Surveying the Sweetpotato Rhizosphere, Endophyte, and Surrounding Soil Microbiomes at Two North Carolina Farms Reveals Underpinnings of Sweetpotato Microbiome Community Assembly

Farmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, ‘Beauregard’ and ‘Covington’. By comparing small subunit rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil, we found the skin microbiome possessed the least composition heterogeneity among samples, lowest alpha-diversity, and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

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Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

10.1101/758359 ◽

2019 ◽

Author(s):

C Pepe-Ranney ◽

C Keyser ◽

J Trimble ◽

B Bissinger

Keyword(s):

North Carolina ◽

Community Assembly ◽

Alpha Diversity ◽

Rrna Gene ◽

Sequence Variant ◽

Skin Microbiome ◽

Microbiome Composition ◽

Pests And Diseases ◽

Sub Saharan ◽

Surrounding Soil

AbstractFarmers grow sweetpotatoes worldwide and some sub-Saharan African and Asian diets include sweetpotato as a staple, yet the sweetpotato microbiome is conspicuously less studied relative to crops such as maize, soybean, and wheat. Studying sweetpotato microbiome ecology may reveal paths to engineer the microbiome to improve sweetpotato yield, and/or combat sweetpotato pests and diseases. We sampled sweetpotatoes and surrounding soil from two North Carolina farms. We took samples from sweetpotato fields under two different land management regimes, conventional and organic, and collected two sweetpotato cultivars, ‘Beauregard’ and ‘Covington’. By comparing SSU rRNA gene amplicon sequence profiles from sweetpotato storage root skin, rhizosphere, and surrounding soil we found the skin microbiome possessed the least composition heterogeneity among samples and lowest alpha-diversity and was significantly nested by the rhizosphere in amplicon sequence variant (ASV) membership. Many ASVs were specific to a single field and/or only found in either the skin, rhizosphere, or surrounding soil. Notably, sweetpotato skin enriched for Planctomycetaceae in relative abundance at both farms. This study elucidates underpinnings of sweetpotato microbiome community assembly, quantifies microbiome composition variance within a single farm, and reveals microorganisms associated with sweetpotato skin that belong to common but uncultured soil phylotypes.

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Characterisation of, and entomopathogenic studies on, Pristionchus aerivorus (Cobb in Merrill & Ford, 1916) Chitwood, 1937 (Rhabditida: Diplogastridae) from North Carolina, USA

Nematology ◽

10.1163/15685411-00002891 ◽

2015 ◽

Vol 17 (5) ◽

pp. 567-580

Author(s):

Weimin Ye ◽

Qing Yu ◽

Natsumi Kanzaki ◽

Paul R. Adams ◽

Yasmin J. Cardoza

Keyword(s):

North Carolina ◽

Helicoverpa Zea ◽

Large Subunit ◽

Small Subunit ◽

Morphological Observation ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Morphological Studies ◽

The Status ◽

Molecular Phylogenetic

During a survey of entomopathogenic nematodes in North Carolina, USA, aPristionchusspecies was recovered using theGalleriabait method. Morphological studies with light microscopy and scanning electron microscopy, mating tests with reference strains, as well as molecular analyses of the near-full-length small subunit rRNA gene (18S) and D2-D3 expansion segments of the large subunit rRNA gene (28S) identified this isolate asPristionchus aerivorus. ExposedGallerialarvae were killed within 48 h and high numbers of nematodes were recovered from the cadavers about 5 days later. Preliminary tests revealed that this nematode is capable of infecting at least two other insect species (Helicoverpa zeaandTenebrio molitor) under laboratory conditions. The status of the genusChroniodiplogasteris discussed and confirmed as a junior synonym ofPristionchusbased on morphological observation and molecular phylogenetic analysis.

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Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions

Microorganisms ◽

10.3390/microorganisms9010021 ◽

2020 ◽

Vol 9 (1) ◽

pp. 21

Author(s):

Abdul Ghafar ◽

Anson V. Koehler ◽

Ross S. Hall ◽

Charles G. Gauci ◽

Robin B. Gasser ◽

...

Keyword(s):

Next Generation Sequencing ◽

Water Buffalo ◽

Hypervariable Region ◽

Small Subunit ◽

Rrna Gene ◽

Next Generation ◽

Small Subunit Rrna ◽

Tropical Theileriosis ◽

Ecological Zones ◽

Generation Sequencing

Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.

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Differences in Microbial Activity and Microbial Populations of Peat Associated with Suppression of Damping-Off Disease Caused by Pythium sylvaticum

Applied and Environmental Microbiology ◽

10.1128/aem.00313-06 ◽

2006 ◽

Vol 72 (10) ◽

pp. 6452-6460 ◽

Cited By ~ 43

Author(s):

Paul J. Hunter ◽

Geoff M. Petch ◽

Leo A. Calvo-Bado ◽

Tim R. Pettitt ◽

Nick R. Parsons ◽

...

Keyword(s):

Microbial Activity ◽

Denaturing Gradient Gel Electrophoresis ◽

Small Subunit ◽

Disease Suppression ◽

Rrna Gene ◽

Damping Off ◽

Small Subunit Rrna ◽

Pythium Sylvaticum ◽

Gradient Gel Electrophoresis ◽

Microbial Groups

ABSTRACT The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for Pythium sylvaticum-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of P. sylvaticum at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the Rhizobium-Agrobacterium group (specifically sequences similar to those for the genera Ochrobactrum and Zoogloea) and the Acidobacteria, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to Basidiomycete yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of Cryptococcus increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of Pythium-induced diseases in peats.

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Detection of Kobe-typeBabesia microtiassociated with Japanese human babesiosis in field rodents in central Taiwan and southeastern mainland China

Parasitology ◽

10.1017/s0031182008004356 ◽

2008 ◽

Vol 135 (6) ◽

pp. 691-699 ◽

Cited By ~ 12

Author(s):

A. SAITO-ITO ◽

N. TAKADA ◽

F. ISHIGURO ◽

H. FUJITA ◽

Y. YANO ◽

...

Keyword(s):

Mainland China ◽

Small Subunit ◽

Human Infection ◽

Babesia Microti ◽

Rrna Gene ◽

Microscopical Examination ◽

Small Subunit Rrna ◽

Central Taiwan ◽

Field Rodents ◽

Human Babesiosis

SUMMARYField rodent surveys forBabesiainfection were performed from 2002 to 2005 in the vicinities of human babesiosis occurrences in Taiwan and mainland China.Babesia microtiwas identified by microscopical examination and/or PCR in 1Rattus coxingaand 1Crocidura horsfieldiiin central Taiwan and in 13Niviventer confucianusand 1Apodemus agrariusin Zhejiang and Fujian Provinces of southeastern China. Of 15B. microtisamples detected by PCR, all except 1 were shown to be the Kobe-type, the aetiological small subunit rRNA gene-type of the first Japanese patient; the exception was also a Kobe-related type. The Kobe-type had been found in rodents only in a few places including the human infection occurrence place in Japan. The internal transcribed spacer 1 to 2 sequences of the Taiwanese and Chinese Kobe-types were very similar to each other but considerably different (approx. 94% pairwise identities) from that of the Japanese Kobe-type. A Taiwanese Kobe-type strain was serologically differentiated from the Kobe strain originating from the Japanese first patient. The distribution of the Kobe-type in the vicinities of human babesiosis occurrences in Taiwan and China as well as in Japan is suggestive of involvement of the Kobe-type in Asian human babesiosis.

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Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences

Molecular and Biochemical Parasitology ◽

10.1016/s0166-6851(02)00246-3 ◽

2003 ◽

Vol 126 (1) ◽

pp. 119-123 ◽

Cited By ~ 62

Author(s):

Christophe Noël ◽

Corinne Peyronnet ◽

Delphine Gerbod ◽

Virginia P Edgcomb ◽

Pilar Delgado-Viscogliosi ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Small Subunit ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Gene Sequences ◽

Small Subunit Rrna Gene

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Comparison of bacterial communities in the Solimões and Negro River tributaries of the Amazon River based on small subunit rRNA gene sequences

Genetics and Molecular Research ◽

10.4238/2011.december.8.8 ◽

2011 ◽

Vol 10 (4) ◽

pp. 3783-3793 ◽

Cited By ~ 3

Author(s):

J.C.C. Peixoto ◽

L. Leomil ◽

J.V. Souza ◽

F.B.S. Peixoto ◽

S. Astolfi-Filho

Keyword(s):

Bacterial Communities ◽

Small Subunit ◽

Amazon River ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Gene Sequences ◽

Negro River ◽

Small Subunit Rrna Gene

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Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

Applied and Environmental Microbiology ◽

10.1128/aem.64.12.5064-5066.1998 ◽

1998 ◽

Vol 64 (12) ◽

pp. 5064-5066 ◽

Cited By ~ 21

Author(s):

Clifford F. Brunk ◽

Nicole Eis

Keyword(s):

Internal Standard ◽

Pcr Amplification ◽

Quantitative Measure ◽

Pcr Primers ◽

Small Subunit ◽

Ssu Rdna ◽

Rdna Sequence ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

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