Species-specific Functions Research Articles

Actin cytoskeletal regulation of ciliogenesis in development and disease.

Primary cilia are antenna-like sensory organelles that are evolutionarily conserved in nearly all modern eukaryotes, from the single-celled green alga, Chlamydomonas reinhardtii, to vertebrates and mammals. Cilia are microtubule-based cellular projections that have adapted to perform a broad range of species-specific functions, from cell motility to detection of light and the transduction of extracellular mechanical and chemical signals. These functions render cilia essential for organismal development and survival. The high conservation of cilia has allowed for discoveries in C. reinhardtii to inform our understanding of the basic biology of mammalian primary cilia, and to provide insight into the genetic etiology of ciliopathies. Over the last two decades, a growing number of studies has revealed that multiple aspects of ciliary homeostasis are regulated by the actin cytoskeleton, including centrosome migration and positioning, vesicle transport to the basal body, ectocytosis, and ciliary-mediated signaling. Here, we review actin regulation of ciliary homeostasis, and highlight conserved and divergent mechanisms in C. reinhardtii and mammalian cells. Further, we compare the disease manifestations of patients with ciliopathies to those with mutations in actin and actin-associated genes, and propose that primary cilia defects caused by genetic alteration of the actin cytoskeleton may underlie certain birth defects.

Surface mapping of gastric motor functions using MRI: a comparative study between humans and rats.

The stomach's ability to store, mix, propel, and empty its content requires highly coordinated motor functions. However, current diagnostic tools cannot simultaneously assess these motor processes. This study aimed to use magnetic resonance imaging (MRI) to map multifaceted gastric motor functions, including accommodation, tonic and peristaltic contractions, and emptying, through a single noninvasive experiment for both humans and rats. Ten humans and 10 Sprague-Dawley rats consumed MRI-visible semisolid meals and underwent MRI scans. We used a surface model to analyze MRI data, capturing the deformation of the stomach wall on ingestion or during digestion. We inferred muscle activity, mapped motor processes, parcellated the stomach into functional regions, and revealed cross-species distinctions. In humans, both the fundus and antrum distended postmeal, followed by sustained tonic contractions to regulate intragastric pressure. Peristaltic contractions initiated from the distal fundus, including three concurrent wavefronts oscillating at 3.3 cycles/min and traveling at 1.7 to 2.9 mm/s. These motor functions facilitated linear gastric emptying with a 61-min half-time. In contrast, rats exhibited peristalsis from the midcorpus, showing two wavefronts oscillating at 5.0 cycles/min and traveling at 0.4 to 0.9 mm/s. For both species, motility features allowed functional parcellation of the stomach along a midcorpus division. This study maps region- and species-specific gastric motor functions. We demonstrate the value of MRI with surface modeling in understanding gastric physiology and its potential to become a new standard for clinical and preclinical investigations of gastric disorders at both individual and group levels.NEW & NOTEWORTHY A novel MRI technique can visualize how the stomach accommodates, mixes, and propels food for digestion in humans and animals alike. Digital models of gastric MRI reveal the functional maps, organization, and distinction of the stomach across individuals and species. This technique holds the unique potential to advance basic and clinical studies of functional gastric disorders.

Structural diversity and carbon stock of forest stands: tradeoff as modified by silvicultural thinning

AbstractIn forest management, merging stand structural diversity with carbon storage is essential for resilience and climate mitigation. This study assesses (1) how structural diversity in stands of spruce (Picea abies (L.) H. Karst.), pine (Pinus sylvestris L.), beech (Fagus sylvatica L.), and oak (Quercus robur L. and Quercus petraea (Matt.) Liebl.) in Central Europe varies with age, site quality, and applied thinning grade; (2) these factors' impact on carbon stock; and (3) the link between structural diversity and carbon stock. Analyzing 26 long-term thinning experiments, we used the Gini coefficient of tree heights to measure structural diversity and species-specific biomass functions for carbon stock assessments. Our results show that structural diversity, highest in beech and spruce, decreases with stand age and on richer sites. Thinning enhances structural diversity in spruce and beech but reduces it in pine and oak. Unthinned or only moderately thinned mature spruce and beech stands outperform pine and oak in carbon stock (200–300 vs. 100–150 Mg C ha−1). C- and D&E-grade thinning halves carbon stock. A decrease in vertical layering with increased carbon storage varies across species. Given the same carbon stock, thinning from above maintains structural diversity in spruce and beech, while non-thinning or thinning from below promotes structural diversity in pine and oak. Based on the current silvicultural practice reflected by the NFI data of Germany, we argue that reduced thinning in previously D&E-grade thinned stands may slightly reduce their structural diversity. However, a suspension or reduction of thinning would strongly improve carbon storage (+ 100–200 Mg C ha−1) in the next 3–5 decades. We discussed options for reconciling structural diversity and carbon storage by silvicultural management of the four considered species in Central Europe.

No detectable influence of the carbonate ion effect on changes in stable carbon isotope ratios (δ13C) of shallow dwelling planktic foraminifera over the past 160 kyr

Abstract. Laboratory experiments showed that the isotopic fractionation of δ13C and of δ18O during calcite formation of planktic foraminifera are species-specific functions of ambient CO32- concentration. This effect became known as the carbonate ion effect (CIE), whose role for the interpretation of marine sediment data will be investigated here in an in-depth analysis of the 13C cycle. For this investigation, we constructed new 160 kyr long mono-specific stacks of changes in both δ13C and δ18O from either the planktic foraminifera Globigerinoides ruber (rub) or Trilobatus sacculifer (sac) from 112 and 40 marine records, respectively, from the wider tropics (latitudes below 38°). Both mono-specific time series Δ(δ13Crub) and Δ(δ13Csac) are very similar to each other, and a linear regression through a scatter plot of both data sets has a slope of ∼ 0.99 – although the laboratory-based CIE for both species differs by a factor of nearly 2, implying that they should record distinctly different changes in δ13C, if we accept that the carbonate ion concentration changes on glacial–interglacial timescales. For a deeper understanding of the 13C cycle, we use the Solid Earth version of the Box model of the Isotopic Carbon cYCLE (BICYLE-SE) to calculate how surface-ocean CO32- should have varied over time in order to be able to calculate the potential offsets which would by caused by the CIE quantified in culture experiments. Our simulations are forced with atmospheric reconstructions of CO2 and δ13CO2 derived from ice cores to obtain a carbon cycle which should at least at the surface ocean be as close as possible to expected conditions and which in the deep ocean largely agrees with the carbon isotope ratio of dissolved inorganic carbon (DIC), δ13CDIC, as reconstructed from benthic foraminifera. We find that both Δ(δ13Crub) and Δ(δ13Csac) agree better with changes in simulated δ13CDIC when ignoring the CIE than those time series which were corrected for the CIE. The combination of data- and model-based evidence for the lack of a role for the CIE in Δ(δ13Crub) and Δ(δ13Csac) suggests that the CIE as measured in laboratory experiments is not directly transferable to the interpretation of marine sediment records. The much smaller CIE-to-glacial–interglacial-signal ratio in foraminifera δ18O, when compared to δ13C, prevents us from drawing robust conclusions on the role of the CIE in δ18O as recorded in the hard shells of both species. However, theories propose that the CIE in both δ13C and δ18O depends on the pH in the surrounding water, suggesting that the CIE should be detectable in neither or both of the isotopes. Whether this lack of role of the CIE in the interpretation of planktic paleo-data is a general feature or is restricted to the two species investigated here needs to be checked with further data from other planktic foraminiferal species.

Predicting Wood Density Using Resistance Drilling: The Effect of Varying Feed Speed and RPM

The IML PD series Resi is a device used to assess the drilling resistance of wood. The IML PD series Resi instrument is being widely adopted for commercial wood quality assessment due to its speed, cost-effectiveness, and precision when combined with web-based trace processing. Collecting Resi data with fixed feed speed and RPM settings is challenging due to inherent basic density variations within and between tree species. Altering these settings affects the drilling resistance amplitude of the Resi data, impacting basic density predictions. This study introduces the concept of chip thickness to combine feed speed and RPM into a single parameter to minimise the effects of different sampling conditions on the basic density predictions. Regression models, with chip thickness as the regressor variable, account for 97% to 99% of variance in mean Resi outerwood amplitude across six species. The demonstrated adaptability of chip thickness for adjusting feed speed and RPM settings, along with species-specific functions correlating it with Resi amplitude, holds promise for standardizing amplitude values across diverse feed speeds and RPM settings. Optimal sampling conditions needed to predict basic density lie within the 30%–40% amplitude range. To drill a ~30 cm diameter tree, the recommended fastest settings were 200 cm/min and 3500 RPM for Southern Pine (Pinus elliottii var. elliottii (Engelm) × Pinus caribaea var. hondurensis (Sénéclauze)) and Radiata Pine (Pinus radiata (D. Don.)), 200 cm/min and 2500 RPM for Hoop Pine (Araucaria cunninghamii (Mudie)), 50 cm/min and 5000 RPM for Spotted Gum (Corymbia citriodora subsp. variegata (F. Muell.)), 200 cm/min and 4500 RPM for White Cypress (Callitris glaucophylla (Thompson & Johnson)), and 150 cm/min and 3500 RPM for Shining Gum (Eucalyptus nitens (H. Deane & Maiden) Maiden) based on the billets sampled.

Adaptive evolution of chloroplast division mechanisms during plant terrestrialization

Despite extensive research, the origin and evolution of the chloroplast division machinery remain unclear. Here, we employ recently sequenced genomes and transcriptomes of Archaeplastida clades to identify the core components of chloroplast division and reconstruct their evolutionary histories, respectively. Our findings show that complete division ring structures emerged in Charophytes. We find that Glaucophytes experienced strong selection pressure, generating diverse variants adapted to the changing terrestrial environments. By integrating the functions of chloroplast division genes (CDGs) annotated in a workflow developed using large-scale multi-omics data, we further show that dispersed duplications acquire more species-specific functions under stronger selection pressures. Notably, PARC6, a dispersed duplicate CDG, regulates leaf color and plant growth in Solanum lycopersicum, demonstrating neofunctionalization. Our findings provide an integrated perspective on the functional evolution of chloroplast division machinery and highlight the potential of dispersed duplicate genes as the primary source of adaptive evolution of chloroplast division.

TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome

THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.

An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between Klebsiella species.

Cas9-based gene editing tools have revolutionized bacterial genetics, yet, their application to non-model gut bacteria is frequently hampered by various limitations. We utilized a two-plasmid Cas9-based system designed for gene deletion in Klebsiella pneumoniae and demonstrate after optimization its utility for gene editing in three members of the Klebsiella oxytoca species complex (KoSC) namely K. oxytoca, Klebsiella michiganensis, and Klebsiella grimontii. We then adapted a recently developed protocol for functional complementation based on universal "bookmark" targets applicable to all tested species. In summary, species-specific adaptation of state-of-the-art genetic tools allows efficient gene deletion and complementation in type strains as well as natural isolates of KoSC members to study microbial interactions.

Emerging role of extracellular vesicles in veterinary practice: novel opportunities and potential challenges

Extracellular vesicles are nanoscale vesicles that transport signals between cells, mediating both physiological and pathological processes. EVs facilitate conserved intercellular communication. By transferring bioactive molecules between cells, EVs coordinate systemic responses, regulating homeostasis, immunity, and disease progression. Given their biological importance and involvement in pathogenesis, EVs show promise as biomarkers for veterinary diagnosis, and candidates for vaccine production, and treatment agents. Additionally, different treatment or engineering methods could be used to boost the capability of extracellular vesicles. Despite the emerging veterinary interest, EV research has been predominantly human-based. Critical knowledge gaps remain regarding isolation protocols, cargo loading mechanisms, in vivo biodistribution, and species-specific functions. Standardized methods for veterinary EV characterization and validation are lacking. Regulatory uncertainties impede veterinary clinical translation. Advances in fundamental EV biology and technology are needed to propel the veterinary field forward. This review introduces EVs from a veterinary perspective by introducing the latest studies, highlighting their potential while analyzing challenges to motivate expanded veterinary investigation and translation.

The genomes of 5 underutilized Papilionoideae crops provide insights into root nodulation and disease resistance.

The Papilionoideae subfamily contains a large amount of underutilized legume crops, which are important for food security and human sustainability. However, the lack of genomic resources has hindered the breeding and utilization of these crops. Here, we present chromosome-level reference genomes for 5 underutilized diploid Papilionoideae crops: sword bean (Canavalia gladiata), scarlet runner bean (Phaseolus coccineus), winged bean (Psophocarpus tetragonolobus), smooth rattlebox (Crotalaria pallida), and butterfly pea (Clitoria ternatea), with assembled genome sizes of 0.62 Gb, 0.59 Gb, 0.71 Gb, 1.22 Gb, and 1.72 Gb, respectively. We found that the long period of higher long terminal repeat retrotransposon activity is the major reason that the genome size of smooth rattlebox and butterfly pea is enlarged. Additionally, there have been no recent whole-genome duplication (WGD) events in these 5 species except for the shared papilionoid-specific WGD event (∼55 million years ago). Then, we identified 5,328 and 10,434 species-specific genes between scarlet runner bean and common bean, respectively, which may be responsible for their phenotypic and functional differences and species-specific functions. Furthermore, we identified the key genes involved in root-nodule symbiosis (RNS) in all 5 species and found that the NIN gene was duplicated in the early Papilionoideae ancestor, followed by the loss of 1 gene copy in smooth rattlebox and butterfly pea lineages. Last, we identified the resistance (R) genes for plant defenses in these 5 species and characterized their evolutionary history. In summary, this study provides chromosome-scale reference genomes for 3 grain and vegetable beans (sword bean, scarlet runner bean, winged bean), along with genomes for a green manure crop (smooth rattlebox) and a food dyeing crop (butterfly pea). These genomes are crucial for studying phylogenetic history, unraveling nitrogen-fixing RNS evolution, and advancing plant defense research.

Acid tolerance of Lactobacillus spp. on root carious lesions: A complex and multifaceted response

Lactobacillus spp. are acidogenic and aciduric bacteria and are among the main cariogenic microorganisms associated with the carious process. Objective: This study aimed to identify genes involved in the acid-tolerance of Lactobacillus spp. and potential functions attributed to these genes within the metatranscriptome of sound root surfaces and carious root surfaces. Design: Genomic libraries were built from mRNA isolated from the biofilm samples (10 from sound root and 9 from carious root using Illumina HiSeq 2500). Reads generated by RNA-seq were mapped against 162 oral microbial genomes and genes potentially related to acid tolerance were manually extracted from the Lactobacillus spp. genomes using L. paracasei ATCC 344 as reference genome. The R package DESeq2 was used to calculate the level of differential gene expression between those two clinical conditions. Results: Fifteen Lactobacillus spp. genomes were identified and a total of 653 acid tolerance genes were overexpressed in carious root surfaces. Multiple functions, as translation, ribosomal structure and biogenesis, transport of nucleotides and amino acids, are involved in Lactobacillus spp. acid tolerance. Species-specific functions also seem to be related to the fitness of Lactobacillus spp. in acidified environments such as that of the cariogenic biofilm associated with carious root lesions. Conclusions: The response of Lactobacillus spp. to an acidic environment is complex and multifaceted. This finding suggests several possible avenues for further research into the adaptive mechanisms of these bacteria.

Unraveling Microbial Endosymbiosis Dynamics in Plant-Parasitic Nematodes with a Genome Skimming Strategy

Bacterial endosymbionts, in genera Wolbachia and Cardinium, infect various arthropods and some nematode groups. Manipulating these microbial symbionts presents a promising biocontrol strategy for managing disease-causing parasites. However, the diversity of Wolbachia and Cardinium in nematodes remains unclear. This study employed a genome skimming strategy to uncover their occurrence in plant-parasitic nematodes, analyzing 52 populations of 12 species. A metagenome analysis revealed varying endosymbiont genome content, leading to the categorization of strong, weak, and no evidence for endosymbiont genomes. Strong evidence for Wolbachia was found in five populations, and for Cardinium in one population, suggesting a limited occurrence. Strong Wolbachia evidence was noted in Pratylenchus penetrans and Radopholus similis from North/South America and Africa. Heterodera glycines from North America showed strong Cardinium evidence. Weak genomic evidence for Wolbachia was observed in Globodera pallida, Meloidogyne incognita, Rotylenchus reniformis, Pratylechus coffeae, Pratylenchus neglectus, and Pratylenchus thornei; for Cardinium was found in G. pallida, R. reniformis and P. neglectus; 27/52 populations exhibited no endosymbiont evidence. Wolbachia and Cardinium presence varied within nematode species, suggesting non-obligate mutualism. Wolbachia and Cardinium genomes differed among nematode species, indicating potential species-specific functionality. This study advances knowledge of plant-parasitic nematode–bacteria symbiosis, providing insights for downstream eco-friendly biocontrol strategies.

Learning from Forest Trees: Improving Urban Tree Biomass Functions

Trees are one of the few carbon sinks in urban areas. Different methods are available to assess the biomass of urban trees, one of these being allometric biomass functions. Biomass functions are well investigated, reliable and easy to apply if the required information is available. Our goal is to use biomass functions to enhance urban forest management tools with information on stored biomass and carbon. In this study, we test several approaches to estimate new species-specific biomass functions. We include data from urban and traditional forest trees since both origins can be modeled by the allometric relationship solely giving different parameter estimates. The tested models include mixed allometric models for urban trees only, the adjustments of available forest tree biomass models and a cross-classified mixed model (CCMM) using both data from urban and forest trees. We then show by cross validation that the CCMM, statistically separating the data into different species and origins, shows greater improvement over the simpler models. Hence, we state that the inclusion of forest tree data improves the performance on biomass predictions for urban trees: the urban tree biomass functions “learned from forest trees”. The CCMM is also compared against the predictions of the above-ground biomass functions applied in the German National Forest Inventory. Comparable RMSE and slightly lower BIAS values are found, both for deciduous and coniferous tree species. With the approach of a cross-classified model, we also enable predictions for non-observed conifers in urban space, assuming comparable growth differences between deciduous and conifer species in forest stands and urban areas. A sample application using the CCMM model shows results for a small subset of data of an urban tree inventory, collected in a residential area in the city of Munich, Germany. It is applied to estimate carbon storage at two points in time and, hence, carbon fluxes in the period under consideration. Such information can help in the decision making and management of urban trees.

Genome-Wide Identification of β-1,3-Glucanase Genes in Hevea brasiliensis

β-1,3-glucanase is one of the pathogenesis-related proteins well-known for their antifungal properties which can be abundantly found in Hevea brasiliensis. Utilization of β-1,3-glucanase in the genetic improvement of H. brasiliensis is very important as the high susceptibility to various fungal infections has challenged the current natural rubber industry. A few nucleotide sequences for β-1,3-glucanase have been reported and their role in biotic stress management has been demonstrated. Being a multigene family, it is necessary to identify and characterize more isoforms of β-1,3-glucanase to select the most suitable isoform to be utilized in genetic improvement. In the current study, we conducted a genome-wide identification of β-1,3-glucanases in H. brasiliensis, their classification based on the functional domains and phylogenetic analysis, using different bioinformatics tools. All publicly available nucleotide sequences were collected and curated by eliminating sequences that lack glycoside hydrolase family 17 (GH 17) domain as well as the partial and closely identical sequences and obtained 14 full-length sequences. The sequences were categorized into 4 distinct classes (I-IV) based on their functional domains and C-terminal extension. Class III and IV which lack the carbohydrate-binding C-terminal X8 domain are the largest classes identified with 5 β-1,3-glucanase each while 4 β-1,3-glucanase contain a variable C-terminal X8 domain. Phylogenetic analysis showed the clustering of β-1,3-glucanases into six major clades (I-VI) based on the domains. Clades I and II were identified as the largest clades with 4 β-1,3-glucanase in each. Several paralogous clusters have been observed for H. brasiliensis indicating the gene family expansion within the species or in the immediate ancestors with possible species-specific function. Further functional characterization is necessary to select the suitable gene to be utilized in genetic improvement and the present study provides a platform for it.

Diet prevents the expansion of segmented filamentous bacteria and ileo-colonic inflammation in a model of Crohn’s disease

BackgroundCrohn’s disease (CD) is associated with changes in the microbiota, and murine models of CD-like ileo-colonic inflammation depend on the presence of microbial triggers. Increased abundance of unknown Clostridiales and the microscopic detection of filamentous structures close to the epithelium of TnfΔARE mice, a mouse model of CD-like ileitis pointed towards segmented filamentous bacteria (SFB), a commensal mucosal adherent bacterium involved in ileal inflammation.ResultsWe show that the abundance of SFB strongly correlates with the severity of CD-like ileal inflammation in two mouse models of ileal inflammation, including TnfΔARE and SAMP/Yit mice. SFB mono-colonization of germ-free TnfΔARE mice confirmed the causal link and resulted in severe ileo-colonic inflammation, characterized by elevated tissue levels of Tnf and Il-17A, neutrophil infiltration and loss of Paneth and goblet cell function. Co-colonization of SFB in human-microbiota associated TnfΔARE mice confirmed that SFB presence is indispensable for disease development. Screening of 468 ileal and colonic mucosal biopsies from adult and pediatric IBD patients, using previously published and newly designed human SFB-specific primer sets, showed no presence of SFB in human tissue samples, suggesting a species-specific functionality of the pathobiont. Simulating the human relevant therapeutic effect of exclusive enteral nutrition (EEN), EEN-like purified diet antagonized SFB colonization and prevented disease development in TnfΔARE mice, providing functional evidence for the protective mechanism of diet in modulating microbiota-dependent inflammation in IBD.ConclusionsWe identified a novel pathogenic role of SFB in driving severe CD-like ileo-colonic inflammation characterized by loss of Paneth and goblet cell functions in TnfΔARE mice. A purified diet antagonized SFB colonization and prevented disease development in TnfΔARE mice in contrast to a fiber-containing chow diet, clearly demonstrating the important role of diet in modulating a novel IBD-relevant pathobiont and supporting a direct link between diet and microbial communities in mediating protective functions.8ntX7JCRAmgBnFgN24WWkMVideo

Phenotypic and Genomic Difference among Four Botryosphaeria Pathogens in Chinese Hickory Trunk Canker.

Botryosphaeria species are amongst the most widespread and important canker and dieback pathogens of trees worldwide, with B. dothidea as one of the most common Botryosphaeria species. However, the information related to the widespread incidence and aggressiveness of B. dothidea among various Botryosphaeria species causing trunk cankers is still poorly investigated. In this study, the metabolic phenotypic diversity and genomic differences of four Chinese hickory canker-related Botryosphaeria pathogens, including B. dothidea, B. qingyuanensis, B. fabicerciana, and B. corticis, were systematically studied to address the competitive fitness of B. dothidea. Large-scale screening of physiologic traits using a phenotypic MicroArray/OmniLog system (PMs) found B. dothidea has a broader spectrum of nitrogen source and greater tolerance toward osmotic pressure (sodium benzoate) and alkali stress among Botryosphaeria species. Moreover, the annotation of B. dothidea species-specific genomic information via a comparative genomics analysis found 143 B. dothidea species-specific genes that not only provides crucial cues in the prediction of B. dothidea species-specific function but also give a basis for the development of a B. dothidea molecular identification method. A species-specific primer set Bd_11F/Bd_11R has been designed based on the sequence of B. dothidea species-specific gene jg11 for the accurate identification of B. dothidea in disease diagnoses. Overall, this study deepens the understanding in the widespread incidence and aggressiveness of B. dothidea among various Botryosphaeria species, providing valuable clues to assist in trunk cankers management.

Long-term cover cropping improved soil bacterial community and soil multifunctionality in a Carya cathayensis plantation

Chinese hickory (Carya cathayensis Sarg.), a nut tree unique to China, is an important source of high-class nuts and oil. However, the intensive management practices, especially removing all the understory, lead to the soil degradation in Chinese hickory plantation. Thus, cover cropping is applied to improve and maintain soil quality and productivity. Soil multifunctionality (SMF) is a practical index to comprehensively assess different soil environmental factors with complicated interactions. However, the long-term effects of cover cropping on soil bacterial community and SMF in Chinese hickory plantations remain unknown. In this study, a field experiment was conducted in a Chinese hickory plantation in Zhejiang province, China, from 2011 to 2021. The effects of cover crops including oilseed rape (Brassica chinensis, OR), Chinese milk vetch (Astragalus sinicus, CMV), and the mixtures of oilseed rape and Chinese milk vetch (OC) on the soil bacterial community and SMF were compared with no cover crop (NC). We employed high throughput sequencing of 16 S rRNA to study soil bacterial community, and adopted the averaging approach to determine the SMF value based on soil carbon (C) and nitrogen (N) storage, potential enzymatic activity, and active nutrient pool. The results revealed that long-term cover cropping significantly improved soil C and N content, which stimulated the soil potential enzymatic activity. And consequently, soil labile nutrient concentrations were increased, suggesting better soil active nutrient pool. The proliferation of bacteria utilizing easily-decomposed organic matter was therefore promoted. Hence, SMF was significantly improved by cover cropping. And OC effectively combined species-specific functions including nutrient retention and utilization. Consequently, OC showed the best improvement of soil environmental factors including C and N storage, active nutrient pool, and potential enzymatic activity among cover cropping treatments. It is therefore that OC manifested better SMF than sole cover crops strategies. Random forest modeling and partial least squares path modeling (PLS-PM) revealed that soil C storage, pH, and potential enzymatic activity, were dominant predictors of SMF. Additionally, C and N storage, and pH directly influenced bacterial richness and composition positively or negatively. This study provides insight into the effects of different cover crops on the soil bacterial community and SMF in Chinese hickory plantations, and highlighted the great potential of the legume-cruciferae cover cropping strategy on SMF improvement. These findings have implications for the optimization of sustainable forest management practices in degraded forest plantations.

Species-specific transcriptional reprogramming during adventitious root initiation.

Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.

Limited water stress modulates expression of circadian clock genes in Brachypodium distachyon roots

Organisms have evolved a circadian clock for the precise timing of their biological processes. Studies primarily on model dicots have shown the complexity of the inner timekeeper responsible for maintaining circadian oscillation in plants and have highlighted that circadian regulation is more than relevant to a wide range of biological processes, especially organ development and timing of flowering. Contribution of the circadian clock to overall plant fitness and yield has also long been known. Nevertheless, the organ- and species-specific functions of the circadian clock and its relation to stress adaptation have only recently been identified. Here we report transcriptional changes of core clock genes of the model monocot Brachypodium distachyon under three different light regimes (18:6 light:dark, 24:0 light and 0:24 dark) in response to mild drought stress in roots and green plant parts. Comparative monitoring of core clock gene expression in roots and green plant parts has shown that both phase and amplitude of expression in the roots of Brachypodium plants differ markedly from those in the green plant parts, even under well-watered conditions. Moreover, circadian clock genes responded to water depletion differently in root and shoot. These results suggest an organ-specific form and functions of the circadian clock in Brachypodium roots.

Effects of hurricane canopy gaps on longleaf pine and upland oak sapling growth

Longleaf pine forests and woodlands are an ecologically important ecosystem that once dominated much of the southeastern U.S. Frequent fire is well-known to be a driver of forest dynamics in these systems, but far less is known about how wind disturbance may reorganize plant communities. To gain a better understanding of how hurricane impacts may alter dynamics in a second-growth longleaf pine woodland, we investigated growth response of saplings from three competing upland species (Pinus palustris, Quercus falcata, Q. margaretta) following Hurricane Michael (2018) in southwest Georgia, United States. We used maximum likelihood to model height and radial growth of saplings as species-specific Michaelis-Menten functions of light availability and examined the effect of sapling size, soil water holding capacity, and annual precipitation using a model comparison approach. The best model for both height and radial growth included species-specific growth rates, a power function for sapling size, and an effect of 2-year lagged precipitation. Overall, we found that height growth rate increased with irradiance for all species, but asymptotic height growth rate for all species was approached at low irradiance. Rates of radial growth also increased with irradiance and were more strongly differentiated among species. Radial growth in longleaf pine and southern red oak responded most strongly to increasing irradiance. Our findings suggest that increases in light availability from hurricanes has direct effects on altering growth dynamics of saplings. Further, because stem radius is a strong predictor of survival from surface fires, hurricane damage may also have an indirect effect on sapling dynamics, by altering survival in future fires. Our results suggest that hurricanes can reinforce the dominance of longleaf pine and potentially play a role in stabilizing community structure. Understanding the effects of common disturbances like wind and fire—together and individually—can reveal important mechanisms that shape the structure and function of fire-prone ecosystems.