scholarly journals Diversity and structure of the rhizosphere microbial communities of wild and cultivated ginseng

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoxue Fang ◽  
Huaying Wang ◽  
Ling Zhao ◽  
Manqi Wang ◽  
Mingzhou Sun
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Human Intervention ◽  
The Sustainable Development ◽  
Rhizosphere Soils ◽  
Soil Microbial ◽  
Operational Taxonomic Units ◽  
Wild Ginseng

Abstract Background The resources of wild ginseng have been reducing sharply, and it is mainly dependent on artificial cultivation in China, Korea and Japan. Based on cultivation modes, cultivated ginseng include understory wild ginseng (the seeds or seedlings of cultivated ginseng were planted under the theropencedrymion without human intervention) and farmland cultivated ginseng (grown in farmland with human intervention). Cultivated ginseng, can only be planted on the same plot of land consecutively for several years owing to soilborne diseases, which is mainly because of the variation in the soil microbial community. In contrast, wild ginseng can grow for hundreds of years. However, the knowledge of rhizosphere microbe communities of the wild ginseng is limited. Result In the present study, the microbial communities in rhizosphere soils of the three types of ginseng were analyzed by high-throughput sequencing of 16 S rRNA for bacteria and internal transcribed spacer (ITS) region for fungi. In total, 4,381 bacterial operational taxonomic units (OTUs) and 2,679 fungal OTUs were identified in rhizosphere soils of the three types of ginseng. Among them, the shared bacterial OTUs was more than fungal OTUs by the three types of ginseng, revealing fungal communities were to be more affected than bacterial communities. In addition, the composition of rhizosphere microbial communities and bacterial diversity were similar between understory wild ginseng and wild ginseng. However, higher bacterial diversity and lower fungal diversity were found in rhizosphere soils of wild ginseng compared with farmland cultivated ginseng. Furthermore, the relative abundance of Chloroflexi, Fusarium and Alternaria were higher in farmland cultivated ginseng compared to wild ginseng and understory wild ginseng. Conclusions Our results showed that composition and diversity of rhizosphere microbial communities were significantly different in three types of ginseng. This study extended the knowledge pedigree of the microbial diversity populating rhizospheres, and provided insights into resolving the limiting bottleneck on the sustainable development of P. ginseng crops, and even the other crops of Panax.

scholarly journals Bacterial diversity and community in Qula from the Qinghai–Tibetan Plateau in China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6044 ◽  
Author(s):  
Yan Zhu ◽  
Yingying Cao ◽  
Min Yang ◽  
Pengchen Wen ◽  
Lei Cao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Different Origins ◽  
Different Levels ◽  
Different Origin

Qula is a cheese-like product usually prepared with unpasteurized yak milk under open conditions, with both endogenous and exogenous microorganisms involved in the fermentation process. In the present study, 15 Qula samples were collected from five different regions in China to investigate the diversity of microbial communities using high-throughput sequencing targeting the V3–V4 region of 16S rRNA gene. The bacterial diversity significantly differed among samples of different origins, indicating a possible effect of geography. The result also showed that microbial communities significantly differed in samples of different origin and these differences were greater at the genus than the phylum level. A total of six phyla were identified in the samples, and Firmicutes and Proteobacteria had a relative abundance >20%. A total of 73 bacterial genera were identified in the samples. Two dominant genera (Lactobacillus and Acetobacter) were common to all samples, and a total of 47 operational taxonomic units at different levels significantly differed between samples of different origin. The predicted functional genes of the bacteria present in samples also indicated differences in bacterial communities between the samples of different origin. The network analysis showed that microbial interactions between bacterial communities in Qula were very complex. This study lays a foundation for further investigations into its food ecology.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Novel Approach to Study the Diversity of Soil Microbial Communities in Qatar

2020 ◽  
Author(s):  
Jane Oja ◽  
Sakeenah Adenan ◽  
Abdel-Fattah Talaat ◽  
Juha Alatalo
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
Mycorrhizal Fungi ◽  
High Throughput Sequencing ◽  
Soil Microbial Communities ◽  
Arbuscular Mycorrhizal ◽  
Soil Microbial ◽  
Fungal Abundance ◽  
Novel Approach ◽  
Soil Climate

A broad diversity of microorganisms can be found in soil, where they are essential for nutrient cycling and energy transfer. Recent high-throughput sequencing methods have greatly advanced our knowledge about how soil, climate and vegetation variables structure the composition of microbial communities in many world regions. However, we are lacking information from several regions in the world, e.g. Middle-East. We have collected soil from 19 different habitat types for studying the diversity and composition of soil microbial communities (both fungi and bacteria) in Qatar and determining which edaphic parameters exert the strongest influences on these communities. Preliminary results indicate that in overall bacteria are more abundant in soil than fungi and few sites have notably higher abundance of these microbes. In addition, we have detected some soil patameters, which tend to have reduced the overall fungal abundance and enhanced the presence of arbuscular mycorrhizal fungi and N-fixing bacteria. More detailed information on the diversity and composition of soil microbial communities is expected from the high-throughput sequenced data.

scholarly journals Phosphorus Reduces Negative Effects of Nitrogen Addition on Soil Microbial Communities and Functions

2020 ◽  
Vol 8 (11) ◽  
pp. 1828 ◽  
Author(s):  
Zongwei Xia ◽  
Jingyi Yang ◽  
Changpeng Sang ◽  
Xu Wang ◽  
Lifei Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Soil Microbial Communities ◽  
N Deposition ◽  
N Fixation ◽  
N Addition ◽  
Soil Bacterial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
P Addition

Increased soil nitrogen (N) from atmospheric N deposition could change microbial communities and functions. However, the underlying mechanisms and whether soil phosphorus (P) status are responsible for these changes still have not been well explained. Here, we investigated the effects of N and P additions on soil bacterial and fungal communities and predicted their functional compositions in a temperate forest. We found that N addition significantly decreased soil bacterial diversity in the organic (O) horizon, but tended to increase bacterial diversity in the mineral (A) horizon soil. P addition alone did not significantly change soil bacterial diversity but mitigated the negative effect of N addition on bacterial diversity in the O horizon. Neither N addition nor P addition significantly influenced soil fungal diversity. Changes in soil microbial community composition under N and P additions were mainly due to the shifts in soil pH and NO3− contents. N addition can affect bacterial functional potentials, such as ureolysis, N fixation, respiration, decomposition of organic matter processes, and fungal guilds, such as pathogen, saprotroph, and mycorrhizal fungi, by which more C probably was lost in O horizon soil under increased N deposition. However, P addition can alleviate or switch the effects of increased N deposition on the microbial functional potentials in O horizon soil and may even be a benefit for more C sequestration in A horizon soil. Our results highlight the different responses of microorganisms to N and P additions between O and A horizons and provides an important insight for predicting the changes in forest C storage status under increasing N deposition in the future.

scholarly journals Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

2019 ◽  
Vol 7 (12) ◽  
pp. 662 ◽  
Author(s):  
Luca Nerva ◽  
Chiara Pagliarani ◽  
Massimo Pugliese ◽  
Matteo Monchiero ◽  
Solène Gonthier ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Microbial Communities ◽  
Defense Mechanisms ◽  
High Throughput Sequencing ◽  
Specific Activity ◽  
Its Region ◽  
Community Analysis ◽  
Its Sequencing ◽  
Viral Community ◽  
Antimicrobial Treatments

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera “Nebbiolo” and “Moscato” cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using BiologTM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, “Moscato” plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the “Nebbiolo” plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.

scholarly journals Best practices in metabarcoding of fungi: from experimental design to results

2021 ◽  
Author(s):  
Leho Tedersoo ◽  
Mohammad Bahram ◽  
Lucie Zinger ◽  
Henrik Nilsson ◽  
Peter Kennedy ◽  
...  
Keyword(s):  
Experimental Design ◽  
Best Practices ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Its Region ◽  
Fungal Communities ◽  
Sequence Variants ◽  
Transcriptomic Data ◽  
Operational Taxonomic Units ◽  
Computational Analyses

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety of ecosystems. Here we provide an overview about current best practices in metabarcoding analysis of fungal communities, from experimental design through molecular and computational analyses. By re-analysing published datasets, we find that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) in recovering fungal diversity, which is particularly evident for long markers. Additionally, analysis of the full-length ITS region allows more accurate taxonomic placement of fungi and other eukaryotes compared with the ITS2 subregion. We conclude that metabarcoding analyses of fungi are especially promising for co-analyses with the functional metagenomic or transcriptomic data, integrating fungi in the entire microbiome, recovery of novel fungal lineages and ancient organisms as well as barcoding of old specimens including type material.

Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Jonathan R Gaiero ◽  
Micaela Tosi ◽  
Elizabeth Bent ◽  
Gustavo Boitt ◽  
Kamini Khosla ◽  
...  
Keyword(s):  
New Zealand ◽  
Acid Phosphatase ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Organic Phosphorus ◽  
Mineral Soil ◽  
Soil Microbial Communities ◽  
Organic P ◽  
Fungal Community Composition ◽  
Soil Microbial

ABSTRACT The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).

scholarly journals Starch Degradation by Microbial Communities in Soils from Oldupai Gorge (Tanzania)

2019 ◽  
Author(s):  
Tolutope Akeju ◽  
Peter Dunfield ◽  
Julio Mercader
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Fungal Species ◽  
Soil Samples ◽  
Model Organisms ◽  
Starch Degradation ◽  
Soil Conditions ◽  
Soil Microbial ◽  
Specific Species ◽  
Microbial Dna

The taphonomy behind ancient starch preservation is very poorly understood in archaeological contexts. This understanding could be aided by biogeochemical experimentation in controlled laboratory environments to isolate degradation pathways in soils, and how this degradation is affected by biotic and abiotic variables. The aims of this project were to:1) Identify and characterize bacterial and fungal species responsible for the degradation of starch in Tanzanian soils2) Determine how factors such as the starch source, soil water, and soil aeration affect the activity of these microbes3) Observe the alterations of starch granules inflicted by degradation by different microbial communities. Field and laboratory studies were designed to achieve these objectives:In the field, bulk soil samples (not adjacent to plant roots/tubers) and tubersphere soil samples (attached to starchy plant tubers) were collected for analysis of microbial communities via high-throughput sequencing of soil microbial DNA. Laboratory analysis of these samples is ongoing, but initial results suggest that particular starch-degrading microbes associate with particular starchy tubers. Secondly, controlled laboratory microcosms of soils amended with various starch types were incubated under different conditions. The microbial communities degrading the starch were followed over time via DNA sequencing and the starch taphonomy observed microscopically. These studies have shown that hardy, spore-forming bacteria of the phylum Firmicutes dominate starch-degrading microbial communities in the Tanzanian soils, but that the specific species change depending on experimental variables. The soil conditions and the source of the starch dramatically affected both the degradation rate and the specific microbial species involved. These findings suggest that starch degradation and taphonomy may be site-specific, that certain starches may be more prone to preservation than others may, and that starch-degradation studies using model organisms may not always be representative of the field conditions.

scholarly journals Environmental characteristics and changes of bacterial communities in the meltwater runoff of glacier in Ny-Alesund, Arctic

2021 ◽  
Author(s):  
Lidong Lin ◽  
Nengfei Wang ◽  
Wenbing Han ◽  
Botao Zhang ◽  
Jiaye Zang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Meltwater Runoff ◽  
Glacial Runoff ◽  
Weighted Correlation

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.

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