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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Isolation of genome-predicted Caldatribacterium ( Atribacterota ) reveals pervasive microbial cultivation problem due to folate precipitation

Most bacterial phyla have few or no pure cultures, including Atribacterota , comprised of ubiquitous anaerobes. Here, we report genome-guided enrichment and isolation of two Atribacterota species representing a new family, Caldatribacterium saccharofermentans from a hot spring, and Caldatribacterium inferamans from a deep aquifer. Both were co-enriched with sulfate-reducing bacteria and initially resisted isolation, which we link to inadvertent removal of precipitated folic acid by filter-sterilization of unbuffered Wolin’s vitamin solution. We then predict folate auxotrophy across the Atribacterota and ~29% of all bacteria, with extensive auxotrophy in 27% of phyla. Since ≥604 of 791 ( ≥ 76%) media with folic acid additions in the MediaDive database use unbuffered vitamin solutions in which folic acid is likely removed during filter-sterilization, we propose that folate auxotrophy limits culturability in defined media en masse. We also uncover unusual features of Caldatribacterium , including three lipid membrane-like layers (LMLs), with the inner LML surrounding the nucleoid, and a high percentage of secreted proteins, supporting a unique cell biology of Atribacterota .

Biological and medical sciences↗
DOE OSTI2024

Impact of Sugarcane Cultivation on C Cycling in Southeastern United States Following Conversion From Grazed Pastures

ABSTRACT The expansion of sugarcane, a tropical high‐yielding feedstock, will likely reshape the Southeastern United States (SE US) bioenergy landscape. However, the sustainability of sugarcane, particularly as it displaces grazed pastures, is highly uncertain. Here, we investigated how pasture conversion to sugarcane in subtropical Florida impacts net ecosystem CO 2 exchange (NEE) and net ecosystem carbon (C) balance (NECB). Measurements were made over three full growth cycles (> 3 years) in sugarcane—plant cane, PC; first ratoon cane, FRC; second ratoon cane, SRC—and in improved (IM) and semi‐native (SN) pastures, which make up ca. 37% of agricultural land in the region. Immediately following conversion, PC was a stronger net source of CO 2 than pastures, indicating the importance of CO 2 losses related to land disturbance. Sugarcane, however, shifted to a strong net sink of CO 2 after first regrowth, and overall sugarcane was a stronger net CO 2 sink than pastures. Both stand age and low water availability during cane emergence and tillering substantially decreased its potential gross CO 2 uptake. Accounting for all C gains and removals (i.e., NECB), greater frequency of burn events and repeated harvest increased removals and overall made sugarcane a stronger C source relative to pastures despite substantial C inputs from the previous land use and a stronger CO 2 sink strength. Time since conversion substantially reduced C losses from sugarcane, and the NECB of SRC was similar to that of IM pasture but lower than that of SN pasture, indicating a rapid shift in the NECB of cane. We conclude that the C‐balance implications following conversion will depend on the proportion of IM versus SN pastures converted to sugarcane. Furthermore, our findings suggest that no‐burn harvest management strategies will be critical to the development of a sustainable bioenergy landscape in SE US.

Gomez‐Casanovas, Nuria↗
DOE OSTI2024

Impacts of Legacy and Contemporary Nitrogen Inputs on N 2 O and CO 2 Emissions in Miscanthus and Maize Cultivated Soils

ABSTRACT Nutrient inputs influence the sustainability of bioenergy crop production through contemporary (shortly after addition) and legacy effects (persisting over years) on microbial nitrogen (N) and carbon cycling, which contribute to greenhouse gas emissions. However, the relative importance of contemporary and legacy effects and how that could vary by crop functional types is poorly understood. Considering its rhizomatous roots and perennial growth, we hypothesized that Miscanthus × giganteus (M×g) would be more sensitive to legacy N fertilization and the historical context of its environment than an annual crop like maize. To test this hypothesis, we examined the effects of legacy and contemporary N inputs on nitrous oxide (N 2 O) and carbon dioxide (CO 2 ) emissions, as well as key N cycling genes in soils where M×g and maize were grown. A 150‐day soil incubation experiment was conducted using soils from a long‐term M×g and maize fertility experiment with three historic N fertilization rates (0, 112, and 336 kg N ha −1 year −1 ) and a contemporary amendment (60 mg N kg −1 ) with negative control (0 mg N kg −1 ). We observed significant increases in cumulative N 2 O emissions in Mxg soils relative to maize soils, particularly at higher legacy fertilization rates, while contemporary N had no significant effect. Bacterial amo A gene abundance, which plays a significant role in nitrification in nutrient‐rich soils, also increased with higher legacy fertilization rates in M×g soils but was unaffected by the contemporary N. In maize soils, legacy and contemporary N did not significantly affect N 2 O emissions, but cumulative CO 2 emissions and amo A gene abundance significantly increased. The abundances of nor B genes were not significantly influenced by either legacy fertilization or contemporary N amendments in either soil. Our findings demonstrate the greater importance of fertilization history over contemporary N in mediating soil N 2 O emissions, particularly for perennial bioenergy crops.

09 BIOMASS FUELS↗
DOE OSTI2025

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.

Kordia↗
DOE OSTI2021

Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveals Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Yarrowia lipolytica is an important industrial oleaginous yeast due to its robust phenotypes for effective conversion of inhibitory lignocellulosic biomass hydrolysates into neutral lipids. While lipid accumulation has been well characterized in this organism, its interconnected lipid degradation phenotype is poorly understood during fermentation of biomass hydrolysates.

proteomic analysis↗
DOE OSTI2021

Cultivating the Bacterial Microbiota of Populus Roots

Microbial communities play an integral role in the health and survival of their plant hosts. Many studies have identified key members in these communities and led to the use of synthetic communities for elucidating their function; however, these studies are limited by the available cultured bacterial representatives.

16S rRNA gene sequencing↗
DOE OSTI2022

Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Planning decentralized urban renewable energy systems using algal cultivation for closed-loop and resilient communities

To tackle climate challenges, communities need to harvest renewable energy and resources on site locally to close the loops for enhancing the resilience of communities facing unpredictable and uncertain future changes. A decentralization planning of urban renewable energy systems is proposed by treating urban waste streams and producing biomass through applying algal biotechnology. When applying algal technology as a renewable and decentralized energy source in urban systems, the overall performance can vary by levels of urban nutrients, solar and CO 2 resources, and the transportation cost when considering its application to different urban densities, urban form, and the spatial scale of urban settings. This research explores three potential impacts on the algal system’s energy performance: (1) urban density, (2) urban form in different contexts, and (3) spatial scale. The research examines the impacts by testing urban settings given in actual contexts in Atlanta, Georgia, USA. Four neighborhoods representing the high-density urban, mid-density urban, mixed suburban, and typical suburban areas are investigated. The density-scale–performance relationships are explored through testing different urban forms of neighborhoods in both hypothetical and actual neighborhood settings. A GIS-based model is developed to estimate the overall energy performance of the decentralized renewable energy system in urban environments. Results show that the energy performance is positive mainly for high-density urban neighborhoods with small-to-medium scales, up to 0.36 MJ per ton of municipal solid wastes for actual settings and 0.37 MJ for hypothetical cases. Neighborhoods with higher density have higher energy performance while up scaling has negative effects on the energy performance with a low degree of significance. Optimal scales are found as a 1-km radius in real test beds and 1.3 km in hypothetical settings, in which the results show trade-offs between scaling effects in the system efficiency gain and the transportation cost increase.

Quan, Steven Jige↗
DOE OSTI2021

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Abstract Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal–methanogen physical associations and fungal cell wall development and remodeling.

09 BIOMASS FUELS↗
DOE OSTI2021

A field guide to cultivating computational biology

Evolving in sync with the computation revolution over the past 30 years, computational biology has emerged as a mature scientific field. While the field has made major contributions toward improving scientific knowledge and human health, individual computational biology practitioners at various institutions often languish in career development. As optimistic biologists passionate about the future of our field, we propose solutions for both eager and reluctant individual scientists, institutions, publishers, funding agencies, and educators to fully embrace computational biology. We believe that in order to pave the way for the next generation of discoveries, we need to improve recognition for computational biologists and better align pathways of career success with pathways of scientific progress. With 10 outlined steps, we call on all adjacent fields to move away from the traditional individual, single-discipline investigator research model and embrace multidisciplinary, data-driven, team science.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Cultivation and Use of Acidithiobacillus ferrooxidans in Tellurium Biorecovery

The use of Acidithiobacillus ferrooxidans, Thiobacillus thiooxidans, and other chemoautotrophic microbes in bioleaching have been implemented in a variety of processes.1 In industry, bioleaching has been studied for its potential to extract valuable metals from low grade ores that would otherwise be cost prohibitive to recover.2 Other applications of bioleaching include the ability of certain microbes to detoxify waste products and even heavy metal contaminated soils.3 Another potential application for such bio-oxidative microbial activity is the extraction of tellurium (Te) from mine tailings, a low-cost abundant resource. Tellurium is one of the least common elements on Earth; it is found in the planetary crust at about 1 µg/kg, a rarity most comparable to that of platinum.4 A major use of Te in the U.S. is in cadmium-telluride (CdTe) solar panels5. Te is primarily imported into the U.S. from Canada, and it is usually recovered as a byproduct of copper refining.6 Since CdTe photovoltaic (PV) cells are the most efficient, cost-effective, and environmentally friendly PV chemistry, the renewables market has seen an increased demand for CdTe PV cells causing some concerns about sustainability and the limited global availability of Te. Acidithiobacillus ferroxidans is a microorganism that can oxidize iron and sulfur to produce ferric iron and sulfuric acid, and it is possible that it could also solubilize Te from sulfidic mine tailings. In this project, different media for growth of A. ferroxidans were evaluated, and a plan for testing the ability of A. ferroxidans to leach Te from mine tailings was developed. Initial characterization of A. ferroxidans cultures grown in the presence of copper tailings suggests that conditions suitable for Te bioleaching can be established.

60 APPLIED LIFE SCIENCES↗