Search Results (61)

Soil organic matter (SOM) is essential for ecosystem health and agricultural productivity. Accurate prediction of SOM content is critical for modern agricultural management and sustainable soil use. Existing digital soil mapping (DSM) models, when processing temporal data, primarily focus on modeling the changes in input data across successive time steps. However, they do not adequately model the relationships among different input variables, which hinders the capture of complex data patterns and limits the accuracy of predictions. To address this problem, this paper proposes a novel deep learning model, 2-Channel Network (2C-Net), leveraging sequential multi-temporal remote sensing images to improve SOM prediction. The network separates input data into temporal and spatial data, processing them through independent temporal and spatial channels. Temporal data includes multi-temporal Sentinel-2 spectral reflectance, while spatial data consists of environmental covariates including climate and topography. The Multi-sequence Feature Fusion Module (MFFM) is proposed to globally model spectral data across multiple bands and time steps, and the Diverse Convolutional Architecture (DCA) extracts spatial features from environmental data. Experimental results show that 2C-Net outperforms the baseline model (CNN-LSTM) and mainstream machine learning model for DSM, with R² = 0.524, RMSE = 0.884 (%), MAE = 0.581 (%), and MSE = 0.781 (%)². Furthermore, this study demonstrates the significant importance of sequential spectral data for the inversion of SOM content and concludes the following: for the SOM inversion task, the bare soil period after tilling is a more important time window than other bare soil periods. 2C-Net model effectively captures spatiotemporal features, offering high-accuracy SOM predictions and supporting future DSM and soil management. Full article

Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species—Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field. Full article

Various prenatal and postnatal factors such as gestational age, mode of delivery, sex, antibiotic exposure, feeding type, duration of feed and other exposures associated with the hospital environment can drive the formation of gut microbiota. In the current study, we examined the role of all these factors in the gut microbiota of healthy Indian preterm infants admitted to NICU in the first four weeks of life. Preterm neonates admitted to the NICU from April 2023 and October 2023 were recruited and fecal samples were collected weekly once beginning from the seventh day till the 30th day of life. 16s rRNA gene sequencing was performed on the NovaSeq 6000 platform. The PICRUSt2 tool was used to predict the functional profiles of the gut microbiome. A total of 61 samples were collected from 16 preterm infants. Alpha and beta diversity showed the administration of probiotics, postnatal age, mode of delivery, and sex of infants as major contributors to altered microbial diversity in preterm infants. The MaAsLin2 analysis showed that the supplementation of probiotics increased Bifidobacterium levels. PICRUSt2 analysis revealed that probiotic supplementation increased the bacterial genes responsible for bile acid metabolism and glycosphingolipid synthesis. Probiotics and postnatal age are responsible for alterations of the gut microbial composition in healthy preterm infants. Full article

Land use change is associated with both higher fossil fuel usage and global cement production, significantly impacting environmental sustainability. Cement dust emission is the third-largest source of anthropogenic CO₂ emissions, right behind fossil fuel usage due to intense agricultural practices like aggressive tillage management. This study’s aim is to determine cement dust emissions impacts on various tillage management methods and the formation of cement dust-affected CO₂ emissions, soil pH, soil organic matter content, total nitrogen content, available phosphorus, CaCO₃ content, bacteria and fungi populations, and enzyme activities. The target of this study is to evaluate how cement dust emissions impact the soil properties and sustainability of different tillage practices. Composite soils from wheat–sugar beet (potato)–fallow cropping sequences under conventional tillage (CT) and no-till (NT) management were collected (0–30 cm depth) with three replications at varying distances from a cement factory (1, 2, 4, 6, 8, and 10 km). To find differences among individual treatments and distances, a two-way ANOVA was employed along with Duncan’s LSD test comparing the various effects of tillage techniques. The associations between soil chemical and biological properties and CO₂ fluxes under the impact of cement dust were examined using Pearson’s correlation analysis. There were notable relationships between soil microbial population, enzyme activities, pH, CaCO₃, and CO₂ fluxes. The sampling distance from the cement plant had a substantial correlation with soil organic carbon, urease activity, pH, CaCO₃, and bacterial populations. According to the study, different tillage methods (CT and NT) affected the diversity and abundance of microorganisms within the soil ecosystem. CT was more beneficial for the microbial population and for sustainable management. Full article

Background: Neuroendocrine carcinomas (NECs) are treated with a frontline platinum–etoposide combination with no standard second-line therapies. We explored a novel combination of nanoliposomal irinotecan (Nal-IRI), 5-fluorouracil (5-FU), and leucovorin (LV) in advanced refractory NECs and investigated the impact of UGT1A1*28 polymorphism on treatment outcomes and toxicity. Methods: We conducted an open-label, single-arm, multi-center Phase 2 trial in advanced NEC patients of gastroenteropancreatic (GEP) or unknown origin with progression or intolerance to first-line therapy. Eligible patients received nal-IRI 70 mg/m² and leucovorin 400 mg/m², followed by 5-FU 2400 mg/m² biweekly till disease progression or unacceptable toxicity. The primary endpoint was the objective response rate (ORR). Secondary endpoints included progression-free survival (PFS), overall survival (OS), and toxicity. Next-generation sequencing (NGS) was performed on blood/tissue samples at baseline and during treatment. Results: Eleven patients were enrolled, with nine evaluable for the primary endpoint. Seven were male, the median age was 66.7 years, and the median Ki-67 was 90%. We observed partial response in one patient, stable disease in six patients, and progressive disease in two patients. The median OS was 9.4 months (95% CI 2.9–29.3), and the median PFS was 4.4 months (95% CI 1.7–6.7). The most common adverse events were diarrhea (45%), nausea (45%), vomiting (45%), and fatigue (45%). The most common genetic mutations on NGS were TP53 (88.9%), CHEK2 (88.9%), and APC (33.3%). Patients with CHEK2 and APC mutation had longer PFS (p = 0.005 and p = 0.013, respectively). UGT1A1*28 polymorphism was not associated with OS, PFS, or toxicity. Conclusion: Nal-IRI with 5-FU/LV is a safe and effective treatment for refractory high-grade NECs of GEP or unknown origin. Future studies should explore novel combinations with Nal-IRI in high-grade NECs both in frontline and refractory settings. Full article

To meet the demands of a growing population, natural wetlands are being converted to arable land, significantly impacting soil biodiversity. This study investigated the effects of land use changes on bacterial communities in wetland, arable land, and forest soils in the Lesser Khingan Mountains using Illumina MiSeq 16S rRNA sequencing. Soil physicochemical properties and enzyme activities were measured using standard methods, while microbial diversity was assessed through sequencing analysis. Our findings revealed that forest soils had significantly higher levels of total potassium (2.62 g·kg⁻¹), electrical conductivity (8.22 mS·cm⁻¹), urease (0.18 mg·g⁻¹·d⁻¹), and nitrate reductase (0.13 mg·g⁻¹·d⁻¹), attributed to rich organic matter and active microbial communities. Conversely, arable soils showed lower total potassium (1.94 g·kg⁻¹), reduced electrical conductivity, and suppressed enzyme activities due to frequent tilling and fertilization. Wetland soils exhibited the lowest values primarily due to water saturation, which limits organic matter decomposition and microbial activity. Land use changes notably reduced microbial diversity, with conversion from forest to arable land leading to habitat loss. Forest soils supported higher abundances of Proteobacteria (37.59%) and Actinobacteriota (34.73%), while arable soils favored nitrogen-fixing bacteria. Wetlands were characterized by chemoheterotrophic and anaerobic bacteria. Overall, these findings underscore the profound influence of land use on soil microbial communities and their functional roles, highlighting the need for sustainable management practices. Full article

Using predicted potential N mineralization (PNM) from its relationship with CO₂ flush at 1 d incubation (CF) of soil samples in recommended N rates can reduce N fertilization rates for crops. This study used predicted PNM at the 0–15 cm depth to reduce N fertilization rates and examined spring wheat (Triticum aestivum L.) yields at two sites (Froid and Sidney) in Montana, USA. Cropping sequences at Froid were fall and spring till continuous spring wheat (FSTCW), no-till continuous spring wheat (NTCW1), no-till spring wheat–pea (Pisum sativum L.) (NTWP1), and spring till spring wheat–fallow (STWF). At Sidney, cropping sequences were conventional till spring wheat–fallow (CTWF), no-till spring wheat–fallow (NTWF), no-till continuous spring wheat (NTCW2), and no-till spring wheat–pea (NTWP2). Soil samples collected to a depth of 15 cm in September 2021 at both sites were analyzed for CF, PNM, and NO₃-N contents, from which the reduction in N fertilization rate (RNFA) and the amount of N fertilizer applied (ANFA) to 2022 spring wheat were determined. In April 2022, spring wheat was grown with or without predicted PNM and annualized crop yields were compared. The CF and PNM were 114–137% greater for NTWP1 than STWF at Froid and 26–80% greater for NTCW2 than CTWF and NTWF at Sidney. The reduction in N fertilization rate was 26–102% greater for NTWP1 at Froid and 8–10% greater for NTCW2 and NTWF than other cropping sequences at Sidney. Annualized crop yield was 26–60% lower for crop–fallow than continuous cropping, but was not significantly different between with or without PNM at both sites. Using PNM can significantly reduce N fertilization rates for crops while sustaining dryland yields. Full article

Premature leaf senescence significantly reduces rice yields. Despite identifying numerous factors influencing these processes, the intricate genetic regulatory networks governing leaf senescence demand further exploration. We report the characterization of a stably inherited, ethyl methanesulfonate(EMS)-induced rice mutant with wilted leaf tips from seedling till harvesting, designated lts2. This mutant exhibits dwarfism and early senescence at the leaf tips and margins from the seedling stage when compared to the wild type. Furthermore, lts2 displays a substantial decline in both photosynthetic activity and chlorophyll content. Transmission electron microscopy revealed the presence of numerous osmiophilic granules in chloroplast cells near the senescent leaf tips, indicative of advanced cellular senescence. There was also a significant accumulation of H₂O₂, alongside the up-regulation of senescence-associated genes within the leaf tissues. Genetic mapping situated lts2 between SSR markers Q1 and L12, covering a physical distance of approximately 212 kb in chr.1. No similar genes controlling a premature senescence leaf phenotype have been identified in the region, and subsequent DNA and bulk segregant analysis (BSA) sequencing analyses only identified a single nucleotide substitution (C-T) in the exon of LOC_Os01g35860. These findings position the lts2 mutant as a valuable genetic model for elucidating chlorophyll metabolism and for further functional analysis of the gene in rice. Full article

In the traditional farming systems, the excessive application of chemical fertilizers to boost crop yields has resulted in a range of issues, such as soil quality degradation, soil structure deterioration, and pollution of the farmland ecological environment. Green manure, as a high-quality biological fertilizer source with rich nutrient content, is of great significance for enhancing the soil quality and establishing a healthy farmland ecosystem. However, there are few studies on the effects of different green manures on the soil nutrient levels, enzyme activities, and soil bacterial community composition in the rice–wheat rotation areas in southern China. Thus, we planted Chinese milk vetch (MV; Astragalus sinicus L.), light leaf vetch (LV; Vicia villosa var.), common vetch (CV; Vicia sativa L.), crimson clover (CC; Trifolium incarnatum L.), Italian ryegrass (RG; Lolium multiflorum L.), and winter fields without any crops as a control in the Taihu Lake area of Jiangsu. The soil samples collected after tilling and returning the green manure to the field during the bloom period were used to analyze the effects of the different green manures on the soil nutrient content, enzyme activity, and the structural composition of the bacterial community. This analysis was conducted using chemical methods and high-throughput sequencing technology. The results showed that the green manure returned to the field increased the soil pH, soil organic matter (SOM), alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), available potassium (AK), sucrose (SC), urease (UE), and neutral phosphatase (NEP) contents compared to the control. They increased by 1.55% to 10.06%, 0.26% to 9.31%, 20.95% to 28.42%, 20.66% to 57.79%, 12.38% to 37.94%, 3.11% to 58.19%, 6.49% to 32.99%, and 50.0% to 80.36%, respectively. In addition, the green manure field increased the relative abundance of the genera Proteobacteria and Haliangium while decreasing the relative abundance of Gemmatimonadetes, Chloroflexi, SBR1031, and Anaeromyxobacter in the soil bacteria. Both the number of ASVs (amplicon sequence variants) and α-diversity of the soil bacterial communities were higher compared to the control, and the β-diversity varied significantly among the treatments. Alkali-hydrolyzed nitrogen and neutral phosphatase had the greatest influence on the soil bacterial community diversity, with alkali-hydrolyzed nitrogen being the primary soil factor affecting the soil bacterial community composition. Meanwhile, the results of the principal component analysis showed that the MV treatment had the most significant impact on soil improvement. Our study provides significant insights into the sustainable management of the soil quality in rice–wheat rotations. It identifies MV as the best choice among the green manure crops for improving the soil quality, offering innovative solutions for reducing chemical fertilizer dependence and promoting ecological sustainability. Full article

Crop sequence and tillage can affect the yield of peanut (Arachis hypogaea L.) and other crops. Research was conducted from 2006 through 2022 to determine the response of peanut to previous crop sequences including corn (Zea mays L.) and cotton (Gossypium hirsutum L.) planted in continuous conventional tillage (e.g., disking, field cultivating, and bedding with in-row sub-soiling) or strip tillage (e.g., tilling a 45 cm section on rows spaced 91 cm apart using fluted coulters, rolling baskets, and in-row sub-soiling). In 2013, 2019, and 2022, the entire test area was planted with peanut. In 2019 and 2022, peanut was planted without or with fluopyram applied in the seed furrow at planting. Decreasing the number of years between peanut planting resulted in lower peanut yields compared with fewer years of peanut planting in the rotation sequence. Continuous conventional tillage and strip tillage resulted in similar peanut yields at one location, while the yield was lower at a second location when peanut was planted in continuous strip tillage. Fluopyram did not affect peanut yield regardless of previous crop rotation sequence, the number of years separating peanut plantings, or the tillage system. However, minor differences in the populations of plant-parasitic nematodes in soil were noted when comparing fluopyram treatment. The results from these experiments indicate that while fluopyram can reduce the populations of some plant-parasitic nematodes in soil, the magnitude of reduction does not translate into increases in peanut yield. Full article

GII.4 noroviruses have caused the overwhelming majority of norovirus-related gastroenteritis cases during the past two decades. However, a trend towards the emergence of new genotypes and novel GII.4 variants provided the impetus to explore further the changing patterns in norovirus epidemiology during the present study. Genotyping of 60 norovirus strains detected during a period of 33 months (January 2016–October 2018) was performed on the basis of the capsid VP1-coding ORF2 gene sequence. All norovirus strains detected were classified into seven genotypes, six of which belonged to genogroup GII. GII.2 was the dominant genotype till February 2017, whereas GII.4 prevailed thereafter. Most of the GII.4 strains were of the Sydney_2012 variant, whereas five strains could not be classified. Further recombination analysis at the ORF1/ORF2 gene junction revealed that 23 out of 24 strains were recombinant, thereby showcasing the significant role of genetic recombination in norovirus evolution and epidemiology. Continuous genomic surveillance and molecular characterization are essential for tracking norovirus evolution, which could contribute to the elucidation of new aspects of virus–host interactions that potentially affect host morbidity and epidemiology. Full article

Fruit ripening is a highly complicated process that is accompanied by the formation of fruit quality. In recent years, a series of studies have demonstrated post-transcriptional control play important roles in fruit ripening and fruit quality formation. Till now, the post-transcriptional mechanisms for watermelon fruit ripening have not been comprehensively studied. In this study, we conducted PacBio single-molecule long-read sequencing to identify genome-wide alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. In total, 6,921,295 error-corrected and mapped full-length non-chimeric (FLNC) reads were obtained. Notably, more than 42,285 distinct splicing isoforms were derived from 5,891,183 intron-containing full-length FLNC reads, including a large number of AS events associated with fruit ripening. In addition, we characterized 21,506 polyadenylation sites from 11,611 genes, 8703 of which have APA sites. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that fructose and mannose metabolism, starch and sucrose metabolism and carotenoid biosynthesis were both enriched in genes undergoing AS and APA. These results suggest that post-transcriptional regulation might potentially have a key role in regulation of fruit ripening in watermelon. Taken together, our comprehensive PacBio long-read sequencing results offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of watermelon fruit ripening. Full article

Managing soil biodiversity using reduced tillage is a popular approach, yet soil bacteriobiomes in the agroecosystems of Siberia has been scarcely studied, especially as they are related to tillage. We studied bacteriobiomes in Chernozem under natural steppe vegetation and cropped for wheat using conventional or no tillage in a long-term field trial in the Novosibirsk region, Russia, by using the sequence diversity of the V3/V4 region of 16S rRNA genes. Actinobacteria, Acidobacteria, and Proteobacteria summarily accounted for 80% of the total number of sequences, with Actinobacteria alone averaging 51%. The vegetation (natural vs. crop) and tillage (ploughed vs. no-till) affected the bacterial relative abundance at all taxonomic levels and many taxa, e.g., hundreds of OTUs. However, such changes did not translate into α-biodiversity changes, i.e., observed and potential OTUs’ richness, Shannon, and Simpson, excepting the slightly higher evenness and equitability in the top 0–5 cm of the undisturbed soil. As for the β-biodiversity, substituting conventional ploughing with no tillage and maintaining the latter for 12 years notably shifted the soil bacteriobiome closer to the one in the undisturbed soil. This study, presenting the first inventory of soil bacteriobiomes under different tillage in the south of West Siberia, underscores the need to investigate the seasonality and longevity aspects of tillage, especially as they are related to crop production. Full article

Soil-borne oomycetes include devastating plant pathogens that cause substantial losses in the agricultural sector. To better manage this important group of pathogens, it is critical to understand how they respond to common agricultural practices, such as tillage and crop rotation. Here, a long-term field experiment was established using a split-plot design with tillage as the main plot factor (conventional tillage (CT) vs. no till (NT), two levels) and rotation as the subplot factor (monocultures of soybean, corn, or wheat, and corn–soybean–wheat rotation, four levels). Post-harvest soil oomycete communities were characterized over three consecutive years (2016–2018) by metabarcoding the Internal Transcribed Spacer 1 (ITS1) region. The community contained 292 amplicon sequence variants (ASVs) and was dominated by Globisporangium spp. (85.1% in abundance, 203 ASV) and Pythium spp. (10.4%, 51 ASV). NT decreased diversity and community compositional structure heterogeneity, while crop rotation only affected the community structure under CT. The interaction effects of tillage and rotation on most oomycetes species accentuated the complexity of managing these pathogens. Soil and crop health represented by soybean seedling vitality was lowest in soils under CT cultivating soybean or corn, while the grain yield of the three crops responded differently to tillage and crop rotation regimes. Full article

Revealing the regional distribution and diversity of fungal sub-communities under different land management practices is essential to conserve biodiversity and predict microbial change trends. In this study, a total of 19 tilled and 25 untilled soil samples across different land-use types were collected from subtropical China to investigate the differences between the spatial distribution patterns, diversity, and community assembly of fungal sub-communities using high-throughput sequencing technology. Our results found that anthropogenic disturbances significantly reduced the diversity of abundant taxa but significantly increased the diversity of rare taxa, suggesting that the small-scale intensive management of land by individual farmers is beneficial for fungal diversity, especially for the conservation of rare taxa. Abundant, intermediate, and rare fungal sub-communities were significantly different in tilled and untilled soils. Anthropogenic disturbances both enhanced the homogenization of fungal communities and decreased the spatial-distance–decay relationship of fungal sub-communities in tilled soils. Based on the null model approach, the changes in the assembly processes of the fungal sub-communities in tilled soils were found to shift consistently to stochastic processes, possibly as a result of the significant changes in the diversity of those fungal sub-communities and associated ecological niches in different land-use types. Our results provide support for the theoretical contention that fungal sub-communities are changed by different land management practices and open the way to the possibility of predicting those changes. Full article