scholarly journals Profiling the Bacterial Diversity in a Typical Karst Tiankeng of China

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 187 ◽  
Author(s):  
Gaozhong Pu ◽  
Yanna Lv ◽  
Lina Dong ◽  
Longwu Zhou ◽  
Kechao Huang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Operational Taxonomic Unit ◽  
Soil Characteristics ◽  
Soil Samples ◽  
Controlling Factors ◽  
Bacterial Composition ◽  
Microbial Distribution ◽  
Significant Difference

While karst tiankengs have a higher capacity to act as safe havens for biodiversity in changing climates, little is known about their soil microorganisms. To fill this gap, we investigate the distribution and driving factors of the bacterial community in karst tiankeng systems. There is a significant difference in the soil characteristics between the inside and the outside of a karst tiankeng. At the karst tiankeng considered in this study, the bacterial composition, in terms of the operational taxonomic unit (OTU), was found to be significantly different in different soil samples, taken from diverse sampling sites within the collapsed doline or the external area, and showed a high habitat heterogeneity. The dominant phylum abundances vary with the sampling sites and have their own indicator taxa from phylum to genus. Unlike the primary controlling factors of plant diversity, the microclimate (soil moisture and temperature), soil pH, and slope dominated the distribution of the bacterial community in karst tiankeng systems. Our results firstly showed the distribution characteristics of bacterial communities and then revealed the importance of microhabitats in predicting the microbial distribution in karst tiankeng systems.

scholarly journals Bacterial Diversity in Soil Surround Subterranean Termites-Damaged Wooden Buildings in Seonamsa Temple and Effect of the Termites on Bacterial Diversity in Humus Soil

2021 ◽  
Vol 37 (4) ◽  
pp. 357-361
Author(s):  
Young Hee Kim ◽  
Boa Lim ◽  
Jeung Min Lee ◽  
Jin Young Hong ◽  
Soo Ji Kim ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Soil Microorganisms ◽  
Operational Taxonomic Unit ◽  
Illumina Miseq ◽  
Subterranean Termites ◽  
Bacterial Composition ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Humus Soil

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple’s soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple’s soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

scholarly journals Skin microbiota differs drastically between co-occurring frogs and newts

2017 ◽  
Vol 4 (4) ◽  
pp. 170107 ◽  
Author(s):  
Molly C. Bletz ◽  
R. G. Bina Perl ◽  
Miguel Vences
Keyword(s):  
Bacterial Communities ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Amphibian Skin ◽  
Skin Microbiota ◽  
Triturus Cristatus ◽  
Bacterial Composition ◽  
Host Ecology ◽  
Rana Dalmatina ◽  
Ichthyosaura Alpestris

Diverse microbial assemblages inhabit amphibian skin and are known to differ among species; however, few studies have analysed these differences in systems that minimize confounding factors, such as season, location or host ecology. We used high-throughput amplicon sequencing to compare cutaneous microbiotas among two ranid frogs ( Rana dalmatina, R. temporaria ) and four salamandrid newts ( Ichthyosaura alpestris, Lissotriton helveticus, L. vulgaris, Triturus cristatus ) breeding simultaneously in two ponds near Braunschweig, Germany. We found that bacterial communities differed strongly and consistently between these two distinct amphibian clades. While frogs and newts had similar cutaneous bacterial richness, their bacterial composition strongly differed. Average Jaccard distances between frogs and newts were over 0.5, while between species within these groups distances were only 0.387 and 0.407 for frogs and newts, respectively. At the operational taxonomic unit (OTU) level, 31 taxa exhibited significantly different relative abundances between frogs and newts. This finding suggests that chemical or physical characteristics of these amphibians' mucosal environments provide highly selective conditions for bacterial colonizers. Multi-omics analyses of hosts and their microbiota as well as directed efforts to understand chemical differences in the mucosal environments (e.g. pH), and the specificities of host-produced compounds against potential colonizers will help to better understand this intriguing pattern.

scholarly journals The response of desert biocrust bacterial communities to hydration-desiccation cycles

2021 ◽  
Author(s):  
Capucine Baubin ◽  
Osnat Gillor ◽  
Noya Ran ◽  
Hagar Siebner
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Photosynthetic Activity ◽  
Biological Soil Crust ◽  
Rain Event ◽  
Arid Environments ◽  
Soil Crust ◽  
Bacterial Composition ◽  
Soil Bacterial Communities ◽  
Rain Events

Rain events in arid environments are highly unpredictable, interspersing extended periods of drought. Therefore, following changes in desert soil bacterial communities during hydration-desiccation cycles in the field, was seldom attempted. Here, we assessed rain-mediated dynamics of active community in the Negev Desert biological soil crust (biocrust), and evaluated the changes in bacterial composition, potential function, and photosynthetic activity. We predicted that increased biocrust moisture would resuscitate the phototrophs, while desiccation would inhibit their activity. Our results show that hydration increased chlorophyll content, resuscitated the biocrust Cyanobacteria, and induced potential phototrophic functions. However, decrease in the soil water content did not immediately decrease the phototrophs activity, though chlorophyll levels decreased. Moreover, while the Cyanobacteria relative abundance significantly increased, Actinobacteria, the former dominant taxa, significantly decreased in abundance. We propose that, following a rain event biocrust moisture significantly decreased, almost to drought levels, yet the response of the active bacterial community lagged, in contrast to topsoil. Possible explanations to the described rain-mediated bacteria dynamics are discussed.

scholarly journals Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

2020 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Photosynthetic Capacity ◽  
Soil Bacterial Communities ◽  
Plant Soil ◽  
Soil Bacterial

Abstract Background: The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. Results: OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.

Comparative analysis of biofilm community on different coloured substrata in relation to mussel settlement

2016 ◽  
Vol 97 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Yi-Feng Li ◽  
Xing-Pan Guo ◽  
Yu-Ru Chen ◽  
De-Wen Ding ◽  
Jin-Long Yang
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
Significant Difference ◽  
The World ◽  
Community Variability ◽  
Biofilm Community

Mussels are typical macrofouling organisms in the world. In this study, the interaction between the settlement ofMytilus coruscusplantigrades and bacterial community on coloured substrata was determined. Bacterial communities in biofilms developed on seven coloured substrata were analysed by Illumina Miseq sequencing. The mussel settlement response to coloured substrata with no biofilms was also examined.Flavobacteria, AlphaproteobacteriaandGammaproteobacteriawere the first, second and third most dominant groups in seven biofilm samples. The results suggest that the inducing activities of these biofilms on plantigrade settlement varied with coloured substrata and the lowest percentage of settlement was observed on biofilms on the green substratum. High-throughput sequencing showed that bacterial community in biofilms also changed with the substratum colour. No significant difference in the inducing activity on plantigrade settlement was observed between the coloured substrata with no biofilms. Thus, difference in plantigrade settlement response may be correlated to the changes in bacterial community on coloured substrata. This finding extends current knowledge of interaction among mussel settlement and bacterial community variability.

scholarly journals Biodiversity of Soil Bacterial Communities from the Sasso Fratino Integral Nature Reserve

2021 ◽  
Vol 12 (4) ◽  
pp. 862-877
Author(s):  
Lara Mitia Castronovo ◽  
Sara Del Duca ◽  
Sofia Chioccioli ◽  
Alberto Vassallo ◽  
Donatella Fibbi ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Dna Analysis ◽  
Nature Reserve ◽  
Random Amplified Polymorphic Dna ◽  
Soil Samples ◽  
Microbial Composition ◽  
Rdna Sequencing ◽  
Soil Bacterial

The Sasso Fratino Integral Nature Reserve (Italy) aims to protect nature and territory. Since no anthropic activities are allowed, it represents a good model to study the bacterial community of a wild environment. The aim of this work was to characterise the cultivable and the total bacterial community of soil samples from the reserve in terms of taxonomy, composition, and structure. Seven soil samples were collected at different altitudes, and the chemical composition, the total and the cultivable microbiota, and the antibiotic resistance profiles of isolates were investigated. Total bacterial communities, studied through Next Generation Sequences analysis, included 390 genera. Samples differed in terms of microbial composition basing on the different altitude/vegetation of collection points. Random Amplified Polymorphic DNA Analysis (RAPD) allowed to identify 82 haplotypes out of 158 bacterial isolates. The taxonomic identification through 16S rDNA sequencing revealed that the strains were affiliated to 21 genera. Antibiotic resistance profiles of bacteria were also investigated, highlighting a high resistance against streptomycin and kanamycin. This work represents the first description of the soil bacterial community from the Natural Reserve of Sasso Fratino, and it is the first study considering the soil microbiota of an Italian integral nature reserve.

scholarly journals Forensic DNA Profiling of Bacterial Communities in Soil

2021 ◽  
Author(s):  
◽  
Rachel Parkinson
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Community Change ◽  
Soil Samples ◽  
Dna Profiling ◽  
The Body ◽  
Soil Bacterial Community ◽  
Preliminary Evaluation ◽  
Soil Bacterial ◽  
Pmi Estimation

<p>Soil is frequently encountered as trace evidence in forensic science case-work, but because of the limitations of current analytical techniques, this evidence is rarely utilised. A technique has been developed that allows comparisons of soil samples to be made, based on molecular analysis of the bacterial communities living in the soil. This project assesses the practicality of using this technique, known as 16S rDNA T-RFLP community profiling, for forensic soil analysis, by refining the basic methodology and performing a preliminary evaluation of its reproducibility and utility. Initial difficulties associated with generating profiles from soil samples have been overcome through methodology improvement, and the technique has been found to be effective for generating simple, visual profiles that clearly demonstrate differences between soil samples. Soil bacterial community DNA profiling is likely to be a powerful yet simple forensic tool, providing the ability to routinely use soil as associative evidence. The potential for using the same technology to develop a time since death or post mortem interval (PMI) estimation tool was also investigated. This study monitored the changes in the soil bacterial community beneath decomposing human cadavers and pig carcasses and showed that community change is dynamic and progressive. These changes are caused by fluctuations in specific bacterial species populations that are able to utilise organic breakdown products released from the body over time. Release of the body’s natural microflora into the underlying soil may also contribute to an altered bacterial community. This project has demonstrated that the soil microbial community clearly changes over the course of decomposition, and potential exists for development of a PMI estimation tool based on soil bacterial community succession.</p>

scholarly journals Long-term effects of maize straw return and manure on the microbial community in cinnamon soil in Northern China using 16S rRNA sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249884
Author(s):  
Zhiping Liu ◽  
Huaiping Zhou ◽  
Wenyan Xie ◽  
Zhenxing Yang ◽  
Qianqian Lv
Keyword(s):  
Bacterial Community ◽  
Soil Fertility ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Soil Samples ◽  
Cattle Manure ◽  
Shanxi Province ◽  
Maize Straw ◽  
Straw Return

Excessive use of chemical fertilizers in agricultural practices have demonstrated a significant impact on microbial diversity and community in soil by altering soil physical and chemical properties, thereby leading to a certain degree of soil salinization and nutritional imbalances. As an organic amendment, maize straw has been widely used to improve soil quality; however, its effect on the soil bacterial community remains limited in Calcarie-Fluvie Cambisols soil in semi-humid arid plateau of North China. In the present experiment, we investigated the effects of continuous straw utilization and fertilization on bacterial communities in Shouyang, Shanxi province, China. Soil samples were collected from 5 different straw utilization and fertilization modes in the following ways: straw mulching (SM), straw crushing (SC), cattle manure (CM), in which way straw is firstly used as silage and then organic fertilizer, control with no straw return (NSR), and control without fertilizers (CK), same amount of N+P fertilizer was applied to the regimes except CK. High-throughput sequencing approaches were applied to the V3-V4 regions of the 16S ribosomal RNA for analysis of the bacterial abundance and community structures. Different long-term straw returning regimes significantly altered the physicochemical properties and bacterial communities of soil, among which CM had the most significant effects on soil fertility and bacterial diversity. Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were consistently dominant in all soil samples, and Redundancy analysis (RDA) showed significant association of total nitrogen (TN), total phosphorus (TP) and available potassium (AK) with alternation of the bacterial community. Cattle manure had the most beneficial effects on soil fertility and bacterial diversity among different straw utilization and fertilization modes.

scholarly journals Dynamic changes in the rhizosphere bacterial community in monoculture and intercropping maize and soybean during various crop growth stages 

2020 ◽  
Author(s):  
Han Li ◽  
Luyun Luo ◽  
Bin Tang ◽  
Huanle Guo ◽  
Zhongyang Cao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Physicochemical Properties ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Crop Growth ◽  
Soil Samples ◽  
Growth Stages ◽  
Soil Physicochemical Properties ◽  
Crop Growth Stages ◽  
Rhizosphere Bacterial Communities

Abstract Although rhizosphere microorganisms have been studied for a long time, rhizosphere microbial communities based on monoculture and intercropping soybean and maize have rarely been studied. To define the effect of crop monoculture and intercropping on soil physicochemical properties and rhizosphere bacterial communities, field experiments were conducted using maize and soybean cultivars at five different crop growth stages, including monoculture maize, monoculture soybean and maize-soybean intercropping. The rhizosphere bacterial communities were analyzed by using the 16S rRNA Illumina sequencing. The pH and soil organic matter (SOM) were the key factors affecting crop rhizosphere soil bacterial communities. The intercropping soybean-maize increased the available phosphorus (AP) content at five different crop growth stages. And the available potassium (AK) content in the intercropping soybean soil samples was higher than corresponding monoculture soil samples. The content of available cadmium (ACd) in monoculture soybean rhizosphere soil samples decreased and then increased, but the intercropping soybean soil samples indicated an opposite trend. Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria and Firmicutes were the dominant phyla in the soybean and maize rhizosphere soil samples. Crops of the same plant species showed little difference in the bacterial community diversity under the two planting modes. The results indicated the intercropping planting pattern altered the absorption of ACd in the maize and soybean soil since the S2 stage and showed a different change in different crop growth stages. And the maize-soybean intercropping system also changed the bacterial community and soil physicochemical properties.

scholarly journals Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

2021 ◽  
Vol 9 (5) ◽  
pp. 1032
Author(s):  
Emily Celeste Fowler ◽  
Prakash Poudel ◽  
Brandon White ◽  
Benoit St-Pierre ◽  
Michael Brown
Keyword(s):  
Striped Bass ◽  
Soybean Meal ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Hybrid Striped Bass ◽  
Bacterial Composition ◽  
Morone Chrysops ◽  
Fish Diets ◽  
Significant Difference

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

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