scholarly journals The Azospirillum brasilense Core Chemotaxis Proteins CheA1 and CheA4 Link Chemotaxis Signaling with Nitrogen Metabolism

mSystems ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Elena E. Ganusova ◽  
Lam T. Vo ◽  
Paul E. Abraham ◽  
Lindsey O’Neal Yoder ◽  
Robert L. Hettich ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogen Metabolism ◽  
Azospirillum Brasilense ◽  
Regulatory Networks ◽  
Growth Promotion ◽  
Bacterial Chemotaxis ◽  
Nitrate Assimilation ◽  
Free Living ◽  
Content Type ◽  
Chemotaxis Proteins

ABSTRACT Bacterial chemotaxis affords motile bacteria the ability to navigate the environment to locate niches for growth and survival. At the molecular level, chemotaxis depends on chemoreceptor signaling arrays that interact with cytoplasmic proteins to control the direction of movement. In Azospirillum brasilense, chemotaxis is mediated by two distinct chemotaxis pathways: Che1 and Che4. Both Che1 and Che4 are critical in the A. brasilense free-living and plant-associated lifestyles. Here, we use whole-cell proteomics and metabolomics to characterize the role of chemotaxis in A. brasilense physiology. We found that mutants lacking CheA1 or CheA4 or both are affected in nonchemotaxis functions, including major changes in transcription, signaling transport, and cell metabolism. We identify specific effects of CheA1 and CheA4 on nitrogen metabolism, including nitrate assimilation and nitrogen fixation, that may depend, at least, on the transcriptional control of rpoN, which encodes RpoN, a global regulator of metabolism, including nitrogen. Consistent with proteomics, the abundance of several nitrogenous compounds (purines, pyrimidines, and amino acids) changed in the metabolomes of the chemotaxis mutants relative to the parental strain. Further, we uncover novel, and yet uncharacterized, layers of transcriptional and posttranscriptional control of nitrogen metabolism regulators. Together, our data reveal roles for CheA1 and CheA4 in linking chemotaxis and nitrogen metabolism, likely through control of global regulatory networks. IMPORTANCE Bacterial chemotaxis is widespread in bacteria, increasing competitiveness in diverse environments and mediating associations with eukaryotic hosts ranging from commensal to beneficial and pathogenic. In most bacteria, chemotaxis signaling is tightly linked to energy metabolism, with this coupling occurring through the sensory input of several energy-sensing chemoreceptors. Here, we show that in A. brasilense the chemotaxis proteins have key roles in modulating nitrogen metabolism, including nitrate assimilation and nitrogen fixation, through novel and yet unknown regulations. These results are significant given that A. brasilense is a model bacterium for plant growth promotion and free-living nitrogen fixation and is used as a bio-inoculant for cereal crops. Chemotaxis signaling in A. brasilense thus links locomotor behaviors to nitrogen metabolism, allowing cells to continuously and reciprocally adjust metabolism and chemotaxis signaling as they navigate gradients.

scholarly journals Cellular Stoichiometry of Chemotaxis Proteins in Sinorhizobium meliloti

2020 ◽  
Vol 202 (14) ◽  
Author(s):  
Timofey D. Arapov ◽  
Rafael Castañeda Saldaña ◽  
Amanda L. Sebastian ◽  
W. Keith Ray ◽  
Richard F. Helm ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Sinorhizobium Meliloti ◽  
Response Regulator ◽  
Bacterial Chemotaxis ◽  
Adaptor Proteins ◽  
Molar Ratio ◽  
Content Type ◽  
Chemotaxis Proteins ◽  
Chemotaxis System

ABSTRACT Chemotaxis systems enable microbes to sense their immediate environment, moving toward beneficial stimuli and away from those that are harmful. In an effort to better understand the chemotaxis system of Sinorhizobium meliloti, a symbiont of the legume alfalfa, the cellular stoichiometries of all ten chemotaxis proteins in S. meliloti were determined. A combination of quantitative immunoblot and mass spectrometry revealed that the protein stoichiometries in S. meliloti varied greatly from those in Escherichia coli and Bacillus subtilis. To compare protein ratios to other systems, values were normalized to the central kinase CheA. All S. meliloti chemotaxis proteins exhibited increased ratios to various degrees. The 10-fold higher molar ratio of adaptor proteins CheW1 and CheW2 to CheA might result in the formation of rings in the chemotaxis array that consist of only CheW instead of CheA and CheW in a 1:1 ratio. We hypothesize that the higher ratio of CheA to the main response regulator CheY2 is a consequence of the speed-variable motor in S. meliloti, instead of a switch-type motor. Similarly, proteins involved in signal termination are far more abundant in S. meliloti, which utilizes a phosphate sink mechanism based on CheA retrophosphorylation to inactivate the motor response regulator versus CheZ-catalyzed dephosphorylation as in E. coli and B. subtilis. Finally, the abundance of CheB and CheR, which regulate chemoreceptor methylation, was increased compared to CheA, indicative of variations in the adaptation system of S. meliloti. Collectively, these results mark significant differences in the composition of bacterial chemotaxis systems. IMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti contributes greatly to host-plant growth by fixing atmospheric nitrogen. The provision of nitrogen as ammonium by S. meliloti leads to increased biomass production of its legume host alfalfa and diminishes the use of environmentally harmful chemical fertilizers. To better understand the role of chemotaxis in host-microbe interaction, a comprehensive catalogue of the bacterial chemotaxis system is vital, including its composition, function, and regulation. The stoichiometry of chemotaxis proteins in S. meliloti has very few similarities to the systems in Escherichia coli and Bacillus subtilis. In addition, total amounts of proteins are significantly lower. S. meliloti exhibits a chemotaxis system distinct from known models by incorporating new proteins as exemplified by the phosphate sink mechanism.

scholarly journals Nutrient-ColimitedTrichodesmiumas a Nitrogen Source or Sink in a Future Ocean

2017 ◽  
Vol 84 (3) ◽  
Author(s):  
Nathan G. Walworth ◽  
Fei-Xue Fu ◽  
Michael D. Lee ◽  
Xiaoni Cai ◽  
Mak A. Saito ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogen Source ◽  
Nitrogen Metabolism ◽  
Organic Nitrogen ◽  
Open Ocean ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Nitrogen Inputs ◽  
Ocean Conditions ◽  
Nitrogen Scavenging

ABSTRACTNitrogen-fixing (N2) cyanobacteria provide bioavailable nitrogen to vast ocean regions but are in turn limited by iron (Fe) and/or phosphorus (P), which may force them to employ alternative nitrogen acquisition strategies. The adaptive responses of nitrogen fixers to global-change drivers under nutrient-limited conditions could profoundly alter the current ocean nitrogen and carbon cycles. Here, we show that the globally important N2fixerTrichodesmiumfundamentally shifts nitrogen metabolism toward organic-nitrogen scavenging following long-term high-CO2adaptation under iron and/or phosphorus (co)limitation. Global shifts in transcripts and proteins under high-CO2/Fe-limited and/or P-limited conditions include decreases in the N2-fixing nitrogenase enzyme, coupled with major increases in enzymes that oxidize trimethylamine (TMA). TMA is an abundant, biogeochemically important organic nitrogen compound that supports rapidTrichodesmiumgrowth while inhibiting N2fixation. In a future high-CO2ocean, this whole-cell energetic reallocation toward organic nitrogen scavenging and away from N2fixation may reduce new-nitrogen inputs byTrichodesmiumwhile simultaneously depleting the scarce fixed-nitrogen supplies of nitrogen-limited open-ocean ecosystems.IMPORTANCETrichodesmiumis among the most biogeochemically significant microorganisms in the ocean, since it supplies up to 50% of the new nitrogen supporting open-ocean food webs. We usedTrichodesmiumcultures adapted to high-CO2conditions for 7 years, followed by additional exposure to iron and/or phosphorus (co)limitation. We show that “future ocean” conditions of high CO2and concurrent nutrient limitation(s) fundamentally shift nitrogen metabolism away from nitrogen fixation and instead toward upregulation of organic nitrogen-scavenging pathways. We show that the responses ofTrichodesmiumto projected future ocean conditions include decreases in the nitrogen-fixing nitrogenase enzymes coupled with major increases in enzymes that oxidize the abundant organic nitrogen source trimethylamine (TMA). Such a shift toward organic nitrogen uptake and away from nitrogen fixation may substantially reduce new-nitrogen inputs byTrichodesmiumto the rest of the microbial community in the future high-CO2ocean, with potential global implications for ocean carbon and nitrogen cycling.

scholarly journals Draft Genome Sequences of Azospirillum brasilense Strains Ab-V5 and Ab-V6, Commercially Used in Inoculants for Grasses and Legumes in Brazil

2018 ◽  
Vol 6 (20) ◽  
Author(s):  
Mariangela Hungria ◽  
Renan Augusto Ribeiro ◽  
Marco Antonio Nogueira
Keyword(s):  
Nitrogen Fixation ◽  
Azospirillum Brasilense ◽  
Draft Genome ◽  
Environmental Adaptation ◽  
Genome Sequences ◽  
Phenotypic Properties ◽  
Content Type ◽  
Commercial Inoculants

ABSTRACT Azospirillum brasilense strains Ab-V5 and Ab-V6 are largely used in commercial inoculants for grasses and legumes in Brazil. Their genomes were estimated at 6,934,595 and 7,197,196 bp, respectively, and encompass genes related to nitrogen fixation, synthesis of phytohormones, and environmental adaptation. Although the strains differ in phenotypic properties, their genomes are highly similar.

scholarly journals Differing Courses of Genetic Evolution of Bradyrhizobium Inoculants as Revealed by Long-Term Molecular Tracing in Acacia mangium Plantations

2014 ◽  
Vol 80 (18) ◽  
pp. 5709-5716 ◽  
Author(s):  
M. M. Perrineau ◽  
C. Le Roux ◽  
A. Galiana ◽  
A. Faye ◽  
R. Duponnois ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Growth Promotion ◽  
Acacia Mangium ◽  
Housekeeping Genes ◽  
Nitrogen Fixing ◽  
Microbial Inoculants ◽  
Nitrogen Fixing Bacteria ◽  
Content Type ◽  
Significant Difference

ABSTRACTIntroducing nitrogen-fixing bacteria as an inoculum in association with legume crops is a common practice in agriculture. However, the question of the evolution of these introduced microorganisms remains crucial, both in terms of microbial ecology and agronomy. We explored this question by analyzing the genetic and symbiotic evolution of twoBradyrhizobiumstrains inoculated onAcacia mangiumin Malaysia and Senegal 15 and 5 years, respectively, after their introduction. Based on typing of several loci, we showed that these two strains, although closely related and originally sampled in Australia, evolved differently. One strain was recovered in soil with the same five loci as the original isolate, whereas the symbiotic cluster of the other strain was detected with no trace of the three housekeeping genes of the original inoculum. Moreover, the nitrogen fixation efficiency was variable among these isolates (either recombinant or not), with significantly high, low, or similar efficiencies compared to the two original strains and no significant difference between recombinant and nonrecombinant isolates. These data suggested that 15 years after their introduction, nitrogen-fixing bacteria remain in the soil but that closely related inoculant strains may not evolve in the same way, either genetically or symbiotically. In a context of increasing agronomical use of microbial inoculants (for biological control, nitrogen fixation, or plant growth promotion), this result feeds the debate on the consequences associated with such practices.

scholarly journals Effects of Engineered Sinorhizobium meliloti on Cytokinin Synthesis and Tolerance of Alfalfa to Extreme Drought Stress

2012 ◽  
Vol 78 (22) ◽  
pp. 8056-8061 ◽  
Author(s):  
Ji Xu ◽  
Xiao-Lin Li ◽  
Li Luo
Keyword(s):  
Nitrogen Fixation ◽  
Drought Stress ◽  
Sinorhizobium Meliloti ◽  
Nitrogenase Activity ◽  
Root Nodules ◽  
Severe Drought ◽  
Control Strain ◽  
Free Living ◽  
Content Type ◽  
Host Tolerance

ABSTRACTCytokinin is required for the initiation of leguminous nitrogen fixation nodules elicited by rhizobia and the delay of the leaf senescence induced by drought stress. A few free-living rhizobia have been found to produce cytokinin. However, the effects of engineered rhizobia capable of synthesizing cytokinin on host tolerance to abiotic stresses have not yet been described. In this study, two engineeredSinorhizobiumstrains overproducing cytokinin were constructed. The tolerance of inoculated alfalfa plants to severe drought stress was assessed. The engineered strains, which expressed theAgrobacterium iptgene under the control of different promoters, synthesized more zeatins than the control strain under free-living conditions, but their own growth was not affected. After a 4-week inoculation period, the effects of engineered strains on alfalfa growth and nitrogen fixation were similar to those of the control strain under nondrought conditions. After being subjected to severe drought stress, most of the alfalfa plants inoculated with engineered strains survived, and the nitrogenase activity in their root nodules showed no apparent change. A small elevation in zeatin concentration was observed in the leaves of these plants. The expression of antioxidant enzymes increased, and the level of reactive oxygen species decreased correspondingly. Although theiptgene was transcribed in the bacteroids of engineered strains, the level of cytokinin in alfalfa nodules was identical to that of the control. These findings suggest that engineeredSinorhizobiumstrains synthesizing more cytokinin could improve the tolerance of alfalfa to severe drought stress without affecting alfalfa nodulation or nitrogen fixation.

scholarly journals Nitrogen Fixation in Pozol, a Traditional Fermented Beverage

2020 ◽  
Vol 86 (16) ◽  
Author(s):  
Jocelin Rizo ◽  
Marco A. Rogel ◽  
Daniel Guillén ◽  
Carmen Wacher ◽  
Esperanza Martinez-Romero ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Acetylene Reduction ◽  
Growth Promotion ◽  
Point Of View ◽  
Intestinal Microbiome ◽  
Acetylene Reduction Activity ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Free Living ◽  
Functional Perspective

ABSTRACT Traditional fermentations have been widely studied from the microbiological point of view, but little is known from the functional perspective. In this work, nitrogen fixation by free-living nitrogen-fixing bacteria was conclusively demonstrated in pozol, a traditional Mayan beverage prepared with nixtamalized and fermented maize dough. Three aspects of nitrogen fixation were investigated to ensure that fixation actually happens in the dough: (i) the detection of acetylene reduction activity directly in the substrate, (ii) the presence of potential diazotrophs, and (iii) an in situ increase in acetylene reduction by inoculation with one of the microorganisms isolated from the dough. Three genera were identified by sequencing the 16S rRNA and nifH genes as Kosakonia, Klebsiella, and Enterobacter, and their ability to fix nitrogen was confirmed. IMPORTANCE Nitrogen-fixing bacteria are found in different niches, as symbionts in plants, in the intestinal microbiome of several insects, and as free-living microorganisms. Their use in agriculture for plant growth promotion via biological nitrogen fixation has been extensively reported. This work demonstrates the ecological and functional importance that these bacteria can have in food fermentations, reevaluating the presence of these genera as an element that enriches the nutritional value of the dough.

scholarly journals Draft Genome Sequences of Chryseobacterium lactis NCTC11390T Isolated from Milk, Chryseobacterium oncorhynchi 701B-08T from Rainbow Trout, and Chryseobacterium viscerum 687B-08T from Diseased Fish

2018 ◽  
Vol 6 (26) ◽  
Author(s):  
Jin-Ju Jeong ◽  
Ye Ji Lee ◽  
Duleepa Pathiraja ◽  
Byeonghyeok Park ◽  
In-Geol Choi ◽  
...  
Keyword(s):  
Growth Promotion ◽  
Bacterial Species ◽  
Draft Genome ◽  
Genome Sequences ◽  
Free Living ◽  
Gram Negative ◽  
Content Type ◽  
The Family ◽  
Diseased Fish ◽  
Type Strains

The genus Chryseobacterium, belonging to the family Flavobacteriaceae, contains Gram-negative, yellow-pigmented, rod-shaped, and non-spore-forming bacterial species, which may be free living or parasitic. Here, we report draft genome sequences of type strains of three species of Chryseobacterium containing genes related to biological control and plant growth promotion.

scholarly journals Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Roberto Siani ◽  
Georg Stabl ◽  
Caroline Gutjahr ◽  
Michael Schloter ◽  
Viviane Radl
Keyword(s):  
Plant Growth ◽  
Plant Pathogens ◽  
Growth Promotion ◽  
Lotus Japonicus ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Free Living ◽  
Single Strain ◽  
Content Type ◽  
Link Type

Beta-proteobacteria belonging to the genus Acidovorax have been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study, we investigated the genomic properties of 52 bacterial strains of the genus Acidovorax , isolated from healthy roots of Lotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays with L. japonicus, performed in a gnotobiotic system, we distinguished seven robust plant-growth promoting strains from strains with no significant effects on plant-growth. We showed that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genus Acidovorax sourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We showed that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-living Acidovorax strains did not harbour any secretion-systems. Overall, our data indicate that Acidovorax strains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.

scholarly journals CheY1 and CheY2 of Azorhizobium caulinodans ORS571 Regulate Chemotaxis and Competitive Colonization with the Host Plant

2020 ◽  
Vol 86 (15) ◽  
Author(s):  
Wei Liu ◽  
Xue Bai ◽  
Yan Li ◽  
Jun Min ◽  
Yachao Kong ◽  
...  
Keyword(s):  
Response Regulator ◽  
Bacterial Chemotaxis ◽  
Nodule Formation ◽  
Sesbania Rostrata ◽  
Azorhizobium Caulinodans ◽  
Response Regulators ◽  
Free Living ◽  
Content Type ◽  
Colonization Ability ◽  
Cell Phenotypes

ABSTRACT The genome of Azorhizobium caulinodans ORS571 encodes two chemotaxis response regulators: CheY1 and CheY2. cheY1 is located in a chemotaxis cluster (cheAWY1BR), while cheY2 is located 37 kb upstream of the cheAWY1BR cluster. To determine the contributions of CheY1 and CheY2, we compared the wild type (WT) and mutants in the free-living state and in symbiosis with the host Sesbania rostrata. Swim plate tests and capillary assays revealed that both CheY1 and CheY2 play roles in chemotaxis, with CheY2 having a more prominent role than CheY1. In an analysis of the swimming paths of free-swimming cells, the ΔcheY1 mutant exhibited decreased frequency of direction reversal, whereas the ΔcheY2 mutant appeared to change direction much more frequently than the WT. Exopolysaccharide (EPS) production in the ΔcheY1 and ΔcheY2 mutants was lower than that in the WT, but the ΔcheY2 mutant had more obvious EPS defects that were similar to those of the ΔcheY1 ΔcheY2 and Δeps1 mutants. During symbiosis, the levels of competitiveness for root colonization and nodule occupation of ΔcheY1 and ΔcheY2 mutants were impaired compared to those of the WT. Moreover, the competitive colonization ability of the ΔcheY2 mutant was severely impaired compared to that of the ΔcheY1 mutant. Taken together, the ΔcheY2 phenotypes are more severe than the ΔcheY1 phenotype in free-living and symbiotic states, and that of the double mutant resembles the ΔcheY2 single-mutant phenotype. These defects of ΔcheY1 and ΔcheY2 mutants were restored to the WT phenotype by complementation. These results suggest that there are different regulatory mechanisms of CheY1 and CheY2 and that CheY2 is a key chemotaxis regulator under free-living and symbiosis conditions. IMPORTANCE Azorhizobium caulinodans ORS571 is a motile soil bacterium that has the dual capacity to fix nitrogen both under free-living conditions and in symbiosis with Sesbania rostrata, forming nitrogen-fixing root and stem nodules. Bacterial chemotaxis to chemoattractants derived from host roots promotes infection and subsequent nodule formation by directing rhizobia to appropriate sites of infection. In this work, we identified and demonstrated that CheY2, a chemotactic response regulator encoded by a gene outside the chemotaxis cluster, is required for chemotaxis and multiple other cell phenotypes. CheY1, encoded by a gene in the chemotaxis cluster, also plays a role in chemotaxis. Two response regulators mediate bacterial chemotaxis and motility in different ways. This work extends the understanding of the role of multiple response regulators in Gram-negative bacteria.

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