Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost

Kitamura, Rika; Ishii, Kazuo; Maeda, Isamu; Kozaki, Toshinori; Iwabuchi, Kazunori; Saito, Takahiro

doi:10.1016/j.jbiosc.2015.05.005

Cited by 26 publications

(21 citation statements)

References 51 publications

(32 reference statements)

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“…Although many more 16S rDNA sequences have been deposited in the database, it is difficult to design the “universal primers” that will amplify all the prokaryotic and eukaryotic algal taxa that correspond to the 16S rDNA region. In fact, most studies that have used the universal primers have been conducted to determine the biodiversity of a specific taxon or group ( Asudi et al , 2016 ; Cruaud et al , 2014 ; Kitamura et al , 2016 ; Logares et al , 2014 ; Valenzuela-González et al , 2016 ; Vierheilig et al , 2015 ). In contrast, our current results with the modified primers that target plastid 23S rDNA indicate that these can be used as “universal primers” for analyzing algal community structure because of their large coverage and the fact that they amplify both prokaryotic and eukaryotic algal species.…”

Section: Discussionmentioning

confidence: 99%

“…Although there is still debate, universal primers targeting 16S rDNA are now most widely used ( Decelle et al , 2015 ; Herlemann et al , 2011 ). However, it has been difficult to design a universal primer set that will amplify all phytoplankton taxa from cyanobacteria to eukaryotic algae in the 16S rDNA region, and most studies have analyzed specific taxonomic groups, especially for the bacterial communities ( Asudi et al , 2016 ; Cruaud et al , 2014 ; Kitamura et al , 2016 ; Le Bescot et al , 2015 ; Logares et al , 2014 ; Massana et al , 2015 ; Valenzuela-González et al , 2016 ; Vierheilig et al , 2015 ). Although the sequence information from the 23S rDNA region is only a subset of that for 16S rDNA in the database, this region is considered an important marker for phytoplankton community structure when designing better universal primer sets that will cover most phytoplankton taxa ( Folmer et al , 1994 ; Sherwood & Presting , 2007 ).…”

Section: Introductionmentioning

confidence: 99%

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Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community

Yoon

Kang

et al. 2016

PeerJ

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We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404–411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community

Yoon

Kang

et al. 2016

PeerJ

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“…The study revealed that Domain Bacteria predominated during the whole process, comprising approximately 90 % of the analyzed sequences and the order Actinomycetales, which includes the Family Mycobacteriaceae , was included among the 10 most abundant orders [ 26 ]. Moreover, Kitamura et al showed that food waste composts contained relatively high amounts of Actinobacteria [ 27 ] and Partanen et al confirmed that Phyllum Actinobacteria was predominantly isolated in the thermophilic phase of the composting process [ 28 ].…”

Section: Resultsmentioning

confidence: 99%

Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U

et al. 2016

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BackgroundA large collection of sequenced mycobacteriophages capable of infecting a single host strain of Mycobacterium smegmatis shows considerable genomic diversity with dozens of distinctive types (clusters) and extensive variation within those sharing evident nucleotide sequence similarity. Here we profiled the mycobacterial components of a large composting system at the São Paulo zoo.ResultsWe isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc2155 as a host. None of these eight phages infected any of mycobacterial strains isolated from the same materials. The phage isolates span considerable genomic diversity, including two phages (Barriga, Nhonho) related to Subcluster A1 phages, two Cluster B phages (Pops, Subcluster B1; Godines, Subcluster B2), three Subcluster F1 phages (Florinda, Girafales, and Quico), and Madruga, a relative of phage Patience with which it constitutes the new Cluster U. Interestingly, the two Subcluster A1 phages and the three Subcluster F1 phages have genomic relationships indicating relatively recent evolution within a geographically isolated niche in the composting system.ConclusionsWe predict that composting systems such as those used to obtain these mycobacteriophages will be a rich source for the isolation of additional phages that will expand our view of bacteriophage diversity and evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0734-3) contains supplementary material, which is available to authorized users.

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“…Although many more 16S rDNA sequences have been deposited in the database, it is difficult to design the "universal primers" that will amplify all the prokaryotic and eukaryotic algal taxa that correspond to the 16S rDNA region. In fact, most studies that have used the universal primers have been conducted to determine the biodiversity of a specific taxon or group (Asudi et al 2016;Cruaud et al 2014;Kitamura et al 2016;Logares et PeerJ reviewing PDF | (2016:01:8848:1:1:CHECK 10 May 2016)…”

Section: Reliability Of the Modified Universal Primers For Algal Commmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Peer Review #2 of "Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community (v0.1)"

2016

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We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404-411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology.

show abstract

Evaluation of bacterial communities by bacteriome analysis targeting 16S rRNA genes and quantitative analysis of ammonia monooxygenase gene in different types of compost

Cited by 26 publications

References 51 publications

Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community

Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community

Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U

Peer Review #2 of "Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community (v0.1)"

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