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>

pH affects bacterial community composition in soils across the Huashan Watershed, China

2016 ◽  
Vol 62 (9) ◽  
pp. 726-734 ◽  
Author(s):  
Rui Huang ◽  
Dayong Zhao ◽  
Jin Zeng ◽  
Feng Shen ◽  
Xinyi Cao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Properties ◽  
Soil Ph ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Mantel Test ◽  
Soil Samples ◽  
Dominant Factor ◽  
Bioinformatics Analyses ◽  
Soil Bacterial

To investigate soil bacterial richness and diversity and to determine the correlations between bacterial communities and soil properties, 8 soil samples were collected from the Huashan watershed in Anhui, China. Subsequently, 454 high-throughput pyrosequencing and bioinformatics analyses were performed to examine the soil bacterial community compositions. The operational taxonomic unit richness of the bacterial community ranged from 3664 to 5899, and the diversity indices, including Chao1, Shannon–Wiener, and Faith’s phylogenetic diversity ranged from 7751 to 15 204, 7.386 to 8.327, and 415.77 to 679.11, respectively. The 2 most dominant phyla in the soil samples were Actinobacteria and Proteobacteria. The richness and diversity of the bacterial community were positively correlated with soil pH. The Mantel test revealed that the soil pH was the dominant factor influencing the bacterial community. The positive modular structure of co-occurrence patterns at the genus level was discovered by network analysis. The results obtained in this study provide useful information that enhances our understanding of the effects of soil properties on the bacterial communities.

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 Soil bacterial community as impacted by addition of rice straw and biochar

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhiqiang Tang ◽  
Liying Zhang ◽  
Na He ◽  
Diankai Gong ◽  
Hong Gao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Rice Straw ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Soil Bacterial Community ◽  
Rice Soil ◽  
Uncultured Bacterium ◽  
Rice Growth ◽  
Rdna Sequencing ◽  
Soil Bacterial

AbstractThe application of straw and biochar can effectively improve soil quality, but whether such application impacts paddy soil bacterial community development remains to be clarified. Herein, the impacts of three different field amendment strategies were assessed including control (CK) treatment, rice straw (RS) application (9000 kg ha−1), and biochar (BC) application (3150 kg ha−1). Soil samples were collected at five different stages of rice growth, and the bacterial communities therein were characterized via high-throughput 16S rDNA sequencing. The results of these analyses revealed that soil bacterial communities were dominated by three microbial groups (Chloroflexi, Proteobacteria and Acidobacteria). Compared with the CK samples, Chloroflexi, Actinobacteria, Nitrospirae and Gemmatimonadetes levels were dominated phyla in the RS treatment, and Acidobacteria, Actinobacteria, Nitrospirae and Patescibacteria were dominated phyla in the BC treatment. Compared with the RS samples, Chloroflexi, Acidobacteria, Actinobacteria, and Verrucomicrobia levels were increased, however, Proteobacteria, Gemmatimonadetes, Nitrospirae, and Firmicute levels were decreased in the BC samples. Rhizosphere soil bacterial diversity rose significantly following RS and BC amendment, and principal component analyses confirmed that there were significant differences in soil bacterial community composition among treatment groups when comparing all stages of rice growth other than the ripening stage. Relative to the CK treatment, Gemmatimonadaceae, Sphingomonadaceae, Thiovulaceae, Burkholderiaceae, and Clostridiaceae-1 families were dominant following the RS application, while Thiovulaceae and uncultured-bacterium-o-C0119 were dominant following the BC application. These findings suggest that RS and BC application can improve microbial diversity and richness in paddy rice soil in Northeast China.

scholarly journals Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

2009 ◽  
Vol 75 (15) ◽  
pp. 5111-5120 ◽  
Author(s):  
Christian L. Lauber ◽  
Micah Hamady ◽  
Rob Knight ◽  
Noah Fierer
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Spatial Scales ◽  
Bacterial Community Composition ◽  
Phylogenetic Structure ◽  
Soil Bacterial Communities ◽  
Soil Bacterial Community Structure ◽  
Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

scholarly journals The role of ecosystem engineers in shaping the diversity and function of arid soil bacterial communities

2020 ◽  
Author(s):  
Capucine Baubin ◽  
Arielle M. Farrell ◽  
Adam Šťovíček ◽  
Lusine Ghazaryan ◽  
Itamar Giladi ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Soil Samples ◽  
Ecosystem Engineers ◽  
Soil Microbiome ◽  
Desert Ecosystems ◽  
Arid Soil ◽  
Soil Bacterial Communities ◽  
Ant Nests ◽  
Soil Bacterial ◽  
And Function

ABSTRACTEcosystem engineers (EEs) are present in every environment and are known to strongly influence ecological processes and thus shape the distribution of species and resources. In this study, we assessed the direct and indirect effect of two EEs (perennial shrubs and ant nests), individually and combined, on the composition and function of arid soil bacterial communities. To that end, top soil samples were collected in the Negev Desert Highlands during the dry season from four patch types: (1) barren soil; (2) under shrubs; (3) near ant nests; or (4) near ant nests situated under shrubs. The bacterial composition was evaluated in the soil samples (fourteen replicates per patch type) using 16S rRNA gene amplicon sequencing, together with physico-chemical measures of the soil, and the potential functions of the community. We have found that the EEs differently affected the community composition. Indeed, barren patches supported a soil microbiome, dominated by Rubrobacter and Proteobacteria, while in EE patches the Deinococcus-Thermus phylum was dominating. The presence of the EEs similarly enhanced the abundance of phototrophic, nitrogen cycle and stress- related genes. In addition, only when both EEs were combined, were the soil characteristics altered. Our results imply that arid landscapes foster unique communities selected by each EE(s), solo or in combination, yet these communities have similar potential biological traits to persist under the harsh arid conditions. Environments with multiple EEs are complicated to study due to the possibility of non-additive effects of EEs and thus further research should be done.IMPORTANCEEcosystem engineers are organisms that can create, modify, or maintain their habitat. They are present in various environments but are particularly conspicuous in desert ecosystems, where their presence is tightly linked to vital resources like water or nutrients. Despite their key role in structuring and controlling desert ecosystems, joint engineering, and their effect on soil function, are unknown. Our study explores the contributions of key ecosystem engineers to the diversity and function of their soil microbiome allowing better understanding of their role in shaping habitats and engineering their activity

scholarly journals Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Mayank Krishna ◽  
Shruti Gupta ◽  
Manuel Delgado – Baquerizo ◽  
Elly Morriën ◽  
Satish Chandra Garkoti ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Bacterial Communities ◽  
Secondary Succession ◽  
Positive Association ◽  
Ecological Networks ◽  
Growth Stages ◽  
Ecosystem Recovery ◽  
Soil Bacterial

Abstract This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

scholarly journals Diversity of Soil Bacterial Community Is Influenced by Spatial Location and Time but Not Potato Cultivar

2020 ◽  
Vol 4 (3) ◽  
pp. 225-238
Author(s):  
Kamrun Nahar ◽  
Jean-Baptiste Floc’h ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
Sean Whitney
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Potato Cultivar ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Streptomyces Spp ◽  
Β Diversity ◽  
Soil Bacterial ◽  
Spatial Locations

Potato cultivars susceptible to common scab were previously reported to harbor five to six times more abundant pathogenic Streptomyces spp. in the rhizosphere soils compared with tolerant cultivars. It is still unclear if the diversity of soil bacterial communities is related to the abundance of pathogenic Streptomyces spp. This study evaluated the effects of potato cultivar on the diversity of bacterial communities in three spatial locations (soil located close to the plant [SCP], in the rhizosphere soil [RS], and in the geocaulosphere soil [GS]) in 2013 and 2014. Common scab tolerant (Goldrush and Hindenburg) and susceptible cultivars (Green Mountain and Agria) were planted in a field infested with pathogenic Streptomyces spp. causing common scab. The β-diversity of the bacterial community was significantly different between years and on dates within each year according to a permutational multivariate analysis of variance. The β-diversity also varied significantly among spatial locations (i.e., SCP, RS, and GS), probably due to changes in soil properties, but did not change significantly among potato cultivars. The architecture of the bacterial network in RS in 2014 was more complex compared with 2013 with a 2.5-fold increase in the number of bacteria included according to a co-occurrence analysis. These results indicated that the soil bacterial community diversity changed temporally and spatially. However, bacterial community diversity and richness were not affected by potato cultivar, suggesting that there were no relationships between bacterial community diversity or richness and the abundance of pathogenic Streptomyces spp.

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 The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China

Forests ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 51 ◽  
Author(s):  
Jiangmei Qiu ◽  
Jianhua Cao ◽  
Gaoyong Lan ◽  
Yueming Liang ◽  
Hua Wang ◽  
...  
Keyword(s):  
Land Use ◽  
Surface Layer ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Yunnan Province ◽  
Soil Bacterial Community ◽  
Land Use Patterns ◽  
Use Patterns ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Land use patterns can change the structure of soil bacterial communities. However, there are few studies on the effects of land use patterns coupled with soil depth on soil bacterial communities in the karst graben basin of Yunnan province, China. Consequently, to reveal the structure of the soil bacterial community at different soil depths across land use changes in the graben basins of the Yunnan plateau, the relationship between soil bacterial communities and soil physicochemical properties was investigated for a given area containing woodland, shrubland, and grassland in Yunnan province by using next-generation sequencing technologies coupled with soil physicochemical analysis. Our results indicated that the total phosphorus (TP), available potassium (AK), exchangeable magnesium (E-Mg), and electrical conductivity (EC) in the grassland were significantly higher than those in the woodland and shrubland, yet the total nitrogen (TN) and soil organic carbon (SOC) in the woodland were higher than those in the shrubland and grassland. Proteobacteria, Verrucomicrobia, and Acidobacteria were the dominant bacteria, and their relative abundances were different in the three land use types. SOC, TN, and AK were the most important factors affecting soil bacterial communities. Land use exerts strong effects on the soil bacterial community structure in the soil’s surface layer, and the effects of land use attenuation decrease with soil depth. The nutrient content of the soil surface layer was higher than that of the deep layer, which was more suitable for the survival and reproduction of bacteria in the surface layer.

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