Cipro at concentrations greater than 160 μg g -1 dry weight when cultivated in 3.05 mg Cipro l -1 , indicating it as a candidate for Cipro recovery from water. Although Cipro was not seen to interfere with the heterocyst/vegetative cell ratios, the antibiotic promoted changes with carbon and nitrogen metabolism in plants. Decreased photosynthesis and nitrogenase activity, and altered plant's amino acid profile, with decreases in cell N concentrations, were observed. The removal of N from the growth medium accentuated the deleterious effects of Cipro, resulting in lower photosynthesis, N-fixation, and assimilation rates, and increased hydrogen peroxide accumulation. Our results shown that Cipro may constrain the use of Azolla as a biofertilizer species due to its interference with nitrogen fixation processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

The nitrogen cycle on Mars

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Mancinelli, Rocco L.

1989-01-01

Nirtogen is an essential element for the evolution of life, because it is found in a variety of biologically important molecules. Therefore, N is an important element to study from a exobiological perspective. In particular, fixed nitrogen is the biologically useful form of nitrogen. Fixed nitrogen is generally defines as NH3, NH4(+), NO(x), or N that is chemically bound to either inorganic or organic molecules, and releasable by hydrolysis to NH3 or NH4(+). On Earth, the vast majority of nitrogen exists as N2 in the atmosphere, and not in the fixes form. On early Mars the same situations probably existed. The partial pressure of N2 on early Mars was thought to be 18 mb, significantly less than that of Earth. Dinitrogen can be fixed abiotically by several mechanisms. These mechanisms include thernal shock from meteoritic infall and lightning, as well as the interaction of light and sand containing TiO2 which produces NH3 that would be rapidly destroyed by photolysis and reaction with OH radicals. These mechanisms could have been operative on primitive Mars.The chemical processes effecting these compounds and possible ways of fixing or burying N in the Martian environment are described. Data gathered in this laboratory suggest that the low abundance of nitrogen along (compared to primitive Earth) may not significantly deter the origin and early evolution of a nitrogen utilizing organisms. However, the conditions on current Mars with respect to nitrogen are quite different, and organisms may not be able to utilize all of the available nitrogen.

An antimicrobial peptide essential for bacterial survival in the nitrogen-fixing symbiosis.

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Kim, Minsoo; Chen, Yuhui; Xi, Jiejun; Waters, Christopher; Chen, Rujin; Wang, Dong

2015-12-08

In the nitrogen-fixing symbiosis between legume hosts and rhizobia, the bacteria are engulfed by a plant cell membrane to become intracellular organelles. In the model legume Medicago truncatula, internalization and differentiation of Sinorhizobium (also known as Ensifer) meliloti is a prerequisite for nitrogen fixation. The host mechanisms that ensure the long-term survival of differentiating intracellular bacteria (bacteroids) in this unusual association are unclear. The M. truncatula defective nitrogen fixation4 (dnf4) mutant is unable to form a productive symbiosis, even though late symbiotic marker genes are expressed in mutant nodules. We discovered that in the dnf4 mutant, bacteroids can apparently differentiate, but they fail to persist within host cells in the process. We found that the DNF4 gene encodes NCR211, a member of the family of nodule-specific cysteine-rich (NCR) peptides. The phenotype of dnf4 suggests that NCR211 acts to promote the intracellular survival of differentiating bacteroids. The greatest expression of DNF4 was observed in the nodule interzone II-III, where bacteroids undergo differentiation. A translational fusion of DNF4 with GFP localizes to the peribacteroid space, and synthetic NCR211 prevents free-living S. meliloti from forming colonies, in contrast to mock controls, suggesting that DNF4 may interact with bacteroids directly or indirectly for its function. Our findings indicate that a successful symbiosis requires host effectors that not only induce bacterial differentiation, but also that maintain intracellular bacteroids during the host-symbiont interaction. The discovery of NCR211 peptides that maintain bacterial survival inside host cells has important implications for improving legume crops.

Drug susceptibility testing in microaerophilic parasites: Cysteine strongly affects the effectivities of metronidazole and auranofin, a novel and promising antimicrobial

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David Leitsch

2017-12-01

Full Text Available The microaerophilic parasites Entamoeba histolytica, Trichomonas vaginalis, and Giardia lamblia annually cause hundreds of millions of human infections which are treated with antiparasitic drugs. Metronidazole is the most often prescribed drug but also other drugs are in use, and novel drugs with improved characteristics are constantly being developed. One of these novel drugs is auranofin, originally an antirheumatic which has been relabelled for the treatment of parasitic infections. Drug effectivity is arguably the most important criterion for its applicability and is commonly assessed in susceptibility assays using in vitro cultures of a given pathogen. However, drug susceptibility assays can be strongly affected by certain compounds in the growth media. In the case of microaerophilic parasites, cysteine which is added in large amounts as an antioxidant is an obvious candidate because it is highly reactive and known to modulate the toxicity of metronidazole in several microaerophilic parasites.In this study, it was attempted to reduce cysteine concentrations as far as possible without affecting parasite viability by performing drug susceptibility assays under strictly anaerobic conditions in an anaerobic cabinet. Indeed, T. vaginalis and E. histolytica could be grown without any cysteine added and the cysteine concentration necessary to maintain G. lamblia could be reduced to 20%. Susceptibilities to metronidazole were found to be clearly reduced in the presence of cysteine. With auranofin the protective effect of cysteine was extreme, providing protection to concentrations up to 100-fold higher as observed in the absence of cysteine. With three other drugs tested, albendazole, furazolidone and nitazoxanide, all in use against G. lamblia, the effect of cysteine was less pronounced. Oxygen was found to have a less marked impact on metronidazole and auranofin than cysteine but bovine bile which is standardly used in growth media for G

Nitrogen symbiotically fixed by cowpea and gliricidia in traditional and agroforestry systems under semiarid conditions

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Júlio César Rodrigues Martins

2015-02-01

Full Text Available The objective of this work was to estimate the amounts of N fixed by cowpea in a traditional system and by cowpea and gliricidia in an agroforestry system in the Brazilian Northeast semiarid. The experiment was carried out in a randomized complete block design, in a split-plot arrangement, with four replicates, in the semiarid region of the state of Paraíba, Brazil. Plots consisted of agroforestry and traditional systems (no trees, and split-plots of the three crops planted between the tree rows in the agroforestry system. To estimate N fixation, plant samples were collected in the fourth growth cycle of the perennial species and in the fourth planting cycle of the annual species. In the agroforestry system with buffel grass and prickly-pear cactus, gliricidia plants symbiotically fix high proportions of N (>50% and contribute with higher N amounts (40 kg ha-1 in leaves than in the traditional system (11 kg ha-1 in grain and 18 kg ha-1 in straw. In the agroforestry system with maize and cowpea, gliricidia plants do not fix nitrogen, and N input is limited to the fixation by cowpea (2.7 kg ha-1, which is lower than in the traditional system due to its lower biomass production.

Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting Pseudomonas Species Isolated from Sugarcane Rhizosphere.

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Li, Hai-Bi; Singh, Rajesh K; Singh, Pratiksha; Song, Qi-Qi; Xing, Yong-Xiu; Yang, Li-Tao; Li, Yang-Rui

2017-01-01

The study was designed to isolate and characterize Pseudomonas spp. from sugarcane rhizosphere, and to evaluate their plant- growth- promoting (PGP) traits and nitrogenase activity. A biological nitrogen-fixing microbe has great potential to replace chemical fertilizers and be used as a targeted biofertilizer in a plant. A total of 100 isolates from sugarcane rhizosphere, belonging to different species, were isolated; from these, 30 isolates were selected on the basis of preliminary screening, for in vitro antagonistic activities against sugarcane pathogens and for various PGP traits, as well as nitrogenase activity. The production of IAA varied from 312.07 to 13.12 μg mL -1 in tryptophan supplemented medium, with higher production in AN15 and lower in CN20 strain. The estimation of ACC deaminase activity, strains CY4 and BA2 produced maximum and minimum activity of 77.0 and 15.13 μmoL mg -1 h -1 . For nitrogenase activity among the studied strains, CoA6 fixed higher and AY1 fixed lower in amounts (108.30 and 6.16 μmoL C 2 H 2 h -1 mL -1 ). All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. The results identified all strains as being similar to Pseudomonas spp. Polymerase chain reaction (PCR) amplification of nifH and antibiotic genes was suggestive that the amplified strains had the capability to fix nitrogen and possessed biocontrol activities. Genotypic comparisons of the strains were determined by BOX, ERIC, and REP PCR profile analysis. Out of all the screened isolates, CY4 ( Pseudomonas koreensis ) and CN11 ( Pseudomonas entomophila ) showed the most prominent PGP traits, as well as nitrogenase activity. Therefore, only these two strains were selected for further studies; Biolog profiling; colonization through green fluorescent protein (GFP)-tagged bacteria; and nifH gene expression using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The Biolog

Global climate change will increase the abundance of symbiotic nitrogen-fixing trees in much of North America.

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Liao, Wenying; Menge, Duncan N L; Lichstein, Jeremy W; Ángeles-Pérez, Gregorio

2017-11-01

Symbiotic nitrogen (N)-fixing trees can drive N and carbon cycling and thus are critical components of future climate projections. Despite detailed understanding of how climate influences N-fixation enzyme activity and physiology, comparatively little is known about how climate influences N-fixing tree abundance. Here, we used forest inventory data from the USA and Mexico (>125,000 plots) along with climate data to address two questions: (1) How does the abundance distribution of N-fixing trees (rhizobial, actinorhizal, and both types together) vary with mean annual temperature (MAT) and precipitation (MAP)? (2) How will changing climate shift the abundance distribution of N-fixing trees? We found that rhizobial N-fixing trees were nearly absent below 15°C MAT, but above 15°C MAT, they increased in abundance as temperature rose. We found no evidence for a hump-shaped response to temperature throughout the range of our data. Rhizobial trees were more abundant in dry than in wet ecosystems. By contrast, actinorhizal trees peaked in abundance at 5-10°C MAT and were least abundant in areas with intermediate precipitation. Next, we used a climate-envelope approach to project how N-fixing tree relative abundance might change in the future. The climate-envelope projection showed that rhizobial N-fixing trees will likely become more abundant in many areas by 2080, particularly in the southern USA and western Mexico, due primarily to rising temperatures. Projections for actinorhizal N-fixing trees were more nuanced due to their nonmonotonic dependence on temperature and precipitation. Overall, the dominant trend is that warming will increase N-fixing tree abundance in much of the USA and Mexico, with large increases up to 40° North latitude. The quantitative link we provide between climate and N-fixing tree abundance can help improve the representation of symbiotic N fixation in Earth System Models. © 2017 John Wiley & Sons Ltd.

Culture-independent molecular approaches reveal a mostly unknown high diversity of active nitrogen-fixing bacteria associated with Pennisetum purpureum—a bioenergy crop

NARCIS (Netherlands)

Videira, Sandy Sampaio; de Cássia Pereira e Silva, Michele; Galisa, Pericles de Souza; Franco Dias, Armando Cavalcante; Nissinen, Riitta; Baldani Divan, Vera Lucia; van Elsas, Jan Dirk; Baldani, Jose Ivo; Salles, Joana Falcao

2013-01-01

Previous studies have shown that elephant grass is colonized by nitrogen-fixing bacterial species; however, these results were based on culture-dependent methods, an approach that introduces bias due to an incomplete assessment of the microbial community. In this study, we used culture-independent

The oceanic fixed nitrogen and nitrous oxide budgets: Moving targets as we enter the anthropocene?

Directory of Open Access Journals (Sweden)

L. A. Codispoti

2001-12-01

Full Text Available New data force us to raise previous estimates of oceanic denitrification. Our revised estimate of ~ 450 Tg N yr-1 (Tg = 1012 g produces an oceanic fixed N budget with a large deficit (~ 200 Tg N yr-1 that can be explained only by positing an ocean that has deviated far from a steady-state, the need for a major upwards revision of fixed N inputs, particularly nitrogen fixation, or both. Oceanic denitrification can be significantly altered by small re-distributions of carbon and dissolved oxygen. Since fixed N is a limiting nutrient, uncompensated changes in denitrification affect the ocean´s ability to sequester atmospheric CO2 via the "biological pump". We have also had to modify our concepts of the oceanic N2O regime to take better account of the extremely high N2O saturations that can arise in productive, low oxygen waters. Recent results from the western Indian Shelf during a period when hypoxic, suboxic and anoxic waters were present produced a maximum surface N2O saturation of > 8000%, a likely consequence of "stop and go" denitrification. The sensitivity of N2O production and consumption to small changes in the oceanic dissolved oxygen distribution and to the "spin-up" phase of denitrification suggests that the oceanic source term for N2O could change rapidly.

Diversity and activity of nitrogen fixing archaea and bacteria associated with micro-environments of wetland rice

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Schmidt, Hannes; Woebken, Dagmar

2017-04-01

Wetland rice is one of the world's most important crop plants. The cultivation on waterlogged paddy soils is strongly limited by nitrogen (N), which is typically supplied by industrial fertilizers that are not only costly but also exhibit hazardous effects on the environment. It has been reported that "Biological Nitrogen Fixation" through N2-fixing bacteria and archaea (diazotrophs) can alleviate the N-shortage in rice cultivation, thus carrying out an important ecosystem function. However, our understanding of the diversity and in situ N2 fixation activity of diazotrophs in flooded rice fields is still rudimentary. Moreover, knowledge on the impact of biochemical gradients established by root activity (i.e. exudation, radial oxygen loss) on the functioning of N-fixing microorganisms in paddy soil ecosystems is limited. We aimed at studying underlying processes on biologically relevant scales. Greenhouse studies were performed to identify key factors that control rice-diazotroph association and related N2 fixation activities. Paddy soils of different geographical origin were cultivated with two commercially used genotypes of wetland rice. Samples were separated into bulk soil, rhizosphere soil, rhizoplane, and roots at flowering stage of rice plant development. These samples were subjected to functional assays and various molecular biological techniques in order to analyze the associated diazotroph communities. Based on Illumina amplicon sequencing of nifH genes and transcripts, we show that the diversity and potential activity of diazotroph communities varies according to micro-environments. We will comparatively discuss the influence of (a) the soil microbial "seed bank" and (b) plant genotype in shaping the respective microbiomes and selecting for potentially active diazotrophs. Actual N2 fixation activities of soil-genotype combinations and micro-environments will be shown on the basis of incubation assays using 15N2-containing atmospheres. Areas of potential

MASS LOSS AND NITROGEN DYNAMICS DURING THE DECOMPOSITION OF A N-LABELED N2-FIXING EPOPHYTIC LICHEN, LOBARIA OREGANA (TUCK.) MULL. ARG.

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We studied mass loss and nitrogen dynamics during fall and spring initiated decomposition of an N2-fixing epiphytic lichen, Lobaria oregana (Tuck.) Mull. Arg. using 15N. We developed a method of labeling lichens with 15N that involved spraying lichen material with a nutrient sol...

Isolation and characterization of a prokaryotic cell organelle from the anammox bacterium

NARCIS (Netherlands)

Neumann, S.; Wessels, H.J.C.T.; Rijpstra, W.I.C.; Sinninghe Damsté, J.S.; Kartal, B.; Jetten, M.S.M.; van Niftrik, L.

2014-01-01

Anaerobic ammonium oxidizing (anammox) bacteria oxidize ammonium with nitrite to nitrogen gas in the absence of oxygen. These microorganisms form a significant sink for fixed nitrogen in the oceans and the anammox process is applied as a cost-effective and environment-friendly nitrogen removal

Iron depletion affects nitrogenase activity and expression of nifH and nifA genes in Herbaspirillum seropedicae.

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Rosconi, Federico; Souza, Emanuel M; Pedrosa, Fabio O; Platero, Raúl A; González, Cecilia; González, Marcela; Batista, Silvia; Gill, Paul R; Fabiano, Elena R

2006-05-01

Herbaspirillum seropedicae Z67 is a nitrogen-fixing bacterium able to colonize the rhizosphere and the interior of several plants. As iron is a key element for nitrogen fixation, we examined the response of this microorganism to iron deficiency under nitrogen fixing conditions. We identified a H. seropedicae exbD gene that was induced in response to iron limitation and is involved in iron homeostasis. We found that an exbD mutant grown in iron-chelated medium is unable to fix nitrogen. Moreover, we provide evidence that expression of the nifH and nifA genes is iron dependent in a H. seropedicae genetic background.

16S Ribosomal DNA Characterization of Nitrogen-Fixing Bacteria Isolated from Banana (Musa spp.) and Pineapple (Ananas comosus (L.) Merril)

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Magalhães Cruz, Leonardo; Maltempi de Souza, Emanuel; Weber, Olmar Baler; Baldani, José Ivo; Döbereiner, Johanna; de Oliveira Pedrosa, Fábio

2001-01-01

Nitrogen-fixing bacteria isolated from banana (Musa spp.) and pineapple (Ananas comosus (L.) Merril) were characterized by amplified 16S ribosomal DNA restriction analysis and 16S rRNA sequence analysis. Herbaspirillum seropedicae, Herbaspirillum rubrisubalbicans, Burkholderia brasilensis, and Burkholderia tropicalis were identified. Eight other types were placed in close proximity to these genera and other alpha and beta Proteobacteria. PMID:11319127

Bacterial nitrogen fixation in sand bioreactors treating winery wastewater with a high carbon to nitrogen ratio.

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Welz, Pamela J; Ramond, Jean-Baptiste; Braun, Lorenz; Vikram, Surendra; Le Roes-Hill, Marilize

2018-02-01

Heterotrophic bacteria proliferate in organic-rich environments and systems containing sufficient essential nutrients. Nitrogen, phosphorus and potassium are the nutrients required in the highest concentrations. The ratio of carbon to nitrogen is an important consideration for wastewater bioremediation because insufficient nitrogen may result in decreased treatment efficiency. It has been shown that during the treatment of effluent from the pulp and paper industry, bacterial nitrogen fixation can supplement the nitrogen requirements of suspended growth systems. This study was conducted using physicochemical analyses and culture-dependent and -independent techniques to ascertain whether nitrogen-fixing bacteria were selected in biological sand filters used to treat synthetic winery wastewater with a high carbon to nitrogen ratio (193:1). The systems performed well, with the influent COD of 1351 mg/L being reduced by 84-89%. It was shown that the nitrogen fixing bacterial population was influenced by the presence of synthetic winery effluent in the surface layers of the biological sand filters, but not in the deeper layers. It was hypothesised that this was due to the greater availability of atmospheric nitrogen at the surface. The numbers of culture-able nitrogen-fixing bacteria, including presumptive Azotobacter spp. exhibited 1-2 log increases at the surface. The results of this study confirm that nitrogen fixation is an important mechanism to be considered during treatment of high carbon to nitrogen wastewater. If biological treatment systems can be operated to stimulate this phenomenon, it may obviate the need for nitrogen addition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of the Symbiotic Nitrogen-Fixing Common Bean Low Phytic Acid (lpa1) Mutant Response to Water Stress.

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Chiozzotto, Remo; Ramírez, Mario; Talbi, Chouhra; Cominelli, Eleonora; Girard, Lourdes; Sparvoli, Francesca; Hernández, Georgina

2018-02-15

The common bean ( Phaseolus vulgaris L.) low phytic acid ( lpa1 ) biofortified genotype produces seeds with improved nutritional characteristics and does not display negative pleiotropic effects. Here we demonstrated that lpa1 plants establish an efficient nitrogen-fixing symbiosis with Rhizobium etli CE3. The lpa1 nodules showed a higher expression of nodule-function related genes than the nodules of the parental wild type genotype (BAT 93). We analyzed the response to water stress of lpa1 vs. BAT 93 plants grown under fertilized or under symbiotic N₂-fixation conditions. Water stress was induced by water withholding (up to 14% soil moisture) to fertilized or R. etli nodulated plants previously grown with normal irrigation. The fertilized lpa1 plants showed milder water stress symptoms during the water deployment period and after the rehydration recovery period when lpa1 plants showed less biomass reduction. The symbiotic water-stressed lpa1 plants showed decreased nitrogenase activity that coincides with decreased sucrose synthase gene expression in nodules; lower turgor weight to dry weight (DW) ratio, which has been associated with higher drought resistance index; downregulation of carbon/nitrogen (C/N)-related and upregulation of stress-related genes. Higher expression of stress-related genes was also observed in bacteroids of stressed lpa1 plants that also displayed very high expression of the symbiotic cbb ₃ oxidase ( fixN d).

Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501

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Lu Wei

2010-01-01

Full Text Available Abstract Background Biological nitrogen fixation is highly controlled at the transcriptional level by regulatory networks that respond to the availability of fixed nitrogen. In many diazotrophs, addition of excess ammonium in the growth medium results in immediate repression of nif gene transcription. Although the regulatory cascades that control the transcription of the nif genes in proteobacteria have been well investigated, there are limited data on the kinetics of ammonium-dependent repression of nitrogen fixation. Results Here we report a global transcriptional profiling analysis of nitrogen fixation and ammonium repression in Pseudomonas stutzeri A1501, a root-associated and nitrogen-fixing bacterium. A total of 166 genes, including those coding for the global nitrogen regulation (Ntr and Nif-specific regulatory proteins, were upregulated under nitrogen fixation conditions but rapidly downregulated as early as 10 min after ammonium shock. Among these nitrogen fixation-inducible genes, 95 have orthologs in each of Azoarcus sp. BH72 and Azotobacter vinelandii AvoP. In particular, a 49-kb expression island containing nif and other associated genes was markedly downregulated by ammonium shock. Further functional characterization of pnfA, a new NifA-σ54-dependent gene chromosomally linked to nifHDK, is reported. This gene encodes a protein product with an amino acid sequence similar to that of five hypothetical proteins found only in diazotrophic strains. No noticeable differences in the transcription of nifHDK were detected between the wild type strain and pnfA mutant. However, the mutant strain exhibited a significant decrease in nitrogenase activity under microaerobic conditions and lost its ability to use nitrate as a terminal electron acceptor for the support of nitrogen fixation under anaerobic conditions. Conclusions Based on our results, we conclude that transcriptional regulation of nif gene expression in A1501 is mediated by the nif

Comparative effectiveness of ACC-deaminase and/or nitrogen-fixing rhizobacteria in promotion of maize (Zea mays L.) growth under lead pollution.

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Hassan, Waseem; Bano, Rizwana; Bashir, Farhat; David, Julie

2014-09-01

Lead (Pb) pollution is appearing as an alarming threat nowadays. Excessive Pb concentrations in agricultural soils result in minimizing the soil fertility and health which affects the plant growth and leads to decrease in crop production. Plant growth promoting rhizobacteria (PGPR) are beneficial bacteria which can protect the plants against many abiotic stresses, and enhance the growth. The study aimed to identify important rhizobacterial strains by using the 1-aminocyclopropane-1-carboxylate (ACC) enrichment technique and examine their inoculation effects in the growth promotion of maize, under Pb pollution. A pot experiment was conducted and six rhizobacterial isolates were used. Pb was added to 2 kg soil in each pot (with 4 seeds/pot) using Pb(NO3)2 at the rate of 0, 100, 200, 300, and 400 mg kg(-1) Pb with three replications in completely randomized design. Rhizobacterial isolates performed significantly better under all Pb levels, i.e., 100 to 400 Pb mg kg(-1) soil, compared to control. Comparing the efficacy of the rhizobacterial isolates under different Pb levels, rhizobacterial isolates having both ACC-deaminase and nitrogen-fixing activities (AN8 and AN12) showed highest increase in terms of the physical, chemical and enzymatic growth parameters of maize, followed by the rhizobacterial isolates having ACC-deaminase activity only (ACC5 and ACC8), and then the nitrogen-fixing rhizobia (Azotobacter and RN5). However, the AN8 isolate showed maximum efficiency, and highest shoot and root length (14.2 and 6.1 cm), seedling fresh and dry weights (1.91 and 0.14 g), chlorophyll a, b, and carotenoids (24.1, 30.2 and 77.7 μg/l), protein (0.82 mg/g), proline (3.42 μmol/g), glutathione S-transferase, peroxidase and catalase (12.3, 4.2 and 7.2 units/mg protein), while the lowest Pb uptake in the shoot and root (0.83 and 0.48 mg/kg) were observed under this rhizobial isolate at the highest Pb level (i.e., 400 Pb mg kg(-1) soil). The results revealed that PGPR

Microencapsulation by spray drying of nitrogen-fixing bacteria associated with lupin nodules.

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Campos, Daniela C; Acevedo, Francisca; Morales, Eduardo; Aravena, Javiera; Amiard, Véronique; Jorquera, Milko A; Inostroza, Nitza G; Rubilar, Mónica

2014-09-01

Plant growth promoting bacteria and nitrogen-fixing bacteria (NFB) used for crop inoculation have important biotechnological potential as a sustainable fertilization tool. However, the main limitation of this technology is the low inoculum survival rate under field conditions. Microencapsulation of bacterial cells in polymer matrices provides a controlled release and greater protection against environmental conditions. In this context, the aim of this study was to isolate and characterize putative NFB associated with lupin nodules and to evaluate their microencapsulation by spray drying. For this purpose, 21 putative NFB were isolated from lupin nodules and characterized (16S rRNA genes). Microencapsulation of bacterial cells by spray drying was studied using a mixture of sodium alginate:maltodextrin at different ratios (0:15, 1:14, 2:13) and concentrations (15 and 30% solids) as the wall material. The microcapsules were observed under scanning electron microscopy to verify their suitable morphology. Results showed the association between lupin nodules of diverse known NFB and nodule-forming bacteria belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Bacteroidetes. In microencapsulation assays, the 1:14 ratio of sodium alginate:maltodextrin (15% solids) showed the highest cell survival rate (79%), with a microcapsule yield of 27% and spherical microcapsules of 5-50 µm in diameter. In conclusion, diverse putative NFB genera and nodule-forming bacteria are associated with the nodules of lupine plants grown in soils in southern Chile, and their microencapsulation by spray drying using sodium alginate:maltodextrin represents a scalable process to generate a biofertilizer as an alternative to traditional nitrogen fertilization.

Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

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Levicán, Gloria; Ugalde, Juan A; Ehrenfeld, Nicole; Maass, Alejandro; Parada, Pilar

2008-01-01

Background Carbon and nitrogen fixation are essential pathways for autotrophic bacteria living in extreme environments. These bacteria can use carbon dioxide directly from the air as their sole carbon source and can use different sources of nitrogen such as ammonia, nitrate, nitrite, or even nitrogen from the air. To have a better understanding of how these processes occur and to determine how we can make them more efficient, a comparative genomic analysis of three bioleaching bacteria isolated from mine sites in Chile was performed. This study demonstrated that there are important differences in the carbon dioxide and nitrogen fixation mechanisms among bioleaching bacteria that coexist in mining environments. Results In this study, we probed that both Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans incorporate CO2 via the Calvin-Benson-Bassham cycle; however, the former bacterium has two copies of the Rubisco type I gene whereas the latter has only one copy. In contrast, we demonstrated that Leptospirillum ferriphilum utilizes the reductive tricarboxylic acid cycle for carbon fixation. Although all the species analyzed in our study can incorporate ammonia by an ammonia transporter, we demonstrated that Acidithiobacillus thiooxidans could also assimilate nitrate and nitrite but only Acidithiobacillus ferrooxidans could fix nitrogen directly from the air. Conclusion The current study utilized genomic and molecular evidence to verify carbon and nitrogen fixation mechanisms for three bioleaching bacteria and provided an analysis of the potential regulatory pathways and functional networks that control carbon and nitrogen fixation in these microorganisms. PMID:19055775

Evaluation of the Effects of Bio Fertilizers Containing non Symbiotic Nitrogen Fixing and Phosphate Solubilizing Bacteria on Quantitative and Qualitative Traits of Wheat

Directory of Open Access Journals (Sweden)

M Mohtadi

2016-02-01

Full Text Available Introduction Wheat crop plays an important role in food security in a country such as Iran. Therefore, serious attention has been paid to ecological farming systems and sustainable management of wheat. For this purpose extensive efforts is done to find proper strategies to improve the quality of soil, agricultural products and started removal pollutants. One of the factors to achieve sustainable agriculture is to use natural agents such as biofertilizers. Several mechanisms are proposed to explain how effective plant growth promoting rhizobacteria is for growth and development of plants. These mechanisms include two groups, direct and indirect in general. Indirect mechanism is to increase absorption and availability of the nutrient elements soluble, producing plant growth regulators, siderophore production of iron chelator, and the phosphate soluble. Through indirect mechanisms such as antagonistic relation, PGPRs moderate the harmful effects of of plant pathogens and thereby lead to increase plant growth. The main goal of this study was to investigate the effect of biofertilizers containing non-symbiotic nitrogen fixing and phosphate solubilizing bacteria on quantitative and qualitative traits of wheat. Materials and Methods This Experiment was conducted in the research farm of Baykola agricultural research stations affiliated by agriculture and natural resources research center of Mazandaran during 2011-12 cropping season. In order to determine physical and chemical properties of the soil samples were taken from the depth of 0-30 cm,. Experimental design was split plots arrangement based on randomized complete block design with three replications. In this experiment chemical fertilizer was assumed as the main plot in 3 levels include: 1- noconsumption (C0, 2- equivalent to 50% of the fertilizer recommendations (C1, 3- equivalent to 100% of the fertilizer recommendations(C2 and two types of biological fertilizers was applied in the sub plot in

Reduction of Mo(VI) by the bacterium Serratia sp. strain DRY5.

Science.gov (United States)

Rahman, M F A; Shukor, M Y; Suhaili, Z; Mustafa, S; Shamaan, N A; Syed, M A

2009-01-01

The need to isolate efficient heavy metal reducers for cost effective bioremediation strategy have resulted in the isolation of a potent molybdenum-reducing bacterium. The isolate was tentatively identified as Serratia sp. strain DRY5 based on the Biolog GN carbon utilization profiles and partial 16S rDNA molecular phylogeny. Strain DRY5 produced 2.3 times the amount of Mo-blue than S. marcescens strain Dr.Y6, 23 times more than E. coli K12 and 7 times more than E. cloacae strain 48. Strain DRY5 required 37 degrees C and pH 7.0 for optimum molybdenum reduction. Carbon sources such as sucrose, maltose, glucose and glycerol, supported cellular growth and molybdate reduction after 24 hr of static incubation. The most optimum carbon source that supported reduction was sucrose at 1.0% (w/v). Ammonium sulphate, ammonium chloride, glutamic acid, cysteine, and valine supported growth and molybdate reduction with ammonium sulphate as the optimum nitrogen source at 0. 2% (w/v). Molybdate reduction was optimally supported by 30 mM molybdate. The optimum concentration of phosphate for molybdate reduction was 5 mM when molybdate concentration was fixed at 30 mM and molybdate reduction was totally inhibited at 100 mM phosphate. Mo-blue produced by this strain shows a unique characteristic absorption profile with a maximum peak at 865 nm and a shoulder at 700 nm, Dialysis tubing experiment showed that 95.42% of Mo-blue was found in the dialysis tubing suggesting that the molybdate reduction seen in this bacterium was catalyzed by enzyme(s). The characteristics of isolate DRY5 suggest that it would be useful in the bioremediation ofmolybdenum-containing waste.

The glnAntrBC operon of Herbaspirillum seropedicae is transcribed by two oppositely regulated promoters upstream of glnA.

Science.gov (United States)

Schwab, Stefan; Souza, Emanuel M; Yates, Marshall G; Persuhn, Darlene C; Steffens, M Berenice R; Chubatsu, Leda S; Pedrosa, Fábio O; Rigo, Liu U

2007-01-01

Herbaspirillum seropedicae is an endophytic bacterium that fixes nitrogen under microaerophilic conditions. The putative promoter sequences glnAp1 (sigma70-dependent) and glnAp2 (sigma54), and two NtrC-binding sites were identified upstream from the glnA, ntrB and ntrC genes of this microorganism. To study their transcriptional regulation, we used lacZ fusions to the H. seropedicae glnA gene, and the glnA-ntrB and ntrB-ntrC intergenic regions. Expression of glnA was up-regulated under low ammonium, but no transcription activity was detected from the intergenic regions under any condition tested, suggesting that glnA, ntrB and ntrC are co-transcribed from the promoters upstream of glnA. Ammonium regulation was lost in the ntrC mutant strain. A point mutation was introduced in the conserved -25/-24 dinucleotide (GG-->TT) of the putative sigma54-dependent promoter (glnAp2). Contrary to the wild-type promoter, glnA expression with the mutant glnAp2 promoter was repressed in the wild-type strain under low ammonium levels, but this repression was abolished in an ntrC background. Together our results indicate that the H. seropedicae glnAntrBC operon is regulated from two functional promoters upstream from glnA, which are oppositely regulated by the NtrC protein.

Demography of Symbiotic Nitrogen-Fixing Trees Explains Their Rarity and Successional Decline in Temperate Forests in the United States.

Science.gov (United States)

Liao, Wenying; Menge, Duncan N L

2016-01-01

Symbiotic nitrogen (N) fixation is the major N input to many ecosystems. Although temperate forests are commonly N limited, symbiotic N-fixing trees ("N fixers") are rare and decline in abundance as succession proceeds-a challenging paradox that remains unexplained. Understanding demographic processes that underlie N fixers' rarity and successional decline would provide a proximate answer to the paradox. Do N fixers grow slower, die more frequently, or recruit less in temperate forests? We quantified demographic rates of N-fixing and non-fixing trees across succession using U.S. forest inventory data. We used an individual-based model to evaluate the relative contribution of each demographic process to community dynamics. Compared to non-fixers, N fixers had lower growth rates, higher mortality rates, and lower recruitment rates throughout succession. The mortality effect contributed more than the growth effect to N fixers' successional decline. Canopy and understory N fixers experienced these demographic disadvantages, indicating that factors in addition to light limitation likely contribute to N fixers' successional decline. We show that the rarity and successional decline of N-fixing trees in temperate forests is due more to their survival disadvantage than their growth disadvantage, and a recruitment disadvantage might also play a large role.

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

NARCIS (Netherlands)

Bollmann, A.; Sedlacek, C.J.; Norton, J.; Laanbroek, H.J.; Suwa, Y.; Stein, L.Y.; Klotz, M.G.; Arp, D.; Sayavedra-Soto, L.; Lu, M.; Bruce, D.; Detter, C.; Tapia, R.; Han, J.; Woyke, T.; Lucas, S.; Pitluck, S.; Pennacchio, L.; Nolan, M.; Land, M.L.; Huntemann, M.; Deshpande, S.; Han, C.; Chen, A.; Kyrpides, N.; Mavromatis, K.; Markowitz, V.; Szeto, E.; Ivanova, N.; Mikhailova, N.; Pagani, I.; Pati, A.; Peters, L.; Ovchinnikova, G.; Goodwin, L.

2013-01-01

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production

Achieving mainstream nitrogen removal through simultaneous partial nitrification, anammox and denitrification process in an integrated fixed film activated sludge reactor.

Science.gov (United States)

Wang, Chao; Liu, Sitong; Xu, Xiaochen; Zhang, Chaolei; Wang, Dong; Yang, Fenglin

2018-07-01

The anaerobic ammonium oxidation (anammox) is becoming a critical technology for energy neutral in mainstream wastewater treatment. However, the presence of chemical oxygen demanding in influent would result in a poor nitrogen removal efficiency during the deammonification process. In this study, the simultaneous partial nitrification, anammox and denitrification process (SNAD) for mainstream nitrogen removal was investigated in an integrated fixed film activated sludge (IFAS) reactor. SNAD-IFAS process achieved a total nitrogen (TN) removal efficiency of 72 ± 2% and an average COD removal efficiency was 88%. The optimum COD/N ratio for mainstream wastewater treatment was 1.2 ± 0.2. Illumina sequencing analysis and activity tests showed that anammox and denitrifying bacteria were the dominant nitrogen removal microorganism in the biofilm and the high COD/N ratios (≥2.0) leaded to the proliferation of heterotrophic bacteria (Hydrogenophaga) and nitrite-oxidizing bacteria (Nitrospira) in the suspended sludge. Network analysis confirmed that anammox bacteria (Candidatus Kuenenia) could survive in organic matter environment due to that anammox bacteria displayed significant co-occurrence through positive correlations with some heterotrophic bacteria (Limnobacter) which could protect anammox bacteria from hostile environments. Overall, the results of this study provided more comprehensive information regarding the community composition and assemblies in SNAD-IFAS process for mainstream nitrogen removal. Copyright © 2018 Elsevier Ltd. All rights reserved.

Incorporating nitrogen fixing cyanobacteria in the global biogeochemical model HAMOCC

Science.gov (United States)

Paulsen, Hanna; Ilyina, Tatiana; Six, Katharina

2015-04-01

Nitrogen fixation by marine diazotrophs plays a fundamental role in the oceanic nitrogen and carbon cycle as it provides a major source of 'new' nitrogen to the euphotic zone that supports biological carbon export and sequestration. Since most global biogeochemical models include nitrogen fixation only diagnostically, they are not able to capture its spatial pattern sufficiently. Here we present the incorporation of an explicit, dynamic representation of diazotrophic cyanobacteria and the corresponding nitrogen fixation in the global ocean biogeochemical model HAMOCC (Hamburg Ocean Carbon Cycle model), which is part of the Max Planck Institute for Meteorology Earth system model (MPI-ESM). The parameterization of the diazotrophic growth is thereby based on available knowledge about the cyanobacterium Trichodesmium spp., which is considered as the most significant pelagic nitrogen fixer. Evaluation against observations shows that the model successfully reproduces the main spatial distribution of cyanobacteria and nitrogen fixation, covering large parts of the tropical and subtropical oceans. Besides the role of cyanobacteria in marine biogeochemical cycles, their capacity to form extensive surface blooms induces a number of bio-physical feedback mechanisms in the Earth system. The processes driving these interactions, which are related to the alteration of heat absorption, surface albedo and momentum input by wind, are incorporated in the biogeochemical and physical model of the MPI-ESM in order to investigate their impacts on a global scale. First preliminary results will be shown.

Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

Directory of Open Access Journals (Sweden)

Ehrenfeld Nicole

2008-12-01

Full Text Available Abstract Background Carbon and nitrogen fixation are essential pathways for autotrophic bacteria living in extreme environments. These bacteria can use carbon dioxide directly from the air as their sole carbon source and can use different sources of nitrogen such as ammonia, nitrate, nitrite, or even nitrogen from the air. To have a better understanding of how these processes occur and to determine how we can make them more efficient, a comparative genomic analysis of three bioleaching bacteria isolated from mine sites in Chile was performed. This study demonstrated that there are important differences in the carbon dioxide and nitrogen fixation mechanisms among bioleaching bacteria that coexist in mining environments. Results In this study, we probed that both Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans incorporate CO2 via the Calvin-Benson-Bassham cycle; however, the former bacterium has two copies of the Rubisco type I gene whereas the latter has only one copy. In contrast, we demonstrated that Leptospirillum ferriphilum utilizes the reductive tricarboxylic acid cycle for carbon fixation. Although all the species analyzed in our study can incorporate ammonia by an ammonia transporter, we demonstrated that Acidithiobacillus thiooxidans could also assimilate nitrate and nitrite but only Acidithiobacillus ferrooxidans could fix nitrogen directly from the air. Conclusion The current study utilized genomic and molecular evidence to verify carbon and nitrogen fixation mechanisms for three bioleaching bacteria and provided an analysis of the potential regulatory pathways and functional networks that control carbon and nitrogen fixation in these microorganisms.

Transformation of nitrogenous fertilizers of surface and deep application in calcareous soil

International Nuclear Information System (INIS)

Zuo Dongfeng

1990-01-01

The transformations of 15 N labelled fertilizer N in calcareous soil were studied under greennhouse conditions. The experimental results indicate that the ratio of fixed ammonium is closely related to the methods of fertilizer application to the soil. When fertilizer N applied as deep dressing the fixation of nitrogen by clay minerals and microorganisms may markedly reduce the losses of nitrogen, but the amount of nitrogen fixed by the clay minerals and that by microorganisms showed negative correlation (r = -0.9185 ** ). The more the amount of fixed nitrogen by clay minerals, the less by microorganisms. No obvious interrelation between the residual utilization of urea, ammonium bicarbonate, ammonium sulfate and the ammount of nitrogen fixed by organisms can be observed, but the residual utilization of these fertilizers by the succeeding crop has been related to the total amount of mineral nitrogen

Biological nitrogen fixation in non-legume plants.

Science.gov (United States)

Santi, Carole; Bogusz, Didier; Franche, Claudine

2013-05-01

Nitrogen is an essential nutrient in plant growth. The ability of a plant to supply all or part of its requirements from biological nitrogen fixation (BNF) thanks to interactions with endosymbiotic, associative and endophytic symbionts, confers a great competitive advantage over non-nitrogen-fixing plants. Because BNF in legumes is well documented, this review focuses on BNF in non-legume plants. Despite the phylogenic and ecological diversity among diazotrophic bacteria and their hosts, tightly regulated communication is always necessary between the microorganisms and the host plant to achieve a successful interaction. Ongoing research efforts to improve knowledge of the molecular mechanisms underlying these original relationships and some common strategies leading to a successful relationship between the nitrogen-fixing microorganisms and their hosts are presented. Understanding the molecular mechanism of BNF outside the legume-rhizobium symbiosis could have important agronomic implications and enable the use of N-fertilizers to be reduced or even avoided. Indeed, in the short term, improved understanding could lead to more sustainable exploitation of the biodiversity of nitrogen-fixing organisms and, in the longer term, to the transfer of endosymbiotic nitrogen-fixation capacities to major non-legume crops.

N2-fixing red alder indirectly accelerates ecosystem nitrogen cycling

Science.gov (United States)

Perakis, Steven S.; Matkins, Joselin J.; Hibbs, David E.

2012-01-01

Symbiotic N2-fixing tree species can accelerate ecosystem N dynamics through decomposition via direct pathways by producing readily decomposed leaf litter and increasing N supply to decomposers, as well as via indirect pathways by increasing tissue and detrital N in non-fixing vegetation. To evaluate the relative importance of these pathways, we compared three-year decomposition and N dynamics of N2-fixing red alder leaf litter (2.34 %N) to both low-N (0.68 %N) and high-N (1.21 %N) litter of non-fixing Douglas-fir, and decomposed each litter source in four forests dominated by either red alder or Douglas-fir. We also used experimental N fertilization of decomposition plots to assess elevated N availability as a potential mechanism of N2-fixer effects on litter mass loss and N dynamics. Direct effects of N2-fixing red alder on decomposition occurred primarily as faster N release from red alder than Douglas-fir litter, but direct increases in N supply to decomposers via fertilization did not stimulate decomposition of any litter. Fixed N indirectly influenced detrital dynamics by increasing Douglas-fir tissue and litter N concentrations, which accelerated litter N release without accelerating mass loss. By increasing soil N, tissue N, and the rate of N release from litter of non-fixers, we conclude that N2-fixing vegetation can indirectly foster plant-soil feedbacks that contribute to the persistence of elevated N availability in terrestrial ecosystems.

Proteomic analysis reveals contrasting stress response to uranium in two nitrogen-fixing Anabaena strains, differentially tolerant to uranium

Energy Technology Data Exchange (ETDEWEB)

Panda, Bandita; Basu, Bhakti; Acharya, Celin; Rajaram, Hema; Apte, Shree Kumar, E-mail: aptesk@barc.gov.in

2017-01-15

Highlights: • Response of two native cyanobacterial strains to uranium exposure was studied. • Anabaena L-31 exhibited higher tolerance to uranium as compared to Anabaena 7120. • Uranium exposure differentially affected the proteome profiles of the two strains. • Anabaena L-31 showed better sustenance of photosynthesis and carbon metabolism. • Anabaena L-31 displayed superior oxidative stress defense than Anabaena 7120. - Abstract: Two strains of the nitrogen-fixing cyanobacterium Anabaena, native to Indian paddy fields, displayed differential sensitivity to exposure to uranyl carbonate at neutral pH. Anabaena sp. strain PCC 7120 and Anabaena sp. strain L-31 displayed 50% reduction in survival (LD{sub 50} dose), following 3 h exposure to 75 μM and 200 μM uranyl carbonate, respectively. Uranium responsive proteome alterations were visualized by 2D gel electrophoresis, followed by protein identification by MALDI-ToF mass spectrometry. The two strains displayed significant differences in levels of proteins associated with photosynthesis, carbon metabolism, and oxidative stress alleviation, commensurate with their uranium tolerance. Higher uranium tolerance of Anabaena sp. strain L-31 could be attributed to sustained photosynthesis and carbon metabolism and superior oxidative stress defense, as compared to the uranium sensitive Anabaena sp. strain PCC 7120. Significance: Uranium responsive proteome modulations in two nitrogen-fixing strains of Anabaena, native to Indian paddy fields, revealed that rapid adaptation to better oxidative stress management, and maintenance of metabolic and energy homeostasis underlies superior uranium tolerance of Anabaena sp. strain L-31 compared to Anabaena sp. strain PCC 7120.

The atherogenic bacterium Porphyromonas gingivalis evades circulating phagocytes by adhering to erythrocytes

DEFF Research Database (Denmark)

Belstrøm, Daniel; Holmstrup, Palle; Damgaard, Christian

2011-01-01

A relationship between periodontitis and coronary heart disease has been investigated intensively. A pathogenic role for the oral bacterium Porphyromonas gingivalis has been suggested for both diseases. We examined whether complement activation by P. gingivalis strain ATCC 33277 allows...... the bacterium to adhere to human red blood cells (RBCs) and thereby evade attack by circulating phagocytes. On incubation with normal human serum, the P. gingivalis strain efficiently fixed complement component 3 (C3). Incubation of bacteria with washed whole blood cells suspended in autologous serum resulted...... in a dose- and time-dependent adherence to RBCs. The adherence required functionally intact complement receptor 1 (CR1; also called CD35) on the RBCs and significantly inhibited the uptake of P. gingivalis by neutrophils and B cells within 1 min of incubation (by 64% and 51%, respectively...

Impact of Crab Bioturbation on Nitrogen-Fixation Rates in Red Sea Mangrove Sediment

KAUST Repository

Qashqari, Maryam S.

2017-05-01

Mangrove plants are a productive ecosystem that provide several benefits for marine organisms and industry. They are considered to be a food source and habitat for many organisms. However, mangrove growth is limited by nutrient availability. According to some recent studies, the dwarfism of the mangrove plants is due to the limitation of nitrogen in the environment. Biological nitrogen fixation is the process by which atmospheric nitrogen is fixed into ammonium. Then, this fixed nitrogen can be uptaken by plants. Hence, biological nitrogen fixation increases the input of nitrogen in the mangrove ecosystem. In this project, we focus on measuring the rates of nitrogen fixation on Red Sea mangrove (Avicennia marina) located at Thuwal, Saudi Arabia. The nitrogen fixation rates are calculated by the acetylene reduction assay. The experimental setup will allow us to analyze the effect of crab bioturbation on nitrogen fixing rates. This study will help to better understand the nitrogen dynamics in mangrove ecosystems in Saudi Arabia. Furthermore, this study points out the importance of the sediment microbial community in mangrove trees development. Finally, the role of nitrogen fixing bacteria should be taken in account for future restoration activities.

The chemical formula of a magnetotactic bacterium.

Science.gov (United States)

Naresh, Mohit; Das, Sayoni; Mishra, Prashant; Mittal, Aditya

2012-05-01

Elucidation of the chemical logic of life is one of the grand challenges in biology, and essential to the progress of the upcoming field of synthetic biology. Treatment of microbial cells explicitly as a "chemical" species in controlled reaction (growth) environments has allowed fascinating discoveries of elemental formulae of a few species that have guided the modern views on compositions of a living cell. Application of mass and energy balances on living cells has proved to be useful in modeling of bioengineering systems, particularly in deriving optimized media compositions for growing microorganisms to maximize yields of desired bio-derived products by regulating intra-cellular metabolic networks. In this work, application of elemental mass balance during growth of Magnetospirillum gryphiswaldense in bioreactors has resulted in the discovery of the chemical formula of the magnetotactic bacterium. By developing a stoichiometric equation characterizing the formation of a magnetotactic bacterial cell, coupled with rigorous experimental measurements and robust calculations, we report the elemental formula of M. gryphiswaldense cell as CH(2.06)O(0.13)N(0.28)Fe(1.74×10(-3)). Remarkably, we find that iron metabolism during growth of this magnetotactic bacterium is much more correlated individually with carbon and nitrogen, compared to carbon and nitrogen with each other, indicating that iron serves more as a nutrient during bacterial growth rather than just a mineral. Magnetotactic bacteria have not only invoked some interest in the field of astrobiology for the last two decades, but are also prokaryotes having the unique ability of synthesizing membrane bound intracellular organelles. Our findings on these unique prokaryotes are a strong addition to the limited repertoire, of elemental compositions of living cells, aimed at exploring the chemical logic of life. Copyright © 2011 Wiley Periodicals, Inc.

Alteration of the exopolysaccharide production and the transcriptional profile of free-living Frankia strain CcI3 under nitrogen-fixing conditions.

Science.gov (United States)

Lee, Hae-In; Donati, Andrew J; Hahn, Dittmar; Tisa, Louis S; Chang, Woo-Suk

2013-12-01

We investigated the effect of different nitrogen (N) sources on exopolysaccharide (EPS) production and composition by Frankia strain CcI3, a N2-fixing actinomycete that forms root nodules with Casuarina species. Frankia cells grown in the absence of NH4Cl (i.e., under N2-fixing conditions) produced 1.7-fold more EPS, with lower galactose (45.1 vs. 54.7 mol%) and higher mannose (17.3 vs. 9.7 mol%) contents than those grown in the presence of NH4Cl as a combined N-source. In the absence of the combined N-source, terminally linked and branched residue contents were nearly twice as high with 32.8 vs. 15.1 mol% and 15.1 vs. 8.7 mol%, respectively, than in its presence, while the content of linearly linked residues was lower with 52.1 mol% compared to 76.2 mol%. To find out clues for the altered EPS production at the transcriptional level, we performed whole-gene expression profiling using quantitative reverse transcription PCR and microarray technology. The transcription profiles of Frankia strain CcI3 grown in the absence of NH4Cl revealed up to 2 orders of magnitude higher transcription of nitrogen fixation-related genes compared to those of CcI3 cells grown in the presence of NH4Cl. Unexpectedly, microarray data did not provide evidence for transcriptional regulation as a mechanism for differences in EPS production. These findings indicate effects of nitrogen fixation on the production and composition of EPS in Frankia strain CcI3 and suggest posttranscriptional regulation of enhanced EPS production in the absence of the combined N-source.

Nitrogen fixation by cyanobacteria stimulates production in Baltic food webs.

Science.gov (United States)

Karlson, Agnes M L; Duberg, Jon; Motwani, Nisha H; Hogfors, Hedvig; Klawonn, Isabell; Ploug, Helle; Barthel Svedén, Jennie; Garbaras, Andrius; Sundelin, Brita; Hajdu, Susanna; Larsson, Ulf; Elmgren, Ragnar; Gorokhova, Elena

2015-06-01

Filamentous, nitrogen-fixing cyanobacteria form extensive summer blooms in the Baltic Sea. Their ability to fix dissolved N2 allows cyanobacteria to circumvent the general summer nitrogen limitation, while also generating a supply of novel bioavailable nitrogen for the food web. However, the fate of the nitrogen fixed by cyanobacteria remains unresolved, as does its importance for secondary production in the Baltic Sea. Here, we synthesize recent experimental and field studies providing strong empirical evidence that cyanobacterial nitrogen is efficiently assimilated and transferred in Baltic food webs via two major pathways: directly by grazing on fresh or decaying cyanobacteria and indirectly through the uptake by other phytoplankton and microbes of bioavailable nitrogen exuded from cyanobacterial cells. This information is an essential step toward guiding nutrient management to minimize noxious blooms without overly reducing secondary production, and ultimately most probably fish production in the Baltic Sea.

Comparative diversity and composition of nitrogen-fixing ...

African Journals Online (AJOL)

Three contrasting land use systems: reserve forests, rice fields and coal fields located at Upper Assam region of North East India were explored for documenting diversity and species composition of N2-fixing cyanobacteria. Altogether 24 taxa (16 heterocystous and 8 non-heterocystous) belonging to nine different genera ...

Nitrogen-Fixing Bacteria in Eucalyptus globulus Plantations

Science.gov (United States)

da Silva, Marliane de Cássia Soares; Paula, Thiago de Almeida; Moreira, Bruno Coutinho; Carolino, Manuela; Cruz, Cristina; Bazzolli, Denise Mara Soares; Silva, Cynthia Canedo; Kasuya, Maria Catarina Megumi

2014-01-01

Eucalypt cultivation is an important economic activity worldwide. In Portugal, Eucalyptus globulus plantations account for one-third of the total forested area. The nutritional requirements of this crop have been well studied, and nitrogen (N) is one of the most important elements required for vegetal growth. N dynamics in soils are influenced by microorganisms, such as diazotrophic bacteria (DB) that are responsible for biological nitrogen fixation (BNF), so the aim of this study was to evaluate and identity the main groups of DB in E. globulus plantations. Samples of soil and root systems were collected in winter and summer from three different Portuguese regions (Penafiel, Gavião and Odemira). We observed that DB communities were affected by season, N fertilization and moisture. Furthermore Bradyrhizobium and Burkholderia were the most prevalent genera in these three regions. This is the first study describing the dynamic of these bacteria in E. globulus plantations, and these data will likely contribute to a better understanding of the nutritional requirements of eucalypt cultivation and associated organic matter turnover. PMID:25340502

Nitrogen-fixing bacteria in Eucalyptus globulus plantations.

Science.gov (United States)

da Silva, Marliane de Cássia Soares; Paula, Thiago de Almeida; Moreira, Bruno Coutinho; Carolino, Manuela; Cruz, Cristina; Bazzolli, Denise Mara Soares; Silva, Cynthia Canedo; Kasuya, Maria Catarina Megumi

2014-01-01

Eucalypt cultivation is an important economic activity worldwide. In Portugal, Eucalyptus globulus plantations account for one-third of the total forested area. The nutritional requirements of this crop have been well studied, and nitrogen (N) is one of the most important elements required for vegetal growth. N dynamics in soils are influenced by microorganisms, such as diazotrophic bacteria (DB) that are responsible for biological nitrogen fixation (BNF), so the aim of this study was to evaluate and identity the main groups of DB in E. globulus plantations. Samples of soil and root systems were collected in winter and summer from three different Portuguese regions (Penafiel, Gavião and Odemira). We observed that DB communities were affected by season, N fertilization and moisture. Furthermore Bradyrhizobium and Burkholderia were the most prevalent genera in these three regions. This is the first study describing the dynamic of these bacteria in E. globulus plantations, and these data will likely contribute to a better understanding of the nutritional requirements of eucalypt cultivation and associated organic matter turnover.

Nitrogen-fixing bacteria in Eucalyptus globulus plantations.

Directory of Open Access Journals (Sweden)

Marliane de Cássia Soares da Silva

Full Text Available Eucalypt cultivation is an important economic activity worldwide. In Portugal, Eucalyptus globulus plantations account for one-third of the total forested area. The nutritional requirements of this crop have been well studied, and nitrogen (N is one of the most important elements required for vegetal growth. N dynamics in soils are influenced by microorganisms, such as diazotrophic bacteria (DB that are responsible for biological nitrogen fixation (BNF, so the aim of this study was to evaluate and identity the main groups of DB in E. globulus plantations. Samples of soil and root systems were collected in winter and summer from three different Portuguese regions (Penafiel, Gavião and Odemira. We observed that DB communities were affected by season, N fertilization and moisture. Furthermore Bradyrhizobium and Burkholderia were the most prevalent genera in these three regions. This is the first study describing the dynamic of these bacteria in E. globulus plantations, and these data will likely contribute to a better understanding of the nutritional requirements of eucalypt cultivation and associated organic matter turnover.

Veillonella Catalase Protects the Growth of Fusobacterium nucleatum in Microaerophilic and Streptococcus gordonii-Resident Environments.

Science.gov (United States)

Zhou, Peng; Li, Xiaoli; Huang, I-Hsiu; Qi, Fengxia

2017-10-01

The oral biofilm is a multispecies community in which antagonism and mutualism coexist among friends and foes to keep an ecological balance of community members. The pioneer colonizers, such as Streptococcus gordonii , produce H 2 O 2 to inhibit the growth of competitors, like the mutans streptococci, as well as strict anaerobic middle and later colonizers of the dental biofilm. Interestingly, Veillonella species, as early colonizers, physically interact (coaggregate) with S. gordonii A putative catalase gene ( catA ) is found in most sequenced Veillonella species; however, the function of this gene is unknown. In this study, we characterized the ecological function of catA from Veillonella parvula PK1910 by integrating it into the only transformable strain, Veillonella atypica OK5, which is catA negative. The strain (OK5- catA ) became more resistant to H 2 O 2 Further studies demonstrated that the catA gene expression is induced by the addition of H 2 O 2 or coculture with S. gordonii Mixed-culture experiments further revealed that the transgenic OK5- catA strain not only enhanced the growth of Fusobacterium nucleatum , a strict anaerobic periodontopathogen, under microaerophilic conditions, but it also rescued F. nucleatum from killing by S. gordonii A potential role of catalase in veillonellae in biofilm ecology and pathogenesis is discussed here. IMPORTANCE Veillonella species, as early colonizers, can coaggregate with many bacteria, including the initial colonizer Streptococcus gordonii and periodontal pathogen Fusobacterium nucleatum , during various stages of oral biofilm formation. In addition to providing binding sites for many microbes, our previous study also showed that Veillonella produces nutrients for the survival and growth of periodontal pathogens. These findings indicate that Veillonella plays an important "bridging" role in the development of oral biofilms and the ecology of the human oral cavity. In this study, we demonstrated that the reducing

Trends in industrial and environmental biotechnology research in ...

African Journals Online (AJOL)

SERVER

2007-12-28

Dec 28, 2007 ... Department of Molecular Biology and Biotechnology, University of Dar es Salaam P. O. Box 35179, Dar es .... digestion of bagasse, maize bran, coconut fibres, water ..... bacterium formicicum has shown nitrogen fixing abilities.

Characterization of carbon dioxide concentrating chemolithotrophic bacterium Serratia sp. ISTD04 for production of biodiesel.

Science.gov (United States)

Kumar, Manish; Morya, Raj; Gnansounou, Edgard; Larroche, Christian; Thakur, Indu Shekhar

2017-11-01

Proteomics and metabolomics analysis has become a powerful tool for characterization of microbial ability for fixation of Carbon dioxide. Bacterial community of palaeoproterozoic metasediments was enriched in the shake flask culture in the presence of NaHCO 3 . One of the isolate showed resistance to NaHCO 3 (100mM) and was identified as Serratia sp. ISTD04 by 16S rRNA sequence analysis. Carbon dioxide fixing ability of the bacterium was established by carbonic anhydrase enzyme assay along with proteomic analysis by LC-MS/MS. In proteomic analysis 96 proteins were identified out of these 6 protein involved in carbon dioxide fixation, 11 in fatty acid metabolism, indicating the carbon dioxide fixing potency of bacterium along with production of biofuel. GC-MS analysis revealed that hydrocarbons and FAMEs produced by bacteria within the range of C 13 -C 24 and C 11 -C 19 respectively. Presence of 59% saturated and 41% unsaturated organic compounds, make it a better fuel composition. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in Alphaproteobacteria

Directory of Open Access Journals (Sweden)

Olga V Tsoy

2016-08-01

Full Text Available Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of Bacteria and Archaea. Being a complex and sensitive process, nitrogen fixation requires a complicated regulatory system, also, on the level of transcription. The transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class Alphaproteobacteria. This regulatory network includes the activator of nitrogen fixation NifA, working in tandem with the alternative sigma-factor RpoN as well as oxygen-responsive regulatory systems, one-component regulators FnrN/FixK and two-component system FixLJ. Here we used a comparative genomics analysis for in silico study of the transcriptional regulatory network in 50 genomes of Alphaproteobacteria. We extended the known regulons and proposed the scenario for the evolution of the nitrogen fixation transcriptional network. The reconstructed network substantially expands the existing knowledge of transcriptional regulation in nitrogen-fixing microorganisms and can be used for genetic experiments, metabolic reconstruction, and evolutionary analysis.

Enzymology of biological nitrogen fixation. Final report, May 1, 1987--April 30, 1996

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-05-01

Biological nitrogen fixation is of central importance in the earth`s nitrogen economy. Fixation of nitrogen is accomplished by a variety of microorganisms, all of them procaryotic. Some operate independently and some function symbiotically or associatively with photosynthesizing plants. Biological nitrogen fixation is accomplished via the reaction: N{sub 2} + 8H{sup +} + 8e{sup {minus}} {yields} 2NH{sub 3} + H{sub 2}. This reaction requires a minimum of 16 ATP under ideal laboratory conditions, so it is obvious that the energy demand of the reaction is very high. When certain nitrogen-fixing organisms are supplied fixed nitrogen (e.g., ammonium) the organisms use the fixed nitrogen and turn off their nitrogenase system, thus conserving energy. When the fixed nitrogen is exhausted, the organism reactivates its nitrogenase. The system is turned off by dinitrogenase reductase ADP-ribosyl transferase (DRAT) and turned back on by dinitrogenase reductase-activating glycohydrolase (DRAG). The authors have investigated the details of how DRAT and DRAG are formed, how they function, and the genetics of their formation and operation.

Complete genome of Pseudomonas sp. strain L10.10, a psychrotolerant biofertilizer that could promote plant growth.

Science.gov (United States)

See-Too, Wah Seng; Lim, Yan-Lue; Ee, Robson; Convey, Peter; Pearce, David A; Yin, Wai-Fong; Chan, Kok Gan

2016-03-20

Pseudomonas sp. strain L10.10 (=DSM 101070) is a psychrotolerant bacterium which was isolated from Lagoon Island, Antarctica. Analysis of its complete genome sequence indicates its possible role as a plant-growth promoting bacterium, including nitrogen-fixing ability and indole acetic acid (IAA)-producing trait, with additional suggestion of plant disease prevention attributes via hydrogen cyanide production. Copyright © 2016 Elsevier B.V. All rights reserved.

Heterotrophic ammonium removal characteristics of an aerobic heterotrophic nitrifying-denitrifying bacterium, Providencia rettgeri YL

Institute of Scientific and Technical Information of China (English)

TAYLOR Shauna M; HE Yiliang; ZHAO Bin; HUANG Jue

2009-01-01

Bacterium Providencia rettgeri YL was found to exhibit an unusual ability to heterotrophically nitrify and aerobically denitrify various concentrations of ammonium (NH4+-N). In order to further analyze its removal ability, several experiments were conducted to identify the growth and ammonium removal response in different carbon to nitrogen (C/N) mass ratios, shaking speeds, temperatures, ammonium concentrations and to qualitatively verify the production of nitrogen gas using gas chromatography techniques. Results showed that under optimum conditions (C/N 10, 30℃, 120 r/min), YL can significantly remove low and high concentrations of ammonium within 12 to 48 h of growth. The nitrification products hydroxylamine (NH2OH), nitrite (NO2-) and nitrate (NO3-) as well as the denitrification product, nitrogen gas (N2), were detected under completely aerobic conditions.

Content of nitrogen in atmospheric precipitation in Sweden

Energy Technology Data Exchange (ETDEWEB)

Angstroem, A; Hoegberg, L

1952-01-01

In the present paper an attempt is made to give a general idea of the geographical distribution of fixed nitrogen (NH/sub 4/-N) transferred to the soil through precipitation in Sweden. Further a map is given showing the distribution af alpha, a quantity proportional to the nitrogen concentration in the precipitation at the beginning of a rain and, it is assumed, representative for the content of fixed nitrogen in the atmosphere before the rain is falling. A discussion of different causes of the concentration of fixed nitrogen in precipitation is presented and a photochemical process is suggested, which would explain the almost constant ratio between NH/sub 4//sup -n/ and NO/sub 3//sup -n/ frequently found within the temperate zones. It is evident, however, that other causes also are at work, especially at lower latitudes. The need of laboratory experiments is emphasized.

Field performance of new cowpea cultivars inoculated with efficient nitrogen-fixing rhizobial strains in the Brazilian Semiarid

Directory of Open Access Journals (Sweden)

Rita de Cássia Nunes Marinho

2014-05-01

Full Text Available The objective of this work was to evaluate the contribution of efficient nitrogen-fixing rhizobial strains to grain yield of new cowpea cultivars, indicated for cultivation in the Brazilian Semiarid region, in the sub-medium of the São Francisco River Valley. Two experiments were set up at the irrigated perimeters of Mandacaru (Juazeiro, state of Bahia and Bebedouro (Petrolina, state of Pernambuco. The treatments consisted of single inoculation of five rhizobial strains - BR 3267, BR 3262, INPA 03-11B, UFLA 03-84 (Bradyrhizobium sp., and BR 3299T (Microvirga vignae -, besides a treatment with nitrogen and a control without inoculation or N application. The following cowpea cultivars were evaluated: BRS Pujante, BRS Tapaihum, BRS Carijó, and BRS Acauã. A randomized complete block design, with four replicates, was used. Inoculated plants showed similar grain yield to the one observed with plants fertilized with 80 kg ha-1 N. The cultivars BRS Tapaihum and BRS Pujante stood out in grain yield and protein contents when inoculated, showing their potential for cultivation in the sub-medium of the São Francisco River Valley.

Synthetic biology approaches to engineering the nitrogen symbiosis in cereals.

Science.gov (United States)

Rogers, Christian; Oldroyd, Giles E D

2014-05-01

Nitrogen is abundant in the earth's atmosphere but, unlike carbon, cannot be directly assimilated by plants. The limitation this places on plant productivity has been circumvented in contemporary agriculture through the production and application of chemical fertilizers. The chemical reduction of nitrogen for this purpose consumes large amounts of energy and the reactive nitrogen released into the environment as a result of fertilizer application leads to greenhouse gas emissions, as well as widespread eutrophication of aquatic ecosystems. The environmental impacts are intensified by injudicious use of fertilizers in many parts of the world. Simultaneously, limitations in the production and supply of chemical fertilizers in other regions are leading to low agricultural productivity and malnutrition. Nitrogen can be directly fixed from the atmosphere by some bacteria and Archaea, which possess the enzyme nitrogenase. Some plant species, most notably legumes, have evolved close symbiotic associations with nitrogen-fixing bacteria. Engineering cereal crops with the capability to fix their own nitrogen could one day address the problems created by the over- and under-use of nitrogen fertilizers in agriculture. This could be achieved either by expression of a functional nitrogenase enzyme in the cells of the cereal crop or through transferring the capability to form a symbiotic association with nitrogen-fixing bacteria. While potentially transformative, these biotechnological approaches are challenging; however, with recent advances in synthetic biology they are viable long-term goals. This review discusses the possibility of these biotechnological solutions to the nitrogen problem, focusing on engineering the nitrogen symbiosis in cereals.

Unusual radioresistance of nitrogen-fixing cultures of Anabaena ...

Indian Academy of Sciences (India)

Prakash

Atlas R M 2004 Handbook of microbiological media; third edition. (Florida: CRC Press) ... nitrogen-fixation, and nodularin production by two Baltic sea cyanobacteria ... Sharma A 1998 Mycotoxins: risk evaluation and management in radiation ...

Nitrogen fixation by the Azolla-Anabaena azollae symbiosis

International Nuclear Information System (INIS)

Becking, J.H.

1985-01-01

A concise outline is presented on the main characteristics of the Azolla association in relation to tropical wetland rice cultivation and the nitrogen economy of paddy soils. Due to the presence of a nitrogen fixing cyanobiont occurring in a special leaf cavity of the Azolla leaf, the water fern Azolla can grow in a nitrogen-deficient environment and is able to contribute considerably to the nitrogen status of the soil. An experimental set-up is presented for how the nitrogen-fixing capacity of Azolla plants can be measured in the field by means of the acetylene reduction assay using a rather simple glass vessel. A comparison was made between 15 N 2 fixation by Azolla and acetylene reduction of Azolla plants under identical conditions

Energy transfer in Anabaena variabilis filaments adapted to nitrogen-depleted and nitrogen-enriched conditions studied by time-resolved fluorescence.

Science.gov (United States)

Onishi, Aya; Aikawa, Shimpei; Kondo, Akihiko; Akimoto, Seiji

2017-09-01

Nitrogen is among the most important nutritious elements for photosynthetic organisms such as plants, algae, and cyanobacteria. Therefore, nitrogen depletion severely compromises the growth, development, and photosynthesis of these organisms. To preserve their integrity under nitrogen-depleted conditions, filamentous nitrogen-fixing cyanobacteria reduce atmospheric nitrogen to ammonia, and self-adapt by regulating their light-harvesting and excitation energy-transfer processes. To investigate the changes in the primary processes of photosynthesis, we measured the steady-state absorption and fluorescence spectra and time-resolved fluorescence spectra (TRFS) of whole filaments of the nitrogen-fixing cyanobacterium Anabaena variabilis at 77 K. The filaments were grown in standard and nitrogen-free media for 6 months. The TRFS were measured with a picosecond time-correlated single photon counting system. Despite the phycobilisome degradation, the energy-transfer paths within phycobilisome and from phycobilisome to both photosystems were maintained. However, the energy transfer from photosystem II to photosystem I was suppressed and a specific red chlorophyll band appeared under the nitrogen-depleted condition.

Growth and foliar nitrogen concentrations of interplanted native woody legumes and pecan

Science.gov (United States)

J.W. Van Sambeek; Nadia E. Navarrete-Tindall; Kenneth L. Hunt

2008-01-01

The interplanting and underplanting of nodulated nitrogen-fixing plants in tree plantings can increase early growth and foliage nitrogen content of hardwoods, especially black walnut and pecan. Recent studies have demonstrated that some non-nodulated woody legumes may be capable of fixing significant levels of atmospheric nitrogen. The following nine nurse crop...

Characterization of Diazotrophs Containing Mo-Independent Nitrogenases, Isolated from Diverse Natural Environments

Science.gov (United States)

Molybdenum-independent nitrogenases were first described in the nitrogen-fixing bacterium Azotobacter vinelandii and have since been described in other diazotrophic bacteria. Previously, we reported the isolation of seven diazotrophs with Molybdenum-independent nitrogenases from aquatic environments...

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria.

Science.gov (United States)

Martínez-Hidalgo, Pilar; Galindo-Villardón, Purificación; Trujillo, Martha E; Igual, José M; Martínez-Molina, Eustoquio

2014-09-17

Biotic interactions can improve agricultural productivity without costly and environmentally challenging inputs. Micromonospora strains have recently been reported as natural endophytes of legume nodules but their significance for plant development and productivity has not yet been established. The aim of this study was to determine the diversity and function of Micromonospora isolated from Medicago sativa root nodules. Micromonospora-like strains from field alfalfa nodules were characterized by BOX-PCR fingerprinting and 16S rRNA gene sequencing. The ecological role of the interaction of the 15 selected representative Micromonospora strains was tested in M. sativa. Nodulation, plant growth and nutrition parameters were analyzed. Alfalfa nodules naturally contain abundant and highly diverse populations of Micromonospora, both at the intra- and at interspecific level. Selected Micromonospora isolates significantly increase the nodulation of alfalfa by Ensifer meliloti 1021 and also the efficiency of the plant for nitrogen nutrition. Moreover, they promote aerial growth, the shoot-to-root ratio, and raise the level of essential nutrients. Our results indicate that Micromonospora acts as a Rhizobia Helper Bacteria (RHB) agent and has probiotic effects, promoting plant growth and increasing nutrition efficiency. Its ecological role, biotechnological potential and advantages as a plant probiotic bacterium (PPB) are also discussed.

Effects of water and nitrogen availability on nitrogen contribution by the legume, Lupinus argenteus Pursh

Science.gov (United States)

Erin Goergen; Jeanne C. Chambers; Robert Blank

2009-01-01

Nitrogen-fixing species contribute to ecosystem nitrogen budgets, but background resource levels influence nodulation, fixation, and plant growth. We conducted a greenhouse experiment to examine the separate and interacting effects of water and N availability on biomass production, tissue N concentration, nodulation, nodule activity, and rhizodeposition of ...

The Purine-Utilizing Bacterium Clostridium acidurici 9a: A Genome-Guided Metabolic Reconsideration

OpenAIRE

Hartwich, Katrin; Poehlein, Anja; Daniel, Rolf

2012-01-01

Clostridium acidurici is an anaerobic, homoacetogenic bacterium, which is able to use purines such as uric acid as sole carbon, nitrogen, and energy source. Together with the two other known purinolytic clostridia C. cylindrosporum and C. purinilyticum, C. acidurici serves as a model organism for investigation of purine fermentation. Here, we present the first complete sequence and analysis of a genome derived from a purinolytic Clostridium. The genome of C. acidurici 9a consists ...

Nitrogen fixation in Red Sea seagrass meadows

KAUST Repository

Abdallah, Malak

2017-05-01

Seagrasses are key coastal ecosystems, providing many ecosystem services. Seagrasses increase biodiversity as they provide habitat for a large set of organisms. In addition, their structure provides hiding places to avoid predation. Seagrasses can grow in shallow marine coastal areas, but several factors regulate their growth and distribution. Seagrasses can uptake different kinds of organic and inorganic nutrients through their leaves and roots. Nitrogen and phosphorous are the most important nutrients for seagrass growth. Biological nitrogen fixation is the conversion of atmospheric nitrogen into ammonia by diazotrophic bacteria. This process provides a significant source of nitrogen for seagrass growth. The nitrogen fixation is controlled by the nif genes which are found in diazotrophs. The main goal of the project is to measure nitrogen fixation rates on seagrass sediments, in order to compare among various seagrass species from the Red Sea. Moreover, we will compare the fixing rates of the Vegetated areas with the bare sediments. This project will help to ascertain the role of nitrogen fixing bacteria in the development of seagrass meadows.

Functional specialization of one copy of glutamine phosphoribosyl pyrophosphate amidotransferase in ureide production from symbiotically fixed nitrogen in Phaseolus vulgaris.

Science.gov (United States)

Coleto, Inmaculada; Trenas, Almudena T; Erban, Alexander; Kopka, Joachim; Pineda, Manuel; Alamillo, Josefa M

2016-08-01

Purines are essential molecules formed in a highly regulated pathway in all organisms. In tropical legumes, the nitrogen fixed in the nodules is used to generate ureides through the oxidation of de novo synthesized purines. Glutamine phosphoribosyl pyrophosphate amidotransferase (PRAT) catalyses the first committed step of de novo purine synthesis. In Phaseolus vulgaris there are three genes coding for PRAT. The three full-length sequences, which are intron-less genes, were cloned, and their expression levels were determined under conditions that affect the synthesis of purines. One of the three genes, PvPRAT3, is highly expressed in nodules and protein amount and enzymatic activity in these tissues correlate with nitrogen fixation activity. Inhibition of PvPRAT3 gene expression by RNAi-silencing and subsequent metabolomic analysis of the transformed roots shows that PvPRAT3 is essential for the synthesis of ureides in P. vulgaris nodules. © 2016 John Wiley & Sons Ltd.

Molecular markers to study competition and diversity of Rhizobium

NARCIS (Netherlands)

Sessitsch, A.

1997-01-01

The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous

Anaerobic Nitrogen Fixers on Mars

Science.gov (United States)

Lewis, B. G.

2000-07-01

The conversion of atmospheric nitrogen gas to the protein of living systems is an amazing process of nature. The first step in the process is biological nitrogen fixation, the transformation of N2 to NH3. The phenomenon is crucial for feeding the billions of our species on Earth. On Mars, the same process may allow us to discover how life can adapt to a hostile environment, and render it habitable. Hostile environments also exist on Earth. For example, nothing grows in coal refuse piles due to the oxidation of pyrite and marcasite to sulfuric acid. Yet, when the acidity is neutralized, alfalfa and soybean plants develop root nodules typical of symbiotic nitrogen fixation with Rhizobium species possibly living in the pyritic material. When split open, these nodules exhibited the pinkish color of leghemoglobin, a protein in the nodule protecting the active nitrogen-fixing enzyme nitrogenase against the toxic effects of oxygen. Although we have not yet obtained direct evidence of nitrogenase activity in these nodules (reduction of acetylene to ethylene, for example), these findings suggested the possibility that nitrogen fixation was taking place in this hostile, non-soil material. This immediately raises the possibility that freeliving anaerobic bacteria which fix atmospheric nitrogen on Earth, could do the same on Mars.

Increased protein content of chickpea (Cicer arietinum L.) inoculated with arbuscular mycorrhizal fungi and nitrogen-fixing bacteria under water deficit conditions.

Science.gov (United States)

Oliveira, Rui S; Carvalho, Patrícia; Marques, Guilhermina; Ferreira, Luís; Nunes, Mafalda; Rocha, Inês; Ma, Ying; Carvalho, Maria F; Vosátka, Miroslav; Freitas, Helena

2017-10-01

Chickpea (Cicer arietinum L.) is a widely cropped pulse and an important source of proteins for humans. In Mediterranean regions it is predicted that drought will reduce soil moisture and become a major issue in agricultural practice. Nitrogen (N)-fixing bacteria and arbuscular mycorrhizal (AM) fungi have the potential to improve plant growth and drought tolerance. The aim of the study was to assess the effects of N-fixing bacteria and AM fungi on the growth, grain yield and protein content of chickpea under water deficit. Plants inoculated with Mesorhizobium mediterraneum or Rhizophagus irregularis without water deficit and inoculated with M. mediterraneum under moderate water deficit had significant increases in biomass. Inoculation with microbial symbionts brought no benefits to chickpea under severe water deficit. However, under moderate water deficit grain crude protein was increased by 13%, 17% and 22% in plants inoculated with M. mediterraneum, R. irregularis and M. mediterraneum + R. irregularis, respectively. Inoculation with N-fixing bacteria and AM fungi has the potential to benefit agricultural production of chickpea under water deficit conditions and to contribute to increased grain protein content. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

NARCIS (Netherlands)

Santos, Henrique F.; Carmo, Flavia L.; Duarte, Gustavo; Dini-Andreote, Francisco; Castro, Clovis B.; Rosado, Alexandre S.; van Elsas, Jan Dirk; Peixoto, Raquel S.

2014-01-01

Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study

Climate change affects key nitrogen-fixing bacterial populations on coral reefs

NARCIS (Netherlands)

Santos, Henrique F.; Carmo, Flavia L.; Duarte, Gustavo; Dini-Andreote, Francisco; Castro, Clovis B.; Rosado, Alexandre S.; van Elsas, Jan Dirk; Peixoto, Raquel S.

Coral reefs are at serious risk due to events associated with global climate change. Elevated ocean temperatures have unpredictable consequences for the ocean's biogeochemical cycles. The nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation. This study

Permanent draft genome of the malachite-green-tolerant bacterium Rhizobium sp. MGL06.

Science.gov (United States)

Liu, Yang; Wang, Runping; Zeng, Runying

2014-12-01

Rhizobium sp. MGL06, the first Rhizobium isolate from a marine environment, is a malachite-green-tolerant bacterium with a broader salinity tolerance (range: 0.5% to 9%) than other rhizobia. This study sequences and annotates the draft genome sequence of this strain. Genome sequence information provides a basis for analyzing the malachite green tolerance, broad salinity adaptation, nitrogen fixation properties, and taxonomic classification of the isolate. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative determination of nitrogen biological fixation by the N-15 isotopic method

International Nuclear Information System (INIS)

Basantes, Emilio; Trivelin, Paulo; Mui Tsai, Siu

1993-01-01

In order to quantify the biological nitrogen fixation (BNF) and to evaluate the mycorrhiza effect in the BNF, an experiment was carried on by applying 1 5 N -ammonium sulphate and mycorrhiza fungi to the soil. The treatments included legumes: mucuna negra(Stizolobium atterrinum Piper et Tracv) and caupi (Vigna unguiculoata L. Walp). Two control plants: non nodulating soybean (Glycine max L.Merril) and rice (Oryza sativa), were used for measuring the fixed N in the legumes by isotope dilution method. Both legumes and control plants assimmilated the same ammounts of nitrogen from the soil and fertilizer. The greater N content in the legumnes was determined as coming from the fixed nitrogen. Rice and non nodulating soybean showed to be good controls for measuring biological nitrogen fixation using isotopic dilution method. The values of fixed nitrogen for legumes calculated using rice as control plant were slightly greater than those with non nodulating soybean, nevertheless there were no significant statistical differences between the values. The mucuna fixed more N than caupi in both mycorrhiza treatments (76.7, 66.6 and 56. 7 per cent of N fixed, respectively). The mycorrhiza increased dry matter yield (13.84 per cent), accumulation of N in the plant(14.85 per cent N) and the biological N fixation (16.06 per cent N-fixed) in caupi

Effect of systemic herbicides on N2-fixing and phosphate solubilizing microorganisms in relation to availability of nitrogen and phosphorus in paddy soils of West Bengal.

Science.gov (United States)

Das, Amal Chandra; Debnath, Anjan

2006-11-01

A field experiment has been conducted with four systemic herbicides viz., butachlor [N-(butoxymethyl)-2-chloro-2',6'-diethyl-acetanilide], fluchloralin [N-(2-chloroethyl)-(2,6-dinitro-N-propyl-4-trifluoromethyl) aniline], oxadiazon [5-terbutyl-3-(2,4-dichloro-5-isopro poxyphenyl)-1,3,4-oxadiazol-2-one] and oxyfluorfen [2-chloro-1-(3-ethoxy-4-nitrophenyl)-4-(trifluoromethyl) benzene] at their recommended field rates (2.0, 1.5, 0.4 and 0.12kga.i.ha(-1), respectively) to investigate their effects on growth and activities of aerobic non-symbiotic N(2)-fixing bacteria and phosphate solubilizing microorganisms in relation to availability of nitrogen and phosphorus in the rhizosphere soils as well as yield of the rice crop (Oryza sativa L cv. IR-36). Application of herbicides, in general, highly stimulated the population and activities of the target microorganisms, which resulted in a greater amount of atmospheric nitrogen fixation and phosphate solubilization in the rhizosphere soils of the test crop. The greater microbial activities subsequently augmented the mineralization and availability of nitrogen and phosphorus in the soil solution, which in turn increased the yield of the crop. Among the herbicides, oxyfluorfen was most stimulative followed by fluchloralin and oxadiazon in augmenting the microbial activities in soil. Butachlor also accentuated the mineralization and availability of nitrogen due to higher incitement of non-symbiotic N(2)-fixing bacteria in paddy soil. The grain and straw yields of the crop were also significantly increased due to the application of oxyfluorfen (20.2% and 21%) followed by fluchloralin (13.1% and 15.4%) and butachlor (9.1% and 10.2%), respectively.

Denitrification, anammox and fixed nitrogen removal in the water column of a tropical great lake

Science.gov (United States)

Darchambeau, François; Roland, Fleur; Crowe, Sean A.; De Brabandere, Loreto; Llirós, Marc; Garcia-Armisen, Tamara; Inceoglu, Ozgul; Michiels, Céline; Servais, Pierre; Morana, Cédric D. T.; Bouillon, Steven; Meysman, Filip; Veuger, Bart; Masilya, Pascal M.; Descy, Jean-Pierre; Borges, Alberto V.

2013-04-01

If rates of microbial denitrification in aquatic systems are poorly constrained, it is much more the case for tropical water bodies. Lake Kivu [2.50° S 1.59° S, 29.37° E 28.83° E] is one of the great lakes of the East African Rift. It is an oligotrophic lake characterized by anoxic deep waters rich in dissolved gases (methane and carbon dioxide) and nutrients, and by well oxygenated and nutrient-depleted surface waters. During the seasonally stratified rainy season (October to May), a nitrogenous zone characterized by the accumulation of nitrite (NO2-) and nitrate (NO3-) is often observed in the lower layer of the mixolimnion. It results from nitrification of ammonium released by decaying organic matter. With the seasonal uplift of the oxygen minimum zone, the nitrogenous zone becomes anoxic and might be the most preferential area for fixed nitrogen (N) removal in Lake Kivu. Our work aimed at identifying and quantifying the processes of N losses by denitrification and/or anammox in the nitrogenous zone of the Lake Kivu water column. During 5 sampling campaigns (March 2010, October 2010, June 2011, February 2012 and September 2012), isotopic labelling experiments were used to quantify denitrification and anammox rates along vertical profiles at two pelagic stations of the main lake. Moreover, N2:Ar ratios were estimated during the September 2012 campaign, and 16S rDNA pyrosequencing was used to describe bacterial community composition during the last 2 campaigns. No bacteria related to organisms performing anammox was observed and labelling experiments failed to detect anammox at any locations and any depths. In Lake Kivu, denitrifying bacteria were mainly related to Denitratisoma and Thiobacillus genus. Significant denitrification rates were observed at several occasions, especially under the oxic-anoxic interface in the bottom of the nitracline. The annual average denitrification rate was estimated at ~150 μmoles N m-2 d-1. Denitrification was not the only

Nitrogen fixation by free-living microorganisms in tropical rice soils using labelled fertilizer. Part of a coordinated programme on isotope techniques in studies of biological nitrogen fixation for the dual purpose of increasing crop production and decreasing nitrogen fertilizer use to conserve the environment

International Nuclear Information System (INIS)

Rao, V.R.

1981-11-01

Both acetylene-reduction and 15 N techniques were used to study heterotrophic N fixation in the rhizosphere of rice plants. Soils subjected to flooding in 4 soil types in both greenhouse and the field were found to stimulate greater heterotrophic nitrogen fixation than moist soils. The addition of organic materials, in particular, cellulose and rice straw, in general, enhanced nitrogen fixed by heterotrophic organisms living in the rhizosphere of rice plants. The highest amount of N fixed was 38 kg N/ha, and was obtained in a flooded lateritic soil to which had been added cellulose. Heterotrophic nitrogen fixation was influenced by soil type. In this study, the lowest value for fixed N was recorded in an acid sulphate soil of low pH. The addition of increasing amounts of inorganic nitrogen fertilizer in the form of ammonium sulphate suppressed rhizospheric nitrogen fixation in all soils, but the extent of suppression differed in the different soils. Benomyl fungicide and methyl carbamate insecticide had a stimulatory effect on heterotrophic nitrogen fixation in soils under rice roots. Different rice cultivars stimulated strains of Azospirillum to varying extent, and thus did not fix nitrogen to the same extent. It is thus possible that varieties of rice could be selected on the basis of their ability to support non-symbiotic N fixation in their rhizosphere

Nitrogen regulates chitinase gene expression in a marine bacterium

DEFF Research Database (Denmark)

Delpin, Marina; Goodman, A.E.

2009-01-01

Ammonium concentration and nitrogen source regulate promoter activity and use for the transcription of chiA, the major chitinase gene of Pseudoalteromonas sp. S91 and S91CX, an S91 transposon lacZ fusion mutant. The activity of chiA was quantified by beta-galactosidase assay of S91CX cultures con...... GlcNAc, transcription initiated from two putative sigma(54)-dependent promoters and (3) glt, transcription initiated from all three putative promoters. The ISME Journal (2009) 3, 1064-1069; doi:10.1038/ismej.2009.49; published online 14 May 2009...

Nitrogen fixation in rice systems: State of knowledge and future prospects

International Nuclear Information System (INIS)

Ladha, J.K.; Reddy, P.M.

2001-01-01

Rice is the most important cereal crop. In the next three decades, the world will need to produce about 60% more rice than today's global production to feed the extra billion people. Nitrogen is the major nutrient limiting rice production. Development of fertilizer-responsive varieties in the Green Revolution, coupled with the realization by farmers of the importance of nitrogen, has led to high rates of N fertilizer use on rice. Increased future demand for rice will entail increased application of fertilizer N. Awareness is growing, however, that such an increase in agricultural production needs to be achieved without endangering the environment. To achieve food security through sustainable agriculture, the requirement for fixed nitrogen must increasingly met by biological nitrogen fixation (BNF) rather than by using nitrogen fixed industrially. It is thus imperative to improve existing BNF systems and develop N 2 -fixing non-leguminous crops such as rice. Here we review the potentials and constraints of conventional BNF systems in rice agriculture, as well as the prospects of achieving in planta nitrogen fixation in rice. (author)

Swivel Joint For Liquid Nitrogen

Science.gov (United States)

Milner, James F.

1988-01-01

Swivel joint allows liquid-nitrogen pipe to rotate through angle of 100 degree with respect to mating pipe. Functions without cracking hard foam insulation on lines. Pipe joint rotates on disks so mechanical stress not transmitted to thick insulation on pipes. Inner disks ride on fixed outer disks. Disks help to seal pressurized liquid nitrogen flowing through joint.

[Assimilation of biological nitrogen by European beaver].

Science.gov (United States)

Vecherskiĭ, M V; Naumova, E I; Kostina, N V; Umarov, M M

2009-01-01

Nitrogenase activity, the abundance of diazotrophic bacteria, the structure and functional characteristics of the complex of microorganisms, and the content of nitrogen and carbon were determined in the contents of the gastrointestinal tract of the European beaver. A high nitrogen-fixing activity in the large intestine correlated with an increase in nitrogen content in the chyme upon its transfer over the gastrointestinal tract. It is assumed that microbial nitrogen fixation plays a major role in nitrogen nutrition of the European beaver.

Biological nitrogen fixation in Crotalaria species estimated using the 15N isotope dilution method

International Nuclear Information System (INIS)

Samba, R.T.; Neyra, M.; Gueye, M.; Sylla, S.N.; Ndoye, I.; Dreyfus, B.

2002-01-01

Growing in Senegal by using 15 N direct isotope dilution technique. Two non-fixing plants, Senna obtusifolia and Senna occidentalis served as reference plants. The amount of nitrogen fixed two months after planting was obtained using the average of the two reference plants. The atom % 15 N excess in the Crotalaria species was significantly lower than that of the reference plants, indicating that significant nitrogen fixation occurred in the three plants. Significant differences were observed between the Crotalaria species; C. ochroleuca yielded more dry matter weight and total nitrogen than did C. perrottetti and C. retusa. The % nitrogen derived from atmosphere (%Ndfa) in leaves and stems was also higher in C. ochroleuca. There was no significant difference in %Ndfa in the whole plant between the three Crotalaria species (47% to 53%). In contrast, interspecific variability was observed based on the %Ndfa. C. ochroleuca significantly exhibited the higher amount of total nitrogen fixed, equivalent to 83 kg of nitrogen fixed per hectare. Based on these data, it was concluded that C. ochroleuca could be used in multiple cropping systems in Senegal for making more nitrogen available to other plants. (author)

Engineering Pseudomonas protegens Pf-5 for Nitrogen Fixation and its Application to Improve Plant Growth under Nitrogen-Deficient Conditions

Science.gov (United States)

Setten, Lorena; Soto, Gabriela; Mozzicafreddo, Matteo; Fox, Ana Romina; Lisi, Christian; Cuccioloni, Massimiliano; Angeletti, Mauro; Pagano, Elba; Díaz-Paleo, Antonio; Ayub, Nicolás Daniel

2013-01-01

Nitrogen is the second most critical factor for crop production after water. In this study, the beneficial rhizobacterium Pseudomonas protegens Pf-5 was genetically modified to fix nitrogen using the genes encoding the nitrogenase of Pseudomonas stutzeri A1501 via the X940 cosmid. Pf-5 X940 was able to grow in L medium without nitrogen, displayed high nitrogenase activity and released significant quantities of ammonium to the medium. Pf-5 X940 also showed constitutive expression and enzymatic activity of nitrogenase in ammonium medium or in nitrogen-free medium, suggesting a constitutive nitrogen fixation. Similar to Pseudomonas protegens Pf-5, Pseudomonas putida, Pseudomonas veronii and Pseudomonas taetrolens but not Pseudomonas balearica and Pseudomonas stutzeri transformed with cosmid X940 showed constitutive nitrogenase activity and high ammonium production, suggesting that this phenotype depends on the genome context and that this technology to obtain nitrogen-fixing bacteria is not restricted to Pf-5. Interestingly, inoculation of Arabidopsis, alfalfa, tall fescue and maize with Pf-5 X940 increased the ammonium concentration in soil and plant productivity under nitrogen-deficient conditions. In conclusion, these results open the way to the production of effective recombinant inoculants for nitrogen fixation on a wide range of crops. PMID:23675499

The effects of arbuscular mycorrhizal fungus and free living nitrogen fixing bacteria on growth, photosynthesis and yield of corn

Directory of Open Access Journals (Sweden)

mohsen jahan

2009-06-01

Full Text Available In recent years, biological fertilizers have received special attention by scientists in sustainable and low input agriculture. In order to study the effects of arbuscular mycorrhizal fungi and free living nitrogen fixing bacteria on growth and photosynthesis characteristics of corn in conventional and ecological cropping systems, a field experiment was conducted at the Research Farm of Ferdowsi University of Mashhad during year 2006. A split plots arrangement based on randomized complete block design with three replications was used. Treatments consisted four cropping systems (1- High input conventional system, 2- Medium input conventional system, 3- Low input conventional system and 4- Ecological system and four inoculations (1- Mycorrhiza fungus, Glomus intraradices, 2- Bacteria, Azotobacter paspali and Azospirillum brasilense, 3- Dual inoculation, Fungus plus bacteria, and 4- No-inoculation, control, which were allocated to main plots and sub plots, respectively. All agronomic practices and inputs application during planting and nursing for each of cropping systems were conducted according to regional traditions. Results showed that the effect of inoculation on photosynthesis rates of corn was significant, as the highest photosynthesis rate obtained in dual inoculation. Single inoculation (fungus or bacteria was ranked second. The effect of all inoculations on corn dry matter production was significant and dual inoculation produced the highest dry matter yield. The cropping systems have significant effect on corn yield and the difference between medium input conventional system and high input conventional system was significant, but the high input, low input and ecological cropping systems showed no differences. Inoculants affected the SPAD readings, and dual inoculation showed the highest SPAD readings. This study showed that utilization of low input conventional and ecological systems in combination with use of dual inoculation of

Biochemical and Molecular Phylogenetic Study of Agriculturally Useful Association of a Nitrogen-Fixing Cyanobacterium and Nodule Sinorhizobium with Medicago sativa L.

Directory of Open Access Journals (Sweden)

E. V. Karaushu

2015-01-01

Full Text Available Seed inoculation with bacterial consortium was found to increase legume yield, providing a higher growth than the standard nitrogen treatment methods. Alfalfa plants were inoculated by mono- and binary compositions of nitrogen-fixing microorganisms. Their physiological and biochemical properties were estimated. Inoculation by microbial consortium of Sinorhizobium meliloti T17 together with a new cyanobacterial isolate Nostoc PTV was more efficient than the single-rhizobium strain inoculation. This treatment provides an intensification of the processes of biological nitrogen fixation by rhizobia bacteria in the root nodules and an intensification of plant photosynthesis. Inoculation by bacterial consortium stimulates growth of plant mass and rhizogenesis and leads to increased productivity of alfalfa and to improving the amino acid composition of plant leaves. The full nucleotide sequence of the rRNA gene cluster and partial sequence of the dinitrogenase reductase (nifH gene of Nostoc PTV were deposited to GenBank (JQ259185.1, JQ259186.1. Comparison of these gene sequences of Nostoc PTV with all sequences present at the GenBank shows that this cyanobacterial strain does not have 100% identity with any organisms investigated previously. Phylogenetic analysis showed that this cyanobacterium clustered with high credibility values with Nostoc muscorum.

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

KAUST Repository

Narita, Yuko; Zhang, Lei; Kimura, Zen-ichiro; Ali, Muhammad; Fujii, Takao; Okabe, Satoshi

2017-01-01

Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium ‘ Candidatus Brocadia sapporoensis’

KAUST Repository

Narita, Yuko

2017-08-18

Anaerobic ammonium-oxidation (anammox) is recognized as an important microbial process in the global nitrogen cycle and wastewater treatment. In this study, we successfully enriched a novel anammox bacterium affiliated with the genus ‘Candidatus Brocadia’ with high purity (>90%) in a membrane bioreactor (MBR). The enriched bacterium was distantly related to the hitherto characterized ‘Ca. Brocadia fulgida’ and ‘Ca. Brocadia sinica’ with 96% and 93% of 16S ribosomal RNA gene sequence identity, respectively. The bacterium exhibited the common structural features of anammox bacteria and the production of hydrazine in the presence of hydroxylamine under anoxic conditions. The temperature range of anammox activity was 20 − 45°C with a maximum activity at 37°C. The maximum specific growth rate (μmax) was determined to be 0.0082h−1 at 37°C, corresponding to a doubling time of 3.5 days. The half-saturation constant (KS) for nitrite was 5±2.5μM. The anammox activity was inhibited by nitrite with 11.6mM representing the 50% inhibitory concentration (IC50) but no significant inhibition was observed in the presence of formate and acetate. The major respiratory quinone was identified to be menaquinone-7 (MK-7). Comparative genome analysis revealed that the anammox bacterium enriched in present study shared nearly half of genes with ‘Ca. Brocadia sinica’ and ‘Ca. Brocadia fulgida’. The bacterium enriched in this study showed all known physiological characteristics of anammox bacteria and can be distinguished from the close relatives by its rRNA gene sequences. Therefore, we proposed the name ‘Ca. Brocadia sapporoensis’ sp. nov.

The nitrogen cycle.

Science.gov (United States)

Stein, Lisa Y; Klotz, Martin G

2016-02-08

Nitrogen is the fourth most abundant element in cellular biomass, and it comprises the majority of Earth's atmosphere. The interchange between inert dinitrogen gas (N2) in the extant atmosphere and 'reactive nitrogen' (those nitrogen compounds that support, or are products of, cellular metabolism and growth) is entirely controlled by microbial activities. This was not the case, however, in the primordial atmosphere, when abiotic reactions likely played a significant role in the inter-transformation of nitrogen oxides. Although such abiotic reactions are still important, the extant nitrogen cycle is driven by reductive fixation of dinitrogen and an enzyme inventory that facilitates dinitrogen-producing reactions. Prior to the advent of the Haber-Bosch process (the industrial fixation of N2 into ammonia, NH3) in 1909, nearly all of the reactive nitrogen in the biosphere was generated and recycled by microorganisms. Although the Haber-Bosch process more than quadrupled the productivity of agricultural crops, chemical fertilizers and other anthropogenic sources of fixed nitrogen now far exceed natural contributions, leading to unprecedented environmental degradation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nutrient and organic matter inputs to Hawaiian anchialine ponds: influences of n-fixing and non-n-fixing trees

Science.gov (United States)

Kehauwealani K. Nelson-Kaula; Rebecca Ostertag; R. Flint Hughes; Bruce D. Dudley

2016-01-01

Invasive nitrogen-fixing plants often increase energy and nutrient inputs to both terrestrial and aquatic ecosystems via litterfall, and these effects may be more pronounced in areas lacking native N2-fixers. We examined organic matter and nutrient inputs to and around anchialine ponds...

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

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Yunlong Yang

Full Text Available ABSTRACT Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.

Photosynthetic and nitrogen fixation capability in several soybean mutant lines

International Nuclear Information System (INIS)

Gandanegara, S.; Hendratno, K.

1987-01-01

Photosynthetic and nitrogen fixation capability in several soybean mutant lines. A greenhouse experiment has been carried out to study photosynthetic and nitrogen fixation capability of five mutant lines and two soybean varieties. An amount of 330 uCi of 14 CO 2 was fed to the plants including of the non-fixing reference crop (Chippewa non-nodulating isoline). Nitrogen fixation measurements was carried out using 15 N isotope dilution technique according to A-value concept. Results showed that beside variety/mutant lines, plant growth also has important role in photosynthetic and N fixing capability. Better growth and a higher photosynthetic capability in Orba, mutant lines nos. 63 and 65 resulted in a greater amount of N 2 fixed (mg N/plant) than other mutant lines. (author). 12 refs.; 5 figs

Symbiotic nitrogen-fixing bacterial populations trapped from soils under agroforestry systems in the Western Amazon

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Paula Marcela Duque Jaramillo

2013-12-01

Full Text Available Cowpea (Vigna unguiculata is an important grain-producing legume that can forego nitrogen fertilization by establishing an efficient symbiosis with nitrogen-fixing bacteria. Although inoculating strains have already been selected for this species, little is known about the genotypic and symbiotic diversity of native rhizobia. Recently, Bradyrhizobium has been shown to be the genus most frequently trapped by cowpea in agricultural soils of the Amazon region. We investigated the genetic and symbiotic diversity of 148 bacterial strains with different phenotypic and cultural properties isolated from the nodules of the trap species cowpea, which was inoculated with samples from soils under agroforestry systems from the western Amazon. Sixty non-nodulating strains indicated a high frequency of endophytic strains in the nodules. The 88 authenticated strains had varying symbiotic efficiency. The SPAD (Soil Plant Analysis Development index (indirect measurement of chlorophyll content was more efficient at evaluating the contribution of symbiotic N2-fixation than shoot dry matter under axenic conditions. Cowpea-nodulating bacteria exhibited a high level of genetic diversity, with 68 genotypes identified by BOX-PCR. Sequencing of the 16S rRNA gene showed a predominance of the genus Bradyrhizobium, which accounted for 70 % of all strains sequenced. Other genera identified were Rhizobium, Ochrobactrum, Paenibacillus, Bosea, Bacillus, Enterobacter, and Stenotrophomonas. These results support the promiscuity of cowpea and demonstrate the high genetic and symbiotic diversity of rhizobia in soils under agroforestry systems, with some strains exhibiting potential for use as inoculants. The predominance of Bradyrhizobium in land uses with different plant communities and soil characteristics reflects the adaptation of this genus to the Amazon region.

Environmental factors influencing milk urea nitrogen in South African ...

African Journals Online (AJOL)

p2492989

following fixed effects model, in matrix notation, was used for the ANOVA: .... Estimation of genetic parameters for milk urea nitrogen and its ... urea nitrogen concentration: Heritability and genetic correlations with reproductive performance and.

Fixed-nitrogen loss associated with sinking zooplankton carcasses in a coastal oxygen minimum zone (Golfo Dulce, Costa Rica)

DEFF Research Database (Denmark)

Stief, Peter; Lundgaard, Ann Sofie Birch; Morales Ramirez, Alvaro

2017-01-01

Oxygen minimum zones (OMZs) in the ocean are of key importance for pelagic fixed-nitrogen loss (N-loss) through microbial denitrification and anaerobic ammonium oxidation (anammox). Recent studies document that zooplankton is surprisingly abundant in and around OMZs and that the microbial community...... associated with carcasses of a large copepod species mediates denitrification. Here, we investigate the complex N-cycling associated with sinking zooplankton carcasses exposed to the steep O2 gradient in a coastal OMZ (Golfo Dulce, Costa Rica). 15N-stable-isotope enrichment experiments revealed...... that the carcasses of abundant copepods and ostracods provide anoxic microbial hotspots in the pelagic zone by hosting intense anaerobic N-cycle activities even in the presence of ambient O2. Carcass-associated anaerobic N-cycling was clearly dominated by dissimilatory nitrate reduction to ammonium (DNRA) at up...

Journal of Biosciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

C. equisetifolia fixes atmospheric nitrogen through a symbiotic relationship with Frankia, a soil bacterium of the actinobacteria group. The roots of C. equisetifolia produce ... As the vegetative propagation method uses inert material (vermiculite) for rooting there is no chance for Frankia association. Therefore after planting of ...

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

KAUST Repository

Wang, Yong

2016-07-01

Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

Nitrogen efficiency of Dutch dairy farms : A shadow cost system approach

NARCIS (Netherlands)

Reinhard, S.; Thijssen, G.J.

2000-01-01

In this paper we analyse the cost efficiency and nitrogen efficiency of an unbalanced panel of Dutch dairy farms. Nitrogen efficiency is defined as the ratio of minimal to observed use of nitrogen (N-containing inputs), conditional on output and quasi-fixed inputs. Nitrogen efficiency is computed in

Achieve efficient nitrogen removal from real sewage in a plug-flow integrated fixed-film activated sludge (IFAS) reactor via partial nitritation/anammox pathway.

Science.gov (United States)

Yang, Yandong; Zhang, Liang; Cheng, Jun; Zhang, Shujun; Li, Baikun; Peng, Yongzhen

2017-09-01

This study tested the feasibility of plug-flow integrated fixed-film activated sludge (IFAS) reactor in applying sewage partial nitritation/anammox (PN/A) process. The IFAS reactor was fed with real pre-treated sewage (C/N ratio=1.3) and operated for 200days. High nitrogen removal efficiency of 82% was achieved with nitrogen removal rates of 0.097±0.019kgN/(m 3 ·d). Therefore, plug-flow IFAS reactor could be an alternative to applying sewage PN/A process. Besides, it was found that the stability of sewage PN/A process was significantly affected by residual ammonium. Nitrate accumulated in effluent and PN/A performance deteriorated when residual ammonium was below 1mg/L. On the contrary, long-term stable PN/A operation was achieved when residual ammonium was over 3mg/L. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of free nitrogen fixing bacteria of the genus Azotobacter in organic vegetable-grown Colombian soils

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Diego Javier Jiménez

2011-09-01

Full Text Available With the purpose of isolating and characterizing free nitrogen fixing bacteria (FNFB of the genus Azotobacter, soil samples were collected randomly from different vegetable organic cultures with neutral pH in different zones of Boyacá-Colombia. Isolations were done in selective free nitrogen Ashby-Sucrose agar obtaining a recovery of 40%. Twenty four isolates were evaluated for colony and cellular morphology, pigment production and metabolic activities. Molecular characterization was carried out using amplified ribosomal DNA restriction analysis (ARDRA. After digestion of 16S rDNA Y1-Y3 PCR products (1487pb with AluI, HpaII and RsaI endonucleases, a polymorphism of 16% was obtained. Cluster analysis showed three main groups based on DNA fingerprints. Comparison between ribotypes generated by isolates and in silico restriction of 16S rDNA partial sequences with same restriction enzymes was done with Gen Workbench v.2.2.4 software. Nevertheless, Y1-Y2 PCR products were analysed using BLASTn. Isolate C5T from tomato (Lycopersicon esculentum grown soils presented the same in silico restriction patterns with A. chroococcum (AY353708 and 99% of similarity with the same sequence. Isolate C5CO from cauliflower (Brassica oleracea var. botrytis grown soils showed black pigmentation in Ashby-Benzoate agar and high similarity (91% with A. nigricans (AB175651 sequence. In this work we demonstrated the utility of molecular techniques and bioinformatics tools as a support to conventional techniques in characterization of the genus Azotobacter from vegetable-grown soils.

Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense

Science.gov (United States)

Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J.; Hirel, Bertrand

2017-01-01

Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

Metabolic profiling of two maize (Zea mays L. inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense.

Directory of Open Access Journals (Sweden)

Liziane Cristina Brusamarello-Santos

Full Text Available Maize roots can be colonized by free-living atmospheric nitrogen (N2-fixing bacteria (diazotrophs. However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2, already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+. The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts

Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense.

Science.gov (United States)

Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J; Hirel, Bertrand

2017-01-01

Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation RID B-8834-2011

DEFF Research Database (Denmark)

Kuypers, MMM; Lavik, G.; Woebken, D.

2005-01-01

) and is commonly attributed to denitrification (reduction of nitrate to N-2 by heterotrophic bacteria). Here, we show that instead, the anammox process (the anaerobic oxidation of ammonium by nitrite to yield N-2) is mainly responsible for nitrogen loss in the OMZ waters of one of the most productive regions......In many oceanic regions, growth of phytoplankton is nitrogen-limited because fixation of N-2 cannot make up for the removal of fixed inorganic nitrogen (NH4+, NO2-, and NO3-) by anaerobic microbial processes. Globally, 30-50% of the total nitrogen loss occurs in oxygen-minimum zones (OMZs...... that anammox bacteria are responsible for massive losses of fixed nitrogen. We have identified and directly linked anammox bacteria to the removal of fixed inorganic nitrogen in the OMZ waters of an open-ocean setting. We hypothesize that anammox could also be responsible for substantial nitrogen loss from...

Interconnection of nitrogen fixers and iron in the Pacific Ocean: Theory and numerical simulations

OpenAIRE

Dutkiewicz, S.; Ward, B. A.; Monteiro, F.; Follows, M. J.

2012-01-01

We examine the interplay between iron supply, iron concentrations and phytoplankton communities in the Pacific Ocean. We present a theoretical framework which considers the competition for iron and nitrogen resources between phytoplankton to explain where nitrogen fixing autotrophs (diazotrophs, which require higher iron quotas, and have slower maximum growth) can co-exist with other phytoplankton. The framework also indicates that iron and fixed nitrogen concentrations can be strongly contro...

Effect of nitrogen on cellular production and release of the neurotoxin anatoxin-a in a nitrogen-fixing cyanobacterium

Directory of Open Access Journals (Sweden)

Alexis eGagnon

2012-06-01

Full Text Available Anatoxin-a (ANTX is a neurotoxin produced by several freshwater cyanobacteria and implicated in lethal poisonings of domesticated animals and wildlife. The factors leading to its production in nature and in culture are not well understood. Resource availability may influence its cellular production as suggested by the carbon-nutrient hypothesis, which links the amount of secondary metabolites produced by plants or microbes to the relative abundance of nutrients. We tested the effects of nitrogen supply on ANTX production and release in a toxic strain of the cyanobacterium Aphanizomenon issatschenkoi (Nostocales. We hypothesized that nitrogen deficiency might constrain the production of ANTX. However, the total concentration and more significantly the cellular content of anatoxin-a peaked (max. 146 µg/L and 1683 µg•g-1 dry weight at intermediate levels of nitrogen supply when N-deficiency was evident based on phycocyanin to chlorophyll a and carbon to nitrogen ratios. The results suggest that the cellular production of anatoxin-a may be stimulated by moderate nutrient stress as described recently for another cyanotoxin (microcystin.

Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.

Science.gov (United States)

Martínez-Aguilar, Lourdes; Salazar-Salazar, Corelly; Méndez, Rafael Díaz; Caballero-Mellado, Jesús; Hirsch, Ann M; Vásquez-Murrieta, María Soledad; Estrada-de los Santos, Paulina

2013-12-01

During a survey of Burkholderia species with potential use in agrobiotechnology, a group of 12 strains was isolated from the rhizosphere and rhizoplane of tomato plants growing in Mexico (Nepantla, Mexico State). A phylogenetic analysis of 16S rRNA gene sequences showed that the strains are related to Burkholderia kururiensis and Burkholderia mimosarum (97.4 and 97.1 %, respectively). However, they induced effective nitrogen-fixing nodules on roots of Phaseolus vulgaris. Based on polyphasic taxonomy, the group of strains represents a novel species for which the name Burkholderia caballeronis sp. nov. is proposed. The type species is TNe-841(T) (= LMG 26416(T) = CIP 110324(T)).

A bacterium that can grow by using arsenic instead of phosphorus

Energy Technology Data Exchange (ETDEWEB)

Wolfe-Simon, F; Blum, J S; Kulp, T R; Gordon, G W; Hoeft, S E; Pett-Ridge, J; Stolz, J F; Webb, S M; Weber, P K; Davies, P W; Anbar, A D; Oremland, R S

2010-11-01

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus. Although these six elements make up nucleic acids, proteins and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, CA, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical significance.

A bacterium that can grow by using arsenic instead of phosphorus.

Science.gov (United States)

Wolfe-Simon, Felisa; Switzer Blum, Jodi; Kulp, Thomas R; Gordon, Gwyneth W; Hoeft, Shelley E; Pett-Ridge, Jennifer; Stolz, John F; Webb, Samuel M; Weber, Peter K; Davies, Paul C W; Anbar, Ariel D; Oremland, Ronald S

2011-06-03

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

Effects of titanium dioxide nanoparticles on red clover and its rhizobial symbiont

NARCIS (Netherlands)

Moll, Janine; Okupnik, Annette; Gogos, Alexander; Knauer, Katja; Bucheli, Thomas D.; Van Der Heijden, Marcel G A; Widmer, Franco

2016-01-01

Titanium dioxide nanoparticles (TiO2 NPs) are in consideration to be used in plant protection products. Before these products can be placed on the market, ecotoxicological tests have to be performed. In this study, the nitrogen fixing bacterium Rhizobium trifolii and red clover were exposed to two

Terrestrial nitrogen cycles: Some unanswered questions

Science.gov (United States)

Vitousek, P.

1984-01-01

Nitrogen is generally considered to be the element which most often limits the growth of plants in both natural and agricultural ecosystems. It regulates plant growth because photosynthetic rates are strongly dependent on the concentration of nitrogen in leaves, and because relatively large mounts of protein are required for cell division and growth. Yet nitrogen is abundant in the biosphere - the well-mixed pool in the atmosphere is considered inexhaustible compared to biotic demand, and the amount of already fixed organic nitrogen in soils far exceeds annual plant uptake in terrestrial ecosystems. In regions where natural vegetation is not nitrogen limited, continuous cultivation induces nitrogen deficiency. Nitrogen loss from cultivated lands is more rapid than that of other elements, and nitrogen fertilization is generally required to maintain crop yield under any continuous system. The pervasiveness of nitrogen deficiency in many natural and most managed sites is discussed.

New insights into the evolutionary history of biological nitrogen fixation

Directory of Open Access Journals (Sweden)

Eric eBoyd

2013-08-01

Full Text Available Nitrogenase, which catalyzes the ATP-dependent reduction of dinitrogen (N2 to ammonia (NH3, accounts for roughly half of the bioavailable nitrogen supporting extant life. The fundamental requirement for fixed forms of nitrogen for life on Earth, both at present and in the past, has led to broad and significant interest in the origin and evolution of this fundamental biological process. One key question is whether the limited availability of fixed nitrogen was a factor in life’s origin or whether there were ample sources of fixed nitrogen produced by abiotic processes or delivered through the weathering of bolide impact materials to support this early life. If the latter, the key questions become what were the characteristics of the environment that precipitated the evolution of this oxygen sensitive process, when did this occur, and how was its subsequent evolutionary history impacted by the advent of oxygenic photosynthesis and the rise of oxygen in the Earth’s biosphere. Since the availability of fixed sources of nitrogen capable of supporting early life is difficult to glean from the geologic record, there are limited means to get direct insights into these questions. Indirect insights, however, can be gained by deep phylogenetic studies of nitrogenase structural gene products and additional gene products involved in the biosynthesis of the complex metal-containing prosthetic groups associated with this enzyme complex. Insights gained from such studies, as reviewed herein, challenge traditional models for the evolution of biological nitrogen fixation and provide the basis for the development of new conceptual models that explain the stepwise evolution of this highly complex and life sustaining process.

Stimulation of nitrogen fixation in soddy-podzolic soils with fungi

Science.gov (United States)

Kurakov, A. V.; Prokhorov, I. S.; Kostina, N. V.; Makhova, E. G.; Sadykova, V. S.

2006-09-01

Stimulation of nitrogen fixation in soddy-podzolic soils is related to the hydrolytic activity of fungi decomposing plant polymers. It was found that the rate of nitrogen fixation upon the simultaneous inoculation of the strains of nitrogen-fixing bacteria Bacillus cereus var. mycoides and the cellulolytic fungus Trichoderma asperellum into a sterile soil enriched with cellulose or Jerusalem artichoke residues is two to four times higher than upon the inoculation of the strains of Bacillus cereus var. mycoides L1 only. The increase in the nitrogen fixation depended on the resistance of the substrates added into the soil to fungal hydrolysis. The biomass of the fungi decomposing plant polymers increased by two-four times. The nitrogen-fixing activity of the soil decreased when the growth of the fungi was inhibited with cycloheximide, which attested to a close correlation between the intensity of the nitrogen fixation and the decomposition of the plant polymers by fungi. The introduction of an antifungal antibiotic, together with starch or with plant residues, significantly (by 60-90%) decreased the rate of nitrogen fixation in the soll.

Enhancing biological nitrogen fixation

Energy Technology Data Exchange (ETDEWEB)

Danso, S.K.A.; Eskew, D.L. (Joint FAO/IAEA Div. of Isotope and Radiation Applications of Atomic Energy for Food and Agricultural Development, Vienna (Austria))

1984-06-01

Several co-ordinated research programmes (CRPs) conducted by the Soil Fertility, Irrigation and Crop Production Section of the Joint FAO/IAEA Division have concentrated on finding the most efficient way of applying nitrogen fertilizers to various crops, using nitrogen-15 (/sup 15/N) as a tracer. The findings of these studies have been adopted in many countries around the world, resulting in savings of nitrogen fertilizers worth many millions of dollars every year. More recently, the Section's CRPs have focused on enhancing the natural process of biological di-nitrogen fixation. The /sup 15/N isotope technique has proven to be very valuable in studies of the legume-Rhizobium symbiosis, allowing many more experiments than before to be done and yielding much new practical information. The Soils Section is now working to extend the use of the technique to other nitrogen-fixing symbioses.

Symbioses with nitrogen-fixing bacteria: nodulation and phylogenetic data across legume genera.

Science.gov (United States)

Afkhami, Michelle E; Luke Mahler, D; Burns, Jean H; Weber, Marjorie G; Wojciechowski, Martin F; Sprent, Janet; Strauss, Sharon Y

2018-02-01

How species interactions shape global biodiversity and influence diversification is a central - but also data-hungry - question in evolutionary ecology. Microbially based mutualisms are widespread and could cause diversification by ameliorating stress and thus allowing organisms to colonize and adapt to otherwise unsuitable habitats. Yet the role of these interactions in generating species diversity has received limited attention, especially across large taxonomic groups. In the massive angiosperm family Leguminosae, plants often associate with root-nodulating bacteria that ameliorate nutrient stress by fixing atmospheric nitrogen. These symbioses are ecologically-important interactions, influencing community assembly, diversity, and succession, contributing ~100-290 million tons of N annually to natural ecosystems, and enhancing growth of agronomically-important forage and crop plants worldwide. In recent work attempting to determine whether mutualism with N-fixing bacteria led to increased diversification across legumes, we were unable to definitively resolve the relationship between diversification and nodulation. We did, however, succeed in compiling a very large searchable, analysis-ready database of nodulation data for 749 legume genera (98% of Leguminosae genera; LPWG 2017), which, along with associated phylogenetic information, will provide a valuable resource for future work addressing this question and others. For each legume genus, we provide information about the species richness, frequency of nodulation, subfamily association, and topological correspondence with an additional data set of 100 phylogenetic trees curated for database compatibility. We found 386 legume genera were confirmed nodulators (i.e., all species examined for nodulation nodulated), 116 were non-nodulating, four were variable (i.e., containing both confirmed nodulators and confirmed non-nodulators), and 243 had not been examined for nodulation in published studies. Interestingly

QTL analysis of symbiotic nitrogen fixation in a black bean RIL population

Science.gov (United States)

Dry bean (Phaseolus vulgaris L) acquires nitrogen (N) from the atmosphere through symbiotic nitrogen fixation (SNF) but it has a low efficiency to fix nitrogen. The objective of this study is to map the genes controlling nitrogen fixation in common bean. A mapping population consisting of 122 recomb...

Molecular characterization of nitrogen-fixing bacteria isolated from brazilian agricultural plants at São Paulo state Caracterização molecular de bactérias fixadoras de nitrogênio isoladas de plantas brasileiras no estado de São Paulo

Directory of Open Access Journals (Sweden)

Érica. L. Reinhardt

2008-09-01

Full Text Available Fourteen strains of nitrogen-fixing bacteria were isolated from different agricultural plant species, including cassava, maize and sugarcane, using nitrogen-deprived selective isolation conditions. Ability to fix nitrogen was verified by the acetylene reduction assay. All potentially nitrogen-fixing strains tested showed positive hybridization signals with a nifH probe derived from Azospirillum brasilense. The strains were characterized by RAPD, ARDRA and 16S rDNA sequence analysis. RAPD analyses revealed 8 unique genotypes, the remaining 6 strains clustered into 3 RAPD groups, suggesting a clonal origin. ARDRA and 16S rDNA sequence analyses allowed the assignment of 13 strains to known groups of nitrogen-fixing bacteria, including organisms from the genera Azospirillum, Herbaspirillum, Pseudomonas and Enterobacteriaceae. Two strains were classified as Stenotrophomonas ssp. Molecular identification results from 16S rDNA analyses were also corroborated by morphological and biochemical data.Quatorze linhagens de bactérias fixadoras de nitrogênio foram isoladas de diferentes espécies de plantas, incluindo cassava, milho e cana-de-açúcar, usando condições seletivas desprovidas de nitrogênio. A capacidade de fixar nitrogênio foi verificada por ensaio de redução de acetileno. Todas as linhagens fixadoras de nitrogênio testadas apresentaram hibridização positiva com sonda de gene nifH derivada de Azospirillum brasilense. As linhagens foram caracterizadas por RAPD, ARDRA e sequenciamento do gene 16S rDNA. As análises de RAPD revelaram 8 genótipos, as 6 linhagens restantes foram agrupadas em 3 grupos de RAPD, sugerindo uma origem clonal. ARDRA e seqüências de 16S rDNA foram alocadas em 13 grupos conhecidos de bactérias fixadoras de nitrogênio, incluindo organismos dos gêneros Azospirillum, Herbaspirillum, Pseudomonas e Enterobacteriaceae. Duas linhagens foram classificadas como Stenotrophomonas ssp. Os resultados da identifica

Two isotopic methods for estimation of soybean nitrogen fixation

International Nuclear Information System (INIS)

Domenach, A.-M.; Chalamet, Alain; Pachiaudi, Christiane

1979-01-01

Measurements of rate of nitrogen symbiotic fixation by Soybean were determined by two different methods: variations in the natural abundance of 15 N in plants; use of 'A' value determined from labelled nitrogen applications to the soil. The results from both methods were in good agreement. Rates of fixed nitrogen were similar when using non nodulated Soybean or Ray-Grass as reference [fr

Two isotopic methods for estimation of soybean nitrogen fixation

Energy Technology Data Exchange (ETDEWEB)

Domenach, A M; Chalamet, A; Pachiaudi, C [Lyon-1 Univ., 69 - Villeurbanne (France)

1979-07-16

Measurements of rate of nitrogen symbiotic fixation by Soybean were determined by two different methods: variations in the natural abundance of /sup 15/N in plants; use of 'A' value determined from labelled nitrogen applications to the soil. The results from both methods were in good agreement. Rates of fixed nitrogen were similar when using non nodulated Soybean or Ray-Grass as reference.

Nitrogen Fixation in Cyanobacteria

NARCIS (Netherlands)

Stal, L.J.

2008-01-01

Cyanobacteria are oxygenic photosynthetic bacteria that are widespread in marine, freshwater and terrestrial environments and many of them are capable of fixing atmospheric nitrogen. But ironically, nitrogenase, the enzyme that is responsible for the reduction of N2, is extremely sensitive to O2.

The marine nitrogen cycle: recent discoveries, uncertainties and the potential relevance of climate change

NARCIS (Netherlands)

Voss, M.; Bange, H.W.; Dippner, J.W.; Middelburg, J.J.; Montoya, J.P.; Ward, B.

2013-01-01

The ocean’s nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation, assimilation, nitrification, anammox and denitrification. Dinitrogen is the most abundant form of nitrogen in sea water but only accessible by nitrogen-fixing microbes. Denitrification and

Isolation and Identification of Phosphate Solubilizing and Nitrogen Fixing Bacteria from Soil in Wamena Biological Garden, Jayawijaya, Papua

Directory of Open Access Journals (Sweden)

SRI WIDAWATI

2005-07-01

Full Text Available A study was undertaken to investigate the occurrence of phosphate solubilizing bacteria (PSB and nitrogen-fixing bacteria (NFB from soil samples of Wamena Biological Garden (WbiG. Eleven soil samples were collected randomly to estimate microbial population which used plate count method. The result showed that the microbial population ranged from 5.0x103-7.5x106 cells of bacteria/gram of soil and 5.0x103-1.5x107 cells of bacteria/gram of soil for PSB and NFB respectively. There were 17 isolates which have been identified till genus and species. The isolated microorganism were identified as PSB i.e. Bacillus sp., B. pantothenticus, B. megatherium, Flavobacterium sp., F. breve, Klebsiella sp., K. aerogenes, Chromobacterium lividum, Enterobacter alvei, E. agglomerans, Pseudomonas sp., Proteus sp. and as NFB i.e. Azotobacter sp., A. chroococcum, A. paspalii, Rhizobium sp., and Azospirillum sp.

Interactions among endophytic bacteria and fungi: effects and ...

Indian Academy of Sciences (India)

Madhu

co-cultures were then prepared. ... From the prepared solution, 0.25, 0.5, 0.75, 1.0 and 1.25 ml of aliquots were mixed .... pathogens and nematodes affecting strawberries; Soil Biol. Biochem. ... P Johnson-Green (Halifax: Atlantic Canada Society for. Microbial ... 1994 Infection of sugar cane by the nitrogen-fixing bacterium.

Transcriptome and metabolome responses of Shewanella oneidensis MR-1 to methyl orange under microaerophilic and aerobic conditions.

Science.gov (United States)

Cao, Xinhua; Qi, Yueling; Xu, Chen; Yang, Yuyi; Wang, Jun

2017-04-01

Shewanella oneidensis MR-1 degrades various azo dyes under microaerophilic and anaerobic conditions, but this process is inhibited under aerobic conditions. The mechanisms underlying azo dye biodegradation and inhibition remain unknown. Therefore, we investigated metabolic and transcriptional changes in strain MR-1, which was cultured under different conditions, to elucidate these mechanisms. At the transcriptional level, genes involved in certain metabolic processes, particularly the tricarboxylic acid (TCA) cycle, amino acid biodegradation, and the electron transfer system, were significantly altered (M ≧ 2, p > 0.8 ) in the presence of methyl orange (MO). Moreover, a high concentration of dissolved oxygen heavily impacted the expression levels of genes involved in fatty acid biodegradation. Metabolome analysis revealed significant alteration (p < 0.05) in the concentrations of nine metabolites when strain MR-1 was cultured under aerobic conditions; the majority of these metabolites were closely associated with amino acid metabolism and DNA replication. Accordingly, we propose a possible pathway for MO biodegradation and discuss the most likely causes of biodegradation inhibition due to dissolved oxygen.

[Regulatory genes of garden pea (Pisum sativum L.) controlling the development of nitrogen-fixing nodules and arbuscular mycorrhiza: a review of basic and applied aspects

DEFF Research Database (Denmark)

Borisov, A Iu; Vasil'chikov, A G; Voroshilova, V A

2007-01-01

The review sums up the long experience of the authors and other researchers in studying the genetic system of garden pea (Pisum sativum L.), which controls sthe development of nitrogen-fixing symbiosis and arbuscular mycorrhiza. A justified phenotypic classification of pea mutants is presented....... Progress in identifying and cloning symbiotic genes is adequately reflected. The feasibility of using double inoculation as a means of increasing the plant productivity is demonstrated, in which the potential of a tripartite symbiotic system (pea plants-root nodule bacteria-arbuscular mycorrhiza...

Moss-nitrogen input to boreal forest soils

DEFF Research Database (Denmark)

Rousk, Kathrin; Jones, Davey; DeLuca, Thomas

2014-01-01

Cyanobacteria living epiphytically on mosses in pristine, unpolluted areas fix substantial amounts of atmospheric nitrogen (N) and therefore represent a primary source of N in N-limited boreal forests. However, the fate of this N is unclear, in particular, how the fixed N2 enters the soil and bec...... and that transfer of N to the soil is not facilitated by fungal hyphae....

Estimation of nitrogen fixation in Saccharum spp. by 15N dilution method

International Nuclear Information System (INIS)

Singh, Mohan

1994-01-01

The amount of nitrogen fixed by bacteria associated with the roots of Saccharum spontaneum, S. sinense, and S. barberi has been estimated by 15 N-isotope dilution method using Sclerotachya fusca as a non-fixing control. S. spontaneum produced highest shoot dry weight among the species tested but maximum nitrogen was accumulated by S. barberi. Highest dilution in the 15 N-enrichment was observed in S. spontaneum followed by S. sinense and S. barberi in comparison to the control plant of Sclerotchya fusca. S. spontaneum derived 60 per cent followed by S. sinense 54 per cent and S. barberi 35 per cent of their total nitrogen requirement through fixation of nitrogen by diazotrophic bacteria associated with their roots. (author). 11 refs., 2 tabs

Transport and partitioning of CO2 fixed by root nodules of ureide and amide producing legumes

International Nuclear Information System (INIS)

Vance, C.P.; Boylan, K.L.M.; Maxwell, C.A.; Heichel, G.H.; Hardman, L.L.

1985-01-01

Nodulated and denodulated roots of adzuki bean (Vigna angularis), soybean (Glycine max), and alfalfa (Medicago sativa) were exposed to 14 CO 2 to investigate the contribution of nodule CO 2 fixation to assimilation and transport of fixed nitrogen. The distribution of radioactivity in xylem sap and partitioning of carbon fixed by nodules to the whole plant were measured. Radioactivity in the xylem sap of nodulated soybean and adzuki bean was located primarily (70 to 87%) in the acid fraction while the basic (amino acid) fraction contained 10 to 22%. In contrast radioactivity in the xylem sap of nodulated alfalfa was primarily in amino acids with about 20% in organic acids. Total ureide concentration was 8.1, 4.7, and 0.0 micromoles per milliliter xylem sap for soybean, adzuki bean, and alfalfa, respectively. While the major nitrogen transport products in soybeans and adzuki beans are ureides, this class of metabolites contained less than 20% of the the total radioactivity. When nodules of plants were removed, radioactivity in xylem sap decreased by 90% or more. Pulse-chase experiments indicated that CO 2 fixed by nodules was rapidly transported to shoots and incorporated into acid stable constituents. The data are consistent with a role for nodule CO 2 fixation providing carbon for the assimilation and transport of fixed nitrogen in amide-based legumes. In contrast, CO 2 fixation by nodules of ureide transporting legumes appears to contribute little to assimilation and transport of fixed nitrogen. 19 references, 2 figures, 5 tables

Impacts of atmospheric anthropogenic nitrogen on the open ocean

NARCIS (Netherlands)

Duce, R.A.; LaRoche, J.; Altieri, K.; Arrigo, K.R.; Baker, A.R.; Capone, D.G.; Cornell, S.; Dentener, F.; Galloway, J.; Ganeshram, R.S.; Geider, R.J.; Jickells, T.; Kuypers, M.M.; Langlois, R.; Liss, P.S.; Liu, S.; Middelburg, J.J.; Moore, C.M.; Nickovic, S.; Oschlies, A.; Pedersen, T.; Prospero, J.; Schlitzer, R.; Seitzinger, S.; Sorensen, L.L.; Uematsu, M.; Ulloa, O.; Voss, M.; Ward, B.; Zamora, L.

2008-01-01

Increasing quantities of atmospheric anthropogenic fixed nitrogen entering the open ocean could account for up to about a third of the ocean's external (nonrecycled) nitrogen supply and up to 3% of the annual new marine biological production, 0.3 petagram of carbon per year. This input could account

An eddy-stimulated hotspot for fixed nitrogen-loss from the Peru oxygen minimum zone

Science.gov (United States)

Altabet, M. A.; Ryabenko, E.; Stramma, L.; Wallace, D. W. R.; Frank, M.; Grasse, P.; Lavik, G.

2012-12-01

Fixed nitrogen (N) loss to biogenic N2 in intense oceanic O2 minimum zones (OMZ) accounts for a large fraction of the global N sink and is an essential control on the ocean's N-budget. However, major uncertainties exist regarding microbial pathways as well as net impact on the magnitude of N-loss and the ocean's overall N-budget. Here we report the discovery of a N-loss hotspot in the Peru OMZ associated with a coastally trapped mesoscale eddy that is marked by an extreme N-deficit matched by biogenic N2 production, high NO2- levels, and the highest isotope enrichments observed so far in OMZ's for the residual NO3-. High sea surface chlorophyll in seaward flowing streamers provides evidence for offshore eddy transport of highly productive, inshore water. Resulting pulses in the downward flux of particles likely stimulated heterotrophic dissimilatory NO3- reduction and subsequent production of biogenic N2 within the OMZ. A shallower biogenic N2 maximum within the oxycline is likely a feature advected by the eddy streamer from the shelf. Eddy-associated temporal-spatial heterogeneity of N-loss, mediated by a local succession of microbial processes, may explain inconsistencies observed among prior studies. Similar transient enhancements of N-loss likely occur within all other major OMZ's exerting a major influence on global ocean N and N isotope budgets.

Ascorbate oxidase: the unexpected involvement of a 'wasteful enzyme' in the symbioses with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi.

Science.gov (United States)

Balestrini, Raffaella; Ott, Thomas; Güther, Mike; Bonfante, Paola; Udvardi, Michael K; De Tullio, Mario C

2012-10-01

Ascorbate oxidase (AO, EC 1.10.3.3) catalyzes the oxidation of ascorbate (AsA) to yield water. AO over-expressing plants are prone to ozone and salt stresses, whereas lower expression apparently confers resistance to unfavorable environmental conditions. Previous studies have suggested a role for AO as a regulator of oxygen content in photosynthetic tissues. For the first time we show here that the expression of a Lotus japonicus AO gene is induced in the symbiotic interaction with both nitrogen-fixing bacteria and arbuscular mycorrhizal (AM) fungi. In this framework, high AO expression is viewed as a possible strategy to down-regulate oxygen diffusion in root nodules, and a component of AM symbiosis. A general model of AO function in plants is discussed. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Is the distribution of nitrogen-fixing cyanobacteria in the oceans related to temperature?

NARCIS (Netherlands)

Stal, L.J.

2009-01-01

Approximately 50% of the global natural fixation of nitrogen occurs in the oceans supporting a considerable part of the new primary production. Virtually all nitrogen fixation in the ocean occurs in the tropics and subtropics where the surface water temperature is 25°C or higher. It is attributed

A novel type of DNA-binding protein interacts with a conserved sequence in an early nodulin ENOD12 promoter.

NARCIS (Netherlands)

Christiansen, H.; Hansen, A.C.; Vijn, I.; Pallisgaard, N.; Larsen, K.; Yang, W.C.; Bisseling, T.; Marcker, K.A.; Jensen, E.O.

1996-01-01

The pea genes PsENOD12A and PsENOD12B are expressed in the root hairs shortly after infection with the nitrogen-fixing bacterium Rhizobium leguminosarum bv. viciae or after application of purified Nod factors. A 199 bp promoter fragment of the PsENOD12B gene contains sufficient information for Nod

Nitrogen transformation under different dissolved oxygen levels by the anoxygenic phototrophic bacterium Marichromatium gracile.

Science.gov (United States)

Hong, Xuan; Chen, Zhongwei; Zhao, Chungui; Yang, Suping

2017-06-01

Marichromatium gracile: YL28 (M. gracile YL28) is an anoxygenic phototrophic bacterial strain that utilizes ammonia, nitrate, or nitrite as its sole nitrogen source during growth. In this study, we investigated the removal and transformation of ammonium, nitrate, and nitrite by M. gracile YL28 grown in a combinatorial culture system of sodium acetate-ammonium, sodium acetate-nitrate and sodium acetate-nitrite in response to different initial dissolved oxygen (DO) levels. In the sodium acetate-ammonium system under aerobic conditions (initial DO = 7.20-7.25 mg/L), we detected a continuous accumulation of nitrate and nitrite. However, under semi-anaerobic conditions (initial DO = 4.08-4.26 mg/L), we observed a temporary accumulation of nitrate and nitrite. Interestingly, under anaerobic conditions (initial DO = 0.36-0.67 mg/L), there was little accumulation of nitrate and nitrite, but an increase in nitrous oxide production. In the sodium acetate-nitrite system, nitrite levels declined slightly under aerobic conditions, and nitrite was completely removed under semi-anaerobic and anaerobic conditions. In addition, M. gracile YL28 was able to grow using nitrite as the sole nitrogen source in situations when nitrogen gas produced by denitrification was eliminated. Taken together, the data indicate that M. gracile YL28 performs simultaneous heterotrophic nitrification and denitrification at low-DO levels and uses nitrite as the sole nitrogen source for growth. Our study is the first to demonstrate that anoxygenic phototrophic bacteria perform heterotrophic ammonia-oxidization and denitrification under anaerobic conditions.

Long-Term Exposure of Agricultural Soil to Veterinary Antibiotics Changes the Population Structure of Symbiotic Nitrogen-Fixing Rhizobacteria Occupying Nodules of Soybeans (Glycine max).

Science.gov (United States)

Revellin, Cécile; Hartmann, Alain; Solanas, Sébastien; Topp, Edward

2018-05-01

Antibiotics are entrained in agricultural soil through the application of manures from medicated animals. In the present study, a series of small field plots was established in 1999 that receive annual spring applications of a mixture of tylosin, sulfamethazine, and chlortetracycline at concentrations ranging from 0.1 to 10 mg · kg -1 soil. These antibiotics are commonly used in commercial swine production. The field plots were cropped continuously for soybeans, and in 2012, after 14 annual antibiotic applications, the nodules from soybean roots were sampled and the occupying bradyrhizobia were characterized. Nodules and isolates were serotyped, and isolates were distinguished using 16S rRNA gene and 16S to 23S rRNA gene intergenic spacer region sequencing, multilocus sequence typing, and RSα fingerprinting. Treatment with the antibiotic mixture skewed the population of bradyrhizobia dominating the nodule occupancy, with a significantly larger proportion of Bradyrhizobium liaoningense organisms even at the lowest dose of 0.1 mg · kg -1 soil. Likewise, all doses of antibiotics altered the distribution of RSα fingerprint types. Bradyrhizobia were phenotypically evaluated for their sensitivity to the antibiotics, and there was no association between in situ treatment and a decreased sensitivity to the drugs. Overall, long-term exposure to the antibiotic mixture altered the composition of bradyrhizobial populations occupying nitrogen-fixing nodules, apparently through an indirect effect not associated with the sensitivity to the drugs. Further work evaluating agronomic impacts is warranted. IMPORTANCE Antibiotics are entrained in agricultural soil through the application of animal or human waste or by irrigation with reused wastewater. Soybeans obtain nitrogen through symbiotic nitrogen fixation. Here, we evaluated the impact of 14 annual exposures to antibiotics commonly used in swine production on the distribution of bradyrhizobia occupying nitrogen-fixing

Putative N₂-fixing heterotrophic bacteria associated with dinoflagellate-Cyanobacteria consortia in the low-nitrogen Indian Ocean

DEFF Research Database (Denmark)

Farnelid, H.; Tarangkoon, Woraporn; Hansen, Gert

2010-01-01

that the symbionts fix gaseous nitrogen (N2). Individual heterotrophic dinoflagellates containing cyanobacterial symbionts were isolated from the open Indian Ocean and off Western Australia, and characterized using light microscopy, transmission electron microscopy (TEM), and nitrogenase (nifH) gene amplification......, cloning, and sequencing. Cyanobacteria, heterotrophic bacteria and eukaryotic algae were recognized as symbionts of the heterotrophic dinoflagellates. nifH gene sequences were obtained from 23 of 37 (62%) specimens of dinoflagellates (Ornithocercus spp. and Amphisolenia spp.). Interestingly, only 2...... specimens contained cyanobacterial nifH sequences, while 21 specimens contained nifH genes related to heterotrophic bacteria. Of the 137 nifH sequences obtained 68% were most similar to Alpha-, Beta-, and Gammaproteobacteria, 8% clustered with anaerobic bacteria, and 5% were related to second alternative...

Higher survival drives the success of nitrogen-fixing trees through succession in Costa Rican rainforests.

Science.gov (United States)

Menge, Duncan N L; Chazdon, Robin L

2016-02-01

Trees capable of symbiotic nitrogen (N) fixation ('N fixers') are abundant in many tropical forests. In temperate forests, it is well known that N fixers specialize in early-successional niches, but in tropical forests, successional trends of N-fixing species are poorly understood. We used a long-term census study (1997-2013) of regenerating lowland wet tropical forests in Costa Rica to document successional patterns of N fixers vs non-fixers, and used an individual-based model to determine the demographic drivers of these trends. N fixers increased in relative basal area during succession. In the youngest forests, N fixers grew 2.5 times faster, recruited at a similar rate and were 15 times less likely to die as non-fixers. As succession proceeded, the growth and survival disparities decreased, whereas N fixer recruitment decreased relative to non-fixers. According to our individual-based model, high survival was the dominant driver of the increase in basal area of N fixers. Our data suggest that N fixers are successful throughout secondary succession in tropical rainforests of north-east Costa Rica, and that attempts to understand this success should focus on tree survival. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Transcriptional Profiling of Nitrogen Fixation in Azotobacter vinelandii▿†

Science.gov (United States)

Hamilton, Trinity L.; Ludwig, Marcus; Dixon, Ray; Boyd, Eric S.; Dos Santos, Patricia C.; Setubal, João C.; Bryant, Donald A.; Dean, Dennis R.; Peters, John W.

2011-01-01

Most biological nitrogen (N2) fixation results from the activity of a molybdenum-dependent nitrogenase, a complex iron-sulfur enzyme found associated with a diversity of bacteria and some methanogenic archaea. Azotobacter vinelandii, an obligate aerobe, fixes nitrogen via the oxygen-sensitive Mo nitrogenase but is also able to fix nitrogen through the activities of genetically distinct alternative forms of nitrogenase designated the Vnf and Anf systems when Mo is limiting. The Vnf system appears to replace Mo with V, and the Anf system is thought to contain Fe as the only transition metal within the respective active site metallocofactors. Prior genetic analyses suggest that a number of nif-encoded components are involved in the Vnf and Anf systems. Genome-wide transcription profiling of A. vinelandiicultured under nitrogen-fixing conditions under various metal amendments (e.g., Mo or V) revealed the discrete complement of genes associated with each nitrogenase system and the extent of cross talk between the systems. In addition, changes in transcript levels of genes not directly involved in N2fixation provided insight into the integration of central metabolic processes and the oxygen-sensitive process of N2fixation in this obligate aerobe. The results underscored significant differences between Mo-dependent and Mo-independent diazotrophic growth that highlight the significant advantages of diazotrophic growth in the presence of Mo. PMID:21724999

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria.

Directory of Open Access Journals (Sweden)

Lisa C Crossman

2008-07-01

Full Text Available This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10 are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

Isolating silkworm genomic DNA without liquid nitrogen suitable for ...

African Journals Online (AJOL)

Genomic DNA was isolated from posterior silk gland of silkworms, Antheraea assama. Absolute alcohol was used as tissue fixing solution instead of grinding in liquid nitrogen, which yielded high molecular weight DNA (>40 kb). Samples yielded similar amount of DNA when fixed in absolute alcohol (400 μmg/g of silk gland ...

Use of 15N methodology to assess biological nitrogen fixation

International Nuclear Information System (INIS)

Hardarson, G.

1990-01-01

One of the most important characteristics of legumes are their ability in symbiosis with Rhizobium bacteria to fix atmospheric nitrogen for growth. For proper management and a full realization of the benefits of this plant-microbial association, it is necessary to estimate how much nitrogen is fixed under different conditions in the field. It is only after this is known that various factors can be manipulated so as to increase the amount and proportion of N a plant derives from biological fixation. A suitable method for accurately measuring the amount of N crops derive from fixation is therefore an important requirement in any programme aimed at maximizing biological nitrogen fixation. There are several methods available to measure N 2 fixation (Bergersen, 1980) based on (1) increment in N yield and plant growth, (2) nitrogen balance (3) acetylene reduction and (4) the use of isotopes of N. Only isotopic methods will be illustrated here. 20 refs, 2 figs, 9 tabs

Quantification of Atmospheric N2 Fixed by Cowpea, Pigeonpea and ...

African Journals Online (AJOL)

at taking advantage of legumes to replenish soil nitrogen (N due to legumes' N2 fixation). Glasshouse pot ... In both cases, maize (Katumani variety) was the non- N2- fixing reference crop. ... Biological N2 fixation is affected by several factors,.

Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria.

Science.gov (United States)

Simonsen, Anna K; Han, Shery; Rekret, Phil; Rentschler, Christine S; Heath, Katy D; Stinchcombe, John R

2015-01-01

Fertilizer application is a common anthropogenic alteration to terrestrial systems. Increased nutrient input can impact soil microbial diversity or function directly through altered soil environments, or indirectly through plant-microbe feedbacks, with potentially important effects on ecologically-important plant-associated mutualists. We investigated the impacts of plant fertilizer, containing all common macro and micronutrients on symbiotic nitrogen-fixing bacteria (rhizobia), a group of bacteria that are important for plant productivity and ecosystem function. We collected rhizobia nodule isolates from natural field soil that was treated with slow-release plant fertilizer over a single growing season and compared phenotypic traits related to free-living growth and host partner quality in these isolates to those of rhizobia from unfertilized soils. Through a series of single inoculation assays in controlled glasshouse conditions, we found that isolates from fertilized field soil provided legume hosts with higher mutualistic benefits. Through growth assays on media containing variable plant fertilizer concentrations, we found that plant fertilizer was generally beneficial for rhizobia growth. Rhizobia isolated from fertilized field soil had higher growth rates in the presence of plant fertilizer compared to isolates from unfertilized field soil, indicating that plant fertilizer application favoured rhizobia isolates with higher abilities to utilize fertilizer for free-living growth. We found a positive correlation between growth responses to fertilizer and mutualism benefits among isolates from fertilized field soil, demonstrating that variable plant fertilizer induces context-dependent genetic correlations, potentially changing the evolutionary trajectory of either trait through increased trait dependencies. Our study shows that short-term application is sufficient to alter the composition of rhizobia isolates in the population or community, either directly

Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria

Directory of Open Access Journals (Sweden)

Anna K. Simonsen

2015-10-01

Full Text Available Fertilizer application is a common anthropogenic alteration to terrestrial systems. Increased nutrient input can impact soil microbial diversity or function directly through altered soil environments, or indirectly through plant-microbe feedbacks, with potentially important effects on ecologically-important plant-associated mutualists. We investigated the impacts of plant fertilizer, containing all common macro and micronutrients on symbiotic nitrogen-fixing bacteria (rhizobia, a group of bacteria that are important for plant productivity and ecosystem function. We collected rhizobia nodule isolates from natural field soil that was treated with slow-release plant fertilizer over a single growing season and compared phenotypic traits related to free-living growth and host partner quality in these isolates to those of rhizobia from unfertilized soils. Through a series of single inoculation assays in controlled glasshouse conditions, we found that isolates from fertilized field soil provided legume hosts with higher mutualistic benefits. Through growth assays on media containing variable plant fertilizer concentrations, we found that plant fertilizer was generally beneficial for rhizobia growth. Rhizobia isolated from fertilized field soil had higher growth rates in the presence of plant fertilizer compared to isolates from unfertilized field soil, indicating that plant fertilizer application favoured rhizobia isolates with higher abilities to utilize fertilizer for free-living growth. We found a positive correlation between growth responses to fertilizer and mutualism benefits among isolates from fertilized field soil, demonstrating that variable plant fertilizer induces context-dependent genetic correlations, potentially changing the evolutionary trajectory of either trait through increased trait dependencies. Our study shows that short-term application is sufficient to alter the composition of rhizobia isolates in the population or community

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24.

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Sang-Yeop Lee

Full Text Available Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs, including benzene, toluene, and xylene (BTX, as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX.

Proteogenomic Characterization of Monocyclic Aromatic Hydrocarbon Degradation Pathways in the Aniline-Degrading Bacterium Burkholderia sp. K24

Science.gov (United States)

Yun, Sung Ho; Choi, Chi-Won; Yi, Yoon-Sun; Kim, Jonghyun; Chung, Young-Ho; Park, Edmond Changkyun; Kim, Seung Il

2016-01-01

Burkholderia sp. K24, formerly known as Acinetobacter lwoffii K24, is a soil bacterium capable of utilizing aniline as its sole carbon and nitrogen source. Genomic sequence analysis revealed that this bacterium possesses putative gene clusters for biodegradation of various monocyclic aromatic hydrocarbons (MAHs), including benzene, toluene, and xylene (BTX), as well as aniline. We verified the proposed MAH biodegradation pathways by dioxygenase activity assays, RT-PCR, and LC/MS-based quantitative proteomic analyses. This proteogenomic approach revealed four independent degradation pathways, all converging into the citric acid cycle. Aniline and p-hydroxybenzoate degradation pathways converged into the β-ketoadipate pathway. Benzoate and toluene were degraded through the benzoyl-CoA degradation pathway. The xylene isomers, i.e., o-, m-, and p-xylene, were degraded via the extradiol cleavage pathways. Salicylate was degraded through the gentisate degradation pathway. Our results show that Burkholderia sp. K24 possesses versatile biodegradation pathways, which may be employed for efficient bioremediation of aniline and BTX. PMID:27124467

Molecular identification of phosphate solubilizing bacterium ...

African Journals Online (AJOL)

A phosphate solubilizing bacterium was isolated from the rhizosphere soil of upland rice and identified by 16S rRNA gene sequencing. The gene sequence showed 99% homology with Alcaligenes faecalis. Based on the gene sequence homology, it was identified as A. faecalis. Interaction effect of this bacterium on growth ...

Microaerophilic conditions permit to mimic in vitro events occurring during in vivo Helicobacter pylori infection and to identify Rho/Ras-associated proteins in cellular signaling.

Science.gov (United States)

Cottet, Sandra; Corthésy-Theulaz, Irène; Spertini, François; Corthésy, Blaise

2002-09-13

Molecular dissection of the mechanisms underlying Helicobacter pylori infection suffers from the lack of in vitro systems mimicking in vivo observations. A system was developed whereby human epithelial cells (Caco-2) grown as polarized monolayers and bacteria can communicate with each other under culture conditions optimal for each partner. Caco-2 cells grown on filter supports were inserted in a vertical position into diffusion chambers equilibrated with air and 5% CO(2) at their basolateral surface (aerophilic conditions) and 5% CO(2), 5% O(2), 90% N(2) (microaerophilic conditions) in the apical compartment. Remarkably, the epithelial polarized layer was stable under these asymmetric culture conditions for at least 24 h, and the presence of Caco-2 cells was necessary to maintain H. pylori growth. In contrast to previous studies conducted with non-polarized Caco-2 cells and other cell lines kept under aerophilic conditions, we found H. pylori-dependent stimulation of cytokine secretion (MCP-1 (monocyte chemoattractant protein-1), GRO-alpha (growth-regulated oncogene-alpha), RANTES (regulated on activation normal T cell expressed and secreted)). This correlated with nuclear translocation of NF-kappaB p50 and p65 subunits. Tyrosine phosphorylation of nine cellular proteins was induced or enhanced; we identified p120(RasGAP), p190(RhoGAP), p62dok (downstream of tyrosine kinases), and cortactin as H. pylori-inducible targets. Moreover, reduction of H. pylori urease expression was observed in adherent bacteria as compared with bacteria in suspension. In addition to mimicking several observations seen in the inflamed gastric mucosa, the novel in vitro system was allowed to underscore complex cellular events not seen in classical in vitro analyses of microaerophilic bacteria-epithelial cell cross-talk.

Buckminsterfullerenes: a non-metal system for nitrogen fixation.

Science.gov (United States)

Nishibayashi, Yoshiaki; Saito, Makoto; Uemura, Sakae; Takekuma, Shin-Ichi; Takekuma, Hideko; Yoshida, Zen-Ichi

2004-03-18

In all nitrogen-fixation processes known so far--including the industrial Haber-Bosch process, biological fixation by nitrogenase enzymes and previously described homogeneous synthetic systems--the direct transformation of the stable, inert dinitrogen molecule (N2) into ammonia (NH3) relies on the powerful redox properties of metals. Here we show that nitrogen fixation can also be achieved by using a non-metallic buckminsterfullerene (C60) molecule, in the form of a water-soluble C60:gamma-cyclodextrin (1:2) complex, and light under nitrogen at atmospheric pressure. This metal-free system efficiently fixes nitrogen under mild conditions by making use of the redox properties of the fullerene derivative.

Removal of hard COD, nitrogenous compounds and phenols from a ...

African Journals Online (AJOL)

The objective of this study was to identify the factors affecting the suspended and fixed biomass in the removal of hard COD, nitrogenous compounds and phenols from a coal gasification wastewater (CGWW) stream using a hybrid fixed-film bioreactor (H-FFBR) process under real-time plant operational conditions and ...

Response of free-living nitrogen-fixing microorganisms to land use change in the Amazon rainforest.

Science.gov (United States)

Mirza, Babur S; Potisap, Chotima; Nüsslein, Klaus; Bohannan, Brendan J M; Rodrigues, Jorge L M

2014-01-01

The Amazon rainforest, the largest equatorial forest in the world, is being cleared for pasture and agricultural use at alarming rates. Tropical deforestation is known to cause alterations in microbial communities at taxonomic and phylogenetic levels, but it is unclear whether microbial functional groups are altered. We asked whether free-living nitrogen-fixing microorganisms (diazotrophs) respond to deforestation in the Amazon rainforest, using analysis of the marker gene nifH. Clone libraries were generated from soil samples collected from a primary forest, a 5-year-old pasture originally converted from primary forest, and a secondary forest established after pasture abandonment. Although diazotroph richness did not significantly change among the three plots, diazotroph community composition was altered with forest-to-pasture conversion, and phylogenetic similarity was higher among pasture communities than among those in forests. There was also 10-fold increase in nifH gene abundance following conversion from primary forest to pasture. Three environmental factors were associated with the observed changes: soil acidity, total N concentration, and C/N ratio. Our results suggest a partial restoration to initial levels of abundance and community structure of diazotrophs following pasture abandonment, with primary and secondary forests sharing similar communities. We postulate that the response of diazotrophs to land use change is a direct consequence of changes in plant communities, particularly the higher N demand of pasture plant communities for supporting aboveground plant growth.

Co-inoculation of arbusculr mycorrhizae and nitrogen fixing bacteria enhance alfalfa yield under saline conditions

International Nuclear Information System (INIS)

Zhu, R.; Tang, F.; Liu, F.; Chen, J.

2016-01-01

The study was to investigate the effects of combined inoculation of Glomus mosseae (arbusculr mycorrhizae fungi, AMF) and Sinorhizobium meliloti (nitrogen-fixing bacteria, i.e., an Rhizobium meliloti, RM) on yield, nutrient contents, nodulation and mycorrhizal colonization of different alfalfa cultivars under saline conditions. An experiment was conducted to test the efficacy of AMF and RM inoculation in development of salt tolerance in alfalfa cultivars (Zhaodong, Nongjing and Longmu) under different salinity levels (0, 60, 120 and 180 mM NaCl). We found that under non stress condition, double inoculation of alfalfa with rhizobium and AM increased the alfalfa yield, nodule weight and number, as well as shoot proline contents, the most when plants were double inoculated followed by AM and rhizobium inoculation, respectively. Whereas under salinity condition, double inoculation of alfalfa with rhizobium and AM increased alfalfa yield, mycorrhizal infection, nodule weight and number as well as increased in shoot proline content, the most followed by AM and rhizobium inoculation, respectively. The Results suggest that growth of alfalfa may be improved by combined inoculation of alfalfa with AM and rhizobium under salt and non-stress conditions. Alleviation of alfalfa growth under saline condition was perhaps due to an increase in mycorrhizal infection and nodule weight and number as well as an increased in shoot proline content by dual inoculation. (author)

Isolation and characterization of a bacterium which utilizes polyester polyurethane as a sole carbon and nitrogen source.

Science.gov (United States)

Nakajima-Kambe, T; Onuma, F; Kimpara, N; Nakahara, T

1995-06-01

Various soil samples were screened for the presence of microorganisms which have the ability to degrade polyurethane compounds. Two strains with good polyurethane degrading activity were isolated. The more active strain was tentatively identified as Comamonas acidovorans. This strain could utilize polyester-type polyurethanes but not the polyether-type polyurethanes as sole carbon and nitrogen sources. Adipic acid and diethylene glycol were probably the main degradation products when polyurethane was supplied as a sole carbon and nitrogen source. When ammonium nitrate was used as nitrogen source, only diethylene glycol was detected after growth on polyurethane.

Regulation of Azorhizobium caulinodans ORS571 nitrogen fixation (NIF/FIX) genes

NARCIS (Netherlands)

Stigter, J.

1994-01-01

Biological nitrogen fixation is the microbial process by which atmospheric dinitrogen (N ₂ ) is reduced to ammonia. In all microbes studied, dinitrogen reduction is catalyzed by a highly conserved enzyme complex, called nitrogenase.

Understanding the contribution of biofilm in an integrated fixed-film-activated sludge system (IFAS) designed for nitrogen removal.

Science.gov (United States)

Moretti, P; Choubert, J M; Canler, J P; Petrimaux, O; Buffiere, P; Lessard, P

2015-01-01

The objective of this study is to improve knowledge on the integrated fixed-film-activated sludge (IFAS) system designed for nitrogen removal. Biofilm growth and its contribution to nitrification were monitored under various operating conditions in a semi-industrial pilot-scale plant. Nitrification rates were observed in biofilms developed on free-floating media and in activated sludge operated under a low sludge retention time (4 days) and at an ammonia loading rate of 45-70 gNH4-N/kgMLVSS/d. Operational conditions, i.e. oxygen concentration, redox potential, suspended solids concentration, ammonium and nitrates, were monitored continuously in the reactors. High removal efficiencies were observed for carbon and ammonium at high-loading rate. The contribution of biofilm to nitrification was determined as 40-70% of total NOx-N production under the operating conditions tested. Optimal conditions to optimize process compacity were determined. The tested configuration responds especially well to winter and summer nitrification conditions. These results help provide a deeper understanding of how autotrophic biomass evolves through environmental and operational conditions in IFAS systems.

Isolation and characterization of Burkholderia fungorum Gan-35 with the outstanding ammonia nitrogen-degrading ability from the tailings of rare-earth-element mines in southern Jiangxi, China.

Science.gov (United States)

Feng, Ai-Juan; Xiao, Xi; Ye, Cong-Cong; Xu, Xiao-Ming; Zhu, Qing; Yuan, Jian-Ping; Hong, Yue-Hui; Wang, Jiang-Hai

2017-12-01

The exploitation of rare-earth-element (REE) mines has resulted in severe ammonia nitrogen pollution and induced hazards to environments and human health. Screening microorganisms with the ammonia nitrogen-degrading ability provides a basis for bioremediation of ammonia nitrogen-polluted environments. In this study, a bacterium with the outstanding ammonia nitrogen-degrading capability was isolated from the tailings of REE mines in southern Jiangxi Province, China. This strain was identified as Burkholderia fungorum Gan-35 according to phenotypic and phylogenetic analyses. The optimal conditions for ammonia-nitrogen degradation by strain Gan-35 were determined as follows: pH value, 7.5; inoculum dose, 10%; incubation time, 44 h; temperature, 30 °C; and C/N ratio, 15:1. Strain Gan-35 degraded 68.6% of ammonia nitrogen under the optimized conditions. Nepeta cataria grew obviously better in the ammonia nitrogen-polluted soil with strain Gan-35 than that without inoculation, and the decrease in ammonia-nitrogen contents of the former was also more obvious than the latter. Besides, strain Gan-35 exhibited the tolerance to high salinities. In summary, strain Gan-35 harbors the ability of both ammonia-nitrogen degradation at high concentrations and promoting plant growth. This work has reported a Burkholderia strain with the ammonia nitrogen-degrading capability for the first time and is also the first study on the isolation of a bacterium with the ammonia nitrogen-degrading ability from the tailings of REE mines. The results are useful for developing an effective method for microbial remediation of the ammonia nitrogen-polluted tailings of REE mines.

Bacterium oxidizing carbon monoxide

Energy Technology Data Exchange (ETDEWEB)

Kistner, A

1953-01-01

Present-day knowledge of the microbiological oxidation of carbon monoxide is based on doubtful observations and imperfect experimental procedures. By making use of shake cultures in contact with gas mixtures containing high concentrations of CO and by employing liquid enrichment media with a low content of organic matter and solid media of the same composition with not more than 1.2% agar, it proved possible to isolate a co-oxidizing bacterium of the genus hydrogenomonas from sewage sludge. For the first time irrefutable proof has been given of the oxidation of carbon monoxide by a pure culture of a bacterium, both in growing cultures and in resting cell suspensions. 12 references.

Analyzing the contribution of climate change to long-term variations in sediment nitrogen sources for reservoirs/lakes

Energy Technology Data Exchange (ETDEWEB)

Xia, Xinghui, E-mail: xiaxh@bnu.edu.cn [School of Environment, Beijing Normal University, State Key Laboratory of Water Environment Simulation/Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing 100875 (China); Wu, Qiong; Zhu, Baotong; Zhao, Pujun [School of Environment, Beijing Normal University, State Key Laboratory of Water Environment Simulation/Key Laboratory of Water and Sediment Sciences of Ministry of Education, Beijing 100875 (China); Zhang, Shangwei [Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research — UFZ, Permoserstraße 15, Leipzig 04318 (Germany); Yang, Lingyan [Beijing Municipal Environmental Monitoring Center, Beijing 100048 (China)

2015-08-01

We applied a mixing model based on stable isotopic δ{sup 13}C, δ{sup 15}N, and C:N ratios to estimate the contributions of multiple sources to sediment nitrogen. We also developed a conceptual model describing and analyzing the impacts of climate change on nitrogen enrichment. These two models were conducted in Miyun Reservoir to analyze the contribution of climate change to the variations in sediment nitrogen sources based on two {sup 210}Pb and {sup 137}Cs dated sediment cores. The results showed that during the past 50 years, average contributions of soil and fertilizer, submerged macrophytes, N{sub 2}-fixing phytoplankton, and non-N{sub 2}-fixing phytoplankton were 40.7%, 40.3%, 11.8%, and 7.2%, respectively. In addition, total nitrogen (TN) contents in sediment showed significant increasing trends from 1960 to 2010, and sediment nitrogen of both submerged macrophytes and phytoplankton sources exhibited significant increasing trends during the past 50 years. In contrast, soil and fertilizer sources showed a significant decreasing trend from 1990 to 2010. According to the changing trend of N{sub 2}-fixing phytoplankton, changes of temperature and sunshine duration accounted for at least 43% of the trend in the sediment nitrogen enrichment over the past 50 years. Regression analysis of the climatic factors on nitrogen sources showed that the contributions of precipitation, temperature, and sunshine duration to the variations in sediment nitrogen sources ranged from 18.5% to 60.3%. The study demonstrates that the mixing model provides a robust method for calculating the contribution of multiple nitrogen sources in sediment, and this study also suggests that N{sub 2}-fixing phytoplankton could be regarded as an important response factor for assessing the impacts of climate change on nitrogen enrichment. - Highlights: • A mixing model was built to analyze sediment N sources of lakes/reservoirs. • Fertilizer/soil and macrophytes showed decreasing trends during

Analyzing the contribution of climate change to long-term variations in sediment nitrogen sources for reservoirs/lakes

International Nuclear Information System (INIS)

Xia, Xinghui; Wu, Qiong; Zhu, Baotong; Zhao, Pujun; Zhang, Shangwei; Yang, Lingyan

2015-01-01

We applied a mixing model based on stable isotopic δ 13 C, δ 15 N, and C:N ratios to estimate the contributions of multiple sources to sediment nitrogen. We also developed a conceptual model describing and analyzing the impacts of climate change on nitrogen enrichment. These two models were conducted in Miyun Reservoir to analyze the contribution of climate change to the variations in sediment nitrogen sources based on two 210 Pb and 137 Cs dated sediment cores. The results showed that during the past 50 years, average contributions of soil and fertilizer, submerged macrophytes, N 2 -fixing phytoplankton, and non-N 2 -fixing phytoplankton were 40.7%, 40.3%, 11.8%, and 7.2%, respectively. In addition, total nitrogen (TN) contents in sediment showed significant increasing trends from 1960 to 2010, and sediment nitrogen of both submerged macrophytes and phytoplankton sources exhibited significant increasing trends during the past 50 years. In contrast, soil and fertilizer sources showed a significant decreasing trend from 1990 to 2010. According to the changing trend of N 2 -fixing phytoplankton, changes of temperature and sunshine duration accounted for at least 43% of the trend in the sediment nitrogen enrichment over the past 50 years. Regression analysis of the climatic factors on nitrogen sources showed that the contributions of precipitation, temperature, and sunshine duration to the variations in sediment nitrogen sources ranged from 18.5% to 60.3%. The study demonstrates that the mixing model provides a robust method for calculating the contribution of multiple nitrogen sources in sediment, and this study also suggests that N 2 -fixing phytoplankton could be regarded as an important response factor for assessing the impacts of climate change on nitrogen enrichment. - Highlights: • A mixing model was built to analyze sediment N sources of lakes/reservoirs. • Fertilizer/soil and macrophytes showed decreasing trends during the past two decades. �

Effect of water and nitrogen additions on free-living nitrogen fixer populations in desert grass root zones.

Science.gov (United States)

Herman, R P; Provencio, K R; Torrez, R J; Seager, G M

1993-01-01

In this study we measured changes in population levels of free-living N2-fixing bacteria in the root zones of potted Bouteloua eriopoda and Sporobolus flexuosus plants as well as the photosynthetic indices of the plants in response to added nitrogen, added water, and added water plus nitrogen treatments. In addition, N2 fixer population changes in response to added carbon source and nitrogen were measured in plant-free soil columns. There were significant increases in the numbers of N2 fixers associated with both plant species in the water and the water plus nitrogen treatments. Both treatments increased the photosynthetic index, suggesting that plant exudates were driving N2 fixer population changes. Population increases were greatest in the water plus nitrogen treatments, indicating that added nitrogen was synergistic with added water and suggesting that nitrogen addition spared bacteria the metabolic cost of N2 fixation, allowing greater reproduction. Plant-free column studies demonstrated a synergistic carbon-nitrogen effect when carbon levels were limiting (low malate addition) but not when carbon was abundant (high malate), further supporting this hypothesis. The results of this study indicate the presence of N2 fixer populations which interact with plants and which may play a role in the nitrogen balance of desert grasslands. PMID:8215373

Nitrogen studies for achieving the whole-year harvest

International Nuclear Information System (INIS)

Boven, G.D.; Danso, K.A.

1987-01-01

The IAEA activity in solving the problems related to recovery of productivity of soils subjected to erosion in tropical regions using nitrogen-fixator plants which include pasture bean crops and trees, is considered. The IAEA activity covers development of appropriate methods of changing fixed nitrogen in perennial plants, determination of practical ways of increasing nitrogen fixation and development of reliable and high-productivity systems of bean-herb pastures. The main attention is paid to methods of farming and selection. Favourable effect of forest planting on recovery and preservation of soil productivity and important role of isotopic and nuclear methods (using 15 N) in care for trees and nitrogen fixation improvement are underlined

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

DEFF Research Database (Denmark)

Stief, P.

2013-01-01

(mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release...... enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide...... of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna...

An eddy-stimulated hotspot for fixed nitrogen-loss from the Peru oxygen minimum zone

Directory of Open Access Journals (Sweden)

M. A. Altabet

2012-12-01

Full Text Available Fixed nitrogen (N loss to biogenic N₂ in intense oceanic O₂ minimum zones (OMZ accounts for a large fraction of the global N sink and is an essential control on the ocean's N-budget. However, major uncertainties exist regarding microbial pathways as well as net impact on the magnitude of N-loss and the ocean's overall N-budget. Here we report the discovery of a N-loss hotspot in the Peru OMZ associated with a coastally trapped mesoscale eddy that is marked by an extreme N-deficit matched by biogenic N₂ production, high NO₂⁻ levels, and the highest isotope enrichments observed so far in OMZ's for the residual NO₃⁻. High sea surface chlorophyll in seaward flowing streamers provides evidence for offshore eddy transport of highly productive, inshore water. Resulting pulses in the downward flux of particles likely stimulated heterotrophic dissimilatory NO₃⁻ reduction and subsequent production of biogenic N₂ within the OMZ. A shallower biogenic N₂ maximum within the oxycline is likely a feature advected by the eddy streamer from the shelf. Eddy-associated temporal-spatial heterogeneity of N-loss, mediated by a local succession of microbial processes, may explain inconsistencies observed among prior studies. Similar transient enhancements of N-loss likely occur within all other major OMZ's exerting a major influence on global ocean N and N isotope budgets.

Nitrogen and Martian Habitability: Insights from Five Years of Curiosity Measurements

Science.gov (United States)

Stern, J. C.; Sutter, B.; Navarro-Gonzalez, R.; McKay, C.; Ming, D. W.; Mahaffy, P. R.; Archer, D., Jr.; Franz, H. B.; Freissinet, C.; Jackson, W. A.; Conrad, P. G.; Glavin, D. P.; Trainer, M. G.; Malespin, C.; McAdam, A.; Eigenbrode, J. L.; Teinturier, S.; Manning, C.

2017-12-01

The detection of "fixed" N on Mars in the form of nitrate by the Sample Analysis at Mars (SAM) instrument suite on the Mars Science Laboratory (MSL) Curiosity Rover [1] has major implications for martian habitability. "Follow the nitrogen" has been proposed as a strategy in the search for both extant and extinct life on Mars [e.g., 2]. Nitrogen is so crucial to life on Earth that life developed metabolic pathways to break the triple bond of N2 and "fix" atmospheric nitrogen to more biologically available molecules for use in proteins and informational polymers. Sequestration of nitrate in regolith has long been predicted to contribute to the removal of N from the martian atmosphere [e.g., 3], and our detections confirm that nitrogen fixation was occurring on ancient Mars. Detections of fixed nitrogen, particularly within the context of the habitable environment in Yellowknife Bay characterized by the MSL payload, are an important tool to assess whether life ever could have existed on ancient Mars. We present 5 years of analyses and interpretation of nitrate in solid martian drilled and scooped samples by SAM on MSL. Nitrate abundance reported by SAM in situ measurements ranges from non-detection to 681 ± 304 mg/kg [1,4] in the samples examined to date. The measured abundances are consistent with nitrogen fixation via impact generated thermal shock on ancient Mars and/or dry deposition from photochemistry of thermospheric NO. We review the integration of SAM data with terrestrial Mars analog work in order to better understand the timing of nitrogen fixation and mobility of nitrogen on Mars, and thus its availability to putative biology. In particular, the relationship between nitrate and other soluble salts, such as perchlorate, may help reveal the timing of nitrogen fixation and post-depositional behavior of nitrate on Mars [4]. Finally, we present a comparison of isotopic composition (δ15N) of nitrate with δ15N of atmospheric nitrogen (δ15N ≈ 574‰, [5

Thiol-based redox signaling in the nitrogen-fixing symbiosis

Directory of Open Access Journals (Sweden)

Pierre eFrendo

2013-09-01

Full Text Available In nitrogen poor soils legumes establish a symbiotic interaction with rhizobia that results in the formation of root nodules. These are unique plant organs where bacteria differentiate into bacteroids, which express the nitrogenase enzyme complex that reduces atmospheric N2 to ammonia. Nodule metabolism requires a tight control of the concentrations of reactive oxygen and nitrogen species (RONS so that they can perform useful signaling roles while avoiding nitro-oxidative damage. In nodules a thiol-dependent regulatory network that senses, transmits and responds to redox changes is starting to be elucidated. A combination of enzymatic, immunological, pharmacological and molecular analyses has allowed to conclude that glutathione and its legume-specific homolog, homoglutathione, are abundant in meristematic and infected cells, their spatio-temporally distribution is correlated with the corresponding (homoglutathione synthetase activities, and are crucial for nodule development and function. Glutathione is at high concentrations in the bacteroids and at moderate amounts in the mitochondria, cytosol and nuclei. Less information is available on other components of the network. The expression of multiple isoforms of glutathione peroxidases, peroxiredoxins, thioredoxins, glutaredoxins and NADPH-thioredoxin reductases has been detected in nodule cells using antibodies and proteomics. Peroxiredoxins and thioredoxins are essential to regulate and in some cases to detoxify RONS in nodules. Further research is necessary to clarify the regulation of the expression and activity of thiol redox-active proteins in response to abiotic, biotic and developmental cues, their interactions with downstream targets by disulfide-exchange reactions, and their participation in signaling cascades. The availability of mutants and transgenic lines will be crucial to facilitate systematic investigations into the function of the various proteins in the legume

Nitrogen research for perennial crops

International Nuclear Information System (INIS)

Bowen, G.D.; Danso, S.K.A.

1987-01-01

The article describes the role of trees in restoring and maintaining soil fertility. Cropping systems that include trees can provide the ecological framework within which food, fuelwood, and fibre production can be intergrated. The IAEA has been actively involved in studies on nitrogen-fixing pasture legumes and is ready to embark on similar studies of trees. 1 tab

The role of symbiotic nitrogen fixation in nitrogen availability, competition and plant invasion into the sagebrush steppe

Science.gov (United States)

Erin M. Goergen

2009-01-01

In the semi-arid sagebrush steppe of the Northeastern Sierra Nevada, resources are both spatially and temporally variable, arguably making resource availability a primary factor determining invasion success. N fixing plant species, primarily native legumes, are often relatively abundant in sagebrush steppe and can contribute to ecosystem nitrogen budgets. ...

Genome Sequence of Rhodoferax antarcticus ANT.BRT; A Psychrophilic Purple Nonsulfur Bacterium from an Antarctic Microbial Mat

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Jennifer M. Baker

2017-02-01

Full Text Available Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BRT, isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp of Rfx. antarcticus has a 59.1% guanine + cytosine (GC content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames that comprises about 5% of the total genetic content. Surprisingly, genes encoding light-harvesting complexes 1 and 3 (LH1 and LH3, but not light-harvesting complex 2 (LH2, were identified in the photosynthesis gene cluster of the Rfx. antarcticus genome, a feature that is unique among purple phototrophs. Consistent with physiological studies that showed a strong capacity for nitrogen fixation in Rfx. antarcticus, a nitrogen fixation gene cluster encoding a molybdenum-type nitrogenase was present, but no alternative nitrogenases were identified despite the cold-active phenotype of this phototroph. Genes encoding two forms of ribulose 1,5-bisphosphate carboxylase/oxygenase were present in the Rfx. antarcticus genome, a feature that likely provides autotrophic flexibility under varying environmental conditions. Lastly, genes for assembly of both type IV pili and flagella are present, with the latter showing an unusual degree of clustering. This report represents the first genomic analysis of a psychrophilic anoxygenic phototroph and provides a glimpse of the genetic basis for maintaining a phototrophic lifestyle in a permanently cold, yet highly variable, environment.

The marine nitrogen cycle: recent discoveries, uncertainties and the potential relevance of climate change

OpenAIRE

Voss, Maren; Bange, Hermann W.; Dippner, Joachim W.; Middelburg, Jack J.; Montoya, Joseph P.; Ward, Bess

2013-01-01

The ocean's nitrogen cycle is driven by complex microbial transformations, including nitrogen fixation, assimilation, nitrification, anammox and denitrification. Dinitrogen is the most abundant form of nitrogen in sea water but only accessible by nitrogen-fixing microbes. Denitrification and nitrification are both regulated by oxygen concentrations and potentially produce nitrous oxide (N2O), a climate-relevant atmospheric trace gas. The world's oceans, including the coastal areas and upwelli...

Use of 15N-isotope dilution for quantification of nitrogen fixation in Saccharum SPP

International Nuclear Information System (INIS)

Singh, M.; Singh, G.B.; Joshi, B.B.

1994-01-01

The objectives of present study were to quantify and compare the amount of nitrogen fixed by diazotrophes associated with roots of Saccharum spontaneum, S. barberi and S. sinense using Sclerotachya fusca as a non-fixing control. 5 refs

Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/Chlorobi group.

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Vitaly V Kadnikov

Full Text Available Melioribacter roseus is a moderately thermophilic facultatively anaerobic organotrophic bacterium representing a novel deep branch within Bacteriodetes/Chlorobi group. To better understand the metabolic capabilities and possible ecological functions of M. roseus and get insights into the evolutionary history of this bacterial lineage, we sequenced the genome of the type strain P3M-2(T. A total of 2838 open reading frames was predicted from its 3.30 Mb genome. The whole proteome analysis supported phylum-level classification of M. roseus since most of the predicted proteins had closest matches in Bacteriodetes, Proteobacteria, Chlorobi, Firmicutes and deeply-branching bacterium Caldithrix abyssi, rather than in one particular phylum. Consistent with the ability of the bacterium to grow on complex carbohydrates, the genome analysis revealed more than one hundred glycoside hydrolases, glycoside transferases, polysaccharide lyases and carbohydrate esterases. The reconstructed central metabolism revealed pathways enabling the fermentation of complex organic substrates, as well as their complete oxidation through aerobic and anaerobic respiration. Genes encoding the photosynthetic and nitrogen-fixation machinery of green sulfur bacteria, as well as key enzymes of autotrophic carbon fixation pathways, were not identified. The M. roseus genome supports its affiliation to a novel phylum Ignavibateriae, representing the first step on the evolutionary pathway from heterotrophic ancestors of Bacteriodetes/Chlorobi group towards anaerobic photoautotrophic Chlorobi.

Insects as a Nitrogen Source for Plants

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Michael J. Bidochka

2013-07-01

Full Text Available Many plants have evolved adaptations in order to survive in low nitrogen environments. One of the best-known adaptations is that of plant symbiosis with nitrogen-fixing bacteria; this is the major route by which nitrogen is incorporated into plant biomass. A portion of this plant-associated nitrogen is then lost to insects through herbivory, and insects represent a nitrogen reservoir that is generally overlooked in nitrogen cycles. In this review we show three specialized plant adaptations that allow for the recovery of insect nitrogen; that is, plants gaining nitrogen from insects. First, we show specialized adaptations by carnivorous plants in low nitrogen habitats. Insect carnivorous plants such as pitcher plants and sundews (Nepenthaceae/Sarraceniaceae and Drosera respectively are able to obtain substantial amounts of nitrogen from the insects that they capture. Secondly, numerous plants form associations with mycorrhizal fungi that can provide soluble nitrogen from the soil, some of which may be insect-derived nitrogen, obtained from decaying insects or insect frass. Finally, a specialized group of endophytic, insect-pathogenic fungi (EIPF provide host plants with insect-derived nitrogen. These soil-inhabiting fungi form a remarkable symbiosis with certain plant species. They can infect a wide range of insect hosts and also form endophytic associations in which they transfer insect-derived nitrogen to the plant. Root colonizing fungi are found in disparate fungal phylogenetic lineages, indicating possible convergent evolutionary strategies between taxa, evolution potentially driven by access to carbon-containing root exudates.

A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria.

Science.gov (United States)

Gaby, John Christian; Buckley, Daniel H

2014-01-01

We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. 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. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm.

Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense

Directory of Open Access Journals (Sweden)

C.Y. Nishikawa

2012-02-01

Full Text Available Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ54 co-factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL. A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH4Cl but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.

Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense

Energy Technology Data Exchange (ETDEWEB)

Nishikawa, C.Y.; Araújo, L.M.; Kadowaki, M.A.S.; Monteiro, R.A.; Steffens, M.B.R.; Pedrosa, F.O.; Souza, E.M.; Chubatsu, L.S. [Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR (Brazil)

2012-01-27

Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ{sup 54} factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH{sub 4}Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.

Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense.

Science.gov (United States)

Nishikawa, C Y; Araújo, L M; Kadowaki, M A S; Monteiro, R A; Steffens, M B R; Pedrosa, F O; Souza, E M; Chubatsu, L S

2012-02-01

Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ(54) co-factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH(4)Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription.

Expression and characterization of an N-truncated form of the NifA protein of Azospirillum brasilense

International Nuclear Information System (INIS)

Nishikawa, C.Y.; Araújo, L.M.; Kadowaki, M.A.S.; Monteiro, R.A.; Steffens, M.B.R.; Pedrosa, F.O.; Souza, E.M.; Chubatsu, L.S.

2012-01-01

Azospirillum brasilense is a nitrogen-fixing bacterium associated with important agricultural crops such as rice, wheat and maize. The expression of genes responsible for nitrogen fixation (nif genes) in this bacterium is dependent on the transcriptional activator NifA. This protein contains three structural domains: the N-terminal domain is responsible for the negative control by fixed nitrogen; the central domain interacts with the RNA polymerase σ 54 factor and the C-terminal domain is involved in DNA binding. The central and C-terminal domains are linked by the interdomain linker (IDL). A conserved four-cysteine motif encompassing the end of the central domain and the IDL is probably involved in the oxygen-sensitivity of NifA. In the present study, we have expressed, purified and characterized an N-truncated form of A. brasilense NifA. The protein expression was carried out in Escherichia coli and the N-truncated NifA protein was purified by chromatography using an affinity metal-chelating resin followed by a heparin-bound resin. Protein homogeneity was determined by densitometric analysis. The N-truncated protein activated in vivo nifH::lacZ transcription regardless of fixed nitrogen concentration (absence or presence of 20 mM NH 4 Cl) but only under low oxygen levels. On the other hand, the aerobically purified N-truncated NifA protein bound to the nifB promoter, as demonstrated by an electrophoretic mobility shift assay, implying that DNA-binding activity is not strictly controlled by oxygen levels. Our data show that, while the N-truncated NifA is inactive in vivo under aerobic conditions, it still retains DNA-binding activity, suggesting that the oxidized form of NifA bound to DNA is not competent to activate transcription

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

Energy Technology Data Exchange (ETDEWEB)

Bollmann, Annette [Miami University, Oxford, OH; Sedlacek, Christopher J [Miami University, Oxford, OH; Laanbroek, Hendrikus J [Netherlands Institute of Ecology (NIOO-KNAW); Suwa, Yuichi [Chuo University, Tokyo, Japan; Stein, Lisa Y [University of California, Riverside; Klotz, Martin G [University of Louisville, Louisville; Arp, D J [Oregon State University; Sayavedra-Soto, LA [Oregon State University; Lu, Megan [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL)

2013-01-01

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

Effect of the major components of industrial air pollution on nonsymbiotic nitrogen-fixation activity in soil

Energy Technology Data Exchange (ETDEWEB)

Islamov, S S; Chunderova, A I

1976-01-01

Industrial pollution of atmosphere inhibits the activity of non-symbiotic nitrogen fixation in soils. The inhibiting effect of polluted air can be explained by the presence of carbon monoxide and nitrogen dioxide in it. Sulfur dioxide does not depress the nitrogenase complex of aerobic and anaerobic nitrogen fixing microorganisms.

Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

Science.gov (United States)

Stief, P.

2013-12-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal-microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal-microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal-microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies reveal that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and

A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation.

Science.gov (United States)

Pislariu, Catalina I; Murray, Jeremy D; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; Benedito, Vagner A; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S; Chen, Rujin; Udvardi, Michael K

2012-08-01

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.

Proteomic analysis of Herbaspirillum seropedicae reveals ammonium-induced AmtB-dependent membrane sequestration of PII proteins.

Science.gov (United States)

Huergo, Luciano F; Noindorf, Lilian; Gimenes, Camila; Lemgruber, Renato S P; Cordellini, Daniela F; Falarz, Lucas J; Cruz, Leonardo M; Monteiro, Rose A; Pedrosa, Fábio O; Chubatsu, Leda S; Souza, Emanuel M; Steffens, Maria B R

2010-07-01

This study was aimed at describing the spectrum and dynamics of proteins associated with the membrane in the nitrogen-fixing bacterium Herbaspirillum seropedicae according to the availability of fixed nitrogen. Using two-dimensional electrophoresis we identified 79 protein spots representing 45 different proteins in the membrane fraction of H. seropedicae. Quantitative analysis of gel images of membrane extracts indicated two spots with increased levels when cells were grown under nitrogen limitation in comparison with nitrogen sufficiency; these spots were identified as the GlnK protein and as a conserved noncytoplasmic protein of unknown function which was encoded in an operon together with GlnK and AmtB. Comparison of gel images of membrane extracts from cells grown under nitrogen limitation or under the same regime but collected after an ammonium shock revealed two proteins, GlnB and GlnK, with increased levels after the shock. The P(II) proteins were not present in the membrane fraction of an amtB mutant. The results reported here suggest that changes in the cellular localization of P(II) might play a role in the control of nitrogen metabolism in H. seropedicae.

Stimulation of Diesel Fuel Biodegradation by Indigenous Nitrogen Fixing Bacterial Consortia.

Science.gov (United States)

Piehler; Swistak; Pinckney; Paerl

1999-07-01

> Abstract Successful stimulation of N2 fixation and petroleum hydrocarbon degradation in indigenous microbial consortia may decrease exogenous N requirements and reduce environmental impacts of bioremediation following petroleum pollution. This study explored the biodegradation of petroleum pollution by indigenous N2 fixing marine microbial consortia. Particulate organic carbon (POC) in the form of ground, sterile corn-slash (post-harvest leaves and stems) was added to diesel fuel amended coastal water samples to stimulate biodegradation of petroleum hydrocarbons by native microorganisms capable of supplying a portion of their own N. It was hypothesized that addition of POC to petroleum amended water samples from N-limited coastal waters would promote the growth of N2 fixing consortia and enhance biodegradation of petroleum. Manipulative experiments were conducted using samples from coastal waters (marinas and less polluted control site) to determine the effects of POC amendment on biodegradation of petroleum pollution by native microbial consortia. Structure and function of the microbial consortia were determined by measurement of N2 fixation (acetylene reduction), hydrocarbon biodegradation (14C hexadecane mineralization), bacterial biomass (AODC), number of hydrocarbon degrading bacteria (MPN), and bacterial productivity (3H-thymidine incorporation). Throughout this study there was a consistent enhancement of petroleum hydrocarbon degradation in response to the addition of POC. Stimulation of diesel fuel biodegradation following the addition of POC was likely attributable to increases in bacterial N2 fixation, diesel fuel bioavailability, bacterial biomass, and metabolic activity. Toxicity of the bulk phase water did not appear to be a factor affecting biodegradation of diesel fuel following POC addition. These results indicate that the addition of POC to diesel-fuel-polluted systems stimulated indigenous N2 fixing microbial consortia to degrade petroleum

Evaluation of early nodulation and Nitrogen fixation a number of Bradyrhizobium Japonicum strains to increase nitrogen fixation ability of soybean cultivars ars by using the A-value (N-15) method

International Nuclear Information System (INIS)

Piervali-Bieranvand, N.; Teimori, S.; Khorasani, A.

2004-01-01

To date significant contribution of atmospheric N fixation to soybean nutrition and growth, is approved. Nevertheless several studies have demonstrated that effectiveness of soybean -rhizobium symbiosis is medium compared with other legumes. The time course study of biological nitrogen fixation in soybean under field conditions has been shown that soybean has limited initial fixation and fixes substantially atmospheric nitrogen just during the reproductive periods (R1 until R 5).So there is the possibility of enhancing nitrogen fixation in soybean during vegetation growth. This could be done by improving inoculation methods or breeding for early nodulation. Hence, the present study was conducted to examine the effect of some Bradyrhizobium japonicum strains on early nodulation and biological nitrogen fixation three soybean cultivars by using a-value method. The experiment, was a factorial on randomized complete block design with three replications under proper glass house condition. Treatments were harvesting times(one , two and three weeks after flowering, respectively.)soybean cultivars(Chippewa, M 112 and clay )and Bradyrhizobium japonicum strains(J 1, J 3 and J 43). Ninety-plastic pots were filled with 1.5 kg of a compound of sand and soil(1:3). Rhizobial inoculation was performed by mixing 10 ml of a suspension(Yeast extract Manitol Broth) containing about 9X10 8 cells per ml to the soil of mixing pots were kept weed-free and watered with demineralized water as well as have received every two weeks 5 ml of a solution containing all the necessary nutrients except nitrogen. For measuring biological nitrogen fixation using a-value approach, two solutions of N-15 enriched ammonium sulfate containing 10.16 and %2 N-15 atom excess in amount of 5 and 25 mg N/Kg soil were mixed with soils in each pot containing fixing and reference plants, respectively. A non-nodulation isoline of soybean C v. M 129 for the all cultivars was used as a reference crop. First harvest was

Nitrogen fixation and induction of pseudo-nodules in grass

International Nuclear Information System (INIS)

Rasul, G.; Hassan, U.; Mehnaz, S.; Malik, K.A.

1993-01-01

The rice grown nitrogen depleted saline sols showed higher values for in-situ ARA. Isolations of N/sub 2/ fixing bacteria were carried out on soil Azotobacter was observed in plant rhizosphere. The 2,4-D (0.5 and 1 ppm) with diazo trophic bacteria induced nodule like structure on the wheat roots. The bacteria were found in nodules in the form of micro colonies or bacterial aggregates which were responsible for nitrogen fixation providing optimum 02 concentrations was incorporations /sup 15/N dilution data indicated that 125-46.5% atmosphere N was incorporated in nitrogen pool of inoculated plants. (author)

Molecular aspects of the nitrogen fixing system in pea root nodules

International Nuclear Information System (INIS)

Bisseling, T.

1980-01-01

The author considers symbiotic nitrogen fixation of Pisum sativum and Rhizobium leguminosarum. Some general aspects of nodule formation and the regulation of the proteins nitrogenase and leghemoglobin (Lb) have been studied. Synthesis of these proteins was studied by 35 SO 4 labelling of intact pea plants. The sequence of appearance of the proteins was determined with specific radioimmunoassays for each protein. (Auth.)

MODELING OF MIXED CHEMOSTAT CULTURES OF AN AEROBIC BACTERIUM, COMAMONAS-TESTOSTERONI, AND AN ANAEROBIC BACTERIUM, VEILLONELLA-ALCALESCENS - COMPARISON WITH EXPERIMENTAL-DATA

NARCIS (Netherlands)

GERRITSE, J; SCHUT, F; GOTTSCHAL, JC

A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation Of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the

Soil-N tagging - a method for measurement of biological nitrogen fixation in cereal-legume intercropping system

International Nuclear Information System (INIS)

Patra, D.D.; Subbiah, B.V.; Sachdev, M.S.

1985-01-01

The quantitative estimates of atmospheric dinitrogen fixed by the legume crop and transferred to the associated cereal in cereal-legume intercropping system of maize-cowpea and wheat-gram using soil and fertilizer nitrogen labelling with 15 N have been reported. The estimates of N-fixation have been compared with the similar data from A-value method. Under field conditions sole cropped cowpea fixed 53.7 per cent of its total N uptake while as intercrop with maize fixed 43.5 per cent. Maize crop got 27.6 per cent of its total N uptake by transference of the nitrogen fixed by the intercropped cowpea. In the wheat-gram intercropping system the corresponding values under greenhouse conditions were 35.0, 44.8 and 20.2 per cent, respectively. (author)

Lactic acid production from xylose by Geobacillus stearothermophilus strain 15

Science.gov (United States)

Kunasundari, B.; Naresh, S.; Chu, J. E.

2017-09-01

Lactic acid is an important compound with a wide range of industrial applications. The present study tested the efficiency of xylose, as a sole carbon source to be converted to lactic acid by Geobacillus stearothermophilus strain 15. To the best of our knowledge, limited information is available on the directed fermentation of xylose to lactic acid by this bacterium. The effects of different parameters such as temperature, pH, incubation time, agitation speed, concentrations of nitrogen and carbon sources on the lactic acid production were investigated statistically. It was found that the bacterium exhibited poor assimilation of xylose to lactic acid. Temperature, agitation rate and incubation time were determined to improve the lactic acid production slightly. The highest lactic acid yield obtained was 8.9% at 45°C, 300 RPM, 96 h, pH of 6.0 with carbon and nitrogen source concentrations were fixed at 5% w/v.

Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi.

Science.gov (United States)

Hoppe, Björn; Kahl, Tiemo; Karasch, Peter; Wubet, Tesfaye; Bauhus, Jürgen; Buscot, François; Krüger, Dirk

2014-01-01

Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase) genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.

Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi.

Directory of Open Access Journals (Sweden)

Björn Hoppe

Full Text Available Nitrogen availability in dead wood is highly restricted and associations with N-fixing bacteria are thought to enable wood-decaying fungi to meet their nitrogen requirements for vegetative and generative growth. We assessed the diversity of nifH (dinitrogenase reductase genes in dead wood of the common temperate tree species Fagus sylvatica and Picea abies from differently managed forest plots in Germany using molecular tools. By incorporating these genes into a large compilation of published nifH sequences and subsequent phylogenetic analyses of deduced proteins we verified the presence of diverse pools corresponding to functional nifH, almost all of which are new to science. The distribution of nifH genes strongly correlated with tree species and decay class, but not with forest management, while higher fungal fructification was correlated with decreasing nitrogen content of the dead wood and positively correlated with nifH diversity, especially during the intermediate stage of wood decay. Network analyses based on non-random species co-occurrence patterns revealed interactions among fungi and N-fixing bacteria in the dead wood and strongly indicate the occurrence of at least commensal relationships between these taxa.

Legume Shrubs Are More Nitrogen-Homeostatic than Non-legume Shrubs.

Science.gov (United States)

Guo, Yanpei; Yang, Xian; Schöb, Christian; Jiang, Youxu; Tang, Zhiyao

2017-01-01

Legumes are characterized as keeping stable nutrient supply under nutrient-limited conditions. However, few studies examined the legumes' stoichiometric advantages over other plants across various taxa in natural ecosystems. We explored differences in nitrogen (N) and phosphorus (P) stoichiometry of different tissue types (leaf, stem, and root) between N 2 -fixing legume shrubs and non-N 2 -fixing shrubs from 299 broadleaved deciduous shrubland sites in northern China. After excluding effects of taxonomy and environmental variables, these two functional groups differed considerably in nutrient regulation. N concentrations and N:P ratios were higher in legume shrubs than in non-N 2 -fixing shrubs. N concentrations were positively correlated between the plants and soil for non-N 2 -fixing shrubs, but not for legume shrubs, indicating a stronger stoichiometric homeostasis in legume shrubs than in non-N 2 -fixing shrubs. N concentrations were positively correlated among three tissue types for non-N 2 -fixing shrubs, but not between leaves and non-leaf tissues for legume shrubs, demonstrating that N concentrations were more dependent among tissues for non-N 2 -fixing shrubs than for legume shrubs. N and P concentrations were correlated within all tissues for both functional groups, but the regression slopes were flatter for legume shrubs than non-N 2 -fixing shrubs, implying that legume shrubs were more P limited than non-N 2 -fixing shrubs. These results address significant differences in stoichiometry between legume shrubs and non-N 2 -fixing shrubs, and indicate the influence of symbiotic nitrogen fixation (SNF) on plant stoichiometry. Overall, N 2 -fixing legume shrubs are higher and more stoichiometrically homeostatic in N concentrations. However, due to excess uptake of N, legumes may suffer from potential P limitation. With their N advantage, legume shrubs could be good nurse plants in restoration sites with degraded soil, but their P supply should be taken care

Concentration and transport of nitrate by the mat-forming sulphur bacterium Thioploca

Science.gov (United States)

Fossing, H.; Gallardo, V. A.; Jørgensen, B. B.; Hüttel, M.; Nielsen, L. P.; Schulz, H.; Canfield, D. E.; Forster, S.; Glud, R. N.; Gundersen, J. K.; Küver, J.; Ramsing, N. B.; Teske, A.; Thamdrup, B.; Ulloa, O.

1995-04-01

MARINE species of Thioploca occur over 3,000 km along the continental shelf off Southern Peru and North and Central Chile1-4. These filamentous bacteria live in bundles surrounded by a common sheath and form thick mats on the sea floor under the oxygen-minimum zone in the upwelling region, at between 40 and 280 m water depth. The metabolism of this marine bacterium5,6 remained a mystery until long after its discovery1,7. We report here that Thioploca cells are able to concentrate nitrate to up to 500 mM in a liquid vacuole that occupies >80% of the cell volume. Gliding filaments transport this nitrate 5-10 cm down into the sediment and reduce it, with concomitant oxidation of hydrogen sulphide, thereby coupling the nitrogen and sulphur cycles in the sediment.

Automatic filling of liquid nitrogen traps auxiliary safety devices of a pumping unit

International Nuclear Information System (INIS)

Chatel, S.

1969-01-01

The liquid nitrogen traps in our laboratories are generally filled at fixed time intervals, the supply being cut when the liquid flowing through the overflow pipe acts on a lever to which is fixed a small cup fitted with a hole which allows the water of condensation to escape. This system is reliable. After a certain time however, the escape hole blocks up, water accumulates and the lever arm no longer works properly. Furthermore the duration of any cuts in the current, is added to the fixed time intervals, and in this case there can be a lack of liquid nitrogen for several hours after the current has been restored. The device described here avoids these problems. A stainless steel tube containing a copper wire passes into the trap and is immersed in the nitrogen which boils at its tip. A mercury manometer with concentric reservoirs, or an oil manometer, acting on two micro switches through a floater, records the pressure corresponding to the difference in level and controls the filling operation. If there is a lack of nitrogen, a valve can be closed by means of a falling weight, or a diffusion pump can be cut off; one time switch and at least two relays are required. One single relay can be used to control, the supply of several similar traps placed in series [fr

Engineering a wild fast-growing Mycoplasma bacterium to generate ...

International Development Research Centre (IDRC) Digital Library (Canada)

2018-01-12

Jan 12, 2018 ... The CCPP bacterium causes sick animals to experience severe symptoms ... because antibiotic treatment does not eliminate the responsible bacterium. ... To develop a fast growing CCPP vaccine for cheaper production and ...

Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation

Science.gov (United States)

Common bean (Phaseolus vulgaris L.) is able to fix atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF). Effective utilization of existing variability for SNF in common bean for genetic improvement requires an understanding of underlying genes and molecular mechanisms. The utility of ...

Production and characterization of bioemulsifier from a marine bacterium, Acinetobacter calcoaceticus subsp. anitratus SM7

Directory of Open Access Journals (Sweden)

Kulnaree Phetrong

2008-05-01

Full Text Available Marine bacterium strain SM7 was isolated as a bioemulsifier-producing bacterium from oil-spilled seawater in Songkhla lagoon, Thailand. It was identified as Acinetobacter calcoaceticus subsp. anitratus based on morphology, biochemicalcharacteristics and 16S rRNA sequence. A. calcoaceticus subsp. anitratus SM7 produced an extracellular emulsifying agent when grown in a minimal salt medium (pH 7.0 containing 0.3% (v/v n-heptadecane and 0.1% (w/v ammoniumhydrogen carbonate as carbon source and nitrogen source, respectively, at 30oC with agitation rate of 200 rpm. Crude bioemulsifier was recovered from the culture supernatant by ethanol precipitation with a yield of 2.94 g/l and had a criticalemulsifier concentration of 0.04 g/ml. The crude bioemulsifier was capable of emulsifying n-hexadecane in a broad pH range (6-12, temperatures (30-121oC and in the presence of NaCl up to 12% (w/v. The bioemulsifier was stable in saltsolution ranging from 0 to 0.1% (w/v of MgCl2 and CaCl2. The broad range of pH stability, thermostability and salt tolerance suggested that the bioemulsifier from A. calcoaceticus subsp. anitratus SM7 could be useful in environmentalapplication, especially bioremediation of oil-polluted seawater.

Nitrogen mass balance in the Brazilian Amazon: an update.

Science.gov (United States)

Martinelli, L A; Pinto, A S; Nardoto, G B; Ometto, J P H B; Filoso, S; Coletta, L D; Ravagnani, E C

2012-08-01

The main purpose of this study is to perform a nitrogen budget survey for the entire Brazilian Amazon region. The main inputs of nitrogen to the region are biological nitrogen fixation occurring in tropical forests (7.7 Tg.yr(-1)), and biological nitrogen fixation in agricultural lands mainly due to the cultivation of a large area with soybean, which is an important nitrogen-fixing crop (1.68 Tg.yr(-1)). The input due to the use of N fertilizers (0.48 Tg.yr(-1)) is still incipient compared to the other two inputs mentioned above. The major output flux is the riverine flux, equal to 2.80 Tg.yr(-1) and export related to foodstuff, mainly the transport of soybean and beef to other parts of the country. The continuous population growth and high rate of urbanization may pose new threats to the nitrogen cycle of the region through the burning of fossil fuel and dumping of raw domestic sewage in rivers and streams of the region.

Incorporation of nitrogen from N2 fixation into amino acids of zooplankton

DEFF Research Database (Denmark)

Loick-Wilde, Natalie; Dutz, Jörg; Miltner, Anja

2012-01-01

quantified the direct incorporation of 15N tracer from N2-fixing N. spumigena (diazotroph nitrogen) and ammonium-utilizing R. salina into the amino acid nitrogen (AA-N) of zooplankton using complementary gas chromatography– combustion–isotope ratio mass spectrometry, gas chromatography–mass spectrometry...... consistently low in E. affinis when exposed to N. spumigena, suggesting that these animals were reluctant to feed on N. spumigena. Essential isoleucine received most of the diazotroph nitrogen in field zooplankton, while nonessential amino acids received most 15N tracer in E. affinis. N. spumigena was clearly...... an important amino acid nitrogen source for Baltic Sea zooplankton...

Zymomonas mobilis: a bacterium for ethanol production

Energy Technology Data Exchange (ETDEWEB)

Baratti, J.C.; Bu' Lock, J.D.

1986-01-01

Zymomonas mobilis is a facultative anaerobic gram negative bacterium first isolated in tropical countries from alcoholic beverages like the African palm wine, the Mexican pulque and also as a contaminant of cider (cider sickness) or beer in the European countries. It is one of the few facultative anaerobic bacteria degrading glucose by the Entner-Doudoroff pathway usually found in strictly aerobic microorganisms. Some work was devoted to this bacterium in the 50s and 60s and was reviewed by Swings and De Ley in their classical paper published in 1977. During the 70s there was very little work on the bacterium until 1979 and the first report by the Australian group of P.L. Rogers on the great potentialities of Z. mobilis for ethanol production. At that time the petroleum crisis had led the developed countries to search for alternative fuel from renewable resources. The Australian group clearly demonstrated the advantages of the bacterium compared to the yeasts traditionally used for the alcoholic fermentation. As a result, there was a considerable burst in the Zymomonas literature which started from nearly zero in the late 70s to attain 70 papers published in the field in 1984. In this article, papers published from 1982 to 1986 are reviewed.

Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

Energy Technology Data Exchange (ETDEWEB)

Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

1994-06-01

The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

Robust biological nitrogen fixation in a model grass-bacterial association.

Science.gov (United States)

Pankievicz, Vânia C S; do Amaral, Fernanda P; Santos, Karina F D N; Agtuca, Beverly; Xu, Youwen; Schueller, Michael J; Arisi, Ana Carolina M; Steffens, Maria B R; de Souza, Emanuel M; Pedrosa, Fábio O; Stacey, Gary; Ferrieri, Richard A

2015-03-01

Nitrogen-fixing rhizobacteria can promote plant growth; however, it is controversial whether biological nitrogen fixation (BNF) from associative interaction contributes to growth promotion. The roots of Setaria viridis, a model C4 grass, were effectively colonized by bacterial inoculants resulting in a significant enhancement of growth. Nitrogen-13 tracer studies provided direct evidence for tracer uptake by the host plant and incorporation into protein. Indeed, plants showed robust growth under nitrogen-limiting conditions when inoculated with an ammonium-excreting strain of Azospirillum brasilense. (11)C-labeling experiments showed that patterns in central carbon metabolism and resource allocation exhibited by nitrogen-starved plants were largely reversed by bacterial inoculation, such that they resembled plants grown under nitrogen-sufficient conditions. Adoption of S. viridis as a model should promote research into the mechanisms of associative nitrogen fixation with the ultimate goal of greater adoption of BNF for sustainable crop production. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

H{sub 2}S Removal in Anaerobic digestion of Sludge by Microaerophilic Processes: Pilot Plant Experience; Eliminacion de H{sub 2}S en digestion anaerobia de lodos por procesos microaerofilico: experiencia en planta piloto

Energy Technology Data Exchange (ETDEWEB)

Fdz-Polanco Iniguez de la Torre, M.; Perez Elvira, S. I.; Diaz Villalobos, I.; Garcia Rodriguez, L.; Torio Acha, R.; Acevedo Alvarez, A. F.

2009-07-01

Anaerobic digestion of sludge produces a biogas with content in H{sub 2}S between 4.000-6.000 ppm, Removal strategies can operate at three different levels: (1) at the source (source control), (2) at process level or (3) at the end (biogas treatment). Process-level control of sulfide presents several advantages when comparing with traditional biogas treatment. Microaerophilic process consists on the supply of small amounts of oxygen in the digester in order to completely remove H{sub 2}S without affect the anaerobic process. (Author) 9 refs.

Microflora of urogenital tract in pregnancy with asymptomatic bacterium

International Nuclear Information System (INIS)

Abdullaeva, R.A.

2006-01-01

The article contains results of research interrelationship from colonization of vagina and urinary tract diseases. E.coli one of the main factors in development asymptomatic bacterium. Presented high effects of penicillin medicaments and nitrofurans in treatment of asymptomatic bacterium

Nitrogen-fixing and uricolytic bacteria associated with the gut of Dendroctonus rhizophagus and Dendroctonus valens (Curculionidae: Scolytinae).

Science.gov (United States)

Morales-Jiménez, Jesús; Vera-Ponce de León, Arturo; García-Domínguez, Aidé; Martínez-Romero, Esperanza; Zúñiga, Gerardo; Hernández-Rodríguez, César

2013-07-01

The bark beetles of the genus Dendroctonus feed on phloem that is a nitrogen-limited source. Nitrogen fixation and nitrogen recycling may compensate or alleviate such a limitation, and beetle-associated bacteria capable of such processes were identified. Raoultella terrigena, a diazotrophic bacteria present in the gut of Dendroctonus rhizophagus and D. valens, exhibited high acetylene reduction activity in vitro with different carbon sources, and its nifH and nifD genes were sequenced. Bacteria able to recycle uric acid were Pseudomonas fluorescens DVL3A that used it as carbon and nitrogen source, Serratia proteomaculans 2A CDF and Rahnella aquatilis 6-DR that used uric acid as sole nitrogen source. Also, this is the first report about the uric acid content in whole eggs, larvae, and adults (male and female) samples of the red turpentine beetle (Dendroctonus valens). Our results suggest that the gut bacteria of these bark beetles could contribute to insect N balance.

Legume Shrubs Are More Nitrogen-Homeostatic than Non-legume Shrubs

OpenAIRE

Guo, Yanpei; Yang, Xian; Schöb, Christian; Jiang, Youxu; Tang, Zhiyao

2017-01-01

Legumes are characterized as keeping stable nutrient supply under nutrient-limited conditions. However, few studies examined the legumes' stoichiometric advantages over other plants across various taxa in natural ecosystems. We explored differences in nitrogen (N) and phosphorus (P) stoichiometry of different tissue types (leaf, stem, and root) between N2-fixing legume shrubs and non-N2-fixing shrubs from 299 broadleaved deciduous shrubland sites in northern China. After excluding effects of ...

A comparative study on phyllosphere nitrogen fixation by newly isolated Corynebacterium sp. & Flavobacterium sp. and their potentialities as biofertilizer.

Science.gov (United States)

Giri, S; Pati, B R

2004-01-01

A number of nitrogen fixing bacteria has been isolated from forest phyllosphere on the basis of nitrogenase activity. Among them two best isolates are selected and identified as Corynebacterium sp. AN1 & Flavobacterium sp. TK2 able to reduce 88 and 132 n mol of acetylene (10(8)cells(-1)h(-1)) respectively. They were grown in large amount and sprayed on the phyllosphere of maize plants as a substitute for nitrogenous fertilizer. Marked improvements in growth and total nitrogen content of the plant have been observed by the application of these nitrogen-fixing bacteria. An average 30-37% increase in yield was obtained, which is nearer to chemical fertilizer treatment. Comparatively better effect was obtained by application of Flavobacterium sp.

Studies on the roles of GlnK and GlnB in regulating Klebsiella pneumoniae NifL-dependent nitrogen control.

NARCIS (Netherlands)

Arcondeguy, T.; van Heeswijk, W.C.; Merrick, M.

1999-01-01

In Klebsiella pneumoniae, nitrogen fixation (nif) genes are regulated in response to fixed nitrogen and oxygen. The activity of the nif-specific transcriptional activator NifA is modulated by NifL, which mediates both oxygen and nitrogen control. The signal transduction protein GlnK is required to

Low temperature delays timing and enhances the cost of nitrogen fixation in the unicellular cyanobacterium Cyanothece

NARCIS (Netherlands)

Brauer, V.S.; Stomp, M.; Rosso, C.; van Beusekom, S.A.M.; Emmerich, B.; Stal, L.J.; Huisman, J.

2013-01-01

Marine nitrogen-fixing cyanobacteria are largely confined to the tropical and subtropical ocean. It has been argued that their global biogeographical distribution reflects the physiologically feasible temperature range at which they can perform nitrogen fixation. In this study we refine this line of

Anaerobic nitrogen turnover by sinking diatom aggregates at varying ambient oxygen levels

DEFF Research Database (Denmark)

Stief, Peter; Kamp, Anja; Thamdrup, Bo

2016-01-01

nitrate supply. Sinking diatom aggregates can contribute directly to fixed-nitrogen loss in low-oxygen environments in the ocean and vastly expand the ocean volume in which anaerobic nitrogen turnover is possible, despite relatively high ambient oxygen levels. Depending on the extent of intracellular......In the world’s oceans, even relatively low oxygen levels inhibit anaerobic nitrogen cycling by free-living microbes. Sinking organic aggregates, however, might provide oxygen-depleted microbial hotspots in otherwise oxygenated surface waters. Here, we show that sinking diatom aggregates can host...

Nitrogen fixation in denitrified marine waters.

Directory of Open Access Journals (Sweden)

Camila Fernandez

Full Text Available Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria, whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria. Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP, a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ. Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m(-2 d(-1. Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m(-2 d(-1 than the oxic euphotic layer (48±68 µmol m(-2 d(-1. Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions.

Nitrogen Fixation in Denitrified Marine Waters

Science.gov (United States)

Fernandez, Camila; Farías, Laura; Ulloa, Osvaldo

2011-01-01

Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m−2 d−1). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m−2 d−1) than the oxic euphotic layer (48±68 µmol m−2 d−1). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions. PMID:21687726

Influence of the compound effect between nitrogen and zinc on the resource of nitrogen of herbage in mixed and pure culture

International Nuclear Information System (INIS)

He Zhongjun; Hua Luo

2002-01-01

Under pot culture, the influence of compound effect between nitrogen and zinc on the resource of nitrogen of ryegrass in mono-culture and ryegrass/clover in mixture were studied on yellow brown earth which collected from sub-tropic mountain sward of southern China. The result showed as follows: (1) The percentage of nitrogen derived from atmosphere (% Ndfa) was decreased by nitrogen application in early growth stage and suitable amount of nitrogen application increased it in later growth stage. The % Ndfa of white clover in mixture was the highest with 6 mg/kg zinc application in all nitrogen levels. The transfer of fixed nitrogen by white clover to ryegrass was decreased by nitrogen application and increased by low amount of zinc application. (2) The percentage of nitrogen derived from fertilizer (% Ndff) was significantly increased by nitrogen application, of which the treatments with 6-20 mg/kg zinc application was higher than other zinc application treatments on ryegrass in monoculture, and the treatments with 6-20 mg/kg zinc application on white clover/ryegrass in mixture was lower than other zinc treatments at the range from 30 to 90 mg/kg nitrogen application. (3) The percentage of nitrogen derived from soil (% Ndfs) of ryegrass both in pure and in mixture was significantly decreased as the increasing of the levels of nitrogen application, of which ryegrass in mono-culture was not obviously influenced by zinc application, and ryegrass/clover in mixture was decreased by 6-20 mg/kg zinc application under all nitrogen levels

Synthesis and review: Tackling the nitrogen management challenge: from global to local scales

Science.gov (United States)

Reis, Stefan; Bekunda, Mateete; Howard, Clare M.; Karanja, Nancy; Winiwarter, Wilfried; Yan, Xiaoyuan; Bleeker, Albert; Sutton, Mark A.

2016-12-01

One of the ‘grand challenges’ of this age is the anthropogenic impact exerted on the nitrogen cycle. Issues of concern range from an excess of fixed nitrogen resulting in environmental pressures for some regions, while for other regions insufficient fixed nitrogen affects food security and may lead to health risks. To address these issues, nitrogen needs to be managed in an integrated fashion, at a variety of scales (from global to local). Such management has to be based on a thorough understanding of the sources of reactive nitrogen released into the environment, its deposition and effects. This requires a comprehensive assessment of the key drivers of changes in the nitrogen cycle both spatially, at the field, regional and global scale and over time. In this focus issue, we address the challenges of managing reactive nitrogen in the context of food production and its impacts on human and ecosystem health. In addition, we discuss the scope for and design of management approaches in regions with too much and too little nitrogen. This focus issue includes several contributions from authors who participated at the N2013 conference in Kampala in November 2013, where delegates compiled and agreed upon the ‘Kampala Statement-for-Action on Reactive Nitrogen in Africa and Globally’. These contributions further underline scientifically the claims of the ‘Kampala Statement’, that simultaneously reducing pollution and increasing nitrogen available in the food system, by improved nitrogen management offers win-wins for environment, health and food security in both developing and developed economies. The specific messages conveyed in the Kampala Statement focus on improving nitrogen management (I), including the reduction of nitrogen losses from agriculture, industry, transport and energy sectors, as well as improving waste treatment and informing individuals and institutions (II). Highlighting the need for innovation and increased awareness among stakeholders (III

Method for optical 15N analysis of small amounts of nitrogen gas released from an automatic nitrogen analyzer

International Nuclear Information System (INIS)

Arima, Yasuhiro

1981-01-01

A method of optical 15 N analysis is proposed for application to small amounts of nitrogen gas released from an automatic nitrogen analyzer (model ANA-1300, Carlo Erba, Milano) subjected to certain set modifications. The ANA-1300 was combined with a vacuum line attached by a molecular sieve 13X column. The nitrogen gas released from the ANA-1300 was introduced with a carrier gas of helium into the molecular sieve column which was pre-evacuated at 10 -4 Torr and cooled with outer liquid nitrogen. After removal of the helium by evacuation, the nitrogen gas fixed on the molecular sieve was released by warming the column, and then, it was sealed into pre-evacuated pyrex glass tubes at 4.5 - 5.0 Torr. In the preparation of discharge tubes, contamination of unlabelled nitrogen occurred from the carrier gas of standard grade helium, and the relative lowering of the 15 N value by it was estimated to be less than 1% when over 700 μg nitrogen was charged on the ANA-1300; when 200 μg nitrogen was charged, it was about 3.5%. However, the effect of the contamination could be corrected for by knowing the amount of contaminant nitrogen. In the analysis of plant materials by the proposed method, the coefficient of variation was less than 2%, and no significant difference was observed between results given by the present method and by the ordinary method in which samples were directly pyrolyzed in the discharge tubes by the Dumas method. The present method revealed about 1.5 μg of cross-contaminated nitrogen and was applicable to more than 200 μg of sample nitrogen. (author)

Potential for nitrogen fixation in fungus-growing termite symbiosis

DEFF Research Database (Denmark)

Sapountzis, Panagiotis; de Verges, Jane; Rousk, Kathrin

2016-01-01

Termites host a gut microbiota of diverse and essential symbionts that enable specialization on dead plant material; an abundant, but nutritionally imbalanced food source. To supplement the severe shortage of dietary nitrogen (N), some termite species make use of diazotrophic bacteria to fix atmo...

Biochemical changes induced by fungicides in nitrogen fixing Nostoc sp.

Science.gov (United States)

Deviram, G V N S; Pant, Gaurav; Prasuna, R Gyana

2013-01-01

The present study indicates the effect of fungicides (approved by WHO) and their behavior on nitrogen fixer of rice eco system Nostoc sp. Application of plant protecting chemicals at recommended levels braced up the growth of blue green algae thereby enhancing heterocyst formation and nitrogenase activity. Nostoc sp demoed varying degrees of sensitivity to fungicides. Biomass yield, protein, carbohydrate content reduced after 3pg/mL concentration. Heterocyst damage was observed from 4μg/mL, Proline content increased with increase in fungicide concentration, utmost yellowing of the culture started from 4μg/mL. The decreasing order of the toxicity to Nostoc sp with fungicides was Mancozeb> Ediphenphos> Carbendazim> Hexaconazole.

Monitoring plant tissue nitrogen isotopes to assess nearshore inputs of nitrogen to Lake Crescent, Olympic National Park, Washington

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Cox, Stephen E.; Moran, Patrick W.; Huffman, Raegan L.; Fradkin, Steven C.

2016-05-31

Mats of filamentous-periphytic algae present in some nearshore areas of Lake Crescent, Olympic National Park, Washington, may indicate early stages of eutrophication from nutrient enrichment of an otherwise highly oligotrophic lake. Natural abundance ratios of stable isotopes of nitrogen (δ15N) measured in plant tissue growing in nearshore areas of the lake indicate that the major source of nitrogen used by these primary producing plants is derived mainly from atmospherically fixed nitrogen in an undeveloped forested ecosystem. Exceptions to this pattern occurred in the Barnes Point area where elevated δ15N ratios indicate that effluent from septic systems also contribute nitrogen to filamentous-periphytic algae growing in the littoral zone of that area. Near the Lyre River outlet of Lake Crescent, the δ15N of filamentous-periphytic algae growing in close proximity to the spawning areas of a unique species of trout show little evidence of elevated δ15N indicating that nitrogen from on-site septic systems is not a substantial source of nitrogen for these plants. The δ15N data corroborate estimates that nitrogen input to Lake Crescent from septic sources is comparatively small relative to input from motor vehicle exhaust and vegetative sources in undeveloped forests, including litterfall, pollen, and symbiotic nitrogen fixation. The seasonal timing of blooms of filamentous-periphytic algal near the lake shoreline is also consistent with nitrogen exported from stands of red alder trees (Alnus rubra). Isotope biomonitoring of filamentous-periphytic algae may be an effective approach to monitoring the littoral zone for nutrient input to Lake Crescent from septic sources.

Characterization of a halophilic heterotrophic nitrification-aerobic denitrification bacterium and its application on treatment of saline wastewater.

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Duan, Jinming; Fang, Hongda; Su, Bing; Chen, Jinfang; Lin, Jinmei

2015-03-01

A novel halophilic bacterium capable of heterotrophic nitrification-aerobic denitrification was isolated from marine sediments and identified as Vibrio diabolicus SF16. It had ability to remove 91.82% of NH4(+)-N (119.77 mg/L) and 99.71% of NO3(-)-N (136.43 mg/L). The nitrogen balance showed that 35.83% of initial NH4(+)-N (119.77 mg/L) was changed to intracellular nitrogen, and 53.98% of the initial NH4(+)-N was converted to gaseous denitrification products. The existence of napA gene further proved the aerobic denitrification ability of strain SF16. The optimum culture conditions were salinity 1-5%, sodium acetate as carbon source, C/N 10, and pH 7.5-9.5. When an aerated biological filter system inoculated with strain SF16 was employed to treat saline wastewater, the average removal efficiency of NH4(+)-N and TN reached 97.14% and 73.92%, respectively, indicating great potential of strain SF16 for future full-scale applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

Impact of climate change and ocean acidification on the marine nitrogen cycle

International Nuclear Information System (INIS)

Martinez-Rey, Jorge

2015-01-01

The marine nitrogen cycle is responsible for two climate feedbacks in the Earth System. Firstly, it modulates the fixed nitrogen pool available for phytoplankton growth and hence it modulates in part the strength of the biological pump, one of the mechanisms contributing to the oceanic uptake of anthropogenic CO 2 . Secondly, the nitrogen cycle produces a powerful greenhouse gas and ozone (O 3 ) depletion agent called nitrous oxide (N 2 O). Future changes of the nitrogen cycle in response to global warming, ocean deoxygenation and ocean acidification are largely unknown. Processes such as N 2 -fixation, nitrification, denitrification and N 2 O production will experience changes under the simultaneous effect of these three stressors. Global ocean biogeochemical models allow us to study such interactions. Using NEMO-PISCES and the CMIP5 model ensemble we project changes in year 2100 under the business-as-usual high CO 2 emissions scenario in global scale N 2 -fixation rates, nitrification rates, N 2 O production and N 2 O sea-to-air fluxes adding CO 2 sensitive functions into the model parameterizations. Second order effects due to the combination of global warming in tandem with ocean acidification on the fixed nitrogen pool, primary productivity and N 2 O radiative forcing feedbacks are also evaluated in this thesis. (author) [fr

Salt-inducible promoter derivable from a lactic acid bacterium, and its use in a lactic acid bacterium for production of a desired protein

NARCIS (Netherlands)

Sanders, Jan Willem; Kok, Jan; Venema, Gerard; Ledeboer, Adrianus Marinus

1998-01-01

The invention provides a salt-inducible promoter present in SEQ ID NO: 10 and derivable from a lactic acid bacterium in isolation from the coding sequence normally controlled by said promoter in a wild-type lactic acid bacterium, with modifications and important parts thereof. Also provided are a

Cyanobacteria in CELSS: Growth strategies for nutritional variation and nitrogen cycling

Science.gov (United States)

Fry, I. V.; Packer, L.

1990-01-01

Cyanobacteria (blue-green algae) are versatile organisms which are capable of adjusting their cellular levels of carbohydrate, protein, and lipid in response to changes in the environment. Under stress conditions there is an imbalance between nitrogen metabolism and carbohydrate/lipid synthesis. The lesion in nitrogen assimilation is at the level of transport: the stress condition diverts energy from the active accumulation of nitrate to the extrusion of salt, and probably inhibits a cold-labile ATP'ace in the case of cold shock. Both situations affect the bioenergetic status of the cell such that the nitrogenous precursors for protein synthesis are depleted. Dispite the inhibition of protein synthesis and growth, photosynthetic reductant generation is relatively unaffected. The high O2 reductant would normally lead to photo-oxidative damage of cellular components; however, the organism copes by channeling the 'excess' reductant into carbon storage products. The increase in glycogen (28 to 35 percent dry weight increase) and the elongation of lipid fatty acid side chains (2 to 5 percent dry weight increase) at the expense of protein synthesis (25 to 34 percent dry weight decrease) results in carbohydrate, lipid and protein ratios that are closer to those required in the human diet. In addition, the selection of nitrogen fixing mutants which excrete ammonium ions present an opportunity to tailor these micro-organisms to meet the specific need for a sub-system to reverse potential loss of fixed nitrogen material.

The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation

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Zhou Bai-Cheng

2010-04-01

Full Text Available Abstract Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant.

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Horváth, Beatrix; Domonkos, Ágota; Kereszt, Attila; Szűcs, Attila; Ábrahám, Edit; Ayaydin, Ferhan; Bóka, Károly; Chen, Yuhui; Chen, Rujin; Murray, Jeremy D; Udvardi, Michael K; Kondorosi, Éva; Kaló, Péter

2015-12-08

Host compatible rhizobia induce the formation of legume root nodules, symbiotic organs within which intracellular bacteria are present in plant-derived membrane compartments termed symbiosomes. In Medicago truncatula nodules, the Sinorhizobium microsymbionts undergo an irreversible differentiation process leading to the development of elongated polyploid noncultivable nitrogen fixing bacteroids that convert atmospheric dinitrogen into ammonia. This terminal differentiation is directed by the host plant and involves hundreds of nodule specific cysteine-rich peptides (NCRs). Except for certain in vitro activities of cationic peptides, the functional roles of individual NCR peptides in planta are not known. In this study, we demonstrate that the inability of M. truncatula dnf7 mutants to fix nitrogen is due to inactivation of a single NCR peptide, NCR169. In the absence of NCR169, bacterial differentiation was impaired and was associated with early senescence of the symbiotic cells. Introduction of the NCR169 gene into the dnf7-2/NCR169 deletion mutant restored symbiotic nitrogen fixation. Replacement of any of the cysteine residues in the NCR169 peptide with serine rendered it incapable of complementation, demonstrating an absolute requirement for all cysteines in planta. NCR169 was induced in the cell layers in which bacteroid elongation was most pronounced, and high expression persisted throughout the nitrogen-fixing nodule zone. Our results provide evidence for an essential role of NCR169 in the differentiation and persistence of nitrogen fixing bacteroids in M. truncatula.

Breeding food and forge legumes for enhancement of nitrogen fixation: a review

International Nuclear Information System (INIS)

Ali, A.; Hussain, S.; Qamar, I.A.; Khan, B.R.

2000-01-01

Nitrogen fixation in legume - root nodules requires the functioning of genes present in the Rhizobia that induce nodule-formation. The plant produces the nodules and the energy required for respiration. Genes in both Rhizobium and the plant are responsible for the efficient use of photosynthesis for N/sub 2/ fixation and assimilation of nitrogen. Genes from Rhizobium and legume hosts that are involved in the symbiosis are being identified, isolated and cloned, to facilitate the manipulation of either partner. The amounts of nitrogen fixed by grain-legumes vary appreciably, between and within, species and are also influenced by environment. With few exceptions, most legumes fix insufficient N/sub 2/ to support substantial seed-yields. Deficits between required N and the combined amounts provide by soil and fertilizer help in estimating the improvements in N/sub 2/ fixation which is possible through breeding. Since the symbiosis is a complex process, heritability of traits is weak, and most methods which estimate fixation are destructive, a breeding method that allows selection of replicated families rather than single plants is preferred. (author)

Elevated enzyme activities in soils under the invasive nitrogen-fixing tree Falcataria moluccana

Science.gov (United States)

Steven D. Allison; Caroline Nielsen; R. Flint. Hughes

2006-01-01

Like other N-fixing invasive species in Hawaii, Falcataria moluccana dramatically alters forest structure, litterfall quality and quantity, and nutrient dynamics. We hypothesized that these biogeochemical changes would also affect the soil microbial community and the extracellular enzymes responsible for carbon and nutrient mineralization. Across...

[Phylogenetic analysis and nitrogen removal characteristics of a heterotrophic nitrifying-aerobic denitrifying bacteria strain from marine environment].

Science.gov (United States)

Sun, Xuemei; Li, Qiufen; Zhang, Yan; Liu, Huaide; Zhao, Jun; Qu, Keming

2012-06-04

We determined the phylogenetic position of a heterotrophic nitrifying-aerobic denitrifying bacterium X3, and detected its nitrogen removal characteristics for providing evidence to explain the principle of heterotrophic nitrification-aerobic denitrification and to improve the process in purification of marine-culture wastewater. The evolutionary position of the strain was determined based on its morphological, physiological, biochemical characteristics and 16SrRNA gene sequence. The nitrification-denitrification ability of this strain was detected by detecting its nitrogen removal efficiency and growth on different inorganic nitrogen source. Strain X3 was identified as Halomonas sp. It grew optimally at salinity 3%, pH 8.5, C:N 10:1 at 28 degrees C, and it could still survive at 15% salinity. The removal of NH4+ -N, NO2(-) -N and NO3(-) -N was 98.29%, 99.07%, 96.48% respectively within 24 h. When three inorganic nitrogen existed simultaneously, it always utilized ammonia firstly, and the total inorganic nitrogen removal was higher than with only one nitrogen, suggesting that strain X3 has the ability of simultaneous nitrification and denitrification and completing the whole nitrogen removing process. Strain X3 belonged to the genus of Halomonas. It had strong simultaneous nitrification and denitrification capability and could live in high-salinity environment.

Descriptions of Roseiarcus fermentans gen. nov., sp. nov., a bacteriochlorophyll a-containing fermentative bacterium related phylogenetically to alphaproteobacterial methanotrophs, and of the family Roseiarcaceae fam. nov.

Science.gov (United States)

Kulichevskaya, Irina S; Danilova, Olga V; Tereshina, Vera M; Kevbrin, Vadim V; Dedysh, Svetlana N

2014-08-01

A light-pink-pigmented, microaerophilic bacterium was obtained from a methanotrophic consortium enriched from acidic Sphagnum peat and designated strain Pf56(T). Cells of this bacterium were Gram-negative, non-motile, thick curved rods that contained a vesicular intracytoplasmic membrane system characteristic of some purple non-sulfur alphaproteobacteria. The absorption spectrum of acetone/methanol extracts of cells grown in the light showed maxima at 363, 475, 505, 601 and 770 nm; the peaks at 363 and 770 nm are characteristic of bacteriochlorophyll a. However, in contrast to purple non-sulfur bacteria, strain Pf56(T) was unable to grow phototrophically under anoxic conditions in the light. Best growth occurred on some sugars and organic acids under micro-oxic conditions by means of fermentation. The fermentation products were propionate, acetate and hydrogen. Slow chemo-organotrophic growth was also observed under fully oxic conditions. Light stimulated growth. C1 substrates were not utilized. Strain Pf56(T) grew at pH 4.0-7.0 (optimum pH 5.5-6.5) and at 15-30 °C (optimum 22-28 °C). The major cellular fatty acids were 19 : 0 cyclo ω8c and 18 : 1ω7c; quinones were represented by ubiquinone Q-10. The G+C content of the DNA was 70.0 mol%. Strain Pf56 displays 93.6-94.7 and 92.7-93.7% 16S rRNA gene sequence similarity to members of the families Methylocystaceae and Beijerinckiaceae, respectively, and belongs to a large cluster of environmental sequences retrieved from various wetlands and forest soils in cultivation-independent studies. Phenotypic, genotypic and chemotaxonomic characteristics of strain Pf56(T) suggest that it represents a novel genus and species of bacteriochlorophyll a-containing fermentative bacteria, for which the name Roseiarcus fermentans gen. nov., sp. nov. is proposed. Strain Pf56(T) ( = DSM 24875(T) = VKM B-2876(T)) is the type strain of Roseiarcus fermentans, and is also the first characterized member of a novel family

Gasification of biomass chars in steam-nitrogen mixture

International Nuclear Information System (INIS)

Haykiri-Acma, H.; Yaman, S.; Kucukbayrak, S.

2006-01-01

Some agricultural and waste biomass samples such as sunflower shell, pinecone, rapeseed, cotton refuse and olive refuse were first pyrolyzed in nitrogen, and then, their chars were gasified in a gas mixture of steam and nitrogen. Experiments were performed using the thermogravimetric analysis technique. Pyrolysis of the biomass samples was performed at a heating rate of 20 K/min from ambient to 1273 K in a dynamic nitrogen atmosphere of 40 cm 3 min -1 . The obtained chars were cooled to ambient temperature and then gasified up to 1273 K in a dynamic atmosphere of 40 cm 3 min -1 of a mixture of steam and nitrogen. Derivative thermogravimetric analysis profiles from gasification of the chars were derived, and the mass losses from the chars were interpreted in terms of temperature. It was concluded that gasification characteristics of biomass chars were fairly dependent on the biomass properties such as ash and fixed carbon contents and the constituents present in the ash. Different mechanisms in the three temperature intervals, namely water desorption at lower temperatures, decomposition of hydroxide minerals to oxide minerals and formation of carbon monoxide at medium temperatures and production of hydrogen at high temperatures govern the behavior of the char during the gasification process. The chars from pinecone and sunflower shell could be easily gasified under the mentioned conditions. In order to further raise the conversion yields, long hold times should be applied at high temperatures. However, the chars from rapeseed and olive refuse were not gasified satisfactorily. Low ash content and high fixed carbon content biomass materials are recommended for use in gasification processes when char from pyrolysis at elevated temperatures is used as a feedstock

Ubiquity of insect-derived nitrogen transfer to plants by endophytic insect-pathogenic fungi: an additional branch of the soil nitrogen cycle.

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Behie, Scott W; Bidochka, Michael J

2014-03-01

The study of symbiotic nitrogen transfer in soil has largely focused on nitrogen-fixing bacteria. Vascular plants can lose a substantial amount of their nitrogen through insect herbivory. Previously, we showed that plants were able to reacquire nitrogen from insects through a partnership with the endophytic, insect-pathogenic fungus Metarhizium robertsii. That is, the endophytic capability and insect pathogenicity of M. robertsii are coupled so that the fungus acts as a conduit to provide insect-derived nitrogen to plant hosts. Here, we assess the ubiquity of this nitrogen transfer in five Metarhizium species representing those with broad (M. robertsii, M. brunneum, and M. guizhouense) and narrower insect host ranges (M. acridum and M. flavoviride), as well as the insect-pathogenic fungi Beauveria bassiana and Lecanicillium lecanii. Insects were injected with (15)N-labeled nitrogen, and we tracked the incorporation of (15)N into two dicots, haricot bean (Phaseolus vulgaris) and soybean (Glycine max), and two monocots, switchgrass (Panicum virgatum) and wheat (Triticum aestivum), in the presence of these fungi in soil microcosms. All Metarhizium species and B. bassiana but not L. lecanii showed the capacity to transfer nitrogen to plants, although to various degrees. Endophytic association by these fungi increased overall plant productivity. We also showed that in the field, where microbial competition is potentially high, M. robertsii was able to transfer insect-derived nitrogen to plants. Metarhizium spp. and B. bassiana have a worldwide distribution with high soil abundance and may play an important role in the ecological cycling of insect nitrogen back to plant communities.

Bioturbation: impact on the marine nitrogen cycle.

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Laverock, Bonnie; Gilbert, Jack A; Tait, Karen; Osborn, A Mark; Widdicombe, Steve

2011-01-01

Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into deeper sediment layers and allows the exchange of solutes between the sediment and water column. Burrows can effectively extend the oxic/anoxic interface into deeper sediment layers, thus providing a unique environment for nitrogen-cycling microbial communities. Recent studies have shown that the abundance and diversity of micro-organisms can be far greater in burrow wall sediment than in the surrounding surface or subsurface sediment; meanwhile, bioturbated sediment supports higher rates of coupled nitrification-denitrification reactions and increased fluxes of ammonium to the water column. In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study.

Determination of biological nitrogen fixation capacities of winter and spring lentil varieties by using ''1''5N methodology

International Nuclear Information System (INIS)

Akin, A.

2001-01-01

In order to determine the biological nitrogen fixation capacities of winter and spring varieties of lentil which have of agronomic importance under the Central Anatolia region, the field experiments (winter and spring) were carried out. In both experiments, the effects of two different iconoclasts and different harvesting times on the biological nitrogen fixation capacities of lentil varieties, were investigated. The field experiments were conducted using by randomized block design as split-split plot for 4 replications. Barley was selected as the reference crop and 20 cm row spacing were used for lentil and barley. Inoculations were done immediately before sowing. 10.0 kg N/ ha for lentil varieties as 10.0 % ''1''5N atom excess and 40.0 kg N/ ha for barley (reference crop) as 2.0 % ''1''5N atom excess ammonium sulphate fertilizer were applied. In addition, 60.0 kgP 2 O 5 / ha were applied as triple superphosphate for all treatments. Plants were harvested at the different growth stages and than plant materials prepared for the analysis. Total nitrogen and % ''1''5N atom excess analysis were done by Kjeldahl method and Emission spectrometer, respectively. The amount of nitrogen fixation capacities of winter and spring lentil varieties were calculated according to the A-Value method (IAEA 1990). The results showed us that the winter varieties of lentil had higher dry matter yields and nitrogen fixation capacities than the spring varieties. Inoculation treatments had no statistically significant effects on the percentage of nitrogen derived from atmosphere (% Ndfa) and the amount of fixed nitrogen (kg N/ ha) for both experiments. In comparison between the harvesting times, the highest amount of fixed nitrogen was found at the pod formation stage for all cultivars. The average amounts of % Ndfa and fixed nitrogen (kg N/ ha) were 75.0 and 70.0 for winter cultivars, 70.0 and 45.0 for spring cultivars, respectively

Symbiotic nitrogen fixation and nitrate uptake by the pea crop

International Nuclear Information System (INIS)

Jensen, E.S.

1986-08-01

Symbiotic nitrogen fixation and nitrate uptake by pea plants (Pisum sativum L.) were studied in field and pot experiments using the 15 N isotope dilution technique and spring barley as a non-fixing reference crop. Barley, although not ideal, seemed to be a suitable reference for pea in the 15 N-technique. Maximum N 2 fixation activity of 10 kg N fixed per ha per day was reached around the flat pod growth stage, and the activity decreased rapidly during pod-filling. The pea crop fixed between 100 and 250 kg N ha -1 , corresponding to from 45 to 80 per cent of total crop N. The amount of symbiotically fixed N 2 depended on the climatic conditions in the experimental year, the level of soil mineral N and the pea cultivar. Field-grown pea took up 60 to 70 per cent of the N-fertilizer supplied. The supply of 50 kg NO 3 -N ha -1 inhibited the N 2 fixation approximately 15 per cent. Small amounts of fertilizer N, supplied at sowing (starter-N), slightly stimulated the vegetative growth of pea, but the yields of seed dry matter and protein were not significantly influenced. In the present field experiments the environmental conditions, especially the distribution of rainfall during the growth season, seemed to be more important in determining the protein and dry matter yield of the dry pea crop, than the ability of pea to fix nitrogen symbiotically. However, fertilizer N supplied to pot-grown pea plants at the flat pod growth stage or as split applications significantly increased the yield of seed dry matter and protein. (author)

The value of symbiotic nitrogen fixation by grain legumes in comparison to the cost of nitrogen fertilizer used in developing countries

International Nuclear Information System (INIS)

Hardarson, G.; Bunning, S.; Montanez, A.; Roy, R.; MacMillan, A.

2001-01-01

A great challenge lies in devising more sustainable farming systems without compromising food production levels and food security. Obviously, increasing productivity is necessary to accommodate growth in the global population. World wide, the environmental factors that most severely restrict plant growth are the availability of water and nitrogen. The challenges in developing countries are to find ways of meeting this additional nitrogen demand without concomitant degrading natural productivity. Widespread adoption of biological nitrogen fixation (BNF) would contribute to this goal. BNF, together with adequate N management in the ecosystem, appears to be the most promising alternative to increasing the use of inorganic fertiliser nitrogen. BNF technologies represent economic, sustainable and environmentally friendly means of ensuring the nitrogen requirement of an agro-ecosystem. Here we investigate the value of BNF by grain legumes and compares it to the cost of nitrogen fertilizer used in developing countries. Our data show that major grain legumes fix approximately 11.1 million metric tons of nitrogen per annum in developing countries. If this N was supplied by inorganic fertiliser one would have to apply at least double that amount to achieve the same yields, and this would cost approximately 6.7 billion US dollars. As the eight major grain legumes grown in developing countries contribute 30 - 40% of the annual N requirement the contribution of BNF is of great economic and environmental importance. (author)

Evaluation of Arthrobacter aurescens Strain TC1 as Bioaugmentation Bacterium in Soils Contaminated with the Herbicidal Substance Terbuthylazine.

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Vera P Silva

Full Text Available In the last years the chloro-s-triazine active substance terbuthylazine has been increasingly used as an herbicide and may leave residues in the environment which can be of concern. The present study aimed at developing a bioaugmentation tool based on the soil bacterium Arthrobacter aurescens strain TC1 for the remediation of terbuthylazine contaminated soils and at examining its efficacy for both soil and aquatic compartments. First, the feasibility of growing the bioaugmentation bacterium inocula on simple sole nitrogen sources (ammonium and nitrate instead of atrazine, while still maintaining its efficiency to biodegrade terbuthylazine was shown. In sequence, the successful and quick (3 days bioremediation efficacy of ammonium-grown A. aurescens TC1 cells was proven in a natural soil freshly spiked or four-months aged with commercial terbuthylazine at a dose 10× higher than the recommended in corn cultivation, to mimic spill situations. Ecotoxicity assessment of the soil eluates towards a freshwater microalga supported the effectiveness of the bioaugmentation tool. Obtained results highlight the potential to decontaminate soil while minimizing terbuthylazine from reaching aquatic compartments via the soil-water pathway. The usefulness of this bioaugmentation tool to provide rapid environment decontamination is particularly relevant in the event of accidental high herbicide contamination. Its limitations and advantages are discussed.

Evaluation of Arthrobacter aurescens Strain TC1 as Bioaugmentation Bacterium in Soils Contaminated with the Herbicidal Substance Terbuthylazine

Science.gov (United States)

Silva, Vera P.; Moreira-Santos, Matilde; Mateus, Carla; Teixeira, Tânia; Ribeiro, Rui; Viegas, Cristina A.

2015-01-01

In the last years the chloro-s-triazine active substance terbuthylazine has been increasingly used as an herbicide and may leave residues in the environment which can be of concern. The present study aimed at developing a bioaugmentation tool based on the soil bacterium Arthrobacter aurescens strain TC1 for the remediation of terbuthylazine contaminated soils and at examining its efficacy for both soil and aquatic compartments. First, the feasibility of growing the bioaugmentation bacterium inocula on simple sole nitrogen sources (ammonium and nitrate) instead of atrazine, while still maintaining its efficiency to biodegrade terbuthylazine was shown. In sequence, the successful and quick (3 days) bioremediation efficacy of ammonium-grown A. aurescens TC1 cells was proven in a natural soil freshly spiked or four-months aged with commercial terbuthylazine at a dose 10× higher than the recommended in corn cultivation, to mimic spill situations. Ecotoxicity assessment of the soil eluates towards a freshwater microalga supported the effectiveness of the bioaugmentation tool. Obtained results highlight the potential to decontaminate soil while minimizing terbuthylazine from reaching aquatic compartments via the soil-water pathway. The usefulness of this bioaugmentation tool to provide rapid environment decontamination is particularly relevant in the event of accidental high herbicide contamination. Its limitations and advantages are discussed. PMID:26662024

Nitrogen Fixed by Pea Plant as Affected by Lead,Cadmium and Rates of N-Fertilizer Using 15N Tracer Technique

International Nuclear Information System (INIS)

Ismail, M.M.; El-Degwy, S.M.; Abdel-Aziz, H.A.; Elbaz, A.S.

2012-01-01

A pot experiment was carried out in greenhouse to investigate the effect Pb and Cd applied on growth, yield and the amount of fixed nitrogen by pea's plants. 15 N-labelled (5 % atom excess) ammonium nitrate was applied at three levels (0,20 and 40 mg N -1 kg soil). The legume pea seeds were inoculated with Rhizobium Leguminesarum. Lead was applied as lead sulfate at rates of 0, 50 and 200 mg Pb kg -1 soil, while the cadmium applied as cadmium sulfate at rates of 0, 5 and 10 mg Cd kg -1 soil. Results indicated that the highest values of Pb uptake were 540,11.55 and 552 mg -1 pot for pea shoot, pods and whole plant at the rate of 200 mg Pb kg -1 soil + 40 mg N kg -1 soil, respectively, While, the highest values of Cd-uptake were 13.90, 6.54 and 20 mg -1 pot at the rate of 10 mg Cd kg -1 + 20 mg N kg -1 soil for the same sequence. The values of Ndff and Ndfa were 43.74 and 278.2 while Ndfs recorded 164.1 mg pot -1 at rate of 5 mg Cd kg -1 soil + 40 mg N kg -1 soil compared to the control.

Draft genome sequence of Paraburkholderia tropica Ppe8 strain, a sugarcane endophytic diazotrophic bacterium.

Science.gov (United States)

Silva, Paula Renata Alves da; Simões-Araújo, Jean Luiz; Vidal, Márcia Soares; Cruz, Leonardo Magalhães; Souza, Emanuel Maltempi de; Baldani, José Ivo

Paraburkholderia tropica (syn Burkholderia tropica) are nitrogen-fixing bacteria commonly found in sugarcane. The Paraburkholderia tropica strain Ppe8 is part of the sugarcane inoculant consortium that has a beneficial effect on yield. Here, we report a draft genome sequence of this strain elucidating the mechanisms involved in its interaction mainly with Poaceae. A genome size of approximately 8.75Mb containing 7844 protein coding genes distributed in 526 subsystems was de novo assembled with ABySS and annotated by RAST. Genes related to the nitrogen fixation process, the secretion systems (I, II, III, IV, and VI), and related to a variety of metabolic traits, such as metabolism of carbohydrates, amino acids, vitamins, and proteins, were detected, suggesting a broad metabolic capacity and possible adaptation to plant association. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Nitrogen modulation of legume root architecture signalling pathways involves phytohormones and small regulatory molecules

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Nadiatul Akmal Mohd-Radzman

2013-10-01

Full Text Available Nitrogen, particularly nitrate is an important yield determinant for crops. However, current agricultural practice with excessive fertilizer usage has detrimental effects on the environment. Therefore, legumes have been suggested as a sustainable alternative for replenishing soil nitrogen. Legumes can uniquely form nitrogen-fixing nodules through symbiotic interaction with specialized soil bacteria. Legumes possess a highly plastic root system which modulates its architecture according to the nitrogen availability in the soil. Understanding how legumes regulate root development in response to nitrogen availability is an important step to improving root architecture. The nitrogen-mediated root development pathway starts with sensing soil nitrogen level followed by subsequent signal transduction pathways involving phytohormones, microRNAs and regulatory peptides that collectively modulate the growth and shape of the root system. This review focuses on the current understanding of nitrogen-mediated legume root architecture including local and systemic regulations by different N-sources and the modulations by phytohormones and small regulatory molecules.

Nitrogen modulation of legume root architecture signaling pathways involves phytohormones and small regulatory molecules.

Science.gov (United States)

Mohd-Radzman, Nadiatul A; Djordjevic, Michael A; Imin, Nijat

2013-10-01

Nitrogen, particularly nitrate is an important yield determinant for crops. However, current agricultural practice with excessive fertilizer usage has detrimental effects on the environment. Therefore, legumes have been suggested as a sustainable alternative for replenishing soil nitrogen. Legumes can uniquely form nitrogen-fixing nodules through symbiotic interaction with specialized soil bacteria. Legumes possess a highly plastic root system which modulates its architecture according to the nitrogen availability in the soil. Understanding how legumes regulate root development in response to nitrogen availability is an important step to improving root architecture. The nitrogen-mediated root development pathway starts with sensing soil nitrogen level followed by subsequent signal transduction pathways involving phytohormones, microRNAs and regulatory peptides that collectively modulate the growth and shape of the root system. This review focuses on the current understanding of nitrogen-mediated legume root architecture including local and systemic regulations by different N-sources and the modulations by phytohormones and small regulatory molecules.

Removal of carbon, nitrogen and phosphorus from the separated liquid phase of hog manure by the multi-zone BioCAST technology.

Science.gov (United States)

Yerushalmi, Laleh; Alimahmoodi, Mahmood; Afroze, Niema; Godbout, Stephane; Mulligan, Catherine N

2013-06-15

The removal of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) at concentrations of 960 ± 38 to 2400 ± 96 mg/L, 143 ± 9 to 235 ± 15 mg/L and 25 ± 2 to 57 ± 4 mg/L, respectively, from the separated liquid phase of hog manure by the multi-zone BioCAST technology is discussed. Despite the inhibitory effect of hog waste toward microbial activities, removal efficiencies up to 89.2% for COD, 69.2% for TN and 47.6% for TP were obtained during 185 d of continuous operation. The free ammonia inhibition was postulated to be responsible for the steady reduction of COD and TP removal with the increase of TN/TP ratio from 3.6 to 5.8. On the contrary, the increase of COD/TN ratio from 4.8 to 14.1 improved the removal of all contaminants. Nitrogen removal did not show any dependence on the COD/TP ratio, despite the steady increase of COD and TP removal with this ratio in the range of 19.3-50.6. The removal efficiencies of organic and inorganic contaminants increased progressively owing to the adaptation of microbial biomass, resulting from the presence of suspended biomass in the mixed liquor that circulated continuously between the three zones of aerobic, microaerophilic and anoxic, as well as the attached biomass immobilized inside the aerobic zone. Copyright © 2013 Elsevier B.V. All rights reserved.

Production of polyhydroxybutyrate and alginate from glycerol by Azotobacter vinelandii under nitrogen-free conditions

OpenAIRE

Yoneyama, Fuminori; Yamamoto, Mayumi; Hashimoto, Wataru; Murata, Kousaku

2015-01-01

Glycerol is an interesting feedstock for biomaterials such as biofuels and bioplastics because of its abundance as a by-product during biodiesel production. Here we demonstrate glycerol metabolism in the nitrogen-fixing species Azotobacter vinelandii through metabolomics and nitrogen-free bacterial production of biopolymers, such as poly-d-3-hydroxybutyrate (PHB) and alginate, from glycerol. Glycerol-3-phosphate was accumulated in A. vinelandii cells grown on glycerol to the exponential phase...

Nitrogen fixation in the activated sludge treatment of thermomechanical pulping wastewater: effect of dissolved oxygen.

Science.gov (United States)

Slade, A H; Anderson, S M; Evans, B G

2003-01-01

N-ViroTech, a novel technology which selects for nitrogen-fixing bacteria as the bacteria primarily responsible for carbon removal, has been developed to treat nutrient limited wastewaters to a high quality without the addition of nitrogen, and only minimal addition of phosphorus. Selection of the operating dissolved oxygen level to maximise nitrogen fixation forms a key component of the technology. Pilot scale activated sludge treatment of a thermomechanical pulping wastewater was carried out in nitrogen-fixing mode over a 15 month period. The effect of dissolved oxygen was studied at three levels: 14% (Phase 1), 5% (Phase 2) and 30% (Phase 3). The plant was operated at an organic loading of 0.7-1.1 kg BOD5/m3/d, a solids retention time of approximately 10 d, a hydraulic retention time of 1.4 d and a F:M ratio of 0.17-0.23 mg BOD5/mg VSS/d. Treatment performance was very stable over the three dissolved oxygen operating levels. The plant achieved 94-96% BOD removal, 82-87% total COD removal, 79-87% soluble COD removal, and >99% total extractives removal. The lowest organic carbon removals were observed during operation at 30% DO but were more likely to be due to phosphorus limitation than operation at high dissolved oxygen, as there was a significant decrease in phosphorus entering the plant during Phase 3. Discharge of dissolved nitrogen, ammonium and oxidised nitrogen were consistently low (1.1-1.6 mg/L DKN, 0.1-0.2 mg/L NH4+-N and 0.0 mg/L oxidised nitrogen). Discharge of dissolved phosphorus was 2.8 mg/L, 0.1 mg/L and 0.6 mg/L DRP in Phases 1, 2 and 3 respectively. It was postulated that a population of polyphosphate accumulating bacteria developed during Phase 1. Operation at low dissolved oxygen during Phase 2 appeared to promote biological phosphorus uptake which may have been affected by raising the dissolved oxygen to 30% in Phase 3. Total nitrogen and phosphorus discharge was dependent on efficient secondary clarification, and improved over the course of

Azospirillum Inoculation Alters Nitrate Reductase Activity and Nitrogen Uptake in Wheat Plant Under Water Deficit Conditions

OpenAIRE

N. Aliasgharzad, N. Aliasgharzad; Heydaryan, Zahra; Sarikhani, M.R

2014-01-01

Water deficit stress usually diminishes nitrogen uptake by plants. There are evidences that some nitrogen fixing bacteria can alleviate this stress by supplying nitrogen and improving its metabolism in plants. Four Azospirillum strains, A. lipoferum AC45-II, A. brasilense AC46-I, A. irakense AC49-VII and A. irakense AC51-VI were tested for nitrate reductase activity (NRA). In a pot culture experiment using a sandy loam soil, wheat plants (Triticum aestivum L. cv. Sardari) were inoculated with...

Improved Eco-Friendly Recombinant Anabaena sp. Strain PCC7120 with Enhanced Nitrogen Biofertilizer Potential▿

Science.gov (United States)

Chaurasia, Akhilesh Kumar; Apte, Shree Kumar

2011-01-01

Photosynthetic, nitrogen-fixing Anabaena strains are native to tropical paddy fields and contribute to the carbon and nitrogen economy of such soils. Genetic engineering was employed to improve the nitrogen biofertilizer potential of Anabaena sp. strain PCC7120. Constitutive enhanced expression of an additional integrated copy of the hetR gene from a light-inducible promoter elevated HetR protein expression and enhanced functional heterocyst frequency in the recombinant strain. The recombinant strain displayed consistently higher nitrogenase activity than the wild-type strain and appeared to be in homeostasis with compatible modulation of photosynthesis and respiration. The enhanced combined nitrogen availability from the recombinant strain positively catered to the nitrogen demand of rice seedlings in short-term hydroponic experiments and supported better growth. The engineered strain is stable, eco-friendly, and useful for environmental application as nitrogen biofertilizer in paddy fields. PMID:21057013

Improved eco-friendly recombinant Anabaena sp. strain PCC7120 with enhanced nitrogen biofertilizer potential.

Science.gov (United States)

Chaurasia, Akhilesh Kumar; Apte, Shree Kumar

2011-01-01

Photosynthetic, nitrogen-fixing Anabaena strains are native to tropical paddy fields and contribute to the carbon and nitrogen economy of such soils. Genetic engineering was employed to improve the nitrogen biofertilizer potential of Anabaena sp. strain PCC7120. Constitutive enhanced expression of an additional integrated copy of the hetR gene from a light-inducible promoter elevated HetR protein expression and enhanced functional heterocyst frequency in the recombinant strain. The recombinant strain displayed consistently higher nitrogenase activity than the wild-type strain and appeared to be in homeostasis with compatible modulation of photosynthesis and respiration. The enhanced combined nitrogen availability from the recombinant strain positively catered to the nitrogen demand of rice seedlings in short-term hydroponic experiments and supported better growth. The engineered strain is stable, eco-friendly, and useful for environmental application as nitrogen biofertilizer in paddy fields.

Symbiotic Burkholderia Species Show Diverse Arrangements of nif/fix and nod Genes and Lack Typical High-Affinity Cytochrome cbb3 Oxidase Genes.

Science.gov (United States)

De Meyer, Sofie E; Briscoe, Leah; Martínez-Hidalgo, Pilar; Agapakis, Christina M; de-Los Santos, Paulina Estrada; Seshadri, Rekha; Reeve, Wayne; Weinstock, George; O'Hara, Graham; Howieson, John G; Hirsch, Ann M

2016-08-01

Genome analysis of fourteen mimosoid and four papilionoid beta-rhizobia together with fourteen reference alpha-rhizobia for both nodulation (nod) and nitrogen-fixing (nif/fix) genes has shown phylogenetic congruence between 16S rRNA/MLSA (combined 16S rRNA gene sequencing and multilocus sequence analysis) and nif/fix genes, indicating a free-living diazotrophic ancestry of the beta-rhizobia. However, deeper genomic analysis revealed a complex symbiosis acquisition history in the beta-rhizobia that clearly separates the mimosoid and papilionoid nodulating groups. Mimosoid-nodulating beta-rhizobia have nod genes tightly clustered in the nodBCIJHASU operon, whereas papilionoid-nodulating Burkholderia have nodUSDABC and nodIJ genes, although their arrangement is not canonical because the nod genes are subdivided by the insertion of nif and other genes. Furthermore, the papilionoid Burkholderia spp. contain duplications of several nod and nif genes. The Burkholderia nifHDKEN and fixABC genes are very closely related to those found in free-living diazotrophs. In contrast, nifA is highly divergent between both groups, but the papilionoid species nifA is more similar to alpha-rhizobia nifA than to other groups. Surprisingly, for all Burkholderia, the fixNOQP and fixGHIS genes required for cbb3 cytochrome oxidase production and assembly are missing. In contrast, symbiotic Cupriavidus strains have fixNOQPGHIS genes, revealing a divergence in the evolution of two distinct electron transport chains required for nitrogen fixation within the beta-rhizobia.

N2-fixing legumes are linked to enhanced mineral dissolution and microbiome modulations in Neotropical rainforests

Science.gov (United States)

Epihov, Dimitar; Batterman, Sarah; Hedin, Lars; Saltonstall, Kristin; Hall, Jefferson; Leake, Jonathan; Beerling, David

2017-04-01

Legumes represent the dominant family of many tropical forests with estimates of 120 billion legume trees in the Amazon basin alone. Many rainforest legume trees form symbioses with N2-fixing bacteria. In the process of atmospheric N2-fixation large amounts of nitrogen-rich litter are generated, supplying half of all nitrogen required to support secondary rainforest succession. However, it is unclear how N2-fixers affect the biogeochemical cycling of other essential nutrients by affecting the rates of mineral dissolution and rock weathering. Here we show that N2-fixing legumes in young Panamanian rainforests promote acidification and enhance silicate rock weathering by a factor of 2 compared to non-fixing trees. We report that N2-fixers also associate with enhanced dissolution of Al- and Fe-bearing secondary minerals native to tropical oxisols. In legume-rich neighbourhoods, non-fixers benefited from raised weathering rates relative to those of legume-free zones thus suggesting a positive community effect driven by N2-fixers. These changes in weathering potential were tracked by parallel functional and structural changes in the soil and rock microbiomes. Our findings support the view that N2-fixing legumes are central components of biogeochemical cycling, associated with enhanced release of Fe- and Al-bound P and primary mineral products (Mg, Mo). Rainforest legume services therefore bear important implications to short-term C cycling related to forest growth and the long-term C cycle related to marine carbonate deposition fuelled by silicate weathering.

Stable Isotope Identification of Nitrogen Sources for United ...

Science.gov (United States)

We used natural abundance stable isotope data to evaluate nitrogen sources to U.S. west coast estuaries. We collected δ15N of macroalgae data and supplemented this with available data from the literature for estuaries from Mexico to Alaska. Stable isotope ratios of green macroalgae were compared to δ15N of dissolved inorganic nitrogen of oceanic and watershed end members. There was a latitudinal gradient in δ15N of macroalgae with southern estuaries being 7 per mil heavier than northern estuaries. Gradients in isotope data were compared to nitrogen sources estimated by the USGS using the SPARROW model. In California estuaries, the elevation of isotope data appeared to be related to anthropogenic nitrogen sources. In Oregon systems, the nitrogen levels of streams flowing into the estuaries are related to forest cover, rather than to developed land classes. In addition, the δ15N of macroalgae suggested that the ocean and nitrogen-fixing trees in the watersheds were the dominant nitrogen sources. There was also a strong gradient in δ15N of macroalgae with heavier sites located near the estuary mouth. In some Oregon estuaries, there was an elevation an elevation of δ15N above marine end members in the vicinity of wastewater treatment facility discharge locations, suggesting isotopes may be useful for distinguishing inputs along an estuarine gradient. Nutrients are the leading cause of water quality impairments in the United States, and as a result too

Dissolved organic nitrogen and carbon release by a marine unicellular diazotrophic cyanobacterium

NARCIS (Netherlands)

Benavides, M.; Agawin, N.S.R.; Aristegui, J.; Peene, J.; Stal, L.J.

2013-01-01

Dinitrogen (N-2) fixation rates may be underestimated when recently fixed N2 is released as dissolved organic nitrogen (DON). DON release (DONr) is substantial in the filamentous cyanobacterium Trichodesmium but has never been reported in unicellular diazotrophic cyanobacteria. We used axenic

Dissolved organic nitrogen and carbon release by a marine unicellular diazotrophic cyanobacterium

NARCIS (Netherlands)

Benavides, M.; Agawin, N.S.R.; Aristegui, J.; Peene, J.; Stal, L.J.

2013-01-01

Dinitrogen (N2) fixation rates may be underestimated when recently fixed N2 is released as dissolved organic nitrogen (DON). DON release (DONr) is substantial in the filamentous cyanobacterium Trichodesmium but has never been reported in unicellular diazotrophic cyanobacteria. We used axenic

Oxygen-Poor Microzones as Potential Sites of Microbial N2 Fixation in Nitrogen-Depleted Aerobic Marine Waters

Science.gov (United States)

Paerl, Hans W.; Prufert, Leslie E.

1987-01-01

The nitrogen-deficient coastal waters of North Carolina contain suspended bacteria potentially able to fix N2. Bioassays aimed at identifying environmental factors controlling the development and proliferation of N2 fixation showed that dissolved organic carbon (as simple sugars and sugar alcohols) and particulate organic carbon (derived from Spartina alterniflora) additions elicited and enhanced N2 fixation (nitrogenase activity) in these waters. Nitrogenase activity occurred in samples containing flocculent, mucilage-covered bacterial aggregates. Cyanobacterium-bacterium aggregates also revealed N2 fixation. In all cases bacterial N2 fixation occurred in association with surficial microenvironments or microzones. Since nitrogenase is oxygen labile, we hypothesized that the aggregates themselves protected their constituent microbes from O2. Microelectrode O2 profiles revealed that aggregates had lower internal O2 tensions than surrounding waters. Tetrazolium salt (2,3,5-triphenyl-3-tetrazolium chloride) reduction revealed that patchy zones existed both within microbes and extracellularly in the mucilage surrounding microbes where free O2 was excluded. Triphenyltetrazolium chloride reduction also strongly inhibited nitrogenase activity. These findings suggest that N2 fixation is mediated by the availability of the appropriate types of reduced microzones. Organic carbon enrichment appears to serve as an energy and structural source for aggregate formation, both of which were required for eliciting N2 fixation responses of these waters. Images PMID:16347337

General metabolism of Laribacter hongkongensis: a genome-wide analysis

Directory of Open Access Journals (Sweden)

Curreem Shirly O

2011-04-01

Full Text Available Abstract Background Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes and pathways of the general metabolism of L. hongkongensis and correlated them with its phenotypic characteristics. Results The L. hongkongensis genome possesses the pentose phosphate and gluconeogenesis pathways and tricarboxylic acid and glyoxylate cycles, but incomplete Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in agreement with its asaccharolytic phenotype. It contains enzymes for biosynthesis and β-oxidation of saturated fatty acids, biosynthesis of all 20 universal amino acids and selenocysteine, the latter not observed in Neisseria gonorrhoeae, Neisseria meningitidis and Chromobacterium violaceum. The genome contains a variety of dehydrogenases, enabling it to utilize different substrates as electron donors. It encodes three terminal cytochrome oxidases for respiration using oxygen as the electron acceptor under aerobic and microaerophilic conditions and four reductases for respiration with alternative electron acceptors under anaerobic conditions. The presence of complete tetrathionate reductase operon may confer survival advantage in mammalian host in association with diarrhea. The genome contains CDSs for incorporating sulfur and nitrogen by sulfate assimilation, ammonia assimilation and nitrate reduction. The existence of both glutamate dehydrogenase and glutamine synthetase/glutamate synthase pathways suggests an importance of ammonia metabolism in the living environments that it may encounter. Conclusions The L. hongkongensis genome possesses a variety of genes and pathways for carbohydrate, amino acid and lipid metabolism, respiratory chain and sulfur and nitrogen metabolism. These allow the bacterium to utilize various substrates for energy production and survive in different environmental niches.

Nitrogen fixation in seedlings of sabia and leucena grown in the caatinga soils under different vegetation covers

International Nuclear Information System (INIS)

Santana, Augusto Cesar de Arruda; Nascimento, Luciana Remigio Santos; Silva, Arthur Jorge da; Freitas, Ana Dolores Santiago de

2013-01-01

The aim of this study was to evaluate the efficiency differences of populations forming bacteria in legume nodules (BNL) in areas under different vegetation cover in semi-arid Pernambuco state, Brazil, using the methodology of the natural abundance of 15 N to estimate the amount of N fixed symbiotically. The highest levels of nitrogen was found in plants of leucena, and the sabia had levels that did not differ from reference species. The analysis by the technique of 15N showed that in all areas the leucena and the sabia showed signs of 15N different of the average signal of the control plants. The largest nitrogen accumulation was observed for leucena in the Caatinga and Capoeira. The sabia got greater accumulation of N from the Caatinga. The areas of Capoeira and Caatinga has showed the native populations of rhizobia with greater ability to fix nitrogen for the leucena

Growth Kinetics of Diazotrophic Bacillus sphaericus UPMB10 Cultured Using Different Types and Concentrations of Carbon and Nitrogen Sources

Directory of Open Access Journals (Sweden)

Ooi, T. C.

2008-01-01

Full Text Available Growth kinetics of newly isolated diazotrophic Bacillus sphaericus UPMB10 grown in various carbon (lactate, acetate, glycerol, malate, fructose, xylose and sucrose and nitrogen (glutamate, yeast extract, arginine, hystadine, glycine, polypeptone, tryptophan, lysine, NH4Cl and urea sources was investigated using 2 L stirred tank fermenter. The highest growth was obtained in a medium containing lactate as a carbon source, which gave the highest maximum cell concentration of 2.30 g/L, which is corresponding to maximum viable cell count of 4.60 x 10^9 cfu/mL. However, the highest cell yield (1.06 g cell/g carbon consumed was obtained in cultivation using glycerol though slightly lower maximum viable cell count was obtained (3.22 x 10^9 cfu/mL. In addition, cost for the production of live cell using glycerol was about 15 times lower than the cost using lactate. Growth performance of this bacterium when yeast extract was used as a nitrogen source was comparable to the use of pure amino acid. The medium containing 1.8 g/L glycerol and 2 g/L yeast extract was suggested as optimal for growth of this bacterium, which gave carbon to nitrogen ratio (C/N of 10:1. The maximum viable cell count obtained in cultivation using optimised medium in 2 L stirred tank fermenter was 3.34 x 10^9 cfu/mL and the cells maintained its capacity for N2 fixation at 18 nmol C2H2/h.mL.

Formation of N{sub 2} during the fixed-bed pyrolysis of coals

Energy Technology Data Exchange (ETDEWEB)

Wu, Zhiheng; Ohtsuka, Yasuo [Tohoku Univ., Sendai (Japan); Furimsky, E. [Natural Resources Canada, Ottawa, Ontario (Canada)

1995-12-31

Research on the fate of the nitrogen in coal during pyrolysis has attracted increased attention, since it is related with the NO{sub x} and N{sub 2}O emissions during subsequent combustion. It has been reported that coal nitrogen is initially released as tar, which is then converted to HCN and NH{sub 3} through secondary decomposition reactions. However, little attention to N{sub 2} has been paid so far. We have recently found that N{sub 2} is the dominant product in slow heating rate pyrolysis of a subbituminous coal, and that the finely dispersed iron catalyst promotes drastically the formation of N{sub 2} from a brown coal. If coal nitrogen can be removed efficiently as N{sub 2} during pyrolysis, this method would contribute to the reduction of the NO{sub x} and N{sub 2}O emissions, since such pollutants originate mostly from coal nitrogen. Therefore the present study aims at making clear the influence of coal type, pyrolysis conditions, demineralization, and iron catalyst on the formation of N{sub 2} during the fix-bed pyrolysis of several coals with different ranks.

Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching

KAUST Repository

Pogoreutz, Claudia; Radecker, Nils; Cardenas, Anny; Gä rdes, Astrid; Voolstra, Christian R.; Wild, Christian

2017-01-01

The disruption of the coral-algae symbiosis (coral bleaching) due to rising sea surface temperatures has become an unprecedented global threat to coral reefs. Despite decades of research, our ability to manage mass bleaching events remains hampered by an incomplete mechanistic understanding of the processes involved. In this study, we induced a coral bleaching phenotype in the absence of heat and light stress by adding sugars. The sugar addition resulted in coral symbiotic breakdown accompanied by a fourfold increase of coral-associated microbial nitrogen fixation. Concomitantly, increased N:P ratios by the coral host and algal symbionts suggest excess availability of nitrogen and a disruption of the nitrogen limitation within the coral holobiont. As nitrogen fixation is similarly stimulated in ocean warming scenarios, here we propose a refined coral bleaching model integrating the cascading effects of stimulated microbial nitrogen fixation. This model highlights the putative role of nitrogen-fixing microbes in coral holobiont functioning and breakdown.

Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching

KAUST Repository

Pogoreutz, Claudia

2017-04-21

The disruption of the coral-algae symbiosis (coral bleaching) due to rising sea surface temperatures has become an unprecedented global threat to coral reefs. Despite decades of research, our ability to manage mass bleaching events remains hampered by an incomplete mechanistic understanding of the processes involved. In this study, we induced a coral bleaching phenotype in the absence of heat and light stress by adding sugars. The sugar addition resulted in coral symbiotic breakdown accompanied by a fourfold increase of coral-associated microbial nitrogen fixation. Concomitantly, increased N:P ratios by the coral host and algal symbionts suggest excess availability of nitrogen and a disruption of the nitrogen limitation within the coral holobiont. As nitrogen fixation is similarly stimulated in ocean warming scenarios, here we propose a refined coral bleaching model integrating the cascading effects of stimulated microbial nitrogen fixation. This model highlights the putative role of nitrogen-fixing microbes in coral holobiont functioning and breakdown.

Dense populations of a giant sulfur bacterium in Namibian shelf sediments

DEFF Research Database (Denmark)

Schulz, HN; Brinkhoff, T.; Ferdelman, TG

1999-01-01

A previously unknown giant sulfur bacterium is abundant in sediments underlying the oxygen minimum zone of the Benguela Current upwelling system. The bacterium has a spherical cell that exceeds by up to 100-fold the biovolume of the largest known prokaryotes. On the basis of 16S ribosomal DNA...

Isolation, Identification, and Optimization of Culture Conditions of a Bioflocculant-Producing Bacterium Bacillus megaterium SP1 and Its Application in Aquaculture Wastewater Treatment.

Science.gov (United States)

Luo, Liang; Zhao, Zhigang; Huang, Xiaoli; Du, Xue; Wang, Chang'an; Li, Jinnan; Wang, Liansheng; Xu, Qiyou

2016-01-01

A bioflocculant-producing bacterium, Bacillus megaterium SP1, was isolated from biofloc in pond water and identified by using both 16S rDNA sequencing analysis and a Biolog GEN III MicroStation System. The optimal carbon and nitrogen sources for Bacillus megaterium SP1 were 20 g L -1 of glucose and 0.5 g L -1 of beef extract at 30°C and pH 7. The bioflocculant produced by strain SP1 under optimal culture conditions was applied into aquaculture wastewater treatment. The removal rates of chemical oxygen demand (COD), total ammonia nitrogen (TAN), and suspended solids (SS) in aquaculture wastewater reached 64, 63.61, and 83.8%, respectively. The volume of biofloc (FV) increased from 4.93 to 25.97 mL L -1 . The addition of Bacillus megaterium SP1 in aquaculture wastewater could effectively improve aquaculture water quality, promote the formation of biofloc, and then form an efficient and healthy aquaculture model based on biofloc technology.

Concentration and Transport of Nitrate by the Mat-Forming Sulfur Bacterium Thioploca Rid E-1821-2011

DEFF Research Database (Denmark)

FOSSING, H.; GALLARDO, VA; JØRGENSEN, BB

1995-01-01

MARINE species of Thioploca occur over 3,000 km along the continental shelf off Southern Peru and North and Central Chile(1-4). These filamentous bacteria live in bundles surrounded by a common sheath and form thick mats on the sea floor under the oxygen-minimum zone in the upwelling region......, at between 40 and 280 m water depth. The metabolism of this marine bacterium(5,6) remained a mystery until long after its discovery(1,7). We report here that Thioploca cells are able to concentrate nitrate to up to 500 mM in a liquid vacuole that occupies >80% of the cell volume. Gliding filaments transport...... this nitrate 5-10 cm down into the sediment and reduce it, with concomitant oxidation of hydrogen sulphide, thereby coupling the nitrogen and sulphur cycles in the sediment....

Estimates of biological nitrogen fixation by Pterocarpus lucens in a ...

African Journals Online (AJOL)

Nitrogen (N2) fixation by Pterocarpus lucens in a natural semi arid ecosystem, in Ferlo, Senegal was estimated using 15N natural abundance (15N) procedure. Other non-fixing trees accompanying P. lucens in the same area were also investigated as control. Results showed an important variation of 15N in leaves between ...

Biological Nitrogen Fixation on Legume

Directory of Open Access Journals (Sweden)

Armiadi

2009-03-01

Full Text Available Nitrogen (N is one of the major limiting factors for crop growth and is required in adequate amount, due to its function as protein and enzyme components. In general, plants need sufficient nitrogen supply at all levels of growth, especially at the beginning of growth phase. Therefore, the availability of less expensive N resources would reduce the production cost. The increasing use of chemical fertilizer would probably disturb soil microorganisms, reduce the physical and chemical characteristics of soil because not all of N based fertilizer applied can be absorbed by the plants. Approximately only 50% can be used by crops, while the rest will be altered by microorganism into unavailable N for crops or else dissappear in the form of gas. Leguminous crops have the capacity to immobilize N2 and convert into the available N if innoculated with Rhizobium. The amount of N2 fixed varies depending on legume species and their environment.

Moritella viscosa, a pathogenic bacterium affecting the fillet quality in fish

DEFF Research Database (Denmark)

Ingerslev, Hans-Christian; Nielsen, Michael Engelbrecht

2011-01-01

Moritella viscosa is a bacterium belonging to the family Moritellaceae and was formerly known as Vibrio viscosus. The name ‘viscosa’ originates from the slimy nature of the bacterium. M. viscosa is considered to be the main causative agent of the phenomenon ‘winter ulcer’ or ‘cold-water ulcer......’ which affects various fish species in seawater during cold periods (Lunder et al. 1995). The bacterium is mainly a problem for farmed salmonid species, such as Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), but has also been isolated from other fish species, including Atlantic...... market price because of a quality downgrade caused by textural changes in the fillet....

Effect of an ntrC mutation on amino acid or urea utilization and on nitrogenase switch-off in Herbaspirillum seropedicae.

Science.gov (United States)

Gusso, Claudio L; de Souza, Emanuel M; Rigo, Liu Un; de Oliveira Pedrosa, Fábio; Yates, M G; de M Rego, Fabiane G; Klassen, Giseli

2008-03-01

Herbaspirillum seropedicae is a nitrogen-fixing bacterium that grows well with ammonium chloride or sodium nitrate as alternative single nitrogen sources but that grows more slowly with L-alanine, L-serine, L-proline, or urea. The ntrC mutant strain DCP286A was able to utilize only ammonium or urea of these nitrogen sources. The addition of 1 mmol.L-1 ammonium chloride to the nitrogen-fixing wild-type strain inhibited nitrogenase activity rapidly and completely. Urea was a less effective inhibitor; approximately 20% of nitrogenase activity remained 40 min after the addition of 1 mmol x L-1 urea. The effect of the ntrC mutation on nitrogenase inhibition (switch-off) was studied in strain DCP286A containing the constitutively expressed gene nifA of H. seropedicae. In this strain, nitrogenase inhibition by ammonium was completely abolished, but the addition of urea produced a reduction in nitrogenase activity similar to that of the wild-type strain. The results suggest that the NtrC protein is required for assimilation of nitrate and the tested amino acids by H. seropedicae. Furthermore, NtrC is also necessary for ammonium-induced switch-off of nitrogenase but is not involved in the mechanism of nitrogenase switch-off by urea.

Biological nitrogen fixation in common bean and faba bean using N-15 methodology and two reference crops

International Nuclear Information System (INIS)

Calvache, Marcelo.

1989-01-01

A field was conducted on a Typic ustropepts soil located at 'La Tola', the experimental campus of the Agricultural Sciences Faculty at Tumbaco, Ecuador. The objectives were to quantify faba bean (Vicia faba) and common bean (Phaseolus vulgaris) biological nitrogen fixation, using quinoa (chenopodium quinoa) and maize (Zea mays) as reference crops. The average values were 80 and 70 per cent for faba bean and 42 and 14 per cent for common bean, respectively. It was assumed that nitrogen use eficiency was the same for fixing crops but observed that a crop with high nitrogen use efficiency overestimates legume biological nitrogen fixation. Results suggests that greater caution is needed when selecting reference crops for legumes with nitrogen fixation

The carbon-nitrogen balance of the nodule and its regulation under elevated carbon dioxide concentration.

Science.gov (United States)

Libault, Marc

2014-01-01

Legumes have developed a unique way to interact with bacteria: in addition to preventing infection from pathogenic bacteria like any other plant, legumes also developed a mutualistic symbiotic relationship with one gender of soil bacteria: rhizobium. This interaction leads to the development of a new root organ, the nodule, where the differentiated bacteria fix for the plant the atmospheric dinitrogen (atmN2). In exchange, the symbiont will benefit from a permanent source of carbon compounds, products of the photosynthesis. The substantial amounts of fixed carbon dioxide dedicated to the symbiont imposed to the plant a tight regulation of the nodulation process to balance carbon and nitrogen incomes and outcomes. Climate change including the increase of the concentration of the atmospheric carbon dioxide is going to modify the rates of plant photosynthesis, the balance between nitrogen and carbon, and, as a consequence, the regulatory mechanisms of the nodulation process. This review focuses on the regulatory mechanisms controlling carbon/nitrogen balances in the context of legume nodulation and discusses how the change in atmospheric carbon dioxide concentration could affect nodulation efficiency.

Plant delta 15N correlates with the transpiration efficiency of nitrogen acquisition in tropical trees.

Science.gov (United States)

Cernusak, Lucas A; Winter, Klaus; Turner, Benjamin L

2009-11-01

Based upon considerations of a theoretical model of (15)N/(14)N fractionation during steady-state nitrate uptake from soil, we hypothesized that, for plants grown in a common soil environment, whole-plant delta(15)N (deltaP) should vary as a function of the transpiration efficiency of nitrogen acquisition (F(N)/v) and the difference between deltaP and root delta(15)N (deltaP - deltaR). We tested these hypotheses with measurements of several tropical tree and liana species. Consistent with theoretical expectations, both F(N)/v and deltaP - deltaR were significant sources of variation in deltaP, and the relationship between deltaP and F(N)/v differed between non-N(2)-fixing and N(2)-fixing species. We interpret the correlation between deltaP and F(N)/v as resulting from variation in mineral nitrogen efflux-to-influx ratios across plasma membranes of root cells. These results provide a simple explanation of variation in delta(15)N of terrestrial plants and have implications for understanding nitrogen cycling in ecosystems.

Evaluation of nodulation and nitrogen fixing potentials of some herbaceous legumes in inland valley soil

International Nuclear Information System (INIS)

Bayorbor, T. B.; Addai, I. K.; Lawson, I. Y. D.; Dogbe, W.; Djagbletey, D.

2006-01-01

A screening experiment was conducted to evaluate the nodulation, nitrogen fixation and biomass production of eleven herbaceous legumes in three soil series mainly used for rice production in the Guinea savannah agro-ecological zone of Ghana. This study was carried out with a view to fully exploiting the potential of N-fixating legumes as a supplement to inorganic N-fertilizers in rice-based cropping systems. The treatment combinations were laid out in a factorial experiment in randomized complete block design (RCBD) with three replications. Plant samples were harvested at flowering for nodule count, biomass production and N-fixation. The study revealed that the mucuna and crotalaria species were the best nitrogen fixers and biomass producers. For increased yields of rice in the study area, these legumes require more intensive field study for their integration into the rice-based cropping systems. (au)

Serpentine endophytic bacterium Pseudomonas azotoformans ASS1 accelerates phytoremediation of soil metals under drought stress.

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Ma, Ying; Rajkumar, Mani; Moreno, António; Zhang, Chang; Freitas, Helena

2017-10-01

This study evaluates the potential of serpentine endophytic bacterium to foster phytoremediation efficiency of Trifolium arvense grown on multi-metal (Cu, Zn and Ni) contaminated soils under drought stress. A drought resistant endophytic bacterial strain ASS1 isolated from the leaves of Alyssum serpyllifolium grown in serpentine soils was identified as Pseudomonas azotoformans based on biochemical tests and partial 16S rRNA gene sequencing. P. azotoformans ASS1 possessed abiotic stress resistance (heavy metals, drought, salinity, antibiotics and extreme temperature) and plant growth promoting (PGP) properties (phosphate solubilization, nitrogen fixation, production of 1-aminocyclopropane-1-carboxylate deaminase, siderophore and ammonia). Inoculation of T. arvense with ASS1 considerably increased the plant biomass and leaf relative water content in both roll towel assay and pot experiments in the absence and presence of drought stress (DS). In the pot experiments, ASS1 greatly enhanced chlorophyll content, catalase, peroxidase, superoxide dismutase activities, and proline content (only in the absence of drought) in plant leaves, whereas they decreased the concentrations of malondialdehyde. Irrespective of water stress, ASS1 significantly improved accumulation, total removal, bio-concentration factor and biological accumulation coefficient of metals (Cu, Zn and Ni), while decreased translocation factors of Cu. The effective colonization and survival in the rhizosphere and tissue interior assured improved plant growth and successful metal phytoremediation under DS. These results demonstrate the potential of serpentine endophytic bacterium ASS1 for protecting plants against abiotic stresses and helping plants to thrive in semiarid ecosystems and accelerate phytoremediation process in metal polluted soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of Frankia and Rhizobial strains as inocula for nitrogen-fixing trees in saline conditions

International Nuclear Information System (INIS)

Hafeez, F.Y.; Hameed, S.; Malik, K.A.

1998-01-01

Frankia strains isolated from various Casuarina species were screened for nodulation and N 2 -fixing ability on C. glauca and C. obesa under controlled-environment conditions. Five out of thirteen strains induced effective root nodules on C. glauca, but none did so on C. obesa; two strains were selected. Similarly, various rhizobial strains were screened for nodulation and N 2 fixation on four Acacia species and finally three were selected for compatibility with A. ampliceps. The two Frankia strains (CcOl and CcI3) and three Rhizobium strains (Abal, Ar2-1 and PMA63/1) were checked for NaCl-tolerance in vitro, and were used as inocula to estimate N 2 fixation in fast-growing trees under highly saline field conditions. The isotope-dilution method was used to estimate the proportion and amount of N 2 -fixed by A. ampliceps and C. glauca with Eucalyptus camaldulensis as the non-fixing check. After a year, A. ampliceps plants formed a few root nodules at low Ec c levels, but during the second and third years profuse nodulation was observed. In 1-year-old plants the fraction of N derived from fixation (Ndfa) ranged from 7 to 55% (average 31%) in A. ampliceps and from 7 to 24% (average 15%) in C. glauca, and after two years %Ndfa for A. ampliceps increased markedly, with values up to 86%. On the other hand, increases in %Ndfa for C. glauca were insignificant, possibly due to the use of E. camaldulensis as the non-fixing reference plant. Infection of tree roots by vesicular arbuscular mycorrhiza (VAM), scored after 3 years, showed a negative relationship with soil electric conductivity, as did VAM spore number. The spores isolated from saline soils had thicker walls than those from a fertile soil. Decreases in the soil salinity levels were observed at the end of the 3-year experiment. (author)

Sensitivity of some nitrogen fixers and the target pest Fusarium oxysporum to fungicide thiram

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Osman, Awad G.; Sherif, Ashraf M.; Elhussein, Adil A.; Mohamed, Afrah T.

2012-01-01

This study was carried out to investigate the toxic effects of the fungicide thiram (TMTD) against five nitrogen fixers and the thiram target pest Fusarium oxysporum under laboratory conditions. Nitrogen fixing bacteria Falvobacterium showed the highest values of LD50 and proved to be the most resistant to the fungicide followed by Fusarium oxysporum, while Pseudomonas aurentiaca was the most affected microorganism. LD50 values for these microorganisms were in 2–5 orders of magnitude lower in...

Nitrogen metabolism in plants using 15N as tracer. Part of a coordinated programme on the use of isotopes in fertilizer efficiency studies on grain legumes

International Nuclear Information System (INIS)

Pate, J.; Atkins, C.

1978-01-01

Techniques are described for studying the economy of carbon and nitrogen in annual nodulated legumes. Budgets for utilization of net photosynthate are constructed for cowpea (Vigna unguiculata (L) Walp.) and white lupin (Lupinus albus L.), including expenditure in respiration and dry matter accumulation of plant parts, carbon consumption in growth, respiration and export of fixed nitrogen by nodules, and the provision of recent photosynthate and earlier-fixed carbon to fruits. Sources of nitrogen to fruits are defined, and efficiencies of conversion of net photosynthate to protein of above-ground vegetative parts and of seeds are computed. Consideration is given to the timing of events associated with loss of symbiotic activity after flowering. Literature giving estimates of the respiratory requirements of nitrogen fixation by nodules is reviewed. Rates of respiration of nodules of cowpea, white lupin and pea (Pisum sativum L.) are assessed from a theoretical viewpoint, basing the estimates on ATP requirements for assimilation of N 2 into nitrogenous solutes, and published values for respiration costs in plant tissues. Expressed as CO 2 output per unit of nitrogen assimilated, these estimates greatly exceed the experimentally-observed CO 2 efflux of nodules of the species. This discrepancy is examined in relation to the capacity of nodules to fix CO 2 and the uncertainty of the in vivo requirement of nitrogenase for ATP

Structural characterization of the RNA chaperone Hfq from the nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1.

Science.gov (United States)

Kadowaki, Marco Antonio Seiki; Iulek, Jorge; Barbosa, João Alexandre Ribeiro Gonçalves; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Chubatsu, Leda Satie; Monteiro, Rose Adele; de Oliveira, Marco Aurélio Schüler; Steffens, Maria Berenice Reynaud

2012-02-01

The RNA chaperone Hfq is a homohexamer protein identified as an E. coli host factor involved in phage Qβ replication and it is an important posttranscriptional regulator of several types of RNA, affecting a plethora of bacterial functions. Although twenty Hfq crystal structures have already been reported in the Protein Data Bank (PDB), new insights into these protein structures can still be discussed. In this work, the structure of Hfq from the β-proteobacterium Herbaspirillum seropedicae, a diazotroph associated with economically important agricultural crops, was determined by X-ray crystallography and small-angle X-ray scattering (SAXS). Biochemical assays such as exclusion chromatography and RNA-binding by the electrophoretic shift assay (EMSA) confirmed that the purified protein is homogeneous and active. The crystal structure revealed a conserved Sm topology, composed of one N-terminal α-helix followed by five twisted β-strands, and a novel π-π stacking intra-subunit interaction of two histidine residues, absent in other Hfq proteins. Moreover, the calculated ab initio envelope based on small-angle X-ray scattering (SAXS) data agreed with the Hfq crystal structure, suggesting that the protein has the same folding structure in solution. Copyright © 2011 Elsevier B.V. All rights reserved.

Altered Nitrogenous Pools Induced by the Azolla-Anabaena Azolla Symbiosis

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Newton, Jack W.; Cavins, James F.

1976-01-01

The free amino acid and ammonia pools of Azolla caroliniana were analyzed by quantitative column chromatography on columns capable of separating all of the nitrogenous constituents normally found in physiological fluids. Comparisons were made of plants containing symbiotic algae and grown on nitrogen-free media, plants grown on media containing nitrate, and algae-free plants also grown on nitrate media. The major feature of the data was a very high level of intracellular ammonia found in plants which contain N2-fixing algal symbionts. In addition to the more usual amino acids, serine and cystathionine were found in the free amino acid pool. PMID:16659770

Rate and time of nitrogen fertilizer application on the growth, nitrogen remobilization and yield of soyabean (Glycine max(L) Merrill)

International Nuclear Information System (INIS)

Bebeley, J. F.; Sarkodie-Addo; Duku, S.

2015-01-01

Two field experiments were conducted in 2012 at the plantation Crop section of the Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, to investigate the effect N availability on nodulation, nitrogen fixation, N remobilization and grain yield of soybean. The design used in both studies was a 3 x 4 factorial arranged in randomized complete block design. Each treatment was replicated three times. The factors studied were rate and time of N fertilizer application. The N rate were 0, 20, 40 and 60kg N/ha and the time of application were early vegetative and early flowering phases. Anidaso, an improved soybean variety of 110 days maturity was used. Following land preparation, seeds were planted at the beginning of the rains at a spacing of 50 x 5cm. All required cultural practices were observed. Data collected were nodule number per plant and nodule dry weight, number of pods per plant, number of seeds per pod, 100 seeds weight, total nitrogen fixed, harvest index, grain yield and remobilized N. The total nitrogen difference method was used in determining the amount of N 2 fixed by the soybean and the micro kjeldahl method was used in determining the total plant N. The results indicated that nodulation was not significantly (p>0.05) affected by N rate and time of N application. However Nitrogen fixation was significantly (p<0.05 in affected time of N application in the minor season. Harvest index was significantly affected time of N application in the major season. Grain yield was also significantly affected by time of N application in both seasons. The results indicate that if farmers would apply N fertilizer to soybean at the vegetative growth phase, there would be increase in yield. The study also demonstrate that N remobilization occurs in soybean during grain filling although rate and time of application used did not significantly (p>0.05) affect N remobilization. (au)

Coffea arabica L., a new host plant for Acetobacter diazotrophicus, and isolation of other nitrogen-fixing acetobacteria.

Science.gov (United States)

Jimenez-Salgado, T; Fuentes-Ramirez, L E; Tapia-Hernandez, A; Mascarua-Esparza, M A; Martinez-Romero, E; Caballero-Mellado, J

1997-09-01

Acetobacter diazotrophicus was isolated from coffee plant tissues and from rhizosphere soils. Isolation frequencies ranged from 15 to 40% and were dependent on soil pH. Attempts to isolate this bacterial species from coffee fruit, from inside vesicular-arbuscular mycorrhizal fungi spores, or from mealybugs (Planococcus citri) associated with coffee plants were not successful. Other acid-producing diazotrophic bacteria were recovered with frequencies of 20% from the coffee rhizosphere. These N2-fixing isolates had some features in common with the genus Acetobacter but should not be assigned to the species Acetobacter diazotrophicus because they differed from A. diazotrophicus in morphological and biochemical traits and were largely divergent in electrophoretic mobility patterns of metabolic enzymes at coefficients of genetic distance as high as 0.950. In addition, these N2-fixing acetobacteria differed in the small-subunit rRNA restriction fragment length polymorphism patterns obtained with EcoRI, and they exhibited very low DNA-DNA homology levels, ranging from 11 to 15% with the A. diazotrophicus reference strain PAI 5T. Thus, some of the diazotrophic acetobacteria recovered from the rhizosphere of coffee plants may be regarded as N2-fixing species of the genus Acetobacter other than A. diazotrophicus. Endophytic diazotrophic bacteria may be more prevalent than previously thought, and perhaps there are many more potentially beneficial N2-fixing bacteria which can be isolated from other agronomically important crops.

Economy of Photosynthate Use in Nitrogen-fixing Legume Nodules: Observations on Two Contrasting Symbioses.

Science.gov (United States)

Layzell, D B; Rainbird, R M; Atkins, C A; Pate, J S

1979-11-01

The economy of C use by root nodules was examined in two symbioses, Vigna unguiculata (L.) Walp. (cv. Caloona):Rhizobium CB756 and Lupinus albus L. (cv. Ultra):Rhizobium WU425 over a 2-week period in early vegetative growth. Plants were grown in minus N water culture with cuvettes attached to the nodulated zone of their primary roots for collection of evolved CO(2) and H(2). Increments in total plant N and in C and N of nodules, and C:N weight ratios of xylem and phloem exudates were studied by periodic sampling from the plant populations. Itemized budgets were constructed for the partitioning and utilization of C in the two species. For each milligram N fixed and assimilated by the cowpea association, 1.54 +/- 0.26 (standard error) milligrams C as CO(2) and negligible H(2) were evolved and 3.11 milligrams of translocated C utilized by the nodules. Comparable values for nodules of the lupin association were 3.64 +/- 0.28 milligrams C as CO(2), 0.22 +/- 0.05 milligrams H(2), and 6.58 milligrams C. More efficient use of C by cowpea nodules was due to a lesser requirement of C for synthesis of exported N compounds, a smaller allocation of C to nodule dry matter, and a lower evolution of CO(2). The activity of phosphoenolpyruvate carboxylase in nodule extracts and the rate of (14)CO(2) fixation by detached nodules were greater for the cowpea symbiosis (0.56 +/- 0.06 and 0.22 milligrams C as CO(2) fixed per gram fresh weight per hour, respectively) than for the lupin 0.06 +/- 0.02 and 0.01 milligrams C as CO(2) fixed per gram fresh weight per hour. The significance of the data was discussed in relation to current information on theoretical costs of nitrogenase functioning and associated nodule processes.

A mechanistic, globally-applicable model of plant nitrogen uptake, retranslocation and fixation

Science.gov (United States)

Fisher, J. B.; Tan, S.; Malhi, Y.; Fisher, R. A.; Sitch, S.; Huntingford, C.

2008-12-01

Nitrogen is one of the nutrients that can most limit plant growth, and nitrogen availability may be a controlling factor on biosphere responses to climate change. We developed a plant nitrogen assimilation model based on a) advective transport through the transpiration stream, b) retranslocation whereby carbon is expended to resorb nitrogen from leaves, c) active uptake whereby carbon is expended to acquire soil nitrogen, and d) biological nitrogen fixation whereby carbon is expended for symbiotic nitrogen fixers. The model relies on 9 inputs: 1) net primary productivity (NPP), 2) plant C:N ratio, 3) available soil nitrogen, 4) root biomass, 5) transpiration rate, 6) saturated soil depth,7) leaf nitrogen before senescence, 8) soil temperature, and 9) ability to fix nitrogen. A carbon cost of retranslocation is estimated based on leaf nitrogen and compared to an active uptake carbon cost based on root biomass and available soil nitrogen; for nitrogen fixers both costs are compared to a carbon cost of fixation dependent on soil temperature. The NPP is then allocated to optimize growth while maintaining the C:N ratio. The model outputs are total plant nitrogen uptake, remaining NPP available for growth, carbon respired to the soil and updated available soil nitrogen content. We test and validate the model (called FUN: Fixation and Uptake of Nitrogen) against data from the UK, Germany and Peru, and run the model under simplified scenarios of primary succession and climate change. FUN is suitable for incorporation into a land surface scheme of a General Circulation Model and will be coupled with a soil model and dynamic global vegetation model as part of a land surface model (JULES).

Toxicity of herbicides used in the sugarcane crop to diazotrophic bacterium Herbaspirillum seropedicae

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Sergio de Oliveira Procópio

2014-10-01

Full Text Available The objective of this work was to identify herbicides used in the sugarcane crop that affects neither the growth, the development, of nor the process of biological nitrogen fixation (BNF by the diazotrophic bacterium Herbaspirillum seropedicae. Eighteen herbicides (paraquat, ametryne, tebuthiuron, amicarbazone, diuron, metribuzin, [hexazinone + diuron], [hexazinone + clomazone], clomazone, isoxaflutole, sulfentrazone, oxyfluorfen, imazapic, imazapyr, [trifloxysulfuron sodium + ametryne], glyphosate, MSMA e 2,4-D were tested in their respective commercial doses regarding their impact on the growth of the bacteria in liquid medium DIGs. For this, we determined the duration of lag phase, generation time and maximum cell density of H. seropedicae, calculated from optical density data obtained at regular intervals during the incubation of cultures for 33 h at 32oC. We also evaluated the impact of herbicides on nitrogenase activity of H. seropedicae grown in semi-solid N-free JNFb medium. The effects of herbicides on the growth variables and the ARA were compared with the untreated control by Dunnett test. A completely randomized design was used. The herbicides paraquat, imazapyr, ametryne, glyphosate and oxyfluorfen inhibited the growth of H. seropedicae in vitro. Ametryne, oxyfluorfen and glyphosate caused a small reduction in the duration of the lag phase of diazotrophic bacteria H. seropedicae. Oxyfluorfen, ametryne and imazapyr resulted in increased the generation time by H. seropedicae. Glyphosate promoted drastic reduction in biological nitrogen fixation in vitro by H. seropedicae. The other tested herbicides did not affect the growth or the same BNF by H. seropedicae.

Draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite strain recommended for cowpea inoculation in Brazil

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Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3267 is a nitrogen-fixing symbiotic bacteria isolated from soil of semi-arid area of Brazilian Northeast using cowpea as the trap plant. This strain is used as commercial inoculant for cowpea and presents high efficient in nitrogen fixation as consequence of its adaptation potential to semi-arid conditions. We report here the draft genome sequence of Bradyrhizobium sp. strain BR 3267, an elite bacterium used as inoculant for cowpea. Whole genome sequencing of BR 3267 using Illumina MiSeq sequencing technology has 55 scaffolds with a total genome size of 7,904,309 bp and C+G 63%. Annotation was added by the RAST prokaryotic genome annotation service and has shown 7314 coding sequences and 52 RNA genes.

Characterization of the orf1glnKamtB operon of Herbaspirillum seropedicae.

Science.gov (United States)

Noindorf, Lilian; Rego, Fabiane G M; Baura, Valter A; Monteiro, Rose A; Wassem, Roseli; Cruz, Leonardo M; Rigo, Liu U; Souza, Emanuel M; Steffens, Maria B R; Pedrosa, Fabio O; Chubatsu, Leda S

2006-03-01

Herbaspirillum seropedicae is an endophytic nitrogen-fixing bacterium that colonizes economically important grasses. In this organism, the amtB gene is co-transcribed with two other genes: glnK that codes for a PII-like protein and orf1 that codes for a probable periplasmatic protein of unknown function. The expression of the orf1glnKamtB operon is increased under nitrogen-limiting conditions and is dependent on NtrC. An amtB mutant failed to transport methylammonium. Post-translational control of nitrogenase was also partially impaired in this mutant, since a complete switch-off of nitrogenase after ammonium addition was not observed. This result suggests that the AmtB protein is involved in the signaling pathway for the reversible inactivation of nitrogenase in H. seropedicae.

Biological and Physicochemical Parameters Related to the Nitrogen Cycle in the Rhizospheric Soil of Native Potato (Solanum phureja Crops of Colombia

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Nathalia Flórez-Zapata

2011-01-01

Full Text Available Nitrogen (N plays an important role in agricultural production. This study was designed to evaluate the presence of cultivable N cycle-associated microorganisms (nitrogen-fixing bacteria—NFB, proteolytic bacteria—PR, ammonifiers—AMO, ammonium-oxidizing bacteria—AOB, nitrite-oxidizing bacteria—NOB, and denitrifiers—DEN, and their relationship with physical-chemical and agronomic soil descriptors, in Solanum phureja rhizospheric soil samples, from traditional and organic crop management farms. A cluster analysis with the physical and chemical properties of soil, allowed to identify the organic matter content as an important factor that determines the outcome of that grouping. Significant differences (<0.05 between farms were found in the abundance of this groups, but correlation analysis showed that proteolytic and nitrogen fixing bacteria were the main nitrogen associated functional groups affected by soils' physical-chemical characteristics. The amount of ammonia available is affected by the agricultural management strategy, which consequently affects the NFB abundance. Finally the results showed that PR, protease activity and soil properties related with organic matter transformation has a positive relationship with productivity, which given the high organic matter content of the Andean soils being studied, we conclude that nitrogen mineralization process has an important role in the nitrogen cycle and its bioavailability in this ecosystem.

Biological and Physicochemical Parameters Related to the Nitrogen Cycle in the Rhizospheric Soil of Native Potato (Solanum phureja) Crops of Colombia

International Nuclear Information System (INIS)

Zapata, N.F; Velez, D.U

2011-01-01

Nitrogen (N) plays an important role in agricultural production. This study was designed to evaluate the presence of cultivable N cycle-associated microorganisms (nitrogen-fixing bacteria NFB, proteolytic bacteria PR, ammonifiers AMO, ammonium-oxidizing bacteria AOB, nitrite-oxidizing bacteria NOB, and denitrifiers DEN), and their relationship with physical-chemical and agronomic soil descriptors, in Solanum phureja rhizospheric soil samples, from traditional and organic crop management farms. A cluster analysis with the physical and chemical properties of soil, allowed to identify the organic matter content as an important factor that determines the outcome of that grouping. Significant differences (P<0.05) between farms were found in the abundance of this groups, but correlation analysis showed that proteolytic and nitrogen fixing bacteria were the main nitrogen associated functional groups affected by soils' physical-chemical characteristics. The amount of ammonia available is affected by the agricultural management strategy, which consequently affects the NFB abundance. Finally the results showed that PR, protease activity and soil properties related with organic matter transformation has a positive relationship with productivity, which given the high organic matter content of the Andean soils being studied, we conclude that nitrogen mineralization process has an important role in the nitrogen cycle and its bioavailability in this ecosystem.

Screening Prosopis (mesquite) germplasm for biomass production and nitrogen fixation

Energy Technology Data Exchange (ETDEWEB)

Felker, P.; Cannell, G.H.; Clark, P.R.; Osborn, J.F.

1980-01-01

The nitrogen-fixing trees of the genus Prosopis (mesquite or algaroba) are well adapted to the semi-arid and often saline regions of the world. These trees may produce firewood or pods for livestock food, they may stabilize sand dunes and they may enrich the soil by production of leaf litter supported by nitrogen fixation. A collection of nearly 500 Prosopis accessions representing North and South American and African germplasm has been established. Seventy of these accessions representing 14 taxa are being grown under field conditions where a 30-fold range in biomass productivity among accessions has been estimated. In a greehouse experiment, 13 Prosopis taxa grew on nitrogen-free medium nodulated, and had a 10-fold difference in nitrogen fixation (acetylene reduction). When Prosopis is propagated by seed the resulting trees are extremely variable in growth rate and presence or absence of thorns. Propagation of 6 Prosopis taxa by stem cuttings has been achieved with low success (1 to 10%) in field-grown plants and with higher success (50 to 100%) with young actively growing greenhouse plants.

Increased root exudation of 14C-compounds by sorghum seedlings inoculated with nitrogen-fixing bacteria

International Nuclear Information System (INIS)

Lee, K.J.; Gaskins, M.H.

1982-01-01

Organic components leaked from Sorghum bicolor seedlings ('root exudates') were examined by recovering 14 C labelled compounds from root solutions of seedlings inoculated with Azospirillum brasilense, Azotobacter vinelandii or Klebsiella pneumoniae nif-. Up to 3.5% of the total 14 C recovered from shoots, roots, and nutrient solutions was found in the root solutions. Inoculation with Azospirillum and Azotobacter increased the amounts of 14 C and decreased the amounts of carbohydrates in the root solutions. When sucrose was added as a carbon source for the bacteria, the increase of 14 C in the solutions did not occur. Quantities of 14 C found in the root solutions were proportional to amounts of mineral nitrogen supplied to the plants. Bacterial growth also was proportional to nitrogen levels. When sorghum plants were grown in soil and labelled with 14 CO 2 , about 15% of the total 14 C recovered within 48 hours exposure was found in soil leachates. (orig.)

Metabolic engineering of a diazotrophic bacterium improves ammonium release and biofertilization of plants and microalgae.

Science.gov (United States)

Ambrosio, Rafael; Ortiz-Marquez, Juan Cesar Federico; Curatti, Leonardo

2017-03-01

The biological nitrogen fixation carried out by some Bacteria and Archaea is one of the most attractive alternatives to synthetic nitrogen fertilizers. However, with the exception of the symbiotic rhizobia-legumes system, progress towards a more extensive realization of this goal has been slow. In this study we manipulated the endogenous regulation of both nitrogen fixation and assimilation in the aerobic bacterium Azotobacter vinelandii. Substituting an exogenously inducible promoter for the native promoter of glutamine synthetase produced conditional lethal mutant strains unable to grow diazotrophically in the absence of the inducer. This mutant phenotype could be reverted in a double mutant strain bearing a deletion in the nifL gene that resulted in constitutive expression of nif genes and increased production of ammonium. Under GS non-inducing conditions both the single and the double mutant strains consistently released very high levels of ammonium (>20mM) into the growth medium. The double mutant strain grew and excreted high levels of ammonium under a wider range of concentrations of the inducer than the single mutant strain. Induced mutant cells could be loaded with glutamine synthetase at different levels, which resulted in different patterns of extracellular ammonium accumulation afterwards. Inoculation of the engineered bacteria into a microalgal culture in the absence of sources of C and N other than N 2 and CO 2 from the air, resulted in a strong proliferation of microalgae that was suppressed upon addition of the inducer. Both single and double mutant strains also promoted growth of cucumber plants in the absence of added N-fertilizer, while this property was only marginal in the parental strain. This study provides a simple synthetic genetic circuit that might inspire engineering of optimized inoculants that efficiently channel N 2 from the air into crops. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All

Effect of free and symbiotic nitrogen fixing bacterial co-inoculation on seed and seedling of soybean seeds produced under deficit water condition

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Hamed Hadi

2016-04-01

Full Text Available Effect of free and symbiotic nitrogen fixing bacteria on seed and seedling produced seeds under deficit irrigation was conducted in laboratory and field experiments in 2006. In laboratory of karaj’s Seed and Plant Research and Certificate Institute an experiment was conducted based on factorial in form of completely randomized design with four replications and in field’s of Islamic Azad University, Varamin Branch were split factorial in form of randomized completely block design with three replications. Treatments included water stress [Irrigation after 50 (Normal irrigation, 100 (Middle stress, 150 (Severe stress mm evaporation from pan class A], Cultivar [Manokin & Williams and SRF×T3 Line] and inoculation [Inoculation with Bradyrhizobium japonicum, Bradyrhizobium japonicum co-inoculated with Azotobacter chroococcum, No seed inoculation]. Results showed that drought stress decreased the uniformity and germination speed and seedling emergence. Bacteria increased leaf dry weight, stem dry weight, leaf area and seedling vigor index but had no effect on emergence. In irrigation levels inoculated treatments had higher seedling length, leaf, stem, seedling dry weight and seedling vigor. Severs stress seeds inoculated with Bradyrhizobium japonicum had higher root dry weight than control. Therefore in seeds which were produced under deficit irrigation conditions, bacteria increased seedlings vigor.

Nitrogen fixation by free-living organisms in rice soils. Studies with 15N

International Nuclear Information System (INIS)

Rao, V.R.; Charyulu, P.B.B.N.; Nayak, D.N.; Ramakrishna, C.

1979-01-01

Heterotrophic nitrogen fixation as influenced by water regime, organic matter, combined nitrogen and pesticides was investigated in several Indian rice soils by means of the 15 N 2 tracer technique. Soil submergence accelerated nitrogen fixation. Addition of cellulose to both non-flooded and flooded soils enhanced nitrogen fixation. Under submerged conditions, addition of sucrose, glucose and malate in that order stimulated nitrogen fixation in alluvial soil, while only sucrose enhanced nitrogen fixation in laterite soil. Nitrogen fixation in flooded alluvial and laterite soils decreased with increasing concentration of combined nitrogen. Nitrogen fixation was appreciable in acid sulphate and saline soils under both flooded and non-flooded conditions, despite high salinity and acidity. Application of certain pesticides at rates equivalent to recommended field level greatly influenced nitrogen fixation in flooded rice soils. Additions of benomyl (carbamate fungicide) and carbofuran (methyl carbamate insecticide) to alluvial and laterite soils resulted in significant stimulation of nitrogen fixation. Gamma-BHC stimulated nitrogen fixation only in alluvial soil, with considerable inhibition in a laterite soil. Nitrogen fixation by Azospirillum lipoferum was investigated by 15 N 2 . Large variations in 15 N 2 incorporation by A. lipoferum isolated from the roots of several rice cultivars was observed. Specific lines of rice harbouring A. lipoferum with high nitrogenase activity might be selected. Nitrogen fixed by heterotrophic organisms in a complex system such as soil could not be evaluated precisely. Indigenous nitrogen fixation in a flooded soil would be in the range of 5-10 kg N/ha, increasable 3 to 4-fold by appropriate fertilizers and cultural practices

Nitrogen deposition, competition and the decline of a regionally threatened legume, Desmodium cuspidatum.

Science.gov (United States)

Skogen, Krissa A; Holsinger, Kent E; Cardon, Zoe G

2011-01-01

Increased nitrogen (N) deposition, resulting from the combustion of fossil fuels, production of synthetic fertilizers, growth of N(2)-fixing crops and high-intensity agriculture, is one of the anthropogenic factors most likely to cause global biodiversity changes over the next century. This influence may be especially large in temperate zone forests, which are highly N limited and occur in regions with the highest levels of N deposition. Within these ecosystems, N(2)-fixing plants, including legumes, may be more sensitive to N deposition than other plant species. Though it has long been recognized that the competitive edge conferred by N(2)-fixation diminishes with increasing soil N availability, the conservation implications of increased N deposition on native N(2)-fixers have received less attention. We focus on Desmodium cuspidatum, which has experienced dramatic population losses in the last 30-40 years in the northeastern United States. We explore competition between this regionally threatened legume and a common non-N(2)-fixing neighbor, Solidago canadensis, across a gradient of N deposition. Our data show that increased N deposition may be detrimental to N(2)-fixers such as D. cuspidatum in two ways: (1) biomass accumulation in the non-N(2)-fixer, S. canadensis, responds more strongly to increasing N deposition, and (2) S. canadensis competes strongly for available mineral nitrogen and can assimilate N previously fixed by D. cuspidatum, resulting in D. cuspidatum relying more heavily on energetically expensive N(2)-fixation when grown with S. canadensis. N deposition may thus reduce or eliminate the competitive advantage of N(2)-fixing species growing in N-limited ecosystems.

Global gene expression under nitrogen starvation in Xylella fastidiosa: contribution of the σ54 regulon

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da Silva Neto José F

2010-08-01

Full Text Available Abstract Background Xylella fastidiosa, a Gram-negative fastidious bacterium, grows in the xylem of several plants causing diseases such as citrus variegated chlorosis. As the xylem sap contains low concentrations of amino acids and other compounds, X. fastidiosa needs to cope with nitrogen limitation in its natural habitat. Results In this work, we performed a whole-genome microarray analysis of the X. fastidiosa nitrogen starvation response. A time course experiment (2, 8 and 12 hours of cultures grown in defined medium under nitrogen starvation revealed many differentially expressed genes, such as those related to transport, nitrogen assimilation, amino acid biosynthesis, transcriptional regulation, and many genes encoding hypothetical proteins. In addition, a decrease in the expression levels of many genes involved in carbon metabolism and energy generation pathways was also observed. Comparison of gene expression profiles between the wild type strain and the rpoN null mutant allowed the identification of genes directly or indirectly induced by nitrogen starvation in a σ54-dependent manner. A more complete picture of the σ54 regulon was achieved by combining the transcriptome data with an in silico search for potential σ54-dependent promoters, using a position weight matrix approach. One of these σ54-predicted binding sites, located upstream of the glnA gene (encoding glutamine synthetase, was validated by primer extension assays, confirming that this gene has a σ54-dependent promoter. Conclusions Together, these results show that nitrogen starvation causes intense changes in the X. fastidiosa transcriptome and some of these differentially expressed genes belong to the σ54 regulon.

Pyrolysis of the lignocellulose fermentation residue by fixed-bed micro reactor

International Nuclear Information System (INIS)

Wang, Ze; Lin, Weigang; Song, Wenli; Wu, Xuexing

2012-01-01

Thermal gravimetric (TG) analysis was conducted to compare the fundamental pyrolytic behaviors between the lignocellulose fermentation residue (LFR) and three other biomass raw materials. It was found that the TG weight loss curve of LFR appeared very close to the curve of acidified alkaline lignin (AAL), but different to the material of dried distillers grains with solubles (DDGS, also a fermentation residue but obtained from liquor producing process). Pyrolysis of LFR by fixed-bed micro reactor in the range of 430 °C–700 °C was carried out. It was found that the liquid yield had a maximum value at the pyrolytic temperature of 475 °C. The oil phase of the liquid was mainly composed of phenols, and the content of dimethyl phenol and fatty acids decreased with increasing pyrolytic temperature. In the aqueous liquid, besides the most abundant phenol derivatives, small acids and nitrogen containing compounds appeared more. -- Highlights: ► The tense of the paper has been revised. ► The description of the experimental procedure was kept in past tense. ► The expression of ‘fixed bed’ was changed to ‘fixed-bed’.

Earth Without Life: A Systems Model of a Global Abiotic Nitrogen Cycle.

Science.gov (United States)

Laneuville, Matthieu; Kameya, Masafumi; Cleaves, H James

2018-03-20

Nitrogen is the major component of Earth's atmosphere and plays important roles in biochemistry. Biological systems have evolved a variety of mechanisms for fixing and recycling environmental nitrogen sources, which links them tightly with terrestrial nitrogen reservoirs. However, prior to the emergence of biology, all nitrogen cycling was abiological, and this cycling may have set the stage for the origin of life. It is of interest to understand how nitrogen cycling would proceed on terrestrial planets with comparable geodynamic activity to Earth, but on which life does not arise. We constructed a kinetic mass-flux model of nitrogen cycling in its various major chemical forms (e.g., N 2 , reduced (NH x ) and oxidized (NO x ) species) between major planetary reservoirs (the atmosphere, oceans, crust, and mantle) and included inputs from space. The total amount of nitrogen species that can be accommodated in each reservoir, and the ways in which fluxes and reservoir sizes may have changed over time in the absence of biology, are explored. Given a partition of volcanism between arc and hotspot types similar to the modern ones, our global nitrogen cycling model predicts a significant increase in oceanic nitrogen content over time, mostly as NH x , while atmospheric N 2 content could be lower than today. The transport timescales between reservoirs are fast compared to the evolution of the environment; thus atmospheric composition is tightly linked to surface and interior processes. Key Words: Nitrogen cycle-Abiotic-Planetology-Astrobiology. Astrobiology 18, xxx-xxx.

The oceanic fixed nitrogen and nitrous oxide budgets: Moving targets as we enter the anthropocene?

Digital Repository Service at National Institute of Oceanography (India)

Codispoti, L; Brandes, J.A.; Christensen, J.P.; Devol, A.H.; Naqvi, S.W.A.; Paerl, H.W.; Yoshinari, T.

New data forced to raise previous estimates of oceanic denitrification. The revised estimate of approx. 450 Tg N yr sup(-1) (Tg = 10 sup(12) g) produces an oceanic fixed N budget with a large deficit (approx. 200 Tg N yr sup(1)) that can...

Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds

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Herrmann, Martina; Rusznyák, Anna; Akob, Denise M.; Schulze, Isabel; Opitz, Sebastian; Totsche, Kai Uwe; Küsel, Kirsten

2015-01-01

The traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed—upper and lower—limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO2 via the Calvin cycle, with abundances of cbbM and cbbL genes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 103 to 6 × 106 genes liter−1 over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO2-assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO2 fixation in environments with strong oxygen and CO2 fluctuations. The genera Sulfuricellaand Nitrosomonas were represented by read fractions of up to 78 and 33%, respectively, within the cbbM and cbbL transcript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO2 fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds.

N2-fixing tropical legume evolution: a contributor to enhanced weathering through the Cenozoic?

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Epihov, Dimitar Z; Batterman, Sarah A; Hedin, Lars O; Leake, Jonathan R; Smith, Lisa M; Beerling, David J

2017-08-16

Fossil and phylogenetic evidence indicates legume-rich modern tropical forests replaced Late Cretaceous palm-dominated tropical forests across four continents during the early Cenozoic (58-42 Ma). Tropical legume trees can transform ecosystems via their ability to fix dinitrogen (N 2 ) and higher leaf N compared with non-legumes (35-65%), but it is unclear how their evolutionary rise contributed to silicate weathering, the long-term sink for atmospheric carbon dioxide (CO 2 ). Here we hypothesize that the increasing abundance of N 2 -fixing legumes in tropical forests amplified silicate weathering rates by increased input of fixed nitrogen (N) to terrestrial ecosystems via interrelated mechanisms including increasing microbial respiration and soil acidification, and stimulating forest net primary productivity. We suggest the high CO 2 early Cenozoic atmosphere further amplified legume weathering. Evolution of legumes with high weathering rates was probably driven by their high demand for phosphorus and micronutrients required for N 2 -fixation and nodule formation. © 2017 The Author(s).

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil.

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Simões-Araújo, Jean Luiz; Leite, Jakson; Marie Rouws, Luc Felicianus; Passos, Samuel Ribeiro; Xavier, Gustavo Ribeiro; Rumjanek, Norma Gouvêa; Zilli, Jerri Édson

The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp) growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems. Published by Elsevier Editora Ltda.

Draft genome sequence of Bradyrhizobium sp. strain BR 3262, an effective microsymbiont recommended for cowpea inoculation in Brazil

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Jean Luiz Simões-Araújo

Full Text Available Abstract The strain BR 3262 was isolated from nodule of cowpea (Vigna unguiculata L. Walp growing in soil of the Atlantic Forest area in Brazil and it is reported as an efficient nitrogen fixing bacterium associated to cowpea. Firstly, this strain was assigned as Bradyrhizobium elkanii, however, recently a more detailed genetic and molecular characterization has indicated it could be a Bradyrhizobium pachyrhizi species. We report here the draft genome sequence of B. pachyrhizi strain BR 3262, an elite bacterium used as inoculant for cowpea. The whole genome with 116 scaffolds, 8,965,178 bp and 63.8% of C+G content for BR 3262 was obtained using Illumina MiSeq sequencing technology. Annotation was added by the RAST prokaryotic genome annotation service and shown 8369 coding sequences, 52 RNAs genes, classified in 504 subsystems.

Lactococcus lactis - a diploid bacterium

DEFF Research Database (Denmark)

Michelsen, Ole; Hansen, Flemming G.; Jensen, Peter Ruhdal

the next division. Thus, the regions of the chromosome that are the last to be replicated are haploid even in fast-growing bacteria. In contrast to this general rule for bacteria, we found that Lactococcus lactis, a bacterium which has been exploited for thousands of years for the production of fermented...... milk products, is born with two complete non-replicating chromosomes. L. lactis therefore remain diploid throughout its entire life cycle....

Determination of the ''1''4N to ''1''5N ratio in nitrogen-containing samples

International Nuclear Information System (INIS)

Aidarhanova, G.; Baktybaev, D.T.; Burtebaeva, N.; Burtebaev, N.; Djazairov-Kakhramanov, V.; Zazulin, D.M.; Urazaliev, R.U.; Ramazanova, S.B.; Baimaganova, G.Sh.; Ramazanova, R.H.

2001-01-01

It is known that nitrogen nutrition plays very important role in increase of plant crop and the albumin content in food rural cultures. Producers widely use nitrogen fertilizers. Their non-controlled or too extensive use can lead to contamination of air and water , resulting in hazardous sequences for human health and environment. The studies related to determination of nitrogen nutrition efficiency are based on utilization of the ''1''5N isotope, in view of determination of the best forms, time and place for introduction of nitrogen fertilizers, in order to provide the most reasonable nitrogen consumption by plants, avoiding waste and reducing the nitrogen fertilizer volumes required for obtaining a desired level of crop. In the course of natural experiments, scientists of various countries studied the processes of nitrogen consumption by plants from fertilizers, the processes responsible for nitrogen fixing in soil, nitrogen losses in a gaseous form or in liquids, in a form of solutions with ground water. The studies have shown that a fresh organic mass (manure) introduced to soil causes acceleration of decomposition of organic substance and renewal of the humus composition in soil. These phenomena can be detected by means of radioactive or stable isotopes

Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives

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Servé W. M. Kengen

2013-01-01

Full Text Available Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit for dark fermentation of 4 mol hydrogen per mol hexose, this organism has proven itself to be an excellent candidate for biological hydrogen production. This review provides an overview of the research on C. saccharolyticus with respect to the hydrolytic capability, sugar metabolism, hydrogen formation, mechanisms involved in hydrogen inhibition, and the regulation of the redox and carbon metabolism. Analysis of currently available fermentation data reveal decreased hydrogen yields under non-ideal cultivation conditions, which are mainly associated with the accumulation of hydrogen in the liquid phase. Thermodynamic considerations concerning the reactions involved in hydrogen formation are discussed with respect to the dissolved hydrogen concentration. Novel cultivation data demonstrate the sensitivity of C. saccharolyticus to increased hydrogen levels regarding substrate load and nitrogen limitation. In addition, special attention is given to the rhamnose metabolism, which represents an unusual type of redox balancing. Finally, several approaches are suggested to improve biohydrogen production by C. saccharolyticus.

[Isolation, Identification and Nitrogen Removal Characteristics of a Heterotrophic Nitrification-Aerobic Denitrification Strain y3 Isolated from Marine Environment].

Science.gov (United States)

Sun, Qing-hua; Yu, De-shuang; Zhang, Pei-yu; Lin, Xue-zheng; Xu, Guang-yao; Li, Jin

2016-03-15

A heterotrophic nitrification--aerobic denitrification bacterium named y3 was isolated from the sludge of Jiaozhou Bay using the enrichment medium with seawater as the matrix. It was identified as Pseudomonas sp. based on the morphological observation, physiological experiments and sequence analysis of 16S rRNA. The experiment results showed that the optimal carbon resource was sodium citrate, the optimal pH was 7.0, and the optimal C/N was 13. The strain could use NH₄Cl, NaNO₂ and KNO₃ as sole nitrogen source, and the removal efficiencies were 98.69%, 78.38% and 72.95% within 20 hours, respectively. There was no nitrate and nitrite accumulation during the heterotrophic nitrification process. Within 20 hours, the nitrogen removal efficiencies were 99.56%, 99.75% and 99.41%, respectively, in the mixed system with NO₃⁻-N: NO²⁻-N of 2:1, 1:1 and 1:2. When the NH₄⁺-N: NO₃⁻-N ratios were 2: 1 , 1: 1 , 1: 2, the nitrogen removal efficiencies were all 100% . When the NH₄⁺-N:NO₂⁻-N ratios were 2:1,1:1,1:2, the nitrogen removal efficiencies were 90.43%, 92.79% and 99.96%, respectively. They were higher than those with single nitrogen source. As a result, strain y3 had good nitrogen removal performance in high saline wastewater treatment.

Nitrogen fixation rates associated with the invasive macroalgae Sargassum horneri around Catalina Island, CA

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DeLiberto, A.

2016-02-01

Nitrogen fixation is an important process which allows organisms access to biologically unavailable dinitrogen gas. Bacteria, known as diazotrophs use the enzyme nitrogenase to convert N2 to NH3. These bacteria, including certain species of heterotrophic bacteria and cyanobacteria, can be symbiotically associated with marine macroalgae, facilitating nutrient cycling in oligotrophic regions. As many species within the genera Sargassum are associated with nitrogen fixation, this study hypothesized that nitrogenase activity would be associated with the benthic invasive Sargassum horneri on Catalina Island. In the past decade, Sargassum horneri, an invasive from Japan, has spread throughout the waters around Catalina Island. Using the acetylene reduction procedure using flame ionization detection, initial nitrogenase activity of S. horneri sampled from Indian Rock was observed. Nitrogen fixation rates increased with decomposition, particularly in dark/anaerobic treatments, suggesting the presence of heterotrophic bacteria. In addition, acetate additions greatly increase nitrogen fixation rates, once again indicating heterotrophic nitrogen fixing bacteria.

Modeling the role of covalent enzyme modification in Escherichia coli nitrogen metabolism

International Nuclear Information System (INIS)

Kidd, Philip B; Wingreen, Ned S

2010-01-01

In the bacterium Escherichia coli, the enzyme glutamine synthetase (GS) converts ammonium into the amino acid glutamine. GS is principally active when the cell is experiencing nitrogen limitation, and its activity is regulated by a bicyclic covalent modification cascade. The advantages of this bicyclic-cascade architecture are poorly understood. We analyze a simple model of the GS cascade in comparison to other regulatory schemes and conclude that the bicyclic cascade is suboptimal for maintaining metabolic homeostasis of the free glutamine pool. Instead, we argue that the lag inherent in the covalent modification of GS slows the response to an ammonium shock and thereby allows GS to transiently detoxify the cell, while maintaining homeostasis over longer times

Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte.

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Michele T Hoffman

Full Text Available Numerous plant pathogens, rhizosphere symbionts, and endophytic bacteria and yeasts produce the important phytohormone indole-3-acetic acid (IAA, often with profound effects on host plants. However, to date IAA production has not been documented among foliar endophytes -- the diverse guild of primarily filamentous Ascomycota that live within healthy, above-ground tissues of all plant species studied thus far. Recently bacteria that live within hyphae of endophytes (endohyphal bacteria have been detected, but their effects have not been studied previously. Here we show not only that IAA is produced in vitro by a foliar endophyte (here identified as Pestalotiopsis aff. neglecta, Xylariales, but that IAA production is enhanced significantly when the endophyte hosts an endohyphal bacterium (here identified as Luteibacter sp., Xanthomonadales. Both the endophyte and the endophyte/bacterium complex appear to rely on an L-tryptophan dependent pathway for IAA synthesis. The bacterium can be isolated from the fungus when the symbiotic complex is cultivated at 36°C. In pure culture the bacterium does not produce IAA. Culture filtrate from the endophyte-bacterium complex significantly enhances growth of tomato in vitro relative to controls and to filtrate from the endophyte alone. Together these results speak to a facultative symbiosis between an endophyte and endohyphal bacterium that strongly influences IAA production, providing a new framework in which to explore endophyte-plant interactions.

Effect of pond depth and lining plastic color on growth and nitrogen ...

African Journals Online (AJOL)

Thus, this study evaluated the effect of pond depth and lining plastic colors on nitrogen fixing capacity of Anabaena species strain E3. Factorial combinations of four pond lining plastic colors and two depths were laid out in a complete randomized design with three replications. The ANOVA results revealed that the 20 cm ...

Identification of NH4+-regulated genes of Herbaspirillum seropedicae by random insertional mutagenesis.

Science.gov (United States)

Schwab, Stefan; Ramos, Humberto J; Souza, Emanuel M; Pedrosa, Fábio O; Yates, Marshall G; Chubatsu, Leda S; Rigo, Liu U

2007-05-01

Random mutagenesis using transposons with promoterless reporter genes has been widely used to examine differential gene expression patterns in bacteria. Using this approach, we have identified 26 genes of the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae regulated in response to ammonium content in the growth medium. These include nine genes involved in the transport of nitrogen compounds, such as the high-affinity ammonium transporter AmtB, and uptake systems for alternative nitrogen sources; nine genes coding for proteins responsible for restoring intracellular ammonium levels through enzymatic reactions, such as nitrogenase, amidase, and arginase; and a third group includes metabolic switch genes, coding for sensor kinases or transcription regulation factors, whose role in metabolism was previously unknown. Also, four genes identified were of unknown function. This paper describes their involvement in response to ammonium limitation. The results provide a preliminary profile of the metabolic response of Herbaspirillum seropedicae to ammonium stress.

Aerobic and heterotrophic nitrogen removal by Enterobacter cloacae CF-S27 with efficient utilization of hydroxylamine.

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Padhi, Soumesh Kumar; Tripathy, Swetaleena; Mohanty, Sriprakash; Maiti, Nikhil Kumar

2017-05-01

Heterotrophic bacterium, Enterobacter cloacae CF-S27 exhibited simultaneous nitrification and aerobic denitrification in presence of high concentration of hydroxylamine. With the initial nitrogen concentration of 100mgL -1 h -1 , ammonium, nitrate and nitrite removal efficiencies were 81%, 99.9% and 92.8%, while the corresponding maximum removal rates reached as high as 11.6, 15.1 and 11.2mgL -1 h -1 respectively. Quantitative amplification by real time PCR and enzyme assay demonstrated that hydroxylamine reductase gene (hao) is actively involved in hetrotrophic nitrification and aerobic denitrification process of Enterobacter cloacae CF-S27. PCR primers were designed targeting amplification of hao gene from diversified environmental soil DNA. The strain Enterobacter cloacae CF-S27 significantly maintained the undetectable amount of dissolved nitrogen throughout 60days of zero water exchange fish culture experiment in domestic wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

The fate of fixed nitrogen in marine sediments with low organic loading: an in situ study

DEFF Research Database (Denmark)

Bonaglia, Stefano; Hylén, Astrid; Rattray, Jane E.

2017-01-01

Given the increasing impacts of human activities on global nitrogen (N) cycle, investigations on N transformation processes in the marine environment have drastically increased in the last years. Benthic N cycling has mainly been studied in anthropogenically impacted estuaries and coasts, while its...... sediments worldwide (range 34–344 µmol N m−2 d−1). Anammox accounted for 18–26 % of the total N2 production. Absence of free hydrogen sulfide and low concentrations of dissolved iron in sediment pore waters suggested that denitrification and DNRA were driven by organic matter oxidation rather than...... chemolithotrophy. DNRA was as important as denitrification at a shallow, coastal station situated in the northern Bothnian Bay. At this pristine and fully oxygenated site, ammonium regeneration through DNRA contributed more than one third to the total dissolved nitrogen (TDN) diffusing from the sediment...

Carbon and nitrogen metabolism of free-living Frankia spp. and of Frankia-alnus symbioses

NARCIS (Netherlands)

Blom, J.

1982-01-01

The research reported in this thesis deals with the symbiosis of Frankia spp. and Alnus glutinosa. Frankia spp. are actinomycetes giving rise to the formation of nitrogen-fixing nodules on the roots of a number of non-leguminous plants. In these nodules

A mechanistic nitrogen limitation model for CLM(ED)

Science.gov (United States)

Ali, A. A.; Xu, C.; McDowell, N. G.; Rogers, A.; Wullschleger, S. D.; Fisher, R.; Vrugt, J. A.

2014-12-01

Photosynthetic capacity is a key plant trait that determines the rate of photosynthesis; however, in Earth System Models it is either a fixed value or derived from a linear function of leaf nitrogen content. A mechanistic leaf nitrogen allocation model have been developed for a DOE-sponsored Community Land Model coupled to the Ecosystem Demography model (CLM-ED) to predict the photosynthetic capacity [Vc,max25 (μmol CO2 m-2 s-1)] under different environmental conditions at the global scale. We collected more than 800 data points of photosynthetic capacity (Vc,max25) for 124 species from 57 studies with the corresponding leaf nitrogen content and environmental conditions (temperature, radiation, humidity and day length) from literature and the NGEE arctic site (Barrow). Based on the data, we found that environmental control of Vc,max25 is about 4 times stronger than the leaf nitrogen content. Using the Markov-Chain Monte Carlo simulation approach, we fitted the collected data to our newly developed nitrogen allocation model, which predict the leaf nitrogen investment in different components including structure, storage, respiration, light capture, carboxylation and electron transport at different environmental conditions. Our results showed that our nitrogen allocation model explained 52% of variance in observed Vc,max25 and 65% variance in observed Jmax25 using a single set of fitted model parameters for all species. Across the growing season, we found that the modeled Vc,max25 explained 49% of the variability in measured Vc,max25. In the context of future global warming, our model predicts that a temperature increase by 5oC and the doubling of atmospheric carbon dioxide reduced the Vc,max25 by 5%, 11%, respectively.

A sensitive spectrophotometric determination of nitrogen dioxide in the working atmosphere

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Prachi Parmar

2009-12-01

Full Text Available In the present investigation, a simple and sensitive spectrophotometric method for the determination of nitrogen dioxide in various environmental samples is described. Nitrogen dioxide in air was fixed as nitrite ion in alkaline sodium arsenite absorbing solution. The nitrite formed was diazotized with p−aminoacetophenone in acidic medium which was subsequently coupled with phloroglucinol to give yellow−orange dye in alkaline medium having an absorption maximum at 420 nm. Beer’s law was obeyed in the range of 0.008 − 0.12 μg mL-1 of nitrogen dioxide and has a molar absorptivity of 2.875 x 105 L mol-1 cm-1. Optimum reaction conditions for diazotization, full colour development and the effect of variables like temperature, time and pH have been studied. Detailed studies to check the collection efficiency and NO2:NO2- stoichiometric ratio has been carried out. The reaction has been successfully applied for the detection of nitrogen dioxide in cigarette smoke, scooter exhaust, and workroom air.

Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer.

Science.gov (United States)

Coelho, Marcia Reed Rodrigues; de Vos, Marjon; Carneiro, Newton Portilho; Marriel, Ivanildo Evódio; Paiva, Edilson; Seldin, Lucy

2008-02-01

The diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (IS 5322-C and IPA 1011) sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg ha(-1)). The nifH gene was amplified directly from DNA extracted from the rhizospheres, and the PCR products cloned and sequenced. Four clone libraries were generated from the nifH fragments and 245 sequences were obtained. Most of the clones (57%) were closely related to nifH genes of uncultured bacteria. NifH clones affiliated with Azohydromonas spp., Ideonella sp., Rhizobium etli and Bradyrhizobium sp. were found in all libraries. Sequences affiliated with Delftia tsuruhatensis were found in the rhizosphere of both cultivars sown with high levels of nitrogen, while clones affiliated with Methylocystis sp. were detected only in plants sown under low levels of nitrogen. Moreover, clones affiliated with Paenibacillus durus could be found in libraries from the cultivar IS 5322-C sown either in high or low amounts of fertilizer. This study showed that the amount of nitrogen used for fertilization is the overriding determinative factor that influenced the nitrogen-fixing community structures in sorghum rhizospheres cultivated in Cerrado soil.

BMAA Inhibits Nitrogen Fixation in the Cyanobacterium Nostoc sp. PCC 7120

Science.gov (United States)

Berntzon, Lotta; Erasmie, Sven; Celepli, Narin; Eriksson, Johan; Rasmussen, Ulla; Bergman, Birgitta

2013-01-01

Cyanobacteria produce a range of secondary metabolites, one being the neurotoxic non-protein amino acid β-N-methylamino-L-alanine (BMAA), proposed to be a causative agent of human neurodegeneration. As for most cyanotoxins, the function of BMAA in cyanobacteria is unknown. Here, we examined the effects of BMAA on the physiology of the filamentous nitrogen-fixing cyanobacterium Nostoc sp. PCC 7120. Our data show that exogenously applied BMAA rapidly inhibits nitrogenase activity (acetylene reduction assay), even at micromolar concentrations, and that the inhibition was considerably more severe than that induced by combined nitrogen sources and most other amino acids. BMAA also caused growth arrest and massive cellular glycogen accumulation, as observed by electron microscopy. With nitrogen fixation being a process highly sensitive to oxygen species we propose that the BMAA effects found here may be related to the production of reactive oxygen species, as reported for other organisms. PMID:23966039

Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer

NARCIS (Netherlands)

Coelho, M.R.R.; Vos, de M.; Carneiro, N.P.; Marriel, I.E.; Paiva, E.; Seldin, L.

2008-01-01

The diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (IS 5322-C and IPA 1011) sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg ha(-1)). The nifH gene was amplified directly from DNA extracted from the rhizospheres,

The independent acquisition of plant root nitrogen-fixing symbiosis in Fabids recruited the same genetic pathway for nodule organogenesis.

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Sergio Svistoonoff

Full Text Available Only species belonging to the Fabid clade, limited to four classes and ten families of Angiosperms, are able to form nitrogen-fixing root nodule symbioses (RNS with soil bacteria. This concerns plants of the legume family (Fabaceae and Parasponia (Cannabaceae associated with the Gram-negative proteobacteria collectively called rhizobia and actinorhizal plants associated with the Gram-positive actinomycetes of the genus Frankia. Calcium and calmodulin-dependent protein kinase (CCaMK is a key component of the common signaling pathway leading to both rhizobial and arbuscular mycorrhizal symbioses (AM and plays a central role in cross-signaling between root nodule organogenesis and infection processes. Here, we show that CCaMK is also needed for successful actinorhiza formation and interaction with AM fungi in the actinorhizal tree Casuarina glauca and is also able to restore both nodulation and AM symbioses in a Medicago truncatula ccamk mutant. Besides, we expressed auto-active CgCCaMK lacking the auto-inhibitory/CaM domain in two actinorhizal species: C. glauca (Casuarinaceae, which develops an intracellular infection pathway, and Discaria trinervis (Rhamnaceae which is characterized by an ancestral intercellular infection mechanism. In both species, we found induction of nodulation independent of Frankia similar to response to the activation of CCaMK in the rhizobia-legume symbiosis and conclude that the regulation of actinorhiza organogenesis is conserved regardless of the infection mode. It has been suggested that rhizobial and actinorhizal symbioses originated from a common ancestor with several independent evolutionary origins. Our findings are consistent with the recruitment of a similar genetic pathway governing rhizobial and Frankia nodule organogenesis.

Using 15N isotope technique on evaluation of starter N effect on soybean-bacteria symbiosis intensity

International Nuclear Information System (INIS)

Sagheb, N.; Majd, F.; Porrdavai, H.; Yousefy, F.

1994-02-01

Nuclear techniques have solved many agricultural research problems during the last two decades, while resolving these problems with classical methods have been very difficult if not impossible. With this technique evaluation of unknown effects of biological nitrogen fixation became possible. The advantage of using 1 5N technique is its ability to e specify and identify exact amount of nitrogen from soil, fertilizer and that existing in the atmosphere as molecular nitrogen. Soybean crop (Elycine max(L.) Merill) is able to receive large portion of its nitrogen through biological nitrogen fixation from symbiosis of Rhizobium-Japonicum bacterium. In this study three soybean cultivars received 20 and 100 Kg of N ha -1 as starter nitrogen fertilizer and in form of 1 5N -labelled ammonium phosphate. In collected plant materials 1 5N /1 4N ratios were determined by the Kjeldahl procedure. By using 1 5N isotope method the amount of nitrogen derived from different sources (Soil, Fertilizer and atmosphere) at 20 and 100 Kg N ha -1 were evaluated. Significant differences were observed in percent and amounts of nitrogen fixed (Kg ha 1 ) from atmosphere. There were no significant differences in total N yield and total dry matter at two different levels of nitrogen fertilizer applied. (author)

Initiation of chromosomal replication in predatory bacterium Bdellovibrio bacteriovorus

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Lukasz Makowski

2016-11-01

Full Text Available Bdellovibrio bacteriovorus is a small Gram-negative predatory bacterium that attacks other Gram-negative bacteria, including many animal, human, and plant pathogens. This bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase and replicating cells (the intracellular-growth phase. The process of chromosomal replication in B. bacteriovorus must therefore be temporally and spatially regulated to ensure that it is coordinated with cell differentiation and cell cycle progression. Recently, B. bacteriovorus has received considerable research interest due to its intriguing life cycle and great potential as a prospective antimicrobial agent. Although we know that chromosomal replication in bacteria is mainly regulated at the initiation step, no data exists about this process in B. bacteriovorus. We report the first characterization of key elements of initiation of chromosomal replication – DnaA protein and oriC region from the predatory bacterium, B. bacteriovorus. In vitro studies using different approaches demonstrate that the B. bacteriovorus oriC (BdoriC is specifically bound and unwound by the DnaA protein. Sequence comparison of the DnaA-binding sites enabled us to propose a consensus sequence for the B. bacteriovorus DnaA box (5’-NN(A/TTCCACA-3’. Surprisingly, in vitro analysis revealed that BdoriC is also bound and unwound by the host DnaA proteins (relatively distantly related from B. bacteriovorus. We compared the architecture of the DnaA–oriC complexes (orisomes in homologous (oriC and DnaA from B. bacteriovorus and heterologous (BdoriC and DnaA from prey, E. coli or P. aeruginosa systems. This work provides important new entry points toward improving our understanding of the initiation of chromosomal replication in this predatory bacterium.

Evaluation of nitrogen fixation rates of soybean and species of rhizobia

International Nuclear Information System (INIS)

Ping Shuzhen; You Chongbiao

1993-01-01

Using 1 '5N dilution technique the nitrogen fixing rates were estimated from symbiosis between 20 varieties of soybean and 2 species of rhizobia: Bradyrhizobium japonicum and Sinorhizobium fredii. The nodulation status such as size and number of nodules differed among the varieties and species of bacteria. The Ndfa% of these varieties ranged from 40% ∼ 59% for S. fredii, 38% ∼ 62% for B. japonicum and 32% ∼ 56% for inoculant of the mixture of the species, respectively. Among 3 inoculants the B. japonicum is the best one. The variety of soybean, however, plays a significant role in the symbiosis. Therefore, improving the soybean and selecting a good partner for raising the yield and nitrogen fixation are important

A Medicago truncatula Tobacco Retrotransposon Insertion Mutant Collection with Defects in Nodule Development and Symbiotic Nitrogen Fixation1[W][OA

Science.gov (United States)

Pislariu, Catalina I.; D. Murray, Jeremy; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; A. Benedito, Vagner; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E.; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S.; Chen, Rujin; Udvardi, Michael K.

2012-01-01

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod−), 51 mutants with totally ineffective nodules (Nod+ Fix−), 17 mutants with partially ineffective nodules (Nod+ Fix+/−), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/− Fix−), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/− Fix+), and 11 supernodulating mutants (Nod++Fix+/−). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN’T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod− lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging. PMID:22679222

Understanding the interplay of carbon and nitrogen supply for ectoines production and metabolic overflow in high density cultures of Chromohalobacter salexigens.

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Salar-García, María J; Bernal, Vicente; Pastor, José M; Salvador, Manuel; Argandoña, Montserrat; Nieto, Joaquín J; Vargas, Carmen; Cánovas, Manuel

2017-02-08

The halophilic bacterium Chromohalobacter salexigens has been proposed as promising cell factory for the production of the compatible solutes ectoine and hydroxyectoine. This bacterium has evolved metabolic adaptations to efficiently grow under high salt concentrations by accumulating ectoines as compatible solutes. However, metabolic overflow, which is a major drawback for the efficient conversion of biological feedstocks, occurs as a result of metabolic unbalances during growth and ectoines production. Optimal production of ectoines is conditioned by the interplay of carbon and nitrogen metabolisms. In this work, we set out to determine how nitrogen supply affects the production of ectoines. Chromohalobacter salexigens was challenged to grow in media with unbalanced carbon/nitrogen ratio. In C. salexigens, overflow metabolism and ectoines production are a function of medium composition. At low ammonium conditions, the growth rate decreased importantly, up to 80%. Shifts in overflow metabolism were observed when changing the C/N ratio in the culture medium. 13 C-NMR analysis of ectoines labelling revealed a high metabolic rigidity, with almost constant flux ratios in all conditions assayed. Unbalanced C/N ratio led to pyruvate accumulation, especially upon N-limitation. Analysis of an ect - mutant demonstrated the link between metabolic overflow and ectoine biosynthesis. Under non ectoine synthesizing conditions, glucose uptake and metabolic overflow decreased importantly. Finally, in fed-batch cultures, biomass yield was affected by the feeding scheme chosen. High growth (up to 42.4 g L -1 ) and volumetric ectoine yields (up to 4.21 g L -1 ) were obtained by minimizing metabolite overflow and nutrient accumulation in high density cultures in a low nitrogen fed-batch culture. Moreover, the yield coefficient calculated for the transformation of glucose into biomass was 30% higher in fed-batch than in the batch culture, demonstrating that the metabolic

Total recovery of nitrogen and phosphorus from three wetland plants by fast pyrolysis technology.

Science.gov (United States)

Liu, Wu-Jun; Zeng, Fan-Xin; Jiang, Hong; Yu, Han-Qing

2011-02-01

Fast pyrolysis of three wetland plants (Alligator weed, Oenanthe javanica and Typha angustifolia) in a vertical drop fixed bed reactor was investigated in this study. The experiments were carried out at different pyrolysis temperatures, and the maximum bio-oil yields achieved were 42.3%, 40.2% and 43.6% for Alligator weed, Oenanthe javanica and Typha angustifolia, respectively. The elemental composition of the bio-oil and char were analyzed, and the results show that a low temperature was appropriate for the nitrogen and phosphorus enrichment in char. GC-MS analysis shows that nitrogenous compounds, phenols and oxygenates were the main categories in the bio-oil. A series of leaching tests were carried out to examine the recovery of the nitrogen and phosphorus in the char, and the results indicate that significant fractions of nitrogen and phosphorus could be recovered by leaching process. Copyright © 2010 Elsevier Ltd. All rights reserved.

Increased root exudation of /sup 14/C-compounds by sorghum seedlings inoculated with nitrogen-fixing bacteria

Energy Technology Data Exchange (ETDEWEB)

Lee, K.J. (Institute of Forest Genetics, Suweon (Republic of Korea)); Gaskins, M.H. (Florida Univ., Gainesville (USA). Dept. of Agriculture)

1982-01-01

Organic components leaked from Sorghum bicolor seedlings ('root exudates') were examined by recovering /sup 14/C labelled compounds from root solutions of seedlings inoculated with Azospirillum brasilense, Azotobacter vinelandii or Klebsiella pneumoniae nif-. Up to 3.5% of the total /sup 14/C recovered from shoots, roots, and nutrient solutions was found in the root solutions. Inoculation with Azospirillum and Azotobacter increased the amounts of /sup 14/C and decreased the amounts of carbohydrates in the root solutions. When sucrose was added as a carbon source for the bacteria, the increase of /sup 14/C in the solutions did not occur. Quantities of /sup 14/C found in the root solutions were proportional to amounts of mineral nitrogen supplied to the plants. Bacterial growth also was proportional to nitrogen levels. When sorghum plants were grown in soil and labelled with /sup 14/CO/sub 2/, about 15% of the total /sup 14/C recovered within 48 hours exposure was found in soil leachates.

Abundance of Alnus incana ssp. rugosa in Adirondack Mountain shrub wetlands and its influence on inorganic nitrogen

International Nuclear Information System (INIS)

Kiernan, B.D.; Hurd, T.M.; Raynal, D.J.

2003-01-01

The presence of the nitrogen-fixing shrub, Alnus incana ssp. rugosa, influences the concentration of inorganic nitrogen in surface waters in the Adirondack Mountain region of northern New York. - The purpose of this research was to determine the abundance of the nitrogen-fixing shrub, Alnus incana ssp. rugosa (speckled alder), in shrub wetlands of the Adirondack Mountain region of New York State and to determine whether its abundance affects the concentration or accumulation of inorganic nitrogen in wetland substrates. Alder/willow wetlands are the second most common wetland type in the Adirondack region. The Adirondack Park Agency's digital GIS database of wetland types was used to determine the areal extent of alder/willow wetlands in the Adirondacks. Randomly selected wetlands were sampled to determine the size and abundance of alder. Alder densities averaged ∼7000 stems ha -1 and alder was present in 75% of the wetlands. As an indication of short-term accumulation of NO 3 - and NH 4 + in wetland substrates, ion exchange resins were used to sample ground water in high and low alder density wetlands as well as from wetlands lacking alder and dominated by conifers. Additionally, NO 3 - and NH 4 + concentrations in ground water samples were measured. NH 4 + accumulation levels from exchange resins were low for all wetland types while groundwater NH 4 + concentration was highest in the low-density alder sites. Wetlands with high alder density had approximately six times higher NO 3 - accumulation than other wetlands. Substrate groundwater NO 3 - concentrations in wetlands of high-density alder exceeded by three times levels in low or no alder wetlands, showing the importance of alder to local N budgets. To assess the recovery of shrub wetlands from acidification, future studies should determine the fate of fixed N in wetland systems

The fixABCX genes in Rhodospirillum rubrum encode a putative membrane complex participating in electron transfer to nitrogenase.

Science.gov (United States)

Edgren, Tomas; Nordlund, Stefan

2004-04-01

In our efforts to identify the components participating in electron transport to nitrogenase in Rhodospirillum rubrum, we used mini-Tn5 mutagenesis followed by metronidazole selection. One of the mutants isolated, SNT-1, exhibited a decreased growth rate and about 25% of the in vivo nitrogenase activity compared to the wild-type values. The in vitro nitrogenase activity was essentially wild type, indicating that the mutation affects electron transport to nitrogenase. Sequencing showed that the Tn5 insertion is located in a region with a high level of similarity to fixC, and extended sequencing revealed additional putative fix genes, in the order fixABCX. Complementation of SNT-1 with the whole fix gene cluster in trans restored wild-type nitrogenase activity and growth. Using Western blotting, we demonstrated that expression of fixA and fixB occurs only under conditions under which nitrogenase also is expressed. SNT-1 was further shown to produce larger amounts of both ribulose 1,5-bisphosphate carboxylase/oxygenase and polyhydroxy alkanoates than the wild type, indicating that the redox status is affected in this mutant. Using Western blotting, we found that FixA and FixB are soluble proteins, whereas FixC most likely is a transmembrane protein. We propose that the fixABCX genes encode a membrane protein complex that plays a central role in electron transfer to nitrogenase in R. rubrum. Furthermore, we suggest that FixC is the link between nitrogen fixation and the proton motive force generated in the photosynthetic reactions.

A Cyanide-Induced 3-Cyanoalanine Nitrilase in the Cyanide-Assimilating Bacterium Pseudomonas pseudoalcaligenes Strain CECT 5344.

Science.gov (United States)

Acera, Felipe; Carmona, María Isabel; Castillo, Francisco; Quesada, Alberto; Blasco, Rafael

2017-05-01

Pseudomonas pseudoalcaligenes CECT 5344 is a bacterium able to assimilate cyanide as a sole nitrogen source. Under this growth condition, a 3-cyanoalanine nitrilase enzymatic activity was induced. This activity was encoded by nit4 , one of the four nitrilase genes detected in the genome of this bacterium, and its expression in Escherichia coli enabled the recombinant strain to fully assimilate 3-cyanoalanine. P. pseudoalcaligenes CECT 5344 showed a weak growth level with 3-cyanoalanine as the N source, unless KCN was also added. Moreover, a nit4 knockout mutant of P. pseudoalcaligenes CECT 5344 became severely impaired in its ability to grow with 3-cyanoalanine and cyanide as nitrogen sources. The native enzyme expressed in E. coli was purified up to electrophoretic homogeneity and biochemically characterized. Nit4 seems to be specific for 3-cyanoalanine, and the amount of ammonium derived from the enzymatic activity doubled in the presence of exogenously added asparaginase activity, which demonstrated that the Nit4 enzyme had both 3-cyanoalanine nitrilase and hydratase activities. The nit4 gene is located downstream of the cyanide resistance transcriptional unit containing cio1 genes, whose expression levels are under the positive control of cyanide. Real-time PCR experiments revealed that nit4 expression was also positively regulated by cyanide in both minimal and LB media. These results suggest that this gene cluster including cio1 and nit4 could be involved both in cyanide resistance and in its assimilation by P. pseudoalcaligenes CECT 5344. IMPORTANCE Cyanide is a highly toxic molecule present in some industrial wastes due to its application in several manufacturing processes, such as gold mining and the electroplating industry. The biodegradation of cyanide from contaminated wastes could be an attractive alternative to physicochemical treatment. P. pseudoalcaligenes CECT 5344 is a bacterial strain able to assimilate cyanide under alkaline conditions, thus

PCR-restriction fragment length polymorphism analysis of indigenous nitrogen-fixing micro organisms lineages

International Nuclear Information System (INIS)

Liew Woan Ying Pauline; Jong Bor Chyan; Khairuddin Abdul Rahim

2006-01-01

The use of PCR-RFLP analysis as a useful microbial identification tool has been evaluated for years. This approach was verified effective worldwide, where differential DNA bands and sequence markers distinctive to specific microbes or microbial groups have been identified. In our study, PCR-RFLP technique has been adopted in the identification of our indigenous N 2 -fixing isolates obtained from several local environments. RFLP was carried out with suitable restriction enzymes and the patterns were documented. Representatives of the different patterns were selected and analysed with the 16S ribosomal DNA sequencing method. The results demonstrated correlation between the differential RFLP patterns and the 16S rDNA identities. (Author)

Studies on the pathogenic bacterium of ulcer disease in Epinephelus awoara

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

Studies were conducted to determine the cause of the acute mortality of cage-cultured Epinephelus awoara in the Tong'an Bay of Xiamen, China during the summer of 2002. Predominant bacteria strain TS-628 was isolated from the diseased grouper. The virulence test confirmed that TS-628 was the pathogenic bacterium. Biochemical characteristics of the isolates were determined using the automatic bacterial identification system and standard tube tests. To further confirm the identification, a 1 121 bp 16S rRNA gene sequence of the isolate was amplified by PCR, which had been deposited into Genbank (accession number: AY747308). According to the biochemical characteristics and by comparing the 16S rRNA gene homology of the isolate, the pathogenic bacterium was identified as Vibrio harveyi. Drug sensitivity tests showed that this pathogenic bacterium was sensitive to 16 antibacterials, especially to chloramphenicol and actinospectacin, but completely resistant to antibacterials likes vancomycin, penicillin, lincomycin, and so on.

Effect of two organophosphorus insecticides on the growth, respiration and (/sup 14/C)-glucose metabolism of Azobacter chroococcum Beij

Energy Technology Data Exchange (ETDEWEB)

Balasubramanian, A; Narayanan, R [Tamil Nadu Agricultural Univ., Coimbatore (India)

1980-01-01

The two organophosphorus insecticides, commonly applied to soil, viz., disulfoton (0,0-diethyl S-2-ethyl thio ethyl phosphorodithioate) and fensulfothion (0,0-diethyl 0-4-methyl sulphinyl phenyl phosphorothioate) did not affect the in vitro growth of Azotobacter chroococcum Beij., the free-living, nitrogen fixing soil bacterium, at 2 ppm (lower level), while the normal dose (5 ppm) and the higher level (10 ppm) suppressed the growth. Respiration of the organism (glucose oxidation) was adversely affected by the insecticides in the growth medium and the inhibition increased with the concentration of the chemical. Both the insecticides suppressed the assimilation of (/sup 14/C)-glucose in the cold-TCA soluble, hot-TCA soluble fractions and insoluble residue of the cells whereas the /sup 14/C-incorporation in the alcohol soluble and alcohol-ether soluble fractions was enhanced indicating that the insecticides considerably altered the glucose metabolism of the bacterium.

Effect of two organophosphorus insecticides on the growth, respiration and (14C)-glucose metabolism of Azobacter chroococcum Beij

International Nuclear Information System (INIS)

Balasubramanian, A.; Narayanan, R.

1980-01-01

The two organophosphorus insecticides, commonly applied to soil, viz., disulfoton (0,0-diethyl S-2-ethyl thio ethyl phosphorodithioate) and fensulfothion (0,0-diethyl 0-4-methyl sulphinyl phenyl phosphorothioate) did not affect the in vitro growth of Azotobacter chroococcum Beij., the free-living, nitrogen fixing soil bacterium, at 2 ppm (lower level), while the normal dose (5 ppm) and the higher level (10 ppm) suppressed the growth. Respiration of the organism (glucose oxidation) was adversely affected by the insecticides in the growth medium and the inhibition increased with the concentration of the chemical. Both the insecticides suppressed the assimilation of ( 14 C)-glucose in the cold-TCA soluble, hot-TCA soluble fractions and insoluble residue of the cells whereas the 14 C-incorporation in the alcohol soluble and alcohol-ether soluble fractions was enhanced indicating that the insecticides considerably altered the glucose metabolism of the bacterium. (author)

"Cold" Fixation: Reconciliation of Nitrogen Fixation Rates and Diazotroph Assemblages in the Arctic Ocean

Science.gov (United States)

Fong, A. A.; Waite, A.; Rost, B.; Richter, K. U.

2016-02-01

Measurements of biological nitrogen fixation are typically conducted in oligotrophic subtropical and tropical marine environments where concentrations of fixed inorganic nitrogen are low. To date, only a handful of nitrogen fixation studies have been conducted in high latitude marine environments, but further investigation is needed to resolve the distribution of cold ocean diazotrophic assemblages. Nitrogen fixation rates and nifH gene distributions were measured at seven stations from 5°E to 20°E, north of 81°N in the Arctic Ocean at the onset of summer 2015. Discrete water samples in ice-covered regions were collected from the sea surface to 200 m for 15N2-tracer additions and targeted nifH gene and transcript analyses. Previous work suggests that heterotrophic bacteria dominate diazotrophic communities in the Arctic Ocean. Therefore, additional nifH gene surveys of sinking particles were conducted to test for enrichment on organic matter-rich microenvironments. Together, these measurements aim to reconcile diazotrophic activity with microbial community composition, further elucidating how nitrogen fixers could impact current concepts in polar carbon and nutrient cycling.

BMAA Inhibits Nitrogen Fixation in the Cyanobacterium Nostoc sp. PCC 7120

Directory of Open Access Journals (Sweden)

Birgitta Bergman

2013-08-01

Full Text Available Cyanobacteria produce a range of secondary metabolites, one being the neurotoxic non-protein amino acid β-N-methylamino-L-alanine (BMAA, proposed to be a causative agent of human neurodegeneration. As for most cyanotoxins, the function of BMAA in cyanobacteria is unknown. Here, we examined the effects of BMAA on the physiology of the filamentous nitrogen-fixing cyanobacterium Nostoc sp. PCC 7120. Our data show that exogenously applied BMAA rapidly inhibits nitrogenase activity (acetylene reduction assay, even at micromolar concentrations, and that the inhibition was considerably more severe than that induced by combined nitrogen sources and most other amino acids. BMAA also caused growth arrest and massive cellular glycogen accumulation, as observed by electron microscopy. With nitrogen fixation being a process highly sensitive to oxygen species we propose that the BMAA effects found here may be related to the production of reactive oxygen species, as reported for other organisms.

A reevaluation of the magnitude and impacts of anthropogenic atmospheric nitrogen inputs on the ocean

NARCIS (Netherlands)

Jickells, T.D.; Buitenhuis, E.; Altieri, K.; Baker, A.R.; Capone, D.; Duce, R.A.; Dentener, Frank; Fennel, F.; Kanakidou, M.; LaRoche, J.; Lee, K.; Liss, P.; Middelburg, Jack J.|info:eu-repo/dai/nl/079665373; Moore, J.K.; Okin, G.; Oschlies, A.; Sarin, M.; Seitzinger, S.; Sharples, J.; Singh, A.; Suntharalingam, P.; Uematsu, M.; Zamora, L.M.

We report a new synthesis of best estimates of the inputs of fixed nitrogen to the world ocean via atmospheric deposition and compare this to fluvial inputs and dinitrogen fixation. We evaluate the scale of human perturbation of these fluxes. Fluvial inputs dominate inputs to the continental shelf,

Potential for Nitrogen Fixation and Nitrification in the Granite-Hosted Subsurface at Henderson Mine, CO

Science.gov (United States)

Swanner, Elizabeth D.; Templeton, Alexis S.

2011-01-01

The existence of life in the deep terrestrial subsurface is established, yet few studies have investigated the origin of nitrogen that supports deep life. Previously, 16S rRNA gene surveys cataloged a diverse microbial community in subsurface fluids draining from boreholes 3000 feet deep at Henderson Mine, CO, USA (Sahl et al., 2008). The prior characterization of the fluid chemistry and microbial community forms the basis for the further investigation here of the source of NH4+. The reported fluid chemistry included N2, NH4+ (5–112 μM), NO2− (27–48 μM), and NO3− (17–72 μM). In this study, the correlation between low NH4+ concentrations in dominantly meteoric fluids and higher NH4+ in rock-reacted fluids is used to hypothesize that NH4+ is sourced from NH4+-bearing biotite. However, biotite samples from the host rocks and ore-body minerals were analyzed by Fourier transform infrared (FTIR) microscopy and none-contained NH4+. However, the nitrogenase-encoding gene nifH was successfully amplified from DNA of the fluid sample with high NH4+, suggesting that subsurface microbes have the capability to fix N2. If so, unregulated nitrogen fixation may account for the relatively high NH4+ concentrations in the fluids. Additionally, the amoA and nxrB genes for archaeal ammonium monooxygenase and nitrite oxidoreductase, respectively, were amplified from the high NH4+ fluid DNA, while bacterial amoA genes were not. Putative nitrifying organisms are closely related to ammonium-oxidizing Crenarchaeota and nitrite-oxidizing Nitrospira detected in other subsurface sites based upon 16S rRNA sequence analysis. Thermodynamic calculations underscore the importance of NH4+ as an energy source in a subsurface nitrification pathway. These results suggest that the subsurface microbial community at Henderson is adapted to the low nutrient and energy environment by their capability of fixing nitrogen, and that fixed nitrogen may support subsurface biomass via

Thermal activation and characterization of clay aiming their use as sorbent in fixed bed columns to remove cadmium

International Nuclear Information System (INIS)

Silva, M.M. da; Rodrigues, M.G.F.; Silva, M.L.P.; Kleinübing, S.J.; Silva, M.G.C.

2011-01-01

In this work we studied the removal of cadmium in a synthetic wastewater using clay of Pernambuco - Brazil, in systems of fixed bed column. Clay was thermally activated at 500 °C. The materials were characterized using X-ray Fluorescence (XRF), X-ray Diffraction (XRD) and nitrogen adsorption (BET method). For tests in fixed bed column, we applied a factorial design 2"2 and found that increasing the flow adversely affects the process of removing cadmium concentration while acting positively. The studies showed these materials as promising for the removal of Cd"2"+ ions in synthetic wastewater containing low levels of this metal. (author)