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At least 613 records · Page 34

Microbial carbon use efficiency promotes global soil carbon storage

Soils store more carbon than other terrestrial ecosystems. How soil organic carbon (SOC) forms and persists remains uncertain, which makes it challenging to understand how it will respond to climatic change. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Optogenetics Illuminates Applications in Microbial Engineering

Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe–host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Lastly, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Positive correlations between soil C stabilization and loss are regulated by roots, minerals, and microbes

Modern conceptual models of soil organic carbon (SOC) cycling place a strong focus on the microbe-mineral interactions that regulate C stabilization. However, the formation of ‘stable’ soil organic matter, which consists mainly of microbial residues bonded to mineral surfaces, is inextricably linked to C loss through microbial respiration. Therefore, what is the net impact of microbial metabolism on the total quantity of C held in the soil? To address this question, we constructed artificial root-soil systems to identify controls on C cycling across the plant-microbe-mineral continuum, simultaneously quantifying the formation of persistent mineral-associated C and C losses to respiration. Roots and minerals interacted to regulate these processes: while roots stimulated respiratory C losses and depleted mineral-associated C pools in low-activity clays, roots triggered formation of stable C in high-activity clays. Moreover, we observed a strong positive correlation between the formation of mineral-associated C and respiration. This suggests that the growth of persistent C pools which can resist subsequent disturbance comes at the expense of C loss from the system.

58 GEOSCIENCES↗

Beyond microbes: Are fauna the next frontier in soil biogeochemical models?

The explicit representation of microbial communities in soil biogeochemical models is improving their projections, promoting new interdisciplinary research, and stimulating novel theoretical developments. However, microbes are the foundation of complicated soil food webs, with highly intricate and non-linear interactions among trophic groups regulating soil biogeochemical cycles. This food web includes fauna, which influence litter decomposition and the structure and activity of the microbial community. Given the early success of microbial-explicit models, should we also consider explicitly representing faunal activity and physiology in soil biogeochemistry models? Herein we explore this question, arguing that the direct effects of fauna on litter decomposition are stronger than on soil organic matter dynamics, and that fauna can have strong indirect effects on soil biogeochemical cycles by influencing microbial population dynamics, but the direction and magnitude of these effects remains too unpredictable for models used to predict global biogeochemical patterns. Given glaring gaps in our understanding of fauna-microbe interactions and how these might play out along climatic and land use gradients, we believe it remains early to explicitly represent fauna in these global-scale models. However, their incorporation into models used for conceptual exploration of food-web interactions or into ecosystem-scale models using site-specific data could provide rich theoretical breakthroughs and provide a starting point for improving model projections across scales.

59 BASIC BIOLOGICAL SCIENCES↗

Decreased growth of wild soil microbes after 15 years of transplant‐induced warming in a montane meadow

Abstract The carbon stored in soil exceeds that of plant biomass and atmospheric carbon and its stability can impact global climate. Growth of decomposer microorganisms mediates both the accrual and loss of soil carbon. Growth is sensitive to temperature and given the vast biological diversity of soil microorganisms, the response of decomposer growth rates to warming may be strongly idiosyncratic, varying among taxa, making ecosystem predictions difficult. Here, we show that 15 years of warming by transplanting plant–soil mesocosms down in elevation, strongly reduced the growth rates of soil microorganisms, measured in the field using undisturbed soil. The magnitude of the response to warming varied among microbial taxa. However, the direction of the response—reduced growth—was universal and warming explained twofold more variation than did the sum of taxonomic identity and its interaction with warming. For this ecosystem, most of the growth responses to warming could be explained without taxon‐specific information, suggesting that in some cases microbial responses measured in aggregate may be adequate for climate modeling. Long‐term experimental warming also reduced soil carbon content, likely a consequence of a warming‐induced increase in decomposition, as warming‐induced changes in plant productivity were negligible. The loss of soil carbon and decreased microbial biomass with warming may explain the reduced growth of the microbial community, more than the direct effects of temperature on growth. These findings show that direct and indirect effects of long‐term warming can reduce growth rates of soil microbes, which may have important feedbacks to global warming.

54 ENVIRONMENTAL SCIENCES↗

Remarkably coherent population structure for a dominant Antarctic Chlorobium species

Background: In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby “feeding” ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. Results: A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 10 8 cells ml –1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. Conclusion: The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species.

59 BASIC BIOLOGICAL SCIENCES↗

Mercury methylation potential in a sand dune on Lake Michigan's eastern shoreline

Lake Michigan hosts the largest freshwater sand dune system in the world and is economically important for the fishery industry and tourism. Due to industrial pollution and atmospheric mercury (Hg) deposition, toxic levels of methylmercury (MeHg) have been found in the Lake biota, but little information is known regarding MeHg sources and Hg methylation potential in the shoreline sand dunes. In this study, we conducted anaerobic incubation experiments with beach sands collected from Ludington, Michigan, and examined the effects of organic carbon substrate addition, inorganic nitrogen, and mineral magnetite on Hg methylation. Despite nutrient poor and low-organic carbon conditions, appreciable Hg methylation activity coupled with carbon degradation was observed in the sands. Addition of acetate as a carbon source substantially increased MeHg production from 2 to 380 ng/kg sediment while acetate was rapidly degraded in the first 19 days of incubation. Ammonium addition showed little influence on carbon degradation or Hg methylation, whereas iron oxide addition (~1% dry weight) significantly inhibited both carbon degradation and MeHg production (by up to 90%), highlighting strongly coupled interactions between microbes, carbon substrates, and minerals. This research demonstrates the potential of microbial Hg methylation in the sand dunes, which may play a role in MeHg input and bioaccumulation in the Lake Michigan ecosystem.

54 ENVIRONMENTAL SCIENCES↗

Correlative Surface Imaging Reveals Chemical Signatures for Bacterial Hotspots on Plant Roots

The rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a highly diverse microbial community (the rhizosphere microbiome)1. Understanding, predicting and controlling plant-microbe interactions in the rhizosphere will allow us to harness the plant microbiome as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage1. To this end, it is imperative to develop new molecular approaches with high spatial resolution to capture interactions at the plant-microbe, microbe-microbe, and plant-plant interfaces. In this work, we designed an imaging sample holder that allows integrated surface imaging tools to map the same locations of a plant root-microbe interface with submicron lateral resolutions, providing novel in vivo analysis of root-microbe interactions. Specifically, confocal fluorescence microscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscope (SEM) were used for the first time for correlative imaging of the Brachypodium distachyon root and its interaction with Pseudomonas SW25, a typical plant growth-promoting soil bacterium. Imaging data suggest that the root surface is inhomogeneous and that the interaction between Pseudomonas and Brachypodium roots was confined to only few spots along the sampled root segments and that the bacterial attachment spots were enriched in Na- and S-related and high-mass organic species. We conclude that attachment of the Pseudomonas cells to the root surface is outcompeted by strong root-soil mineral interactions but facilitated by formation of extracellular polymeric substances (EPS).

Plant root, Plant growth-promoting bacteria, soil,↗

GenomeDepot: data management system for microbial comparative genomics

Summary GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of websites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, Basic Local Alignment Search Tool (BLAST) search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools. Availability and implementation GenomeDepot is open source and distributed under the GNU General Public License via GitHub (https://github.com/aekazakov/genome-depot). GenomeDepot is implemented in Python and was tested in Ubuntu Linux. Full installation instructions and documentation are available at https://aekazakov.github.io/genome-depot/. GenomeDepot demo server is freely accessible at https://iseq.lbl.gov/demogd/.

Kazakov, Alexey [Lawrence Berkeley National Labora↗

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation

A site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilized in situ through intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A paired t test indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion. Castellaniella had the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing genera Geothrix, Desulfovibrio, Ferribacterium, and Geobacter decreased significantly, whereas the denitrifying Acidovorax abundance increased significantly after groundwater invasion. Additionally, seven genera, i.e., Castellaniella, Ignavibacterium, Simplicispira, Rhizomicrobium, Acidobacteria Gp1, Acidobacteria Gp14, and Acidobacteria Gp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Social Evolution and Cheating in Plant Pathogens

Plant pathogens are a critical component of the microbiome that exist as populations undergoing ecological and evolutionary processes within their host. Many aspects of virulence rely on social interactions mediated through multiple forms of public goods, including quorum-sensing signals, exoenzymes, and effectors. Virulence and disease progression involve life-history decisions that have social implications with large effects on both host and microbe fitness, such as the timing of key transitions. Considering the molecular basis of sequential stages of plant–pathogen interactions highlights many opportunities for pathogens to cheat, and there is evidence for ample variation in virulence. Case studies reveal systems where cheating has been demonstrated and others where it is likely occurring. Harnessing the social interactions of pathogens, along with leveraging novel sensing and -omics technologies to understand microbial fitness in the field, will enable us to better manage plant microbiomes in the interest of plant health.

Plant Sciences↗

GenomeDepot v1.0

GenomeDepot is a web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid creation of web-sites for user-defined genome collections that include bioinformatic tools for interactive genome browsing, BLAST search, annotation search, comparative genomic neighborhood visualization, and sequence download. Gene function annotations are generated by a customizable annotation pipeline. The pipeline runs annotation tools in Conda environments and can be easily extended with additional user-specified tools.

Kazakov, Alexey [Lawrence Berkeley National Labora↗

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA). Final report

The goal of the Stahl lab is to use a combination of isotopic, genomic, and activity-based analyses in the field, of selected field isolates, and defined synthetic communities to identify sources and sinks of different nitrogen species in the field, focusing on the FRC at the ORNL. The most general research objective is to characterize variants in the pathway for denitrification among field isolates and synthetic microbial assemblies as a foundation for predicting the biotic and abiotic controls of nitrogen and carbon transformations in the field. Specifically, we have focused on characterizing environmental controls of nitrous oxide emissions, an important greenhouse gas and ozone depleting molecule. Studies have mapped the flux of nitrous oxide and controlling genetic elements within the FRC subsurface, indicating the importance of different enzyme variants in nitrous oxide production and consumption in controlling surface emissions. We have developed methods to quantify and catalog the isotopic signatures imparted on nitrous oxide by different nitrous oxide reductase variants in isolated organisms and model synthetic communities. We have developed methods to quantify and catalog the nitrous oxide affinity of field relevant isolates and their biomass yield when respiring nitrous oxide on different carbon substrates. We continue to expand the collection of field-relevant microbial isolates within ENIGMA by focused enrichment and isolation from field material. These objectives have been facilitated by the development of new technologies, including: 1) the development of a multiplexed automated optical density measurement system for quantifying growth kinetics of microorganisms dependent on gaseous substrates in monoculture or gas exchange in synthetic communities and 2) the development of a microcalorimetric analysis format to quantify the impact of environmental stress on microbial maintenance energy. Since field relevant processes are mediated by assemblies of organisms interacting with each other and their local environment, we have also collaborated with other ENIGMA investigators on the assembly and characterization of synthetic communities. These studies have evaluated the role of organisms lacking a complete pathway for denitrification in the control of field processes, measuring process rates of assemblies of organisms that individually lack the full denitrification pathway but mediate the complete denitrification when growing together. These efforts have so far resulted in the publication of 18 peer reviewed papers ranging from ecological and physiological drivers of pathway optimization to field-scale process characterization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

EnviroNET

EnviroNET is a service/facility that provides users with on-line, dial-up technical information concerning environmental conditions likely to be encountered by instruments and experimental arrangements carried aboard spacecraft. EnviroNET incorporates at present a combination of expository text and numerical tables amounting to about two million characters (bytes), plus FORTRAN programs that model the space environment. The topics covered are presented in viewgraph form and include the following: advantages of EnviroNET; thermal and humidity; vibration and acoustics; electromagnetic interference; loads and low frequency dynamics; microbial and toxic contaminants; molecular contamination; natural environment; orbiter motion; particulate environment; surface interactions; spacecraft anomalies; and interactive graphics facility.

Vansant, Tim↗

Squeezing Every Last 'Bit' of Information from Enceladus Mass Spectrometry

Potential opportunities to return to Enceladus in Discovery and Flagship class missions inspire development of next-generation instruments and creative approaches to sample collection, sample analysis, and data analysis and transmission strategies. Mass spectrometers (MS) are ideally suited to future Enceladus missions due to their analytical power in identifying a range of molecular and ionic compositions – including complex organics – and potentially astrobiologically-important features such as isotope ratios, chirality, and enantiomeric excess. However, long communication delays from Enceladus and limited bandwidth limits the data transmission from these higher-data-volume instruments, likely delaying mission-related response to new data. We explore the utility of data science and machine learning (ML) on isotope ratio (IR)MS data collected from laboratory analogs of Enceladus to: 1) process data quickly for rapid ground-based analyses, 2) understand if compositional and biosignature information could be extracted from IRMS data, and 3) evaluate whether onboard ML techniques could improve sample analysis, cadence, and transmission prioritization. Laboratory analogs analyzed isotopes of volatile CO2 that interacted with seawaters of varying composition, and include both abiotic and biotic (microbially-influenced) experiments. Enceladus’s alkaline oceans promote speciation of carbon into multiple forms (e.g., H2CO3 / CO2, HCO3-, and CO32-), each of which could be isotopically fractionated by abiotic or biotic reactions. Large (>2‰) changes in carbon isotopes (δ13C) are observed from some biotic experiments inoculated with complex microbial ecosystems relative to the abiotic seawaters. ML training and classification suggests that microbial samples can be distinguished from abiotic samples, yet that a broad range of microbial experiments are necessary to train ML models to cover a range of complexities including disequilibria, and isotopic and compositional fractionation.

geochemistry↗

Effect of CO 2 Concentration on the Microbial Activity of Orenia metallireducens (Strain Z6) in Surface Inert Materials

Carbon dioxide (CO 2 ) sequestration has garnered widespread attention as a key strategy for mitigating CO 2 emissions and combating the greenhouse effect. However, the mechanisms underlying the interactions between CO 2 , widespread siliceous minerals and biological processes remain unclear. The present study explored the potential impacts of different CO 2 concentrations on microbial activity, environmental conditions and their feedback on the fate of CO 2 . A total of 20 experimental conditions was created, with the variables including different natural and synthetic siliceous minerals (e.g., quartz sand and a type of commercial glass beads), the presence or absence of the iron-reducing microorganism Orenia metallireducens (strain Z6) and varying CO 2 concentrations (0%, 20%, 50%, 100%) in the presence of ferrihydrite and pyruvate. Geochemical, microbial and mineralogical analyses revealed that elevated CO 2 concentrations significantly inhibited microbial Fe(III) reduction and pyruvate metabolism. Interestingly, compared to cultures without mineral amendments or those with glass beads alone, the addition of quartz sand enabled strain Z6 to better withstand the environmental stress caused by elevated CO 2 , promoting pyruvate fermentation and iron reduction. In addition to an increased pH, the formation of siderite, hematite and vivianite was also observed in the bioactive systems. Although both glass beads and quartz sand were primarily composed of silica, differences in the mineral structure, elemental composition and acid neutralization capacity rendered quartz sand more chemically active and unexpectedly led to greater CO 2 sequestration.

CO2 stress↗

Automating the Study of Microbial Adaptation Dynamics on and off the ISS

The International Space Station (ISS) not only serves as a unique environment for humans, but also the microorganisms that join alongside. Many microbes present on the spacecraft arrive via humans, and as they interact with different surfaces they begin to inhabit those locations. Much like how human health has shown to be impacted by these extreme environments, microbial viability and response to stress also changes. Experimental evolution (EE) can aid in studying how microbes’ growth and activity changes within the ISS environments by applying controlled stressors to microbial cultures and monitoring their response over generations. EE studies are commonly done manually in laboratories, but, with multiple environmental variables to measure and adjust, it becomes highly labor-intensive, prone to human error, and challenging to scale. A multipurpose automated EE system named the AADEC has been developed to address these problems. This system integrates multiple sensors into a single fluidic chamber using UV-C flux, temperature, and media composition as stressors. AADEC contains five sensors: oxidation-reduction potential, electrical conductivity, pH, dissolved oxygen, and optical density. On their own, each is able to provide certain information on growth rate or metabolism; together, they show in detail how stressors affect life. AADEC studies can be conducted on Earth and repeated aboard the ISS to see how behavior changes when exposed to space mission stressors such as microgravity and radiation. AADEC’s auxiliary systems include peristaltic pumps for media exchange, magnetic rods for agitation, and a Raspberry Pi microprocessor to monitor, store, and adjust stressor levels real-time. This allows researchers to gather information within rapid generations, data and accuracy which is challenging to achieve through manual studies. With further miniaturization and automation, such as a more robust single-piece fluidics card, AADEC has the potential to be developed as a spacecraft payload. Support: NASA Ames CIF Award

Automating↗

Soil gas probes for monitoring trace gas messengers of microbial activity

Abstract Soil microbes vigorously produce and consume gases that reflect active soil biogeochemical processes. Soil gas measurements are therefore a powerful tool to monitor microbial activity. Yet, the majority of soil gases lack non-disruptive subsurface measurement methods at spatiotemporal scales relevant to microbial processes and soil structure. To address this need, we developed a soil gas sampling system that uses novel diffusive soil probes and sample transfer approaches for high-resolution sampling from discrete subsurface regions. Probe sampling requires transferring soil gas samples to above-ground gas analyzers where concentrations and isotopologues are measured. Obtaining representative soil gas samples has historically required balancing disruption to soil gas composition with measurement frequency and analyzer volume demand. These considerations have limited attempts to quantify trace gas spatial concentration gradients and heterogeneity at scales relevant to the soil microbiome. Here, we describe our new flexible diffusive probe sampling system integrated with a modified, reduced volume trace gas analyzer and demonstrate its application for subsurface monitoring of biogeochemical cycling of nitrous oxide (N 2 O) and its site-specific isotopologues, methane, carbon dioxide, and nitric oxide in controlled soil columns. The sampling system observed reproducible responses of soil gas concentrations to manipulations of soil nutrients and redox state, providing a new window into the microbial response to these key environmental forcings. Using site-specific N 2 O isotopologues as indicators of microbial processes, we constrain the dynamics of in situ microbial activity. Unlocking trace gas messengers of microbial activity will complement -omics approaches, challenge subsurface models, and improve understanding of soil heterogeneity to disentangle interactive processes in the subsurface biome.

04 OIL SHALES AND TAR SANDS↗