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1. Host-Associated Rhizobial Fitness: Dependence on Nitrogen, Density, Community Complexity, and Legume Genotype

   https://doi.org/10.1128/aem.00526-22  

   Burghardt, Liana T.; Epstein, Brendan; Hoge, Michelle; Trujillo, Diana I.; Tiffin, Peter (August 2022, Applied and Environmental Microbiology)

   Glass, Jennifer B. (Ed.)

   ABSTRACT The environmental context of the nitrogen-fixing mutualism between leguminous plants and rhizobial bacteria varies over space and time. Variation in resource availability, population density, and composition likely affect the ecology and evolution of rhizobia and their symbiotic interactions with hosts. We examined how host genotype, nitrogen addition, rhizobial density, and community complexity affected selection on 68 rhizobial strains in the Sinorhizobium meliloti – Medicago truncatula mutualism. As expected, host genotype had a substantial effect on the size, number, and strain composition of root nodules (the symbiotic organ). The understudied environmental variable of rhizobial density had a stronger effect on nodule strain frequency than the addition of low nitrogen levels. Higher inoculum density resulted in a nodule community that was less diverse and more beneficial but only in the context of the more selective host genotype. Higher density resulted in more diverse and less beneficial nodule communities with the less selective host. Density effects on strain composition deserve additional scrutiny as they can create feedback between ecological and evolutionary processes. Finally, we found that relative strain rankings were stable across increasing community complexity (2, 3, 8, or 68 strains). This unexpected result suggests that higher-order interactions between strains are rare in the context of nodule formation and development. Our work highlights the importance of examining mechanisms of density-dependent strain fitness and developing theoretical predictions that incorporate density dependence. Furthermore, our results have translational relevance for overcoming establishment barriers in bioinoculants and motivating breeding programs that maintain beneficial plant-microbe interactions across diverse agroecological contexts. IMPORTANCE Legume crops establish beneficial associations with rhizobial bacteria that perform biological nitrogen fixation, providing nitrogen to plants without the economic and greenhouse gas emission costs of chemical nitrogen inputs. Here, we examine the influence of three environmental factors that vary in agricultural fields on strain relative fitness in nodules. In addition to manipulating nitrogen, we also use two biotic variables that have rarely been examined: the rhizobial community's density and complexity. Taken together, our results suggest that (i) breeding legume varieties that select beneficial strains despite environmental variation is possible, (ii) changes in rhizobial population densities that occur routinely in agricultural fields could drive evolutionary changes in rhizobial populations, and (iii) the lack of higher-order interactions between strains will allow the high-throughput assessments of rhizobia winners and losers during plant interactions. 

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2. Sinorhizobium medicae WSM419 Genes That Improve Symbiosis between Sinorhizobium meliloti Rm1021 and Medicago truncatula Jemalong A17 and in Other Symbiosis Systems

   https://doi.org/10.1128/AEM.03004-20  

   Ghosh, Prithwi; Adolphsen, Katie N.; Yurgel, Svetlana N.; Kahn, Michael L. (July 2021, Applied and Environmental Microbiology)

   Stabb, Eric V. (Ed.)

   ABSTRACT Some soil bacteria, called rhizobia, can interact symbiotically with legumes, in which they form nodules on the plant roots, where they can reduce atmospheric dinitrogen to ammonia, a form of nitrogen that can be used by growing plants. Rhizobium-plant combinations can differ in how successful this symbiosis is: for example, Sinorhizobium meliloti Rm1021 forms a relatively ineffective symbiosis with Medicago truncatula Jemalong A17, but Sinorhizobium medicae WSM419 is able to support more vigorous plant growth. Using proteomic data from free-living and symbiotic S. medicae WSM419, we previously identified a subset of proteins that were not closely related to any S. meliloti Rm1021 proteins and speculated that adding one or more of these proteins to S. meliloti Rm1021 would increase its effectiveness on M. truncatula A17. Three genes, Smed_3503, Smed_5985, and Smed_6456, were cloned into S. meliloti Rm1021 downstream of the E. coli lacZ promoter. Strains with these genes increased nodulation and improved plant growth, individually and in combination with one another. Smed_3503, renamed iseA ( i ncreased s ymbiotic e ffectiveness), had the largest impact, increasing M. truncatula biomass by 61%. iseA homologs were present in all currently sequenced S. medicae strains but were infrequent in other Sinorhizobium isolates. Rhizobium leguminosarum bv. viciae 3841 containing iseA led to more nodules on pea and lentil. Split-root experiments with M. truncatula A17 indicated that S. meliloti Rm1021 carrying the S. medicae iseA is less sensitive to plant-induced resistance to rhizobial infection, suggesting an interaction with the plant’s regulation of nodule formation. IMPORTANCE Legume symbiosis with rhizobia is highly specific. Rhizobia that can nodulate and fix nitrogen on one legume species are often unable to associate with a different species. The interaction can be more subtle. Symbiotically enhanced growth of the host plant can differ substantially when nodules are formed by different rhizobial isolates of a species, much like disease severity can differ when conspecific isolates of pathogenic bacteria infect different cultivars. Much is known about bacterial genes essential for a productive symbiosis, but less is understood about genes that marginally improve performance. We used a proteomic strategy to identify Sinorhizobium genes that contribute to plant growth differences that are seen when two different strains nodulate M. truncatula A17. These genes could also alter the symbiosis between R. leguminosarum bv. viciae 3841 and pea or lentil, suggesting that this approach identifies new genes that may more generally contribute to symbiotic productivity. 

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3. On the Effect of Biochar Application on the Hydraulic Properties of Salt-affected Green Stormwater Infrastructure

   Finnegan, Maxwell; Khatei, Ganesh; Rinaldo, Tobia; Caplan, Joshua; Van_Pelt, Scott; D'Odorico, Paolo; Ravi, Sujith (December 2024, American Geophysical Union)

   Soil salinization is an increasing global problem, especially in agricultural, coastal, and roadside environments. The increasing intensity of precipitation events due to climate change may be exacerbating these effects, such as through larger pulses of deicing salts entering roadside green stormwater infrastructure (GSI) and stronger coastal storms bringing seawater further inland. Although soils are often amended with biochar to remove pollutants and improve hydraulic properties, it may also mitigate the impact of salinity. Here, we compared the water retention properties and unsaturated hydraulic conductivities of both biochar-amended and unamended GSI soil media with varying salinity levels (1-25 dS m-1, using Na+ salts). The effects of salinity on both matric and osmotic potential included shifts in the plant-available water range, with the magnitude depending on the salt concentration and biochar content. Overall, biochar addition decreased the salinity and improved plant water availability in salt-affected soils. There was an increase in the integral water capacity (which describes the total amount of water the soil media can hold and release to a plant) for biochar-amended saline soils, demonstrating that biochar can reduce the total osmo-matric stress. On a macro scale, the high density of pores in biochar appears to increase soil hydraulic conductivity while reducing osmotic potential by adsorbing salt ions. On a micro scale, the negative surface charge of biochar likely counteracts the impact of the electric double layer of saline soils, reducing the total osmo-matric force on water molecules in soil solution. In effect, this helps the plant's osmotic potential to overcome the forces holding water molecules to soil grains. As soils become more saline due to ongoing climate-related snow events, biochar application might be an effective management technique for roadside and other saline soils. 

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4. Mycorrhizal and rhizobial interactions influence model grassland plant community structure and productivity

   https://doi.org/10.1007/s00572-021-01061-2  

   Zhou, Jiqiong; Wilson, Gail W.; Cobb, Adam B.; Zhang, Yingjun; Liu, Lin; Zhang, Xinquan; Sun, Feida (January 2022, Mycorrhiza)

   Arbuscular mycorrhizal (AM) fungi and rhizobium are likely important drivers of plant coexistence and grassland productivity due to complementary roles in supplying limiting nutrients. However, the interactive effects of mycorrhizal and rhizobial associations on plant community productivity and competitive dynamics remain unclear. To address this, we conducted a greenhouse experiment to determine the influences of these key microbial functional groups on communities comprising three plant species by comparing plant communities grown with or without each symbiont. We also utilized N-fertilization and clipping treatments to explore potential shifts in mycorrhizal and rhizobial benefits across abiotic and biotic conditions. Our research suggests AM fungi and rhizobium co-inoculation was strongly facilitative for plant community productivity and legume (Medicago sativa) growth and nodulation. Plant competitiveness shifted in the presence of AM fungi and rhizobium, favoring M. sativa over a neighboring C4 grass (Andropogon gerardii) and C 3 forb (Ratibida pinnata). This may be due to rhizobial symbiosis as well as the relatively greater mycorrhizal growth response of M. sativa, compared to the other model plants. Clipping and N-fertilization altered relative costs and benefits of both symbioses, presumably by altering host-plant nitrogen and carbon dynamics, leading to a relative decrease in mycorrhizal responsiveness and proportional biomass of M. sativa relative to the total biomass of the entire plant community, with a concomitant relative increase in A. gerardii and R. pinnata proportional biomass. Our results demonstrate a strong influence of both microbial symbioses on host-plant competitiveness and community dynamics across clipping and N-fertilization treatments, suggesting the symbiotic rhizosphere community is critical for legume establishment in grasslands. 

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5. Adaptive Remodeling of the Proteome in Pistachio Roots Under Salt Stress: Implications for Food and Energy Security in Arid Regions

   https://doi.org/10.1002/fes3.70151  

   Akbari, Mohammad; Singh, Rakesh K; Andriūnaitė, Elena; Reddy, Umesh; Farajpour, Mostafa; Simmons, Sanaa; Vishnudasan, Dalia; Charles, Sona; Suravajhala, Prashanth; Mahna, Nasser; et al (November 2025, Food and Energy Security)

   ABSTRACT Pistachio thrives in semi‐arid and arid environments and is highly adaptable to various abiotic stresses. However, soil salinization significantly threatens productivity, leading to considerable osmotic and ionic stress for these plants. Roots are the primary sites for stress perception and response; however, they remain understudied in woody crops, such asPistachio. This study examines the alterations in root protein expression and metabolic pathways in response to sodium chloride‐induced salt stress through biochemical and proteomic analyses. One‐year‐old pistachio rootstocks were treated with four different saline water regimes over a 100‐day period, and the total proteins were isolated from these samples. Over 1600 protein identifiers were detected, with comparative analysis revealing 245 proteins that were more abundant and 190 that were less abundant across three stress levels. Key pathways associated with stress tolerance, such as protein modification, folding, and heat shock protein (HSP) protection, were upregulated. An increase in secondary metabolites played a crucial role in detoxification. As salt stress intensified, the abundance of trafficking proteins increased, enhancing transporter activities. Active signaling pathways were observed at lower stress levels, while structural proteins became more critical at higher stress levels for maintaining cell membrane integrity. This cultivar exhibited enhanced kinase activities that regulate lipid and carbohydrate metabolism, thereby aiding in ion homeostasis and maintaining redox balance. The protein interaction network, mapped to orthologous proteins inArabidopsis thaliana, revealed clusters associated with cytosolic, carbohydrate, and amino acid metabolism contributing to salinity stress tolerance. The validation of proteomic data was performed by assessing corresponding changes in transcript levels. The study expands upon previous work by providing a comprehensive proteomic map of UCB‐1 pistachio rootstock across multiple salinity levels. The findings have practical implications for developing more resilient cultivars, supporting sustainable pistachio production in regions prone to salinity. 

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