Bibliographic record
Abstract
This review describes plant microbiomes and then addresses whether they can be engineered to encourage beneficial organisms, and discourage undesirable ones. This Microbe Wiki page deals broadly with plant-associated microorganisms. It contains some useful references at the end. This open source research article begins to address the complex issue of hub species and how microbiome composition influences plant growth and health. This news-type article highlights the complexity of plant microbiomes and suggests that engineering them for beneficial traits will likely prove to be more complex than many people currently suggest. This news article discusses Indigo, a relatively new company using the knowledge from metagenomic sequencing to help produce microbial seed coatings that deliver beneficial properties. This project at the Joint Genome Institute describes a project to connect plant genotypes and phenotypes to the composition of their microbiomes. This article reviews plant microbiome research and makes some suggestions for translating findings to applications in crop science. This article discusses potential benefits of plant microbiome research that can lead to adding beneficial bacteria or fungi via seed coatings, sprayings, or mixing into mulches. This commentary links to a report in the journal Science suggesting that plants play a significant role in organizing the microbiome associated with the plant. The phytobiome association provides links for conferences, funding opportunities, and job postings related to plant microbiome research. This research suggests that plant genotype and abiotic factors effect certain “hub” species within the microbiome and that those hubs networks are critical for maintaining community structure. This review provides an excellent overview of recent research focused on the root-microbe interface. In this study, the researchers transplanted microbiomes between plants and showed enhanced growth. The study was conducted with Arabidopsis. This personal website describes research on microbiomes of sugarcane and peat moss. The former is an important agricultural crop and the latter is important in global carbon cycling. This C&E News article provides a lot of useful information on plant microbiomes with many links to personal websites of scientists in the field and other information. AgBiome is a start-up in the plant microbiome field striving to create new products derived from biologicals discovered in the plant rhizosphere. This is a web page derived from the Genome Canada initiative that is dedicated to using genomics to improve crop yield, resistance to heat stress and water efficiency. This organization in the Netherlands is directed towards promoting research on plant microbiomes. This interesting series of interviews makes the case broadly for microbial metagenomic research, including research into soil environments. This study will investigate the microbial metagenome in and around rice plants. It will also involve transcriptomic studies. This United States government initiative details plans to support microbiome research, including that for agricultural advancement. It describes plans for foundation and government agency financial support. This commercial site contains significant useful information with a resource library, videos, etc. This personal site describes research on the ability of plant immune systems to discriminate between helpful and harmful bacteria in their environment. This site has a collection of 726 papers as of this date related to the topic. This is a good place to start for references if interested in this topic. Pinterest holds a large collection of photographs and has photos related to plant roots, mycorrhizal fungi and other root–microbe associations.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.004 | 0.003 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.003 | 0.002 |
| Insufficient payload (model declined to judge) | 0.011 | 0.004 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".