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DOE OSTI2020

Proteomic Tissue-Based Classifier for Early Prediction of Prostate Cancer Progression

Although ~40% of screen-detected prostate cancers (PCa) are indolent, advanced-stage PCa is a lethal disease with 5-year survival rates around 29%. Identification of biomarkers for early detection of aggressive disease is a key challenge. Starting with 52 candidate biomarkers, selected from existing PCa genomics datasets and known PCa driver genes, we used targeted mass spectrometry to quantify proteins that significantly differed in primary tumors from PCa patients treated with radical prostatectomy (RP) across three study outcomes: (i) metastasis ≥1-year post-RP, (ii) biochemical recurrence ≥1-year post-RP, and (iii) no progression after ≥10 years post-RP. Sixteen proteins that differed significantly in an initial set of 105 samples were evaluated in the entire cohort (n = 338). A five-protein classifier which combined FOLH1, KLK3, TGFB1, SPARC, and CAMKK2 with existing clinical and pathological standard of care variables demonstrated significant improvement in predicting distant metastasis, achieving an area under the receiver-operating characteristic curve of 0.92 (0.86, 0.99, p = 0.001) and a negative predictive value of 92% in the training/testing analysis. This classifier has the potential to stratify patients based on risk of aggressive, metastatic PCa that will require early intervention compared to low risk patients who could be managed through active surveillance.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Stand Age and Climate Change Effects on Carbon Increments and Stock Dynamics

Carbon assimilation and wood production are influenced by environmental conditions and endogenous factors, such as species auto-ecology, age, and hierarchical position within the forest structure. Disentangling the intricate relationships between those factors is more pressing than ever due to climate change’s pressure. We employed the 3D-CMCC-FEM model to simulate undisturbed forests of different ages under four climate change (plus one no climate change) Representative Concentration Pathways (RCP) scenarios from five Earth system models. In this context, carbon stocks and increment were simulated via total carbon woody stocks and mean annual increment, which depends mainly on climate trends. We find greater differences among different age cohorts under the same scenario than among different climate scenarios under the same age class. Increasing temperature and changes in precipitation patterns led to a decline in above-ground biomass in spruce stands, especially in the older age classes. On the contrary, the results show that beech forests will maintain and even increase C-storage rates under most RCP scenarios. Scots pine forests show an intermediate behavior with a stable stock capacity over time and in different scenarios but with decreasing mean volume annual increment. These results confirm current observations worldwide that indicate a stronger climate-related decline in conifers forests than in broadleaves.

Forestry↗

DOE OSTI2020

Antibiotic Treatment Prior to Injury Improves Post-Traumatic Osteoarthritis Outcomes in Mice

Osteoarthritis (OA) is a painful and debilitating disease characterized by the chronic and progressive degradation of articular cartilage. Post-traumatic OA (PTOA) is a secondary form of OA that develops in ~50% of cases of severe articular injury. Inflammation and re-occurring injury have been implicated as contributing to the progression of PTOA after the initial injury. However, there is very little known about external factors prior to injury that could affect the risk of PTOA development. To examine how the gut microbiome affects PTOA development we used a chronic antibiotic treatment regimen starting at weaning for six weeks prior to ACL rupture, in mice. A six-weeks post-injury histological examination showed more robust cartilage staining on the antibiotic (AB)-treated mice than the untreated controls (VEH), suggesting slower disease progression in AB cohorts. Injured joints also showed an increase in the presence of anti-inflammatory M2 macrophages in the AB group. Molecularly, the phenotype correlated with a significantly lower expression of inflammatory genes Tlr5, Ccl8, Cxcl13, and Foxo6 in the injured joints of AB-treated animals. Our results indicate that a reduced state of inflammation at the time of injury and a lower expression of Wnt signaling modulatory protein, Rspo1, caused by AB treatment can slow down or improve PTOA outcomes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Sclerostin Depletion Induces Inflammation in the Bone Marrow of Mice

Romosozumab, a humanized monoclonal antibody specific for sclerostin (SOST), has been approved for treatment of postmenopausal women with osteoporosis at a high risk for fracture. Previous work in sclerostin global knockout (Sost-/- ) mice indicated alterations in immune cell development in the bone marrow (BM), which could be a possible side effect in romosozumab-treated patients. Here, we examined the effects of short-term sclerostin depletion in the BM on hematopoiesis in young mice receiving sclerostin antibody (Scl-Ab) treatment for 6 weeks, and the effects of long-term Sost deficiency on wild-type (WT) long-term hematopoietic stem cells transplanted into older cohorts of Sost-/- mice. Our analyses revealed an increased frequency of granulocytes in the BM of Scl-Ab-treated mice and WT→Sost -/- chimeras, indicating myeloid-biased differentiation in Sost-deficient BM microenvironments. This myeloid bias extended to extramedullary hematopoiesis in the spleen and was correlated with an increase in inflammatory cytokines TNFα, IL-1α, and MCP-1 in Sost-/- BM serum. Additionally, we observed alterations in erythrocyte differentiation in the BM and spleen of Sost-/- mice. Taken together, our current study indicates novel roles for Sost in the regulation of myelopoiesis and control of inflammation in the BM.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study

Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2"), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec 57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Proteomic Determinants of Variation in Cholesterol Efflux: Observations from the Dallas Heart Study

High-density lipoproteins (HDLs) are promising targets for predicting and treating atherosclerotic cardiovascular disease (ASCVD), as they mediate removal of excess cholesterol from lipid-laden macrophages that accumulate in the vasculature. This functional property of HDLs, termed cholesterol efflux capacity (CEC), is inversely associated with ASCVD. HDLs are compositionally diverse, associating with >250 different proteins, but their relative contribution to CEC remains poorly understood. Our goal was to identify and define key HDL-associated proteins that modulate CEC in humans. The proteomic signature of plasma HDL was quantified in 36 individuals in the multi-ethnic population-based Dallas Heart Study (DHS) cohort that exhibited persistent extremely high (>=90th%) or extremely low CEC (<=10th%) over 15 years. Levels of apolipoprotein (Apo)A-I associated ApoC-II, ApoC-III, and ApoA-IV were differentially correlated with CEC in high (r = 0.49, 0.41, and —0.21 respectively) and low (r = —0.46, —0.41, and 0.66 respectively) CEC groups (p for heterogeneity (pHet) = 0.03, 0.04, and 0.003 respectively). Further, we observed that levels of ApoA-I with ApoC-III, complement C3 (CO3), ApoE, and plasminogen (PLMG) were inversely associated with CEC in individuals within the low CEC group (r = —0.11 to —0.25 for subspecies with these proteins vs. r = 0.58 to 0.65 for subspecies lacking these proteins; p < 0.05 for heterogeneity). These findings suggest that enrichment of specific proteins on HDLs and, thus, different subspecies of HDLs, differentially modulate the removal of cholesterol from the vasculature.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Characterizing Families of Spectral Similarity Scores and Their Use Cases for Gas Chromatography–Mass Spectrometry Small Molecule Identification

Metabolomics provides a unique snapshot into the world of small molecules and the complex biological processes that govern the human, animal, plant, and environmental ecosystems encapsulated by the One Health modeling framework. However, this “molecular snapshot” is only as informative as the number of metabolites confidently identified within it. The spectral similarity (SS) score is traditionally used to identify compound(s) in mass spectrometry approaches to metabolomics, where spectra are matched to reference libraries of candidate spectra. Unfortunately, there is little consensus on which of the dozens of available SS metrics should be used. This lack of standard SS score creates analytic uncertainty and potentially leads to issues in reproducibility, especially as these data are integrated across other domains. In this work, we use metabolomic spectral similarity as a case study to showcase the challenges in consistency within just one piece of the One Health framework that must be addressed to enable data science approaches for One Health problems. Here, using a large cohort of datasets comprising both standard and complex datasets with expert-verified truth annotations, we evaluated the effectiveness of 66 similarity metrics to delineate between correct matches (true positives) and incorrect matches (true negatives). We additionally characterize the families of these metrics to make informed recommendations for their use. Our results indicate that specific families of metrics (the Inner Product, Correlative, and Intersection families of scores) tend to perform better than others, with no single similarity metric performing optimally for all queried spectra. This work and its findings provide an empirically-based resource for researchers to use in their selection of similarity metrics for GC-MS identification, increasing scientific reproducibility through taking steps towards standardizing identification workflows.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Associations between Frequency of Culinary Herb Use and Gut Microbiota

While evidence suggests that culinary herbs have the potential to modulate gut microbiota, much of the current research investigating the interactions between diet and the human gut microbiome either largely excludes culinary herbs or does not assess use in standard culinary settings. As such, the primary objective of this study was to evaluate how the frequency of culinary herb use is related to microbiome diversity and the abundance of certain taxa, measured at the phylum level. In this secondary data analysis of the INCLD Health cohort, we examined survey responses assessing frequency of culinary herb use and microbiome analysis of collected stool samples. We did not observe any associations between frequency of culinary herb use and Shannon Index, a measure of alpha diversity. Regarding the abundance of certain taxa, the frequency of use of polyphenol-rich herbs and herbs with certain quantities of antibacterial compounds was positively associated with Firmicutes abundance, and negatively associated with Proteobacteria abundance. Additionally, the total number of herbs used with high frequency, defined as over three times per week, was also positively associated with Firmicutes abundance, independent of adjustments, and negatively associated with Proteobacteria abundance, after adjusting for dietary factors. Frequency of culinary herb use was not associated with Bacteroidota or Actinobacteria abundance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Specific Bacterial Taxa and Their Metabolite, DHPS, May Be Linked to Gut Dyshomeostasis in Patients with Alzheimer’s Disease, Parkinson’s Disease, and Amyotrophic Lateral Sclerosis

Background: Neurodegenerative diseases (NDDs) are multifactorial disorders frequently associated with gut dysbiosis, oxidative stress, and inflammation; however, the pathophysiological mechanisms remain poorly understood. Methods: Using untargeted mass spectrometry-based metabolomics and 16S sequencing of human stool, we investigated bacterial and metabolic dyshomeostasis in the gut microbiome associated with early disease stages across three NDDs—amyotrophic lateral sclerosis (ALS), Alzheimer’s disease (AD), Parkinson’s disease (PD)—and healthy controls (HC). Results: We discovered a previously unrecognized link between a microbial-derived metabolite with an unknown role in human physiology, 2,3-dihydroxypropane-1-sulfonate (DHPS), and gut dysbiosis in NDDs. DHPS was downregulated in AD, ALS, and PD, while bacteria involved in DHPS metabolism, Eubacterium and Desulfovibrio, were increased in all disease cohorts. Additionally, select taxa within the Clostridia class had strong negative correlations to DHPS, suggesting a potential role in DHPS metabolism. A catabolic product of DHPS is hydrogen sulfide, and when in excess, it is known to promote inflammation, oxidative stress, mitochondrial damage, and gut dysbiosis, known hallmarks of NDDs. Conclusions: These findings suggest that cryptic sulfur metabolism via DHPS is a potential missing link in our current understanding of gut dysbiosis associated with NDD onset and progression. As this was a hypothesis generating study, more work is needed to elucidate the role of DHPS in gut dysbiosis and neurodegenerative diseases.

Nutrition & Dietetics↗

DOE OSTI2024

Transcriptomic and Proteomic Insights into Host Immune Responses in Pediatric Severe Malarial Anemia: Dysregulation in HSP60-70-TLR2/4 Signaling and Altered Glutamine Metabolism

Severe malarial anemia (SMA, Hb < 6.0 g/dL) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission zones. This study explored the entire expressed human transcriptome in whole blood from 66 Kenyan children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25), focusing on host immune response networks. RNA-seq analysis revealed 6862 differentially expressed genes, with equally distributed up-and down-regulated genes, indicating a complex host immune response. Deconvolution analyses uncovered leukocytic immune profiles indicative of a diminished antigenic response, reduced immune priming, and polarization toward cellular repair in SMA. Weighted gene co-expression network analysis revealed that immune-regulated processes are central molecular distinctions between non-SMA and SMA. A top dysregulated immune response signaling network in SMA was the HSP60-HSP70-TLR2/4 signaling pathway, indicating altered pathogen recognition, innate immune activation, stress responses, and antigen recognition. Validation with high-throughput gene expression from a separate cohort of Kenyan children (n = 50) with varying severities of malarial anemia (n = 38 non-SMA and n = 12 SMA) confirmed the RNA-seq findings. Proteomic analyses in 35 children with matched transcript and protein abundance (n = 19 non-SMA and n = 16 SMA) confirmed dysregulation in the HSP60-HSP70-TLR2/4 signaling pathway. Additionally, glutamine transporter and glutamine synthetase genes were differentially expressed, indicating altered glutamine metabolism in SMA. This comprehensive analysis underscores complex immune dysregulation and novel pathogenic features in SMA.

Microbiology↗

DOE OSTI2023

Gender Gaps in Mode Usage, Vehicle Ownership, and Spatial Mobility When Entering Parenthood: A Life Course Perspective

Entry into parenthood is a major disruptive event to travel behavior, and gender gaps in mobility choices are often widened during parenthood. The exact timing of gender gap formation and their long-term effects on different subpopulations are less studied in the literature. Leveraging a longitudinal dataset from the 2018 WholeTraveler Study, this paper examines the effects of parenthood on a diverse set of short- to long-term outcomes related to the three hierarchical domains of mobility biography: mode choice, vehicle ownership, spatial mobility, and career decisions. The progress of the effects is evaluated over a sequential set of parenting stages and differentiated across three subpopulations. We find that individuals classified as “Have-it-alls”, who start their careers, partner up, and have children concurrently and early, significantly increase their car uses two years prior to childbirth (“nesting period”), and they then relocate to less transit-accessible areas and consequently reduce their reliance on public transportation while they have children in the household. In contrast, individuals categorized as “Couples”, who start careers and partnerships early but delay parenthood, and “Singles”, who postpone partnership and parenthood, have less pronounced changes in travel behavior throughout the parenting stages. The cohort-level effects are found to be driven primarily by women, whose career development is on average more negatively impacted by parenting events than men, regardless of their life course trajectory. Early career decisions made by women upon entering parenthood contribute to gender gaps in mid- to longer-term mobility decisions, signifying the importance of early intervention.

Yang, Hung-Chia (ORCID:0000000161439904)↗

DOE OSTI2021

Genetic Subtypes and Natural Resistance Mutations in HCV Genotype 4 Infected Saudi Arabian Patients

This study aimed to characterize the HCV genetic subtypes variability and the presence of natural occurring resistance-associated substitutions (RASs) in Saudi Arabia patients. A total of 17 GT patients were analyzed. Sequence analysis of NS3, NS5A, and NS5B regions was performed by direct sequencing, and phylogenetic analyses were used to determine genetic subtypes, RAS, and polymorphisms. Nine patients were infected by GT 4a, two with GT 4o and three with GT 4d. Two patients were infected with apparent recombinant virus (4a/4o/4a in NS3/NS5A/NS5B), and one patient was infected with a previously unknown, unclassifiable, virus of GT 4. Natural RASs were found in six patients (35%), including three infected by GT 4a, two by GT 4a/GT 4o/GT 4a, and one patient infected by an unknown, unclassifiable, virus of GT 4. In particular, NS3-RAS V170I was demonstrated in three patients, while NS5A-RASs (L28M, L30R, L28M + M31L) were detected in the remaining three patients. All patients were treated with sofosbuvir plus daclatasvir; three patients were lost to follow-up, whereas 14 patients completed the treatment. A sustained virological response (SVR) was obtained in all but one patient carrying NS3-RAS V170I who later relapsed. GT 4a is the most common subtype in this small cohort of Saudi Arabia patients infected with hepatitis C infection. Natural RASs were observed in about one-third of patients, but only one of them showed a treatment failure.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Molecular Epidemiology of HIV-1 in Ghana: Subtype Distribution, Drug Resistance and Coreceptor Usage

The greatest HIV-1 genetic diversity is found in West/Central Africa due to the pandemic’s origins in this region, but this diversity remains understudied. We characterized HIV-1 subtype diversity (from both sub-genomic and full-genome viral sequences), drug resistance and coreceptor usage in 103 predominantly (90%) antiretroviral-naive individuals living with HIV-1 in Ghana. Full-genome HIV-1 subtyping confirmed the circulating recombinant form CRF02_AG as the dominant (53.9%) subtype in the region, with the complex recombinant 06_cpx (4%) present as well. Unique recombinants, most of which were mosaics containing CRF02_AG and/or 06_cpx, made up 37% of sequences, while “pure” subtypes were rare (<6%). Pretreatment resistance to at least one drug class was observed in 17% of the cohort, with NNRTI resistance being the most common (12%) and INSTI resistance being relatively rare (2%). CXCR4-using HIV-1 sequences were identified in 23% of participants. Overall, our findings advance our understanding of HIV-1 molecular epidemiology in Ghana. Extensive HIV-1 genetic diversity in the region appears to be fueling the ongoing creation of novel recombinants, the majority CRF02_AG-containing, in the region. The relatively high prevalence of pretreatment NNRTI resistance but low prevalence of INSTI resistance supports the use of INSTI-based first-line regimens in Ghana.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1–V3, V3–V5) and internal transcribed spacer (ITS1, ITS2) regions. Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. In conclusion, these results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Serum bile acid and unsaturated fatty acid profiles of non-alcoholic fatty liver disease in type 2 diabetic patients

The understanding of bile acid (BA) and unsaturated fatty acid (UFA) profiles, as well as their dysregulation, remains elusive in individuals with type 2 diabetes mellitus (T2DM) coexisting with non-alcoholic fatty liver disease (NAFLD). Investigating these metabolites could offer valuable insights into the pathophy-siology of NAFLD in T2DM. Our aim is to identify potential metabolite biomarkers capable of distinguishing between NAFLD and T2DM. A training model was developed involving 399 participants, comprising 113 healthy controls (HCs), 134 individuals with T2DM without NAFLD, and 152 individuals with T2DM and NAFLD. External validation encompassed 172 participants. NAFLD patients were divided based on liver fibrosis scores. The analytical approach employed univariate testing, orthogonal partial least squares-discriminant analysis, logistic regression, receiver operating characteristic curve analysis, and decision curve analysis to pinpoint and assess the diagnostic value of serum biomarkers. Compared to HCs, both T2DM and NAFLD groups exhibited diminished levels of specific BAs. In UFAs, particular acids exhibited a positive correlation with NAFLD risk in T2DM, while the ω-6:ω-3 UFA ratio demonstrated a negative correlation. Levels of α-linolenic acid and γ-linolenic acid were linked to significant liver fibrosis in NAFLD. The validation cohort substantiated the predictive efficacy of these biomarkers for assessing NAFLD risk in T2DM patients. This study underscores the connection between altered BA and UFA profiles and the presence of NAFLD in individuals with T2DM, proposing their potential as biomarkers in the pathogenesis of NAFLD.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Do Piperonyl Butoxide Long-Lasting Insecticide Treated Nets Provide Additional Protection Against Malaria Infections Compared with Conventional Nets in an Operational Setting in Western Kenya?

Malaria control in sub-Saharan Africa has stagnated despite widespread adoption of control measures such as long-lasting insecticidal nets (LLINs). Progress has stalled, in part, because of pyrethroid insecticide resistance, driving the need for retooling to increase the effectiveness of bed nets. Consequently, LLINs have been treated with the chemical synergist piperonyl butoxide (PBO). Piperonyl butoxide LLINs have been shown to be efficacious in controlled settings; however, their effectiveness in real-world settings warrants investigation. In Bungoma County, Western Kenya, a cohort of 768 participants was followed from June 2017 to December 2023 via active and passive surveillance. Household visits were conducted monthly, during which LLIN use for nets distributed in 2017 and 2021 was recorded, and symptomatic malaria cases were identified using rapid diagnostic tests (RDTs). The comparative effectiveness of PBO versus conventional LLINs was assessed in terms of malaria infections. A multilevel logistic regression model was fit with monthly RDT results as the dependent variable. The study results indicate that PBO LLINs provide greater protection against malaria at the individual level than conventional LLINs (odds ratio: 0.70; 95% CI: 0.47–1.03), although the findings were not statistically significant. The added protection against malaria infections provided by PBO LLINs compared with conventional LLINs observed in the current study aligns with findings from most previous studies, although this finding was not statistically significant. In areas with documented pyrethroid resistance, the use of LLINs with an added synergist, such as PBO, can provide additional protection against malaria infections (compared with pyrethroid-only LLINs) and should be considered for scaled-up scenarios despite the additional cost.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Assessing impacts of selective logging on water, energy, and carbon budgets and ecosystem dynamics in Amazon forests using the Functionally Assembled Terrestrial Ecosystem Simulator

Abstract. Tropical forest degradation from logging, fire, and fragmentation not only alters carbon stocks and carbon fluxes, but also impacts physical land surface properties such as albedo and roughness length. Such impacts are poorly quantified to date due to difficulties in accessing and maintaining observational infrastructures, as well as the lack of proper modeling tools for capturing the interactions among biophysical properties, ecosystem demography, canopy structure, and biogeochemical cycling in tropical forests. As a first step to address these limitations, we implemented a selective logging module into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) by mimicking the ecological, biophysical, and biogeochemical processes following a logging event. The model can specify the timing and aerial extent of logging events, splitting the logged forest patch into disturbed and intact patches; determine the survivorship of cohorts in the disturbed patch; and modifying the biomass and necromass (total mass of coarse woody debris and litter) pools following logging. We parameterized the logging module to reproduce a selective logging experiment at the Tapajós National Forest in Brazil and benchmarked model outputs against available field measurements. Our results suggest that the model permits the coexistence of early and late successional functional types and realistically characterizes the seasonality of water and carbon fluxes and stocks, the forest structure and composition, and the ecosystem succession following disturbance. However, the current version of FATES overestimates water stress in the dry season and therefore fails to capture seasonal variation in latent and sensible heat fluxes. Moreover, we observed a bias towards low stem density and leaf area when compared to observations, suggesting that improvements are needed in both carbon allocation and establishment of trees. The effects of logging were assessed by different logging scenarios to represent reduced impact and conventional logging practices, both with high and low logging intensities. The model simulations suggest that in comparison to old-growth forests the logged forests rapidly recover water and energy fluxes in 1 to 3 years. In contrast, the recovery times for carbon stocks, forest structure, and composition are more than 30 years depending on logging practices and intensity. This study lays the foundation to simulate land use change and forest degradation in FATES, which will be an effective tool to directly represent forest management practices and regeneration in the context of Earth system models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Inclusion of a cold hardening scheme to represent frost tolerance is essential to model realistic plant hydraulics in the Arctic–boreal zone in CLM5.0-FATES-Hydro

As temperatures decrease in autumn, vegetation of temperate and boreal ecosystems increases its tolerance to freezing. This process, known as hardening, results in a set of physiological changes at the molecular level that initiate modifications of cell membrane composition and the synthesis of anti-freeze proteins. Together with the freezing of extracellular water, anti-freeze proteins reduce plant water potentials and xylem conductivity. To represent the responses of vegetation to climate change, land surface schemes increasingly employ “hydrodynamic” models that represent the explicit fluxes of water from soil and through plants. The functioning of such schemes under frozen soil conditions, however, is poorly understood. Nonetheless, hydraulic processes are of major importance in the dynamics of these systems, which can suffer from, e.g., winter “frost drought” events. In this study, we implement a scheme that represents hardening into CLM5.0-FATES-Hydro. FATES-Hydro is a plant hydrodynamics module in FATES, a cohort model of vegetation physiology, growth, and dynamics hosted in CLM5.0. We find that, in frozen systems, it is necessary to introduce reductions in plant water loss associated with hardening to prevent winter desiccation. This work makes it possible to use CLM5.0-FATES-Hydro to model realistic impacts from frost droughts on vegetation growth and photosynthesis, leading to more reliable projections of how northern ecosystems respond to climate change.

58 GEOSCIENCES↗