scholarly journals Changes in the Physicochemical Properties and Microbial Communities of Rhizospheric Soil after Cassava/Peanut Intercropping

2019 ◽  
Author(s):  
Xiumei Tang ◽  
Saiyun Luo ◽  
Zhipeng Huang ◽  
Haining Wu ◽  
Jin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Physicochemical Properties ◽  
Microbial Community Structure ◽  
Enzyme Activities ◽  
Southern China ◽  
Nutrient Content ◽  
Rrna Gene ◽  
Rhizospheric Soil

ABSTRACTCassava/peanut intercropping is a popular cultivation method in southern China and has the advantages of apparently increased yield and economic efficiency compared with monoculture, however, the ecological benefits of this method are poorly understood. This study aimed to investigate the effects of intercropping on the physicochemical properties and microbial community structures of soil. Field trials were performed to determine the effects of cassava/peanut intercropping on rhizospheric soil nutrient content, enzyme activities, microbial quantity and microbial community structure. The microbial community was characterized by 16S rRNA tag-based high-throughput sequencing on the Illumina MiSeq platform. Results showed that cassava/peanut intercropping could improve the physicochemical properties of rhizospheric soil by increasing the available nutrient content, pH, bacterial quantity, and some enzyme activities and by altering the microbial community structure. 16S rRNA gene sequencing demonstrated that the microbial community structure varied between the intercropping and monoculture systems. Nitrospirae, Verrucomicrobia and Gemmatimonadetes were more abundant in the intercropping system than in the monocultures. Redundancy analysis (RDA) revealed that the abundances ofDA101,PilimeliaandRamlibacterwere positively correlated with environmental parameters such as available nitrogen and pH, and these were dominant genera in the rhizospheric soil of the intercropped peanut plants.

scholarly journals Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community

2021 ◽  
Vol 12 ◽  
Author(s):  
Ziqin Pang ◽  
Fei Dong ◽  
Qiang Liu ◽  
Wenxiong Lin ◽  
Chaohua Hu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Physicochemical Properties ◽  
Microbial Community Structure ◽  
Fungal Communities ◽  
Sulfur Cycling ◽  
Dissimilatory Sulfate Reduction ◽  
Continuous Cropping ◽  
Rhizospheric Soil ◽  
Functional Pathway

The continuous cropping of plants can result in the disruption of the soil microbial community and caused significant declines in yields. However, there are few reports on the effects of continuous cropping of sugarcane on the microbial community structure and functional pathway. In the current study, we analyzed the structural and functional changes of microbial community structure in the rhizospheric soil of sugarcane in different continuous cropping years using Illumina Miseq high-throughput sequencing and metagenomics analysis. We collected rhizosphere soils from fields of no continuous cropping history (NCC), 10 years of continuous cropping (CC10), and 30 years of continuous cropping (CC30) periods in the Fujian province. The results demonstrated that continuous sugarcane cropping resulted in significant changes in the physicochemical properties of soil and the composition of soil bacterial and fungal communities. With the continuous cropping, the crop yield dramatically declined from NCC to CC30. Besides, the redundancy analysis (RDA) of the dominant bacterial and fungal phyla and soil physicochemical properties revealed that the structures of the bacterial and fungal communities were mainly driven by pH and TS. Analysis of potential functional pathways during the continuous cropping suggests that different KEGG pathways were enriched in different continuous cropping periods. The significant reduction of bacteria associated with rhizospheric soil nitrogen and sulfur cycling functions and enrichment of pathogenic bacteria may be responsible for the reduction of effective nitrogen and total sulfur content in rhizospheric soil of continuous sugarcane as well as the reduction of sugarcane yield and sugar content. Additionally, genes related to nitrogen and sulfur cycling were identified in our study, and the decreased abundance of nitrogen translocation genes and AprAB and DsrAB in the dissimilatory sulfate reduction pathway could be the cause of declined biomass. The findings of this study may provide a theoretical basis for uncovering the mechanism of obstacles in continuous sugarcane cropping and provide better guidance for sustainable development of the sugarcane.

scholarly journals Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure

2018 ◽  
Author(s):  
Lauren Gillies Campbell ◽  
J. Cameron Thrash ◽  
Nancy N. Rabalais ◽  
Olivia U. Mason
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gulf Of Mexico ◽  
Dissolved Oxygen ◽  
Microbial Community Structure ◽  
Rrna Gene ◽  
Hypoxic Zone ◽  
Low Do

AbstractRich geochemical datasets generated over the past 30 years have provided fine-scale resolution on the northern Gulf of Mexico (nGOM) coastal hypoxic (≤ 2 mg of O2 L-1) zone. In contrast, little is known about microbial community structure and activity in the hypoxic zone despite the implication that microbial respiration is responsible for forming low dissolved oxygen (DO) conditioXSns. Here, we hypothesized that the extent of the hypoxic zone is a driver in determining microbial community structure, and in particular, the abundance of ammonia-oxidizing archaea (AOA). Samples collected across the shelf for two consecutive hypoxic seasons in July 2013 and 2014 were analyzed using 16S rRNA gene sequencing, oligotyping, microbial co-occurrence analysis and quantification of thaumarchaeal 16S rRNA and archaeal ammonia-monooxygenase (amoA) genes. In 2014 Thaumarchaeota were enriched and inversely correlated with DO while Cyanobacteria, Acidimicrobiia and Proteobacteria where more abundant in oxic samples compared to hypoxic. Oligotyping analysis of Nitrosopumilus 16S rRNA gene sequences revealed that one oligotype was significantly inversely correlated with dissolved oxygen (DO) in both years and that low DO concentrations, and the high Thaumarchaeota abundances, influenced microbial co-occurrence patterns. Taken together, the data demonstrated that the extent of hypoxic conditions could potentially influence patterns in microbial community structure, with two years of data revealing that the annual nGOM hypoxic zone is emerging as a low DO adapted AOA hotspot.

scholarly journals Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0132253 ◽  
Author(s):  
Guoqin Yu ◽  
Doug Fadrosh ◽  
James J. Goedert ◽  
Jacques Ravel ◽  
Alisa M. Goldstein
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Nested Pcr ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

scholarly journals Distribution of Microbial Community Structure in Sediment from the Suyeong River and Bay of Busan, Republic of Korea, Determined by 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (46) ◽  
Author(s):  
Ilwon Jeong ◽  
Junho Lee ◽  
Jong-Oh Kim ◽  
Seokjin Yoon ◽  
Kyunghoi Kim
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Republic Of Korea ◽  
Rrna Gene ◽  
Sediment Samples

Here, we report a 16S rRNA gene amplicon sequence analysis presenting the microbial community in sediments from the Suyeong River and Suyeong Bay, Republic of Korea. The dominant phyla in all sediment samples were Proteobacteria (39.69 to 53.62%) and Bacteroidetes (29.78 to 33.89%).

scholarly journals Methane related changes in prokaryotic activity along geochemical profiles in sediments of Lake Kinneret (Israel)

2014 ◽  
Vol 11 (6) ◽  
pp. 9813-9852 ◽  
Author(s):  
I. Bar Or ◽  
E. Ben-Dov ◽  
A. Kushmaro ◽  
W. Eckert ◽  
O. Sivan
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Microbial Community Structure ◽  
Iron Reduction ◽  
Lake Kinneret ◽  
Community Diversity ◽  
Rrna Gene ◽  
Anaerobic Oxidation Of Methane ◽  
Deep Sediments

Abstract. Microbial methane oxidation process (methanotrophy) is the primary control on the emission of the greenhouse gas methane (CH4) to the atmosphere. In terrestrial environments, aerobic methanotrophic bacteria are mainly responsible for oxidizing the methane. In marine sediments the coupling of the anaerobic oxidation of methane (AOM) with sulfate reduction, often by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria, was found to consume almost all the upward diffusing methane. Recently, we showed geochemical evidence for AOM driven by iron reduction in Lake Kinneret (LK) (Israel) deep sediments and suggested that this process can be an important global methane sink. The goal of the present study was to link the geochemical gradients found in the porewater (chemical and isotope profiles) with possible changes in microbial community structure. Specifically, we examined the possible shift in the microbial community in the deep iron-driven AOM zone and its similarity to known sulfate driven AOM populations. Screening of archaeal 16S rRNA gene sequences revealed Thaumarchaeota and Euryarchaeota as the dominant phyla in the sediment. Thaumarchaeota, which belongs to the family of copper containing membrane-bound monooxgenases, increased with depth while Euryarchaeota decreased. This may indicate the involvement of Thaumarchaeota, which were discovered to be ammonia oxidizers but whose activity could also be linked to methane, in AOM in the deep sediment. ANMEs sequences were not found in the clone libraries, suggesting that iron-driven AOM is not through sulfate. Bacterial 16S rRNA sequences displayed shifts in community diversity with depth. Proteobacteria and Chloroflexi increased with depth, which could be connected with their different dissimilatory anaerobic processes. The observed changes in microbial community structure suggest possible direct and indirect mechanisms for iron-driven AOM in deep sediments.

scholarly journals Analysis of the Microbial Community Structure in Coastal Sediment of an Ascidian Farm in South Korea through 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Ilwon Jeong ◽  
Jong-Oh Kim ◽  
Seokjin Yoon ◽  
Kyunghoi Kim
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Community Structure ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Content Type ◽  
Styela Clava ◽  
Structure Changes

Aquaculture places contamination pressure on the coastal environment. We investigated the microbial community structure changes in sediment in an ascidian Styela clava farm. Data profiling of the 16S rRNA gene amplicon sequence shows that the microbial diversity of sediment in the Styela clava farm is dominated by Proteobacteria phyla (relative abundance, 95.34 to 97.85%).

scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G H Guilford ◽  
HyunWoo Lee ◽  
Camilla L Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Solid State ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Waste Paper ◽  
Rrna Gene ◽  
Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

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