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Weston, David

Publications and source records attributed to Weston, David.

Leveraging hyperspectral imaging to identify drought tolerant Populus species and genotypes within species

The aim of this study was to identity variation in drought tolerance across genotypes of Populus deltoides, Populus trichocarpa, and hybrids of the two species. A panel of 102 Populus genotypes, comprising 37 genotypes of P. trichocarpa, 37 of P. deltoides and 28 unique hybrid genotypes (P. trichocarpa x P. deltoides and P. deltoides x P. trichocarpa) were evaluated in the greenhouse under two treatments, well-watered (WW) and drought (DS). Plant physiological data were collected throughout the experiment once the drought treatment began. Throughout the experiment, we tracked soil volumetric water content, pot weight, stomatal conductance, quantum yield of photosystem II, and electron transport rate. In addition to those measurements, upon completion of the experiment, we assessed above and belowground plant biomass, plant height and stem diameter, leaf number, specific leaf area, relative water content, total protein, and total chlorophyll. We obtained hyperspectral signatures of one leaf from each plant at the end of the experiment. Columns BC – LL are hyperspectral averages for one leaf from each plant at each wavelength as described in the column header.

Hyper-spectral imaging, Populus, plant stress tole↗

Probabilistic measures for biological adaptation and resilience

This paper introduces an approach to quantifying ecological resilience in biological systems, particularly focusing on noisy systems responding to episodic disturbances with sudden adaptations. Incorporating concepts from nonequilibrium statistical mechanics, we propose a measure termed “ecological resilience through adaptation,” specifically tailored to noisy, forced systems that undergo physiological adaptation in the face of stressful environmental changes. Randomness plays a key role, accounting for model uncertainty and the inherent variability in the dynamical response among components of biological systems. Our measure of resilience is rooted in the probabilistic description of states within these systems and is defined in terms of the dynamics of the ensemble average of a model-specific observable quantifying success or well-being. Our approach utilizes stochastic linear response theory to compute how the expected success of a system, originally in statistical equilibrium, dynamically changes in response to a environmental perturbation and a subsequent adaptation. Importantly, the resulting mathematical derivations allow for the estimation of resilience in terms of ensemble averages of simulated or experimental data. Finally, through a simple but clear conceptual example, we illustrate how our resilience measure can be interpreted and compared to other existing frameworks in the literature. The methodology is general but inspired by applications in plant systems, with the potential for broader application to complex biological processes.

60 APPLIED LIFE SCIENCES↗

Sulfur speciation in Sphagnum peat moss modified by mutualistic interactions with cyanobacteria

Peat moss ( Sphagnum spp.) develops mutualistic interactions with cyanobacteria by providing carbohydrates and S compounds in exchange for N-rich compounds, potentially facilitating N inputs into peatlands. Here, we evaluate how colonization of Sphagnum angustifolium hyaline cells by Nostoc muscorum modifies S abundance and speciation at the scales of individual cells and across whole leaves. For the first time, S K-edge X-ray Absorption Spectroscopy was used to identify bulk and micron-scale S speciation across isolated cyanobacteria colonies, and in colonized and uncolonized leaves. Uncolonized leaves contained primarily reduced organic S and oxidized sulfonate- and sulfate-containing compounds. Increasing Nostoc colonization resulted in an enrichment of S and changes in speciation, with increases in sulfate relative to reduced S and sulfonate. Further, at the scale of individual hyaline cells, colonized cells exhibited localized enrichment of reduced S surrounded by diffuse sulfonate, similar to observations of cyanobacteria colonies cultured in the absence of leaves. We infer that colonization stimulates plant S uptake and the production of sulfate-containing metabolites that are concentrated in stem tissues. Sulfate compounds that are produced in response to colonization become depleted in colonized cells where they may be converted into reduced S metabolites by cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering Crassulacean Acid Metabolism in C3 and C4 Plants

Carbon dioxide (CO2) is a major greenhouse gas contributing to changing climatic conditions, which is a grand challenge affecting the security of food, energy, and environment. Photosynthesis plays the central role in plant-based CO2 reduction. Plants performing CAM (crassulacean acid metabolism) photosynthesis have a much higher water use efficiency than those performing C3 or C4 photosynthesis. Therefore, there is a great potential for engineering CAM in C3 or C4 crops to enhance food/biomass production and carbon sequestration on arid, semiarid, abandoned, or marginal lands. Recent progresses in CAM plant genomics and evolution research, along with new advances in plant biotechnology, have provided a solid foundation for bioengineering to convert C3/C4 plants into CAM plants. Here, we first discuss the potential strategies for CAM engineering based on our current understanding of CAM evolution. Then we describe the technical approaches for engineering CAM in C3 and C4 plants, with a focus on an iterative four-step pipeline: (1) designing gene modules, (2) building the gene modules and transforming them into target plants, (3) testing the engineered plants through an integration of molecular biology, biochemistry, metabolism, and physiological approaches, and (4) learning to inform the next round of CAM engineering. Finally, we discuss the challenges and future opportunities for fully realizing the potential of CAM engineering.

Yang, Xiaohan↗

Clonality, local population structure, and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex

Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with approximately 300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. Here, we assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. 405 samples of the four species, representing 57 populations, were subjected to RADseq. Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Differences in fitness between genets was estimated as the numbers of ramets each genet comprised. Degree of clonality (numbers of genets/numbers of ramets [samples]) within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but 2-8 ramets were detected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St. Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets, and sexes were not detected. Within S. divinum, however, female gametophytes harbored 2-3 times the number oi of microbial taxa as males. These four Sphagnum species all exhibit a similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns where genets abut one another but do not extensively mix, because of limited ramet fragmentation, and the guerrilla patterns where extensive genet fragmentation and dispersal results in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

59 BASIC BIOLOGICAL SCIENCES↗

SPRUCE Sphagnum Phytobiome Responses to Whole Ecosystem Warming and Elevated Atmospheric CO2 in July, 2017-2021

This dataset reports the carbon (C) and nitrogen (N) isotopic composition of Sphagnum moss tissue collected from the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experimental site within the Marcell Experimental Forest in northern Minnesota, USA. Tissues were collected inside the SPRUCE experimental study plot, where air and peat warming are combined in whole-ecosystem warming treatments, from 2019-2021. Additionally, rates of nitrogen fixation and methane oxidation measured for Sphagnum from 2017, 2019, and 2021. Sphagnum tissue % water content was measured at all timepoints. This dataset was used to conduct analyses within Petro et al (2023). Sphagnum C and N concentrations and 13C and 15N isotopic natural abundance were determined for three replicate Sphagnum tissue samples collected from inside the SPRUCE enclosures in July 2019-2021. Elemental and isotope analyses were conducted at the University of Georgia – Center for Applied Isotope Studies (CAIS; https://cais.uga.edu/). Plant elemental analysis was performed by the micro-Dumas method, while isotopic natural abundance was measured by isotope ratio mass spectrometry. 13C natural abundance is expressed as the per mille (‰) deviation from the Pee Dee Belemnite standard (PDB) 13C:12C ratio (δ13C), while 15N natural abundance is expressed as the ‰ deviation from the N2 atmospheric 15N:14N ratio (δ15N). Rates of nitrogen fixation and methane oxidation were measured using serum bottle incubations performed with Sphagnum collected inside the SPRUCE enclosures in July 2017, 2019, and 2021. Rates were calculated according to the amount of 15N-N2 or 13C-CH4 (methane) incorporated into the Sphagnum tissue or incubation headspace over the 48-hour intion period. In 2017, incubations were performed in growth chambers set to the temperature of the experimental plots during Sphagnum sampling. In 2019 and 2021, the incubations were performed directly inside the experimental plots. The 13C and 15N isotopic natural abundance data and rate measurements presented in this dataset provide insight into the impacts of whole-ecosystem warming and elevated atmospheric carbon dioxide (CO2) on N and C cycling within the Sphagnum phytobiome. This dataset contains two data files in comma-separate values (*.csv) format. Additional metadata are provided: two data dictionaries and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format. Additional datasets on NH4-N availability, porewater concentrations of CH4 and CO2, and Sphagnum groundcover within the SPRUCE experimental plots are available. These are outlined in the Related Datasets section in the user guide.

delta 13 carbon↗

Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems

Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum-associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (nifH) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of 13 CH 4 and 15 N 2 isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (Methyloferula spp. of the Rhizobiales) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.

54 ENVIRONMENTAL SCIENCES↗

Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal

A grand challenge facing society is climate change caused mainly by rising CO 2 concentration in Earth’s atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO 2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO 2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO 2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.

59 BASIC BIOLOGICAL SCIENCES↗

Photosynthetic parameters and nutrient content of trees at the Panama crane sites.

This data package contains leaf chemistry and photosynthetic traits data from trees within the NGEE Tropics Parque Natural Metropolitano (PA-PNM) and Bosque Protector San Lorenzo (PA-SLZ) sites in Panama. Photosynthetic parameters including maximum photosynthesis, Vcmax, Jmax, and TPU, were calculated from A/Ci curves. Foliar nitrogen and phosphorus concentrations and leaf mass per unit leaf area of the leaves also were determined. The plants that were sampled were classified as to species, family, order, clade, and growth form (tree, liana, perennial herb, or other). Wood density of the tree and the source of that data also are included. Included in this data package is a zip file with a single Excel data file and CSV copies.

54 ENVIRONMENTAL SCIENCES↗

amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool

Antimicrobial peptides (AMPs) are promising alternative antimicrobial agents. Currently, however, portable, user-friendly and efficient methods for predicting AMP sequences from genome-scale data are not readily available. In this work, we present amPEPpy, an open-source, multi-threaded command-line application for predicting AMP sequences using a random forest classifier.

59 BASIC BIOLOGICAL SCIENCES↗

DISCo-microbe: design of an identifiable synthetic community of microbes

Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts’ phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97–100% of community members using two different post-processing workflows. Furthermore, 97–99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host–associated microbiome, ultimately yielding a diverse community of 784 members. DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub and Python Package Index (PYPI).

16S rRNA↗

Physiological Responses of Populus trichocarpa to Warming

This data set contains empirical physiological, morphological, and chemical data collected over time on Western Black Cottonwood (Populs trichocarpa Torr. & A.Gray ex Hook., Salicaceae) clones, between July and December 2019 at Oak Ridge National Lab. The project was designed to experimentally warm P. trichocarpa clones and assess their physiological acclimation of leaves versus roots. Branch cuttings of the Nisqually-1 genotype were obtained from the US Department of Energy Joint Genome Institute (JGI) in Stanford, California, and propagated in leach tubes. Ninety genetically identical clones were planted into specially constructed mesocosm growth boxes and grown for an initial six weeks in the greenhouse, and then grown at three temperature treatments for ten weeks. The daytime air temperatures of treatments were approximately 25°C, 29°C, and 33°C. Measurements on plant physiology and growth were conducted at various intervals throughout the experiment. This dataset contains nine data files in comma separate (*.csv) format.

54 ENVIRONMENTAL SCIENCES↗