xiulingao / california-grass-allometry

California-grass-allometry

This repo is for hosting data, scripts, and results (git ignored however) for allometry study of 12 common California grasses. See each section for details on study design, data structure, and how to use each script for data analysis.

Study design

This is a greenhouse experiment on grass allometry. Study species see Table 1. We grew all plants from seeds, all seeds are requested from the USDA germplasm program. Seeds were germinated on flats in Feb. 2022 with no stratification. Once there were at least 20 seedlings for each species with mean height greater than 5cm, we transplanted all secpeis into either nursery cones or 42cm (depth) * 15cm (diameter)pots. Plants in small cones were harvested in the first 2 months (March, 2022 - April, 2022) after transplant. Plants in deep pots were harvested between late April, 2022 and March, 2023. Nursery cones were used for early-stage, small-sized plants to allow for more samples across wide size range given limited greenhouse space.

Table 1. Study species informaiton.

Species	USDA code	Photosynthesis	Life form
Avena barbata	AVBA	C3	annual
Bromus hordeaceus	BRHO2	C3	annual
Brachypodium distachyon	BRDI2	C3	annual
Vulpia myuros	VUMY	C3	annual
Elymus glaucus	ELGL	C3	perennial
Festuca californica	FECA	C3	perennial
Nassella pulchra	NAPU4	C3	perennial
Aristida oligantha	AROL	C4	annual
Setaria pumila	SEPU8	C4	annual
Sporobolus airoides	SPAI	C4	perennial
Aristida purpurea	ARPU9	C4	perennial
Muhlenbergia rigens	MURI2	C4	perennial

A block design was applied. We set up 5 blocks in a glassroom at the Oxford facility at University of California, Berkeley. For each block, we assigned 7 (if total samples were 35) or 4 (if total samples were 20) individuals of the same species. Individuals within the same block were randomly located on the workbench. We randomized locations of all plants within the same block every other month. On each sampling day, one plant (randomly chosen either from cones during March- mid April 2022 or pots during late April, 2022-March, 2023) from each sampled species was taken from each block. Given growth rate varied among species, we sampled all annual species in the spring and early summer of 2022. However, smapling of perennial species will not be finished till March, 2023 in order for all perennial plants to reach a reasonable size (e.g. sexually mature). Sampling frequency and species to sample were chosen based on measurements of plant size to maximize the size range of samples.

All plants were watered frequently to maintain moist soil surface during wet season in California. However, watering frequency was reduced to every other day during June, 2022 - September, 2022 for mimicking dry season precipitation. This watering regime was chosen to drought stress the plants but also keep all plants alive and growing during hot summer. We applied fertilizer (100 ppm N 20-20-20 CaNO3) once each month to all plants. A 16-hour photoperiod was applied using medal halide.

Data structure

Data are stored in repo Dir/data. All files are organized in the same way. For instance, biomass.csv stores biomass measurement of different plant organs for each sample, while biomass-metadata.csv stores all the metadata information for biomass.csv Relevant scripts used for data analysis are under repo Dir/scripts, all are written in R. the results dir meant to store figures and tables produced by scripts, but due to large size of the files, they are all git ignored here.

Usage of scripts

inside each script, there is a brief description for what each script is used for and in-line comments. If there's any question, please contact the author for more information at [email protected]