Different Distribution of Soil Core Microbiota in two Places of Huabei Plain, Central China

Soils harbor diverse bacteria, and these bacteria play important roles in soil nutrition cycling and carbon storage. Numerous investigations of soil microbiota had been performed, and the core microbiota in different soil or vegetation soil types had been described. However, the complexity of soil environments and relatively limited information of many geographic areas had attracted great attention on comprehensive exploration of soil microbes in enormous types of soil. To reveal the core soil microbiota in Huabei plain, soil samples from metropolis and countryside regions in the Huabei plain were investigated using high-throughput sequencing strategy. The results showed that the most dominant bacteria are Proteobacteria (38.34%), Actinobacteria (20.56%), and Acidobacteria (15.18%). At the genus-level, the most abundant known genera are Gaiella (3.66%), Sphingomonas (3.6%), Acidobacteria Gp6 (2.1%), and Arthrobacter (2%). Moreover, several dominant operational taxanomy units (OTU), such as OTU_3 and OTU_17, were identified to be associated with the soil environment. Microbial distributions of the metropolis samples were different from the countryside samples, which may reflect the environments in the countryside were more diverse than in the metropolis. Microbial diversity and evenness were higher in the metropolis than in the countryside, which might due to the fact that human activity increased the microbial diversity in the metropolis. The soil core microbiota of the Huabei plain were complex, and microbial distributions in the Huabei plain might be mainly affected by the human activity and environmental factors, not by the distance. Our data highlights the soil core microbiota in Huabei Plain, and provides insights for future soil microbiota distribution studies in central China.

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Effects of husbandry systems and Chinese indigenous chicken strain on cecum microbial diversity

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.19.0157 ◽

2020 ◽

Vol 33 (10) ◽

pp. 1610-1616 ◽

Cited By ~ 1

Author(s):

Xiuxue Dong ◽

Bing Hu ◽

Wenlong Wan ◽

Yanzhang Gong ◽

Yanping Feng

Keyword(s):

Microbial Diversity ◽

High Throughput Sequencing ◽

Stocking Density ◽

Operational Taxonomic Unit ◽

Indigenous Chicken ◽

Microbial Composition ◽

Core Microbiota ◽

Free Range ◽

The Core ◽

Individual Cage

Objective: This study was to evaluate the effect of husbandry systems and strains on cecum microbial diversity of Jingyang chickens under the same dietary conditions.Methods: A total of 320 laying hens (body weight, 1.70±0.15 kg; 47 weeks old) were randomly allocated to one of the four treatments: i) Silver-feathered hens in enrichment cages (SEC) with an individual cage (70×60×75 cm), ii) Silver-feathered hens in free range (SFR) with the stocking density of 1.5 chickens per ten square meters, iii) Gold-feathered hens in enrichment cages (GEC), iv) Gold-feathered hens in free range (GFR). The experiment lasted 8 weeks and the cecum fecal samples were collected for 16S rDNA high throughput sequencing at the end of experiment.Results: i) The core microbiota was composed of Bacteroidetes (49% to 60%), Firmicutes (21% to 32%) and Proteobacteria (2% to 4%) at the phylum level. ii) The core bacteria were Bacteroides (26% to 31%), Rikenellaceae (9% to 16%), Parabacteroides (2% to 5%) and Lachnoclostridium (2% to 6%) at the genus level. iii) The indexes of operational taxonomic unit, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. iv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens.Conclusion: The core microbiota were not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes only for silver feathered hens. However, the cecum microbial composition was similar in two strain treatments under the same dietary conditions.

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Comparative Evaluation of Microbiota Dynamics and Metabolites Correlation Between Spontaneous and Inoculated Fermentations of Nanfeng Tangerine Wine

Frontiers in Microbiology ◽

10.3389/fmicb.2021.649978 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiangyu Qiu ◽

Linlin Yu ◽

Weiying Wang ◽

Riming Yan ◽

Zhibin Zhang ◽

...

Keyword(s):

High Throughput Sequencing ◽

Wine Fermentation ◽

Gas Chromatography Mass Spectrometry ◽

Microbial Succession ◽

Spontaneous Fermentation ◽

Core Microbiota ◽

The Core ◽

Volatile Flavor ◽

Functional Shift ◽

Dominant Bacteria

Understanding the evolution of microorganisms and metabolites during wine fermentation is essential for controlling its production. The structural composition and functional capacity of the core microbiota determine the quality and quantity of fruit wine. Nanfeng tangerine wine fermentation involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this product fermentation remain unclear. Therefore, high-throughput sequencing (HTS) and headspace-gas chromatography-mass spectrometry (HS/GC-MS) were employed to reveal the core functional microbiota for the production of volatile flavors during spontaneous fermentation (SF) and inoculated fermentation (IF) with Saccharomyces cerevisiae of Nanfeng tangerine wine. A total of 13 bacterial and 8 fungal genera were identified as the core microbiota; Lactobacillus and Acetobacter were the dominant bacteria in SF and IF, respectively. The main fungal genera in SF and IF were Hanseniaspora, Pichia, and Saccharomyces with a clear succession. In addition, the potential correlations analysis between microbiota succession and volatile flavor dynamics revealed that Lactobacillus, Acetobacter, Hanseniaspora, and Saccharomyces were the major contributors to the production of the volatile flavor of Nanfeng tangerine wine. The results of the present study provide insight into the effects of the core functional microbiota in Nanfeng tangerine wine and can be used to develop effective strategies for improving the quality of fruit wines.

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An Active Gelatin Coating Containing Eugenol and Vacuum Delays the Decay of Chinese Seabass (Lateolabrax maculatus) Fillets during Cold Storage: A Microbiome Perspective

Coatings ◽

10.3390/coatings11020147 ◽

2021 ◽

Vol 11 (2) ◽

pp. 147

Author(s):

Xuan Ma ◽

Qianqian Zhou ◽

Weiqiang Qiu ◽

Jun Mei ◽

Jing Xie

Keyword(s):

Microbial Diversity ◽

High Throughput Sequencing ◽

Vacuum Treatment ◽

C Storage ◽

Basic Nitrogen ◽

Spoilage Bacteria ◽

Lateolabrax Maculatus ◽

Gelatin Coating ◽

Microbial Enumeration ◽

Growth And Reproduction

The purpose of this study was to evaluate the effect of an active gelatin coating containing eugenol and vacuum on the microbial diversity of Chinese seabass (Lateolabrax maculatus) during cold (−0.9 °C) storage. The bacterial sequences in Chinese seabass were observed using a high-throughput sequencing technique targeting the V3–V4 region of the 16S Ribosomal DNA (rDNA) on 0, 12th, and 24th day, which showed a more comprehensive estimate of the microbial diversity in seabass samples compared with microbial enumeration. The results revealed that the species diversity of fresh seabass was rich, mainly including Carnobacterium, Glutamicibacter, and Pseudomonas, with abundance ratios of 0.286, 0.160, and 0.130, respectively. Pseudomonas and Shewanella were the primary contaminants in the spoiled control samples, where the abundance ratios increased from 0.220 and 0.174 on the 12th day to 0.802 and 0.163 on the 24th day, respectively. Vacuum treatment could inhibit the growth of Pseudomonas and Shewanella such that when stored on the 12th day, Brochothrix became the superior genus. However, Pseudomonas and Shewanella dominated the storage until the 24th day, where their abundance ratios were 0.343 and 0.279, respectively. The inhibition of Pseudomonas and Carnobacterium was gradually enhanced with increasing concentrations of eugenol. Furthermore, an active gelatin coating containing eugenol and vacuum treatment was more effective at inhibiting the increase of the total volatile basic nitrogen. This study confirmed that an active gelatin coating containing eugenol and vacuum could reduce the species of bacteria, inhibit the growth and reproduction of the main dominant spoilage bacteria, and delay the spoilage of seabass.

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Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

Applied and Environmental Microbiology ◽

10.1128/aem.00560-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4757-4766 ◽

Cited By ~ 55

Author(s):

Caterina R. Giner ◽

Irene Forn ◽

Sarah Romac ◽

Ramiro Logares ◽

Colomban de Vargas ◽

...

Keyword(s):

Microbial Diversity ◽

High Throughput ◽

Relative Abundance ◽

Ribosomal Dna ◽

18S Rdna ◽

High Throughput Sequencing ◽

454 Sequencing ◽

Epifluorescence Microscopy ◽

Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

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Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing

Scientific Reports ◽

10.1038/srep45697 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 16

Author(s):

Mao Li ◽

Hanlin Zhou ◽

Xiangyu Pan ◽

Tieshan Xu ◽

Zhenwen Zhang ◽

...

Keyword(s):

Microbial Diversity ◽

High Throughput Sequencing ◽

Animal Feed ◽

Control Diet ◽

Intestinal Microbiome ◽

Sequencing Technology ◽

Experimental Diet ◽

Taxonomic Analysis ◽

Rrna Sequencing ◽

Dietary Treatments

Abstract Geese are extremely adept in utilizing plant-derived roughage within their diet. However, the intestinal microbiome of geese remains limited, especially the dietary effect on microbial diversity. Cassava foliage was widely used in animal feed, but little information is available for geese. In this study, the geese were fed with control diet (CK), experimental diet supplemented with 5% cassava foliage (CF5) or 10% (CF10) for 42 days, respectively. The cecal samples were collected after animals were killed. High-throughput sequencing technology was used to investigate the microbial diversity in the caecum of geese with different dietary supplements. Taxonomic analysis indicated that the predominant phyla were distinct with different dietary treatments. The phyla Firmicutes (51.4%), Bacteroidetes (29.55%) and Proteobacteria (7.90%) were dominant in the CK group, but Bacteroidetes (65.19% and 67.29%,) Firmicutes (18.01% and 17.39%), Proteobacteria (8.72% and 10.18%), Synergistete (2.51% and 1.76%) and Spirochaetes (2.60% and 1.46%) were dominant in CF5 and CF10 groups. The abundance of Firmicutes was negatively correlated with the supplementation of cassava foliage. However, the abundance of Bacteroidetes and Proteobacteria were positively correlated with the supplementation of cassava foliage. Our study also revealed that the microbial communities were significantly different at genus levels. Genes related to nutrient and energy metabolism, immunity and signal transduction pathways were primarily enriched by the microbiome.

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Technology Imperative in Managerial Decision-Making

Advances in Human Resources Management and Organizational Development - Collaborative Communication Processes and Decision Making in Organizations ◽

10.4018/978-1-4666-4478-6.ch009 ◽

2014 ◽

pp. 158-176 ◽

Cited By ~ 6

Author(s):

Neeta Baporikar

Keyword(s):

Decision Making ◽

Decision Makers ◽

Limited Information ◽

Managerial Decision ◽

Managerial Decision Making ◽

Face To Face ◽

The Core ◽

Use Of Technology ◽

Management Approaches ◽

Virtual Setting

Decisions can make or mar an organization. Decision-making is a multifaceted and intricate process. This process becomes even more complicated and complex when it comes to organizations, especially in this competitive world. Today, decisions are made not only under uncertainty, with available and/or limited information, but may also be made in a virtual setting. Decision makers may not be engaged in face-to-face deliberations. Hence, understanding the challenges, complexity, and rewards of the use of technology, especially information technology in managerial decision-making, is important. Such an understanding is not only vital in determining the efficacy of managers and their organizations, but also significant in designing future management approaches and organizations. This is the core objective of this chapter.

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Cover Crop Impact on Soil Organic Carbon, Nitrogen Dynamics and Microbial Diversity in a Mediterranean Semiarid Vineyard

Sustainability ◽

10.3390/su12083256 ◽

2020 ◽

Vol 12 (8) ◽

pp. 3256 ◽

Cited By ~ 2

Author(s):

Agata Novara ◽

Valentina Catania ◽

Marco Tolone ◽

Luciano Gristina ◽

Vito Armando Laudicina ◽

...

Keyword(s):

Organic Carbon ◽

Soil Organic Carbon ◽

Microbial Diversity ◽

Cover Crop ◽

High Throughput Sequencing ◽

Intergenic Spacer ◽

Conventional Tillage ◽

Nitrate Content ◽

Relevant Effect ◽

Management Protocol

Cover crop (CC) management in vineyards increases sustainability by improving soil chemical and biological fertility, but knowledge on its effects in semiarid soils is lacking. This study evaluated the effect of leguminous CC management on soil organic carbon (SOC) sequestration, soil nitrate content and microbial diversity in a semiarid vineyard, in comparison to conventional tillage (CT). SOC and nitrate were monitored during vine-growing season; soil respiration, determined by incubation experiments, microbial biomass and diversity was analyzed after CC burial. The microbial diversity was evaluated by bacterial and fungal automated ribosomal intergenic spacer analysis (ARISA) and high-throughput sequencing of 16SrDNA. CC increased nitrate content and, although it had no relevant effect on SOC, almost doubled its active microbial component, which contributes to SOC stabilization. An unexpected stability of the microbial communities under different soil managements was assessed, fungal diversity being slightly enhanced under CT while bacterial diversity increased under CC. The complete nitrifying genus Nitrospira and plant growth-promoting genera were increased under CC, while desiccation-tolerant genera were abundant in CT. Findings showed that temporary CC applied in semiarid vineyards does not optimize the provided ecosystem services, hence a proper management protocol for dry environments should be set up.

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Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland)

Microorganisms ◽

10.3390/microorganisms7100416 ◽

2019 ◽

Vol 7 (10) ◽

pp. 416 ◽

Cited By ~ 2

Author(s):

Dyda ◽

Pyzik ◽

Wilkojc ◽

Kwiatkowska-Kopka ◽

Sklodowska

Keyword(s):

Microbial Community ◽

Microbial Diversity ◽

High Throughput Sequencing ◽

Extreme Environment ◽

Microbial Colonization ◽

Marker Genes ◽

Lime Mortar ◽

Preventive Actions ◽

Important Challenge ◽

Cultural Heritage Objects

Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e. g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.

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Altitude influences microbial diversity and herbage fermentation in the rumen of yaks

BMC Microbiology ◽

10.1186/s12866-020-02054-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Qingshan Fan ◽

Metha Wanapat ◽

Tianhai Yan ◽

Fujiang Hou

Keyword(s):

Bacterial Community ◽

Microbial Diversity ◽

Volatile Fatty Acids ◽

Rumen Fluid ◽

Energy Requirement ◽

Tibet Plateau ◽

Limited Information ◽

Principal Coordinates Analysis ◽

Rumen Microbiota ◽

Principal Coordinates

Abstract Background Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level. Results The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks. Conclusions Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.

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