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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

KBase Narrative - Comparing Proteomes of Cupriavidus basilensis 4G11 and Cupriavidus necator H16

Species of Cupriavidus are among the best bioplastic producing microorganisms known, though intracellular poly-hydroxybutyrate (PHB) is made exclusively during unbalanced growth (e.g. nitrogen limitation), a state characterized by poor growth and cellular stress. Much work has been done studying bioplastic production in the model/type strain C. necator H16. We use an RB-TnSeq library of the closely related C. basilensis 4G11 to assess for genes which decouple PHB production from growth state. In this narrative we compute genome-wide protein homology between these two organisms, and generate a synteny plot across the genomes as well.

Sander, Kyle↗
DOE OSTI2023

An efficient virus–induced gene silencing (VIGS) system for gene functional studies in Miscanthus

Virus-induced gene silencing (VIGS) is a powerful tool for transient gene functional analysis in plants, especially for monocot species (e.g., grasses) that are recalcitrant to transformation. Despite various VIGS systems that have been developed in different plant species, none was previously available for the bioenergy crop Miscanthus. Here, we report the establishment of an efficient and robust VIGS system mediated by Tobacco Rattle Virus (TRV) in Miscanthus. We first investigated the impact of various factors that may affect gene silencing efficiency using the Miscanthus sinensis Phytoene Desaturase (MsPDS) gene as a visual indicator of photobleaching. Then, we optimized the TRV-elicited VIGS procedure using an orthogonal experimental design with four factors (sprout size, Agrobacterium concentration, vacuum infiltration time, and co-incubation time) each at three levels. The following led to the highest silencing efficiency (~76%): inoculation of germinating seedlings (1.0–2.0 mm), Agrobacterium tumefaciens culture grown to optical density at 600 nm (OD 600 ) of 0.4, vacuum infiltration for 90 min, and co-incubation for 5 h. The VIGS system established was applicable for both M. sinensis and M. lutarioriparius, with comparable gene silencing efficiency. We verified the efficacy of the VIGS system via the functional characterization of the role of a MYB transcription factor, MsMYB112, in salt stress tolerance. Expression of MsMYB112 was successfully knocked down using the VIGS system, and this led to compromised salt tolerance in the silenced Miscanthus plants. The TRV-based VIGS system established may, therefore, substantially facilitate functional genomic studies in Miscanthus.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation

Abstract Knowing how switchgrass ( Panicum virgatum L . ) responds and adapts to phosphorus (P)‐limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P‐stress on genome transcription and whole‐plant metabolism, physiology and development in switchgrass. P‐limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P‐stress, and decreased root diameter with increased density and length of root hairs at severe P‐stress. RNA‐seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P‐stress in roots and/or shoots compared to P‐replete plants, with many stress‐induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P‐acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P‐stress in shoots and roots, although this trend reversed under severe P‐stress, especially in shoots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Hemiptera phylogenomic resources: Tree‐based orthology prediction and conserved exon identification

Abstract High‐throughput sequencing of transcriptomes and targeted genomic regions are advancing our knowledge of The Tree of Life. Building phylogenies with regions of the genome requires 1‐to‐1 orthologue resources of genes and noncoding loci. One organismal group that has received little attention in this area is the Hemiptera, the fifth largest insect order represented by ~103,590 named species. Here, we present a set of 3,872 Hemiptera 1‐to‐1 orthogroups based on tree‐based orthology inference of eight Hemiptera species with publicly available genome sequences. We also estimate a set of 406 orthologous exons with similar mRNA splice sites that can be used for Sanger sequencing and develop enrichment probes for targeted genome sequencing for phylogenomic inference. We show this novel set of orthologues is informative at the protein, coding sequence and exon molecular levels and provides robust branch support in both gene tree–species tree methods and concatenated sequence phylogenies. In addition, we demonstrate the utility of these loci to resolve relationships in whiteflies, Bemisia tabaci , a large species complex with few phylogenomic resources. Last, we compare our Hemiptera phylogeny with previously published phylogenies and other orthologue databases, while providing suggestions on further improvement to this phylogenomic resource.

Owen, Christopher L.↗
DOE OSTI2023

DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Summary Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 ( DDM1 ) and two demethylases DEMETER‐LIKE ( DML ) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor . We compared the ectomycorrhizas formed between transgenic and wild‐type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi‐ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX‐ dml and RNAi‐ ddm1 ) and 120 genes/1441 TEs in the fungal genome suggesting a host‐induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes ( cis and trans effects) in common with 17 being differentially methylated ( cis ). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate‐mediated pathways, and immune response but also terpenoid metabolism.

Vigneaud, Julien↗
DOE OSTI2020

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.

Microbiology↗
DOE OSTI2020

Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms

Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched ß-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) employed secondary metabolite (SM) synthesis in response to a competitor, as shown by the upregulation of several SM-synthesizing genes in the interaction. R. placenta (Antrodia clade) instead upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that an oxidative burst may be a response to competitors in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving abundant unknowns on the battlefield. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure of Lipopolysaccharide from Liberibacter crescens Is Low Molecular Weight and Offers Insight into Candidatus Liberibacter Biology

Huanglongbing (HLB) disease, also known as citrus greening disease, was first reported in the US in 2005. Since then, the disease has decimated the citrus industry in Florida, resulting in billions of dollars in crop losses and the destruction of thousands of acres of citrus groves. The causative agent of citrus greening disease is the phloem limited pathogen Candidatus Liberibacter asiaticus. As it has not been cultured, very little is known about the structural biology of the organism. Liberibacter are part of the Rhizobiaceae family, which includes nitrogen-fixing symbionts of legumes as well as the Agrobacterium plant pathogens. To better understand the Liberibacter genus, a closely related culturable bacterium (Liberibacter crescens or Lcr) has attracted attention as a model organism for structural and functional genomics of Liberibacters. Given that the structure of lipopolysaccharides (LPS) from Gram-negative bacteria plays a crucial role in mediating host-pathogen interactions, we sought to characterize the LPS from Lcr. We found that the major lipid A component of the LPS consisted of a pentaacylated molecule with a β-6-GlcN disaccharide backbone lacking phosphate. The polysaccharide portion of the LPS was unusual compared to previously described members of the Rhizobiaceae family in that it contained ribofuranosyl residues. The LPS structure presented here allows us to extrapolate known LPS structure/function relationships to members of the Liberibacter genus which cannot yet be cultured. It also offers insights into the biology of the organism and how they manage to effectively attack citrus trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Deletion of African Swine Fever Virus Histone-like Protein, A104R from the Georgia Isolate Drastically Reduces Virus Virulence in Domestic Pigs

African swine fever virus (ASFV) is the etiological agent of a frequently lethal disease, ASF, affecting domestic and wild swine. Currently, ASF is causing a pandemic affecting pig production in Eurasia. There are no vaccines available, and therefore control of the disease is based on culling infected animals. We report here that deletion of the ASFV gene A104R, a virus histone-like protein, from the genome of the highly virulent ASFV-Georgia2010 (ASFV-G) strain induces a clear decrease in virus virulence when experimentally inoculated in domestic swine. A recombinant virus lacking the A104R gene, ASFV-G-ΔA104R, was developed to assess the role of the A104R gene in disease production in swine. Domestic pigs were intramuscularly inoculated with 10 2 HAD 50 of ASFV-G-ΔA104R, and compared with animals that received a similar dose of virulent ASFV-G. While all ASFV-G inoculated animals developed a fatal form of the disease, animals receiving ASFV-G-ΔA104R survived the challenge, remaining healthy during the 28-day observational period, with the exception of only one showing a protracted but fatal form of the disease. ASFV-G-ΔA104R surviving animals presented protracted viremias with reduced virus titers when compared with those found in animals inoculated with ASFV-G, and all of them developed a strong virus-specific antibody response. This is the first report demonstrating that the A104R gene is involved in ASFV virulence in domestic swine, suggesting that A104R deletion may be used to increase the safety profile of currently experimental vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genetic variation associated with adult migration timing in lineages of Steelhead and Chinook Salmon in the Columbia River

Abstract With the discovery of a major effect region (GREB1L, ROCK1) for adult migration timing in genomes of both Chinook Salmon and Steelhead, several subsequent studies have investigated the effect size and distribution of early and late migration alleles among populations in the Columbia River. Here, we synthesize the results of these studies for the major lineages of Chinook Salmon and Steelhead that include highly distinct groups in the interior Columbia River that exhibit atypical life histories from most coastal lineage populations of these two species. Whole‐genome studies with high marker density have provided extensive insight into SNPs most associated with adult migration timing, and suites of markers for each species have been genotyped in large numbers of individuals to further validate phenotypic effects. For Steelhead, the largest phenotypic effect sizes have been observed in the coastal lineage (36% of variation for passage timing at Bonneville Dam; 43% of variation for tributary arrival timing) compared to the inland lineage (7.5% of variation for passage timing at Bonneville Dam; 8.4% of variation for tributary arrival timing) that overwinter in freshwater prior to spawning. For Chinook Salmon, large effect sizes have been observed in all three lineages for multiple adult migration phenotypes (Coastal lineage: percentage of variation of 27.9% for passage timing at Bonneville Dam, 28.7% for arrival timing for spawning; Interior ocean type: percentage of variation of 47.6% for passage timing at Bonneville Dam, 39.6% for tributary arrival timing, 77.9% for arrival timing for spawning; Interior stream type: percentage of variation of 35.3% for passage at Bonneville Dam, 9.8% for tributary arrival timing, 4.7% for arrival timing for spawning). Together, these results have extended our understanding of genetic variation associated with life history diversity in distinct populations of the Columbia River, however, much research remains necessary to determine the causal mechanism for this major effect region on migration timing in these species.

Narum, Shawn R.↗
DOE OSTI2020

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Abstract Through advanced mechanistic modeling and the generation of large high-quality datasets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show that mechanistic and machine learning models can be combined to enable accurate genotype-to-phenotype predictions. We use a genome-scale model to pinpoint engineering targets, efficient library construction of metabolic pathway designs, and high-throughput biosensor-enabled screening for training diverse machine learning algorithms. From a single data-generation cycle, this enables successful forward engineering of complex aromatic amino acid metabolism in yeast, with the best machine learning-guided design recommendations improving tryptophan titer and productivity by up to 74 and 43%, respectively, compared to the best designs used for algorithm training. Thus, this study highlights the power of combining mechanistic and machine learning models to effectively direct metabolic engineering efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

Background: Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. Results: In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls. Conclusion: Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mutations that confer resistance to broadly-neutralizing antibodies define HIV-1 variants of transmitting mothers from that of non-transmitting mothers

Despite considerable reduction of mother-to-child transmission (MTCT) of HIV through use of maternal and infant antiretroviral therapy (ART), over 150,000 infants continue to become infected with HIV annually, falling far short of the World Health Organization goal of reaching <20,000 annual pediatric HIV cases worldwide by 2020. Prior to the widespread use of ART in the setting of pregnancy, over half of infants born to HIV-infected mothers were protected against HIV acquisition. Yet, the role of maternal immune factors in this protection against vertical transmission is still unclear, hampering the development of synergistic strategies to further reduce MTCT. It has been established that infant transmitted/founder (T/F) viruses are often resistant to maternal plasma, yet it is unknown if the neutralization resistance profile of circulating viruses predicts the maternal risk of transmission to her infant. In this study, we amplified HIV-1 envelope genes ( env ) by single genome amplification and produced representative Env variants from plasma of 19 non-transmitting mothers from the U.S. Women Infant Transmission Study (WITS), enrolled in the pre-ART era. Maternal HIV Env variants from non-transmitting mothers had similar sensitivity to autologous plasma as observed for non-transmitting variants from transmitting mothers. In contrast, infant variants were on average 30% less sensitive to paired plasma neutralization compared to non-transmitted maternal variants from both transmitting and non-transmitting mothers (p = 0.015). Importantly, a signature sequence analysis revealed that motifs enriched in env sequences from transmitting mothers were associated with broadly neutralizing antibody (bnAb) resistance. Altogether, our findings suggest that circulating maternal virus resistance to bnAb-mediated neutralization, but not autologous plasma neutralization, near the time of delivery, predicts increased MTCT risk. These results caution that enhancement of maternal plasma neutralization through passive or active vaccination during pregnancy may potentially drive the evolution of variants fit for vertical transmission.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism

Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism based on its genomic sequence and associated data. The model includes 1773 genes, 3025 reactions, and 1956 metabolites, was developed in a reproducible manner using CarveMe, and was evaluated through Metabolic Model tests (MEMOTE). We combine the model with two Constraint-Based Reconstruction and Analysis (COBRA) methods that use transcriptomics data to predict growth rates and fluxes: E-Flux2 and SPOT (Simplified Pearson Correlation with Transcriptomic data). Growth rates are best predicted by E-Flux2. Flux profiles are more accurately predicted by E-Flux2 than flux balance analysis (FBA) and parsimonious FBA (pFBA), when compared to 44 central carbon fluxes measured by 13C-Metabolic Flux Analysis (13C-MFA). Under glucose-fed conditions, E-Flux2 presents an R2 value of 0.54, while predictions based on pFBA had an inferior R2 of 0.28. We attribute this improved performance to the extra activity information provided by the transcriptomics data. For phenol-fed metabolism, in which the substrate first enters the TCA cycle, E-Flux2’s flux predictions display a high R2 of 0.96 while pFBA showed an R2 of 0.93. We also show that glucose metabolism and phenol metabolism function with similar relative ATP maintenance costs. These findings demonstrate that iGR1773 can help the metabolic engineering community predict aromatic substrate utilization patterns and perform computational strain design.

Roell, Garrett W.↗
DOE OSTI2021

Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity

How soil is managed, particularly for agriculture, exerts stresses upon soil microbiomes, resulting in altered community structures and functional states. Understanding how soil microbiomes respond to combined stresses is important for predicting system performance under different land use scenarios, aids in identification of the most environmentally benign managements, and provides insight into how system function can be recovered in degraded soils. We use a long-established field experiment to study the effects of combined chronic (press) disturbance of the magnitude of organic carbon inputs with acute (pulse) effects of physical disturbance by tillage and chemical disturbance due to inorganic fertilization and pesticide application. We show that because of the variety of ways it can be assessed, biodiversity—here based on microbial small subunit rRNA gene phylotypes—does not provide a consistent view of community change. In contrast, aggregated traits associated with soil microbiomes indicate general loss of function, measured as a reduction of average genome lengths, associated with chronic reduction of organic inputs in arable or bare fallow soils and altered growth strategies associated with rRNA operon copy number in prokaryotes, as well as a switch to pathogenicity in fungal communities. In addition, pulse disturbance by soil tillage is associated with an increased influence of stochastic processes upon prokaryote community assembly, but fungicide used in arable soils results in niche assembly of fungal communities compared to untilled grassland. Overall, bacteria, archaea, and fungi do not share a common response to land management change, and estimates of biodiversity do not capture important facets of community adaptation to stresses adequately.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Life history strategies of soil bacterial communities across global terrestrial biomes

The life history strategies of soil microbes determine their metabolic potential and their response to environmental changes. Yet these strategies remain poorly understood. Here we use shotgun metagenomes from terrestrial biomes to characterize overarching covariations of the genomic traits that capture dominant life history strategies in bacterial communities. The emerging patterns show a triangle of life history strategies shaped by two trait dimensions, supporting previous theoretical and isolate-based studies. The first dimension ranges from streamlined genomes with simple metabolisms to larger genomes and expanded metabolic capacities. As metabolic capacities expand, bacterial communities increasingly differentiate along a second dimension that reflects a trade-off between increasing capacities for environmental responsiveness or for nutrient recycling. Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution. Finally, our findings provide a trait-based framework to compare life history strategies of soil bacteria.

59 BASIC BIOLOGICAL SCIENCES↗