Enabling Biological Nitrogen Fixation for Cereal Crops in Fertilized Fields

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This article references 67 other publications.

1. 1

   Rütting, T.; Aronsson, H.; Delin, S. Efficient Use of Nitrogen in Agriculture. Nutr. Cycling Agroecosyst. 2018, 110, 1– 5,  DOI: 10.1007/s10705-017-9900-8

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   How a century of ammonia synthesis changed the world

   Erisman, Jan Willem; Sutton, Mark A.; Galloway, James; Klimont, Zbigniew; Winiwarter, Wilfried

   Nature Geoscience (2008), 1 (10), 636-639CODEN: NGAEBU; ISSN:1752-0894. (Nature Publishing Group)

   On 13 Oct. 1908, Fritz Haber filed his patent on the "synthesis of ammonia from its elements" for which he was later awarded the 1918 Nobel Prize in Chem. A hundred years on we live in a world transformed by and highly dependent upon Haber-Bosch nitrogen.
5. 5

   Keeler, B. L.; Gourevitch, J. D.; Polasky, S.; Isbell, F.; Tessum, C. W.; Hill, J. D.; Marshall, J. D. The Social Costs of Nitrogen. Sci. Adv. 2016, 2, e1600219  DOI: 10.1126/sciadv.1600219

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   Venterea, R. T.; Halvorson, A. D.; Kitchen, N.; Liebig, M. A.; Cavigelli, M. A.; Grosso, S. J. D.; Motavalli, P. P.; Nelson, K. A.; Spokas, K. A.; Singh, B. P. Challenges and Opportunities for Mitigating Nitrous Oxide Emissions from Fertilized Cropping Systems. Front. Ecol. Environ. 2012, 10, 562– 570,  DOI: 10.1890/120062

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   Fowler, D.; Coyle, M.; Skiba, U.; Sutton, M. A.; Cape, J. N.; Reis, S.; Sheppard, L. J.; Jenkins, A.; Grizzetti, B.; Galloway, J. N. The Global Nitrogen Cycle in the Twenty-First Century. Philos. Trans. R. Soc., B 2013, 368, 20130164,  DOI: 10.1098/rstb.2013.0164

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   The global nitrogen cycle in the twenty-first century

   Fowler, David; Coyle, Mhairi; Skiba, Ute; Sutton, Mark A.; Cape, J. Neil; Reis, Stefan; Sheppard, Lucy J.; Jenkins, Alan; Grizzetti, Bruna; Galloway, James N.; Vitousek, Peter; Leach, Allison; Bouwman, Alexander F.; Butterbach-Bahl, Klaus; Dentener, Frank; Stevenson, David; Amann, Marcus; Voss, Maren

   Philosophical Transactions of the Royal Society, B: Biological Sciences (2013), 368 (1621), 20130164/1-20130164/13CODEN: PTRBAE; ISSN:0962-8436. (Royal Society)

   A review. Global nitrogen fixation contributes 413 TG of reactive nitrogen (Nr) to terrestrial and marine ecosystems annually of which anthropogenic activities are responsible for half, 210 Tg N. The majority of the transformations of anthropogenic Nr are on land (240 TG N yr-1) within soils and vegetation where reduced Nr contributes most of the input through the use of fertilizer nitrogen in agriculture. Leakages from the use of fertilizer Nr contribute to nitrate (NO-3) in drainage waters from agricultural land and emissions of trace Nr compds. to the atm. Emissions, mainly of ammonia (NH3) from land together with combustion related emissions of nitrogen oxides (NOx), contribute 100 TG N yr-1 to the atm., which are transported between countries and processed within the atm., generating secondary pollutants, including ozone and other photochem. oxidants and aerosols, esp. ammonium nitrate (NH4NO3) and ammonium sulfate (NH4)2SO4. Leaching and riverine transport of NO3 contribute 40-70 TG N yr-1 to coastal waters and the open ocean, which together with the 30 Tg input to oceans from atm. deposition combine with marine biol. nitrogen fixation (140 Tg N yr-1) to double the ocean processing of Nr. Some of the marine Nr is buried in sediments, the remainder being denitrified back to the atm. as N2 or N2O. The marine processing is of a similar magnitude to that in terrestrial soils and vegetation, but has a larger fraction of natural origin. The lifetime of Nr in the atm., with the exception of N2O, is only a few weeks, while in terrestrial ecosystems, with the exception of peatlands (it can be 102-103 years), the lifetime is a few decades. In the ocean, the lifetime of Nr is less known but seems to be longer than in terrestrial ecosystems and may represent an important long-term source of N2O that will respond very slowly to control measures on the sources of Nr from which it is produced.
8. 8

   Sobota, D. J.; Compton, J. E.; McCrackin, M. L.; Singh, S. Cost of Reactive Nitrogen Release from Human Activities to the Environment in the United States. Environ. Res. Lett. 2015, 10, 025006,  DOI: 10.1088/1748-9326/10/2/025006

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   Cost of reactive nitrogen release from human activities to the environment in the United States

   Sobota, Daniel J.; Compton, Jana E.; McCrackin, Michelle L.; Singh, Shweta

   Environmental Research Letters (2015), 10 (2), 025006/1-025006/13CODEN: ERLNAL; ISSN:1748-9326. (IOP Publishing Ltd.)

   Leakage of reactive nitrogen (N) from human activities to the environment can cause human health and ecol. problems. Often these harmful effects are not reflected in the costs of food, fuel, and fiber that derive from N use. Spatial analyses of damage costs attributable to source at management relevant scales could inform decisions in areas where anthropogenic N leakage causes harm. We used recently compiled data describing N inputs in the conterminous United States (US) to assess potential damage costs assocd. with anthropogenic N. We estd. fates of N leaked to the environment (air/deposition, surface freshwater, groundwater, and coastal zones) in the early 2000s by multiplying watershed-level N inputs (8-digit US Geol. Survey Hydrol. Unit Codes; HUC8s) with published coeffs. describing nutrient uptake efficiency, leaching losses, and gaseous emissions. We scaled these N leakage ests. with mitigation, remediation, direct damage, and substitution costs assocd. with human health, agriculture, ecosystems, and climate (per kg of N) to calc. annual damage cost (US dollars in 2008 or as reported) of anthropogenic N per HUC8. Ests. of N leakage byHUC8 ranged from <1 to 125 kg N ha-1 yr-1, with most N leaked to freshwater ecosystems. Ests. of potential damages (based on median ests.) ranged from $1.94 to $2255 ha-1 yr-1 across watersheds, with a median of $252 ha-1 yr-1. Eutrophication of freshwater ecosystems and respiratory effects of atm. N pollution were important across HUC8s. However, significant data gaps remain in our ability to fully assess N damages, such as damage costs from harmful algal blooms and drinking water contamination. Nationally, potential health and environmental damages of anthropogenic N in the early 2000s totaled $210 billion yr-1 USD (range: $81-$441 billion yr-1). While a no. of gaps and uncertainties remain in these ests., overall this work represents a starting point to inform decisions and engage stakeholders on the costs of N pollution.
9. 9

   Campbell, B. M.; Beare, D. J.; Bennett, E. M.; Hall-Spencer, J. M.; Ingram, J. S. I.; Jaramillo, F.; Ortiz, R.; Ramankutty, N.; Sayer, J. A.; Shindell, D. Agriculture Production as a Major Driver of the Earth System Exceeding Planetary Boundaries. Ecol. Soc. 2017, 22, 8,  DOI: 10.5751/ES-09595-220408

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10. 10

    Bloch, S. E.; Ryu, M.-H.; Ozaydin, B.; Broglie, R. Harnessing Atmospheric Nitrogen for Cereal Crop Production. Curr. Opin. Biotechnol. 2020, 62, 181– 188,  DOI: 10.1016/j.copbio.2019.09.024

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    Harnessing atmospheric nitrogen for cereal crop production

    Bloch, Sarah E.; Ryu, Min-Hyung; Ozaydin, Bilge; Broglie, Richard

    Current Opinion in Biotechnology (2020), 62 (), 181-188CODEN: CUOBE3; ISSN:0958-1669. (Elsevier B.V.)

    While synthetic nitrogen fuels modern agriculture, its prodn. is energy-intensive, and its application leads to aquatic pollution and greenhouse gas emissions. Sustainable intensification of agriculture to provide both food for humans and feedstocks for bio-based fuels and materials requires alternative options for nitrogen management. For nearly fifty years, nitrogen fixation in cereal crops has been pursued to address this challenge. Efforts to engineer plants for nitrogen fixation have made strides through eukaryotic nitrogenase expression and a deepened understanding of root nodulation pathways, but deployment of transgenic nitrogen fixing cereals may be outpaced by population growth. By contrast, a root-assocd. bacterium that can fix and supply nitrogen to cereals could offer a sustainable soln. for nitrogen management on a shorter timescale.
11. 11

    Mus, F.; Crook, M. B.; Garcia, K.; Garcia Costas, A.; Geddes, B. A.; Kouri, E. D.; Paramasivan, P.; Ryu, M.-H.; Oldroyd, G. E. D.; Poole, P. S. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl. Environ. Microbiol. 2016, 82, 3698– 3710,  DOI: 10.1128/AEM.01055-16

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    Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes

    Mus, Florence; Crook, Matthew B.; Garcia, Kevin; Costas, Amaya Garcia; Geddes, Barney A.; Kouri, Evangelia D.; Paramasivan, Ponraj; Ryu, Min-Hyung; Oldroyd, Giles E. D.; Poole, Philip S.; Udvardi, Michael K.; Voigt, Christopher A.; Ane, Jean-Michel; Peters, John W.

    Applied and Environmental Microbiology (2016), 82 (13), 3698-3710CODEN: AEMIDF; ISSN:1098-5336. (American Society for Microbiology)

    Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food prodn. Nitrogenous fertilizer prodn. currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biol. nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biol. nitrogen fixation is the conversion of atm. N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biol. nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biol. approaches. This minireview highlights the fundamental advances in our understanding of biol. nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biol.
12. 12

    Smercina, D. N.; Evans, S. E.; Friesen, M. L.; Tiemann, L. K. To Fix or Not To Fix: Controls on Free-Living Nitrogen Fixation in the Rhizosphere. Appl. Environ. Microbiol. 2019, 85, e02546  DOI: 10.1128/AEM.02103-19

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    To fix or not to fix: controls on free-living nitrogen fixation in the rhizosphere

    Smercina, Darian N.; Evans, Sarah E.; Friesen, Maren L.; Tiemanna, Lisa K.

    Applied and Environmental Microbiology (2019), 85 (6), e02546-18/1-e02546-18/14CODEN: AEMIDF; ISSN:1098-5336. (American Society for Microbiology)

    A review. Free-living nitrogen fixation (FLNF) in the rhizosphere, or N fixation by heterotrophic bacteria living on/near root surfaces, is ubiquitous and a significant source of N in some terrestrial systems. FLNF is also of interest in crop prodn. as an alternative to chem. fertilizer, potentially reducing prodn. costs and ameliorating neg. environmental impacts of fertilizer N addns. Despite this interest, a mechanistic understanding of controls (e.g., carbon, oxygen, nitrogen, and nutrient availability) on FLNF in the rhizosphere is lacking but necessary. FLNF is distinct from and occurs under more diverse and dynamic conditions than symbiotic N fixation; therefore, predicting FLNF rates and understanding controls on FLNF has proven difficult. This has led to large gaps in our understanding of FLNF, and studies aimed at identifying controls on FLNF are needed. Here, we provide a mechanistic overview of FLNF, including how various controls may influence FLNF in the rhizosphere in comparison with symbiotic N fixation occurring in plant nodules where environmental conditions are moderated by the plant. We apply this knowledge to a real-world example, the bioenergy crop switchgrass (Panicum virgatum), to provide context of how FLNF may function in a managed system. We also highlight future challenges to assessing FLNF and understanding how FLNF functions in the environment and significantly contributes to plant N availability and productivity.
13. 13

    Heffer, P. Assessment of Fertilizer Use by Crop at the Global Level; IFA, 2013.

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14. 14

    Bennett, A. B.; Pankievicz, V. C. S.; Ané, J.-M. A Model for Nitrogen Fixation in Cereal Crops. Trends Plant Sci. 2020, 25, 226– 235,  DOI: 10.1016/j.tplants.2019.12.004

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    A Model for Nitrogen Fixation in Cereal Crops

    Bennett, Alan B.; Pankievicz, Vania C. S.; Ane, Jean-Michel

    Trends in Plant Science (2020), 25 (3), 226-235CODEN: TPSCF9; ISSN:1360-1385. (Elsevier Ltd.)

    Nitrogen-fixing microbial assocns. with cereals have been of intense interest for more than a century. A recent report demonstrated that an indigenous Sierra Mixe maize landrace, characterized by an extensive development of aerial roots that secrete large amts. of mucilage, can acquire 28-82% of its nitrogen from atm. dinitrogen. Although the Sierra Mixe maize landrace is unique in the large quantity of mucilage produced, other cereal crops secrete mucilage from underground and aerial roots and we hypothesize that this may represent a general mechanism for cereals to support assocns. with microbial diazotrophs. We propose a model for the assocn. of nitrogen-fixing microbes with maize mucilage and identify the four main functionalities for such a productive diazotrophic assocn.
15. 15

    Parnell, J. J.; Berka, R.; Young, H. A.; Sturino, J. M.; Kang, Y.; Barnhart, D. M.; Dileo, M. V. From the Lab to the Farm: An Industrial Perspective of Plant Beneficial Microorganisms. Front. Plant Sci. 2016, 7, 1– 12,  DOI: 10.3389/fpls.2016.01110

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16. 16

    Schmitz, R. A.; Klopprogge, K.; Grabbe, R. Regulation of Nitrogen Fixation in Klebsiella Pneumoniae and Azotobacter Vinelandii: NifL, Transducing Two Environmental Signals to the Nif Transcriptional Activator NifA. J. Mol. Microbiol. Biotechnol. 2002, 4, 235– 242

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    Regulation of nitrogen fixation in Klebsiella pneumoniae and Azotobacter vinelandii: NifL, transducing two environmental signals to the nif transcriptional activator NifA

    Schmitz, Ruth A.; Klopprogge, Kai; Grabbe, Roman

    Journal of Molecular Microbiology and Biotechnology (2002), 4 (3), 235-242CODEN: JMMBFF; ISSN:1464-1801. (Horizon Scientific Press)

    A review that focuses on the regulation of nitrogen fixation in Klebsiella pneumoniae and Azotobacter vinelandii. The review specifically focuses on the transduction of signals for the presence of mol. oxygen and combined nitrogen in these organisms, and compares the mechanism by which these signals are mediated by the NifL/NifA system in the two organisms. The enzymic redn. of mol. nitrogen to ammonia requires high amts. of energy, and the presence of oxygen causes the catalyzing nitrogenase complex to be irreversible inactivated. Thus nitrogen-fixing microorganisms tightly control both the synthesis and activity of nitrogenase to avoid the unnecessary consumption of energy. In the free-living diazotrophs K. pneumoniae and A. vinelandii, products of the nitrogen fixation nifLA operon regulate transcription of the other nif operons. NifA activates transcription of nif genes by the alternative form of RNA-polymerase, σ54-holoenzyme; NifL modulates the activity of the transcriptional activator NifA in response to the presence of combined nitrogen and mol. oxygen. The translationally-coupled synthesis of the two regulatory proteins, in addn. to evidence from studies of NifL/NifA complex formation, imply that the inhibition of NifA activity by NifL occurs via direct protein-protein interaction in vivo. The inhibitory function of the neg. regulator NifL appears to lie in the C-terminal domain, whereas the N-terminal domain binds FAD as a redox-sensitive cofactor, which is required for signal transduction of the internal oxygen status. Recently it was shown, that NifL acts as a redox-sensitive regulatory protein, which modulates NifA activity in response to the redox-state of its FAD cofactor, and allows NifA activity only in the absence of oxygen. In K. pneumoniae, the primary oxygen sensor appears to be Fnr (fumarate nitrate redn. regulator), which is presumed to transduce the signal of anaerobiosis towards NifL by activating the transcription of gene(s) whose product(s) function to relieve NifL inhibition through redn. of the FAD cofactor. In contrast, the redn. of A. vinelandii-NifL appears to occur unspecific in response to the availability of reducing equiv. in the cell. Nitrogen status of the cells is transduced towards the NifL/NifA regulatory system by the GlnK protein, a paralogue PII-protein, which appears to interact with the NifL/NifA regulatory system via direct protein-protein interaction. It is not currently known whether GlnK interacts with NifL alone or affects the NifL/NifA-complex; moreover the effects appear to be the opposite in K. pneumoniae and A. vinelandii. In addn. to these environmental signals, adenine nucleotides also affect the inhibitory function of NifL; in the presence of ATP or ADP the inhibitory effect on NifA activity in vitro is increased. The NifL proteins from the two organisms differ, however, in that stimulation of K. pneumoniae-NifL occurs only when synthesized under nitrogen excess, and is correlated with the ability to hydrolyze ATP. In general, transduction of environmental signals to the nif regulatory system appears to involve a conformational change of NifL or the NifL/NifA complex. However, exptl. data suggest that K. pneumoniae and A. vinelandii employ significantly different species-specific mechanisms of signal transduction.
17. 17

    Batista, M. B.; Dixon, R. Manipulating Nitrogen Regulation in Diazotrophic Bacteria for Agronomic Benefit. Biochem. Soc. Trans. 2019, 47, 603– 614,  DOI: 10.1042/BST20180342

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    Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit

    Batista, Marcelo Bueno; Dixon, Ray

    Biochemical Society Transactions (2019), 47 (2), 603-614CODEN: BCSTB5; ISSN:0300-5127. (Portland Press Ltd.)

    A review. Biol. nitrogen fixation (BNF) is controlled by intricate regulatory mechanisms to ensure that fixed nitrogen is readily assimilated into biomass and not released to the environment. Understanding the complex regulatory circuits that couple nitrogen fixation to ammonium assimilation is a prerequisite for engineering diazotrophic strains that can potentially supply fixed nitrogen to non-legume crops. In this review, we explore how the current knowledge of nitrogen metab. and BNF regulation may allow strategies for genetic manipulation of diazotrophs for ammonia excretion and provide a contribution towards solving the nitrogen crisis.
18. 18

    Triplett, E. W. Diazotrophic Endophytes: Progress and Prospects for Nitrogen Fixation in Monocots. Plant Soil 1996, 186, 29– 38,  DOI: 10.1007/BF00035052

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    Diazotrophic endophytes: progress and prospects for nitrogen fixation in monocots

    Triplett, Eric W.

    Plant and Soil (1996), 186 (1), 29-38CODEN: PLSOA2; ISSN:0032-079X. (Kluwer)

    A review with 79 refs. As nitrogen fertilization is one of the highest costs of corn prodn., the development of a symbiosis between diazotrophic bacteria and corn would be of enormous economic value. Such a discovery would also improve human health as it would decrease the amt. of nitrate in groundwater as well as in corn cultured for human consumption. Proposals have been made toward this end include: (a) the transfer of root nodulation genes from a legume to maize; (b) the expression of the bacterial nif regulon in maize organelles; and (c) the development of corn lines with the ability to accept fixed nitrogen from diazotrophs in the rhizosphere. All of these proposals have enormous tech. problems to overcome such that the development of nitrogen-fixing corn in the near term has been considered unlikely. An alternative and less-tech. challenging approach may be a thorough study of nonpathogenic bacterial endophytes that already inhabit the corn plant. The discovery of a nitrogen-fixing bacterial-sugarcane assocn. by J. Dobereiner and coworkers (1988) in Brazil illustrates the enormous potential of endophytic bacteria to enhance grass biomass in the absence of nitrogen fertilizer. Dobereiner and coworkers have discovered diazotrophic strains of Acetobacter diazotrophicus and Herbaspirillum seropedicae in lines of sugarcane that were bred in the absence of nitrogen fertilizer. The Brazilian group has also demonstrated that sugarcane plants infected with these diazotrophs are capable of deriving all of their nitrogen needs from N2. Recently, the presence of nonpathogenic endophytic bacteria in corn has been shown. Based on this evidence and using the sugarcane paradigm as an example, investigators are working toward the discovery and anal. of diazotrophic endophytes in corn which includes the search for corn germplasm that would readily benefit from an assocn. with these bacteria. Several diazotrophic endophytes have been identified in grass species that are members of the α-, β-, and γ-subclasses of the proteobacteria. Understanding of the ability of these bacteria to enhance the growth of grasses through nitrogen fixation is only beginning to be explored, but this approach is thought to be far less tech. challenging than are other proposals to develop 'nitrogen fixation' in maize.
19. 19

    Ladha, J. K.; Tirol-Padre, A.; Reddy, C. K.; Cassman, K. G.; Verma, S.; Powlson, D. S.; van Kessel, C.; de B. Richter, D.; Chakraborty, D.; Pathak, H. Global nitrogen budgets in cereals: A 50-year assessment for maize, rice and wheat production systems. Sci. Rep. 2016, 6, 19355,  DOI: 10.1038/srep19355

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    19

    Global nitrogen budgets in cereals: A 50-year assessment for maize, rice, and wheat production systems

    Ladha, J. K.; Tirol-Padre, A.; Reddy, C. K.; Cassman, K. G.; Verma, Sudhir; Powlson, D. S.; van Kessel, C.; Richter, Daniel de B.; Chakraborty, Debashis; Pathak, Himanshu

    Scientific Reports (2016), 6 (), 19355CODEN: SRCEC3; ISSN:2045-2322. (Nature Publishing Group)

    Industrially produced N-fertilizer is essential to the prodn. of cereals that supports current and projected human populations. We constructed a top-down global N budget for maize, rice, and wheat for a 50-yr period (1961 to 2010). Cereals harvested a total of 1551 Tg of N, of which 48% was supplied through fertilizer-N and 4% came from net soil depletion. An estd. 48% (737 Tg) of crop N, equal to 29, 38, and 25 kg ha-1 yr-1 for maize, rice, and wheat, resp., is contributed by sources other than fertilizer- or soil-N. Non-symbiotic N2 fixation appears to be the major source of this N, which is 370 Tg or 24% of total N in the crop, corresponding to 13, 22, and 13 kg ha-1 yr-1 for maize, rice, and wheat, resp. Manure (217 Tg or 14%) and atm. deposition (96 Tg or 6%) are the other sources of N. Crop residues and seed contribute marginally. Our scaling-down approach to est. the contribution of non-symbiotic N2 fixation is robust because it focuses on global quantities of N in sources and sinks that are easier to est., in contrast to estg. N losses per se, because losses are highly soil-, climate-, and crop-specific.
20. 20

    Van Deynze, A.; Zamora, P.; Delaux, P.-M.; Heitmann, C.; Jayaraman, D.; Rajasekar, S.; Graham, D.; Maeda, J.; Gibson, D.; Schwartz, K. D. Nitrogen Fixation in a Landrace of Maize Is Supported by a Mucilage-Associated Diazotrophic Microbiota. PLoS Biol. 2018, 16, e2006352  DOI: 10.1371/journal.pbio.2006352

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    20

    Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota

    Van Deynze, Allen; Zamora, Pablo; Delaux, Pierre-Marc; Heitmann, Cristobal; Jayaraman, Dhileepkumar; Rajasekar, Shanmugam; Graham, Danielle; Maeda, Junko; Gibson, Donald; Schwartz, Kevin D.; Berry, Alison M.; Bhatnagar, Srijak; Jospin, Guillaume; Darling, Aaron; Jeannotte, Richard; Lopez, Javier; Weimer, Bart C.; Eisen, Jonathan A.; Shapiro, Howard-Yana; Ane, Jean-Michel; Bennett, Alan B.

    PLoS Biology (2018), 16 (8), e2006352/1-e2006352/21CODEN: PBLIBG; ISSN:1545-7885. (Public Library of Science)

    Plants are assocd. with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial assocns. are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Anal. of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene redn. and 15N2 incorporation assays. Field expts. in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atm. nitrogen fixation contributed 29%-82% of the nitrogen nutrition of Sierra Mixe maize.
21. 21

    Bloch, S. E.; Ryu, M.-H.; Ozaydin, B.; Broglie, R. Harnessing Atmospheric Nitrogen for Cereal Crop Production. Curr. Opin. Biotechnol. 2020, 62, 181– 188,  DOI: 10.1016/J.COPBIO.2019.09.024

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    21

    Harnessing atmospheric nitrogen for cereal crop production

    Bloch, Sarah E.; Ryu, Min-Hyung; Ozaydin, Bilge; Broglie, Richard

    Current Opinion in Biotechnology (2020), 62 (), 181-188CODEN: CUOBE3; ISSN:0958-1669. (Elsevier B.V.)

    While synthetic nitrogen fuels modern agriculture, its prodn. is energy-intensive, and its application leads to aquatic pollution and greenhouse gas emissions. Sustainable intensification of agriculture to provide both food for humans and feedstocks for bio-based fuels and materials requires alternative options for nitrogen management. For nearly fifty years, nitrogen fixation in cereal crops has been pursued to address this challenge. Efforts to engineer plants for nitrogen fixation have made strides through eukaryotic nitrogenase expression and a deepened understanding of root nodulation pathways, but deployment of transgenic nitrogen fixing cereals may be outpaced by population growth. By contrast, a root-assocd. bacterium that can fix and supply nitrogen to cereals could offer a sustainable soln. for nitrogen management on a shorter timescale.
22. 22

    Voigt, C. A. Synthetic biology 2020-2030: six commercially-available products that are changing our world. Nat. Commun. 2020, 11, 6379,  DOI: 10.1038/s41467-020-20122-2

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    Synthetic biology 2020-2030: six commercially-available products that are changing our world

    Voigt, Christopher A.

    Nature Communications (2020), 11 (1), 6379CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)

    Synthetic biol. will transform how we grow food, what we eat, and where we source materials and medicines. Here I have selected six products that are now on the market, highlighting the underlying technologies and projecting forward to the future that can be expected over the next ten years.
23. 23

    Carlson, R. Laying the foundations for a bio-economy. Synth. Syst. Biol. 2007, 1, 109– 117,  DOI: 10.1007/s11693-007-9010-z

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    Laying the foundations for a bio-economy

    Carlson Robert

    Systems and synthetic biology (2007), 1 (3), 109-17 ISSN:1872-5325.

    Biological technologies are becoming an important part of the economy. Biotechnology already contributes at least 1% of US GDP, with revenues growing as much as 20% annually. The introduction of composable biological parts will enable an engineering discipline similar to the ones that resulted in modern aviation and information technology. As the sophistication of biological engineering increases, it will provide new goods and services at lower costs and higher efficiencies. Broad access to foundational engineering technologies is seen by some as a threat to physical and economic security. However, regulation of access will serve to suppress the innovation required to produce new vaccines and other countermeasures as well as limiting general economic growth.
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    Thaiss, C. A.; Levy, M.; Korem, T.; Dohnalová, L.; Shapiro, H.; Jaitin, D. A.; David, E.; Winter, D. R.; Gury-BenAri, M.; Tatirovsky, E. Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations. Cell 2016, 167, 1495– 1510,  DOI: 10.1016/j.cell.2016.11.003

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    Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

    Thaiss, Christoph A.; Levy, Maayan; Korem, Tal; Dohnalova, Lenka; Shapiro, Hagit; Jaitin, Diego A.; David, Eyal; Winter, Deborah R.; Gury-BenAri, Meital; Tatirovsky, Evgeny; Tuganbaev, Timur; Federici, Sara; Zmora, Niv; Zeevi, David; Dori-Bachash, Mally; Pevsner-Fischer, Meirav; Kartvelishvily, Elena; Brandis, Alexander; Harmelin, Alon; Shibolet, Oren; Halpern, Zamir; Honda, Kenya; Amit, Ido; Segal, Eran; Elinav, Eran

    Cell (Cambridge, MA, United States) (2016), 167 (6), 1495-1510.e12CODEN: CELLB5; ISSN:0092-8674. (Cell Press)

    The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeog. localization and metabolome patterns that det. the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day. This diurnal microbial behavior drives, in turn, the global programming of the host circadian transcriptional, epigenetic, and metabolite oscillations. Surprisingly, disruption of homeostatic microbiome rhythmicity not only abrogates normal chromatin and transcriptional oscillations of the host, but also incites genome-wide de novo oscillations in both intestine and liver, thereby impacting diurnal fluctuations of host physiol. and disease susceptibility. As such, the rhythmic biogeog. and metabolome of the intestinal microbiota regulates the temporal organization and functional outcome of host transcriptional and epigenetic programs.
25. 25

    Barrangou, R.; Doudna, J. A. Applications of CRISPR Technologies in Research and Beyond. Nat. Biotechnol. 2016, 34, 933,  DOI: 10.1038/nbt.3659

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    25

    Applications of CRISPR technologies in research and beyond

    Barrangou, Rodolphe; Doudna, Jennifer A.

    Nature Biotechnology (2016), 34 (9), 933-941CODEN: NABIF9; ISSN:1087-0156. (Nature Publishing Group)

    Programmable DNA cleavage using CRISPR-Cas9 enables efficient, site-specific genome engineering in single cells and whole organisms. In the research arena, versatile CRISPR-enabled genome editing has been used in various ways, such as controlling transcription, modifying epigenomes, conducting genome-wide screens and imaging chromosomes. CRISPR systems are already being used to alleviate genetic disorders in animals and are likely to be employed soon in the clinic to treat human diseases of the eye and blood. Two clin. trials using CRISPR-Cas9 for targeted cancer therapies have been approved in China and the United States. Beyond biomedical applications, these tools are now being used to expedite crop and livestock breeding, engineer new antimicrobials and control disease-carrying insects with gene drives.
26. 26

    Berg, G.; Eberl, L.; Hartmann, A. The Rhizosphere as a Reservoir for Opportunistic Human Pathogenic Bacteria. Environ. Microbiol. 2005, 7, 1673– 1685,  DOI: 10.1111/j.1462-2920.2005.00891.x

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    26

    The rhizosphere as a reservoir for opportunistic human pathogenic bacteria

    Berg, Gabriele; Eberl, Leo; Hartmann, Anton

    Environmental Microbiology (2005), 7 (11), 1673-1685CODEN: ENMIFM; ISSN:1462-2912. (Blackwell Publishing Ltd.)

    A review. During the last years, the no. of human infections caused by opportunistic pathogens has increased dramatically. One natural reservoir of opportunistic pathogens is the rhizosphere, the zone around roots that is influenced by the plant. Due to a high content of nutrients, this habitat is a 'microbial hot-spot', where bacterial abundances including those with strong antagonistic traits are enhanced. Various bacterial genera, including Burkholderia, Enterobacter, Herbaspirillum, Ochrobactrum, Pseudomonas, Ralstonia, Staphylococcus and Stenotrophomonas, contain root-assocd. strains that can encounter bivalent interactions with both plant and human hosts. Mechanisms responsible for colonization of the rhizosphere and antagonistic activity against plant pathogens are similar to those responsible for colonization of human organs and tissues, and pathogenicity. Multiple resistances against antibiotics are not only found with clin. strains but also with strains isolated from the rhizosphere. High competition, the occurrence of diverse antibiotics in the rhizosphere, and enhanced horizontal gene transfer rates in this microenvironment appear to contribute to the high levels of natural resistances. While opportunistic bacteria from the rhizosphere have some properties in common, each of these emerging pathogens has its own features, which are discussed in detail for Burkholderia, Ochrobactrum and Stenotrophomonas.
27. 27

    Kanter, D. R.; Zhang, X.; Mauzerall, D. L. Reducing Nitrogen Pollution while Decreasing Farmers’ Costs and Increasing Fertilizer Industry Profits. J. Environ. Qual. 2015, 44, 325– 335,  DOI: 10.2134/jeq2014.04.0173

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    Reducing nitrogen pollution while decreasing farmers' costs and increasing fertilizer industry profits

    Kanter, David R.; Zhang, Xin; Mauzerall, Denise L.

    Journal of Environmental Quality (2015), 44 (2), 325-335CODEN: JEVQAA; ISSN:1537-2537. (American Society of Agronomy)

    Nitrogen (N) pollution is emerging as one of the most important environmental issues of the 21st Century, contributing to air and water pollution, climate change, and stratospheric ozone depletion. With agriculture being the dominant source, we tested whether it is possible to reduce agricultural N pollution in a way that benefits the environment, reduces farmers' costs, and increases fertilizer industry profitability, thereby creating a "sweet spot" for decision-makers that could significantly increase the viability of improved N management initiatives. Although studies of the economic impacts of improved N management have begun to take into account farmers and the environment, this is the first study to consider the fertilizer industry. Our "sweet spot" hypothesis is evaluated via a cost-benefit anal. of moderate and ambitious N use efficiency targets in U.S. and China corn sectors over the period 2015-2035. We use a blend of publicly available crop and energy price projections, original time-series modeling, and expert elicitation. The results present a mixed picture: although the potential for a "sweet spot" exists in both countries, it is more likely that one occurs in China due to the currently extensive overapplication of fertilizer, which creates a greater potential for farmers and the fertilizer industry to gain economically from improved N management. Nevertheless, the environmental benefits of improving N management consistently dwarf the economic impacts on farmers and the fertilizer industry in both countries, suggesting that viable policy options could include incentives to farmers and the fertilizer industry to increase their support for N management policies.
28. 28

    Bloch, S. E.; Clark, R.; Gottlieb, S. S.; Wood, L. K.; Shah, N.; Mak, S.-M.; Lorigan, J. G.; Johnson, J.; Davis-Richardson, A. G.; Williams, L. Biological Nitrogen Fixation in Maize: Optimizing Nitrogenase Expression in a Root-Associated Diazotroph. J. Exp. Bot. 2020, 71, 4591– 4603,  DOI: 10.1093/jxb/eraa176

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    28

    Biological nitrogen fixation in maize: optimizing nitrogenase expression in a root-associated diazotroph

    Bloch, Sarah E.; Clark, Rosemary; Gottlieb, Shayin S.; Wood, Kent L.; Shah, Neal; Mak, San-Ming; Lorigan, James G.; Johnson, Jenny; Davis-Richardson, Austin G.; Williams, Lorena; McKellar, Megan; Soriano, Dominic; Petersen, Max; Horton, Alana; Smith, Olivia; Wu, Leslie; Tung, Emily; Broglie, Richard; Tamsir, Alvin; Temme, Karsten

    Journal of Experimental Botany (2020), 71 (15), 4591-4603CODEN: JEBOA6; ISSN:1460-2431. (Oxford University Press)

    Plants depend upon beneficial interactions between roots and root-assocd. microorganisms for growth promotion, disease suppression, and nutrient availability. This includes the ability of free-living diazotrophic bacteria to supply nitrogen, an ecol. role that has been long underappreciated in modern agriculture for efficient crop prodn. systems. Long-term ecol. studies in legume-rhizobia interactions have shown that elevated nitrogen inputs can lead to the evolution of less cooperative nitrogen-fiing mutualists. Here we describe how reprogramming the genetic regulation of nitrogen fixation and assimilation in a novel root-assocd. diazotroph can restore ammonium prodn. in the presence of exogenous nitrogen inputs. We isolated a strain of the plant-assocd. proteobacterium Kosakonia sacchari from corn roots, characterized its nitrogen regulatory network, and targeted key nodes for gene editing to optimize nitrogen fixation in corn. While the wild-type strain exhibits repression of nitrogen fixation in conditions replete with bioavailable nitrogen, such as fertilized greenhouse and field expts., remodeled strains show elevated levels in the rhizosphere of corn in the greenhouse and field even in the presence of exogenous nitrogen. Such strains could be used in com. applications to supply fixed nitrogen to cereal crops.
29. 29

    Wei, C.-Y.; Lin, L.; Luo, L.-J.; Xing, Y.-X.; Hu, C.-J.; Yang, L.-T.; Li, Y.-R.; An, Q. Endophytic Nitrogen-Fixing Klebsiella Variicola Strain DX120E Promotes Sugarcane Growth. Biol. Fertil. Soils 2014, 50, 657– 666,  DOI: 10.1007/s00374-013-0878-3

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    29

    Endophytic nitrogen-fixing Klebsiella variicola strain DX120E promotes sugarcane growth

    Wei, Chun-Yan; Lin, Li; Luo, Li-Jing; Xing, Yong-Xiu; Hu, Chun-Jin; Yang, Li-Tao; Li, Yang-Rui; An, Qianli

    Biology and Fertility of Soils (2014), 50 (4), 657-666CODEN: BFSOEE; ISSN:0178-2762. (Springer)

    We identified a nitrogen-fixing bacterium, DX120E, which was isolated from surface-sterilized roots of the ROC22 sugarcane cultivar, as Klebsiella variicola by phylogenetic analyses of its 16S rRNA gene, RNA polymerase β-subunit gene, and DNA gyrase subunit A gene sequences. Gfp-tagged DX120E was found to colonize at the roots and aerial parts of micropropagated sugarcane plantlets by fluorescence microscopy and confocal microscopy. DX120E was able to survive in soils and colonize in root epidermal cells, intercellular spaces in root cortices, and leaf mesophyll and vascular tissues. DX120E preferentially colonized at root maturation and elongation zones and entered roots via cracks at the emergence site of lateral roots and at disrupted epidermis. DX120E may penetrate root epidermal cells with the aid of their cellulose-degrading enzymes. 15N isotope diln. assay demonstrated that DX120E was able to fix N2 in assocn. with ROC22 sugarcane plants under gnotobiotic condition. DX120E was also able to promote GT21 cultivar growth and plant uptake of N, P, and K under greenhouse condition. Together, this study for the 1st time shows that a K. variicola strain is able to colonize in its sugarcane plant hosts, to fix N2 in assocn. with plants, and to promote plant growth.
30. 30

    Chelius, M. K.; Triplett, E. W. Immunolocalization of Dinitrogenase Reductase Produced by Klebsiella Pneumoniae in Association with Zea Mays L. Appl. Environ. Microbiol. 2000, 66, 783– 787,  DOI: 10.1128/AEM.66.2.783-787.2000

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    Immunolocalization of dinitrogenase reductase produced by Klebsiella pneumoniae in association with Zea mays L.

    Chelius, Marisa K.; Triplett, Eric W.

    Applied and Environmental Microbiology (2000), 66 (2), 783-787CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    The endophytic lifestyle of Klebsiella pneumoniae is described, including the prodn. of dinitrogenase reductase by bacteria residing in maize root tissue. The green fluorescent protein (GFP) was used to detect the colonization of maize by K. pneumoniae strains 2028 and 342. These strains were found to reside in intercortical layers of the stem and within the region of maturation in the root. The prodn. of dinitrogenase reductase by GFP-tagged bacteria was visualized using immunolocalization. This activity was only apparent when bacteria were supplied with an exogenous carbon source. Thus, maize provides a suitable habitat for K. pneumoniae and this species is capable of producing nitrogenase under the appropriate plant cultivation conditions.
31. 31

    Kifle, M. H.; Laing, M. D. Isolation and Screening of Bacteria for Their Diazotrophic Potential and Their Influence on Growth Promotion of Maize Seedlings in Greenhouses. Front. Plant Sci. 2016, 6, 1225,  DOI: 10.3389/fpls.2015.01225

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32. 32

    Martínez, J.; Martínez, L.; Rosenblueth, M.; Silva, J.; Martínez-Romero, E. How Are Gene Sequence Analyses Modifying Bacterial Taxonomy? The Case of Klebsiella. Int. Microbiol. 2004, 7, 261– 268

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    32

    How are gene sequence analyses modifying bacterial taxonomy? The case of Klebsiella

    Martinez, Julio; Martinez, Lucia; Rosenblueth, Monica; Silva, Jesus; Martinez-Romero, Esperanza

    International Microbiology (2004), 7 (4), 261-268CODEN: INMIFW; ISSN:1139-6709. (Viguera Editores)

    A review. Bacterial names are continually being changed in order to more adequately describe natural groups (the units of microbial diversity) and their relationships. The problems in Klebsiella taxonomy are illustrative and common to other bacterial genera. Like other bacteria, Klebsiella spp. were isolated long ago, when methods to identify and classify bacteria were limited. However, recently developed mol. approaches have led to taxonomic revisions in several cases or to sound proposals of novel species.
33. 33

    Chen, M.; Li, Y.; Li, S.; Tang, L.; Zheng, J.; An, Q. Genomic identification of nitrogen-fixingKlebsiella variicola,K. pneumoniaeandK. quasipneumoniae. J. Basic Microbiol. 2016, 56, 78– 84,  DOI: 10.1002/jobm.201500415

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    Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae

    Chen, Mingyue; Li, Yuanyuan; Li, Shuying; Tang, Lie; Zheng, Jingwu; An, Qianli

    Journal of Basic Microbiology (2016), 56 (1), 78-84CODEN: JBMIEQ; ISSN:0233-111X. (Wiley-VCH Verlag GmbH & Co. KGaA)

    It was difficult to differentiate Klebsiella pneumoniae, K. quasipneumoniae and K. variicola by biochem. and phenotypic tests. Genomics increase the resoln. and credibility of taxonomy for closely-related species. Here, we obtained the complete genome sequence of the K. variicola type strain DSM 15968T (=F2R9T). The genome of the type strain is a circular chromosome of 5,521,203 bp with 57.56% GC content. From 540 Klebsiella strains whose genomes had been publicly available as at 3 March 2015, we identified 21 strains belonging to K. variicola and 8 strains belonging to K. quasipneumoniae based on the genome av. nucleotide identities (ANI). All the K. variicola strains, one K. pneumoniae strain and five K. quasipneumoniae strains contained nitrogen-fixing genes. A phylogenomic anal. showed clear species demarcations for these nitrogen-fixing bacteria. In accordance with the key biochem. characteristics of K. variicola, the idnO gene encoding 5-keto-D-gluconate 5-reductase for utilization of 5-keto-D-gluconate and the sorCDFBAME operon for catabolism of L-sorbose were present whereas the rbtRDKT operon for catabolism of adonitol was absent in the genomes of K. variicola strains. Therefore, the genomic analyses supported the ANI-based species delineation; the genome sequence of the K. variicola type strain provides the ref. genome for genomic identification of K. variicola, which is a nitrogen-fixing species.
34. 34

    Goris, J.; Konstantinidis, K. T.; Klappenbach, J. A.; Coenye, T.; Vandamme, P.; Tiedje, J. M. DNA-DNA Hybridization Values and Their Relationship to Whole-Genome Sequence Similarities. Int. J. Syst. Evol. Microbiol. 2007, 57, 81– 91,  DOI: 10.1099/ijs.0.64483-0

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    34

    DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

    Goris, Johan; Konstantinidis, Konstantinos T.; Klappenbach, Joel A.; Coenye, Tom; Vandamme, Peter; Tiedje, James M.

    International Journal of Systematic and Evolutionary Microbiology (2007), 57 (1), 81-91CODEN: ISEMF5; ISSN:1466-5026. (Society for General Microbiology)

    DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to det. relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their resp. genomic sequences, we examd. the quant. relationship between DDH values and genome sequence-derived parameters, such as the av. nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were detd. for 28 strains for which genome sequences were available. The strains belong to 6 important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was >94%. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70% DDH for species delineation corresponded to 95% ANI and 69% conserved DNA. When the anal. was restricted to the protein-coding portion of the genome, 70% DDH corresponded to 85% conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of 'species'. Examn. of reciprocal values indicated that the level of exptl. error assocd. with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.
35. 35

    Long, S. W.; Linson, S. E.; Ojeda Saavedra, M.; Cantu, C.; Davis, J. J.; Brettin, T.; Olsen, R. J. Whole-Genome Sequencing of Human Clinical Klebsiella Pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella Pneumoniae, Klebsiella Variicola, and Klebsiella Quasipneumoniae. mSphere 2017, 2, e00290  DOI: 10.1128/mspheredirect.00290-17

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    Whole-genome sequencing of human clinical Klebsiella pneumoniae isolates reveals misidentification and misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae

    Long, S. Wesley; Linson, Sarah E.; Saavedra, Matthew Ojeda; Cantu, Concepcion; Davis, James J.; Brettin, Thomas; Olsen, Randall J.

    mSphere (2017), 2 (4), e00290-17/1-e00290-17/15/1-e00290-17/1-e00290-17/15/15CODEN: MSPHCI; ISSN:2379-5042. (American Society for Microbiology)

    Klebsiella pneumoniae is a major threat to public health, causing significant morbidity and mortality worldwide. The emergence of highly drug-resistant strains is particularly concerning. There has been a recognition and division of Klebsiella pneumoniae into three distinct phylogenetic groups: Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. K. variicola and K. quasipneumoniae have often been described as opportunistic pathogens that have less virulence in humans than K. pneumoniae does. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates recovered from human infections and discovered that 28 strains were phylogenetically related to K. variicola and K. quasipneumoniae. Whole-genome sequencing of 95 addnl. non-ESBL-producing K. pneumoniae isolates recovered from patients found 12 K. quasipneumoniae strains. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) anal. initially identified all patient isolates as K. pneumoniae, suggesting a potential pitfall in conventional clin. microbiol. lab. identification methods. Whole-genome sequence anal. revealed extensive sharing of core gene content and plasmid replicons among the Klebsiella species. For the first time, strains of both K. variicola and K. quasipneumoniae were found to carry the Klebsiella pneumoniae carbapenemase (KPC) gene, while another K. variicola strain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene. K. variicola and K. quasipneumoniae infections were not less virulent than K. pneumoniae infections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in one K. variicola strain, as well as one strain from a novel Klebsiella species, which challenge the current understanding of interrelationships between clades of Klebsiella.
36. 36

    Potter, R. F.; Lainhart, W.; Twentyman, J.; Wallace, M. A.; Wang, B.; Burnham, C.-A. D.; Rosen, D. A.; Dantas, G. Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella Variicola. mBio 2018, 9, 1– 17,  DOI: 10.1128/mBio.02481-18

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    There is no corresponding record for this reference.
37. 37

    Barney, B. M.; Eberhart, L. J.; Ohlert, J. M.; Knutson, C. M.; Plunkett, M. H. Gene Deletions Resulting in Increased Nitrogen Release by Azotobacter Vinelandii: Application of a Novel Nitrogen Biosensor. Appl. Environ. Microbiol. 2015, 81, 4316– 4328,  DOI: 10.1128/AEM.00554-15

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    37

    Gene deletions resulting in increased nitrogen release by Azotobacter vinelandii: application of a novel nitrogen biosensor

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

    Applied and Environmental Microbiology (2015), 81 (13), 4316-4328CODEN: AEMIDF; ISSN:1098-5336. (American Society for Microbiology)

    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 prodn. Several disruptions were identified in the ammonium transporter gene amtB that resulted in the prodn. 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.
38. 38

    Bali, A.; Blanco, G.; Hill, S.; Kennedy, C. Excretion of Ammonium by a NifL Mutant of Azotobacter Vinelandii Fixing Nitrogen. Appl. Environ. Microbiol. 1992, 58, 1711– 1718,  DOI: 10.1128/aem.58.5.1711-1718.1992

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    38

    Excretion of ammonium by a nifL mutant of Azotobacter vinelandii fixing nitrogen

    Bali, Anil; Blanco, Gonzalo; Hill, Susan; Kennedy, Christina

    Applied and Environmental Microbiology (1992), 58 (5), 1711-18CODEN: AEMIDF; ISSN:0099-2240.

    A mutation in the gene upstream of nifA in A. vinelandii was introduced into the chromosome to replace the corresponding wild-type region. The resulting mutant, MV376, produced nitrogenase constitutively in the presence of 15 mM NH4+. When introduced into a nifH-lacZ fusion strain, the mutation permitted β-galactosidase prodn. in the presence of NH4+. The gene upstream of nifA is therefore designated nifL because of its similarity to the Klebsiella pneumoniae nifL gene in proximity to nifA, in mutant phenotype, and in amino acid sequence of the gene product. The A. vinelandii nifL mutant MV376 excreted significant quantities of NH4+ (∼10 mM) during diazotrophic growth. In contrast, NH4+ excretion during diazotrophy was much lower in a K. pneumoniae nifL deletion mutant (max., 0.15 mM) but significantly higher than in NifL+ K. pneumoniae. The expression of the A. vinelandii nifA gene, unlike that of K. pneumoniae, was not repressed by NH4+.
39. 39

    Bageshwar, U. K.; Srivastava, M.; Pardha-Saradhi, P.; Paul, S.; Gothandapani, S.; Jaat, R. S.; Shankar, P.; Yadav, R.; Biswas, D. R.; Kumar, P. A. An Environmentally Friendly Engineered Azotobacter Strain That Replaces a Substantial Amount of Urea Fertilizer While Sustaining the Same Wheat Yield. Appl. Environ. Microbiol. 2017, 83, 1– 14,  DOI: 10.1128/AEM.00590-17

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    There is no corresponding record for this reference.
40. 40

    Fox, A. R.; Soto, G.; Valverde, C.; Russo, D.; Lagares, A.; Zorreguieta, Á.; Alleva, K.; Pascuan, C.; Frare, R.; Mercado-Blanco, J. Major Cereal Crops Benefit from Biological Nitrogen Fixation When Inoculated with the Nitrogen-Fixing Bacterium Pseudomonas Protegens Pf-5 X940. Environ. Microbiol. 2016, 18, 3522,  DOI: 10.1111/1462-2920.13376

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    40

    Major cereal crops benefit from biological nitrogen fixation when inoculated with the nitrogen-fixing bacterium Pseudomonas protegens Pf-5 X940

    Fox, Ana Romina; Soto, Gabriela; Valverde, Claudio; Russo, Daniela; Lagares, Antonio, Jr; Zorreguieta, Angeles; Alleva, Karina; Pascuan, Cecilia; Frare, Romina; Mercado-Blanco, Jesus; Dixon, Ray; Ayub, Nicolas Daniel

    Environmental Microbiology (2016), 18 (10), 3522-3534CODEN: ENMIFM; ISSN:1462-2912. (Wiley-Blackwell)

    Summary : A main goal of biol. nitrogen fixation research has been to expand the nitrogen-fixing ability to major cereal crops. In this work, we demonstrate the use of the efficient nitrogen-fixing rhizobacterium Pseudomonas protegens Pf-5 X940 as a chassis to engineer the transfer of nitrogen fixed by BNF to maize and wheat under non-gnotobiotic conditions. Inoculation of maize and wheat with Pf-5 X940 largely improved nitrogen content and biomass accumulation in both vegetative and reproductive tissues, and this beneficial effect was pos. assocd. with high nitrogen fixation rates in roots. 15N isotope diln. anal. showed that maize and wheat plants obtained substantial amts. of fixed nitrogen from the atm. Pf-5 X940-GFP-tagged cells were always reisolated from the maize and wheat root surface but never from the inner root tissues. Confocal laser scanning microscopy confirmed root surface colonization of Pf-5 X940-GFP in wheat plants, and microcolonies were mostly visualized at the junctions between epidermal root cells. Genetic anal. using biofilm formation-related Pseudomonas mutants confirmed the relevance of bacterial root adhesion in the increase in nitrogen content, biomass accumulation and nitrogen fixation rates in wheat roots. To our knowledge, this is the first report of robust BNF in major cereal crops.
41. 41

    Temme, K.; Zhao, D.; Voigt, C. A. Refactoring the Nitrogen Fixation Gene Cluster from Klebsiella Oxytoca. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 7085– 7090,  DOI: 10.1073/pnas.1120788109

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    41

    Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca

    Temme Karsten; Zhao Dehua; Voigt Christopher A

    Proceedings of the National Academy of Sciences of the United States of America (2012), 109 (18), 7085-90 ISSN:.

    Bacterial genes associated with a single trait are often grouped in a contiguous unit of the genome known as a gene cluster. It is difficult to genetically manipulate many gene clusters because of complex, redundant, and integrated host regulation. We have developed a systematic approach to completely specify the genetics of a gene cluster by rebuilding it from the bottom up using only synthetic, well-characterized parts. This process removes all native regulation, including that which is undiscovered. First, all noncoding DNA, regulatory proteins, and nonessential genes are removed. The codons of essential genes are changed to create a DNA sequence as divergent as possible from the wild-type (WT) gene. Recoded genes are computationally scanned to eliminate internal regulation. They are organized into operons and placed under the control of synthetic parts (promoters, ribosome binding sites, and terminators) that are functionally separated by spacer parts. Finally, a controller consisting of genetic sensors and circuits regulates the conditions and dynamics of gene expression. We applied this approach to an agriculturally relevant gene cluster from Klebsiella oxytoca encoding the nitrogen fixation pathway for converting atmospheric N(2) to ammonia. The native gene cluster consists of 20 genes in seven operons and is encoded in 23.5 kb of DNA. We constructed a "refactored" gene cluster that shares little DNA sequence identity with WT and for which the function of every genetic part is defined. This work demonstrates the potential for synthetic biology tools to rewrite the genetics encoding complex biological functions to facilitate access, engineering, and transferability.
42. 42

    Schreiter, S.; Ding, G.-C.; Grosch, R.; Kropf, S.; Antweiler, K.; Smalla, K. Soil Type-Dependent Effects of a Potential Biocontrol Inoculant on Indigenous Bacterial Communities in the Rhizosphere of Field-Grown Lettuce. FEMS Microbiol. Ecol. 2014, 90, 718– 730,  DOI: 10.1111/1574-6941.12430

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    42

    Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce

    Schreiter, Susanne; Ding, Guo-Chun; Grosch, Rita; Kropf, Siegfried; Antweiler, Kai; Smalla, Kornelia

    FEMS Microbiology Ecology (2014), 90 (3), 718-730CODEN: FMECEZ; ISSN:0168-6496. (Wiley-Blackwell)

    Bacterial biocontrol strains used as an alternative to chem. fungicides may influence bacterial communities in the rhizosphere and effects might differ depending on the soil type. Here we present baseline data on the effects of Pseudomonas jessenii RU47 on the bacterial community compn. in the rhizosphere of lettuce grown in diluvial sand, alluvial loam and loess loam at the same field site. 16S rRNA gene fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. DGGE fingerprints revealed that in three consecutive years (2010-2012) RU47 had a slight but statistically significant effect on the bacterial community compn. in one (2010), two (2011) or all the three soils (2012). However, these effects were much less pronounced compared with the influence of soil types. Addnl. pyrosequence anal. of samples from 2011 showed that significant changes in bacterial community compns. in response to RU47 inoculation occurred only in alluvial loam. Different taxonomic groups responded to the RU47 application depending on the soil type. Most remarkable was the increased relative abundance of OTUs belonging to the genera Bacillus and Paenibacillus in alluvial loam. Pyrosequencing allowed side-effects of the application of bacterial inoculants into the rhizosphere to be identified.
43. 43

    Rosenblueth, M.; Martínez, L.; Silva, J.; Martínez-Romero, E. Klebsiella Variicola, A Novel Species with Clinical and Plant-Associated Isolates. Syst. Appl. Microbiol. 2004, 27, 27– 35,  DOI: 10.1078/0723-2020-00261

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    43

    Klebsiella variicola, a novel species with clinical and plant-associated isolates

    Rosenblueth, Monica; Martinez, Lucia; Silva, Jesus; Martinez-Romero, Esperanza

    Systematic and Applied Microbiology (2004), 27 (1), 27-35CODEN: SAMIDF; ISSN:0723-2020. (Elsevier GmbH)

    A new Klebsiella species, K. variicola, is proposed on the basis of total DNA-DNA hybridization, on the monophyly obsd. in the phylogenetic anal. derived from the sequences of rpoB, gyrA, mdh, infB, phoE and nifH genes and on distinct phenotypic traits. The bacteria from this new species seem to be genetically isolated from K. pneumoniae strains, do not ferment adonitol and were obtained from plants (such as banana, rice, sugar cane and maize) and hospitals. The type strain is F2R9T (= ATCC BAA-830T = CFNE 2004T).
44. 44

    Potter, R. F.; Lainhart, W.; Twentyman, J.; Wallace, M. A.; Wang, B.; Burnham, C.-A. D.; Rosen, D. A.; Dantas, G. Population Structure, Antibiotic Resistance, and Uropathogenicity of Klebsiella Variicola. mBio 2018, 9, 1– 17,  DOI: 10.1128/mBio.02481-18

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    There is no corresponding record for this reference.
45. 45

    Barrios-Camacho, H.; Aguilar-Vera, A.; Beltran-Rojel, M.; Aguilar-Vera, E.; Duran-Bedolla, J.; Rodriguez-Medina, N.; Lozano-Aguirre, L.; Perez-Carrascal, O. M.; Rojas, J.; Garza-Ramos, U. Molecular Epidemiology of Klebsiella Variicola Obtained from Different Sources. Sci. Rep. 2019, 9, 1– 10,  DOI: 10.1038/s41598-019-46998-9

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    45

    Molecular epidemiology of Klebsiella variicola obtained from different sources

    Barrios-Camacho, Humberto; Aguilar-Vera, Alejandro; Beltran-Rojel, Marilu; Aguilar-Vera, Edgar; Duran-Bedolla, Josefina; Rodriguez-Medina, Nadia; Lozano-Aguirre, Luis; Perez-Carrascal, Olga Maria; Rojas, Jesus; Garza-Ramos, Ulises

    Scientific Reports (2019), 9 (1), 1-10CODEN: SRCEC3; ISSN:2045-2322. (Nature Research)

    Klebsiella variicola is considered an emerging pathogen in humans and has been described in different environments. K. variicola belongs to Klebsiella pneumoniae complex, which has expanded the taxonomic classification and hindered epidemiol. and evolutionary studies. The present work describes the mol. epidemiol. of K. variicola based on MultiLocus Sequence Typing (MLST) developed for this purpose. In total, 226 genomes obtained from public data bases and 28 isolates were evaluated, which were mainly obtained from humans, followed by plants, various animals, the environment and insects. A total 166 distinct sequence types (STs) were identified, with 39 STs comprising at least two isolates. The mol. epidemiol. of K. variicola showed a global distribution for some STs was obsd., and in some cases, isolates obtained from different sources belong to the same ST. Several examples of isolates corresponding to kingdom-crossing bacteria from plants to humans were identified, establishing this as a possible route of transmission. goeBURST anal. identified Clonal Complex 1 (CC1) as the clone with the greatest distribution. Whole-genome sequencing of K. variicola isolates revealed extended-spectrum β-lactamase- and carbapenemase-producing strains with an increase in pathogenicity. MLST of K. variicola is a strong mol. epidemiol. tool that allows following the evolution of this bacterial species obtained from different environments.
46. 46

    Leggett, M.; Newlands, N. K.; Greenshields, D.; West, L.; Inman, S.; Koivunen, M. E. Maize Yield Response to a Phosphorus-Solubilizing Microbial Inoculant in Field Trials. J. Agric. Sci. 2015, 153, 1464– 1478,  DOI: 10.1017/S0021859614001166

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    46

    Maize yield response to a phosphorus-solubilizing microbial inoculant in field trials

    Leggett, M.; Newlands, N. K.; Greenshields, D.; West, L.; Inman, S.; Koivunen, M. E.

    Journal of Agricultural Science (2015), 153 (8), 1464-1478CODEN: JASIAB; ISSN:0021-8596. (Cambridge University Press)

    Findings from multi-year, multi-site field trial expts. measuring maize yield response to inoculation with the phosphorus-solubilizing fungus, Penicillium bilaiae Chalabuda are presented. The main objective was to evaluate representative data on crop response to the inoculant across a broad set of different soil, agronomic management and climate conditions. A statistical anal. of crop yield response and its variability was conducted to guide further implementation of a stratified trial and sampling plan. Field trials, analyzed in the present study, were conducted across the major maize producing agricultural cropland of the United States (2005-11) comprising 92 small (with sampling replication) and 369 large (without replication) trials. The multi-plot design enabled both a detn. of how sampling area affects the estn. of maize yield and yield variance and an estn. of the ability of inoculation with P. bilaiae to increase maize yield. Inoculation increased maize yield in 66 of the 92 small and 295 of the 369 large field trials (within the small plots, yield increased significantly at the 95% confidence level, by 0·17 ± 0·044 t/ha or 1·8%, while in the larger plots, yield increases were higher and less variable (i.e., 0·33 ± 0·026 t/ha or 3·5%). There was considerable inter-annual variability in maize yield response attributed to inoculation compared to the un-inoculated control, with yield increases varying from 0·7 ± 0·75 up to 3·7 ± 0·73%. No significant correlation between yield response and soil acidity (i.e., pH) was detected, and it appears that pH redn. (through org. acid or proton efflux) was unlikely to be the primary pathway for better phosphorus availability measured as increased yield. Seed treatment and granular or dribble band formulations of the inoculant were found to be equally effective. Inoculation was most effective at increasing maize yield in fields that had low or very low soil phosphorus status for both small and large plots. At higher levels of soil phosphorus, yield in the large plots increased more with inoculation than in the small plots, which could be explained by phosphorus fertilization histories for the different field locations, as well as transient (e.g., rainfall) and topog. effects.
47. 47

    Martínez-Romero, E.; Rodríguez-Medina, N.; Beltrán-Rojel, M.; Silva-Sánchez, J.; Barrios-Camacho, H.; Pérez-Rueda, E.; Garza-Ramos, U. Genome Misclassification of Klebsiella Variicola and Klebsiella Quasipneumoniae Isolated from Plants, Animals and Humans. Salud Publica Mex. 2018, 60, 56– 62,  DOI: 10.21149/8149

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    47

    Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans

    Martinez-Romero Esperanza; Rodriguez-Medina Nadia; Beltran-Rojel Marilu; Silva-Sanchez Jesus; Barrios-Camacho Humberto; Garza-Ramos Ulises; Perez-Rueda Ernesto; Perez-Rueda Ernesto

    Salud publica de Mexico (2018), 60 (1), 56-62 ISSN:.

    OBJECTIVE: Due to the fact that K. variicola, K. quasipneumoniae and K. pneumoniae are closely related bacterial species, misclassification can occur due to mistakes either in normal biochemical tests or during submission to public databases. The objective of this work was to identify K. variicola and K. quasipneumoniae genomes misclassified in GenBank database. MATERIALS AND METHODS: Both rpoB phylogenies and average nucleotide identity (ANI) were used to identify a significant number of misclassified Klebsiella spp. genomes. RESULTS: Here we report an update of K. variicola and K. Quasipneumoniae genomes correctly classified and a list of isolated genomes obtained from humans, plants, animals and insects, described originally as K. pneumoniae or K. variicola, but known now to be misclassified. CONCLUSIONS: This work contributes to recognize the extensive presence of K. variicola and K. quasipneumoniae isolates in diverse sites and samples.
48. 48

    Pinto-Tomás, A. A.; Anderson, M. A.; Suen, G.; Stevenson, D. M.; Chu, F. S. T.; Cleland, W. W.; Weimer, P. J.; Currie, C. R. Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants. Science 2009, 326, 1120– 1123,  DOI: 10.1126/science.1173036

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    Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants

    Pinto-Tomas, Adrian A.; Anderson, Mark A.; Suen, Garret; Stevenson, David M.; Chu, Fiona S. T.; Cleland, W. Wallace; Weimer, Paul J.; Currie, Cameron R.

    Science (Washington, DC, United States) (2009), 326 (5956), 1120-1123CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)

    Bacteria-mediated acquisition of atm. N2 serves as a crit. source of nitrogen in terrestrial ecosystems. Here we reveal that symbiotic nitrogen fixation facilitates the cultivation of specialized fungal crops by leaf-cutter ants. By using acetylene redn. and stable isotope expts., we demonstrated that N2 fixation occurred in the fungus gardens of eight leaf-cutter ant species and, further, that this fixed nitrogen was incorporated into ant biomass. Symbiotic N2-fixing bacteria were consistently isolated from the fungus gardens of 80 leaf-cutter ant colonies collected in Argentina, Costa Rica, and Panama. The discovery of N2 fixation within the leaf-cutter ant-microbe symbiosis reveals a previously unrecognized nitrogen source in neotropical ecosystems.
49. 49

    Lin, L.; Guo, W.; Xing, Y.; Zhang, X.; Li, Z.; Hu, C.; Li, S.; Li, Y.; An, Q. The actinobacterium Microbacterium sp. 16SH accepts pBBR1-based pPROBE vectors, forms biofilms, invades roots, and fixes N2 associated with micropropagated sugarcane plants. Appl. Microbiol. Biotechnol. 2012, 93, 1185– 1195,  DOI: 10.1007/s00253-011-3618-3

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    49

    The actinobacterium Microbacterium sp. 16SH accepts pBBR1-based pPROBE vectors, forms biofilms, invades roots, and fixes N2 associated with micropropagated sugarcane plants

    Lin, Li; Guo, Wei; Xing, Yongxiu; Zhang, Xincheng; Li, Zhengyi; Hu, Chunjin; Li, Song; Li, Yangrui; An, Qianli

    Applied Microbiology and Biotechnology (2012), 93 (3), 1185-1195CODEN: AMBIDG; ISSN:0175-7598. (Springer)

    Members of the genus Microbacterium lineage of Gram-pos. actinobacteria are increasingly being reported to display significant traits assocd. with environmental biotechnol. and bioengineering. 16SH is a nitrogen-fixing bacterial strain isolated from a surface-sterilized stem of sugarcane grown in Guangxi, China. Anal. of 16S rRNA gene sequences revealed that 16SH belonged to the genus Microbacterium. pPROBE-pTetr plasmids were constructed by cloning the promoter region of the Tet r gene into the promoterless pPROBE-AT, -OT, and -TT vectors derived from the pBBR1 plasmid that has a broad host range of Gram-neg. bacteria and sequence similarities to plasmids from Gram-pos. bacteria. The pPROBE-pTetr plasmids expressed the gfp reporter gene and were stably maintained in 16SH cells without antibiotic selection in free-living state and in planta. Confocal microscopy on intact roots of micropropagated sugarcane plantlets showed that gfp-tagged 16SH cells formed biofilms on root maturation and elongation zones but not on root meristem zones and root caps, and colonized in intercellular spaces of root cortices. Inoculation of 16SH significantly increased biomass and nitrogen content of micropropagated sugarcane seedlings grown with a nitrogen fertilization of 6.3 mg N/kg soil. 15 N isotope diln. assays demonstrated that biol. nitrogen fixation contributed to this plant growth promotion. This study for the first time demonstrated that the pBBR1-based pPROBE plasmids provided an efficient genetic transfer system for a Gram-pos. Microbacterium strain, and that a nitrogen-fixing Microbacterium endophyte colonized in intact host plants and fixed N2 assocd. with the host plants.
50. 50

    Iniguez, A. L.; Dong, Y.; Triplett, E. W. Nitrogen Fixation in Wheat Provided by Klebsiella Pneumoniae 342. Mol. Plant-Microbe Interact. 2004, 17, 1078– 1085,  DOI: 10.1094/MPMI.2004.17.10.1078

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    50

    Nitrogen fixation in wheat provided by Klebsiella pneumoniae 342

    Iniguez, A. Leonardo; Dong, Yuemei; Triplett, Eric W.

    Molecular Plant-Microbe Interactions (2004), 17 (10), 1078-1085CODEN: MPMIEL; ISSN:0894-0282. (APS Press)

    Nitrogen fixation in wheat (Triticum aestivum L.) is shown upon inoculation with a nitrogen-fixing bacterium, Klebsiella pneumoniae 342 (Kp342). Kp342 relieved nitrogen (N) deficiency symptoms and increased total N and N concn. in the plant. Nitrogen fixation was confirmed by 15N isotope diln. in the plant tissue and in a plant product, chlorophyll. All of these observations were in contrast to uninoculated plants, plants inoculated with a nitrogen-fixing mutant of Kp342, and plants inoculated with dead Kp342 cells. Nitrogenase reductase was produced by Kp342 in the intercellular space of the root cortex. Wild-type Kp342 and the nifH mutant colonized the interior of wheat roots in equal nos. on a fresh wt. basis. The nitrogen fixation phenotype described here was specific to cv. Trenton. Inoculation of cvs. Russ or Stoa with Kp342 resulted in no relief of nitrogen deficiency symptoms.
51. 51

    Ortiz-Marquez, J. C. F.; Do Nascimento, M.; Dublan, M. d. l. A.; Curatti, L. Association with an Ammonium-Excreting Bacterium Allows Diazotrophic Culture of Oil-Rich Eukaryotic Microalgae. Appl. Environ. Microbiol. 2012, 78, 2345– 2352,  DOI: 10.1128/AEM.06260-11

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    51

    Association with an ammonium-excreting bacterium allows diazotrophic culture of oil-rich eukaryotic microalgae

    Ortiz-Marquez, Juan Cesar Federico; Do Nascimento, Mauro; de los Angeles Dublan, Maria; Curatti, Leonardo

    Applied and Environmental Microbiology (2012), 78 (7), 2345-2352CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    Concerns regarding the depletion of the world's reserves of oil and global climate change have promoted an intensification of research and development toward the prodn. of biofuels and other alternative sources of energy during the last years. There is much interest in developing the technol. for third-generation biofuels from microalgal biomass mainly because of its potential for high yields and reduced land use changes in comparison with biofuels derived from plant feedstocks. Regardless of the nature of the feedstock, the use of fertilizers, esp. nitrogen, entails a potential economic and environmental drawback for the sustainability of biofuel prodn. Here, the authors have studied the possibility of nitrogen biofertilization by diazotrophic bacteria applied to cultured microalgae as a promising feedstock for next-generation biofuels. They have obtained an Azotobacter vinelandii mutant strain that accumulates several times more ammonium in culture medium than wild-type cells. The ammonium excreted by the mutant cells is bioavailable to promote the growth of nondiazotrophic microalgae. Moreover, this synthetic symbiosis was able to produce an oil-rich microalgal biomass using both carbon and nitrogen from the air. This work provides a proof of concept that artificial symbiosis may be considered an alternative strategy for the low-N-intensive cultivation of microalgae for the sustainable prodn. of next-generation biofuels and other bioproducts.
52. 52

    Andrade, B. G. N.; de Veiga Ramos, N.; Marin, M. F. A.; Fonseca, E. L.; Vicente, A. C. P. The genome of a clinicalKlebsiella variicolastrain reveals virulence-associated traits and a pl9-like plasmid. FEMS Microbiol. Lett. 2014, 360, 13– 16,  DOI: 10.1111/1574-6968.12583

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    52

    The genome of a clinical Klebsiella variicola strain reveals virulence-associated traits and a pl9-like plasmid

    Andrade, Bruno Gabriel N.; de Veiga Ramos, Nilceia; Marin, Michel F. Abanto; Fonseca, Erica L.; Vicente, Ana Carolina P.

    FEMS Microbiology Letters (2014), 360 (1), 13-16CODEN: FMLED7; ISSN:0378-1097. (Wiley-Blackwell)

    Klebsiella species frequently cause clin. relevant human infections worldwide. We report the draft genome sequence of a Brazilian clin. isolate (Bz19) of the recently recognized species Klebsiella variicola. The comparison of Bz19 genome content with the At-22 (environmental K. variicola) and several clin. Klebsiella pneumoniae shows that these species share a set of virulence-assocd. determinants. Of note, this K. variicola strain harbors a plasmid-like element that shares the same backbone present in a multidrug-resistant plasmid found in a clin. K. pneumoniae isolated in USA.
53. 53

    Martínez-Romero, E.; Rodríguez-Medina, N.; Beltrán-Rojel, M.; Toribio-Jiménez, J.; Garza-Ramos, U. Klebsiella Variicola and Klebsiella Quasipneumoniae with Capacity to Adapt to Clinical and Plant Settings. Salud Publica Mex. 2018, 60, 29– 40,  DOI: 10.21149/8156

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    53

    Klebsiella variicola and Klebsiella quasipneumoniae with capacity to adapt to clinical and plant settings

    Martinez-Romero Esperanza; Rodriguez-Medina Nadia; Beltran-Rojel Marilu; Garza-Ramos Ulises; Toribio-Jimenez Jeiry

    Salud publica de Mexico (2018), 60 (1), 29-40 ISSN:.

    OBJECTIVE: To compare the genetic determinants involved in plant colonization or virulence in the reported genomes of K. variicola, K. quasipneumoniae and K. pneumoniae. MATERIALS AND METHODS: In silico comparisons and Jaccard analysis of genomic data were used. Fimbrial genes were detected by PCR. Biological assays were performed with plant and clinical isolates. RESULTS: Plant colonization genes such as cellulases, catalases and hemagglutinins were mainly present in K. variicola genomes. Chromosomal β-lactamases were characteristic of this species and had been previously misclassified. K. variicola and K. pneumoniae isolates produced plant hormones. CONCLUSIONS: A mosaic distribution of different virulence- and plant-associated genes was found in K. variicola and in K. quasipneumoniae genomes. Some plant colonizing genes were found mainly in K. variicola genomes. The term plantanosis is proposed for plant-borne human infections.
54. 54

    Basso, B.; Shuai, G.; Zhang, J.; Robertson, G. P. Yield Stability Analysis Reveals Sources of Large-Scale Nitrogen Loss from the US Midwest. Sci. Rep. 2019, 9, 5774,  DOI: 10.1038/s41598-019-42271-1

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    Yield stability analysis reveals sources of large-scale nitrogen loss from the US Midwest

    Basso Bruno; Shuai Guanyuan; Zhang Jinshui; Basso Bruno; Robertson G Philip; Basso Bruno; Robertson G Philip; Zhang Jinshui; Robertson G Philip

    Scientific reports (2019), 9 (1), 5774 ISSN:.

    Loss of reactive nitrogen (N) from agricultural fields in the U.S. Midwest is a principal cause of the persistent hypoxic zone in the Gulf of Mexico. We used eight years of high resolution satellite imagery, field boundaries, crop data layers, and yield stability classes to estimate the proportion of N fertilizer removed in harvest (NUE) versus left as surplus N in 8 million corn (Zea mays) fields at subfield resolutions of 30 × 30 m (0.09 ha) across 30 million ha of 10 Midwest states. On average, 26% of subfields in the region could be classified as stable low yield, 28% as unstable (low yield some years, high others), and 46% as stable high yield. NUE varied from 48% in stable low yield areas to 88% in stable high yield areas. We estimate regional average N losses of 1.12 (0.64-1.67) Tg N y(-1) from stable and unstable low yield areas, corresponding to USD 485 (267-702) million dollars of fertilizer value, 79 (45-113) TJ of energy, and greenhouse gas emissions of 6.8 (3.4-10.1) MMT CO2 equivalents. Matching N fertilizer rates to crop yield stability classes could reduce regional reactive N losses substantially with no impact on crop yields, thereby enhancing the sustainability of corn-based cropping systems.
55. 55

    Bruulsema, T. Managing Nutrients to Mitigate Soil Pollution. Environ. Pollut. 2018, 243, 1602– 1605,  DOI: 10.1016/j.envpol.2018.09.132

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    Managing nutrients to mitigate soil pollution

    Bruulsema, Tom

    Environmental Pollution (Oxford, United Kingdom) (2018), 243 (Part_B), 1602-1605CODEN: ENPOEK; ISSN:0269-7491. (Elsevier Ltd.)

    The health of soils is key not only to agricultural productivity, but to all the ecosystem services provided in terms of maintaining the quality of water, air, and food. Nutrient inputs to agricultural soils produce large benefits to human health, including the provisioning of calories and protein supporting at least half the human population, enhancing micronutrient bioavailability in food, improving crop quality, and strengthening tolerance to plant disease. With appropriate nutrient stewardship, such inputs contribute to soil health and prevent soil degrdn. When mismanaged and applied inappropriately, either mineral or org. sources of nutrients can become pollutants both in soils and in water and air. The soln. being embraced by industry and governments around the world is the implementation of principles of 4R Nutrient Stewardship, ensuring that the right source of nutrient is applied at the right time, in the right place and at the right rate.
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    Gaby, J. C.; Buckley, D. H. A Comprehensive Evaluation of PCR Primers to Amplify the NifH Gene of Nitrogenase. PLoS One 2012, 7, e42149  DOI: 10.1371/journal.pone.0042149

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    A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase

    Gaby, John Christian; Buckley, Daniel H.

    PLoS One (2012), 7 (7), e42149CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)

    The nifH gene is the most widely sequenced marker gene used to identify nitrogen-fixing Bacteria and Archaea. Numerous PCR primers have been designed to amplify nifH, but a comprehensive evaluation of nifH PCR primers has not been performed. We performed an in silico anal. of the specificity and coverage of 51 universal and 35 group-specific nifH primers by using an aligned database of 23,847 nifH sequences. We found that there are 15 universal nifH primers that target 90% or more of nitrogen fixers, but that there are also 23 nifH primers that target less than 50% of nifH sequences. The nifH primers we evaluated vary in their phylogenetic bias and their ability to recover sequences from commonly sampled environments. In addn., many of these primers will amplify genes that do not mediate nitrogen fixation, and thus it would be advisable for researchers to screen their sequencing results for the presence of non-target genes before anal. Universal primers that performed well in silico were tested empirically with soil samples and with genomic DNA from a phylogenetically diverse set of nitrogen-fixing strains. This anal. will be of great utility to those engaged in mol. anal. of nifH genes from isolates and environmental samples.
57. 57

    Frank, J. A.; Reich, C. I.; Sharma, S.; Weisbaum, J. S.; Wilson, B. A.; Olsen, G. J. Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S RRNA Genes. Appl. Environ. Microbiol. 2008, 74, 2461– 2470,  DOI: 10.1128/AEM.02272-07

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    Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes

    Frank, Jeremy A.; Reich, Claudia I.; Sharma, Shobha; Weisbaum, Jon S.; Wilson, Brenda A.; Olsen, Gary J.

    Applied and Environmental Microbiology (2008), 74 (8), 2461-2470CODEN: AEMIDF; ISSN:0099-2240. (American Society for Microbiology)

    RRNA-based studies, which have become the most common method for assessing microbial communities, rely upon faithful amplification of the corresponding genes from the original DNA sample. We report here an anal. and reevaluation of commonly used primers for amplifying the DNA between positions 27 and 1492 of bacterial 16S rRNA genes (numbered according to the Escherichia coli rRNA). We propose a formulation for a forward primer (27f) that includes three sequences not usually present. We compare our proposed formulation to two common alternatives by using linear amplification-providing an assessment that is independent of a reverse primer-and in combination with the 1492 reverse primer (1492r) under the PCR conditions appropriate for making community rRNA gene clone libraries. For analyses of DNA from human vaginal samples, our formulation was better at maintaining the original rRNA gene ratio of Lactobacillus spp. to Gardnerella spp., particularly under stringent amplification conditions. Because our 27f formulation remains relatively simple, having seven distinct primer sequences, there is minimal loss of overall amplification efficiency and specificity.
58. 58

    Sanger, F.; Nicklen, S.; Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A. 1977, 74, 5463– 5467,  DOI: 10.1073/pnas.74.12.5463

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    DNA sequencing with chain-terminating inhibitors

    Sanger, F.; Nicklen, S.; Coulson, A. R.

    Proceedings of the National Academy of Sciences of the United States of America (1977), 74 (12), 5463-7CODEN: PNASA6; ISSN:0027-8424.

    A new method for detg. nucleotide sequences in DNA is described. It is similar to the plus and minus method (Sanger, F., Coulson, A. R., 1975) but makes use of the 2',3'-dideoxy and arabinonucleoside analogs of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique was applied to the DNA of bacteriophage φX174 and was more rapid and more accurate than either the plus or the minus method.
59. 59

    Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic Local Alignment Search Tool. J. Mol. Biol. 1990, 215, 403– 410,  DOI: 10.1016/S0022-2836(05)80360-2

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    Basic local alignment search tool

    Altschul, Stephen F.; Gish, Warren; Miller, Webb; Myers, Eugene W.; Lipman, David J.

    Journal of Molecular Biology (1990), 215 (3), 403-10CODEN: JMOBAK; ISSN:0022-2836.

    A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent math. results on the stochastic properties of MSP scores allow an anal. of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a no. of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the anal. of multiple regions of similarity in long DNA sequences. In addn. to its flexibility and tractability to math. anal., BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
60. 60

    Seemann, T. Prokka: Rapid Prokaryotic Genome Annotation. Bioinformatics 2014, 30, 2068– 2069,  DOI: 10.1093/bioinformatics/btu153

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    Prokka: rapid prokaryotic genome annotation

    Seemann, Torsten

    Bioinformatics (2014), 30 (14), 2068-2069CODEN: BOINFP; ISSN:1367-4803. (Oxford University Press)

    Summary: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces stds.-compliant output files for further anal. or viewing in genome browsers. Availability and implementation: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. Contact: torsten.seemann@monash.edu.
61. 61

    Edgar, R. C. MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput. Nucleic Acids Res. 2004, 32, 1792– 1797,  DOI: 10.1093/nar/gkh340

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    MUSCLE: multiple sequence alignment with high accuracy and high throughput

    Edgar, Robert C.

    Nucleic Acids Research (2004), 32 (5), 1792-1797CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)

    We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estn. using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of ref. alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves av. accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large nos. of sequences, aligning 5000 sequences of av. length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5.com/muscle.
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    Price, M. N.; Dehal, P. S.; Arkin, A. P. Fasttree: Computing Large Minimum Evolution Trees with Profiles Instead of a Distance Matrix. Mol. Biol. Evol. 2009, 26, 1641– 1650,  DOI: 10.1093/molbev/msp077

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    FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

    Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.

    Molecular Biology and Evolution (2009), 26 (7), 1641-1650CODEN: MBEVEO; ISSN:0737-4038. (Oxford University Press)

    Gene families are growing rapidly, but std. methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estg. their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N2) space and O(N2L) time, but FastTree requires just O(NLa + N) memory and O(Nlog (N)La) time. To est. the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S rRNAs in 17 h and 2.4 GB of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 h and 50 GB of memory. In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.
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    Ondov, B. D.; Treangen, T. J.; Melsted, P.; Mallonee, A. B.; Bergman, N. H.; Koren, S.; Phillippy, A. M. Mash: Fast Genome and Metagenome Distance Estimation Using MinHash. Genome Biol. 2016, 17, 132,  DOI: 10.1186/s13059-016-0997-x

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    Mash: fast genome and metagenome distance estimation using MinHash

    Ondov, Brian D.; Treangen, Todd J.; Melsted, Pall; Mallonee, Adam B.; Bergman, Nicholas H.; Koren, Sergey; Phillippy, Adam M.

    Genome Biology (2016), 17 (), 132/1-132/14CODEN: GNBLFW; ISSN:1474-760X. (BioMed Central Ltd.)

    Mash extends the MinHash dimensionality-redn. technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections. Mash reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estd. We demonstrate several use cases, including the clustering of all 54,118 NCBI RefSeq genomes in 33 CPU h; real-time database search using assembled or unassembled Illumina, Pacific Biosciences, and Oxford Nanopore data; and the scalable clustering of hundreds of metagenomic samples by compn. Mash is freely released under a BSD license.
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    Temme, K.; Zhao, D.; Voigt, C. A. Refactoring the Nitrogen Fixation Gene Cluster from Klebsiella Oxytoca. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 7085– 7090,  DOI: 10.1073/pnas.1120788109

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    Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca

    Temme Karsten; Zhao Dehua; Voigt Christopher A

    Proceedings of the National Academy of Sciences of the United States of America (2012), 109 (18), 7085-90 ISSN:.

    Bacterial genes associated with a single trait are often grouped in a contiguous unit of the genome known as a gene cluster. It is difficult to genetically manipulate many gene clusters because of complex, redundant, and integrated host regulation. We have developed a systematic approach to completely specify the genetics of a gene cluster by rebuilding it from the bottom up using only synthetic, well-characterized parts. This process removes all native regulation, including that which is undiscovered. First, all noncoding DNA, regulatory proteins, and nonessential genes are removed. The codons of essential genes are changed to create a DNA sequence as divergent as possible from the wild-type (WT) gene. Recoded genes are computationally scanned to eliminate internal regulation. They are organized into operons and placed under the control of synthetic parts (promoters, ribosome binding sites, and terminators) that are functionally separated by spacer parts. Finally, a controller consisting of genetic sensors and circuits regulates the conditions and dynamics of gene expression. We applied this approach to an agriculturally relevant gene cluster from Klebsiella oxytoca encoding the nitrogen fixation pathway for converting atmospheric N(2) to ammonia. The native gene cluster consists of 20 genes in seven operons and is encoded in 23.5 kb of DNA. We constructed a "refactored" gene cluster that shares little DNA sequence identity with WT and for which the function of every genetic part is defined. This work demonstrates the potential for synthetic biology tools to rewrite the genetics encoding complex biological functions to facilitate access, engineering, and transferability.
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    Ye, J.; Coulouris, G.; Zaretskaya, I.; Cutcutache, I.; Rozen, S.; Madden, T. L. Primer-BLAST: A Tool to Design Target-Specific Primers for Polymerase Chain Reaction. BMC Bioinf. 2012, 13, 134,  DOI: 10.1186/1471-2105-13-134

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    Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction

    Ye, Jian; Coulouris, George; Zaretskaya, Irena; Cutcutache, Ioana; Rozen, Steve; Madden, Thomas L.

    BMC Bioinformatics (2012), 13 (), 134CODEN: BBMIC4; ISSN:1471-2105. (BioMed Central Ltd.)

    Background: Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR). Specific amplification of the intended target requires that primers do not have matches to other targets in certain orientations and within certain distances that allow undesired amplification. The process of designing specific primers typically involves two stages. First, the primers flanking regions of interest are generated either manually or using software tools; then they are searched against an appropriate nucleotide sequence database using tools such as BLAST to examine the potential targets. However, the latter is not an easy process as one needs to examine many details between primers and targets, such as the no. and the positions of matched bases, the primer orientations and distance between forward and reverse primers. The complexity of such anal. usually makes this a time-consuming and very difficult task for users, esp. when the primers have a large no. of hits. Furthermore, although the BLAST program has been widely used for primer target detection, it is in fact not an ideal tool for this purpose as BLAST is a local alignment algorithm and does not necessarily return complete match information over the entire primer range. Results: We present a new software tool called Primer-BLAST to alleviate the difficulty in designing target-specific primers. This tool combines BLAST with a global alignment algorithm to ensure a full primer-target alignment and is sensitive enough to detect targets that have a significant no. of mismatches to primers. Primer-BLAST allows users to design new target-specific primers in one step as well as to check the specificity of pre-existing primers. Primer-BLAST also supports placing primers based on exon/intron locations and excluding single nucleotide polymorphism (SNP) sites in primers. Conclusions: We describe a robust and fully implemented general purpose primer design tool that designs target-specific PCR primers. Primer-BLAST offers flexible options to adjust the specificity threshold and other primer properties. This tool is publicly available at online.
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    Draize, J. H.; Woodard, G.; Calvery, H. O. Methods for the Study of Irritation and Toxicity of Subtances Applied Topically to the Skin and Mucous Membranes. J. Pharmacol. Exp. Ther. 1944, 82, 377

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    Methods for the study of irritation and toxicity of substances applied topically to the skin and mucous membranes

    Draize, John H.; Woodard, Geoffrey; Calvery, Herbert O.

    (1944), 82 (), 377-90 ISSN:.

    Various techniques are discussed. Racks for holding rabbits and small dogs, and sleeves and screens for protecting the exptl. areas from interference by the animals are described.