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Research Output

2020

Fast, sensitive, and reliable detection of waterborne pathogens by digital PCR after coagulation and foam concentration

Jikumaru, A., Ishii, S., Fukudome, T., Kawahara, Y., Iguchi, A., Masago, Y., Nukazawa, K. & Suzuki, Y., Jan 1 2020, (Accepted/In press) In : Journal of Bioscience and Bioengineering.

Research output: Contribution to journalArticle

Isolation and characterization of denitrifiers from woodchip bioreactors for bioaugmentation application

Anderson, E. L., Jang, J., Venterea, R. T., Feyereisen, G. W. & Ishii, S., Jan 1 2020, (Accepted/In press) In : Journal of Applied Microbiology.

Research output: Contribution to journalArticle

Open Access

Role of wastewater treatment plants on environmental abundance of Antimicrobial Resistance Genes in Chilean rivers

Bueno, I., Verdugo, C., Jimenez-Lopez, O., Alvarez, P. P., Gonzalez-Rocha, G., Lima, C. A., Travis, D. A., Wass, B., Zhang, Q., Ishii, S. & Singer, R. S., Jan 2020, In : International Journal of Hygiene and Environmental Health. 223, 1, p. 56-64 9 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Simple and reliable enumeration of Escherichia coli concentrations in wastewater samples by measuring β-D-glucuronidase (GUS) activities via a microplate reader

Satoh, H., Kikuchi, K., Katayose, Y., Tsuda, S., Hirano, R., Hirakata, Y., Kitajima, M., Ishii, S., Oshiki, M., Hatamoto, M., Takahashi, M. & Okabe, S., May 1 2020, In : Science of the Total Environment. 715, 136928.

Research output: Contribution to journalArticle

2019

A microfluidic platform for the simultaneous quantification of methanogen populations in anaerobic digestion processes

Mathai, P. P., Dunn, H. M., Venkiteshwaran, K., Zitomer, D. H., Maki, J. S., Ishii, S. & Sadowsky, M. J., May 2019, In : Environmental microbiology. 21, 5, p. 1798-1808 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

Antibiotic resistance genes in freshwater trout farms in a watershed in Chile

Bueno, I., Travis, D., Gonzalez-Rocha, G., Alvarez, J., Lima, C., Benitez, C. G., Phelps, N. B. D., Wass, B., Johnson, T. J., Zhang, Q., Ishii, S. & Singer, R. S., Jan 1 2019, In : Journal of Environmental Quality. 48, 5, p. 1462-1471 10 p.

Research output: Contribution to journalArticle

3 Scopus citations
2 Scopus citations

Complete genome sequence of a novel Myoviridae phage, SF01, infecting Shigella spp.

Kitajima, M., Ishii, S., Takagi, T. & Okabe, S., Jun 6 2019, In : Microbiology Resource Announcements. 8, 23, e0034919.

Research output: Contribution to journalArticle

Open Access

Denitrifying bacteria active in woodchip bioreactors at low-temperature conditions

Jang, J., Anderson, E. L., Venterea, R. T., Sadowsky, M. J., Rosen, C. J., Feyereisen, G. W. & Ishii, S., Jan 1 2019, In : Frontiers in Microbiology. 10, APR, 635.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Ecology of pathogens and antibiotic-resistant bacteria in environments: Challenges and opportunities

Ishii, S., Jan 1 2019, In : Microbes and environments. 34, 1, p. 1-4 4 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Growth and antibiotic resistance acquisition of Escherichia coli in a river that receives treated sewage effluent

Suzuki, Y., Hashimoto, R., Xie, H., Nishimura, E., Nishiyama, M., Nukazawa, K. & Ishii, S., Nov 10 2019, In : Science of the Total Environment. 690, p. 696-704 9 p.

Research output: Contribution to journalArticle

2 Scopus citations

Impact of long-term grazing exclusion on soil microbial community composition and nutrient availability

Wang, Z., Zhang, Q., Staley, C., Gao, H., Ishii, S., Wei, X., Liu, J., Cheng, J., Hao, M. & Sadowsky, M. J., Feb 1 2019, In : Biology and Fertility of Soils. 55, 2, p. 121-134 14 p.

Research output: Contribution to journalArticle

7 Scopus citations

Multiplex PCR coupled with direct amplicon sequencing for simultaneous detection of numerous waterborne pathogens

Li, B., Saingam, P., Ishii, S. & Yan, T., Jan 18 2019, In : Applied Microbiology and Biotechnology. 103, 2, p. 953-961 9 p.

Research output: Contribution to journalArticle

2 Scopus citations

Potentially mobile denitrification genes identified in Azospirillum sp. Strain TSH58

Jang, J., Sakai, Y., Senoo, K. & Ishiia, S., Jan 1 2019, In : Applied and environmental microbiology. 85, 2, 02474.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2018
10 Scopus citations

Complete genome sequence of Klebsiella quasipneumoniae strain S05, a fouling-causing bacterium isolated from a membrane bioreactor

Kitajima, M., Ishizaki, S., Jang, J., Ishii, S. & Okabe, S., Jun 1 2018, In : Genome Announcements. 6, 23, e00471-18.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
Open Access

Experimental Evidence for in Situ Nitric Oxide Production in Anaerobic Ammonia-Oxidizing Bacterial Granules

Rathnayake, R. M. L. D., Oshiki, M., Ishii, S., Segawa, T., Satoh, H. & Okabe, S., May 15 2018, In : Environmental Science and Technology. 52, 10, p. 5744-5752 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

High-throughput flaA short variable region sequencing to assess campylobacter diversity in fecal samples from birds

Zhang, Q., Al-Ghalith, G. A., Kobayashi, M., Segawa, T., Maeda, M., Okabe, S., Knights, D. & Ishii, S., Sep 1 2018, In : Frontiers in Microbiology. 9, 2201.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
9 Scopus citations

Microfluidic PCR amplification and MiSeq amplicon sequencing techniques for high-throughput detection and genotyping of human pathogenic RNA viruses in human feces, sewage, and oysters

Oshiki, M., Miura, T., Kazama, S., Segawa, T., Ishii, S., Hatamoto, M., Yamaguchi, T., Kubota, K., Iguchi, A., Tagawa, T., Okubo, T., Uemura, S., Harada, H., Kobayashi, N., Araki, N. & Sano, D., Apr 27 2018, In : Frontiers in Microbiology. 9, APR, 830.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations
4 Scopus citations

Nitrogen cycle evaluation (NiCE) chip for simultaneous analysis of multiple N cycleassociated genes

Oshiki, M., Segawa, T. & Ishii, S., Apr 1 2018, In : Applied and environmental microbiology. 84, 8, e02615-17.

Research output: Contribution to journalArticle

Open Access
8 Scopus citations

Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters

Ahmed, W., Zhang, Q., Lobos, A., Senkbeil, J., Sadowsky, M. J., Harwood, V. J., Saeidi, N., Marinoni, O. & Ishii, S., Jul 2018, In : Environment International. 116, p. 308-318 11 p.

Research output: Contribution to journalArticle

26 Scopus citations

Presence of cu-type (Nirk) and cd1-type (nirs) nitrite reductase genes in the denitrifying bacterium bradyrhizobium nitroreducens sp. nov.

Jang, J., Ashida, N., Kai, A., Isobe, K., Nishizawa, T., Otsuka, S., Yokota, A., Senoo, K. & Ishii, S., Jan 1 2018, In : Microbes and environments. 33, 3, p. 326-331 6 p.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations
2017

Environmental Escherichia coli: ecology and public health implications—a review

Jang, J., Hur, H. G., Sadowsky, M. J., Byappanahalli, M. N., Yan, T. & Ishii, S., Sep 2017, In : Journal of Applied Microbiology. 123, 3, p. 570-581 12 p.

Research output: Contribution to journalReview article

Open Access
62 Scopus citations

Generation of small colony variants in biofilms by Escherichia coli harboring a conjugative F plasmid

Tashiro, Y., Eida, H., Ishii, S., Futamata, H. & Okabe, S., Jan 1 2017, In : Microbes and environments. 32, 1, p. 40-46 7 p.

Research output: Contribution to journalArticle

Open Access
7 Scopus citations

Microbial competition among anammox bacteria in nitrite-limited bioreactors

Zhang, L., Narita, Y., Gao, L., Ali, M., Oshiki, M., Ishii, S. & Okabe, S., Jan 1 2017, In : Water Research. 125, p. 249-258 10 p.

Research output: Contribution to journalArticle

23 Scopus citations
Open Access
8 Scopus citations

Target virus log10 reduction values determined for two reclaimed wastewater irrigation scenarios in Japan based on tolerable annual disease burden

Ito, T., Kitajima, M., Kato, T., Ishii, S., Segawa, T., Okabe, S. & Sano, D., Jan 1 2017, In : Water Research. 125, p. 438-448 11 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

Chun, C. L., Peller, J. R., Shively, D., Byappanahalli, M. N., Whitman, R. L., Staley, C., Zhang, Q., Ishii, S. & Sadowsky, M. J., Jan 1 2017, In : Science of the Total Environment. 574, p. 872-880 9 p.

Research output: Contribution to journalArticle

9 Scopus citations
2016

Bacterial histo-blood group antigens contributing to genotype-dependent removal of human noroviruses with a microfiltration membrane

Amarasiri, M., Hashiba, S., Miura, T., Nakagomi, T., Nakagomi, O., Ishii, S., Okabe, S. & Sano, D., May 15 2016, In : Water Research. 95, p. 383-391 9 p.

Research output: Contribution to journalArticle

Open Access
16 Scopus citations

Correlations between pathogen concentration and fecal indicator marker genes in beach environments

Zhang, Q., Eichmiller, J. J., Staley, C., Sadowsky, M. J. & Ishii, S., Dec 15 2016, In : Science of the Total Environment. 573, p. 826-830 5 p.

Research output: Contribution to journalArticle

19 Scopus citations

Denitrification and nitrate-dependent Fe(II) oxidation in various Pseudogulbenkiania strains

Ishii, S., Joikai, K., Otsuka, S., Senoo, K. & Okabe, S., Jan 1 2016, In : Microbes and environments. 31, 3, p. 293-298 6 p.

Research output: Contribution to journalArticle

Open Access
19 Scopus citations

Estimation of concentration ratio of indicator to pathogen-related gene in environmental water based on left-censored data

Kato, T., Kobayashi, A., Ito, T., Miura, T., Ishii, S., Okabe, S. & Sano, D., Feb 2016, In : Journal of Water and Health. 14, 1, p. 14-25 12 p.

Research output: Contribution to journalReview article

Open Access
3 Scopus citations

Evaluation of virus reduction efficiency in wastewater treatment unit processes as a credit value in the multiplebarrier system for wastewater reclamation and reuse

Ito, T., Kato, T., Hasegawa, M., Katayama, H., Ishii, S., Okabe, S. & Sano, D., Dec 2016, In : Journal of Water and Health. 14, 6, p. 879-889 11 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Genome sequence of Enterobacter cloacae strain SENG-6, a bacterium producing histo-blood group antigen-like substances that can bind with human noroviruses

Ishii, S., Amarasiri, M., Hashiba, S., Yang, P., Okabe, S. & Sano, D., Jan 1 2016, In : Genome Announcements. 4, 4, e00893-16.

Research output: Contribution to journalArticle

Open Access

Membrane fouling potentials and cellular properties of bacteria isolated from fouled membranes in a MBR treating municipal wastewater

Ishizaki, S., Fukushima, T., Ishii, S. & Okabe, S., Sep 1 2016, In : Water Research. 100, p. 448-457 10 p.

Research output: Contribution to journalArticle

Open Access
33 Scopus citations

Source identification of nitrous oxide emission pathways from a single-stage nitritation-anammox granular reactor

Ali, M., Rathnayake, R. M. L. D., Zhang, L., Ishii, S., Kindaichi, T., Satoh, H., Toyoda, S., Yoshida, N. & Okabe, S., Oct 1 2016, In : Water Research. 102, p. 147-157 11 p.

Research output: Contribution to journalArticle

Open Access
54 Scopus citations
5 Scopus citations
2015

Application of a Microfluidic Quantitative Polymerase Chain Reaction Technique to Monitor Bacterial Pathogens in Beach Water and Complex Environmental Matrices

Byappanahalli, M. N., Nevers, M. B., Whitman, R. L. & Ishii, S., Nov 17 2015, In : Environmental Science and Technology Letters. 2, 12, p. 347-351 5 p.

Research output: Contribution to journalArticle

13 Scopus citations

Effects of dissolved oxygen and pH on nitrous oxide production rates in autotrophic partial nitrification granules

Rathnayake, R. M. L. D., Oshiki, M., Ishii, S., Segawa, T., Satoh, H. & Okabe, S., Dec 1 2015, In : Bioresource Technology. 197, p. 15-22 8 p.

Research output: Contribution to journalArticle

51 Scopus citations

Rapid and successful start-up of anammox process by immobilizing the minimal quantity of biomass in PVA-SA gel beads

Ali, M., Oshiki, M., Rathnayake, L., Ishii, S., Satoh, H. & Okabe, S., Aug 1 2015, In : Water Research. 79, p. 147-157 11 p.

Research output: Contribution to journalArticle

80 Scopus citations
2014

Identification of key nitrous oxide production pathways in aerobic partial nitrifying granules

Ishii, S., Song, Y., Rathnayake, L., Tumendelger, A., Satoh, H., Toyoda, S., Yoshida, N. & Okabe, S., Jan 1 2014, In : Environmental Microbiology. 16, 10, p. 3168-3180 13 p.

Research output: Contribution to journalArticle

29 Scopus citations

Inoculation with N2-generating denitrifier strains mitigates N2O emission from agricultural soil fertilized with poultry manure

Nishizawa, T., Quan, A., Kai, A., Tago, K., Ishii, S., Shen, W., Isobe, K., Otsuka, S. & Senoo, K., Aug 2014, In : Biology and Fertility of Soils. 50, 6, p. 1001-1007 7 p.

Research output: Contribution to journalArticle

16 Scopus citations

Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples

Ishii, S., Kitamura, G., Segawa, T., Kobayashi, A., Miura, T., Sano, D. & Okabe, S., Jan 1 2014, In : Applied and environmental microbiology. 80, 24, p. 7505-7511 7 p.

Research output: Contribution to journalArticle

43 Scopus citations

The nitrogen cycle in cryoconites: Naturally occurring nitrification-denitrification granules on a glacier

Segawa, T., Ishii, S., Ohte, N., Akiyoshi, A., Yamada, A., Maruyama, F., Li, Z., Hongoh, Y. & Takeuchi, N., Oct 1 2014, In : Environmental microbiology. 16, 10, p. 3250-3262 13 p.

Research output: Contribution to journalArticle

37 Scopus citations

Water quality monitoring and risk assessment by simultaneous multipathogen quantification

Ishii, S., Nakamura, T., Ozawa, S., Kobayashi, A., Sano, D. & Okabe, S., May 6 2014, In : Environmental Science and Technology. 48, 9, p. 4744-4749 6 p.

Research output: Contribution to journalArticle

33 Scopus citations
2013

Chicken- and duck-associated Bacteroides-Prevotella genetic markers for detecting fecal contamination in environmental water

Kobayashi, A., Sano, D., Hatori, J., Ishii, S. & Okabe, S., Aug 1 2013, In : Applied Microbiology and Biotechnology. 97, 16, p. 7427-7437 11 p.

Research output: Contribution to journalArticle

35 Scopus citations