Plant-Microbes Interactions in Enhanced Fertilizer-Use Efficiency

The continued use of chemical fertilizers and manures for enhanced soil fertility and crop productivity often results in unexpected harmful environmental effects, including leaching of nitrate into groundwater, surface runoff of phosphorus and nitrogen runoff, and eutrophication of aquatic ecosystems. Integrated nutrient management systems are needed to maintain agricultural productivity and protect the environment. Microbial inoculants are promising components of such management systems. This review is a critical summary of the efforts in using microbial inoculants, including plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi for increasing the use efficiency of fertilizers. Studies with microbial inoculants and nutrients have demonstrated that some inoculants can improve plant uptake of nutrients and thereby increase the use efficiency of applied chemical fertilizers and manures. These proofs of concept studies will serve as the basis for vigorous future research into integrated nutrient management in agriculture

Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum

To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32- 90%, with 2,839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization

Plant-Microbes Interactions in Enhanced Fertilizer-Use Efficiency

The continued use of chemical fertilizers and manures for enhanced soil fertility and crop productivity often results in unexpected harmful environmental effects, including leaching of nitrate into groundwater, surface runoff of phosphorus and nitrogen runoff, and eutrophication of aquatic ecosystems. Integrated nutrient management systems are needed to maintain agricultural productivity and protect the environment. Microbial inoculants are promising components of such management systems. This review is a critical summary of the efforts in using microbial inoculants, including plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi for increasing the use efficiency of fertilizers. Studies with microbial inoculants and nutrients have demonstrated that some inoculants can improve plant uptake of nutrients and thereby increase the use efficiency of applied chemical fertilizers and manures. These proofs of concept studies will serve as the basis for vigorous future research into integrated nutrient management in agriculture

Spatial and temporal distribution of a bioluminescent-marked Pseudomonas putida on soybean root

The ability of rhizobacteria to compete with other microorganisms for root colonization may be critical for its establishment on a root. Over a 6 day period, visualization of the spatial and temporal rhizosphere distribution of a bioluminescent-marked rhizobacterium, Pseudomonas putida, strain GR7.4lux, was examined on soybean grown in non-sterile soil conditions. Luminometry technologies showed a rapid root distribution of rhizobacteria where bioluminescence was particularly intense on the seed and upper root parts. The results provide new information on rhizobial root distribution, where, using enrichment broth, 50% of the root tips were still colonized by rhizobacteria up to 6 days after sowing. This suggests that rhizobial enrichment is required to detect low populations at the root tip. Bioluminescent technology represents a promising alternative to previous methods for studying rhizobial growth and distribution on root

Variation in Bat Guano Bacterial Community Composition With Depth

Bats are known to be reservoirs for a variety of mammalian pathogens, including viruses, fungi, and bacteria. Many of the studies examining the microbial community inhabiting bats have investigated bacterial taxa found within specific bat tissues and isolated bat guano pellets, but relatively few studies have explored bacterial diversity within bat guano piles. In large bat caves, bat guano can accumulate over time, creating piles several meters deep and forming complex interactions with coprophagous organisms in a habitat with low light and oxygen. As the guano decays, the nutrient composition changes, but the bacterial communities deep within the pile have not been characterized. Here, we assess the bacterial communities across varying depths within the guano pile using both culture-independent and culture-dependent methods. We found that although similar taxa are found throughout the guano pile, the relative abundances of taxa within the pile shift, allowing certain taxa to dominate the bacterial community at varying depths. We also identified potential bacterial functions being performed within the bat guano as various depths within the pile and found little variation in terms of the dominant predicted functions, suggesting that although the relative abundances of bacterial taxa are changing, the functions being performed are similar. Additionally, we cultured 15 different bacterial species, including 2 not present in our culture-independent analysis, and discuss the pathogenicity potential of these taxa. This study represents the first characterization of the bacterial community from the extreme environment within a bat guano pile and demonstrates the potential for bat caves as resources for identifying new bacterial species

Root colonization of faba bean (Vicia faba L.) and pea (Pisum sativum L.) by Rhizobium leguminosarum bv. viciae in the presence of nitrate–nitrogen

There is a lack of knowledge concerning the effect of nitrate–nitrogen (NO3– –N) at levels known to inhibit nodule formation and functioning on root colonization of dinitrogen-fixing legumes. Firstly, this study investigated potential differences between Rhizobium leguminosarum bv. viciae 175F9 and its bioluminescent-labeled strain 175F9.lux on root colonization of faba bean (Vicia faba L.) and pea (Pisum sativum L.). These two strains similarly colonized the roots of both hosts. Secondly, this study evaluated the effects of 0 and 10 mol·m–3 NO3– –N on root colonization of faba bean and pea by strain 175F9.lux, over time. Averaged over both hosts and harvest dates, the presence of NO3– –N increased the rhizobial population and the root length colonized. In addition, our results showed that bioluminescence activity increased from 7 to 14 days after sowing and was not correlated to rhizobial population. Finally, to demonstrate that an increase in bioluminescence activity was not an indirect effect of nitrate on R. leguminosarum bv. viciae 175F9.lux, this study investigated the effects of increasing carbon (mannitol) and nitrogen (NO3– –N) concentrations on the rhizobial population and bioluminescence activity. The carbon source was more important than the nitrogen source to increase the rhizobial population and bioluminescence activity, which increased with increasing mannitol concentration, but not with increasing nitrate concentration. Results from this study demonstrated that NO3– –N increased rhizobial population, especially for faba bean, and the length of root colonized.Il manque de connaissances concernant les effets de l’azote sous forme de nitrate (NO3– –N), à des concentrations connues pour inhiber la formation de nodosités, sur la colonisation des racines des légumineuses fixatrices d’azote. Dans un premier temps, les différences potentielles entre la souche mère, 175F9, de Rhizobium leguminosarum bv. viciae et la souche 175F9.lux porteuse d’un marqueur de bioluminescence ont été étudiées sur la colonisation des racines de la féverole (Vicia faba L.) et du pois (Pisum sativum L.). Les deux souches ont colonisé les racines de ces deux plantes hôtes de façon similaire. Dans un deuxième temps, cette étude a évalué l’effet de 0 et 10 mol·m–3 de NO3– –N sur la colonisation de la féverole et du pois par la souche 175F9.lux. Selon la moyenne des deux souches aux deux dates de récolte, la présence de NO3– –N a augmenté la population des rhizobia et la longueur des racines colonisées. Les résultats ont aussi révélé que l’activité de la bioluminescence a augmenté de 7 à 14 jours après les semis, mais il n’y a pas eu de corrélation avec la population des rhizobia. Finalement, pour démontrer que l’augmentation de l’activité de la bioluminescence n’était pas une conséquence indirecte de l’effet de l’azote sur le R. leguminosarum bv. viciae, 175F9.lux, les effets d’une augmentation du carbone (mannitol) et de l’azote (NO3– –N) sur la population des rhizobia et de l’activité de la bioluminescence ont été mesurés. La source de carbone s’est révélée plus importante que la source d’azote pour augmenter la population des rhizobia et l’activité de la bioluminescence, qui a augmenté avec l’accroissement des concentrations de mannitol mais non avec celles de l’azote. Les résultats de cette étude ont démontré que le NO3– –N a favorisé la population des rhizobiums ainsi que la longueur des racines colonisées, particulièrement chez la féverole