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Raw data for publication: Moni Qiande and Fredy Altpeter. 2025. Comparing four heat-inducible promoters in stably transformed sugarcane regarding spatial and temporal control of transgene expression reveals candidates to drive stem preferred transgene expression. Frontiers in Plant Science (accepted for publication).
Animals may select habitat to maximize the benefits of foraging on growth and reproduction, while balancing competing factors like the risk of predation or mortality from other sources. Variation in the distribution of food resources may lead animals to forage at times or in places that carry greater predation risk, with individuals in poor quality habitats expected to take greater risks while foraging. We studied Mojave desert tortoises ( Gopherus agassizii ) in habitats with variable forage availability to determine if risk aversion in their selection of habitat relative was related to abundance of forage. As a measure of risk, we examined tortoise surface activity and mortality. We also compared tortoise body size and body condition between habitats with ample forage plants and those with less forage plants. Tortoises from low forage habitats selected areas where more annual plants were nutritious herbaceous flowering plants but did not favor areas of greater perennial shrub cover that could shelter them or their burrows. In contrast, tortoises occupying high forage habitats showed no preference for forage characteristics, but used burrows associated with more abundant and larger perennial shrubs. Tortoises in high forage habitats were larger and active above ground more often but did not have better body condition. Mortality was four times higher for females occupying low forage habitat than those in high forage habitat. Our results are consistent with the idea that tortoises may minimize mortality risk where food resources are high, but may accept some tradeoff of greater mortality risk in order to forage optimally when food resources are limiting.
ABSTRACT Cyclodextrinases are carbohydrate-active enzymes involved in the linearization of circular amylose oligosaccharides. Primarily thought to function as part of starch metabolism, there have been previous reports of bacterial cyclodextrinases also having additional enzymatic activities on linear malto-oligosaccharides. This substrate class also includes environmentally rare α-diglucosides such as kojibiose (α−1,2), nigerose (α−1,3), and isomaltose (α−1,6), all of which have valuable properties as prebiotics or low-glycemic index sweeteners. Previous genome sequencing of threeCellvibrio japonicusstrains adapted to utilize these α-diglucosides identified multiple, but uncharacterized, mutations in each strain. One of the mutations identified was in theamy13Egene, which was annotated to encode a neopullulanase. In this report, we functionally characterized this gene and determined that it in fact encodes a cyclodextrinase with additional activities on α-diglucosides. Deletion analysis ofamy13Efound that this gene was essential for kojibiose and isomaltose metabolism inC. japonicus. Interestingly, a Δamy13Emutant was not deficient for cyclodextrin or pullulan utilization inC. japonicus; however, heterologous expression of the gene inE. coliwas sufficient for cyclodextrin-dependent growth. Biochemical analyses found thatCjAmy13E cleaved multiple substrates but preferred cyclodextrins and maltose, but had no activity on pullulan. Our characterization of theCjAmy13E cyclodextrinase is useful for refining functional enzyme predictions in related bacteria and for engineering enzymes for biotechnology or biomedical applications. IMPORTANCE Understanding the bacterial metabolism of cyclodextrins and rare α-diglucosides is increasingly important, as these sugars are becoming prevalent in the foods, supplements, and medicines humans consume that subsequently feed the human gut microbiome. Our analysis of a cyclomaltodextrinase with an expanded substrate range is significant because it broadens the potential applications of the GH13 family of carbohydrate active enzymes (CAZymes) in biotechnology and biomedicine. Specifically, this study provides a workflow for the discovery and characterization of novel activities in bacteria that possess a high number of CAZymes that otherwise would be missed due to complications with functional redundancy. Furthermore, this study provides a model from which predictions can be made why certain bacteria in crowded niches are able to robustly utilize rare carbon sources, possibly to gain a competitive growth advantage.
The environmental impacts of packaging and food service ware (FSW) are increasingly the subject of government policy, public discourse, and industry commitments. While some consideration is given to reducing the impacts of packaging across its entire life cycle, most of the focus is on packaging waste or feedstock substitution. Efforts typically focus on specific packaging characteristics, or material attributes, commonly perceived to be environmentally preferable. This article summarizes an extensive meta-review of existing published literature that was performed to determine whether the material attributes recyclability, recycled content, compostability, and biobased, commonly considered to be environmentally beneficial, correlate with lower net environmental impacts across the full life cycle of the packaging and FSW. Seventy-one unique life cycle assessment (LCA) studies that quantify the environmental impacts throughout the entire life cycle of packaging and FSW were analyzed. These studies included over 5000 comparisons for 13 impact categories commonly analyzed in LCA studies. The results from the meta-review identified a number of instances where material attributes do not correlate with environmental benefits for packaging and FSW. Rather, other characteristics such as material choice or mass of the packaging/FSW products can have higher influence in determining life cycle impacts.
The optimal macronutrient composition of the diet is controversial and many adults attempt to regulate the intake of specific macronutrients for various health-related reasons. The objective was to compare stability and ranges of intakes of different macronutrients across diverse adult populations in the USA and globally. US dietary intake data from NHANES 2009–2014 were used to determine macronutrient intake as a percentage of total energy intake. Variability in macronutrient intake was estimated by calculating the difference between 75th and 25th percentile (Q3–Q1) IQRs of macronutrient intake distributions. In addition, intake data from 13 other countries with per capita gross domestic product (GDP) over $10,000 US dollars (USD) were used to assess variability of intake internationally since there are large differences in types of foods consumed in different countries. Protein, carbohydrate, and fat intake (NHANES 2009–2014) was 15.7 ± 0.1, 48.1 ± 0.1, and 32.9 ± 0.1% kcal, respectively, in US adults. The IQR of protein intake distribution (3.73 ± 0.11% kcal) was 41% of carbohydrate intake distribution (9.18 ± 0.20% kcal) and 58% of fat intake distribution (6.40 ± 0.14% kcal). The IQRs of carbohydrate and fat intake distributions were significantly (P <0.01) influenced by age and race; however, the IQR of protein intake was not associated with demographic and lifestyle factors including sex, race, income, physical activity, and body weight. International mean protein intake was 16.3 ± 0.2% kcal, similar to US intake, and there was less variation in protein than carbohydrate or fat intake. Protein intake of the US population and multiple international populations, regardless of demographic and lifestyle factors, was consistently ~16% of total energy, suggesting biological control mechanism(s) tightly regulate protein intake and, consequently, influence intake of other macronutrients and food constituents. Substantial differences in intake of the other macronutrients observed in US and international populations had little influence on protein intake. This trial was registered at the ISRCTN registry as ISRCTN46157745
Organic waste streams generated by wastewater treatment plants, agricultural operations, and food processing industries represent an important yet underutilized opportunity for renewable energy production in the United States. Through anaerobic digestion, these waste streams can produce biogas, a mixture primarily composed of methane (CH4) and carbon dioxide (CO2), that can be upgraded to pipeline-quality natural gas. However, most existing upgrading technologies remove CO2 from biogas rather than utilizing it, leaving a significant portion of the potential energy unused. This project investigates a novel biological upgrading approach that converts CO2 into additional CH4 by supplying hydrogen (H2) to specialized microorganisms capable of performing hydrogenotrophic methanation. The main challenges associated with biological biogas upgrading are related to hydrogen supply, gas-liquid mass transfer, and process stability. First, due to the high cost of hydrogen gas, it is preferable that H2 be produced on-site using renewable energy sources such as wind or solar power. Second, hydrogen has low solubility in liquids, which limits its availability to microorganisms and requires strategies to improve gas dissolution and transfer within the reactor. Third, process inhibition may occur as a result of increased pH caused by CO2 consumption or elevated H2 partial pressure, both of which can negatively affect methanogenic activity. Although research in these areas has advanced during the course of this project, these challenges have not yet been fully resolved. To date, the biological systems that have achieved the highest methane concentrations are typically ex-situ reactors, where operational conditions can be more easily controlled. For this reason, the findings of the present project remain highly relevant. The project goal was to develop an innovative system that can accomplish biogas upgrading via biological conversion of CO2 to CH4, in a novel hybrid approach that combines the advantages of both in-situ and ex-situ systems. The proposed system employs a three-phase upflow anaerobic bioreactor with H2 delivery through a gas-permeable membrane, enabling efficient hydrogen transfer and microbial conversion. Under optimized operating conditions, the system achieved 99% H2 consumption and 90% CO2 conversion. A subsequent gas cleaning stage was implemented to further improve gas quality and meet target purity standards. The upgraded gas composition reached 97.7% CH4, 2.2% CO2, and 0.97% O2, while H2S concentrations remained below detection limits. In addition, a flue gas-driven inorganic thermoelectric generator (TEG) system was designed and experimentally validated as a potential source of electricity for H2 production. The system consisted of six TEG modules connected in series and achieved an open-circuit voltage of 4.5 V and a maximum power output of 224 mW at a temperature difference of approximately 53.5 °C, demonstrating effective conversion of waste heat into electrical power under simulated flue gas conditions. Finally, a comprehensive techno-economic analysis was completed to evaluate the capital and operating costs associated with the proposed system. The results provide important insights to guide future scale-up, optimization, and potential deployment of integrated biological biogas upgrading technologies.
Abstract Roots are a primary source of organic carbon input in most soils. The consumption of living and detrital root inputs involves multi-trophic processes and multiple kingdoms of microbial life, but typical microbial ecology studies focus on only one or two major lineages. We used Illumina shotgun RNA sequencing to conduct PCR-independent SSU rRNA community analysis (“community RNA-Seq”) and simultaneously assess the bacteria, archaea, fungi, and microfauna surrounding both living and decomposing roots of the annual grass, Avena fatua. Plants were grown in 13CO2-labeled microcosms amended with 15N-root litter to identify the preferences of rhizosphere organisms for root exudates (13C) versus decaying root biomass (15N) using NanoSIMS microarray imaging (Chip-SIP). When litter was available, rhizosphere and bulk soil had significantly more Amoebozoa, which are potentially important yet often overlooked top-down drivers of detritusphere community dynamics and nutrient cycling. Bulk soil containing litter was depleted in Actinobacteria but had significantly more Bacteroidetes and Proteobacteria. While Actinobacteria were abundant in the rhizosphere, Chip-SIP showed Actinobacteria preferentially incorporated litter relative to root exudates, indicating this group’s more prominent role in detritus elemental cycling in the rhizosphere. Our results emphasize that decomposition is a multi-trophic process involving complex interactions, and our methodology can be used to track the trajectory of carbon through multi-kingdom soil food webs.
Abstract Fishery discards supplement food for many seabirds, but the impacts of declining discards are poorly understood. Discards may be beneficial for some populations but have negative impacts by increasing bycatch risk or because they are junk-food. The Falkland Islands support > 70% of global black-browed albatross Thalassarche melanophris populations, which feed on discards. However, the effect of discards on population demographics, and implications of fishery management changes, are unknown. We analysed stomach contents of black-browed albatross chicks across eight breeding seasons (2004–2020) from New Island, Falkland Islands, to assess variation in discard consumption and how this relates to foraging conditions and breeding success. Across years, 68%–98% of samples contained natural prey, whilst 23%–88% of samples contained fishery discards. Discard consumption was positively related to fishery catches of hoki Macruronus magellanicus and sea surface temperature anomalies SSTA (°C), and negatively related to breeding success. These results suggest a diet-switching behaviour for Falkland Islands albatrosses, whereby birds switch from preferred natural prey to suboptimal discards when environmental conditions, and hence natural feeding opportunities, are unfavourable. Crucially, this study highlights that fishery discards do not compensate for poor natural foraging conditions for breeding albatrosses in the long term.
The complex topography of submarine canyons may result in different composition of benthic foraminifera assemblages. To understand how trophic, hydrological and sedimentological conditions in submarine canyons can influence the distribution of benthic foraminifera, and to use this information to corroborate paleoenvironmental interpretations for the Holocene, we investigated recent benthic foraminiferal assemblages (total fauna >63 μm) and sedimentological data in two canyons (CANWN and CAND) in the Espírito Santo Basin (ESB) between 18°20' and 21°20' S. Surface sediment samples (0–2 cm) were collected inside the canyons (150 to 1300 m water depth) and in shelf-slope adjacent transects (50 to 1300 m water depth). The density, taxonomic diversity, and assemblage composition of benthic foraminifera change with depth and location. The distinct ecological preferences of the most abundant taxa allowed us to recognize five benthic foraminiferal groups. Three groups (V, III, and I) are present in different bathymetric sectors; Group V: outer shelf (50 m), Group III: upper, and middle – lower slope (150 to 400 m), and Group I: middle – lower slope (1000 to 1300 m). Groups II and IV show no characteristic bathymetric distribution and are present only in CAND and in CANWN, respectively. Group V consists of Hanzawaia boueana, Peneroplis planatus, and Quinqueloculina lamarckiana; Group III is dominated by Globocassidulina rossensis and Trifarina spp.; Group I consists of Globocassidulina crassa, Bolivina lowmani, Gavelinopsis versiformis, Alabaminella weddellensis, and Epistominella exigua. The main species in Group II (CAND, 150, 1000 to 1300 m) are Trifarina angulosa, Globocassidulina subglobosa, and Discorbis vilardeboanus. Group IV (middle – lower CANWN, 1000 to 1300 m), consists mainly of agglutinated species Glomospira charoides, Rhabdammina abyssorum, and Psammosphaera fusca. Further, our data suggest that the quantity (and quality) of food supply, hydrodynamic conditions and sediment properties are the main drivers controlling the bathymetric distribution of benthic foraminiferal assemblages in both canyons. The middle – lower CANNW revealed unstable trophic conditions, related to terrigenous sediment input due to turbidity currents. In CAND, the foraminiferal assemblages ecology indicated sufficient organic matter supply that favors species establishment and diversity, indicating a more productive and less unstable environment than in CANWN.
Agrivoltaic systems allow for the simultaneous production of solar-generated electricity and agriculture. As the climate change related impacts of conventional energy and food production intensify, finding strategies to increase the deployment of solar photovoltaic systems, preserve agricultural land, and minimize competing land uses is urgent. Given the proven technical, economic, and environmental advantages provided by agrivoltaic systems, increased proliferation is anticipated, which necessitates accounting for the nuances of community resistance to solar development on farmland. Minimizing siting conflict and addressing agricultural communities’ concerns will be key in promoting public support for agrivoltaics, as localized acceptance of solar is a critical determinant of project success. This survey study assessed if public support for solar development increases when energy and agricultural production are combined in an agrivoltaic system. Results show that 81.8% of respondents would be more likely to support solar development in their community if it combined the production of both energy and agriculture. This increase in support for solar given the agrivoltaic approach highlights a development strategy that can improve local social acceptance and the deployment rate of solar photovoltaics. Survey respondents prefer agrivoltaic projects that a) are designed to provide economic opportunities for farmers and the local community b) are located on private property or existing agricultural land c) do not threaten local interests and d) ensure fair distribution of economic benefits. Proactively identifying what the public perceives as opportunities and concerns related to agrivoltaic development can help improve the design, business model, and siting of systems in the U.S.
Ectomycorrhizal fungi (EMF) produce mycelia with variable extension and complexity, which can be classified according to soil ‘exploration types’ (ETs). ETs have received attention as one of the few mycorrhizal trait frameworks, but without an empirical classification of ET functional diversity and environmental preferences, understanding and interpreting EMF biogeographic patterns has been difficult. We conducted a synthesis combining: comparative EMF genomics to describe functional divergence in decomposition and nutrient cycling genes across ETs; and EMF trait distribution modeling across continental Europe, pairing soil and root EMF surveys to establish biogeographic ET niche profiles. We demonstrate a signature of ETs encoded in EMF genomes, which is independent from phylogeny and linked to biomass production strategies. EMF ET relative abundances were separated by soil, root, and dominant tree leaf type habitats and exhibited unique correlations with forest biotic (e.g. plant productivity and plant pathogen densities) and abiotic (e.g. nitrogen deposition and soil pH) conditions. These findings support a theory that EMF niche partitioning can be partially explained by extraradical mycelial traits, with underlying variation in ET biogeography likely arising from distinct decomposition and nutrient cycling potentials. We also identify important limitations to this trait framework and provide a guided outlook for future research.