Photorespiration Research Articles

Isotopic analysis of modern sorghum and finger millet from different altitudes in Ethiopia: implications for ancient farming practices

C4 crops such as sorghum (Sorghum bicolor) and finger millet (Eleusine coracana) have played a significant role in the economic livelihood in arid and semi-arid zones of tropical and sub-tropical Africa since prehistoric times. However, to date, our knowledge of their past management practices is limited. Stable isotope analysis of archaeobotanical remains has been recognized as a valuable tool for reconstructing past agricultural practices, e.g. water management, and fertilization. Nonetheless, our limited understanding of the isotopic variability of C4 plants calls for further research on modern plant before application to archaeobotanical remains. In this paper, we aim to enhance our understanding of modern C4 botanical remains' isotopic variability by analyzing sorghum and finger millet plants. These crops were cultivated according to traditional local practices and collected from ten villages located in the Konso Zone (South Ethiopia) and Tigray Regional State (North Ethiopia), where they are among the daily ingredients for food, and traditional alcoholic and non-alcoholic drinks. We analyzed carbon and nitrogen stable isotopes of seeds and biosilica content in chaff, as it has been suggested that a relationship can exist between silicon and C:N. Carbon isotope values show significant variability, positively correlated with altitude. By demonstrating the sensitivity of C4 grain carbon stable isotope to altitude variations, which are likely connected to water availability, this study offers invaluable insights for the accurate assessment of isotopic values derived from ancient C4 crops. The absence of significant correlations with δ15N suggests that nitrogen isotope values may be less effective for understanding environmental variations in this kind of context. This highlights the limitations of nitrogen isotope data for interpreting ancient agricultural practices and underscores the importance of relying more on carbon isotopes for insights related to environmental conditions and altitude. Furthermore, we confirm that the amount of assimilated carbon may depend also on the biosilica content, which is in turn modulated by environmental parameters such as water availability or soil silicon levels.

Genome-wide comparative analysis of photosynthetic enzymatic genes provides novel insights into foxtail millet and other cereals

C4 crops have more efficient photosynthetic pathways that enable their higher photosynthetic capacities as well as nitrogen and water use efficiencies than C3 crops. Previous research has demonstrated that the genomes of C3 species include and express every gene needed for the C4 photosynthesis pathway. However, very little is known about the dynamics and evolutionary history of such genetic evolution in C4 plants. In this study, the genes encoding five key photosynthetic pathway enzymes in the genomes of C3 (rice), C4 (maize, sorghum, and foxtail millet), and CAM (pineapple) crops were identified and compared systematically. The numbers of genes in these photosynthetic enzymes were highest in the C4 crops like sorghum and foxtail millet, while only eight genes were identified in the CAM plant. However, 16 genes were identified in the C3 crop rice. Furthermore, we performed physical, chemical, gene structure and, cis-element analyses to obtain complete insights into these key genes. Tissue-specific expressions showed that most of the photosynthetic genes are expressed in the leaf tissues. Comparisons of the expression characteristics confirmed that the expression patterns of non-photosynthetic gene copies were relatively conserved among the species, while the C4 gene copies in the C4 species acquired new tissue expression patterns during evolution. Additionally, multiple sequence features that could affect C4 gene expressions and subcellular localization were found in the coding and promoter regions. Our research also highlights the variations in how different genes have evolved within the C4 photosynthetic pathway, and we confirmed that specific high expressions in the leaves and right distribution within the cells were crucial for the development of the C4 photosynthetic abilities. The findings of this study are expected to aid in understanding the evolutionary process of the C4 photosynthetic pathway in grasses as well as offer insights for modifying the C4 photosynthetic pathways in wheat, rice, and other significant C3 cereal crops.

Engineered production of 5-aminolevulinic acid in recombinant Escherichia coli BL21.

5-aminolevulinic acid (ALA) is a non-protein amino acid that has been widely used in the fields of medicine and agriculture. This study aims to engineer the C5 pathway of the ALA biosynthesis in Escherichia coli BL21 to enhance ALA production. The ALA synthase genes gltX, hemA, and hemL were overexpressed in E. coli BL21 to lead to the increase in the production of ALA. The sRNA RyhB was also overexpressed to downregulate the expression of ALA dehydratase to reduce the downstream bioconversion of ALA to porphobilinogen. Next, the gene arcA was knocked out by CRISPR-Cas9 technology to open the TCA cycle to promote the respiratory metabolism of the strain to reduce the feedback inhibition of heme to ALA. The fermentation conditions of the engineered strain were optimized by response surface experiments. The time-course analysis of the ALA production was carried out in a 1 L shake flask. Through these efforts, the production of ALA in engineered strain reached 2953 mg/L in a 1 L shake flask. This study contributes to the industrial production of ALA by the engineered E. coli in the future.

Radiocarbon dating and isotopic paleoecology of Notiomastodon platensis (Mammalia: Proboscidea) from the late Pleistocene of Minas Gerais, Brazil

Proboscidea is a group of large mammals abundant in the fossil record and in Brazil it is represented by Notiomastodon platensis (Ameghino, 1888). To improve the understanding on its taxonomy, chronology, annual diet, and habitats paleoenvironmental aspects, we conducted a morphological description, absolute dating, and analysis of stable isotopes of carbon and oxygen (δ13C and δ18O) in Notiomastodon' remains from the northern (Norte de Minas) and western (Triângulo Mineiro) mesoregions of Minas Gerais State, Brazil. The material includes isolated teeth, mandibular portions, and postcranial bones at different levels of fragmentation, associated with at least eight adults and one juvenile. The only individual from Triângulo, found in Campina Verde municipality, was dated at 27,715–27,903 Cal yr BP. It presented a mixed diet based on C4 plants (piC4 = 90 %; δ13C = 0.5 ‰), which implies the occupation of an open environment, mostly pasture. The region was relatively humid (δ18O = 24.7 ‰), which is supported by the existence of humidity corridors in the Amazon region. A similar phytophysiognomy was inferred for the Norte de Minas region between at least 21,966–22,279 Cal yr BP and 18,944–19,157 Cal yr BP. However, one specimen showed a different δ13C value (piC3 = 0.87 %; δ13C = −10.2 ‰). This indicates it lived in a transitional environment between low-density forest and arboreal savannah. This likely occurred during a period that favored the expansion of trees and shrubs. The region underwent climate change, from relatively humid conditions (δ18O = 25.6 ± 0.2 ‰) to expressively dry (δ18O = 34.6 ‰) between the dated periods, a change corroborated by some palynological data. The multiannual paleoecological analysis, based on sequential sampling of three dentin layers of an incisor, indicated the relative stability of vegetation and climate despite fluctuations in hydrology. The perceived disassociation between vegetation dynamics and local hydrology corroborates the idea that factors other than precipitation may play a significant role in the environmental dynamics of the Cerrado biome.

Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots.

Plasmodesmata (PD) are nanochannels that facilitate cell-to-cell transport in plants. More productive and photosynthetically efficient C4 plants form more PD at the mesophyll (M)-bundle sheath (BS) interface in their leaves than their less efficient C3 relatives. In C4 leaves, PD play an essential role in facilitating the rapid metabolite exchange between the M and BS cells to operate a biochemical CO2 concentrating mechanism, which increases the CO2 partial pressure at the site of Rubisco in the BS cells and hence photosynthetic efficiency. The genetic mechanism controlling PD formation in C3 and C4 leaves is largely unknown, especially in monocot crops, due to the technical challenge of quantifying these nanostructures with electron microscopy. To address this issue, we have generated stably transformed lines of Oryza sativa (rice, C3) and Setaria viridis (setaria, C4) with fluorescent protein-tagged PD to build the first spatiotemporal atlas of leaf pit field (cluster of PD) density in monocots without the need for electron microscopy. Across leaf development, setaria had consistently more PD connections at the M-BS wall interface than rice while the difference in M-M pit field density varied. While light was a critical trigger of PD formation, cell type and function determined leaf pit field density. Complementary temporal mRNA sequencing and gene co-expression network analysis revealed that the pattern of pit field density correlated with differentially expressed PD-associated genes and photosynthesis-related genes. PD-associated genes identified from our co-expression network analysis are related to cell wall expansion, translation and chloroplast signalling.

Prehistoric Italian foodways: Meta-analysis of stable isotope data from the Neolithic to the Iron Age

Italian Later Prehistory was characterised by profound changes that impacted everyday life in many aspects. Whether or not and how such changes were reflected in the subsistence practices of ancient populations is an ongoing question in the archaeological debate. This question has been investigated using stable carbon and nitrogen isotope analysis for several decades. Here, we present a 6000-year-long review of isotopic studies in the Italian Peninsula from the Neolithic to the Iron Age. We reconstruct chronological variations in food practices by observing δ13C and δ15N trends for 776 humans, 382 animals, and 432 C3 plants from 111 archaeological sites. During the Neolithic, when farming is first introduced, a homogenous signal characterised by terrestrial protein consumption is visible. The Copper Age, instead, shows a more varied pattern, possibly representative of a more diversified use of the landscape, characteristic of those millennia. The new cultural paradigm that invested Europe during the Bronze Age is also reflected in food practices in Italy, with the introduction of millets - signalled by high δ13C values in the Northern regions - possibly representing a pivotal shift. Not much data is available for the Iron Age, as only two sites from Northern Italy, showing a diffused consumption of C4 plants, and one site from Southern Italy, with a diet centred around C3 plants, are available for this period. The analysis of this extensive set of data suggests that the “Secondary Products Revolution” probably meant a shift in subsistence practices, with secondary sources substituting meat rather than integrating it.

New Cingulata (Mammalia, Xenarthra) from the late Neogene Palo Pintado Formation (Northwestern Argentina)

Cingulata (Early Eocene-Recent) is a very well-diversified clade that reached a high diversity during the early Neogene. In southern South America, there is an evident imbalance in our knowledge of the Neogene diversity along the Northwestern region of Argentina (NWA) compared to the Pampean region (PR), despite the importance of NWA to understanding the hypothetical evolutionary scenarios of several clades. The Palo Pintado Formation (ca. 10–5 Ma) is one of the richest units in NWA, involving both the global warming of the Tortonian (ca. 11.6–7.25 Ma) and the global cooling event of the Messinian (ca. 7.25–5.33), coeval with the widespread of the C4 plants. Despite this, Cingulata from this Formation are still poorly known. Interdisciplinary fieldwork at Calchaqui Valley (Angastaco Basin) yielded several new remains, including Chlamyphoridae Euphractinae Proeuphractus limpidus, Chorobates villossisimus and Prozaedyus sp.; Dasypodidae Dasypus sp.; Pampatheriidae Kraglievichia paranensis; and Glyptodontidae Cranithlastus xibiensis. The “armadillos” P. limpidus, Prozaedyus sp., and Dasypus sp. increase the previously known diversity. The record of Dasypus sp. reinforces recent hypotheses extending the biochron of the genus to the Late Miocene in NWA. The recognized taxonomic diversity of glyptodonts, limited to one species, contrasts with that known from other coeval formations placed both in the south (Andalhuala and Corral Quemado formations, Catamarca Province) and the north (Maimará and Tafna formations, Jujuy Province), revealing a complex biogeographic scenario for this clade during this period. The analyzed deposits are interpreted as accumulated within the channel and formed during episodes of large discharges of water and sediment mostly under a warm subtropical climate, tough there is an aridization recorded at ca. 6 Ma, which is probably related to the increase in the taxonomic diversification of Cingulata along the stratigraphic sequence.

Over-expression of SiADCL1 in Arabidopsis modulates folate and amino acid metabolism to impact on flowering time

Foxtail millet is a C4 crop rich in folate (FA). This study explores the roles of the 4-amino-4-deoxychorismate lyase (ADCL) – a member of the transaminase IV group of enzymes – in FA metabolism and conferred phenotypes. Phylogenetic comparisons identified diversity in the transaminase IV/ADCL gene family in the foxtail millet genome which was associated with genomic duplications. Molecular docking studies suggested that SiADCL1 bound most strongly to aminodeoxychorismate (ADC) and most likely had the highest catalytic activities. SiADCL1 which was highly expressed in roots, peduncles and flag leaves. Over-expression of SiADCL1 in Arabidopsis significantly increased total FA content (1.14–1.84 fold) and this was linked to a delayed flowering time. Metabolomic and transcriptomic characterization of the derived over-expression lines, found that FA promotes the change of methylation-related genes, ethylene synthesis, amino acid metabolism and flowering-related genes. This study revealed a potential gene coexpression network linked with FA and targeted key genes that could be exploited in foxtail millet breeding programs.

Diversified subsistence patterns and their influencing factors revealed by ancestral paleodiet during the first millenium BC in Northwest Yunnan, China

The in-depth research into how prehistoric human subsistence patterns responded to environmental shifts during the transcontinental spread of crops, livestock, and cultural interactions between the second and first millenium BC is a pivotal scientific endeavor that has aroused widespread attention. Northwest Yunnan, as a vital corridor for human migration, facilitated ancient human dispersals and fostered cultural exchanges. Analyzing prehistoric subsistence patterns in Yunnan, particularly in Northwest Yunnan, is crucial for understanding the dynamics and repercussions of agricultural expansion in Eurasia during prehistory. This study examined stable isotopes extracted from human bone and plant microfossils extracted from dental calculus samples collected from two sites in Northwest Yunnan. The comprehensive analysis revealed that the inhabitants of Northwest Yunnan during the first millenium BC primarily consumed C3 plants (including rice, wheat, barley, buckwheat, legumes, roots and tubers, etcetera), with C4 plants as supplements (such as millets), alongside a high intake of animal protein. With the integration of existing archaeobotanical and zooarchaeological data from neighboring sites, what emerges is a composite subsistence strategy developed by the ancestors in Northwest Yunnan during the first millenium BC, characterized by coexisting practices of planting-gathering and animal husbandry-fishing/hunting. These diversified subsistence patterns were shaped by the cultural influences from Northwest China and the local natural environment, indicating an adaptation to geographical constraints and a strategic response to climatic fluctuations during periods of low productivity.

Stable isotope of Mesolithic remains of Pila wernei of the Nile area, Sudan: A tool for palaeoenvironment reconstruction

The article deals with stable isotopes of oxygen and carbon on current and archaeological semi-aquatic gastropod shell of the Pila wernei from Sudan and reports some new 14C analyses on archaeological Pila specimens. This, with the aim of obtaining new information on climatic and environmental changes in the al-Khiday area during the first phase of Holocene. The Pila shells come from a well-preserved shell midden present at al-Khiday and dated 8700-7000 cal yr BP. The area of al-Khiday was inhabited since at least 10 ka. Pila wernei species has never been studied in detail; this study demonstrates that the O and C isotope composition of aragonite shell is able to record the environmental and diet changes during the gastropod life. The comparison between the isotope data obtained on present-day and archaeological shells show a prevalence of C4 plants and higher rainfall during the Mesolithic. Two climatic fluctuations have been recognised: the first one indicating wetter conditions from 8650-8400 to 8500-8050 cal yr BP (decrease of the δ18O values), the second one pointing less wetter conditions from 8500-8050 to 7850-7600 cal yr BP (increase of δ18O values). Despite the difficulties in studying semi-aquatic gastropods due to their lifestyle habit, the identification of climatic fluctuations in the Early Holocene confirms the reliability of this proxy for climatic reconstructions. Despite the high number of isotopic analyses (1556) used in this work, they were not sufficient to mirror the fast climate changes characterising the studied period and finally obtain a detailed reconstruction for nearly the two millennia considered. Nonetheless, future projects may benefit greatly from unveiling the shell-environment relationship of the species.

Cyclic electron flow and Photosystem II-less photosynthesis.

Oxygenic photosynthesis is characterised by the cooperation of two photo-driven complexes, Photosystem II (PSII) and Photosystem I (PSI), sequentially linked through a series of redox-coupled intermediates. Divergent evolution has resulted in photosystems exhibiting complementary redox potentials, spanning the range necessary to oxidise water and reduce CO2 within a single system. Catalysing nature's most oxidising reaction to extract electrons from water is a highly specialised task that limits PSII's metabolic function. In contrast, potential electron donors in PSI span a range of redox potentials, enabling it to accept electrons from various metabolic processes. This metabolic flexibility of PSI underpins the capacity of photosynthetic organisms to balance energy supply with metabolic demands, which is key for adaptation to environmental changes. Here, we review the phenomenon of 'PSII-less photosynthesis' where PSI functions independently of PSII by operating cyclic electron flow using electrons derived from non-photochemical reactions. PSII-less photosynthesis enables supercharged ATP production and is employed, for example, by cyanobacteria's heterocysts to host nitrogen fixation and by bundle sheath cells of C4 plants to boost CO2 assimilation. We discuss the energetic benefits of this arrangement and the prospects of utilising it to improve the productivity and stress resilience of photosynthetic organisms.

Protective role of reactive aluminum phases to stabilize soil organic matter against long-term cultivation in the humid tropics under volcanic influence

ABSTRACT Cultivation can cause rapid depletion of soil organic matter (SOM), particularly in the humid tropics. Understanding the factors controlling SOM storage is a key step toward effective soil management for sustainable crop production. While clay + silt content is known to be an important factor for soil organic carbon (SOC) storage, recent studies have shown greater importance of oxalate-extracted Al (Alo; roughly corresponds to short-range-order aluminosilicate minerals and organo-Al complexes) and Fe (Feo). However, the extent to which these mineralogical factors control the response of SOM pool to land-use changes remains unclear, especially in the tropics. This study aimed to clarify the factors regulating SOM content in croplands compared to secondary forests or home gardens in Negros Occidental, Philippines. Along two line transects having a wide range of Alo contents, soil samples were collected at a depth of 0 − 10 cm from sugarcane sites (n = 33; long-term continuous cultivation of >70 years) that were paired with either secondary forests (n = 10) or home gardens (n = 20). Sugarcane sites had significantly lower SOC and total nitrogen (N) contents than secondary forest and home garden sites, whereas there was no clear difference between the latter two land uses. Both SOC and total N contents showed significant positive correlations with Alo content and, to a much less extent, with Feo content, but not with clay + silt content. The slope of the regression line between SOC and Alo was indifferent between sugarcane and the other two land uses, while the intercept was significantly lower in the sugarcane sites. These results suggest the protective role of Alo phases in both agricultural and forest soils and the presence of unprotected SOM (e.g. plant litter) in the latter sites. Furthermore, δ13C analysis suggested that the proportion of forest (C3 plant) derived carbon remaining in the sugarcane soils ranged between 10% and 50% and increased with Alo content. Together, our study showed indirect evidence of Alo-induced stabilization of SOM against long-term cultivation under the humid tropical environment.

A life course study of the Beixin culture residents from the Neolithic site of Xiaheqiadong, Shandong Province, China

AbstractThe Xiaheqiadong site located in Zhangqiu district, Jinan city, Shandong province, China, was excavated in 2016 by the Jinan Institute of Archaeology, which revealed six single burials dating to the Beixin culture period (ca. 5,300–4,500 BC to ca. 4,100–3,600 BC). This paper used bioarchaeological methods to study the human skeletal remains to reconstruct the life course of the residents of the Beixin culture at the Xiaheqiadong site, focusing on stable isotope analysis, evaluation of stress, tooth ablation, and intentional skull modification. Based on stable isotope analysis of carbon, it is evident that the dietary structure of the ancient residents of Xiaheqiadong was mainly dependent on C4 plants or animals that ate mainly C4 plants. The stable isotope analysis of nitrogen indicated that the ancient residents of the Xiaheqiadong site exhibited a relatively sufficient consumption of animal protein. Furthermore, this result also reveals that a subsistence economic model was established consisting of farming, gathering, and hunting. Observations of the stress indicators (including cribra orbitalia, porotic hyperostosis, and linear enamel hypoplasia) revealed that they experienced poor health conditions and were under high levels of stress during infancy and early childhood. However, this situation improved with increasing age, suggesting that residents from the Xiaheqiadong site had the capacity to withstand severe living conditions and adapt after experiencing stress events. The tooth ablation and occipital modification cases from the Xiaheqiadong site are the earliest cases among the individuals with accurate dating results found in China.

Fast dehydration reduces bundle sheath conductance in C4 maize and sorghum.

In the face of anthropogenic warming, drought poses an escalating threat to food production. C4 plants offer promise in addressing this threat. C4 leaves operate a biochemical CO2 concentrating mechanism that exchanges metabolites between two partially isolated compartments (mesophyll and bundle sheath), which confers high-productivity potential in hot climates boosting water use efficiency. However, when C4 leaves experience dehydration, photosynthesis plummets. This paper explores the physiological mechanisms behind this decline. In a fast dehydration experiment, we measured the fluxes and isotopic composition of water and CO2 in the gas exchanged by leaves, and we interpreted results using a novel biochemical model and analysis of elasticity. Our findings show that, while CO2 supply to the mesophyll and to the bundle sheath persisted during dehydration, there was a decrease in CO2 conductance at the bundle sheath-mesophyll interface. We interpret this as causing a slowdown of intercellular metabolite exchange - an essential feature of C4 photosynthesis. This would impede the supply of reducing power to the bundle sheath, leading to phosphoglycerate accumulation and feedback inhibition of Rubisco carboxylation. The interplay between this rapid sensitivity and the effectiveness of coping strategies that C4 plants deploy may be an overlooked driver of their competitive performance.

C4 grasses employ distinct strategies to acclimate rubisco activase to heat stress.

Rising temperatures due to the current climate crisis will soon have devastating impacts on crop performance and resilience. In particular, CO2 assimilation is dramatically limited at high temperatures. CO2 assimilation is accomplished by rubisco, which is inhibited by the binding of inhibitory sugar phosphates to its active site. Plants therefore utilize the essential chaperone rubisco activase (RCA) to remove these inhibitors and enable continued CO2 fixation. However, RCA does not function at moderately high temperatures (42°C), resulting in impaired rubisco activity and reduced CO2 assimilation. We set out to understand temperature-dependent RCA regulation in four different C4 plants, with a focus on the crop plants maize (two cultivars) and sorghum, as well as the model grass Setaria viridis (setaria) using gas exchange measurements, which confirm that CO2 assimilation is limited by carboxylation in these organisms at high temperatures (42°C). All three species express distinct complements of RCA isoforms and each species alters the isoform and proteoform abundances in response to heat; however, the changes are species-specific. We also examine whether the heat-mediated inactivation of RCA is due to biochemical regulation rather than simple thermal denaturation. We reveal that biochemical regulation affects RCA function differently in different C4 species, and differences are apparent even between different cultivars of the same species. Our results suggest that each grass evolved different strategies to maintain RCA function during stress and we conclude that a successful engineering approach aimed at improving carbon capture in C4 grasses will need to accommodate these individual regulatory mechanisms.

Time-course analysis of the transcriptome of Arabidopsis thaliana leaves under high-concentration ammonium sulfate treatment

ABSTRACT Ammonium fertilization is of great interest for future agriculture, as unlike nitrate, ammonium use efficiency does not decrease in C3 plants, even in environments with elevated CO2 concentrations. However, excess ammonium often results in toxic effects such as growth suppression and chlorosis, i.e. ammonium toxicity. The addition of nitrate, a major source of nitrogen commonly found in soils, has been shown to alleviate these toxic effects. Understanding the mechanisms of ammonium toxicity in the presence of nitrate is crucial for the effective use of ammonium fertilizers in crop cultivation. To elucidate these responses, a time-course analysis of the transcriptome was performed on A. thaliana leaves treated with high concentrations of ammonium sulfate in the presence of sufficient nitrate. The expression of nitrate-inducible genes tended to be downregulated by the treatment. The expression of genes relating to abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), and membrane trafficking was upregulated, whereas that of photosynthesis-, auxin-, and cytokinin-related genes involved in growth and development was downregulated. The induction of many osmotic stress-responsive genes and nitric oxide (NO)-inducible genes suggests the involvement of osmotic stress and NO signaling in the response. This study provides a novel and comprehensive overview of transcriptional changes occurring in response to high ammonium sulfate concentrations with sufficient nitrate, and sheds light on potential pathways involved in ammonium toxicity under these conditions.

Geographic variability of carbon and nitrogen isotope ratios of nonvolant terrestrial small mammals (Rodentia) across 3 Brazilian biomes

Abstract In this study, we investigated landscape variability of the carbon and nitrogen isotopic composition of nonvolant small mammals in the 3 main Brazilian biomes (Amazon, Atlantic Forest, and Cerrado) while also considering the differential spatial distribution of C4 plants in these biomes. We compiled a subset of data on stable carbon and nitrogen isotope ratios from nonvolant small mammals of the order Rodentia and compared the aggregated isotopic variability at the biome level using classical δ13C–δ15N biplot. The concept of isotopic niche width was used to test whether different foraging attributes drive their isotopic composition, while a Bayesian isotopic mixing model was used to estimate the proportion of 3 main food categories available to these small mammals. We also developed isoscapes in the Brazilian biomes, interpolating animals δ13C and δ15N based on the geographic coordinates of each sample and “sourcescapes” considering geographic variation of the dietary sources. The findings of this study advance our understanding of the foraging ecology of small mammals in biodiversity-rich regions of the Neotropics. Classical methodologies such as stomach content confirmed dietary choices revealed by the stable isotopic composition and also highlighted the importance of C3 and C4 plants in the diet of this group of animals, especially in biomes such as the Atlantic Forest and Cerrado, where there is a predominance of highly altered landscapes. These results confirm that replacing the original vegetation with C4 crops has altered the feeding patterns of small mammals, which could lead to critical ecological changes in the trophic structure of these areas. Vertical stratification of the dietary niche and the interaction between biome and foraging lifestyle were also observed. However, in each biome, there was significant intraspecific and interspecific variation caused by preferences for ingestion of plant and animal material, leading to different degrees of omnivory. Finally, the high local variability between individuals and species requires a larger sampling design that may also contribute to improved spatial resolution of the isoscapes.

Transcriptome dynamics in developing leaves from C3 and C4 Flaveria species.

C4 species have evolved more than 60 times independently from C3 ancestors. This multiple and parallel evolution of the complex C4 trait suggests common underlying evolutionary mechanisms, which could be identified by comparative analysis of closely related C3 and C4 species. Efficient C4 function depends on a distinctive leaf anatomy that is characterised by enlarged, chloroplast-rich bundle sheath cells and narrow vein spacing. To elucidate the molecular mechanisms that generate the Kranz anatomy, we analysed a developmental series of leaves from the C4 plant Flaveria bidentis and the closely related C3 species Flaveria robusta by comparing anatomies and transcriptomes. Vascular density measurements of all nine leaf developmental stages identified three leaf anatomical zones whose proportions vary with respect to the developmental stage. We then deconvoluted the transcriptome datasets using non-negative matrix factorisation, which identified four distinct transcriptome patterns in the growing leaves of both species. By integrating the leaf anatomy and transcriptome data, we were able to correlate the different transcriptional profiles with different developmental zones in the leaves. These comparisons revealed an important role for auxin metabolism, in particular auxin homeostasis (conjugation and deconjugation), in establishing the high vein density typical of C4 species.

Effects of maize residue and biochar applications on soil δ13C and organic carbon sources in a subtropical paddy rice ecosystem

AbstractThis study investigates the utility of plant δ¹3C natural labeling in predicting the impacts of environmental shifts on carbon cycling within ecosystems, particularly focusing on paddy fields treated with maize (Zea mays L.) residues and biochar. Specifically, it examines how soil δ¹3C and the sources of soil organic carbon (SOC), respond in paddy fields (which cultivate C3 plants like rice) when amended with maize residues, maize biochar, and silica‐enriched biochar (derived from C4 plants). Conducted in the Fuzhou paddy fields, the experiment included control groups and treatment groups with maize residue (4 t ha⁻¹), maize biochar (4 t ha⁻¹), and silicon‐modified maize biochar (4 t ha⁻¹) during both the early and late rice growth periods. The results indicate that all soil treatments increased soil δ¹3C. The application of maize residues notably affected the δ¹3C of the upper soil profile (0–15 cm) differently from the deeper layers (15–30 cm), and it increased soil organic C more than biochar or silicon‐modified maize biochar. Soil available P (AP) and pH emerged as significant factors linking δ¹3C, influencing rice yield through changes in soil physicochemical properties. Unlike maize residues, which reduced rice yields, applications of biochar and silicon‐modified maize biochar increased rice yields. The latter, which was particularly effective in lowering SOC decomposition rates and addressing rice's silica needs, emerged as the preferred option. The study highlights maize biochar and silicon‐modified maize biochar as sustainable alternatives to maize residues for rice cultivation, enhancing soil fertility, carbon pool stability, and yields.

Production of 1,4-butanediol through Clostridia C4 pathways

1,4-butanediol (1,4-BDO) is an important building block in the chemical industry that has been mainly produced from fossil fuels, but now biosynthesis of 1,4-BDO has received more and more attention due to environmental issues. The Clostridia C4 pathway produces an intermediate crotonyl-CoA which could be diverted to 1,4-BDO by 4-hydroxybutyryl-CoA dehydratase (4HBD). Here, we compared this pathway with other 1,4-BDO biosynthesis pathways and illustrated its potential advantages regarding cellular energy conservation and theoretical yield. Then, the feasibility of 1,4-BDO production in this way was tested by introducing a single 4HBD in Clostridium acetobutylicum that natively produced the C4 intermediate and a variety of aldehyde/alcohol dehydrogenases (AdhE). Five different 4HBD genes were screened and the Cbei-2100 gene from Clostridium beijerinckii was the most effective, producing 0.066 mg/mL of 1,4-BDO. To block the metabolic flux towards the main product butanol, disruption of butyryl-CoA dehydrogenase (Bcd) was tried but failed, while inactivation of its homologue (FAD/FMN-containing dehydrogenase, Fcd) obtained little effect. Alternatively, the electron-transferring flavoprotein EtfA coupled with Bcd was inactivated, and 1,4-BDO production was greatly increased to 0.182 mg/mL. In conclusion, this study demonstrated the feasibility of 1,4-BDO production through the Clostridia C4 pathway. Further blocking of the competing flux towards butanol would be effective to improve the production of in the future.