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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Polar algae flaunt their zinc assets

Metal ions have been at the centre of pivotal points in the evolution of extant life. Oxygen-evolving photosynthesis, which irrevocably reshaped the geochemistry and biology of our planet, has an absolute requirement for metal ions to harvest light, split water and transfer electrons. Access to abundant oxygen then led to the propagation of organisms capable of oxidative metabolism, a process that is also dependent on metal ions for electron transfer and reduction of molecular oxygen. Because of the essential links between metal ions and the proteins that require them to function, as well as changes in metal bioavailability through time, metals have shaped the trajectories that evolution can take. Iron typically steals this show, but with access to whole-genome sequences and transcriptomes, the imprint that zinc has made on biology is coming into focus. Writing in Nature Ecology & Evolution, Ye and colleagues present new insights into the complex connections between zinc bioavailability, adaptation of algae to the polar oceans and the evolution of regulatory networks. By combining field and laboratory-based analyses, the authors suggest that expanded families of zinc-binding proteins have enabled the green alga Microglena sp. YARC to flourish in the harsh conditions of the polar Southern Ocean (Fig. 1). As the waters where this alga occurs are known for their enrichment of zinc, the authors further propose that availability of this metal ion was directly responsible for successful microalgal colonization of polar oceans. To test this hypothesis, the authors compare meta-transcriptomes collected from pole-to-pole and find positive correlations between higher copy numbers for transcripts encoding putative zinc-binding proteins, higher latitudes, lower surface temperatures and dissolved zinc.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO 2 -driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus “Altiarchaeum sp.” and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. “Altiarchaeum”. Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N 2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth’s environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Human age and skin physiology shape diversity and abundance of Archaea on skin

The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or younger than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. In conclusion, amplicon sequencing of selected samples revealed the prevalence of specific eury- and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Spatial complexity of carcass location influences vertebrate scavenger efficiency and species composition

Scavenging plays an important role in shaping communities through inter- and intra-specific interactions. Although vertebrate scavenger efficiency and species composition is likely influenced by the spatial complexity of environments, heterogeneity in carrion distribution has largely been disregarded in scavenging studies. We tested this hypothesis by experimentally placing juvenile bird carcasses on the ground and in nests in trees to simulate scenarios of nestling bird carrion availability. We used cameras to record scavengers removing carcasses and elapsed time to removal. Carrion placed on the ground was scavenged by a greater diversity of vertebrates and at > 2 times the rate of arboreal carcasses, suggesting arboreal carrion may represent an important resource to invertebrate scavengers, particularly in landscapes with efficient vertebrate scavenging communities. Nonetheless, six vertebrate species scavenged arboreal carcasses. Rat snakes (Elaphe obsolete), which exclusively scavenged from trees, and turkey vultures (Cathartes aura) were the primary scavengers of arboreal carrion, suggesting such resources are potentially an important pathway of nutrient acquisition for some volant and scansorial vertebrates. Our results highlight the intricacy of carrion-derived food web linkages, and how consideration of spatial complexity in carcass distribution (i.e., arboreal) may reveal important pathways of nutrient acquisition by invertebrate and vertebrate scavenging guilds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Improving membrane protein expression and function using genomic edits

Expression of membrane proteins often leads to growth inhibition and perturbs central metabolism and this burden varies with the protein being overexpressed. There are also known strain backgrounds that allow greater expression of membrane proteins but that differ in efficacy across proteins. Here, we hypothesized that for any membrane protein, it may be possible to identify a modified strain background where its expression can be accommodated with less burden. To directly test this hypothesis, we used a bar-coded transposon insertion library in tandem with cell sorting to assess genome-wide impact of gene deletions on membrane protein expression. The expression of five membrane proteins (CyoB, CydB, MdlB, YidC, and LepI) and one soluble protein (GST), each fused to GFP, was examined. We identified Escherichia coli mutants that demonstrated increased membrane protein expression relative to that in wild type. For two of the proteins (CyoB and CydB), we conducted functional assays to confirm that the increase in protein expression also led to phenotypic improvement in function. This study represents a systematic approach to broadly identify genetic loci that can be used to improve membrane protein expression, and our method can be used to improve expression of any protein that poses a cellular burden.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Unusually warm Indian Ocean sea surface temperatures help to arrest development of El Nino in 2014

In early 2014, strong westerly wind bursts (WWBs) and high heat content in the equatorial Pacific favored development of a major El Niño. However, significant coupling between the Pacific Ocean and atmosphere failed to take hold during boreal summer of 2014 such that only borderline El Niño conditions were evident by the end of the year. Observational analysis suggests that warm sea surface temperatures (SSTs) in the Indian Ocean in 2014 weakened westerly wind anomalies in the Pacific and may have helped to arrest the development of the El Niño. We test this hypothesis using an ensemble of coupled numerical experiments in which observed Indian Ocean SST anomalies in 2014–15 are prescribed but the Pacific Ocean-atmosphere system is free to evolve. Results confirm that warm SST anomalies in the Indian Ocean created conditions that would have favored a weakening of El Niño by suppressing the Bjerknes feedback in boreal summer of 2014. Furthermore, this process does not preclude others that have been proposed in the unusual evolution of El Niño SSTs in 2014, but it adds to the list a forcing mechanism external to the Pacific basin.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Increased mechanical loading through controlled swimming exercise induces bone formation and mineralization in adult zebrafish

Exercise promotes gain in bone mass through adaptive responses of the vertebrate skeleton. This mechanism counteracts age- and disease-related skeletal degradation, but remains to be fully understood. In life sciences, zebrafsh emerged as a vertebrate model that can provide new insights into the complex mechanisms governing bone quality. To test the hypothesis that musculoskeletal exercise induces bone adaptation in adult zebrafsh and to characterize bone reorganization, animals were subjected to increased physical exercise for four weeks in a swim tunnel experiment. Cellular, structural and compositional changes of loaded vertebrae were quantifed using integrated high-resolution analyses. Exercise triggered rapid bone adaptation with substantial increases in bone-forming osteoblasts, bone volume and mineralization. Clearly, modeling processes in zebrafsh bone resemble processes in human bone. This study highlights how exercise experiments in adult zebrafsh foster in-depth insight into aging-related bone diseases and can thus catalyze the search for appropriate prevention and new treatment options.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Cu Transport by the Extended Family of CcoA-like Transporters (CalT) in Proteobacteria

Comparative genomic studies of the bacterial MFS-type copper importer CcoA, required for cbb 3 -type cytochrome c oxidase (cbb 3 -Cox) biogenesis, revealed a widespread CcoA-like transporters (CalT) family, containing the conserved CcoA Cu-binding MxxxM and HxxxM motifs. Surprisingly, this family also included the RfnT-like proteins, earlier suggested to transport riboflavin. However, presence of the Cu-binding motifs in these proteins raised the possibility that they might be Cu transporters. To test this hypothesis, the genomic context of the corresponding genes was examined, and three of such genes from Ochrobactrum anthropi , Rhodopseudomonas palustris and Agrobacterium tumefaciens were expressed in Escherichia coli (ΔribB) and Rhodobacter capsulatus (ΔccoA) mutants. Copper and riboflavin uptake abilities of these strains were compared with those expressing R. capsulatus CcoA and Rhizobium leguminosarum RibN as bona fide copper and riboflavin importers, respectively. Altogether data demonstrated that the “RfnT-like” CalT proteins are unable to efficiently transport riboflavin, but they import copper like CcoA. Nevertheless, even though expressed and membrane-localized in a R. capsulatus mutant lacking CcoA, these transporters were unable to accumulate Cu or complement for cbb 3 -Cox defect. This lack of functional exchangeability between the different subfamilies of CalT homologs suggests that MFS-type bacterial copper importers might be species-specific.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Functional compartmentalization in the hemocoel of insects

The insect circulatory system contains an open hemocoel, in which the mechanism of hemolymph flow control is ambiguous. As a continuous fluidic structure, this cavity should exhibit pressure changes that propagate quickly. Narrow-waisted insects create sustained pressure differences across segments, but their constricted waist provides an evident mechanism for compartmentalization. Insects with no obvious constrictions between segments may be capable of functionally compartmentalizing the body, which could explain complex hemolymph flows. Here, we test the hypothesis of functional compartmentalization by measuring pressures in a beetle and recording abdominal movements. We found that the pressure is indeed uniform within the abdomen and thorax, congruent with the predicted behavior of an open system. However, during some abdominal movements, pressures were on average 62% higher in the abdomen than in the thorax, suggesting that functional compartmentalization creates a gradient within the hemocoel. Synchrotron tomography and dissection show that the arthrodial membrane and thoracic muscles may contribute to this dynamic pressurization. Analysis of volume change suggests that the gut may play an important role in regulating pressure by translating between body segments. Overall, this study suggests that functional compartmentalization may provide an explanation for how fluid flows are managed in an open circulatory system.

Science & Technology - Other Topics↗
DOE OSTI2025

Novel adaptive immune systems in pristine Antarctic soils

Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The time since land-use transition drives changes in fire activity in the Amazon-Cerrado region

Abstract Deforestation and climate change are expected to alter fire regimes along the Cerrado-Amazon transition, one of the world’s most active agricultural frontiers. Here we tested the hypothesis that the time since land-use transition (age of frontier) and agricultural intensification also drive changes in the region’s fire regimes by reducing fire probability in both drought and non-drought years. We modeled fire probability as a function of the time since land-use transitions based on MapBiomas Project datasets from 1986 to 2020. We find that, while burned area declined as pasturelands aged and croplands advanced, deforestation abruptly increased fire activity before (Amazon: 4 years; Cerrado: 3 years) and after (Amazon: 8 years; Cerrado: 7 years) land clearing for pasture, especially in the Amazon. Additionally, the combination of ignition risk, drought, and air-dryness increased the likelihood of large extents of burned areas associated with deforestation. Incorporating frontier age as a proxy for governance in fire modeling is crucial, given the ecological implications of changing fire regimes despite declining rates of fire probability. Most importantly, protecting against deforestation and preserving native vegetation are vital.

Environmental Sciences & Ecology↗
DOE OSTI2016

Intrinsic mechanical behavior of femoral cortical bone in young, osteoporotic and bisphosphonate-treated individuals in low- and high energy fracture conditions

Bisphosphonates are a common treatment to reduce osteoporotic fractures. This treatment induces osseous structural and compositional changes accompanied by positive effects on osteoblasts and osteocytes. Here, we test the hypothesis that restored osseous cell behavior, which resembles characteristics of younger, healthy cortical bone, leads to improved bone quality. Microarchitecture and mechanical properties of young, treatment-naïve osteoporosis, and bisphosphonate-treated cases were investigated in femoral cortices. Tissue strength was measured using three-point bending. Collagen fibril-level deformation was assessed in non-traumatic and traumatic fracture states using synchrotron small-angle x-ray scattering (SAXS) at low and high strain rates. The lower modulus, strength and fibril deformation measured at low strain rates reflects susceptibility for osteoporotic low-energy fragility fractures. Independent of age, disease and treatment status, SAXS revealed reduced fibril plasticity at high strain rates, characteristic of traumatic fracture. We find the significantly reduced mechanical integrity in osteoporosis may originate from porosity and alterations to the intra/extrafibrillar structure, while the fibril deformation under treatment indicates improved nano-scale characteristics. In conclusion, losses in strength and fibril deformation at low strain rates correlate with the occurrence of fragility fractures in osteoporosis, while improvements in structural and mechanical properties following bisphosphonate treatment may foster resistance to fracture during physiological strain rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. As a result, this work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Ecosystem Composition Controls the Fate of Rare Earth Elements during Incipient Soil Genesis

The rare earth elements (REE) are increasingly important in a variety of science and economic fields, including (bio)geosciences, paleoecology, astrobiology, and mining. However, REE distribution in early rock-microbe-plant systems has remained elusive. We tested the hypothesis that REE mass-partitioning during incipient weathering of basalt, rhyolite, granite and schist depends on the activity of microbes, vascular plants (Buffalo grass), and arbuscular mycorrhiza. Pore-water element abundances revealed a rapid transition from abiotic to biotic signatures of weathering, the latter associated with smaller aqueous loss and larger plant uptake. Abiotic dissolution was 39% of total denudation in plant-microbes-mycorrhiza treatment. Microbes incremented denudation, particularly in rhyolite, and this resulted in decreased bioavailable solid pools in this rock. Total mobilization (aqueous + uptake) was ten times greater in planted compared to abiotic treatments, REE masses in plant generally exceeding those in water. Larger plants increased bioavailable solid pools, consistent with enhanced soil genesis. Mycorrhiza generally had a positive effect on total mobilization. The main mechanism behind incipient REE weathering was carbonation enhanced by biotic respiration, the denudation patterns being largely dictated by mineralogy. A consistent biotic signature was observed in La:phosphate and mobilization: solid pool ratios, and in the pattern of denudation and uptake.

58 GEOSCIENCES↗
DOE OSTI2017

Albedo feedbacks to future climate via climate change impacts on dryland biocrusts

Drylands represent the planet’s largest terrestrial biome and evidence suggests these landscapes have large potential for creating feedbacks to future climate. Recent studies also indicate that dryland ecosystems are responding markedly to climate change. Biological soil crusts (biocrusts) - soil surface communities of lichens, mosses, and/or cyanobacteria - comprise up to 70% of dryland cover and help govern fundamental ecosystem functions, including soil stabilization and carbon uptake. Drylands are expected to experience significant changes in temperature and precipitation regimes, and such alterations may impact biocrust communities by promoting rapid mortality of foundational species. In turn, biocrust community shifts affect land surface cover and roughness—changes that can dramatically alter albedo. We tested this hypothesis in a full-factorial warming (+4 °C above ambient) and altered precipitation (increased frequency of 1.2 mm monsoon-type watering events) experiment on the Colorado Plateau, USA. We quantified changes in shortwave albedo via multi-angle, solar-reflectance measurements. Warming and watering treatments each led to large increases in albedo (>30%). This increase was driven by biophysical factors related to treatment effects on cyanobacteria cover and soil surface roughness following treatment-induced moss and lichen mortality. A rise in dryland surface albedo may represent a previously unidentified feedback to future climate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Metabolic spatial variability in electrode-respiring Geobacter sulfurreducens biofilms

Certain bacteria are capable of transferring electrons derived from respiratory metabolism to solid extracellular electron-accepting materials1-4. This ability allows the organisms to use conductive substrata as their sole electron sink, generating electricity that is available for practical applications5-7. Geobacter is a biofilm-forming genus capable of this extracellular electron transfer8-11. Evidence in the literature suggests that Geobacter cells produce a conductive matrix to gain access to electron-accepting surfaces12,13. It has been hypothesized that cells that are more than tens of microns from the electron-accepting surface cannot respire because of electrical resistance in the matrix and thus remain metabolically inactive14-16. To test this hypothesis, we sought to determine whether the entire biofilm remains metabolically active and able to respire on an electron-accepting surface as the biofilm thickness increases. We developed and used a novel electrochemical-nuclear magnetic resonance (EC-NMR) microimaging system capable of sustaining an electrochemically active biofilm on a polarized electrode inside a superconducting magnet, allowing for simultaneous NMR and electrochemical investigation of a biofilm for the first time. Here, we show that Geobacter biofilms can grow to several hundred microns thick while respiring on an electrode and that the top of the biofilm remains metabolically active. This is only possible if the cells near the top are able to transfer electrons through the initial biofilm matrix to the electrode. We used X-ray absorption spectroscopy to verify electron transfer to uranium ions by metabolically active cells near the top of the biofilm. Our results reveal that extracellular electron transfer is not prevented by electrical resistance, even when the biofilm is hundreds of microns thick. Furthermore, the electron donor may be the limiting factor for respiration and the base of the biofilm may be less active despite being in close proximity to the electrode. Long-range electron transfer across metabolically inactive regions within Geobacter biofilms adds a novel facet to our comprehension of electrochemically active biology.

ANODE↗
DOE OSTI2017

Zinc sparks induce physiochemical changes in the egg zona pellucida that prevent polyspermy

During fertilization or chemically-induced egg activation, the mouse egg releases billions of zinc atoms in brief bursts known as ‘zinc sparks.’ The zona pellucida (ZP), a glycoprotein matrix surrounding the egg, is the first structure zinc ions encounter as they diffuse away from the plasma membrane. Following fertilization, the ZP undergoes changes described as ‘hardening’, which prevent multiple sperm from fertilizing the egg and thereby establish a block to polyspermy. A major event in zona hardening is cleavage of ZP2 proteins by ovastacin; however, the overall physiochemical changes contributing to zona hardening are not well understood. Using x-ray fluorescence microscopy, transmission and scanning electron microscopy, and biological function assays, we tested the hypothesis that zinc release contributes to ZP hardening. We found that the zinc content in the ZP increases by 300% following activation and that zinc exposure modulates the architecture of the ZP matrix. Importantly, zinc-induced structural changes of the ZP have a direct biological consequence; namely, they reduce the ability of sperm to bind to the ZP. These results provide a paradigm-shifting model in which fertilization-induced zinc sparks contribute to the polyspermy block by altering conformations of the ZP matrix. Finally, this adds a previously unrecognized factor, namely zinc, to the process of ZP hardening.

59 BASIC BIOLOGICAL SCIENCES↗