Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth
A review of this paper appeared on the Phys.org site as Helping plants and bacteria work together reduces fertilizer need, finds new study, but it is restricted by copyright so we can only quote from it. "As the population grows and crop yields are threatened by climate change, scientists are keen to help promote plant growth in a natural and sustainable way." This primarily means by that reducing the use of fertilizers, "an input to agriculture which can be harmful for the environment. Fertilizers can run into waterways, or get broken down by microbes in the soil, releasing the potent greenhouse gas nitrous oxide into the atmosphere." That said, it is a good starting point to understand what the research is about. They summarize the work:
Using different bacteria strains, the team measured the plant's molecular responses and the amount of minerals in the plant. The bacterial and fungal communities were also recorded in different locations: in the soil, around the root and inside the root. By combining all of these types and locations of data, an understanding of the impact of "symbiotic efficiency" was established.
Medicago truncatula is a small low-growing plant with the common names of barrelclover or barrel medic. The clover-like plant is a legume that is native to the Mediterranean region and is "studied as a model organism for legume biology because it has a small diploid genome, is self-fertile, has a rapid generation time and prolific seed production, is amenable to genetic transformation, and its genome has been sequenced" (Wikipedia). The plant's genome was sequenced in 2011 by an international group of research laboratories and published in the journal Nature.
The upshot for this research is that targeted bacteria inoculation can help boost plant efficiency, within the constraint of soil types and health. Just as we know that the use of Mycorrhizae has a benefit to all plants to take up nutrients from the soil in general, this study looks at pairing particular bacterial communities with the types of crop plants that will benefit most from their presence. The soil health is a factor, and bearing in mind that fertilizer does not contribute to soil health, the goal is the have healthier soil and a more effective biome producing better crops. The paper's authors note that "For both bacterial and fungal communities, soil type explains a much higher percentage of microbial community composition than inoculation strain"(8,9). This doesn't fix things that are wrong with soil, but it can enhance the nutrient output when the soil is generally healthy. Symbiosis, or nodulation, are the terms for the efficiency of plant-bacterial relationships investigated in this paper. The authors have also shed "light on how this natural phenomenon impacts interactions with other microbes in the soil."
The authors of this paper have created many graphs and charts, and for those readers who are interested in just how carefully everything was set up (pots used, soil type, soil preparation, seed source, seed scarification, bacteria inoculation, sampling, weighing, and measuring), it's all in there. The second half of the paper is a detailed discussion of how the experiment was set up.
As an open source document, this research paper is available to anyone to open and read and download. The publication Microbiome uses the Creative Commons Attribution License 4.0 International Public License that gives a great deal of latitude to the public as readers or users of the information. Copyright is still held by all of the authors, but the use is less restricted than traditional publication models. The authors are Beatriz Lagunas, Luke Richards, Chrysi Sergaki, Jamie Burgess, Alonso Javier Pardal, Rana M. F. Hussain, Bethany L. Richmond, Laura Baxter, Proyash Roy, Anastasia Pakidi, Gina Stovold, Saúl Vázquez, Sascha Ott, Patrick Schäfer, and Miriam L. Gifford.
Background: Despite the knowledge that the soil–plant–microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of nitrogen-fixing rhizobia with legumes is impacted according to soil type, yet this knowledge is crucial if we are to harness or improve it. We asked how the plant, soil and microbiome are modulated by symbiosis between the model legume Medicago truncatula and different strains of Sinorhizobium meliloti or Sinorhizobium medicae whose nitrogen-fixing efficiency varies, in three distinct soil types that differ in nutrient fertility, to examine the role of the soil environment upon the plant–microbe interaction during nodulation.
Results: The outcome of symbiosis results in installment of a potentially beneficial microbiome that leads to increased nutrient uptake that is not simply proportional to soil nutrient abundance. A number of soil edaphic factors including Zn and Mo, and not just the classical N/P/K nutrients, group with microbial community changes, and alterations in the microbiome can be seen across different soil fertility types. Root endosphere emerged as the plant microhabitat more affected by this rhizobial efficiency-driven community reshaping, manifested by the accumulation of members of the phylum Actinobacteria. The plant in turn plays an active role in regulating its root community, including sanctioning low nitrogen efficiency rhizobial strains, leading to nodule senescence in particular plant–soil–rhizobia strain combinations.
Conclusions: (From Abstract) The microbiome–soil–rhizobial dynamic strongly influences plant nutrient uptake and growth, with the endosphere and rhizosphere shaped differentially according to plant–rhizobial interactions with strains that vary in nitrogen-fixing efficiency levels. These results open up the possibility to select inoculation partners best suited for plant, soil type and microbial community.
Full conclusion at end of paper: By analysing not only plant and soil microbiome and nutrition but also plant growth and gene expression, we have characterised a mechanism for how soil impacts the outcome of symbiosis. We identified specific soil edaphic factors that correlate with bulk soil microbial community composition and suggest how those, plus rhizobial partner efficiency, shape the endosphere microbiome. Finally, we identified transcriptional changes that characterise high N fixation systems and that may account for the differential recruitment of endosphere microbial communities. These findings help to explain how highly efficient symbiosis may impact the soil and potentially soil health when legume crops are used in intercropping or field rotation. Overall, our findings highlight the importance of selecting the right inoculum for legume crops but one that is also right for the soil type and microbial community for optimal soil–plant–microbial interactions. Understanding this tri-partite association is thus crucial for crop improvement and for generating increased yield in a sustainable way. Analysis of the microbes identified from the endosphere in the high-efficiency symbiotic conditions will lead to a better understanding of the functional role of naturally co-occurring strains in soil. This could advance fine-tuning of microbial inoculums to significantly improve legume plant production.
Of particular interest (because we are happy to have information about how both bacteria and fungus work in our healthy soil), this quote from the paper:
For both bacterial and fungal communities, soil type explains a much higher percentage of microbial community composition than inoculation strain (Fig. 4A). Although this percentage is highest in bulk soil fungal community composition (78.7%), this substantially decreases towards the endosphere to 33.1%. This reduction is far less drastic in bacterial communities, from 60.4% in bulk soil to 47.6% in the endosphere. This suggests that the fungal community structure is less dependent on soil type than the bacterial community. Endosphere fungal community structure might be influenced by currently unknown factors in the soil, such as microbe–microbe interactions  or metabolites not measured in this study. Contrastingly, rhizobial inoculation has a higher impact in bacterial community structure in the endosphere, explaining 12.3% in this compartment and a reduced 7.9% in the rhizosphere (Fig. 8). In contrast with previous findings in the widely studied Arabidopsis thaliana , we did not observe this effect in fungal communities, suggesting that bacterial endophyte inoculation might have a more specific effect in legume plants.(13)