Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes

Abstract To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide rang...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Manuel Harringer, Albin Alfreider
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c8debd63495b44e4807417ea553a7a8b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c8debd63495b44e4807417ea553a7a8b
record_format	dspace
spelling	oai:doaj.org-article:c8debd63495b44e4807417ea553a7a8b2021-12-02T10:44:21ZPrimer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes10.1038/s41598-021-82613-62045-2322https://doaj.org/article/c8debd63495b44e4807417ea553a7a8b2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82613-6https://doaj.org/toc/2045-2322Abstract To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers, which target the α-subunit of the ammonia monooxygenase, generated non-specific PCR products or did not amplify target genes from lake water and other habitats. Therefore, a new primer set has been designed for specific detection of Comammox in lakes. The high specificity of the PCR assay was confirmed by sequencing analysis. Quantification of Comammox amoA genes in lake water samples based on droplet digital PCR (ddPCR) revealed very low abundances (not exceeding 85 amoA copies ml−1), which suggest that Comammox is of minor importance for the nitrification process in the water column of the study sites. Surprisingly, samples taken from the sediment/water-interface along an oxygen gradient in dimictic Piburger See showed Comammox abundances three to four magnitudes higher than in the pelagic realm of the lake, which indicates a preference of Comammox to a particle-attached lifestyle.Manuel HarringerAlbin AlfreiderNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Manuel Harringer Albin Alfreider Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes
description	Abstract To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers, which target the α-subunit of the ammonia monooxygenase, generated non-specific PCR products or did not amplify target genes from lake water and other habitats. Therefore, a new primer set has been designed for specific detection of Comammox in lakes. The high specificity of the PCR assay was confirmed by sequencing analysis. Quantification of Comammox amoA genes in lake water samples based on droplet digital PCR (ddPCR) revealed very low abundances (not exceeding 85 amoA copies ml−1), which suggest that Comammox is of minor importance for the nitrification process in the water column of the study sites. Surprisingly, samples taken from the sediment/water-interface along an oxygen gradient in dimictic Piburger See showed Comammox abundances three to four magnitudes higher than in the pelagic realm of the lake, which indicates a preference of Comammox to a particle-attached lifestyle.
format	article
author	Manuel Harringer Albin Alfreider
author_facet	Manuel Harringer Albin Alfreider
author_sort	Manuel Harringer
title	Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes
title_short	Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes
title_full	Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes
title_fullStr	Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes
title_full_unstemmed	Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes
title_sort	primer evaluation and development of a droplet digital pcr protocol targeting amoa genes for the quantification of comammox in lakes
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/c8debd63495b44e4807417ea553a7a8b
work_keys_str_mv	AT manuelharringer primerevaluationanddevelopmentofadropletdigitalpcrprotocoltargetingamoagenesforthequantificationofcomammoxinlakes AT albinalfreider primerevaluationanddevelopmentofadropletdigitalpcrprotocoltargetingamoagenesforthequantificationofcomammoxinlakes
_version_	1718396789212577792

Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes

Ejemplares similares