Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing

Hirakata, Yuga; Hatamoto, Masashi; Oshiki, Mamoru; Watari, Takahiro; Kuroda, Kyohei; Araki, Nobuo; Yamaguchi, Takashi

doi:10.1038/s41598-019-49290-y

Cited by 34 publications

(25 citation statements)

References 80 publications

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“…Several previous studies reported that the Shannon diversity and inverse Simpson indexes for V4 region were lower than those for V9 region 20,21,33 . Conversely, Hirakata et al 30 reported that the Shannon diversity and inverse Simpson indexes for V4 region were higher than those for the V9 region, consistent with our results. Probably, this difference may be due to the fraction of different OTUs, intra-individual polymorphism, and/or different sampling locations 18,21,30,34 .…”

Section: Scientific Reports |supporting

confidence: 92%

“…207 OTUs of the total 1,122 OTUs) from the V4 region sequencing data are similar to those from the V9 region sequencing data (i.e. 219 OTUs of total 1,632 OTUs), implying that non-eukaryotic sequences are often detected in the V4 and V9 region datasets due to capability of the primer sets to amplify the small subunit rDNA of all three domains 30 (i.e. archaea, bacteria, and eukaryotes).…”

Section: Scientific Reports |mentioning

confidence: 54%

“…Furthermore, Heterolobosea was revealed to be the second most abundant group www.nature.com/scientificreports www.nature.com/scientificreports/ (38.6% of total read counts) in the supergroup 'Excavata' using the V9 region, but this group was not detected using the V4 region. Heterolobosea, including amoeba, amoeboflagellate, and flagellate forms, represents one of rare taxa in environmental surveys 17,30,35 , but were commonly isolated from freshwater, marine, soil, and extreme environments [36][37][38][39][40][41][42][43][44][45][46] . Pawlowski et al 17 reported that Heterolobosea comprises <1% of total reads using NGS technology with only the V9 region.…”

Section: Scientific Reports |mentioning

confidence: 99%

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Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

Choi

Park

2020

Sci Rep

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Illumina sequencing is a representative tool for understanding the massive diversity of microbial eukaryotes in natural ecosystems. Here, we investigated the eukaryotic community in a pond (salinity of 2-4) on Dokdo (island) in the East Sea, Korea, using Illumina sequencing with primer sets for the V4 and V9 regions of 18S rDNA from 2016 to 2018 for the first time. Totally, 1,413 operational taxonomic units (OTUs) and 915 OTUs were detected using the V9 and V4 primer sets, respectively. Taxonomic analyses of these OTUs revealed that although the V4 primer set failed to describe the extant diversity for some major sub-division groups, the V9 primer set represented their diversity. Moreover, the rare taxa with <1% of total reads were exclusively detected using V9 primer set. Hence, the diversity of the eukaryotic community can vary depending on the choice of primers. The Illumina sequencing data of the V9 region of 18S rDNA may be advantageous for estimating the richness of the eukaryotic community including a rare biosphere, whereas the simultaneous application of two biomarkers may be suitable for understanding the molecular phylogenetic relationships. We strongly recommend both biomarkers be used to assess the diversity and phylogenetic relationship within the eukaryotic community in natural samples.The advent of next-generation sequencing (NGS) led to a substantial change in the previous knowledge about the microbial diversity in natural ecosystems 1,2 . NGS targeting the 18S rDNA is usually used to evaluate the diversity within all domains of life and provides large quantities of sequencing data for individual investigators. The 454 platform is hardly used anymore and a lot of other platforms are currently used far more widely. The Illumina platforms are representative tools for the investigation of the microbial community although this method can read a relatively short fragment of sequence (200 bp-500 bp) due to the technical limitations 3,4 . Illumina platform is a cost-effective tool per base (priced ~100 times lower than the 454 platform) and can now read longer sequences (200 bp-300 bp) than the initial platform 5,6 . Furthermore, the error rate of the Illumina platform is lower than that of the 454 platform 7 . However, considering the revolutionary application of the Illumina platform, our knowledge about the diversity and phylogenetic relationship of eukaryotes remains poor in field surveys such as those for brackish water 8 .Several studies on the diversity of eukaryotes noted that the V1-V2, V3, V4, and V9 regions of 18S rDNA have been used for better understanding the massive diversity of microbial community 9-11 . The V4 (expected amplicon size, 270 bp-387 bp) and V9 (expected amplicon size, 96 bp-134 bp) regions are considered to be the popular for metabarcoding 12,13 . Based on an in silico analysis, the V9 region of 18S rDNA offers the advantage to reveal the extant diversity of eukaryotes, whereas the V4 region of 18S rDNA is commonly used for studying the phylogenetic relationship of eukaryot...

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Section: Scientific Reports |supporting

confidence: 92%

Section: Scientific Reports |mentioning

confidence: 54%

Section: Scientific Reports |mentioning

confidence: 99%

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Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

Choi

Park

2020

Sci Rep

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“…DNA extraction was performed using a MonoFas Bacterial Genomic Kit VII (Animos Corporation, Saitama, Japan). Polymerase chain reaction (PCR) amplification of the 18S rRNA gene V4 and V9 region (Hirakata et al 2019) and 16S rRNA gene V3-V4 region (Caporaso et al 2012) was performed using a Sapphire Amp Fast PCR Master Mix (Takara, Shiga, Japan). PCR products were purified using AMPure XP SPRI beads (Beckman).…”

Section: Microbial Community Analysismentioning

confidence: 99%

Direct resource recovery from sewage using a combined system of anaerobic-aerobic biological treatment and food production

Tanikawa

Shimomura

Motokawa

et al. 2021

Water Practice and Technology

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A combined system of an anaerobic baffled reactor (ABR), a down-flow hanging sponge (DHS) reactor, an aquarium tank (AT), and a constructed wetland (CWL) was proposed as a new concept for sewage treatment. The ABR and DHS reactor, AT, and CWL were applied for biological sewage treatment, bioassay, and nutrient removal with food production, respectively. Killifishes and tomatoes were cultivated in the AT and CWL, respectively. In the ABR, 81.3% of total chemical oxygen demand and 76.5% of total biochemical oxygen demand were removed at 5.1 h of the hydraulic retention time (HRT). Most remaining organic matter and 47.1% of ammonia were removed in the DHS reactor. In the CWL, 97.0% of total inorganic nitrogen and 78.6% of phosphate were removed with a 3.87 kg/m2 of tomatoes producing yield at 4.4 days of the HRT. In addition, anaerobic ammonium-oxidizing bacteria Candidatus Scalindua and ammonia-oxidizing bacteria Nitrospira and Nitorosococcus were considered as contributors to nitrogen removal in the CWL. The final effluent's water can be utilized as recycled water by installation of sand filtration and disinfection processes. Therefore, the proposed system can be applied as a low-energy, low-cost sewage treatment system with direct resource recovery.

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“…Besides marker genes, metagenomics and metatranscriptomics can be used to estimate the abundance and activity, respectively, of individual immigrants with higher resolution. In addition, the immigration of viruses [61] and eukaryotes [62] from an upstream process to a downstream process can be monitored and quantified, in addition to prokaryotic populations.…”

Section: Quantifying Immigration Impact At Individual Population Levementioning

confidence: 99%

Quantifying the contribution of microbial immigration in engineered water systems

Mei

Liu

2019

Microbiome

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Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counting shared microbial species, microbial source tracking, and neutral community model, rely on abundance profile to reveal the extent of overlapping between the upstream and downstream communities. Thus, they cannot suggest the quantitative contribution of immigrants to the downstream community function because activities of individual immigrants are not considered after entering the receiving environment. This limitation can be overcome by using an approach that couples a mass balance model with high-throughput DNA sequencing, i.e., ecogenomics-based mass balance. It calculates the net growth rate of individual microbial immigrants and partitions the entire community into active populations that contribute to the community function and inactive ones that carry minimal function. Linking activities of immigrants to their abundance further provides quantification of the contribution from an upstream environment to the downstream community. Considering only active populations can improve the accuracy of identifying key environmental parameters dictating process performance using methods such as machine learning.

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Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing

Cited by 34 publications

References 80 publications

Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform

Direct resource recovery from sewage using a combined system of anaerobic-aerobic biological treatment and food production

Quantifying the contribution of microbial immigration in engineered water systems

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