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1. Distribution of Nitrogen‐Fixation Genes in Prokaryotes Containing Alternative Nitrogenases

   https://doi.org/10.1002/cbic.202000022  

   Addo, Maame A.; Dos Santos, Patricia C. (April 2020, ChemBioChem)
2. Multidimensional specialization and generalization are pervasive in soil prokaryotes

   https://doi.org/10.1038/s41559-023-02149-y  

   Hernandez, Damian J.; Kiesewetter, Kasey N.; Almeida, Brianna K.; Revillini, Daniel; Afkhami, Michelle E. (September 2023, Nature Ecology & Evolution)

   Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analysed 236 environmental soil microbiomes across the United States and demonstrate that 90% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had many ecological and evolutionary consequences. First, multidimensional specialization and generalization are highly conserved with very few transitions between these two trajectories. Second, multidimensional generalists dominated communities because they were 73 times more abundant than specialists. Lastly, multidimensional specialists played important roles in community structure with ~220% more connections in microbiome networks. These results indicate that multidimensional generalization and specialization are evolutionarily stable with multidimensional generalists supporting larger populations and multidimensional specialists playing important roles within communities, probably stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that the vast majority of soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for evolutionary transitions, microbial dominance and community roles. 

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3. Root-Knot-Nematode-Encoded CEPs Increase Nitrogen Assimilation

   https://doi.org/10.3390/life13102020  

   Mishra, Shova; Hu, Weiming; DiGennaro, Peter (October 2023, Life)

   C-terminally encoded peptides (CEPs) are plant developmental signals that regulate growth and adaptive responses to nitrogen stress conditions. These small signal peptides are common to all vascular plants, and intriguingly have been characterized in some plant parasitic nematodes. Here, we sought to discover the breadth of root-knot nematode (RKN)-encoded CEP-like peptides and define the potential roles of these signals in the plant–nematode interaction, focusing on peptide activity altering plant root phenotypes and nitrogen uptake and assimilation. A comprehensive bioinformatic screen identified 61 CEP-like sequences encoded within the genomes of six root-knot nematode (RKN; Meloidogyne spp.) species. Exogenous application of an RKN CEP-like peptide altered A. thaliana and M. truncatula root phenotypes including reduced lateral root number in M. truncatula and inhibited primary root length in A. thaliana. To define the role of RKN CEP-like peptides, we applied exogenous RKN CEP and demonstrated increases in plant nitrogen uptake through the upregulation of nitrate transporter gene expression in roots and increased 15N/14N in nematode-formed root galls. Further, we also identified enhanced nematode metabolic processes following CEP application. These results support a model of parasite-induced changes in host metabolism and inform endogenous pathways to regulate plant nitrogen assimilation. 

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4. Quantifying Soil Phosphorus Dynamics: A Data Assimilation Approach

   https://doi.org/10.1029/2018JG004903  

   Hou, Enqing; Lu, Xingjie; Jiang, Lifen; Wen, Dazhi; Luo, Yiqi (July 2019, Journal of Geophysical Research: Biogeosciences)

   Abstract The dynamics of soil phosphorus (P) control its bioavailability. Yet it remains a challenge to quantify soil P dynamics. Here we developed a soil P dynamics (SPD) model. We then assimilated eight data sets of 426‐day changes in Hedley P fractions into the SPD model, to quantify the dynamics of six major P pools in eight soil samples that are representative of a wide type of soils. The performance of our SPD model was better for labile P, secondary mineral P, and occluded P than for nonoccluded organic P (Po) and primary mineral P. All parameters describing soil P dynamics were approximately constrained by the data sets. The average turnover rates were labile P 0.040 g g⁻¹day⁻¹, nonoccluded Po 0.051 g g⁻¹day⁻¹, secondary mineral P 0.023 g g⁻¹day⁻¹, primary mineral P 0.00088 g g⁻¹day⁻¹, occluded Po 0.0066 g g⁻¹day⁻¹, and occluded inorganic P 0.0065 g g⁻¹day⁻¹, in the greenhouse environment studied. Labile P was transferred on average more to nonoccluded Po (transfer coefficient of 0.42) and secondary mineral P (0.38) than to plants (0.20). Soil pH and organic C concentration were the key soil properties regulating the competition for P between plants and soil secondary minerals. The turnover rate of labile P was positively correlated with that of nonoccluded Po and secondary mineral P. The pool size of labile P was most sensitive to its turnover rate. Overall, we suggest data assimilation can contribute significantly to an improved understanding of soil P dynamics. 

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5. Nitrogen Assimilation Varies Among Clades of Nectar- and Insect-Associated Acinetobacters

   https://doi.org/10.1007/s00248-020-01671-x  

   Álvarez-Pérez, Sergio; Tsuji, Kaoru; Donald, Marion; Van Assche, Ado; Vannette, Rachel L.; Herrera, Carlos M.; Jacquemyn, Hans; Fukami, Tadashi; Lievens, Bart (January 2021, Microbial Ecology)

   null (Ed.)

   Floral nectar is commonly colonized by yeasts and bacteria, whose growth largely depends on their capacity to assimilate nutrient resources, withstand high osmotic pressures, and cope with unbalanced carbon-to-nitrogen ratios. Although the basis of the ecological success of these microbes in the harsh environment of nectar is still poorly understood, it is reasonable to assume that they are efficient nitrogen scavengers that can consume a wide range of nitrogen sources in nectar. Furthermore, it can be hypothesized that phylogenetically closely related strains have more similar phenotypic characteristics than distant relatives. We tested these hypotheses by investigating the growth performance on different nitrogen-rich substrates of a collection of 82 acinetobacters isolated from nectar and honeybees, representing members of five species (Acinetobacter nectaris, A. boissieri, A. apis, and the recently described taxa A. bareti and A. pollinis). We also analyzed possible links between growth performance and phylogenetic affiliation of the isolates, while taking into account their geographical origin. Results demonstrated that the studied isolates could utilize a wide variety of nitrogen sources, including common metabolic by-products of yeasts (e.g., ammonium and urea), and that phylogenetic relatedness was associated with the variation in nitrogen assimilation among the studied acinetobacters. Finally, nutrient source and the origin (sample type and country) of isolates also predicted the ability of the acinetobacters to assimilate nitrogen-rich compounds. Overall, these results demonstrate inter-clade variation in the potential of the acinetobacters as nitrogen scavengers and suggest that nutritional dependences might influence interactions between bacteria and yeasts in floral nectar. 

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