Response to Edaphoclimatic Conditions and Crop Management of the Bacterial Microbiome of Musa acuminata Rhizosphere Profiled by 16S rRNA Gene Amplicon Sequencing

ABSTRACT Bacterial rhizospheric microbiomes of Musa acuminata cultivated in farms close to the west and east Mexican coasts and with different climate, soils, and crop management practices were characterized by 16S rRNA gene amplicon sequencing. Results showed that rhizospheric microbiome composition changed along with seasonal weather but were mostly indifferent to soil type.

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Comparison of paperpoint and curette sampling of subgingival microbiome composition as analyzed by 16S rRNA gene amplicon sequencing

Journal of Oral Microbiology ◽

10.1080/20002297.2017.1325260 ◽

2017 ◽

Vol 9 (sup1) ◽

pp. 1325260

Author(s):

K. Beyer ◽

B.W. Brandt ◽

M.J. Buijs ◽

J.G. Brun ◽

W. Crielaard ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Microbiome Composition

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Growth and Population Dynamics of the Anaerobic Fe(II)-Oxidizing and Nitrate-Reducing Enrichment Culture KS

Applied and Environmental Microbiology ◽

10.1128/aem.02173-17 ◽

2018 ◽

Vol 84 (9) ◽

Cited By ~ 15

Author(s):

Claudia Tominski ◽

Helene Heyer ◽

Tina Lösekann-Behrens ◽

Sebastian Behrens ◽

Andreas Kappler

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Community Composition ◽

Enrichment Culture ◽

Operational Taxonomic Unit ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Organic Substrates ◽

Content Type ◽

Heterotrophic Denitrification

ABSTRACTMost isolated nitrate-reducing Fe(II)-oxidizing microorganisms are mixotrophic, meaning that Fe(II) is chemically oxidized by nitrite that forms during heterotrophic denitrification, and it is debated to which extent Fe(II) is enzymatically oxidized. One exception is the chemolithoautotrophic enrichment culture KS, a consortium consisting of a dominant Fe(II) oxidizer,Gallionellaceaesp., and less abundant heterotrophic strains (e.g.,Bradyrhizobiumsp.,Nocardioidessp.). Currently, this is the only nitrate-reducing Fe(II)-oxidizing culture for which autotrophic growth has been demonstrated convincingly for many transfers over more than 2 decades. We used 16S rRNA gene amplicon sequencing and physiological growth experiments to analyze the community composition and dynamics of culture KS with various electron donors and acceptors. Under autotrophic conditions, an operational taxonomic unit (OTU) related to known microaerophilic Fe(II) oxidizers within the familyGallionellaceaedominated culture KS. With acetate as an electron donor, most 16S rRNA gene sequences were affiliated withBradyrhizobiumsp.Gallionellaceaesp. not only was able to oxidize Fe(II) under autotrophic and mixotrophic conditions but also survived over several transfers of the culture on only acetate, although it then lost the ability to oxidize Fe(II).Bradyrhizobiumspp. became and remained dominant when culture KS was cultivated for only one transfer under heterotrophic conditions, even when conditions were reverted back to autotrophic in the next transfer. This study showed a dynamic microbial community in culture KS that responded to changing substrate conditions, opening up questions regarding carbon cross-feeding, metabolic flexibility of the individual strains in KS, and the mechanism of Fe(II) oxidation by a microaerophile in the absence of O2.IMPORTANCENitrate-reducing Fe(II)-oxidizing microorganisms are present in aquifers, soils, and marine and freshwater sediments. Most nitrate-reducing Fe(II) oxidizers known are mixotrophic, meaning that they need organic carbon to continuously oxidize Fe(II) and grow. In these microbes, Fe(II) was suggested to be chemically oxidized by nitrite that forms during heterotrophic denitrification, and it remains unclear whether or to what extent Fe(II) is enzymatically oxidized. In contrast, the enrichment culture KS was shown to oxidize Fe(II) autotrophically coupled to nitrate reduction. This culture contains the designated Fe(II) oxidizerGallionellaceaesp. and several heterotrophic strains (e.g.,Bradyrhizobiumsp.). We showed that culture KS is able to metabolize Fe(II) and a variety of organic substrates and is able to adapt to dynamic environmental conditions. When the community composition changed andBradyrhizobiumbecame the dominant community member, Fe(II) was still oxidized byGallionellaceaesp., even when culture KS was cultivated with acetate/nitrate [Fe(II) free] before being switched back to Fe(II)/nitrate.

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16S rRNA Gene Amplicon Sequencing Data of Tailing and Nontailing Rhizosphere Soils of Mimosa pudica from a Heavy Metal-Contaminated Ex-Tin Mining Area

Microbiology Resource Announcements ◽

10.1128/mra.00761-20 ◽

2020 ◽

Vol 9 (42) ◽

Author(s):

Saidu Abdullahi ◽

Hazzeman Haris ◽

Kamarul Z. Zarkasi ◽

Hamzah G. Amir

Keyword(s):

Heavy Metal ◽

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Mimosa Pudica ◽

Sequencing Data ◽

Content Type ◽

Rhizosphere Soils

ABSTRACT The 16S rRNA gene amplicon sequence data from tailing and nontailing rhizosphere soils of Mimosa pudica from a heavy metal-contaminated area are reported here. Diverse bacterial taxa were represented in the results, and the most dominant phyla were Proteobacteria (41.2%), Acidobacteria (17.1%), and Actinobacteria (14.4%).

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16S rRNA Gene Amplicon Sequencing of Gut Microbiota from Naked Carp (Gymnocypris przewalskii) in Qinghai Lake, China

Microbiology Resource Announcements ◽

10.1128/mra.00374-21 ◽

2021 ◽

Vol 10 (23) ◽

Author(s):

Fayan Wang ◽

Yu Liu ◽

Guangxin Li ◽

Xi Yang ◽

Qiang Gao

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Qinghai Lake ◽

Second Grade ◽

Rrna Gene ◽

Content Type ◽

Gymnocypris Przewalskii ◽

State Protection

Naked carp ( Gymnocypris przewalskii ) is a second-grade animal under state protection of China. We report 16S rRNA gene amplicon analysis of the gut microbiota of Gymnocypris przewalskii . The three most abundant phyla are Tenericutes , Proteobacteria , and Fusobacteria , and the six most abundant genera are Aeromonas , Clostridium , Cetobacterium , Shewanella , Prochlorococcus , and Vibrio .

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Bacterial Diversity Profiling of the New Zealand Parasitic Blowfly Lucilia sericata Based on 16S rRNA Gene Amplicon Sequencing

Microbiology Resource Announcements ◽

10.1128/mra.00257-21 ◽

2021 ◽

Vol 10 (19) ◽

Author(s):

Nikola Palevich ◽

Paul H. Maclean ◽

Luis Carvalho ◽

Ruy Jauregui

Keyword(s):

New Zealand ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Sequence Data ◽

Amplicon Sequencing ◽

Lucilia Sericata ◽

Rrna Gene ◽

Data Set ◽

Content Type

ABSTRACT Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of larval and adult Lucilia sericata, collected from Ashhurst, New Zealand (May 2020). The two dominant genera among adult male and female L. sericata were Serratia and Morganella (phylum Proteobacteria), while the larvae were also dominated by the genera Lactobacillus, Carnobacterium, and Lactococcus (phylum Firmicutes).

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Deciphering the Root Endosphere Microbiome of the Desert Plant Alhagi sparsifolia for Drought Resistance-Promoting Bacteria

Applied and Environmental Microbiology ◽

10.1128/aem.02863-19 ◽

2020 ◽

Vol 86 (11) ◽

Author(s):

Lei Zhang ◽

Weipeng Zhang ◽

Qiqi Li ◽

Rui Cui ◽

Zhuo Wang ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Drought Resistance ◽

Amplicon Sequencing ◽

Disease Suppression ◽

Rrna Gene ◽

Desert Plant ◽

Desert Plants ◽

Alhagi Sparsifolia ◽

Content Type

ABSTRACT Drought is among the most destructive abiotic stresses limiting crop growth and yield worldwide. Although most research has focused on the contribution of plant-associated microbial communities to plant growth and disease suppression, far less is known about the microbes involved in drought resistance among desert plants. In the present study, we applied 16S rRNA gene amplicon sequencing to determine the structure of rhizosphere and root endosphere microbiomes of Alhagi sparsifolia. Compared to those of the rhizosphere, endosphere microbiomes had lower diversity but contained several taxa with higher relative abundance; many of these taxa were also present in the roots of other desert plants. We isolated a Pseudomonas strain (LTGT-11-2Z) that was prevalent in root endosphere microbiomes of A. sparsifolia and promoted drought resistance during incubation with wheat. Complete genome sequencing of LTGT-11-2Z revealed 1-aminocyclopropane-1-carboxylate deaminases, siderophore, spermidine, and colanic acid biosynthetic genes, as well as type VI secretion system (T6SS) genes, which are likely involved in biofilm formation and plant-microbe interactions. Together, these results indicate that drought-enduring plants harbor bacterial endophytes favorable to plant drought resistance, and they suggest that novel endophytic bacterial taxa and gene resources may be discovered among these desert plants. IMPORTANCE Understanding microbe-mediated plant resistance to drought is important for sustainable agriculture. We performed 16S rRNA gene amplicon sequencing and culture-dependent functional analyses of Alhagi sparsifolia rhizosphere and root endosphere microbiomes and identified key endophytic bacterial taxa and their genes facilitating drought resistance in wheat. This study improves our understanding of plant drought resistance and provides new avenues for drought resistance improvement in crop plants under field conditions.

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

Microbiology Resource Announcements ◽

10.1128/mra.00584-21 ◽

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%).

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Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽

10.1186/s40168-021-01012-1 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Janis R. Bedarf ◽

Naiara Beraza ◽

Hassan Khazneh ◽

Ezgi Özkurt ◽

David Baker ◽

...

Keyword(s):

Parkinson’S Disease ◽

16S Rrna ◽

16S Rrna Gene ◽

False Positive ◽

Gene Sequencing ◽

Bacterial Biomass ◽

16S Rrna Gene Sequencing ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

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Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.052993-0 ◽

2014 ◽

Vol 64 (Pt_3) ◽

pp. 781-786 ◽

Cited By ~ 33

Author(s):

Maximo Sánchez ◽

Martha-Helena Ramírez-Bahena ◽

Alvaro Peix ◽

María J. Lorite ◽

Juan Sanjuán ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Carbon Sources ◽

Lotus Corniculatus ◽

Culture Conditions ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

ISME Communications ◽

10.1038/s43705-021-00033-z ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Sandra Reitmeier ◽

Thomas C. A. Hitch ◽

Nicole Treichel ◽

Nikolaos Fikas ◽

Bela Hausmann ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Diversity Analysis ◽

Careful Attention ◽

Operational Taxonomic Units ◽

Basic Concepts ◽

Gnotobiotic Mice ◽

Mock Communities

Abstract16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.

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