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At least 55 records · Page 3

Ocean liming effect on a North Atlantic microbial community: changes in composition and rates

The ongoing rise in atmospheric CO 2 levels and the consequent global warming make it increasingly difficult to maintain the global temperature within the 1.5 - 2°C target set by the Paris Agreement. Therefore, strategies to remove carbon dioxide from the atmosphere are being developed, with ocean alkalinity enhancement (OAE) gaining most attention. Within OAE, ocean liming- the addition of quicklime (CaO) or hydrated lime (Ca(OH) 2 )- can not only remove CO 2 from the atmosphere but potentially counteract the effects of ocean acidification. Although quite attractive, these technologies have yet to be tested regarding ecological safety and efficacy. Here we report the impacts of ocean liming on the abundance, composition and extracellular enzymatic activity (EEA) rates of a North Atlantic planktonic community. The results demonstrate that OAE led to a decreased phytoplankton development, mainly diatoms. The bacterial response to OAE was community-specific, with a consistent increase in the relative abundance of the order Oceanospirillales. OAE also led to increased EEA rates, especially within the bacterial community. These findings suggest that while initial effects on phytoplankton may be limited, the specific impacts on bacterial groups suggest that OAE could influence the remineralization of organic matter. If our results apply to other communities, OAE might initially affect marine microbial dynamics, but further studies are needed to determine if these effects are long-term.

16S↗

Microbial Pathways for Cost-Effective Low-Carbon Renewable Indigoidine

Indigoidine is a bioadvantaged platform molecule with diverse applications, including use as a textile dye, biotransistor, biosolar cell, biosensor, and food coloring. There are multiple microbial hosts and carbon sources that can be used and optimized for its production, yet there is limited guidance for which options have the greatest commercial potential. Here, we consider five different host microbes and combine genome-scale metabolic models with techno-economic and lifecycle assessment models. Pseudomonas putida currently outperforms synthetic indigo production and other indigoidine-producing hosts, using glucose, xylose, and lignin-derived aromatics to produce indigoidine at a minimum selling price of $2.9/kg and a greenhouse gas (GHG) footprint of 3.5 kgCO 2e /kg. Optimizing pathways-achieving 90% of the theoretical indigoidine yield from sugars and aromatics-can reduce costs 6-7-fold and GHG emissions 3-10-fold. From a cost perspective, microbes that co-utilize aromatics are advantageous, while selecting hosts that coproduce other value-added molecules can reduce GHG emissions. System-wide improvements and the use of a low-cost, low-carbon nitrogen source are crucial for commercial viability in all cases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigating drivers of microbial activity and respiration in a forested bog

Northern peatlands store nearly one-third of terrestrial carbon (C) stocks while covering only 3% of the global landmass; nevertheless, the drivers of C cycling in these often-waterlogged ecosystems are different from those that control C dynamics in upland forested soils. To explore how multiple abiotic and biotic characteristics of bogs interact to shape microbial activity in a northern, forested bog, we added a labile C tracer ( 13 C-labeled starch) to in situ peat mesocosms and correlated heterotrophic respiration with natural variation in several microbial predictor variables, such as enzyme activity and microbial biomass, as well as with a suite of abiotic variables and proximity to vascular plants aboveground. We found that peat moisture content was positively correlated with respiration and microbial activity, even when moisture levels exceeded total saturation, suggesting that access to organic matter substrates in drier environments may be limiting for microbial activity. Proximity to black spruce trees decreased total and labile heterotrophic respiration. This negative relationship may reflect the influence of tree evapotranspiration and peat shading effects; i.e., microbial activity may decline as peat dries and cools near trees. Here, we isolated the response of heterotrophic respiration to explore the variation in, and interactions among, multiple abiotic and biotic drivers that influence microbial activity. This approach allowed us to reveal the relative influence of individual drivers on C respiration in these globally important C sinks.

59 BASIC BIOLOGICAL SCIENCES↗

Underground Hydrogen Storage: Transforming Subsurface Science into Sustainable Energy Solutions

As the global economy moves toward net-zero carbon emissions, large-scale energy storage becomes essential to tackle the seasonal nature of renewable sources. Underground hydrogen storage (UHS) offers a feasible solution by allowing surplus renewable energy to be transformed into hydrogen and stored in deep geological formations such as aquifers, salt caverns, or depleted reservoirs, making it available for use on demand. This study thoroughly evaluates UHS concepts, procedures, and challenges. This paper analyzes the most recent breakthroughs in UHS technology and identifies special conditions needed for its successful application, including site selection guidelines, technical and geological factors, and the significance of storage characteristics. The integrity of wells and caprock, which is important for safe and efficient storage, can be affected by the operating dynamics of the hydrogen cycle, notably the fluctuations in pressure and stress within storage formations. To evaluate its potential for broader adoption, we also examined economic elements such as cost-effectiveness and the technical practicality of large-scale storage. We also reviewed current UHS efforts and identified key knowledge gaps, primarily in the areas of hydrogen–rock interactions, geochemistry, gas migration control, microbial activities, and geomechanical stability. Resolving these technological challenges, regulatory frameworks, and environmental sustainability are essential to UHS’s long-term and extensive integration into the energy industry. This article provides a roadmap for UHS research and development, emphasizing the need for further research to fully realize the technology’s promise as a pillar of the hydrogen economy.

25 ENERGY STORAGE↗

Depth-dependent links between microbial taxa and nitrous oxide emissions in a long-term cotton cropping system employing soil health practices

Long-term management practices can shape soil microbial communities in ways that influence nitrogen (N) dynamics and nitrous oxide (N 2 O) emissions. We leverage a 41-year continuous cotton cropping experiment with contrasting tillage, cover cropping, and N fertilization regimes to investigate how these long-term strategies influence soil microbial communities and their associations with N 2 O fluxes during the cotton growing season. Using 16S rRNA gene metabarcoding, we assessed microbial composition in surface and subsurface soils and evaluated its relationship with temporal N 2 O emissions. Among the management practices, N fertilization – a known driver of N 2 O emissions – had the strongest effect on microbial community composition and was linked to a greater number of taxa correlated to N 2 O emissions, particularly in surface soils. Soil pH emerged as a key variable influencing microbial structure across depth and was negatively associated with both N 2 O emissions and microbial composition in the surface layers of fertilized soils. In total, 57 archaeal/bacterial taxa were correlated with N 2 O fluxes, but only seven were shared across depths, suggesting distinct microbial contributors in surface and subsurface soils. Several of these taxa have been previously reported to be associated with N and C cycling processes such as nitrate respiration or carbon turnover, indicating functional context to their correlation with N 2 O fluxes. Temporal shifts in the abundance of key taxa aligned with seasonal peaks in N 2 O emissions, notably in early and late August, and were most pronounced under conventional tillage, hairy vetch cover cropping, and N fertilization. While 16S-based associations cannot confirm functional gene presence or activity, these findings demonstrate that long-term fertilization and associated soil acidification are dominant drivers of microbial shifts linked to N 2 O emissions and highlight the importance of accounting for depth-specific and seasonal microbial dynamics when evaluating management impacts on greenhouse gas emissions.

16S rRNA gene sequencing↗

Geochemical, Biological, and Clumped Isotopologue Evidence for Substantial Microbial Methane Production Under Carbon Limitation in Serpentinites of the Samail Ophiolite, Oman

In hyperalkaline (pH > 10) fluids that have participated in low-temperature (<150°C) serpentinization reactions, the dominant form of C is often methane (CH 4 ), but the origin of this CH 4 is uncertain. To assess CH 4 origin in serpentinite aquifers within the Samail Ophiolite, Oman, we determined fluid chemical compositions, analyzed taxonomic profiles of fluid-hosted microbial communities, and measured isotopic compositions of hydrocarbon gases. We found that 16S rRNA gene sequences affiliated with methanogens were widespread in the aquifer. We measured clumped isotopologue ( 13 CH 3 D and 12 CH 2 D 2 ) relative abundances less than equilibrium, consistent with substantial microbial CH 4 production. Furthermore, we observed an inverse relationship between dissolved inorganic C concentrations and δ 13 C CH 4 across fluids bearing microbiological evidence of methanogenic activity, suggesting that the apparent C isotope effect of microbial methanogenesis is modulated by C availability. An additional source of CH 4 is evidenced by the presence of CH 4 -bearing fluid inclusions in the Samail Ophiolite and our measurement of high δ 13 C values of ethane and propane, which are similar to those reported in studies of CH 4 -rich inclusions in rocks from the oceanic lithosphere. In addition, we observed 16S rRNA gene sequences affiliated with aerobic methanotrophs and, in lower abundance, anaerobic methanotrophs, indicating that microbial consumption of CH 4 in the ophiolite may further enrich CH 4 in 13 C. We conclude that substantial microbial CH 4 is produced under varying degrees of C limitation and mixes with abiotic CH 4 released from fluid inclusions. This study lends insight into the functioning of microbial ecosystems supported by water/rock reactions.

58 GEOSCIENCES↗

Scientists’ call to action: Microbes, planetary health, and the Sustainable Development Goals

Microorganisms, including bacteria, archaea, viruses, fungi, and protists, are essential to life on Earth and the functioning of the biosphere. Here, we discuss the key roles of microorganisms in achieving the United Nations Sustainable Development Goals (SDGs), highlighting recent and emerging advances in microbial research and technology that can facilitate our transition toward a sustainable future. Given the central role of microorganisms in the biochemical processing of elements, synthesizing new materials, supporting human health, and facilitating life in managed and natural landscapes, microbial research and technologies are directly or indirectly relevant for achieving each of the SDGs. More importantly, the ubiquitous and global role of microbes means that they present new opportunities for synergistically accelerating progress toward multiple sustainability goals. By effectively managing microbial health, we can achieve solutions that address multiple sustainability targets ranging from climate and human health to food and energy production. Emerging international policy frameworks should reflect the vital importance of microorganisms in achieving a sustainable future.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO 2 levels). For this purpose, we combined 18 O-water vapor equilibration with quantitative stable isotope probing (termed ‘vapor-qSIP’) to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO 2 ) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗

Climate-Driven Legacies in Simulated Microbial Communities Alter Litter Decomposition Rates

The mechanisms underlying diversity-functioning relationships have been a consistent area of inquiry in biogeochemistry since the 1950s. Though these mechanisms remain unresolved in soil microbiomes, many approaches at varying scales have pointed to the same notion—composition matters. Confronting the methodological challenge arising from the complexity of microbiomes, this study used the model DEMENTpy, a trait-based modeling framework, to explore trait-based drivers of microbiome-dependent litter decomposition. We parameterized DEMENTpy for five sites along a climate gradient in Southern California, United States, and conducted reciprocal transplant simulations analogous to a prior empirical study. The simulations demonstrated climate-dependent legacy effects of microbial communities on plant litter decomposition across the gradient. This result is consistent with the previous empirical study across the same gradient. An analysis of community-level traits further suggests that a 3-way tradeoff among resource acquisition, stress tolerance, and yield strategies influences community assembly. Simulated litter decomposition was predictable with two community traits (indicative of two of the three strategies) plus local environment, regardless of the system state (transient vs. equilibrium). Although more empirical confirmation is still needed, community traits plus local environmental factors (e.g., environment and litter chemistry) may robustly predict litter decomposition across spatial-temporal scales. In conclusion, this study offers a potential trait-based explanation for climate-dependent community effects on litter decomposition with implications for improved understanding of whole-ecosystem functioning across scales.

54 ENVIRONMENTAL SCIENCES↗

Influence of microorganisms on uranium release from mining-impacted lake sediments under various oxygenation conditions

Microbial processes can be involved in the remobilization of uranium (U) from reduced sediments under O 2 reoxidation events such as water table fluctuations. Such reactions could be typically encountered after U-bearing sediment dredging operations. Solid U(IV) species may thus reoxidize into U(VI) that can be released in pore waters in the form of aqueous complexes with organic and inorganic ligands. Non-uraninite U(IV) species may be especially sensitive to reoxidation and remobilization processes. Nevertheless, little is known regarding the effect of microbially mediated processes on the behaviour of U under these conditions.

54 ENVIRONMENTAL SCIENCES↗

Relaxation behavior in low-frequency complex conductivity of sands caused by bacterial growth and biofilm formation by Shewanella oneidensis under a high-salinity condition

Complex electrical conductivity is increasingly used to monitor subsurface processes associated with microbial activities because microbial cells mostly have surface charges and thus electrical double layers. Although highly saline environments are frequently encountered in coastal and marine sediments, there are limited data available on the complex conductivity associated with microbial activities under a high-salinity condition. Therefore, we have developed the spectral responses of complex conductivity of sand associated with bacterial growth and biofilm formation under a highly saline condition of approximately 1% salinity and approximately 2 S/m pore water conductivity with an emphasis on relaxation behavior. A column test is performed, in which the model bacteria Shewanella oneidensis MR-1 are stimulated for cell growth and biofilm formation in a sand pack, whereas the complex conductivity is monitored from 0.01 Hz to 10 kHz. The test results indicate that the real conductivity increases in the early stage due to the microbial metabolites and the increased surface conduction with cell growth but soon begin to decrease because of the reduction of charge passages due to bioclogging. However, the imaginary conductivity significantly increases with time, and clear bell-shaped relaxation behaviors are observed with the peak frequency of 0.1–1 Hz, associated with the double-layer polarization of cells and electrically conductive pili and biofilms. The Cole-Cole relaxation model appears to capture such relaxation behaviors well, and the modeling results indicate gradual increases in normalized chargeability and decreases in relaxation time during bacterial growth and biofilm formation in the highly saline condition. Comparison with previous literature confirms that the high-salinity condition further increases the normalized chargeability, whereas it suppresses the phase shift and thus the imaginary conductivity. Our results suggest that the complex conductivity can effectively capture microbial biomass formation in sands under a highly saline condition.

58 GEOSCIENCES↗

Qualitative and quantitative profiles of jejunal oligosaccharides and cecal short–chain fatty acids in broiler chickens receiving different dietary levels of fiber, protein and exogenous enzymes

Dietary supplemental carbohydrases are able to degrade non-starch polysaccharides and generate oligosaccharides in the gastrointestinal tract. This study was conducted to investigate the influence of dietary fiber and protein levels on growth performance, nutrient utilization, digesta oligosaccharides profile and cecal short-chain fatty acid (SCFA) profile in broilers receiving diets supplemented with xylanase or protease individually or in combination. Enzyme supplementation had no effect on growth performance. There was significant (P < 0.05) fiber × protein × xylanase interaction for ileal nitrogen digestibility and significant (P < 0.01) protein × xylanase × protease interaction for nitrogen-corrected apparent metabolizable energy. Birds fed high-fiber diets had higher (P < 0.05) jejunal oligosaccharides and cecal SCFA concentrations. Xylanase and protease combination produced the greatest pentose (Pent) levels in low fiber–adequate protein diets but lowest levels in highfiber–low protein diets. There was significant (P < 0.05) fiber × xylanase × protease interaction explained by the digesta concentrations of (Pent) 3 , (Pent) 4 and (Pent) 5 being greatest (P < 0.5) in protease-only supplemented high-fiber diets but lowest in protease-only supplemented low-fiber diets. Furthermore, these results suggest that, of all the factors investigated, dietary fiber level had the greatest effect on modulating digesta concentration of oligosaccharides and cecal SCFA. Evidence points to the fact that there is considerable capacity for generating pentose oligosaccharides in the digestive tract of broilers receiving diets rich in fibrous feedstuffs, and that this may have a beneficial effect on microbial profile in the digestive tract.

59 BASIC BIOLOGICAL SCIENCES↗

Microscale spatiotemporal patterns of water, soil organic carbon, and enzymes in plant litter detritusphere

Understanding biophysical and biochemical processes in detritusphere is critical to quantifying and modeling plant residue decomposition dynamics and subsequent soil organic carbon (C) accrual. The objectives of the study were to explore (i) micro-environmental conditions within the detritusphere formed around decomposing corn and soybean leaves, and (ii) the relationships between moisture distribution, enzyme activity, and C dynamics during decomposition. We assessed spatial and temporal dynamics of moisture distribution using X-ray and neutron computed tomography, and activities of β-glucosidase and chitinase, two enzymes involved in soil C and N processing, using zymography. We used 13 C labeled residue to track residue contribution to atmospheric CO 2 and soil organic C. Moisture redistribution pattern varied depending on the residue type. While the water was immediately absorbed by the corn leaves and maintained afterward, switchgrass leaves absorbed water more slowly and created water-deficient zones within ~1mm from the residue. This initial moisture depletion led to lower chitinase activity and residue-derived CO 2 emissions in switchgrass. In contrast to chitinase, β-glucosidase activity was influenced by a combination of vegetation history and residue type, and it was higher when the origin of the residue matched the vegetation history of the soil. Pore size had an opposite impact on the studied enzymes, supporting the notion that contrasting soil pore architecture can stimulate activities of different enzymes through a selection of dominant enzyme producers. We concluded that the decomposition dynamics of plant residues is not only a simple function of residue chemistry, but rather a combined effect of the vegetation history, in part through its effect on microbial community composition, the plant residue chemical and likely physical characteristics, and the soil pore structure in the detritusphere. Together, they create temporally dynamic micro-environmental conditions influencing decomposition. Specifically, our study demonstrated that the initial micro-environment formulated in detritusphere can play an important role in enzyme activities and consequent C dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Effects of the microalgae Chlamydomonas on gastrointestinal health

The effects of consuming whole-cell biomass of the green algae Chlamydomonas reinhardtii on gastrointestinal health in mice and humans was examined. A 14-day murine model of acute colitis revealed significantly less weight loss in mice that received C. reinhardtii biomass by oral gavage. Based on this result, human volunteers with varying gastrointestinal symptoms were asked to consume 1 or 3 g of C. reinhardtii daily for 30 days. Participants reported changes in their gastrointestinal health through a questionnaire and provided stool samples to analyze the composition of their gut microbiome. Those who typically experience frequent gastrointestinal symptoms reported significantly less bowel discomfort or diarrhea, significantly less gas or bloating, more regular bowel movements, and better stool consistency when regularly consuming C. reinhardtii. Analysis of participant stool samples suggested the gut microbiome composition in all groups remained complex, and no signs of dysbiosis or adverse effect on microbial composition were observed.

60 APPLIED LIFE SCIENCES↗

AquaMEND: Reconciling multiple impacts of salinization on soil carbon biogeochemistry

Soil salinization, exacerbated by climate change, poses a global threat to coastal ecosystem function and soil quality. Salinity influences carbon cycling through direct effects on microbial activity and indirect alterations to soil physicochemical properties including cation exchange, pH, and soil organic carbon availability. Current models inadequately represent these complexities, relying on linear reduction functions that overlook specific physicochemical changes induced by salinity. To address this gap, we propose an integrated model framework, AquaMEND, that combines microbial-explicit carbon decomposition and geochemical models. This model allows cation exchange and surface complexation processes to capture solute chemistry and nutrient availability in soils upon saltwater intrusion. Using response functions that capture salinity impacts on both salt-sensitive and salt-resistant microbial processes, AquaMEND simulates how the abiotic and biotic mechanisms work individually and collectively to regulate organic and inorganic pools and fluxes. Here, the parallel structure of aqueous and non-aqueous phases, together with microbial functions, result in a versatile model for solving dynamic coupling of organics, minerals and microbes under various environmental settings.

54 ENVIRONMENTAL SCIENCES↗

Roadmap for naming uncultivated Archaea and Bacteria

The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.

59 BASIC BIOLOGICAL SCIENCES↗

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome

Abstract Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac -like and iad -like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad -like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad -like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

Bacterial and fungal composition and exometabolites control the development and persistence of soil water repellency

Soil water repellency (SWR), the reduced affinity of soil for water, is a phenomenon that affects soils globally. With worsening climate change, SWR is expected to increase emphasizing the need to understand the mechanisms driving SWR development and persistence. The importance of the soil microbes in SWR has been postulated for decades, but limited research has been conducted into whole-community interactions and the role of community metabolic activity. To address this gap in knowledge, we investigated the direct effect of microbial community composition, activity, and diversity, as well as their associated metabolites on the development and persistence of SWR by inoculating microcosms containing model soils with 15 different microbial communities and quantified respiration and SWR over time. Six communities that consistently produced either a hydrophobic or hydrophilic phenotype were characterized using metagenomics and metabolomics to determine the impact of microbial and metabolite composition and diversity on SWR. We identified several bacterial genera with significant changes in abundance between SWR phenotypes including Nocardiopsis and Kocuria in hydrophilic and Streptomyces and Cutibacterium in hydrophobic. We discovered that hydrophilic communities were more positively connected when compared to hydrophobic communities, which could be due to an increase in defense mechanism genes. Additionally, we identified specific metabolites associated with hydrophilic and hydrophobic phenotypes including an increase in the osmolyte ectoine in hydrophilic and an increase in plant-derived decomposition products in hydrophobic communities. Finally, our research suggests that fungi, previously thought to cause hydrophobicity, may actually contribute to hydrophilicity through their preferential consumption of hydrophobic compounds.

54 ENVIRONMENTAL SCIENCES↗