bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture
Authors: Oshiki Mamoru , Morimoto Emi , Kobayashi Kanae , Satoh Hisashi , Okabe Satoshi 
Published: January 2024

Abstract
Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2−. Remineralization of organic nitrogen compounds including urea and cyanate (OCN−) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN−- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN− degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN− degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN− was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32–42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).
Homogenization of bacterial plastisphere community in soil: a continental-scale microcosm study
Authors: Sun Yuanze , Wu Mochen , Xie Siyuan , Zang Jingxi , Wang Xiang , Yang Yuyi , Li Changchao , Wang Jie 
Published: January 2024

Abstract
Microplastics alter niches of soil microbiota by providing trillions of artificial microhabitats, termed the “plastisphere.” Because of the ever-increasing accumulation of microplastics in ecosystems, it is urgent to understand the ecology of microbes associated with the plastisphere. Here, we present a continental-scale study of the bacterial plastisphere on polyethylene microplastics compared with adjacent soil communities across 99 sites collected from across China through microcosm experiments. In comparison with the soil bacterial communities, we found that plastispheres had a greater proportion of Actinomycetota and Bacillota, but lower proportions of Pseudomonadota, Acidobacteriota, Gemmatimonadota, and Bacteroidota. The spatial dispersion and the dissimilarity among plastisphere communities were less variable than those among the soil bacterial communities, suggesting highly homogenized bacterial communities on microplastics. The relative importance of homogeneous selection in plastispheres was greater than that in soil samples, possibly because of the more uniform properties of polyethylene microplastics compared with the surrounding soil. Importantly, we found that the degree to which plastisphere and soil bacterial communities differed was negatively correlated with the soil pH and carbon content and positively related to the mean annual temperature of sampling sites. Our work provides a more comprehensive continental-scale perspective on the microbial communities that form in the plastisphere and highlights the potential impacts of microplastics on the maintenance of microbial biodiversity and ecosystem functioning.
Functional prediction of proteins from the human gut archaeome
Authors: Novikova Polina V , Bhanu Busi Susheel , Probst Alexander J , May Patrick , Wilmes Paul 
Published: January 2024

Abstract
The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal–bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.
Interspecific competition prevents the proliferation of social cheaters in an unstructured environment
Authors: Lin Hui , Wang Donglin , Wang Qiaojuan , Mao Jie , Bai Yaohui , Qu Jiuhui 
Published: January 2024

Abstract
Bacterial communities are intricate ecosystems in which various members interact, compete for resources, and influence each other’s growth. Antibiotics intensify this complexity, posing challenges in maintaining biodiversity. In this study, we delved into the behavior of kin bacterial communities when subjected to antibiotic perturbations, with a particular focus on how interspecific interactions shape these responses. We hypothesized that social cheating—where resistant strains shield both themselves and neighboring cheaters—obstructed coexistence, especially when kin bacteria exhibited varied growth rates and antibiotic sensitivities. To explore potential pathways to coexistence, we incorporated a third bacterial member, anticipating a shift in the dynamics of community coexistence. Simulations and experimental bacterial communities confirmed our predictions, emphasizing the pivotal role of interspecific competition in promoting coexistence under antibiotic interference. These insights are crucial for understanding bacterial ecosystem stability, interpreting drug–microbiome interactions, and predicting bacterial community adaptations to environmental changes.
Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron
Authors: Du Xueyuan , Liu Ning , Yan Bingfa , Li Yisong , Liu Minghao , Huang Ying 
Published: January 2024

Abstract
Microorganisms living in soil maintain intricate interactions among themselves, forming the soil microbiota that influences the rhizosphere microbiome and plant growth. However, the mechanisms underlying the soil microbial interactions remain unclear. Streptomyces and Mesorhizobium are commonly found in soil and serve as plant growth-promoting rhizobacteria (PGPR). Here, we identified an unprecedented interaction between the colonies of red-soil-derived Streptomyces sp. FXJ1.4098 and Mesorhizobium sp. BAC0120 and referred to it as “proximity-based defensive mutualism (PBDM).” We found that metabolite-mediated iron competition and sharing between the two microorganisms were responsible for PBDM. Streptomyces sp. FXJ1.4098 produced a highly diffusible siderophore, desferrioxamine, which made iron unavailable to co-cultured Mesorhizobium sp. BAC0120, thereby inhibiting its growth. Streptomyces sp. FXJ1.4098 also released poorly diffusible iron-porphyrin complexes, which could be utilized by Mesorhizobium sp. BAC0120, thereby restoring the growth of nearby Mesorhizobium sp. BAC0120. Furthermore, in ternary interactions, the PBDM strategy contributed to the protection of Mesorhizobium sp. BAC0120 close to Streptomyces sp. FXJ1.4098 from other microbial competitors, resulting in the coexistence of these two PGPR. A scale-up pairwise interaction screening suggested that the PBDM strategy may be common between Mesorhizobium and red-soil-derived Streptomyces. These results demonstrate the key role of iron in complex microbial interactions and provide novel insights into the coexistence of PGPR in soil.
Limits to the adaptation of herbivorous spider mites to metal accumulation in homogeneous and heterogeneous environments
Authors: Godinho Diogo P , Fragata Inês , Majer Agnieszka , Rodrigues Leonor R , Magalhães Sara 
Published: January 2024

Abstract
Metal accumulation is used by some plants as a defence against herbivores. Yet, herbivores may adapt to these defences, becoming less susceptible. Moreover, ecosystems often contain plants that do and do not accumulate metals, but whether such heterogeneity affects herbivore adaptation remains understudied. Here, we performed experimental evolution to test whether the spider mite Tetranychus evansi adapts to plants with high cadmium concentrations, in homogeneous (plants with cadmium) or heterogeneous (plants with or without cadmium) environments. For that we used tomato plants, which accumulate cadmium, thus affecting the performance of these spider mites. We measured mite fecundity, hatching rate, and the number of adult offspring after 12 and 33 generations and habitat choice after 14 and 51 generations, detecting no trait change, which implies the absence of adaptation. We then tested whether this was due to a lack of genetic variation in the traits measured and, indeed, additive genetic variance was low. Interestingly, despite no signs of adaptation, we observed a decrease in fecundity and number of adult offspring produced on cadmium-free plants, in the populations evolving in environments with cadmium. Therefore, evolving in environments with cadmium reduces the growth rate of spider mite populations on non-accumulating plants. Possibly, other traits contributed to population persistence on plants with cadmium. This calls for more studies addressing herbivore adaptation to plant metal accumulation.
Transcription factors NtNAC028 and NtNAC080 form heterodimers to regulate jasmonic acid biosynthesis during leaf senescence in Nicotiana tabacum
Authors: Lu Mingyue , Fu Boyang , Meng Xiao , Jia Tiantian , Lu Xiaoyue , Yang Chaosha , Li Ke , Yin Pengcheng , Guo Yongfeng , Li Wei , Chi Jina , Wang Geng , Zhou Chunjiang 
Published: January 2024

Abstract
Plant senescence, as a highly integrated developmental stage, involves functional degeneration and nutrient redistribution. NAM/ATAF1/CUC (NAC) transcription factors orchestrate various senescence-related signals and mediate the fine-tuning underlying plant senescence. Previous data revealed that knockout of either NtNAC028 or NtNAC080 leads to delayed leaf senescence in tobacco (Nicotiana tabacum), which implies that NtNAC028 and NtNAC080 play respective roles in the regulation of leaf senescence, although they share 91.87% identity with each other. However, the mechanism underlying NtNAC028- and NtNAC080-regulated leaf senescence remains obscure. Here, we determined that NtNAC028 and NtNAC080 activate a putative jasmonic acid (JA) biosynthetic gene, NtLOX3, and enhance the JA level in vivo. We found that NtNAC028 and NtNAC080 interact with each other and themselves through their NA-terminal region. Remarkably, only the dimerization between NtNAC028 and NtNAC080 stimulated the transcriptional activation activity, but not the DNA binding activity of this heterodimer on NtLOX3. Metabolome analysis indicated that overexpression of either NtNAC028 or NtNAC080 augments both biosynthesis and degradation of nicotine in the senescent stages. Thus, we conclude that NtNAC028 cooperates with NtNAC080 and forms a heterodimer to enhance NtLOX3 expression and JA biosynthesis to trigger the onset of leaf senescence and impact secondary metabolism in tobacco.
Wheat ESCRT-III protein TaSAL1 regulates male gametophyte transmission and controls tillering and heading date
Authors: Song Chengxiang , Xie Kaidi , Chen Hao , Xu, Shuhao , Mao Hailiang 
Published: January 2024

Abstract
Charged multivesicular protein 1 (CHMP1) is a member of the endosomal sorting complex required for transport-III (ESCRT-III) complex that targets membrane localized signaling receptors to intralumenal vesicles in the multivesicular body of the endosome and eventually to the lysosome for degradation. Although CHMP1 plays roles in various plant growth and development processes, little is known about its function in wheat. In this study, we systematically analysed the members of the ESCRT-III complex in wheat (Triticum aestivum) and found that their orthologs were highly conserved in eukaryotic evolution. We identified CHMP1 homologous genes, TaSAL1s, and found that they were constitutively expressed in wheat tissues and essential for plant reproduction. Subcellular localization assays showed these proteins aggregated with and closely associated with the endoplasmic reticulum when ectopically expressed in tobacco leaves. We also found these proteins were toxic and caused leaf death. A genetic and reciprocal cross analysis revealed that TaSAL1 leads to defects in male gametophyte biogenesis. Moreover, phenotypic and metabolomic analysis showed that TaSAL1 may regulate tillering and heading date through phytohormone pathways. Overall, our results highlight the role of CHMP1 in wheat, particularly in male gametophyte biogenesis, with implications for improving plant growth and developing new strategies for plant breeding and genetic engineering.
Parsec-scale evolution of the gigahertz-peaked spectrum quasar PKS 0858 − 279
Authors: Kosogorov N A , Kovalev Y Y , Perucho M , Kovalev Yu A 
Published: January 2024

ABSTRACT
We conducted multi-epoch, multifrequency parsec-scale studies on the gigahertz-peaked spectrum quasar PKS 0858 − 279 with the Very Long Baseline Array (VLBA). Our observations on 2005 November 26 elucidated a weak core, characterized by an inverted spectrum, and a distinctly bent jet that exhibited a notable bright feature in its Stokes I emission. Through comprehensive analysis of polarization and spectral data, we inferred the formation of a shock wave within this feature, stemming from interactions with a dense cloud in the ambient medium. In this paper, Very Long Baseline Interferometry-Gaia astrometry further reinforces the core identification. With a deep analysis of six additional VLBA epochs spanning from 2007 to 2018, we observed that while the quasar’s parsec-scale structure remained largely consistent, there were discernible flux density changes. These variations strongly imply the recurrent ejection of plasma into the jet. Complementing our VLBA data, RATAN-600 observations of the integrated spectra suggested an interaction between standing and travelling shock waves in 2005. Moreover, our multi-epoch polarization analysis revealed a drastic drop in rotation measure values from 6000 to 1000 rad m−2 within a single year, attributable to diminishing magnetic fields and particle density in an external cloud. This change is likely instigated by a shock in the cloud, triggered by the cloud’s interaction with the jet, subsequently prompting its expansion. Notably, we also observed a significant change in the magnetic field direction of the jet, from being perpendicular post its observed bend to being perpendicular prior to the bend – an alteration possibly induced by the dynamics of shock waves.
The local Universe in the era of large surveys – III. Radial activity profiles of S0 galaxies
Authors: Tous J L , Solanes J M , Perea J D , Domínguez-Sánchez H 
Published: January 2024

ABSTRACT
Spatially resolved MaNGA’s optical spectra of 1072 present-day lenticular (S0) galaxies, dimensionally reduced from a principal component analysis (PCA), are used to determine their radial activity structure shaped by any possible nebular ionization source. Activity profiles within $1.5\,$Re are examined in tandem with the mass, age, ellipticity, and kinematics of the stars, as well as environmental density. Among the results of this comparison, we find that the sign of the radial activity gradient of S0s is tightly related to their PCA classification, BPT designation, and star formation status. PCA-passive lenticulars often show low-level, flat activity profiles, although there is also a significant number of systems with positive gradients, while their less common active counterparts generally have negative gradients, usually associated with high SSFRs and, sometimes, moderate Seyfert emission. A fraction of the latter also shows radial activity profiles with positive gradients, which become more abundant with increasing stellar mass regardless of environmental density. Our analysis also reveals that the subset of active S0s with negative gradients experiences at all galactocentric radii a systematic reduction in its median activity level with stellar mass, consistent with expectations for main-sequence galaxies. In contrast, passive S0s with positive gradients show the opposite behaviour. Furthermore, systems whose activity is dominated by star formation are structurally rounder than the rest of S0s, while those classified as Seyfert exhibit higher rotational support. The possibility that negative and positive activity gradients in S0s may result from rejuvenation by two distinct types of minor mergers is raised.
Intra-night optical variability of peculiar narrow-line Seyfert 1 galaxies with enigmatic jet behaviour
Authors: Ojha Vineet , Singh Veeresh , Berton M , Järvelä E 
Published: January 2024

ABSTRACT
Variability studies of active galactic nuclei are a powerful diagnostic tool in understanding the physical processes occurring in disc-jet regions, unresolved by direct imaging with currently available techniques. Here, we report the first attempt to systematically characterize intra-night optical variability (INOV) for a sample of seven apparently radio-quiet narrow-line Seyfert 1 galaxies (RQNLSy1s) that had shown recurring flaring at 37 GHz in the radio observations at Metsähovi Radio Observatory, indicating the presence of relativistic jets in them, but no evidence for relativistic jets in the recent radio observations of Karl G. Jansky Very Large Array at 1.6, 5.2, and 9.0 GHz. We have conducted a total of 28 intra-night sessions, each lasting ≥3 h for this sample, resulting in an INOV duty cycle ($\overline{\mathrm{ DC}} ~\sim$ 20 per cent) similar to that reported for γ-ray-NLSy1s (DC ∼ 25 per cent–30 per cent), that display blazar-like INOV. This in turn infers the presence of relativistic jet in our sample sources. Thus, it appears that even lower mass (MBH ∼ 106 M⊙) RQNLSy1 galaxies can maintain blazar-like activities. However, we note that the magnetic reconnection in the magnetosphere of the black hole can also be a viable mechanism to give rise to the INOV from these sources.
Do Oral Cholera Vaccine and Water, Sanitation, and Hygiene Combine to Provide Greater Protection Against Cholera? Results From a Cluster-Randomized Trial of Oral Cholera Vaccine in Kolkata, India
Authors: Im Justin , Islam Md Taufiqul , Ahmmed Faisal , Kim Deok Ryun , Tadesse Birkneh Tilahun , Kang Sophie , Khanam Farhana , Chowdhury Fahima , Ahmed Tasnuva , Firoj Md Golam , Aziz Asma Binte , Hoque Masuma , Jeon Hyon Jin , Kanungo Suman , Dutta Shanta , Zaman Khalequ , Khan Ashraful Islam , Marks Florian , Kim Jerome H , Qadri Firdausi , Clemens John D 
Published: January 2024

Abstract

Background
Oral cholera vaccine (OCV) and incremental improvements in household water, sanitation, and hygiene (WASH) within cholera-endemic areas can reduce cholera risk. However, we lack empiric evaluation of their combined impact.

Methods
We evaluated a cluster-randomized, placebo-controlled trial of OCV (Shanchol) in Kolkata, India. The study population included 108 777 individuals, and 106 879 nonpregnant individuals &gt;1 year of age were eligible to receive 2 doses of OCV or placebo. We measured cholera risk in all household members assigned to OCV vs placebo and in all members of households with “Better” vs “Not Better” WASH, where WASH was classified according to validated criteria. Protection was measured by Cox proportional hazard models.

Results
Residence in an OCV household was associated with protective effectiveness (PE) of 54% (95% CI, 42%–64%; P &lt; .001) and was similar regardless of Better (PE, 57%; 95% CI, 26%–75%; P = .002) or Not Better (PE, 53%; 95% CI, 40%–64%; P &lt; .001) household WASH. Better WASH household residence was associated with PE of 30% (95% CI, 5%–48%; P = .023) and was similar in OCV (PE, 24%; 95% CI, −26% to 54%; P = .293) and placebo (PE, 29%; 95% CI, −3% to 51%; P = .069) households. When assessed conjointly, residence in OCV households with Better WASH was associated with the greatest PE against cholera at 69% (95% CI, 49%–81%; P &lt; .001).

Conclusions
These findings suggest that the combination of a vaccine policy and improved WASH reduces cholera risk more than either would alone, although the magnitude of either intervention was not affected by the other. Future randomized trials investigating OCV and WASH interventions separately and together are recommended to further understand the interaction between OCV and WASH.
A genome-wide association study identifies genes associated with cuticular wax metabolism in maize
Authors: Xu Liping , Hao Jiaxin , Lv Mengfan , Liu Peipei , Ge Qidong , Zhang Sainan , Yang Jianping , Niu Hongbin , Wang Yiru , Xue Yadong , Lu Xiaoduo , Tang Jihua , Zheng Jun , Gou Mingyue 
Published: January 2024

Abstract
The plant cuticle is essential in plant defense against biotic and abiotic stresses. To systematically elucidate the genetic architecture of maize (Zea mays L.) cuticular wax metabolism, 2 cuticular wax–related traits, the chlorophyll extraction rate (CER) and water loss rate (WLR) of 389 maize inbred lines, were investigated and a genome-wide association study (GWAS) was performed using 1.25 million single nucleotide polymorphisms (SNPs). In total, 57 nonredundant quantitative trait loci (QTL) explaining 5.57% to 15.07% of the phenotypic variation for each QTL were identified. These QTLs contained 183 genes, among which 21 strong candidates were identified based on functional annotations and previous publications. Remarkably, 3 candidate genes that express differentially during cuticle development encode β-ketoacyl-CoA synthase (KCS). While ZmKCS19 was known to be involved in cuticle wax metabolism, ZmKCS12 and ZmKCS3 functions were not reported. The association between ZmKCS12 and WLR was confirmed by resequencing 106 inbred lines, and the variation of WLR was significant between different haplotypes of ZmKCS12. In this study, the loss-of-function mutant of ZmKCS12 exhibited wrinkled leaf morphology, altered wax crystal morphology, and decreased C32 wax monomer levels, causing an increased WLR and sensitivity to drought. These results confirm that ZmKCS12 plays a vital role in maize C32 wax monomer synthesis and is critical for drought tolerance. In sum, through GWAS of 2 cuticular wax–associated traits, this study reveals comprehensively the genetic architecture in maize cuticular wax metabolism and provides a valuable reference for the genetic improvement of stress tolerance in maize.