scholarly journals Bacterial Community Is Affected by Locations and Time Rather Than Potato Varieties but Streptomyces spp. Are Related to Potato Varieties

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 659
Author(s):  
Geon Seung Lee ◽  
Mahesh Adhikari ◽  
Jae E. Yang ◽  
Hyuck Soo Kim ◽  
Kyu Suk Han ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Soil Samples ◽  
Metagenomic Sequencing ◽  
Potato Varieties ◽  
Bacterial Phyla ◽  
Streptomyces Spp ◽  
The Common ◽  
Spatial Locations

Improved knowledge and a better understanding of the functions of bacterial communities are vital for effective crop disease management. This study was conducted to study a bacterial community’s relationship with the common scab in four different potato varieties (Dejima, DJ; Atlantic, DS; Seohong, SH; Haryeong, HY) at two different locations (Gangneung and Chuncheon) and spatial locations (rhizosphere and furrow) at two different times (preharvest and postharvest). In addition, metagenomic sequencing was performed by extracting genomic DNA from soil samples to observe the dominant bacterial microbes and disease severity of the common scab in all the tested varieties in spatial location and time. The results suggest that the most dominant bacterial phyla in all the soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Additionally, Streptomyces spp. were found to be more abundant in the susceptible variety (DJ) than in other varieties (DS, SH, and HY). Interestingly, bacterial communities were found to be more diverse across the two different geographical locations, spatial locations, and harvesting times, rather than the variety of potato, according to PCoA analysis. There were no interlinked changes in bacterial communities among the varieties. Moreover, the 14 most dominant bacterial genus correlation networks with Streptomyces spp. suggested that there was a significant positive and negative correlation to some extent. Alpha and beta diversity results clearly indicated that the possible reason for differences in bacterial communities might have been due to the different spatial locations, in comparison with varieties, which suggests that there was no significant correlation between bacterial community richness and diversity among the varieties.

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 Network Analysis Reveals Seasonal Patterns of Bacterial Community Networks in Lake Taihu under Aquaculture Conditions

Water ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1868 ◽  
Author(s):  
Lin ◽  
Zhao ◽  
Zeng ◽  
Cao ◽  
Jiao
Keyword(s):  
Network Analysis ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Lake Taihu ◽  
Bacterial Species ◽  
Community Networks ◽  
Seasonal Patterns ◽  
Community Interactions ◽  
Important Species ◽  
Bacterial Phyla

Bacterial communities play essential roles in multiple ecological processes, such as primary production and nutrient recycling in aquatic systems. However, although the composition, diversity and function of bacterial communities have been well studied, little is known about the interactions and co-occurrence characteristics of these communities, let alone their seasonal patterns. To investigate the seasonal variations of bacterial community interactions, we collected water samples from four seasons in Lake Taihu and applied network analysis to reveal bacterial community interactions. Bacterial community networks were non-random in structure, and interactions among bacterial taxa in the networks varied markedly in different seasons. The autumnal bacterial network was the largest and most complex among obtained networks, whereas the spring correlation network was the simplest, having no module hubs or connectors. The important species of the networks were the dominant bacterial phyla/classes (e.g., Alphaproteobacteria and Bacteroidetes), although their relative abundance varied among seasons. The relationships between species and measured environmental variables changed over seasons; fewer environmental factors were correlated with bacterial species in the spring bacterial network, while we observed a greater number of species-environment correlations in the winter network. Our study highlights the seasonal differences in bacterial community interactions and expands our understanding of freshwater microbial ecology in systems affected by aquaculture.

scholarly journals Impact of long-term industrial contamination on the bacterial communities in urban river sediments

2020 ◽  
Author(s):  
lei zhang ◽  
Demei Tu ◽  
Xingchen Li ◽  
Wenxuan Lu ◽  
Jing Li
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Industrial Pollution ◽  
River Sediments ◽  
Urban River ◽  
Bacterial Phyla ◽  
Different Types

Abstract Background: The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks.Results: Although the composition of dominant bacterial phyla in different sediment samples was similar, their relative abundance was different. These dominant bacterial phyla showed significant differences in different types of industrial contaminated sediment. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P <0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution.Conclusions: Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

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 Novel bacterial lineages associated with boreal moss species

2017 ◽  
Author(s):  
Hannah Holland-Moritz ◽  
Julia Stuart ◽  
Lily R. Lewis ◽  
Samantha Miller ◽  
Michelle C. Mack ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Carbon Fixation ◽  
Net Primary Productivity ◽  
Bacterial Community Composition ◽  
Marker Gene ◽  
Metagenomic Sequencing ◽  
Moss Species ◽  
Anoxygenic Phototrophs ◽  
Bacterial Phyla ◽  
Bacterial Lineages

AbstractMosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbor diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local environmental conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with eight boreal moss species collected near Fairbanks, AK USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbor diverse lineages of potential N2- fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.

scholarly journals Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China

2015 ◽  
Vol 81 (19) ◽  
pp. 6567-6576 ◽  
Author(s):  
Lihua Niu ◽  
Yi Li ◽  
Peifang Wang ◽  
Wenlong Zhang ◽  
Chao Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Elevation Gradient ◽  
Ammonia Nitrogen ◽  
Phosphorus Concentration ◽  
Total Phosphorus Concentration ◽  
Content Type ◽  
Bacterial Phyla ◽  
Operational Variables

ABSTRACTTo understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla.Betaproteobacteria,Bacteroidetes, andFirmicutesdisplayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations.

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.

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