Microbial Colonizers in an Agroecosystem Under Diverse Cover Crop Treatments
Bibliographic record
Abstract
Cover crops are often incorporated between cash crop seasons to improve or maintain soil health. Although their effects on certain soil properties (e.g., erosion control) are well described, their potential to steer soil microbial composition and function remains poorly understood. Most studies use direct soil sampling to investigate this relationship, but long-dormant microorganisms and legacy DNA can mask treatment effects, leading to signals that may not reflect active contributors to key functions such as biogeochemical cycling and decomposition. In this study, we deployed microbial traps (i.e., sterile soil enclosed in permeable mesh) to contrast active recolonization with direct soil sampling across 11 cover crop treatments applied after fall cash crop harvests in the northeast United States. Bulk and recolonized soil were collected for 16S rRNA gene and internal transcribed spacer region amplicon sequencing before (i) winter and (ii) spring planting. We hypothesized that different cover crop mixtures would stimulate distinct pools of microbial colonizers, with stronger between-treatment effects in recolonized soil compared with bulk. Our results showed that crop treatments significantly influenced microbial composition of active colonizers; however, effect sizes were similar in both bulk and recolonized (explaining 12 to 18% of community variance). The presence or absence of plant cover was the strongest driver of compositional differences in both soil compartments, suggesting microbial traps and bulk soil can capture similar signals despite containing ecologically distinct microbiome subsets. Future work coupling community assembly in situ with functionally informative methods may further resolve whether active colonizers overlap with root-associated taxa and can lead to management-relevant outcomes. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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".