A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

Lv, Xiaofei; Yu, Junbao; Fu, Yuqin; Ma, Ben; Qu, Fanzhu; Ning, Kai; Wu, Huifeng

doi:10.1155/2014/437684

Cited by 73 publications

(54 citation statements)

References 65 publications

(88 reference statements)

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“…Chloroflexi are green non-sulfur bacteria, generally found in intertidal sediment and moderately acidic wetlands (Lv et al, 2014). In this study, the phylum Chloroflexi preferred both low-and high-salinity soils.…”

Section: Saline-responsive Bacterial Speciesmentioning

confidence: 63%

Shifts in the soil bacterial community along a salinity gradient in the Yellow River Delta

et al. 2020

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Soil salinization has rapidly encroached from the coastline to inland areas over the past two decades in the Yellow River Delta (YRD). Soil samples were collected from low-(LSW), medium-(MSW), and high-(HSW) salinity wetlands at a depth of 0-20 cm for 16S rRNA sequencing and bioinformatic analyses. The richness and α-diversity indices were significantly lower in saline soils (ECe > 15 dS/m, HSW) than in soils those were not saline (ECe < 15 dS/m, LSW and MSW) (p < 0.05), generally showing a decreasing trend with increasing salinities. The phyla, Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria and Planctomycetes, represented more than 70% of the bacterial community in the three wetlands, indicating the wide adaption of these phyla to salinity changes. Specifically, Proteobacteria was recognized as the most dominant (35.30%-38.59%) phylum regardless of salinity. Furthermore, bacterial composition was different among the wetlands, as revealed by β-diversity indices and analysis of similarities. Linear discriminant analysis (LDA) effect size revealed the presence of 11, 2, and 10 discriminating bacterial taxa (LDA > 4) among LSW, MSW, and HSW, respectively, implying that they can serve as bioindicators of soil salinization. Redundancy analysis, Spearman correlation analysis, and the Mantel test suggested that salinity parameters (EC, Na + , K + , Mg 2+ , Ca 2+ , Cl − , and SO 4 2−) prominently structured the bacterial community in the current study. These results suggest that the changes of bacterial composition would be induced in these LSW and MSW soils once seawater intrusion occurs.

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Section: Saline-responsive Bacterial Speciesmentioning

confidence: 63%

Shifts in the soil bacterial community along a salinity gradient in the Yellow River Delta

et al. 2020

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“…An interesting feature of the obtained sequencing data was the dominance (38.4% of total sequences) of Flavobacteriia in B1 sample. Oil pollution was shown to favor the growth of Flavobacteriia (Lv et al 2014) and this group contains species that are able to degrade hydrocarbons (Hemalatha et al 2011). Flavobacteriia also known to possess PGP features, such as their ability to hydrolyse organic phosphate (Fitriatin et al 2011) and their ability to solubilize sulfate ester (Fitzgerald 1976).…”

Section: Flavobacteriia In Rhizosphere Soilsmentioning

confidence: 99%

Bacterial communities in the rhizosphere of Phragmites australis from an oil-polluted wetland

Abed

Al-Kharusi

Gkorezis

et al. 2017

Archives of Agronomy and Soil Science

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Although Phragmites australis is commonly planted in constructed wetlands, very little is known about its roots-associated bacterial communities, especially in wetlands used for the remediation of oil produced waters. Here, we describe the bacterial diversity, using molecular (illumina MiSeq sequencing) and cultivation techniques, in the rhizosphere soils of P. australis from an oil-polluted wetland in Oman. The obtained isolates were tested for their plant-growth promoting properties. Most sequences belonged to Proteobacteria, Bacteriodetes and Firmicutes. Sequences of potential hydrocarbondegrading bacteria (e.g. Ochrobactrum, and Pseudomonas) were frequently encountered. All soils contained sequences of known sulfur-oxidizing (e.g. Thiobacillus, Thiofaba, Rhodobacter and Sulfurovum) and sulfate-reducing bacteria, although the latter group made up only 0.1% to 3% of total sequences. The obtained isolates from the rhizosphere soils were phylogenetically affiliated to Serratia, Acinetobacter, Xenorhabdus, Escherichia and Salmonella. All strains were able to solubilize phosphate and about half were capable of producing organic acids and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Around 42% of the strains had the ability to produce indole acetic acid and siderophores. We conclude that the rhizosphere soils of P. australis in oil polluted wetlands harbor diverse bacterial communities that could enhance the wetland performance through hydrocarbon degradation, nutrient cycling and supporting plant growth.

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“…Reasons for this include a continual decrease in cost and an ever greater appreciation of the ability of NGS to more comprehensively characterise microbial communities than traditional culture based methods. NGS has been advantageous in determining the role of the microbiome in disorders like Inflammatory Bowel Disease [ 1 ], diabetes [ 2 ], and obesity [ 3 ], or environmental communities like wetland soils [ 4 ] and oceans [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

et al. 2016

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Rapid advancements in sequencing technologies along with falling costs present widespread opportunities for microbiome studies across a vast and diverse array of environments. These impressive technological developments have been accompanied by a considerable growth in the number of methodological variables, including sampling, storage, DNA extraction, primer pairs, sequencing technology, chemistry version, read length, insert size, and analysis pipelines, amongst others. This increase in variability threatens to compromise both the reproducibility and the comparability of studies conducted. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading next-generation sequencing technologies. These were applied to six human stool samples using Illumina HiSeq, MiSeq and Ion PGM shotgun sequencing, as well as amplicon sequencing across two variable 16S rRNA gene regions. Notably, we found that the factor responsible for the greatest variance in microbiota composition was the chosen methodology rather than the natural inter-individual variance, which is commonly one of the most significant drivers in microbiome studies. Amplicon sequencing suffered from this to a large extent, and this issue was particularly apparent when the 16S rRNA V1-V2 region amplicons were sequenced with MiSeq. Somewhat surprisingly, the choice of taxonomic binning software for shotgun sequences proved to be of crucial importance with even greater discriminatory power than sequencing technology and choice of amplicon. Optimal N50 assembly values for the HiSeq was obtained for 10 million reads per sample, whereas the applied MiSeq and PGM sequencing depths proved less sufficient for shotgun sequencing of stool samples. The latter technologies, on the other hand, provide a better basis for functional gene categorisation, possibly due to their longer read lengths. Hence, in addition to highlighting methodological biases, this study demonstrates the risks associated with comparing data generated using different strategies. We also recommend that laboratories with particular interests in certain microbes should optimise their protocols to accurately detect these taxa using different techniques.

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A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

Cited by 73 publications

References 65 publications

Shifts in the soil bacterial community along a salinity gradient in the Yellow River Delta

Shifts in the soil bacterial community along a salinity gradient in the Yellow River Delta

Bacterial communities in the rhizosphere of Phragmites australis from an oil-polluted wetland

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

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