Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass

Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although...
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Autor*in:	Toshiaki Jo [verfasserIn] Mio Arimoto [verfasserIn] Hiroaki Murakami [verfasserIn] Reiji Masuda [verfasserIn] Toshifumi Minamoto [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2020

Schlagwörter:	environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR

Übergeordnetes Werk:	In: Environmental DNA - Wiley, 2019, 2(2020), 2, Seite 140-151
Übergeordnetes Werk:	volume:2 ; year:2020 ; number:2 ; pages:140-151

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1002/edn3.51

Katalog-ID:	DOAJ003843297

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520			\|a Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance.
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653		0	\|a Environmental sciences
653		0	\|a Microbial ecology
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700	0		\|a Hiroaki Murakami \|e verfasserin \|4 aut
700	0		\|a Reiji Masuda \|e verfasserin \|4 aut
700	0		\|a Toshifumi Minamoto \|e verfasserin \|4 aut
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912			\|a GBV_ILN_213
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912			\|a GBV_ILN_293
912			\|a GBV_ILN_602
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allfields	10.1002/edn3.51 doi (DE-627)DOAJ003843297 (DE-599)DOAJ8de70c9b8aa44188aa19abdf8401397c DE-627 ger DE-627 rakwb eng GE1-350 QR100-130 Toshiaki Jo verfasserin aut Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance. environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR Environmental sciences Microbial ecology Mio Arimoto verfasserin aut Hiroaki Murakami verfasserin aut Reiji Masuda verfasserin aut Toshifumi Minamoto verfasserin aut In Environmental DNA Wiley, 2019 2(2020), 2, Seite 140-151 (DE-627)1683467949 (DE-600)3001165-6 26374943 nnns volume:2 year:2020 number:2 pages:140-151 https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/article/8de70c9b8aa44188aa19abdf8401397c kostenfrei https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/toc/2637-4943 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2020 2 140-151
spelling	10.1002/edn3.51 doi (DE-627)DOAJ003843297 (DE-599)DOAJ8de70c9b8aa44188aa19abdf8401397c DE-627 ger DE-627 rakwb eng GE1-350 QR100-130 Toshiaki Jo verfasserin aut Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance. environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR Environmental sciences Microbial ecology Mio Arimoto verfasserin aut Hiroaki Murakami verfasserin aut Reiji Masuda verfasserin aut Toshifumi Minamoto verfasserin aut In Environmental DNA Wiley, 2019 2(2020), 2, Seite 140-151 (DE-627)1683467949 (DE-600)3001165-6 26374943 nnns volume:2 year:2020 number:2 pages:140-151 https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/article/8de70c9b8aa44188aa19abdf8401397c kostenfrei https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/toc/2637-4943 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2020 2 140-151
allfields_unstemmed	10.1002/edn3.51 doi (DE-627)DOAJ003843297 (DE-599)DOAJ8de70c9b8aa44188aa19abdf8401397c DE-627 ger DE-627 rakwb eng GE1-350 QR100-130 Toshiaki Jo verfasserin aut Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance. environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR Environmental sciences Microbial ecology Mio Arimoto verfasserin aut Hiroaki Murakami verfasserin aut Reiji Masuda verfasserin aut Toshifumi Minamoto verfasserin aut In Environmental DNA Wiley, 2019 2(2020), 2, Seite 140-151 (DE-627)1683467949 (DE-600)3001165-6 26374943 nnns volume:2 year:2020 number:2 pages:140-151 https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/article/8de70c9b8aa44188aa19abdf8401397c kostenfrei https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/toc/2637-4943 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2020 2 140-151
allfieldsGer	10.1002/edn3.51 doi (DE-627)DOAJ003843297 (DE-599)DOAJ8de70c9b8aa44188aa19abdf8401397c DE-627 ger DE-627 rakwb eng GE1-350 QR100-130 Toshiaki Jo verfasserin aut Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance. environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR Environmental sciences Microbial ecology Mio Arimoto verfasserin aut Hiroaki Murakami verfasserin aut Reiji Masuda verfasserin aut Toshifumi Minamoto verfasserin aut In Environmental DNA Wiley, 2019 2(2020), 2, Seite 140-151 (DE-627)1683467949 (DE-600)3001165-6 26374943 nnns volume:2 year:2020 number:2 pages:140-151 https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/article/8de70c9b8aa44188aa19abdf8401397c kostenfrei https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/toc/2637-4943 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2020 2 140-151
allfieldsSound	10.1002/edn3.51 doi (DE-627)DOAJ003843297 (DE-599)DOAJ8de70c9b8aa44188aa19abdf8401397c DE-627 ger DE-627 rakwb eng GE1-350 QR100-130 Toshiaki Jo verfasserin aut Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance. environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR Environmental sciences Microbial ecology Mio Arimoto verfasserin aut Hiroaki Murakami verfasserin aut Reiji Masuda verfasserin aut Toshifumi Minamoto verfasserin aut In Environmental DNA Wiley, 2019 2(2020), 2, Seite 140-151 (DE-627)1683467949 (DE-600)3001165-6 26374943 nnns volume:2 year:2020 number:2 pages:140-151 https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/article/8de70c9b8aa44188aa19abdf8401397c kostenfrei https://doi.org/10.1002/edn3.51 kostenfrei https://doaj.org/toc/2637-4943 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_21 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_171 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_636 GBV_ILN_2004 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2007 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2026 GBV_ILN_2027 GBV_ILN_2034 GBV_ILN_2037 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2049 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2059 GBV_ILN_2061 GBV_ILN_2064 GBV_ILN_2068 GBV_ILN_2088 GBV_ILN_2106 GBV_ILN_2108 GBV_ILN_2110 GBV_ILN_2111 GBV_ILN_2118 GBV_ILN_2122 GBV_ILN_2143 GBV_ILN_2144 GBV_ILN_2147 GBV_ILN_2148 GBV_ILN_2152 GBV_ILN_2153 GBV_ILN_2232 GBV_ILN_2336 GBV_ILN_2470 GBV_ILN_2507 GBV_ILN_2522 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4037 GBV_ILN_4046 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4242 GBV_ILN_4249 GBV_ILN_4251 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4326 GBV_ILN_4333 GBV_ILN_4334 GBV_ILN_4335 GBV_ILN_4336 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 2 2020 2 140-151
language	English
source	In Environmental DNA 2(2020), 2, Seite 140-151 volume:2 year:2020 number:2 pages:140-151
sourceStr	In Environmental DNA 2(2020), 2, Seite 140-151 volume:2 year:2020 number:2 pages:140-151
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR Environmental sciences Microbial ecology
isfreeaccess_bool	true
container_title	Environmental DNA
authorswithroles_txt_mv	Toshiaki Jo @@aut@@ Mio Arimoto @@aut@@ Hiroaki Murakami @@aut@@ Reiji Masuda @@aut@@ Toshifumi Minamoto @@aut@@
publishDateDaySort_date	2020-01-01T00:00:00Z
hierarchy_top_id	1683467949
id	DOAJ003843297
language_de	englisch
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callnumber-first	G - Geography, Anthropology, Recreation
author	Toshiaki Jo
spellingShingle	Toshiaki Jo misc GE1-350 misc QR100-130 misc environmental DNA misc internal transcribed spacer‐1 misc Japanese Jack Mackerel (Trachurus japonicus) misc mitochondrial DNA misc nuclear DNA misc quantitative real‐time PCR misc Environmental sciences misc Microbial ecology Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass
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topic_title	GE1-350 QR100-130 Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass environmental DNA internal transcribed spacer‐1 Japanese Jack Mackerel (Trachurus japonicus) mitochondrial DNA nuclear DNA quantitative real‐time PCR
topic	misc GE1-350 misc QR100-130 misc environmental DNA misc internal transcribed spacer‐1 misc Japanese Jack Mackerel (Trachurus japonicus) misc mitochondrial DNA misc nuclear DNA misc quantitative real‐time PCR misc Environmental sciences misc Microbial ecology
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title	Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass
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title_full	Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass
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title_sort	estimating shedding and decay rates of environmental nuclear dna with relation to water temperature and biomass
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title_auth	Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass
abstract	Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance.
abstractGer	Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance.
abstract_unstemmed	Abstract Background Environmental DNA (eDNA) analysis has been recently applied to the surveillance of species distribution and composition in aquatic ecosystems. However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance.
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title_short	Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass
url	https://doi.org/10.1002/edn3.51 https://doaj.org/article/8de70c9b8aa44188aa19abdf8401397c https://doaj.org/toc/2637-4943
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However, most eDNA studies have used mitochondrial DNA markers, and those using nuclear DNA markers are quite scarce. Moreover, although some studies reported the availability of nuclear DNA markers for eDNA analyses, the characteristics and dynamics of nuclear environmental DNA (nu‐eDNA) of macro‐organisms remain unknown. Herein, we re‐analyzed eDNA samples described in a previously published paper to investigate the shedding and decay rates of nu‐eDNA from Japanese Jack Mackerel (Trachurus japonicus) and compared them to those of mt‐eDNA (mitochondrial environmental DNA). Materials & Methods Tank experiments consisting of 12 combinations of four temperatures and three fish biomass levels were performed, and four tank replicates were prepared for each treatment level. Before and after removing the fish from the tanks, we sampled rearing water over time to quantify nu‐eDNA copy numbers. Results & Discussion Model fitting to eDNA decay curves demonstrated that nu‐eDNA decay rates increased in higher water temperature and with larger fish biomass. The estimated shedding rates of nu‐eDNA also increased with higher temperature and larger biomass. These results were generally consistent with those of mt‐eDNA. Moreover, the ratio of mt‐eDNA to nu‐eDNA shedding and concentration decreased with larger fish biomass levels, which implied that these values may be among the potential indices for estimating the age and body size of organisms from environmental samples. Our findings contribute to the understanding of eDNA characteristics and dynamics between different DNA markers and may help us to interpret future results of eDNA surveillance.</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">environmental DNA</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">internal transcribed spacer‐1</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">Japanese Jack Mackerel (Trachurus japonicus)</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">mitochondrial DNA</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">nuclear DNA</subfield></datafield><datafield tag="650" ind1=" " ind2="4"><subfield code="a">quantitative real‐time PCR</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Environmental sciences</subfield></datafield><datafield tag="653" ind1=" " ind2="0"><subfield code="a">Microbial ecology</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Mio Arimoto</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Hiroaki Murakami</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Reiji Masuda</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="700" ind1="0" ind2=" "><subfield code="a">Toshifumi Minamoto</subfield><subfield code="e">verfasserin</subfield><subfield code="4">aut</subfield></datafield><datafield tag="773" ind1="0" ind2="8"><subfield code="i">In</subfield><subfield code="t">Environmental DNA</subfield><subfield code="d">Wiley, 2019</subfield><subfield code="g">2(2020), 2, Seite 140-151</subfield><subfield code="w">(DE-627)1683467949</subfield><subfield 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Estimating shedding and decay rates of environmental nuclear DNA with relation to water temperature and biomass

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