scholarly journals Time-dependent Effect of Graphene on the Microbial Activity of the Soil Under Single and Repeated Exposures

2022 ◽  
Author(s):  
wenjuan liu ◽  
yufeng guo ◽  
guoli chai ◽  
wenbo deng
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Soil Bacterial Community ◽  
Single Exposure ◽  
Time Dependent Effect ◽  
Soil Bacterial ◽  
And Function ◽  
Clustering Tree ◽  
The Impact

Abstract Graphene (GR) has huge industrial and biomedical potential, and its adverse effect on soil microorganisms has been evaluated in ecotoxicological studies. These studies focus on a single exposure to GR, but repeated exposures are more likely to occur. In this study, we compared the impact of single and repeated exposures of GR on structure, abundance and function of soil bacterial community based on soil enzyme activity and high-throughput sequencing. The activities of urease and fluorescein diacetate esterase and alpha diversity demonstrate that repeated exposure to GR increase the diversity of soil bacteria. The PCoA and sample level clustering tree showed single exposure to GR after 4 days alter the soil bacterial community to some extent. During the entire incubation process, no matter what kind of exposure scenarios to GR, the majority of bacterial phylotypes remained unchanged except for Proteobacteria and Actinobacteria according to the relative abundance of phylotypes.

scholarly journals Time-Dependent Effect of Graphene on the Microbial Activity of the Soil Under Single and Repeated Exposures

2021 ◽  
Author(s):  
Wenjuan Liu ◽  
Yufeng Guo ◽  
Guoli Chai ◽  
Wenbo Deng
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Soil Bacterial Community ◽  
Soil Bacterial Diversity ◽  
Single Exposure ◽  
Soil Bacterial ◽  
The Difference ◽  
And Function ◽  
The Impact

Abstract Graphene (GR) has huge industrial and biomedical potential, and its adverse effect on soil microorganisms has been evaluated in some ecotoxicological studies. These studies focus on a single exposure to GR, but repeated exposures are more likely to occur in soil. In this study, we compared the impact of single and repeated exposures (one, two and three exposures that resulted in the same final concentration) of GR on structure, abundance and function of soil bacterial community based on soil enzyme activity and high-throughput sequencing. The activities of urease and fluorescein diacetate esterase and alpha diversity demonstrate that repeated exposure to GR increase the diversity of soil bacterial diversity after 4 days of incubation following the last application of GR to soil. And the PCoA and sample level clustering tree showed single exposure to GR after 4 days alter the soil bacterial community to some extent, but the difference has been narrowed with the extension of time. During the entire incubation process, no matter what kind of exposure scenarios to GR, the majority of bacterial phylotypes remained unchanged except for Proteobacteria and Actinobacteria according to the relative abundance of phylotypes.

scholarly journals Diversity and composition of soil bacterial community respond to A. palmeri invasion under heterogeneous habitats

2021 ◽  
Author(s):  
Mei Zhang ◽  
Jianhua Han ◽  
Xueying Li ◽  
Pufan Zheng ◽  
Zhenlu Qiu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Alpha Diversity ◽  
Soil Bacterial Community ◽  
Soil Bacterial Diversity ◽  
Core Microbiome ◽  
Non Invasive ◽  
Heterogeneous Habitats ◽  
Soil Bacterial ◽  
The Impact ◽  
Nmds Analysis

Abstract The impact of A. palmeri invasion on soil bacterial community under different habitats is unclear. In this work, the influence of A. palmeri invasion on soil bacterial diversity and community structure were investigated using full-length 16S rRNA sequencing technology under four typical habitats of riverbank (A), roadside (B), wasteland (C) and farmland (D). A two-way ANOVA analysis showed that habitat, invasion and the interaction of them had little effect on alpha diversity, expect for habitat factor had a significant effect on Simpson indices (P<0.05). NMDS analysis demonstrated that soil bacterial community structures among different invasive habitats were clearly distinguished. In addition, the most abundant phyla in the non-invasive plots were Proteobacteria, Planctomycetes and Gemmatimonadetes. However, the third predominant phyla converted from Bacteroidetes to Gemmatimonadetes with the invasion of A. palmeri. LEfSe analysis revealed that the core microbiome, Burkholderiaceae and Betaproteobacteriales (riverbank habitat), Gemmatimonadetes and Gemmatimonadaceae (wasteland habitat), Sphingomonas_sediminicola (roadside habitat), Nitrosomonadaceae (farmland habitat), which played important roles in facilitating the establishment of A. palmeri to heterogeneous habitats.

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

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12105
Author(s):  
Fangnan Xiao ◽  
Yuanyuan Li ◽  
Guifang Li ◽  
Yaling He ◽  
Xinhua Lv ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Soil Bacteria ◽  
High Throughput Sequencing ◽  
Soil Bacterial Community ◽  
Tarim River ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
And Function

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

scholarly journals Conservation tillage regulates soil bacterial community assemblies, network structures and ecological functions in black soils

2021 ◽  
Author(s):  
Zhuxiu Liu ◽  
Haidong Gu ◽  
Aizhen Liang ◽  
Lujun Li ◽  
Qin Yao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Carbon ◽  
High Throughput Sequencing ◽  
Conservation Tillage ◽  
Conventional Tillage ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Tillage Practices ◽  
Degrading Bacteria ◽  
Soil Bacterial

Abstract Aims Conventional tillage is a serious threat to the stability of soil ecosystems. Understanding the response mechanisms of soil microbial community assemblies to anthropogenic activities is a major topic of ecological research. Methods Here, we investigated the bacterial community structures and assemblies in bulk and rhizosphere soils of soybeans grown with conventional tillage (moldboard plow, MP) and with conservation tillage that involved no-tillage (NT) or ridge tillage (RT) using high-throughput sequencing methods. Results We found that soil bacterial community compositions, structures and assembly processes were primarily altered by tillage practices. Briefly, in comparison to MP, NT and RT increased the relative abundances of the nitrogen-fixing bacteria Mesorhizobium sp., Bradyrhizobium sp. and Burkholderia sp., but decreased the abundance of soil carbon-degrading bacteria, especially Blastococcus sp., Streptomyces sp. and Sphingomonas sp. In addition, in comparison to MP, NT and RT resulted in more stable bacterial networks and more lower the relative contribution of homogenizing dispersal. Soil pH was the primary soil factor regulating both the bacterial community structures and assembly processes under the three tillage practices. Conclusions The altered functional bacteria under conservation tillage was mostly affiliated with biomarkers and keystone taxa, inferring that conservation tillage might contribute to biological nitrogen fixation and soil carbon sequestration.

scholarly journals Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4514 ◽  
Author(s):  
Jun Lou ◽  
Li Yang ◽  
Haizhen Wang ◽  
Laosheng Wu ◽  
Jianming Xu
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Laboratory Strain ◽  
Soil Bacterial Community ◽  
Absolute Abundance ◽  
Internal Reference ◽  
Biodegradation Study ◽  
Soil Bacterial

Microbial ecological studies have been remarkably promoted by the high-throughput sequencing approach with explosive information of taxonomy and relative abundance. However, relative abundance does not reflect the quantity of the microbial community and the inter-sample differences among taxa. In this study, we refined and applied an integrated high-throughput absolute abundance quantification (iHAAQ) method to better characterize soil quantitative bacterial community through combining the relative abundance (by high-throughput sequencing) and total bacterial quantities (by quantitative PCR). The proposed iHAAQ method was validated by an internal reference strain EDL933 and a laboratory strain WG5. Application of the iHAAQ method to a soil phenanthrene biodegradation study showed that for some bacterial taxa, the changes of relative and absolute abundances were coincident, while for others the changes were opposite. With the addition of a microbial activity inhibitor (NaN3), the absolute abundances of soil bacterial taxa, including several dominant genera of Bacillus, Flavobacterium, and Paenibacillus, decreased significantly, but their relative abundances increased after 28 days of incubation. We conclude that the iHAAQ method can offer more comprehensive information to reflect the dynamics of soil bacterial community with both relative and absolute abundances than the relative abundance from high-throughput sequencing alone.

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