Environmental Information Processing Research Articles

Characteristics of Bacterial Community Structure in Fluvo-aquic Soil Under Different Rotation Fallow

The aim of this study was to provide a reference for promoting ecological restoration of farmland and the green development of agriculture in the alluvial plain of the lower Yellow River by determining the effects of different rotation fallow patterns on the bacterial community of the fluvo-aquic soil. Farmland soil subject to a long-term rotation fallow experiment since 2018 was studied using Illumina MiSeq high-throughput sequencing technology, and the 'Tax4Fun' bacterial function prediction tool was used to analyze differences in soil bacterial community structure and function under the following four rotation fallow regimes:long fallow(LF), winter wheat and summer fallow(WF), winter fallow and summer maize(FM), and annual rotation of winter wheat and summer maize(WM). The environmental factors affecting changes in the soil bacterial community structure and function were also analyzed. In total, 44 phyla, 146 classes, 338 orders, 530 families, 965 genera, and 2073 species of bacteria were detected in the soil samples from the different rotation fallow regimes, and the dominant bacterial groups were Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi in 0-20 cm and 20-40 cm soil layers. However, the relative abundances of the dominant bacteria groups were varied between the rotation fallow regimes. In the 0-20 cm layer of the seasonal fallow soils(WF and FM), bacteria were more abundant and community diversity was higher than that of the WM and LF soils. In 20-40 cm soil layer, the WF soil was more abundant in bacterial and the community was more diverse. Based on the prediction function of the 'Tax4Fun' tool, six primary metabolic pathways, 40 secondary metabolic pathways(18 types with relative abundance greater than 1%), and 264 tertiary metabolic pathways were identified in the soil bacteria of the different rotation fallow regimes. Seasonal fallow(WF and FM) was found to increase the relative abundance of beneficial bacterial metabolic pathways involved in metabolism, environmental information processing, and genetic information processing. According to RDA analysis, the soil bacterial community in the 0-20 cm soil layer was significantly affected by soil moisture, total phosphorus, available phosphorus, available potassium, pH, and C/N ratio(P<0.05), and the soil bacterial community in 20-40 cm soil layer was significantly affected by soil total phosphorus and available phosphorus(P<0.05). Therefore, different fallow patterns were linked to variation in the structure, diversity, and metabolic functions of soil bacterial communities. Based on these results, seasonal fallow practices could promote the health and stability of farmland soil ecosystems.

Enviromic Assembly Increases Accuracy and Reduces Costs of the Genomic Prediction for Yield Plasticity in Maize.

Quantitative genetics states that phenotypic variation is a consequence of the interaction between genetic and environmental factors. Predictive breeding is based on this statement, and because of this, ways of modeling genetic effects are still evolving. At the same time, the same refinement must be used for processing environmental information. Here, we present an “enviromic assembly approach,” which includes using ecophysiology knowledge in shaping environmental relatedness into whole-genome predictions (GP) for plant breeding (referred to as enviromic-aided genomic prediction, E-GP). We propose that the quality of an environment is defined by the core of environmental typologies and their frequencies, which describe different zones of plant adaptation. From this, we derived markers of environmental similarity cost-effectively. Combined with the traditional additive and non-additive effects, this approach may better represent the putative phenotypic variation observed across diverse growing conditions (i.e., phenotypic plasticity). Then, we designed optimized multi-environment trials coupling genetic algorithms, enviromic assembly, and genomic kinships capable of providing in-silico realization of the genotype-environment combinations that must be phenotyped in the field. As proof of concept, we highlighted two E-GP applications: (1) managing the lack of phenotypic information in training accurate GP models across diverse environments and (2) guiding an early screening for yield plasticity exerting optimized phenotyping efforts. Our approach was tested using two tropical maize sets, two types of enviromics assembly, six experimental network sizes, and two types of optimized training set across environments. We observed that E-GP outperforms benchmark GP in all scenarios, especially when considering smaller training sets. The representativeness of genotype-environment combinations is more critical than the size of multi-environment trials (METs). The conventional genomic best-unbiased prediction (GBLUP) is inefficient in predicting the quality of a yet-to-be-seen environment, while enviromic assembly enabled it by increasing the accuracy of yield plasticity predictions. Furthermore, we discussed theoretical backgrounds underlying how intrinsic envirotype-phenotype covariances within the phenotypic records can impact the accuracy of GP. The E-GP is an efficient approach to better use environmental databases to deliver climate-smart solutions, reduce field costs, and anticipate future scenarios.

Exploring microbiome from sediments of River Ganga using a metagenomic approach

Abstract The Ganga is a major riverine system of India providing ecosystem services to millions of households. However, this river is under stress due to various anthropogenic activities. River sediment harbours a variety of microorganisms which has a tremendous influence on river health. In the present study, metagenomic approach for microbial community characterization of three sediment samples collected from River Ganga at Farakka stretch was carried out. The sediment samples were sequenced using a high-throughput Next Generation Sequencing platform. Taxonomical classification study showed that the occurrence of bacteria is higher than other groups of microbes. The bacterial classes, such as Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and archaeal phylum, Thaumarchaeota, and Crenarchaeota were relatively higher than other communities. KEGG pathway analysis of three samples revealed that the number of genes associated with environmental information processing is higher in the Lalbag sample in comparison to Farakka barrage and Dhulian samples. The microbial community was categorized by functional classification using SEED analysis. Both COG and SEED analysis revealed that genes associated with carbohydrate metabolism are higher than other functional categories. The genus-level study confirms the higher occurrence of Pseudomonas, which corresponds to anthropogenic activities like mass bathing. The presence of bacterial genus Nitrospira and archaeal phylum Thaumarchaeota confirms a healthy nitrogen cycle in the environment. Moreover, the generated information would help in understanding the importance of microbial communities and their imperative function in maintaining the riverine ecosystem health.

High throughput sequencing-based analysis of the soil bacterial community structure and functions of Tamarix shrubs in the lower reaches of the Tarim River.

Tamarix is a dominant species in the Tarim River Basin, the longest inland river in China. Tamarix plays an important role in the ecological restoration of this region. In this study, to investigate the soil bacterial community diversity in Tamarix shrubs, we collected soil samples from the inside and edge of the canopy and the edge of nebkhas and non-nebkhas Tamarix shrubs located near the Yingsu section in the lower reaches of Tarim River. High throughput sequencing technology was employed to discern the composition and function of soil bacterial communities in nebkhas and non-nebkhas Tamarix shrubs. Besides, the physicochemical properties of soil and the spatial distribution characteristics of soil bacteria and their correlation were analyzed. The outcomes of this analysis demonstrated that different parts of Tamarix shrubs had significantly different effects on soil pH, total K (TK), available K (AK), ammonium N (NH4+), and available P (AP) values (P < 0.05), but not on soil moisture (SWC), total salt (TDS), electrical conductivity (EC), organic matter (OM), total N (TN), total P (TP), and nitrate N (NO3−) values. The soil bacterial communities identified in Tamarix shrubs were categorized into two kingdoms, 71 phyla, 161 classes, 345 orders, 473 families, and 702 genera. Halobacterota, unidentified bacteria, and Proteobacteria were found to be dominant phyla. The correlation between the soil physicochemical factors and soil bacterial community was analyzed, and as per the outcomes OM, AK, AP, EC, and NH4+ were found to primarily affect the structure of the soil bacterial community. SWC, TK and pH were positively correlated with each other, but negatively correlated with other soil factors. At the phyla level, a significantly positive correlation was observed between the Halobacterota and AP, OM as well as Bacteroidota and AK (P < 0.01), but a significantly negative correlation was observed between the Chloroflexi and AK, EC (P < 0.01). The PICRUSt software was employed to predict the functional genes. A total of 6,195 KEGG ortholog genes were obtained. The function of soil bacteria was annotated, and six metabolic pathways in level 1, 41 metabolic pathways in level 2, and 307 metabolic pathways in level 3 were enriched, among which the functional gene related to metabolism, genetic information processing, and environmental information processing was found to have the dominant advantage. The results showed that the nebkhas and canopy of Tamarix shrubs had a certain enrichment effect on soil nutrients content, and bacterial abundance and significant effects on the structure and function of the soil bacterial community.

Diversity, Composition, Taxa Biomarkers, and Functional Genes of Fish Gut Microbes in Peat Swamp Forests and its Converted Areas in North Selangor, Malaysia

The aquatic organisms in peat swamp forests are under threat due to habitat degradation resulting from human activities. This study determines the fish gut microbes’ diversity, composition, taxa biomarkers, and functional genes in peat swamp forests and its converted areas in North Selangor, Malaysia. Three undisturbed and disturbed areas nearby the peat swamp forests were selected. First, the 16S amplicon metagenomic analysis was conducted to assess the composition and diversity of bacterial communities in fish gut contents from both areas. Then, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Linear discriminant analysis Effect Size (LEfSe) were used to predict disease/pathogen related functional genes. This study revealed Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria as the predominant phyla in both studied areas. In contrast, bacterial community profiles of disturbed and undisturbed areas were slightly dissimilar. Metagenome predictions revealed that genes are related to metabolism, environmental information processing, genetic information processing, cellular processes, human diseases, and organismal systems. Further investigation revealed six potential biomarker genes, including chronic myeloid leukaemia in an undisturbed area, Vibrio cholerae infection, bladder cancer, pathogenic Escherichia coli infection, Staphylococcus aureus infection, and pertussis in disturbed areas. This study revealed that the fish gut microbiome could be used as an indicator in comparing the undisturbed and disturbed ecosystems.

The Intestinal Bacterial Community and Functional Potential of Litopenaeus vannamei in the Coastal Areas of China.

Intestinal bacteria are crucial for the healthy aquaculture of Litopenaeus vannamei, and the coastal areas of China are important areas for concentrated L. vannamei cultivation. In this study, we evaluated different compositions and structures, key roles, and functional potentials of the intestinal bacterial community of L. vannamei shrimp collected in 12 Chinese coastal cities and investigated the correlation between the intestinal bacteria and functional potentials. The dominant bacteria in the shrimp intestines included Proteobacteria, Bacteroidetes, Tenericutes, Firmicutes, and Actinobacteria, and the main potential functions were metabolism, genetic information processing, and environmental information processing. Although the composition and structure of the intestinal bacterial community, potential pathogenic bacteria, and spoilage organisms varied from region to region, the functional potentials were homeostatic and significantly (p < 0.05) correlated with intestinal bacteria (at the family level) to different degrees. The correlation between intestinal bacteria and functional potentials further suggested that L. vannamei had sufficient functional redundancy to maintain its own health. These findings help us understand differences among the intestinal bacterial communities of L. vannamei cultivated in different regions and provide a basis for the disease management and healthy aquaculture of L. vannamei.

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves.

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study.

Biosorption of Copper in Swine Manure Using Aspergillus and Yeast: Characterization and Its Microbial Diversity Study.

Dietary copper supplementation in the feed of piglets generally exceeds 250–800 mg/kg, where a higher quantity (>250 mg/kg) can promote growth and improve feed conversion. Despite the reported positive effects, 90% of copper is excreted and can accumulate and pollute the soil. Data indicate that fungi have a biosorptive capacity for copper. Thus, the objectives of the present experiment were to study the effects of adding different strains of fungi on the biosorptive capacity for copper in swine manure and to evaluate potential effects on microbiota profiles. Aspergillus niger (AN), Aspergillus oryzae (AO), and Saccharomyces cerevisiae (SC) were selected, and each added 0.4% into swine manure, which contain 250 mg/kg of copper. The incubations lasted for 29 days, and biosorption parameters were analyzed on the 8th (D8), 15th (D15), 22nd (D22), and 29th (D29) day. Results showed that after biosorption, temperature was 18.47–18.77°C; pH was 6.33–6.91; and content of aflatoxin B1, ochratoxin A, and deoxynivalenol were low. In addition, residual copper concentration with AN was the lowest on D15, D22, and D29. The copper biosorption rate was also highest with AN, averaging 84.85% on D29. Biosorption values for AO reached 81.12% and for SC were lower than 80%. Illumina sequencing of 16S and ITS rRNA gene revealed that fungal treatments reduced the diversity and richness of fungal abundance, but had no effect on bacterial abundance. Unknown_Marinilabiliaceae, Proteiniphilum, Tissierella, and Curvibacter were the dominant bacteria, while Aspergillus and Trichoderma were the dominant fungi. However, the added strain of S. cerevisiae was observed to be lower than the dominant fungi, which contained less than 0.05%. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment predicted via PICRUSt2 that there were bacterial genes potentially related to various aspects of metabolism and environmental information processing. Overall, data indicated that Aspergillus can provide microbial materials for adsorption of copper.

The dosage-effect of biochar on anaerobic digestion under the suppression of oily sludge: Performance variation, microbial community succession and potential detoxification mechanisms

This study investigated the dosage-effect of biochar on the suppressed mesophilic digestion of oily sludge (OS) containing naphthalene (recalcitrant compound) and starch (easily bioavailable substrate). Methanogenesis was inhibited in control with OS, where biomethane yield (63.33 mL/gVS) was obviously lower than theoretical yield (260.55 mL/gVS). With adding optimal dose of biochar (0.60 g/gVS OS), the highest CH4 yield (138.41 mL/gVS) was 2.19 times of control. Meanwhile, the efficiencies of hydrolysis, acidogenesis and acetogenesis were significantly enhanced. However, excessive biochar (4.80 g/gVS OS) caused negative effects with methanogenic efficiency diminished by 32.5% and lag phase prolonged by 5.72 h. Dissolved organic matter (DOM) analysis showed that humic acid-like and fulvic acid-like components percentages of fluorescence regional integration were decreased because of the adsorption of biochar. In addition, biochar mediating interspecies electron transfer selectively enriched electroactive fermentation bacteria (Clostridium and Bacteroides) and acetoclastic Methanosaeta, which was responsible for promoting mesophilic digestion performance. The functional genes related to metabolism and environmental information processing were potentially activated by biochar. Above results indicate that moderate biochar application may mitigate the bio-toxicity suppression of OS, which help to provide a promising pathway for reinforcing oily wastes bio-treatment.

Analysis of bacterial community functional diversity in late-stage shrimp (Litopenaeus vannamei) ponds using Biolog EcoPlates and PICRUSt2

The role of microorganisms in the environment is reflective of the function of the community; however, our understanding of the functional diversity of the bacterial microbiome found in water and sediment from shrimp ponds is currently fragmentary. This study utilized high-throughput sequencing techniques and community level physiological profiling (CLPP) methods to study the structural and functional diversity of the bacterial communities found in water samples and sediment from three intensive Litopenaeus vannamei culture ponds at late stage. The correlation between the presumptive functions using PICRUSt2 and the actual metabolic profiles via Biolog EcoPlates was evaluated. Results revealed that the genetic and functional diversity of the microbial community in the sediment of the aquaculture ponds was significantly higher than that of the water samples. In the water samples, the most dominant carbon sources utilized by the microbial community included carboxylic acids (35.08%), polymers (24.91%), and carbohydrates (23.16%); while polymers (25.61%) and amino acids (21.31%) were utilized most often in the sediment samples. Proteobacteria (38.67%), Cyanobacteria (15.96%), and Actinobacteria (16.48%) were the most dominant bacteria phyla found in the water samples. Proteobacteria (40.96%), Chloroflexi (11.79%), Bacteroidetes (9.66%) were the most dominant bacteria phyla in the sediment. Importantly, our results demonstrated that Actinobacteria, Verrucomicrobia, and Firmicutes were significantly positively correlated with the carbon source uses of the microbial community in the Biolog EcoPlates in the water samples, Proteobacteria were significantly positively correlated in the sediment. Besides, Linear discriminant analyses of predicted function of the microbial community showed that the metabolism and the cellular processes were significantly enriched in the water samples and sediment, the difference was that environmental information processing were significantly enriched in the water samples, genetic information processing were significantly enriched in the sediment. Moreover, there was a significant correlation between the predicted function and the actual metabolic profiles of the microbial community in the water samples and sediment. These findings facilitate an understanding of the relationship between the microbial community structure and the function in shrimp ponds and also provide a reference for water purification and the future commercial development of novel aquatic probiotics.

Retraction of "Quorum Sensing System in Bacteroides thetaiotaomicron Strain Identified by Genome Sequence Analysis".

[This retracts the article DOI: 10.1021/acsomega.0c03986.].

Comparative Transcriptome Analyses of the Developmental Stages of Taenia multiceps.

Cerebral coenurosis, caused by the larvae of Taenia multiceps (Coenurus cerebralis), is a fatal central nervous system disease in sheep and other herbivores and occasionally humans. Comparative transcriptomic profiles of the developmental stages of the parasite remain unknown. In this study, RNA sequencing was used to determine the transcriptome profiles of different stages of the life cycle of T. multiceps, including Oncosphere, Coenurus cerebralis (Pro with Cyst), and Adult (Adu), as well as scolex-neck proglottids (Snp), immature–mature proglottids (Imp), and gravid proglottids (Grp) of the adult stage. A total of 42.6 Gb (average 6.1 Gb) Illumina pair-end reads with a 125-bp read length were generated for seven samples. The total number of differentially expressed genes (DEGs) in the various life stages ranged from 2,577 to 3,879; however, for the tissues of the adult worm, the range was from 1,229 to 1,939. Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs mainly participated in cellular and metabolic processes, binding and catalytic activity, genetic information processing, and environmental information processing. In addition, a large number of genes related to development and parasite–host interaction were identified. Quantitative reverse transcription-polymerase chain reaction confirmed that the levels of 28 selected DEGs were consistent with those determined using RNA sequencing. The present study provides insights into the mechanisms of the development and parasitic life of T. multiceps.

Characterization of an Ex Vivo Equine Endometrial Tissue Culture Model Using Next-Generation RNA-Sequencing Technology.

Simple SummaryNotwithstanding extensive research into fertility problems in mares, pregnancy rates have remained low mainly because of endometrial inflammation (endometritis). In the field of equine research, endometrial explants have been used to carry out in vitro studies of the mare’s endometrium. However, there has been no wide-ranging assessment of relative stability of this model over time. The aim of this study was to perform an in-depth transcriptomic assessment of endometrial explants over a culture period of 72 h and assess if they are representative of the whole mare. Explants at 24 h demonstrated significant changes when compared to biopsies at 0 h as expected. Even though gene expression changes were seen between 24 and 48 h of culture, prior to this window changes were dominated by the effects of explanting and culture and subsequently, transcription was generally compromised. Our results, therefore have defined the optimal period when explants can be used to study equine endometritis and how the endometrium is modulated during inflammation. It highlights the use of abattoir derived samples to understand the physiology and pathophysiology of the equine endometrium, negating the need to collect repeated uterine biopsies from living mares.Persistent mating-induced endometritis is a major cause of poor fertility rates in the mare. Endometritis can be investigated using an ex vivo equine endometrial explant system which measures uterine inflammation using prostaglandin F2α as a biomarker. However, this model has yet to undergo a wide-ranging assessment through transcriptomics. In this study, we assessed the transcriptomes of cultured endometrial explants and the optimal temporal window for their use. Endometrium harvested immediately post-mortem from native pony mares (n = 8) were sampled (0 h) and tissue explants were cultured for 24, 48 and 72 h. Tissues were stored in RNALater, total RNA was extracted and sequenced. Differentially expressed genes (DEGs) were defined using DESeq2 (R/Bioconductor). Principal component analysis indicated that the greatest changes in expression occurred in the first 24 h of culture when compared to autologous biopsies at 0 h. Fewer DEGs were seen between 24 and 48 h of culture suggesting the system was more stable than during the first 24 h. No genes were differentially expressed between 48 and 72 h but the low number of background gene expression suggested that explant viability was compromised after 48 h. ESR1, MMP9, PTGS2, PMAIP1, TNF, GADD45B and SELE genes were used as biomarkers of endometrial function, cell death and inflammation across tissue culture timepoints. STRING assessments of gene ontology suggested that DEGs between 24 and 48 h were linked to inflammation, immune system, cellular processes, environmental information processing and signal transduction, with an upregulation of most biomarker genes at 24 h. Taken together our observations indicated that 24–48 h is the optimal temporal window when the explant model can be used, as explants restore microcirculation, perform wound healing and tackle inflammation during this period. This key observation will facilitate the appropriate use of this as a model for further research into the equine endometrium and potentially the progression of mating-induced endometritis to persistent inflammation between 24 and 48 h.

Organic matter- and temperature-driven deterministic assembly processes govern bacterial community composition and functionality during manure composting.

Although many studies have shown that microbial communities play important roles in organic waste composting due to the involvement of specific microbial taxa with metabolic functions, the underlying ecological processes of community assembly and governing factors remain elusive. Thus, a chicken manure composting experiment as a model system of microbially mediated organic waste composting was conducted. Ecological null modeling and metabolic functional prediction combined with electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were used to quantify assembly processes governing bacterial community composition and functions during composting. The results showed the predominant role of deterministic assembly processes in shifting community compositions both across and within composting stages. Stochastic assembly processes also concomitantly influenced microbial community compositions. Changes in the organic matter (OM) content and its chemical properties and temperature governed bacterial community assembly processes throughout the stages by selecting specific bacterial taxa such as Cardiobacteriales, Bacteroidales, and Lachnospiraceae on day 1, Firmicutes on days 6, 25 and 37, and Sphingobacteriales, Thermoactinomycetaceae, Actinobacteria, and Novibacillus on day 45. These taxa ultimately influenced community functions such as environmental information processing, carbohydrate and amino acid metabolism, cellular processes, and genetic information processes involved in composting. Taken together, this study indicates that deterministic assembly processes governed by OM content and quality as well as temperature influenced microbial community turnover and determined community functions during composting. These results are important for better understanding and predicting microbial-driven composting and for ultimately manipulating microorganisms for environmentally-friendly composting outcomes.

Repeated exposure to fungicide tebuconazole alters the degradation characteristics, soil microbial community and functional profiles

Tebuconazole is a broad-spectrum triazole fungicide that has been extensively applied in agriculture, but its toxicity on soil ecology remains unknown after repeated introduction to soil. This study investigated the degradation of tebuconazole and the changes in soil microbial community composition and functional diversity as well as network complexity in soil repeatedly treated with tebuconazole. Tebuconazole degraded slowly as the degradation half-life initially increased and then decreased during the four repeated treatments. High concentration of tebuconazole treatment significantly delayed the degradation of tebuconazole. The soil microbial functional diversity in tebuconazole-treated soils showed an inhibition-recovery-stimulation trend with increasing treatment frequency, which was related to the increased degradation rates of tebuconazole. Tebuconazole significantly decreased soil microbial biomass and bacterial community diversity, and this decreasing trend became more pronounced with increasing treatment frequency and concentration. Moreover, tebuconazole significantly decreased soil bacterial community network complexity, particularly at high concentration of tebuconazole treatment. Notably, four bacterial genera, Methylobacterium, Burkholderia, Hyphomicrobium, and Dermacoccus, were identified as the potential tebuconazole-degrading bacteria, with the relative abundances in the tebuconazole treatment significantly increasing by 42.1–34687.1% compared to the control. High concentration of tebuconazole treatment delayed increases in the relative abundances of Methylobacterium but promoted those of Burkholderia, Hyphomicrobium and Dermacoccus. Additionally, repeated tebuconazole treatments improved only four metabolic pathways, cell motility, membrane transport, environmental information processing, and xenobiotics biodegradation and metabolism, which were associated with the degradation of tebuconazole. The above results indicated that repeated tebuconazole treatments resulted in the significant accumulation of residues and long-term negative effects on soil ecology, and also emphasized the potential roles of dominant indigenous microbial bacteria in the degradation of tebuconazole.

Habitat environmental factors influence intestinal microbial diversity of the short-faced moles (Scaptochirus moschata)

The short-faced moles (Scaptochirus moschata) are unique Chinese mammal that live in burrows for life. They have complex ecological adaptation mechanisms to adapt to perennial underground life. Intestinal microbes play an important role in the ecological adaptation of wild animals. The gut microbiota diversity and its function in short-faced moles’ ecological adaptation is a scientific issue worth exploring. In this study, the Illumina HiSeq sequencing platform was used to sequence the V3-V4 hypervariable regions of the 16S rRNA genes of 22 short-faced moles’ intestinal samples to study the composition and functional structure of their intestinal microbiota. The results showed that in the short-faced moles’ intestine, there are four main phyla, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidete. At the family level, Peptostreptococcaceae and Enterobacteriaceae have the highest abundance. At the genus level, Romboutsia is the genus with the highest microbial abundance. According to the KEGG database, the main functions of short-faced mole gut microbes are metabolism, genetic information processing, environmental information processing, and cellular processes. The function of short-faced mole intestinal microbiota is suitable for its long-term burrowing life. No gender difference is found in the composition and function of the short-faced mole intestinal microbiota. There are significant differences in the composition and functional structure of the short-faced mole gut microbiota between samples collected from different habitats. We conferred that this is related to the different environment factors in which they live, especially to the edaphic factors.

Molecular subtypes based on CNVs related gene signatures identify candidate prognostic biomarkers in lung adenocarcinoma

The classical factors for predicting prognosis currently cannot meet the developing requirements of individualized and accurate prognostic evaluation in lung adenocarcinoma (LUAD). With the rapid development of high-throughput DNA sequencing technologies, genomic changes have been discovered. These sequencing data provide unprecedented opportunities for identifying cancer molecular subtypes. In this article, we classified LUAD into two distinct molecular subtypes (Cluster 1 and Cluster 2) based on Copy Number Variations (CNVs) and mRNA expression data from the Cancer Genome Atlas (TCGA) based on non-negative matrix factorization. Patients in Cluster 1 had worse outcomes than that in Cluster 2. Molecular features in subtypes were assessed to explain this phenomenon by analyzing differential expression genes expression pattern, which involved in cellular processes and environmental information processing. Analysis of immune cell populations suggested different distributions of CD4+ T cells, CD8+ T cells, and dendritic cells in the two subtypes. Subsequently, two novel genes, TROAP and RASGRF1, were discovered to be prognostic biomarkers in TCGA, which were confirmed in GSE31210 and Tianjin Medical University Cancer Institute and Hospital LUAD cohorts. We further proved their crucial roles in cancers by vitro experiments. TROAP mediates tumor cell proliferation, cycle, invasion, and migration, not apoptosis. RASGRF1 has a significant effect on tumor microenvironment. In conclusion, our study provides a novel insight into molecular classification based on CNVs related genes in LUAD, which may contribute to identify new molecular subtypes and target genes.

Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

Grouper and Asian seabass are among the economically important cultured marine fish in Malaysia. However, fry productions in large scale tend to introduce stress that changes the fish microbiota and increases susceptibility to diseases. Currently, high-throughput sequencing is used to study fish microbiota and their respective gene functions. In this study, we investigate the diversity, abundance and functional genes of intestinal microbiota of tiger grouper and Asian seabass that were reared in a semi-closed hatchery during dry and wet seasons. Intestinal samples were collected from tiger grouper and Asian seabass of different sizes before proceeded to DNA extraction. The extracted DNA were then subjected to 16S rRNA gene amplicon sequencing using the Illumina Miseq platform targeting V3 and V4 regions for determination of the bacterial diversity, abundance and functional genes in both seasons. The results revealed that intestinal microbiota of Asian seabass were dominated by the phylum Proteobacteria and order Vibrionales in both seasons. Meanwhile, intestinal microbiome of tiger groupers were shifted from domination of phylum Firmicutes and order Clostridiales in dry season to Proteobacteria and order Lactobacillales in wet season. PICRUSt analysis revealed that the functional genes that were dominantly present were the genes encoded for metabolism, genetic information processing, environmental information processing, cellular process and human diseases. Remarkably, SIMPER analysis showed several potential metagenomics biomarker genes in dry and wet seasons. This study revealed the importance of utilizing amplicon metagenomics approaches in microbiome studies for better identification of the microbial profiling in aquaculture systems.

Adaptive Differences in Gene Expression in Farm-Impacted Seedbeds of the Native Blue Mussel Mytilus chilensis.

The study of adaptive population differences is relevant for evolutionary biology, as it evidences the power of selective local forces relative to gene flow in maintaining adaptive phenotypes and their underlying genetic determinants. However, human-mediated hybridization through habitat translocations, a common and recurrent aquaculture practice where hybrids could eventually replace local genotypes, risk populations’ ability to cope with perturbations. The endemic marine mussel Mytilus chilensis supports a booming farming industry in the inner sea of Chiloé Island, southern Chile, which entirely relies on artificially collected seeds from natural beds that are translocated to ecologically different fattening centers. A matter of concern is how farm-impacted seedbeds will potentially cope with environmental shifts and anthropogenic perturbations. This study provides the first de novo transcriptome of M. chilensis; assembled from tissue samples of mantles and gills of individuals collected in ecologically different farm-impacted seedbeds, Cochamó (41°S) and Yaldad (43°S). Both locations and tissue samples differentially expressed transcripts (DETs) in candidate adaptive genes controlling multiple fitness traits, involved with metabolism, genetic and environmental information processing, and cellular processes. From 189,743 consensus contigs assembled: 1,716 (Bonferroni pvalue ≤ 0.05) were DETs detected in different tissues of samples from different locations, 210 of them (fold change ≥ | 100|) in the same tissue of samples from a different location, and 665 (fold change ≥ | 4|) regardless of the tissue in samples from a different location. Site-specific DETs in Cochamó (169) and Yaldad (150) in candidate genes controlling tolerance to temperature and salinity shifts, and biomineralization exhibit a high number of nucleotide genetic variants with regular occurrence (frequency > 99%). This novel M. chilensis transcriptome should help assessing and monitoring the impact of translocations in wild and farm-impacted mussel beds in Chiloé Island. At the same time, it would help designing effective managing practices for conservation, and translocation traceability.

Asymmetric expression of homoeologous genes contributes to dietary adaption of an allodiploid hybrid fish derived from Megalobrama amblycephala (\u2640) \xd7 Culter alburnus (\u2642)

BackgroundHybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with one another in a single nucleus, which may cause subgenome interaction and dominance at the gene expression level and has been observed in some allopolyploid plants. In our previous studies, newly formed allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) had herbivorous characteristic. It is thus interesting to further characterize whether the subgenome interaction and dominance derive dietary adaptation of this hybrid fish.ResultsDifferential expression, homoeolog expression silencing and bias were investigated in the hybrid fish after 70 days of adaptation to carnivorous and herbivorous diets. A total of 2.65 × 108 clean reads (74.06 Gb) from the liver and intestinal transcriptomes were mapped to the two parent genomes based on specific SNPs. A total of 2538 and 4385 differentially expressed homoeologous genes (DEHs) were identified in the liver and intestinal tissues between the two groups of fish, respectively, and these DEHs were highly enriched in fat digestion and carbon metabolism, amino acid metabolism and steroid biosynthesis. Furthermore, subgenome dominance were observed in tissues, with paternal subgenome was more dominant than maternal subgenome. Moreover, subgenome expression dominance controlled functional pathways in metabolism, disease, cellular processes, environment and genetic information processing during the two dietary adaptation processes. In addition, few but sturdy villi in the intestine, significant fat accumulation and a higher concentration of malondialdehyde in the liver were observed in fish fed carnivorous diet compared with fish fed herbivorous diet.ConclusionsOur results indicated that diet drives phenotypic and genetic variation, and the asymmetric expression of homoeologous genes (including differential expression, expression silencing and bias) may play key roles in dietary adaptation of hybrid fish. Subgenome expression dominance may contribute to uncovering the mechanistic basis of heterosis and also provide perspectives for fish genetic breeding and application.