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At least 163 records · Page 9

Physical protection regulates microbial thermal responses to chronic soil warming

Climate warming can affect the temperature sensitivity of microbial activity and growth efficiency, possibly explained by changes to microbially unavailable carbon (C) protected within in soil aggregates. Here, we assessed physical protection by crushing macroaggregates (250–2000 μm) and microaggregates (<250 μm) isolated from mineral soils exposed to 27 years of experimental warming (+5 °C). We hypothesized that removal of physical protection would increase microbial activity and reduce C use efficiency (CUE). We found that crushing increased microbial respiration and biomass turnover rate, but did not affect CUE. We also hypothesized that long-term warming would reduce the effect of physical protection on microbial activity, and that physical protection would attenuate microbial temperature sensitivity in heated compared to control soils. We found that long-term warming was associated with a smaller effect of physical protection for microbial respiration but with a larger effect for biomass turnover rate in macroaggregates. Physical protection reduced the temperature sensitivity of respiration but enhanced the temperature sensitivity of microbial biomass turnover rate in heated compared to control soils. Our work shows that long-term warming has contrasting effects on how microbial respiration, biomass turnover rate, and their thermal responses are mediated by physical protection within soil aggregates.

59 BASIC BIOLOGICAL SCIENCES↗

CarbStor: Development, Analysis and Modification of Carbon Storing Model Soil Communities

Soil microbial communities carry out a number of key processes including plant growth promotion, bioremediation and cycling of nutrients. Carbon cycling is among the most important of these nutrients that are metabolized and processed by the soil microbial community. Many of the carbon inputs are converted to alternative organic forms of carbon that can be used by plants or act as biomass for microbial growth. However, inorganic forms of carbon can also be produced by soil microbial communities including calcium carbonate (CaCO 3 ). Production of calcium carbonate is beneficial for the ecosystem in several ways: it can stabilize soils and improve soil health, especially denser soils with high clay content, it can act as a method of bioremediation, it can serve as an alternative carbon source for plants and it can be a way to store carbon in soil in a stable, inorganic manner for the long term. While the chemistry surrounding individual species carrying out this process is well known what is lacking is an understanding of how species interact in a community to drive carbonate production. As all microbial species in soil exist in a community setting gaining this knowledge is critical to our predicting and controlling this microbial phenotype to greatly improve soil health. The CarbStor project is focused on developing, analyzing and modifying defined microbial soil consortia that express phenotypes at both the species and community level to convert carbon into recalcitrant stable sources such as precipitated carbonate or microbial necromass. To take full advantage of the soil community for this process we will need to fill several key knowledge gaps (KG), three of which are the focus of CarbStor. KG1: Whether and to what degree microbial communities can be developed that produce precipitated carbon via microbial metabolism. KG2: What interspecies interactions drive the individual member phenotypes in defined communities that lead to carbon precipitation. KG3: How can these interactions be modified to enhance carbon sequestration beyond what native communities are capable of. We hypothesize that in a carbon sequestering community only a subset of species will express phenotypes related to carbon storage processes. We also hypothesize that these phenotypes are expressed as a result of interactions with other species in the community that are not involved in carbon storage processes and that these interactions can be harnessed to enhance community carbon sequestration.

54 ENVIRONMENTAL SCIENCES↗

Characterization of the Biomass Degrading Enzyme GuxA from Acidothermus cellulolyticus

Microbial conversion of biomass relies on a complex combination of enzyme systems promoting synergy to overcome biomass recalcitrance. Some thermophilic bacteria have been shown to exhibit particularly high levels of cellulolytic activity, making them of particular interest for biomass conversion. These bacteria use varying combinations of CAZymes that vary in complexity from a single catalytic domain to large multi-modular and multi-functional architectures to deconstruct biomass. Since the discovery of CelA from Caldicellulosiruptor bescii which was identified as one of the most active cellulase so far identified, the search for efficient multi-modular and multi-functional CAZymes has intensified. One of these candidates, GuxA (previously Acel_0615), was recently shown to exhibit synergy with other CAZymes in C. bescii, leading to a dramatic increase in growth on biomass when expressed in this host. GuxA is a multi-modular and multi-functional enzyme from Acidothermus cellulolyticus whose catalytic domains include a xylanase/endoglucanase GH12 and an exoglucanase GH6, representing a unique combination of these two glycoside hydrolase families in a single CAZyme. These attributes make GuxA of particular interest as a potential candidate for thermophilic industrial enzyme preparations. Here, we present a more complete characterization of GuxA to understand the mechanism of its activity and substrate specificity. In addition, we demonstrate that GuxA exhibits high levels of synergism with E1, a companion endoglucanase from A. cellulolyticus. We also present a crystal structure of one of the GuxA domains and dissect the structural features that might contribute to its thermotolerance.

09 BIOMASS FUELS↗

Biomass Burning and the Production of Greenhouse Gases

Biomass burning is a source of greenhouse gases, carbon dioxide, methane, and nitrous oxide. In addition, biomass burning is a source of chemically active gases, including carbon monoxide, nonmethane hydrocarbons, and nitric oxide. These gases, along with methane, lead to the chemical production of tropospheric ozone (another greenhouse gas) as well as control the concentration of the hydroxyl radical, which regulates the lifetime of almost every atmospheric gas. Following biomass burning, biogenic emissions of nitrous oxide, nitric oxide, and methane are significantly enhanced. It is hypothesized that enhanced postburn biogenic emissions of these gases are related to fire-induced changes in soil chemistry and/or microbial ecology. Biomass burning, once believed to be a tropical phenomenon, has been demonstrated by satellite imagery to also be a regular feature of the world's boreal forests. One example of biomass burning is the extensive 1987 fire that destroyed more than 12 million acres of boreal forest in the People's Republic of China and across its border in the Soviet Union. Recent estimates indicate that almost all biomass burning is human-initiated and that it is increasing with time. With the formation of greenhouse and chemically active gases as direct combustion products and a longer-term enhancement of biogenic emissions of gases, biomass burning may be a significant driver for global change.

Levine, Joel S.↗

Recycling crop residues for use in recirculating hydroponic crop production

As part of bioregenerative life support feasibility testing by NASA, crop residues are being used to resupply elemental nutrients to recirculating hydroponic crop production systems. Methods for recovering nutrients from crop residues have evolved from water soaking (leaching) to rapid aerobic bioreactor processing. Leaching residues recovered the majority of elements but it also recovered significant amounts of soluble organics. The high organic content of leachates was detrimental to plant growth. Aerobic bioreactor processing reduced the organic content ten-fold, which reduced or eliminated phytotoxic effects. Wheat and potato production studies were successful using effluents from reactors having with 8- to 1-day retention times. Aerobic bioreactor effluents supplied at least half of the crops elemental mass needs in these studies. Descriptions of leachate and effluent mineral content, biomass productivity, microbial activity, and nutrient budgets for potato and wheat are presented.

NASA Center KSC↗

Modeling microbial carbon fluxes and stocks in global soils from 1901 to 2016

Abstract. Soil microbes play a crucial role in the carbon (C) cycle; however, they have been overlooked in predicting the terrestrial C cycle. We applied a microbial-explicit Earth system model – the Community Land Model-Microbe (CLM-Microbe) – to investigate the dynamics of soil microbes during 1901 to 2016. The CLM-Microbe model was able to reproduce the variations of gross (GPP) and net (NPP) primary productivity, heterotrophic (HR) and soil (SR) respiration, microbial (MBC) biomass C in fungi (FBC) and bacteria (BBC) in the top 30 cm and 1 m, and dissolved (DOC) and soil organic C (SOC) in the top 30 cm and 1 m during 1901–2016. During the study period, simulated C variables increased by approximately 12 PgC yr−1 for HR, 25 PgC yr−1 for SR, 1.0 PgC for FBC and 0.4 PgC for BBC in 0–30 cm, and 1.2 PgC for FBC and 0.7 PgC for BBC in 0–1 m. Increases in microbial C fluxes and pools were widely found, particularly at high latitudes and in equatorial regions, but we also observed their decreases in some grids. Overall, the area-weighted averages of HR, SR, FBC, and BBC in the top 1 m were significantly correlated with those of soil moisture and soil temperature in the top 1 m. These results suggested that microbial C fluxes and pools were jointly governed by vegetation C input and soil temperature and moisture. Our simulations revealed the spatial and temporal patterns of microbial C fluxes and pools in response to environmental change, laying the foundation for an improved understanding of soil microbial roles in the global terrestrial C cycle.

He, Liyuan↗

Pick-and-Eat Salad-Crop Productivity, Nutritional Value, and Acceptability to Supplement the ISS Food System

The capability to grow nutritious, palatable food for crew consumption during spaceflight has the potential to provide health-promoting, bioavailable nutrients, enhance the dietary experience, and reduce launch mass as we move toward longer-duration missions. However, studies of edible produce during spaceflight have been limited, leaving a significant knowledge gap in the methods required to grow safe, acceptable, nutritious crops for consumption in space. Researchers from Kennedy Space Center, Johnson Space Center, Purdue University and ORBITEC have teamed up to explore the potential for plant growth and food production on the International Space Station (ISS) and future exploration missions. KSC, Purdue, and ORBITEC bring a history of plant and plant-microbial interaction research for ISS and for future bioregenerative life support systems. JSC brings expertise in Advanced Food Technology (AFT), Behavioral Health and Performance (BHP), and statistics. The Veggie vegetable-production system on the ISS offers an opportunity to develop a pick-and-eat fresh vegetable component to the ISS food system as a first step to bioregenerative supplemental food production. We propose growing salad plants in the Veggie unit during spaceflight, focusing on the impact of light quality and fertilizer formulation on crop morphology, edible biomass yield, microbial food safety, organoleptic acceptability, nutritional value, and behavioral health benefits of the fresh produce. The first phase of the project will involve flight tests using leafy greens, with a small Chinese cabbage variety, Tokyo bekana, previously down selected through a series of research tests as a suitable candidate. The second phase will focus on dwarf tomato. Down selection of candidate varieties have been performed, and the dwarf cultivar Red Robin has been selected as the test crop. Four light treatments and three fertilizer treatments will be tested for each crop on the ground, to down select to two light treatments and one fertilizer treatment to test on ISS. Our work will help define light colors, levels, and horticultural best practices to achieve high yields of safe, nutritious leafy greens and tomatoes to supplement a space diet of prepackaged food. Our final deliverable will be the development of growth protocols for these crops in a spaceflight vegetable production system. With this work, and potentially with other pending joint projects, we will continue the synergistic research to help close gaps in the human research roadmap, and enable humans to venture to Mars and beyond. This research was co-funded by the Human Research Program and Space Biology (MTL1075) in the ILSRA 2015 NRA call.

Behavioral Health↗

Comparison of automated chemical-guided segmentation and human annotation of soil organic matter in X-ray microcomputed tomography imaging in contrasted soil types

Soil organic matter (OM) formation and persistence is strongly influenced by the spatial distribution of organic substrates and microscale soil heterogeneity by dictating OM accessibility to microorganisms. However, traditional size and/or density fractionation techniques disrupt aggregate architecture, eliminating spatial information needed to fully understand intra-aggregate OM distribution. To quantify three-dimensional OM spatial distribution and automate segmentation in X-ray microcomputed tomography (µCT) imaging without human annotation bias, we developed an iodine gas vapor (I2) based staining workflow that eliminates labor-intensive manual annotation while maintaining segmentation accuracy, using aggregates from four taxonomically diverse soils (Xerofluvent, Haploxeroll Sphagnofibrist, Palehumult) with an 8-fold range of soil organic carbon. Human annotation of 10 µCT slices by the experienced and inexperienced annotators resulted in variations up to 3% in the Dice similarity coefficient (DSC), reflecting a degree of inherent subjectivity of manual labeling. Such inconsistencies are expected to compound as the number of manually annotated slices increases. Dual-energy µCT imaging at 33.1 keV (below the iodine (I) K-edge) and 33.2 keV (above the I K-edge) was used to resolve aggregate microstructure following I2 staining. The automated image subtraction pipeline identified OM regions by the I Kedge induced brightness increases, achieving DSC values of 0.58–0.83 relative to an experienced annotator. Sensitivity analyses revealed that the reconstruction alpha value—optimized via the open-source tool TomocuPy—and the 3D registration slice count were the primary determinants of accuracy, providing a novel benchmark for dual-energy soil imaging. The pipeline without GPU acceleration achieved 9.6 to 43.2 times faster than manual annotation. Using GPU-accelerated image post-processing and affine transformation matrices, the pipeline successfully segmented OM elements for large-scale datasets (3232×3232 pixel, 2048 slices) within ~5200 s from raw file acquisition to segmented output. The high-throughput approach enables the quantification of OM spatial distribution across diverse and heterogeneous soil.

Soil microbial biomass↗

Long-term nitrogen loading alleviates phosphorus limitation in terrestrial ecosystems

Increased human-derived nitrogen (N) deposition to terrestrial ecosystems has resulted in widespread phosphorus (P) limitation of net primary productivity. However, it remains unclear if and how N-induced P limitation varies over time. Soil extracellular phosphatases catalyze the hydrolysis of P from soil organic matter, an important adaptive mechanism for ecosystems to cope with N-induced P limitation. In this study we show, using a meta-analysis of 140 studies and 668 observations worldwide, that N stimulation of soil phosphatase activity diminishes over time. Whereas short-term N loading (≤5 years) significantly increased soil phosphatase activity by 28%, long-term N loading had no significant effect. Nitrogen loading did not affect soil available P and total P content in either short- or long-term studies. Together, these results suggest that N-induced P limitation in ecosystems is alleviated in the long-term through the initial stimulation of soil phosphatase activity, thereby securing P supply to support plant growth. Our results suggest that increases in terrestrial carbon uptake due to ongoing anthropogenic N loading may be greater than previously thought.

59 BASIC BIOLOGICAL SCIENCES↗

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗

Forearc Carbon Sink Reduces Long-Term Volatile Recycling Into the Mantle

Carbon and other volatiles are transported from Earth’s surface into the mantle at subduction margins. The efficiency of this transfer has profound implications for the nature and scale of geochemical heterogeneities in Earth’s deep (mantle) and shallow (crustal) reservoirs, as well as Earth’s oxidation state. However, the proportion of volatiles released in the forearc and backarc are not well constrained compared to fluxes from the volcanic front. Here, we use helium and carbon isotope data from deeply sourced springs along two cross-arc transects to show that ~91% of carbon released from the slab/mantle beneath the Costa Rica forearc is sequestered within the crust by calcite deposition, and an additional ~3% is incorporated into biomass through microbial chemolithoautotrophy. We estimate that ~1.2 × 10(exp 8) to 1.3 × 10(exp 10) mol CO2/yr are released from the slab beneath the forearc, resulting in up to ~19% less carbon being transferred to Earth’s deep mantle than previously estimated.

Carbon cycle↗

NREL's Biochemical Conversion Pilot Plant Capabilities

NREL's biochemical conversion plant is a flexible pilot plant for testing a wide range of bio-based technologies for producing renewable fuels and byproducts. The biochemical conversion pilot plant is housed in the Integrated Biorefinery Research Facility located on the National Renewable Energy Laboratory's (NREL's) main campus. The facility provides industry partners the opportunity to test and develop their own biorefining technology using NREL equipment or rental equipment that can be brought into the plant. The pilot plant can process materials up to one dry ton per day in an integrated fashion using a variety of operating modes including batch, fed-batch, and continuous processing.

biochemical↗

Necromass responses to warming: A faster microbial turnover in favor of soil carbon stabilisation

Microbial byproducts and residues (hereafter ‘necromass’) potentially play the most critical role in soil organic carbon (SOC) sequestration. However, little is known about the influence of climate warming on necromass accumulation in the agroecosystem and the underlying mechanisms associated with microbial life strategies. Here, in order to address these knowledge gaps, we used amino sugars as biomarkers of microbial necromass, and investigated their variation through an 8-year trial in an agroecosystem with two warming levels (+1.6 and + 3.2 °C) compared to ambient temperature. The results showed that the lower warming level had no impact on total microbial necromass carbon. Conversely, warming the soil 3.2 °C above ambient increased total microbial necromass by 17 % and its contribution to SOC by 21.3 %, mainly by increasing fungal necromass (+19.8 %), whereas +3.2 °C warming had no impact on bacterial necromass. At the phylum level, compared with the ambient control, +3.2 °C warming induced an increase in the abundance of Proteobacteria and a decrease in both Acidobacteria and Actinobacteria, whereas in the fungal community, Ascomycota increased and Mortierellomycota decreased. This indicates that r-strategists outcompete K-strategists in warmer climates, which led to increased microbial necromass production and accumulation, as supported by the positive correlation between r-strategists and microbial necromass. Stronger microbial competition for resources also resulted in a higher biomass turnover rate, greater cell death, and greater production of microbial necromass. This was supported by the lower bacterial and fungal network complexity and trophic links under warming conditions. In addition, the necromass generated from accelerated microbial turnover further offsets warming-induced deceases in microbial biomass. Consequently, bulk SOC did not change, despite microbial necromass having a much greater response to warming than the soil C pool. Therefore, future climate warming may influence the composition and persistence of SOC during microbial degradation.

54 ENVIRONMENTAL SCIENCES↗

Switchgrass cropping systems affect soil carbon and nitrogen and microbial diversity and activity on marginal lands

Abstract Switchgrass ( Panicum virgatum L.), as a dedicated bioenergy crop, can provide cellulosic feedstock for biofuel production while improving or maintaining soil quality. However, comprehensive evaluations of how switchgrass cultivation and nitrogen (N) management impact soil and plant parameters remain incomplete. We conducted field trials in three years (2016–2018) at six locations in the North Central Great Lakes Region to evaluate the effects of cropping systems (switchgrass, restored prairie, undisturbed control) and N rates (0, 56 kg N ha −1 year −1 ) on biomass yield and soil physicochemical, microbial, and enzymatic parameters. Switchgrass cropping system yielded an aboveground biomass 2.9–3.3 times higher than the other two systems (Jayawardena et al., unpublished data) but our study found that this biomass accumulation did not reduce soil dissolved organic C, total dissolved N (TDN), or bacterial diversity. The annual aboveground biomass removal for bioenergy feedstock, however, reduced soil microbial biomass C (MBC) and microbial biomass N (MBN) and bacterial richness in the second and third years; despite this, continuous monocropping of switchgrass improved soil TDN, inorganic N, bacterial diversity, and shoot biomass in the second and/or third years compared with the first year. N fertilization increased aboveground biomass yield by 1.2 times and significantly increased soil TDN, MBN, and the shoot biomass of switchgrass compared with the unfertilized control. Locations with higher C and N contents and lower C:N ratio had higher aboveground biomass, MBC, MBN, and the activity of BG, CBH, and UREA enzymes; by contrast, locations with higher pH had higher soil TDN and activity of NAG and LAP enzymes. Our research demonstrates that switchgrass cultivation could improve or maintain soil N content and N fertilization can increase plant biomass yield. The comprehensive data also can inform future biogeochemical models to successfully implement switchgrass for bioenergy production.

09 BIOMASS FUELS↗

Corynebacterium glutamicum as an Efficient Omnivorous Microbial Host for the Bioconversion of Lignocellulosic Biomass

Corynebacterium glutamicum has been successfully employed for the industrial production of amino acids and other bioproducts, partially due to its native ability to utilize a wide range of carbon substrates. We demonstrated C. glutamicum as an efficient microbial host for utilizing diverse carbon substrates present in biomass hydrolysates, such as glucose, arabinose, and xylose, in addition to its natural ability to assimilate lignin-derived aromatics. As a case study to demonstrate its bioproduction capabilities, L-lactate was chosen as the primary fermentation end product along with acetate and succinate. C. glutamicum was found to grow well in different aromatics (benzoic acid, cinnamic acid, vanillic acid, and p-coumaric acid) up to a concentration of 40 mM. Besides, 13 C-fingerprinting confirmed that carbon from aromatics enter the primary metabolism via TCA cycle confirming the presence of β-ketoadipate pathway in C. glutamicum . 13 C-fingerprinting in the presence of both glucose and aromatics also revealed coumarate to be the most preferred aromatic by C. glutamicum contributing 74 and 59% of its carbon for the synthesis of glutamate and aspartate respectively. 13 C-fingerprinting also confirmed the activity of ortho-cleavage pathway, anaplerotic pathway, and cataplerotic pathways. Finally, the engineered C. glutamicum strain grew well in biomass hydrolysate containing pentose and hexose sugars and produced L-lactate at a concentration of 47.9 g/L and a yield of 0.639 g/g from sugars with simultaneous utilization of aromatics. Succinate and acetate co-products were produced at concentrations of 8.9 g/L and 3.2 g/L, respectively. Our findings open the door to valorize all the major carbon components of biomass hydrolysate by using C. glutamicum as a microbial host for biomanufacturing.

13C-fingerprinting↗

Rapid System to Quantitatively Characterize the Airborne Microbial Community

Bioaerosols have been linked to a wide range of different allergies and respiratory illnesses. Currently, microorganism culture is the most commonly used method for exposure assessment. Such culture techniques, however, generally fail to detect between 90-99% of the actual viable biomass. Consequently, an unbiased technique for detecting airborne microorganisms is essential. In this Phase II proposal, a portable air sampling device his been developed for the collection of airborne microbial biomass from indoor (and outdoor) environments. Methods were evaluated for extracting and identifying lipids that provide information on indoor air microbial biomass, and automation of these procedures was investigated. Also, techniques to automate the extraction of DNA were explored.

Macnaughton, Sarah J.↗

Seeding Advanced Treated Wastewater for Purposes of Direct Potable Reuse

Direct potable reuse (DPR) is a promising solution to address water scarcity. However, a better understanding of how introducing advanced treated water (ATW) affects microbial communities present in distribution systems is needed. Here, in this study, we measured changes to the microbial water quality in simulated distribution systems that were conditioned using treated, unimpaired surface water (SW) and then transitioned to ATW. In addition, we investigated whether adding a biological filtration step would seed the microbial community of the ATW and whether the influence would persist in the simulated distribution systems. We found that the bulk water in the ATW-fed distribution systems had lower cell counts and ATP concentrations and a distinct microbial community (based on 16S amplicon sequencing) compared to the SW-fed or the seeded ATW-fed systems. However, biofilm community composition and biomass remained consistent regardless of the feedwater. Increased microbial biomass and diversity were present in the seeded ATW, with several amplicon sequence variants identified as being introduced by the biological filter. Our results suggest that directly introducing ATW to distribution systems could disturb the existing microbial community. Preparing ATW for distribution via biological filtration may deliver more predictable and stable microbial water quality than introducing unseeded ATW.

16S↗