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At least 91 records · Page 5

The influence of increasing atmospheric CO 2 , temperature, and vapor pressure deficit on seawater-induced tree mortality

We report increasing seawater exposure is killing coastal trees globally, with expectations of accelerating mortality with rising sea levels. However, the impact of concomitant changes in atmospheric CO 2 concentration, temperature, and vapor pressure deficit (VPD) on seawater-induced tree mortality is uncertain. We examined the mechanisms of seawater-induced mortality under varying climate scenarios using a photosynthetic gain and hydraulic cost optimization model validated against observations in a mature stand of Sitka-spruce (Picea sitchensis) trees in the Pacific Northwest, USA, that were dying from recent seawater exposure. The simulations matched well with observations of photosynthesis, transpiration, nonstructural carbohydrates concentrations, leaf water potential, the percentage loss of xylem conductivity, and stand-level mortality rates. The simulations suggest that seawater-induced mortality could decrease by ~16.7% with increasing atmospheric CO 2 levels due to reduced risk of carbon starvation. Conversely, rising VPD could increase mortality by ~5.6% because of increasing risk of hydraulic failure. Across all scenarios, seawater-induced mortality was driven by hydraulic failure in the first two years after seawater exposure began, with carbon starvation becoming more important in subsequent years. Changing CO 2 and climate appear unlikely to have a significant impact on coastal tree mortality under rising sea levels.

54 ENVIRONMENTAL SCIENCES↗

Effects of Eucalyptus wood and leaf litter on saproxylic insects in the southeastern United States

Although Eucalyptus is widely planted outside its native range for timber and pulp production, the effects of these exotic plantations on biodiversity relative to native semi-natural forests or plantations of native tree species remain incompletely understood. Here, we compare the diversity of saproxylic beetles (Coleoptera) and true bugs (Hemiptera) between non-native Eucalyptus benthamii Maiden and Cambage (Camden white gum) and native Pinus taeda L. (loblolly pine) stands on the upper Coastal Plain of South Carolina, U.S.A. We sampled insects emerging from logs of both species placed in both stand types after 1, 2, 6, and 12 months in the field. Beetle and true bug richness and diversity were both significantly lower from eucalypt than from pine wood. Moreover, the two communities were compositionally distinct. Whereas pine supported many species of host-specific phloeoxylophagous beetles, most species collected from eucalypts were mycophagous or predatory taxa capable of utilizing a wide range of hosts. Species richness did not differ between logs placed in eucalypt vs. pine stands but Shannon’s diversity was significantly higher in the eucalypt stands, possibly due to greater sun exposure in the latter. Contrary to a previous study, we found no support for the idea that eucalypt litter reduces the diversity of saproxylic insects. Our findings add to the growing body of evidence that non-native plantations are less favorable to biodiversity than those consisting of native tree species.

59 BASIC BIOLOGICAL SCIENCES↗

Disentangling the drivers of non-stationarity in tree growth

Tree-ring chronologies are an invaluable data source that provides insight into the ecology and physiology of forests across broad spatial and temporal scales. Furthermore, these data have a foundation in paleoclimatic research and have been used for decades to reconstruct climate, fire and other disturbances for several centuries to millennia into the past. Contemporary ecological studies have also used growth data to examine the responses of trees to environmental variability or biotic and abiotic stressors.

59 BASIC BIOLOGICAL SCIENCES↗

Structural Design Variations in Beetle Elytra

Abstract Beetles typically use their protective wing coverings or elytra to shield their membranous hindwings from the environment. Elytra in some terrestrial species have evolved a greater protective role capable of shielding the organism from powerful antagonistic predators. The structure–function relationships of these biological composites identify how architectural and chemical variations of the cuticle are tuned to create light‐weight, impact resistant composites. Specifically, the elytral structures of a tree dwelling beetle capable of flight, Trypoxylus dichotomus , and a terrestrial beetle incapable of flight, Phloeodes diabolicus , are compared to understand how their varied environmental needs forged the elytra to facilitate fight or resist fatal predator strikes. Mechanical and microstructural analysis reveals P . diabolicus has a harder, stiffer elytra that incorporate through‐thickness fibers to resist greater mechanical stresses imposed by bending and puncture. Conversely, the elytra of T . dichotomus have a compliant structure with large voids that facilitates localized deformation. Variations in flexural strength and puncture resistance remain attributed to P . diabolicus possessing a thicker cuticle with a greater degree of cross‐linking and an increased amount of endocuticular layers. These findings may provide useful insight into the design and manufacturing of composite materials for use in light‐weight or energy‐absorbing applications.

Rivera, Jesus↗

Graph-based machine learning improves just-in-time defect prediction

The increasing complexity of today’s software requires the contribution of thousands of developers. This complex collaboration structure makes developers more likely to introduce defect-prone changes that lead to software faults. Determining when these defect-prone changes are introduced has proven challenging, and using traditional machine learning (ML) methods to make these determinations seems to have reached a plateau. In this work, we build contribution graphs consisting of developers and source files to capture the nuanced complexity of changes required to build software. By leveraging these contribution graphs, our research shows the potential of using graph-based ML to improve Just-In-Time (JIT) defect prediction. We hypothesize that features extracted from the contribution graphs may be better predictors of defect-prone changes than intrinsic features derived from software characteristics. We corroborate our hypothesis using graph-based ML for classifying edges that represent defect-prone changes. This new framing of the JIT defect prediction problem leads to remarkably better results. We test our approach on 14 open-source projects and show that our best model can predict whether or not a code change will lead to a defect with an F1 score as high as 77.55% and a Matthews correlation coefficient (MCC) as high as 53.16%. This represents a 152% higher F1 score and a 3% higher MCC over the state-of-the-art JIT defect prediction. We describe limitations, open challenges, and how this method can be used for operational JIT defect prediction.

59 BASIC BIOLOGICAL SCIENCES↗

Whole-proteome tree of life suggests a deep burst of organism diversity

An organism tree of life (organism ToL) is a conceptual and metaphorical tree to capture a simplified narrative of the evolutionary course and kinship among the extant organisms. Such a tree cannot be experimentally validated but may be reconstructed based on characteristics associated with the organisms. Since the whole-genome sequence of an organism is, at present, the most comprehensive descriptor of the organism, a whole-genome sequence-based ToL can be an empirically derivable surrogate for the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. We have constructed three types of ToLs for diversely sampled organisms using the sequences of whole genome, of whole transcriptome, and of whole proteome. Of the three, whole-proteome sequence-based ToL (whole-proteome ToL), constructed by applying information theory-based feature frequency profile method, an “alignment-free” method, gave the most topologically stable ToL. Here, we describe the main features of a whole-proteome ToL for 4,023 species with known complete or almost complete genome sequences on grouping and kinship among the groups at deep evolutionary levels. The ToL reveals 1) all extant organisms of this study can be grouped into 2 “Supergroups,” 6 “Major Groups,” or 35+ “Groups”; 2) the order of emergence of the “founders” of all of the groups may be assigned on an evolutionary progression scale; 3) all of the founders of the groups have emerged in a “deep burst” at the very beginning period near the root of the ToL—an explosive birth of life’s diversity.

59 BASIC BIOLOGICAL SCIENCES↗

Functional Diversification of Populus FLOWERING LOCUS D-LIKE3 Transcription Factor and Two Paralogs in Shoot Ontogeny, Flowering, and Vegetative Phenology

Both the evolution of tree taxa and whole-genome duplication (WGD) have occurred many times during angiosperm evolution. Transcription factors are preferentially retained following WGD suggesting that functional divergence of duplicates could contribute to traits distinctive to the tree growth habit. We used gain- and loss-of-function transgenics, photoperiod treatments, and circannual expression studies in adult trees to study the diversification of three Populus FLOWERING LOCUS D-LIKE (FDL) genes encoding bZIP transcription factors. Expression patterns and transgenic studies indicate that FDL2.2 promotes flowering and that FDL1 and FDL3 function in different vegetative phenophases. Study of dominant repressor FDL versions indicates that the FDL proteins are partially equivalent in their ability to alter shoot growth. Like its paralogs, FDL3 overexpression delays short day-induced growth cessation, but also induces distinct heterochronic shifts in shoot development—more rapid phytomer initiation and coordinated delay in both leaf expansion and the transition to secondary growth in long days, but not in short days. Our results indicate that both regulatory and protein coding sequence variation contributed to diversification of FDL paralogs that has led to a degree of specialization in multiple developmental processes important for trees and their local adaptation.

59 BASIC BIOLOGICAL SCIENCES↗

Ectomycorrhizal and Dark Septate Fungal Associations of Pinyon Pine Are Differentially Affected by Experimental Drought and Warming

Changing climates can cause shifts in temperature and precipitation, resulting in warming and drought in some regions. Although each of these factors has been shown to detrimentally affect forest ecosystems worldwide, information on the impacts of the combined effects of warming and drought is lacking. Forest trees rely on mutualistic root-associated fungi that contribute significantly to plant health and protection against climate stresses. We used a six-year, ecosystem-scale temperature and precipitation manipulation experiment targeted to simulate the climate in 2100 in the Southwestern United States to quantify the effects of drought, warming and combined drought and warming on the root colonization (abundance), species composition and diversity of ectomycorrhizal fungi (EMF), and dark septate fungal endophytes in a widespread woodland tree, pinyon pine (Pinus edulis E.). Our results show that pinyon shoot growth after 6 years of these treatments was reduced more by drought than warming. The combined drought and warming treatment reduced the abundance and diversity of EMF more than either treatment alone. Individual ectomycorrhizal fungal taxa, including the drought tolerant Cenococcum geophilum, were present in all treatments but the combined drought and warming treatment. The combined drought and warming treatment also reduced the abundance of dark septate endophytes (DSE), but did not affect their diversity or species composition. The current year shoot growth of the trees correlated positively with ectomycorrhizal fungal diversity, highlighting the importance of diversity in mutualistic relationships to plant growth. Our results suggest that EMF may be more important than DSE to aboveground growth in P. edulis, but also more susceptible to the negative effects of combined climate stressors.

59 BASIC BIOLOGICAL SCIENCES↗

Disturbance-accelerated succession increases the production of a temperate forest

Many secondary deciduous forests of eastern North America are approaching a transition in which maturing early successional tree species are declining, resulting in an uncertain future for these forests’ century-long carbon (C) sink. We initiated the Forest Accelerated Succession Experiment (FASET) at the University of Michigan Biological Station to examine the patterns and mechanisms underlying forest C cycling following the stem-girdling induced mortality of >6,700 early successional Populus spp. (aspen) and Betula papyrifera (paper birch). Since 2008, meteorological flux tower-based C cycling observations from the 33-ha treatment forest have been paired with those from a nearby unmanipulated forest. Following over a decade of observations, herein we revisit our core hypothesis: that net ecosystem production (NEP) would increase following the transition to mid-late successional species dominance due to increased canopy structural complexity. Supporting our hypothesis, NEP was stable, briefly declined, and then increased relative to the control in the decade following disturbance; however, increasing NEP was not associated with rising structural complexity but rather the rapid 1-year recovery of total LAI as mid-late successional Acer, Quercus, and Pinus assumed canopy dominance. The transition to mid-late successional species dominance improved carbon-use efficiency (CUE = NEP/gross primary production) as ecosystem respiration declined. Similar soil respiration rates in control and treatment forests, along with species differences in leaf physiology and the rising relative growth rates of mid-late successional species in the treatment forest, suggest changes in aboveground plant respiration and growth, respectively, were primarily responsible for increases in NEP. We conclude that deciduous forests transitioning from early to middle succession are capable of sustained or increased NEP, even when experiencing extensive tree mortality. This adds to mounting evidence that aging deciduous forests in the region will function as C sinks for decades to come.

54 ENVIRONMENTAL SCIENCES↗

HPTLC Analysis and Chemical Composition of Selected Melaleuca Essential Oils

Tea tree oil (TTO) is a volatile essential oil obtained by distillation, mainly from the Australian native plant Melaleuca alternifolia (Maiden & Betche) Cheel (Myrtaceae). In this study, a comparative analysis of the chemical constituents of seven tea tree oils (M. alternifolia) and four other Melaleuca spp. oils (M. cajuputi, (M Ca ), two chemotypes of M. quinquenervia, (M Ne and M Ni ), and M. ericifolia (M Ro )) was carried out using gas chromatography–mass spectrometry (GC-MS) and high-performance thin-layer chromatography (HPTLC). Among the seven TTOs, terpinen-4-ol (37.66–44.28%), γ-terpinene (16.42–20.75%), α-terpinene (3.47–12.62%), α-terpineol (3.11–4.66%), and terpinolene (2.75–4.19%) were the most abundant compounds. On the other hand, the most abundant compounds of the other Melaleuca oils varied, such as 1,8-cineole (64.63%) in M Ca oil, (E)-nerolidol (48.40%) and linalool (33.30%) in M Ne oil, 1,8-cineole (52.20%) in M Ni oil, and linalool (38.19%) and 1,8-cineole (27.57%) in M Ro oil. HPTLC fingerprinting of Melaleuca oils enabled the discrimination of TTO oils from other Melaleuca spp. oils. Variation was observed in the profile of the R f values among EOs. The present study shows that HPTLC is one of the best ways to identify and evaluate the quality control in authenticating TTOs, other Melaleuca EOs, or EOs from other species within the Myrtaceae.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Human limits in machine learning: prediction of potato yield and disease using soil microbiome data

Abstract Background The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide one of the first comprehensive investigations into the predictive potential of machine learning models for understanding the connections between soil and biological phenotypes. We investigate an integrative framework performing accurate machine learning-based prediction of plant performance from biological, chemical, and physical properties of the soil via two models: random forest and Bayesian neural network. Results Prediction improves when we add environmental features, such as soil properties and microbial density, along with microbiome data. Different preprocessing strategies show that human decisions significantly impact predictive performance. We show that the naive total sum scaling normalization that is commonly used in microbiome research is one of the optimal strategies to maximize predictive power. Also, we find that accurately defined labels are more important than normalization, taxonomic level, or model characteristics. ML performance is limited when humans can’t classify samples accurately. Lastly, we provide domain scientists via a full model selection decision tree to identify the human choices that optimize model prediction power. Conclusions Our study highlights the importance of incorporating diverse environmental features and careful data preprocessing in enhancing the predictive power of machine learning models for soil and biological phenotype connections. This approach can significantly contribute to advancing agricultural practices and soil health management.

Aghdam, Rosa↗

Radical SAM enzymes: Nature's choice for radical reactions

Enzymes that use a [4Fe-4S] 1+ cluster plus S-adenosyl-L-methionine (SAM) to initiate radical reactions (radical SAM) form the largest enzyme superfamily, with over half a million members across the tree of life. This review summarizes recent work revealing the radical SAM reaction pathway, which ultimately liberates the 5´-deoxyadenosyl (5´-dAdo•) radical to perform extremely diverse, highly regio- and stereo-specific, transformations. Most surprising was the discovery of an organometallic intermediate Ω exhibiting an Fe-C5´-adenosyl bond. Ω liberates 5´-dAdo• through homolysis of the Fe-C5´ bond, in analogy to Co-C5´ bond homolysis in B12, previously viewed as biology’s paradigmatic radical generator. The 5´-dAdo• has been trapped and characterized in radical SAM enzymes via a recently-discovered photoreactivity of the [4Fe- 4S] + /SAM complex, and has been confirmed as a catalytically active intermediate in enzyme catalysis. The regioselective SAM S-C bond cleavage to produce 5´-dAdo• originates in the JahnTeller effect. The simplicity of SAM as a radical precursor, and the exquisite control of 5´-dAdo• reactivity in radical SAM enzymes, may be why radical SAM enzymes pervade the tree of life, while B12 enzymes are only a few.

deoxyadenosyl radical↗

Research Development and Partnership Pilot (RDPP): Developing plans and partnerships for incorporating tree reproduction to understand Earth system change

The goals for this Research Development and Partnership Pilot (RDPP) proposal were to i) learn about Department of Energy (DOE) research and use the PI’s expertise on patterns and environmental drivers of tree reproduction as a basis to make connections with individuals and research groups at DOE National Laboratories, and ii) to develop plans and form partnerships that will both enhance the PI’s research. The objectives of the proj ect were for the PI to i) participate in the Department of Energy's Office of Science program in Biological and Environmental Research training and outreach activities, ii) conduct directed fact-finding on Earth and Environmental Systems Sciences Division (EESSD) research projects and new partnerships with individuals and groups at National Laboratories, ii) conduct meetings with potential collaborators at National Laboratories to discuss EESSD-relevant research ideas, and iv) to develop a plan for future research efforts. During the period of the award, the objectives of the proposal were met, as the PI attended Environmental System Sciences meetings, American Geophysical Union meetings, SPRUCE experiment meetings, and visited the Oak Ridge National Lab. These activities led to increased understanding of the research being conducted by DOE scientists and the PI had meetings with potential collaborators to develop future research plans that leverage expertise at DOE and the research interests of the PI to increase understanding of the role of tree reproduction in future carbon allocation and in tree regeneration models in boreal ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Demographic composition, not demographic diversity, predicts biomass and turnover across temperate and tropical forests

The growth and survival of individual trees determine the physical structure of a forest with important consequences for forest function. However, given the diversity of tree species and forest biomes, quantifying the multitude of demographic strategies within and across forests and the way that they translate into forest structure and function remains a significant challenge. Here, we quantify the demographic rates of 1961 tree species from temperate and tropical forests and evaluate how demographic diversity (DD) and demographic composition (DC) differ across forests, and how these differences in demography relate to species richness, aboveground biomass (AGB), and carbon residence time. We find wide variation in DD and DC across forest plots, patterns that are not explained by species richness or climate variables alone. There is no evidence that DD has an effect on either AGB or carbon residence time. Rather, the DC of forests, specifically the relative abundance of large statured species, predicted both biomass and carbon residence time. Our results demonstrate the distinct DCs of globally distributed forests, reflecting biogeography, recent history, and current plot conditions. Linking the DC of forests to resilience or vulnerability to climate change, will improve the precision and accuracy of predictions of future forest composition, structure, and function.

59 BASIC BIOLOGICAL SCIENCES↗

Diacylglycerol enantiomer selectivity of diacylglycerol acyltransferases highlights metabolic specialization in triacylglycerol synthesis across the tree of life

Triacylglycerols are the major energy storage lipids in plants, animals, and microorganisms, and are predominantly produced by acyl-CoA:diacylglycerol (DAG) acyltransferases (DGATs). Two enantiomers of the DAG substrate, sn -1,2 and sn -2,3, can be produced by different biological mechanisms; however, little is known about which species produce each enantiomer, the selectivity of DGAT isoforms for either enantiomer, or whether DGAT enantiomer selectivity varies across organisms. Here, DAG enantiomer selectivity of DGAT1 and DGAT2 was measured from eight seed plants, two mammals, one oleaginous yeast, and one photosynthetic microalga using enantiomer-specific in vitro DGAT assays. Across most plants, DGAT1 favored sn -1,2-DAG, whereas DGAT2 preferentially utilized sn -2,3-DAG. However, there were several exceptions. Mammalian DGAT1, DGAT2, and microbial DGAT1s efficiently used both DAG enantiomers, while microbial DGAT2s had unique selectivity. The selectivity of several DGATs for combined acyl-CoA and DAG enantiomer molecular species were also evaluated for biotechnical applications. Therefore, DGAT DAG enantiomer selectivity is common yet strongly dependent on lineage and isoform and likely shaped in part by species-specific metabolic context of triacylglycerol synthesis, turnover, and remodeling. This work expands our understanding of DGAT function and establishes a foundation for leveraging enantiomer-selective acyltransferases in metabolic engineering of tailored lipid products.

Arabidopsis thaliana↗

Genetic Modification of KNAT7 Transcription Factor Expression Enhances Saccharification and Reduces Recalcitrance of Woody Biomass in Poplars

The precise role of KNAT7 transcription factors (TFs) in regulating secondary cell wall (SCW) biosynthesis in poplars has remained unknown, while our understanding of KNAT7 functions in other plants is continuously evolving. To study the impact of genetic modifications of homologous and heterologous KNAT7 gene expression on SCW formation in transgenic poplars, we prepared poplar KNAT7 ( PtKNAT7 ) overexpression ( PtKNAT7 -OE) and antisense suppression ( PtKNAT7 -AS) vector constructs for the generation of transgenic poplar lines via Agrobacterium -mediated transformation. Since the overexpression of homologous genes can sometimes result in co-suppression, we also overexpressed Arabidopsis KNAT7 ( AtKNAT7-OE ) in transgenic poplars. In all these constructs, the expression of KNAT7 transgenes was driven by developing xylem (DX)-specific promoter, DX15. Compared to wild-type (WT) controls, many SCW biosynthesis genes downstream of KNAT7 were highly expressed in poplar PtKNAT7-OE and AtKNAT7-OE lines. Yet, no significant increase in lignin content of woody biomass of these transgenic lines was observed. PtKNAT7-AS lines, however, showed reduced expression of many SCW biosynthesis genes downstream of KNAT7 accompanied by a reduction in lignin content of wood compared to WT controls. Syringyl to Guaiacyl lignin (S/G) ratios were significantly increased in all three KNAT7 knockdown and overexpression transgenic lines than WT controls. These transgenic lines were essentially indistinguishable from WT controls in terms of their growth phenotype. Saccharification efficiency of woody biomass was significantly increased in all transgenic lines than WT controls. Overall, our results demonstrated that developing xylem-specific alteration of KNAT7 expression affects the expression of SCW biosynthesis genes, impacting at least the lignification process and improving saccharification efficiency, hence providing one of the powerful tools for improving bioethanol production from woody biomass of bioenergy crops and trees.

59 BASIC BIOLOGICAL SCIENCES↗

Light-Dependence of Formate (C1) and Acetate (C2) Transport and Oxidation in Poplar Trees

Although apparent light inhibition of leaf day respiration is a widespread reported phenomenon, the mechanisms involved, including utilization of alternate respiratory pathways and substrates and light inhibition of TCA cycle enzymes are under active investigation. Recently, acetate fermentation was highlighted as a key drought survival strategy mediated through protein acetylation and jasmonate signaling. Here, we evaluate the light-dependence of acetate transport and assimilation in Populus trichocarpa trees using the dynamic xylem solution injection (DXSI) method developed here for continuous studies of C1 and C2 organic acid transport and light-dependent metabolism. Over 7 days, 1.0 L of [13C]formate and [13C2]acetate solutions were delivered to the stem base of 2-year old potted poplar trees, while continuous diurnal observations were made in the canopy of CO2, H2O, and isoprene gas exchange together with δ13CO2. Stem base injection of 10 mM [13C2]acetate induced an overall pattern of canopy branch headspace 13CO2 enrichment (δ13CO2 +27‰) with a diurnal structure in δ13CO2 reaching a mid-day minimum followed by a maximum shortly after darkening where δ13CO2 values rapidly increased up to +12‰. In contrast, 50 mM injections of [13C]formate were required to reach similar δ13CO2 enrichment levels in the canopy with δ13CO2 following diurnal patterns of transpiration. Illuminated leaves of detached poplar branches pretreated with 10 mM [13C2]acetate showed lower δ13CO2 (+20‰) compared to leaves treated with 10 mM [13C]formate (+320‰), the opposite pattern observed at the whole plant scale. Following dark/light cycles at the leaf-scale, rapid, strong, and reversible enhancements in headspace δ13CO2 by up to +60‰ were observed in [13C2]acetate-treated leaves which showed enhanced dihydrojasmonic acid and TCA cycle intermediate concentrations. The results are consistent with acetate in the transpiration stream as an effective activator of the jasmonate signaling pathway and respiratory substrate. The shorter lifetime of formate relative to acetate in the transpiration stream suggests rapid formate oxidation to CO2 during transport to the canopy. In contrast, acetate is efficiently transported to the canopy where an increased allocation towards mitochondrial dark respiration occurs at night. The results highlight the potential for an effective integration of acetate into glyoxylate and TCA cycles and the light-inhibition of citrate synthase as a potential regulatory mechanism controlling the diurnal allocation of acetate between anabolic and catabolic processes.

59 BASIC BIOLOGICAL SCIENCES↗