Methods of In Situ Quantitative Root Biology

When dealing with plant roots, a multiscale description of the functional root structure is needed. Since the beginning of 21st century, new devices such as laser confocal microscopes have been accessible for coarse root structure measurements, including three-dimensional (3D) reconstruction. Most researchers are familiar with using simple 2D geometry visualization that does not allow quantitative determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for 3D analysis of root features at single-cell resolution, including root asymmetry, lateral root analysis, cell size and nuclear organization, cell-cycle kinetics, and chromatin structure analysis. Quantitative maps of the root apical meristem (RAM) are shown for different species, including Arabidopsis thaliana (L.), Heynh, Nicotiana tabacum L., Medicago sativa L., and Setaria italica (L.) P. Beauv. The 3D analysis of the RAM in these species showed divergence in chromatin organization and cell volume distribution that might be used to study root zonation for each root tissue. Detailed protocols and possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.

Coarse root distribution of Vatica pauciflora (Korth.) Blume in different soil slopes as revealed by root detector

Tree roots have an essential role in absorbing water and nutrients from the soil and supporting tree stability. As an anchor for the tree, the environment can significantly affect root structure but it is rarely investigated due to below ground distribution. The study was aimed to determine the distribution of coarse roots of Vatica trees (Vatica pauciflora) which grows in different soil slopes. Six mature Vatica trees at Bogor Botanical Garden were selected in this study. Root detector as the main tool based on acoustic method was used to evaluate the root distribution. Analysis photogrammetry was carried out to complement the root detector results. The results found that the root detector only can evaluate the radial distribution of coarse root, while root distribution on downward soil cannot be detected. The condition of the site with different slope categories (e.g., flat to steep) affected root distribution patterns. A study on root distribution was useful to assist the evaluation of tree stability and to support arboriculture study.

Seasonal Differences in Water-Use Sources of Impatiens hainanensis (Balsaminaceae), a Limestone-Endemic Plant Based on “Fissure-Soil” Habitat Function

The southwestern mountains of Hainan Island are the southernmost region with tropical karst landform in China. The frequent alternation of dry and wet seasons leads to the loss of the mineral nutrients of limestone, creating karst fissure habitats. Plants living in karst fissure habitats for long periods of time have developed local adaptation mechanisms correspondingly. In the paper, hydrogen–oxygen stable isotope technology was applied to determine the water-use sources of Impatiens hainanensis in the dry and wet seasons, hoping to expound the adaptation mechanism of I. hainanensis in karst fissure habitats to the moisture dynamics in the wet and dry seasons. In the wet season (May to October, 2018), the air humidity is relatively high in the I. hainanensis habitat; in the dry season (November 2018 to April 2019), there is a degree of evaporation. In the wet season, fine-root biomass increases with soil depths, while coarse-root biomass decreases with soil depths; in the dry season, fine-root biomass is lower and coarse-root biomass is higher compared with the wet season. It was found that the average rainfall reached 1523 mm and the main water-use sources were shallow (0–5 cm) and middle (5–10 cm) soil water, epikarst water, and shallow karst fissure water during the wet season; the average rainfall reached 528 mm, and the deep (10–15 cm) soil water and shallow karst fissure water were the main water-use sources during the dry season. Fog water has a partial complementary effect in the dry season. The differences in the distribution of root biomass and each source of water in the wet and dry seasons of I. hainanensis also reflect the different water-use strategies of I. hainanensis in the wet and dry seasons. In both dry and wet seasons, I. hainanensis formed a water-use pattern dominated by soil water and shallow fissure water (0–15 cm) under the influence of the “fissure-soil-plant” system in the karst region.

Methods for in situ quantitative root biology

When dealing with plant roots, a multi-scale description of the functional root structure is needed. Since the beginning of XXI century, new devices like laser confocal microscopes have been accessible for coarse root structure measurements, including 3D reconstruction. Most re-searchers are familiar with using simple 2D geometry visualization that does not allow quantitatively determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for three-dimensional (3D) analysis of root features at single cell resolution, including root asymmetry, lateral root analysis, xylem and phloem structure, cell cycle kinetics, and chromatin determination. Quantitative maps of the distal and proximal root meristems are shown for different species, including Arabidopsis thaliana, Nicotiana tabacum and Medicago sativa. A 3D analysis of the primary root tip showed divergence in chromatin organization and cell volume distribution between cell types and precisely mapped root zonation for each cell file. Detailed protocols are also provided. Possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.

GPR-Based Automatic Identification of Root Zones of Influence Using HDBSCAN

The belowground root zone of influence (ZOI) is fundamental to the study of the root–root and root–soil interaction mechanisms of plants and is vital for understanding changes in plant community compositions and ecosystem processes. However, traditional root research methods have a limited capacity to measure the actual ZOIs within plant communities without destroying them in the process. This study has developed a new approach to determining the ZOIs within natural plant communities. First, ground-penetrating radar (GPR), a non-invasive near-surface geophysical tool, was used to obtain a dataset of the actual spatial distribution of the coarse root system in a shrub quadrat. Second, the root dataset was automatically clustered and analyzed using the hierarchical density-based spatial clustering of applications with noise (HDBSCAN) algorithm to determine the ZOIs of different plants. Finally, the shape, size, and other characteristics of each ZOI were extracted based on the clustering results. The proposed method was validated using GPR-obtained root data collected in two field shrub plots and one simulation on a dataset from existing literature. The results show that the shrubs within the studied community exhibited either segregated and aggregated ZOIs, and the two types of ZOIs were distinctly in terms of shape and size, demonstrating the complexity of root growth in response to changes in the surrounding environment. The ZOIs extracted based on GPR survey data were highly consistent with the actual growth pattern of shrub roots and can thus be used to reveal the spatial competition strategies of plant roots responding to changes in the soil environment and the influence of neighboring plants.

From Propagation to Field: Influence of Tray Design on Tree Seedling Quality and Performance1

This study evaluated the effects of low, moderate and high substrate exposure air-pruning propagation trays on eastern cottonwood (Populus deltoides W. Bartram ex Marshall ssp. deltoides) and black cherry (Prunus serotina Ehrh.) seedling root system quality and overall performance. Root system quality was characterized primarily by proportion of coarse root defects within the container imprint. Seedlings were evaluated after a nearly four-month commercial greenhouse production phase and one year after transplanting into a nursery field. Above and below-ground growth were measured at both time points. Proportions of coarse root defects, indicating degree of root deflection in container production, were persistent between greenhouse and field production phases. The Open (high substrate exposure) tray produced seedlings with roughly three times less deflected coarse root weight compared to the Closed Wall (low substrate exposure) tray for both species in both production phases. At neither production phase were there significant differences in above-ground growth among trays. This corroborates findings from other research studies that have found that variable root system quality does not always result in above-ground growth differences; and that when it does, differences in growth may take several years to manifest. Index words:, tree seedling quality, root defects, transplant performance, above-ground growth. Species used in this study: eastern cottonwood (Populus deltoides W. Bartram ex Marshall ssp. deltoides), black cherry (Prunus serotina Ehrh.).

Climate implications on forest above- and belowground carbon allocation patterns along a tropical elevation gradient on Mt. Kilimanjaro (Tanzania)

Tropical forests represent the largest store of terrestrial biomass carbon (C) on earth and contribute over-proportionally to global terrestrial net primary productivity (NPP). How climate change is affecting NPP and C allocation to tree components in forests is not well understood. This is true for tropical forests, but particularly for African tropical forests. Studying forest ecosystems along elevation and related temperature and moisture gradients is one possible approach to address this question. However, the inclusion of belowground productivity data in such studies is scarce. On Mt. Kilimanjaro (Tanzania), we studied aboveground (wood increment, litter fall) and belowground (fine and coarse root) NPP along three elevation transects (c. 1800–3900 m a.s.l.) across four tropical montane forest types to derive C allocation to the major tree components. Total NPP declined continuously with elevation from 8.5 to 2.8 Mg C ha−1 year−1 due to significant decline in aboveground NPP, while fine root productivity (sequential coring approach) remained unvaried with around 2 Mg C ha−1 year−1, indicating a marked shift in C allocation to belowground components with elevation. The C and N fluxes to the soil via root litter were far more important than leaf litter inputs in the subalpine Erica forest. Thus, the shift of C allocation to belowground organs with elevation at Mt. Kilimanjaro and other tropical forests suggests increasing nitrogen limitation of aboveground tree growth at higher elevations. Our results show that studying fine root productivity is crucial to understand climate effects on the carbon cycle in tropical forests.

Drought-Induced Root Pressure in Sorghum bicolor

Root pressure, also manifested as profusive sap flowing from cut stems, is a phenomenon in some species that has perplexed biologists for much of the last century. It is associated with increased crop production under drought, but its function and regulation remain largely unknown. In this study, we investigated the initiation, mechanisms, and possible adaptive function of root pressure in six genotypes of Sorghum bicolor during a drought experiment in the greenhouse. We observed that root pressure was induced in plants exposed to drought followed by re-watering but possibly inhibited by 100% re-watering in some genotypes. We found that root pressure in drought stressed and re-watered plants was associated with greater ratio of fine: coarse root length and shoot biomass production, indicating a possible role of root allocation in creating root pressure and adaptive benefit of root pressure for shoot biomass production. Using RNA-Seq, we identified gene transcripts that were up- and down-regulated in plants with root pressure expression, focusing on genes for aquaporins, membrane transporters, and ATPases that could regulate inter- and intra-cellular transport of water and ions to generate positive xylem pressure in root tissue.