Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters

ABSTRACT Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed...

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Autores principales:	Margarita Lopez-Fernandez, Elias Broman, Domenico Simone, Stefan Bertilsson, Mark Dopson
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	deep biosphere groundwaters metatranscriptomes protein-coding RNA rRNA Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/abc5f52717b346efbbd540ad540260f0
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spelling	oai:doaj.org-article:abc5f52717b346efbbd540ad540260f02021-11-15T16:22:11ZStatistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters10.1128/mBio.01470-192150-7511https://doaj.org/article/abc5f52717b346efbbd540ad540260f02019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01470-19https://doaj.org/toc/2150-7511ABSTRACT Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two “modern marine” waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic “thoroughly mixed” water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or “geogases.” IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth’s carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.Margarita Lopez-FernandezElias BromanDomenico SimoneStefan BertilssonMark DopsonAmerican Society for Microbiologyarticledeep biospheregroundwatersmetatranscriptomesprotein-coding RNArRNAMicrobiologyQR1-502ENmBio, Vol 10, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	deep biosphere groundwaters metatranscriptomes protein-coding RNA rRNA Microbiology QR1-502
spellingShingle	deep biosphere groundwaters metatranscriptomes protein-coding RNA rRNA Microbiology QR1-502 Margarita Lopez-Fernandez Elias Broman Domenico Simone Stefan Bertilsson Mark Dopson Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
description	ABSTRACT Life in water-filled bedrock fissures in the continental deep biosphere is broadly constrained by energy and nutrient availability. Although these communities are alive, robust studies comparing active populations and metabolic processes across deep aquifers are lacking. This study analyzed three oligotrophic Fennoscandian Shield groundwaters, two “modern marine” waters that are replenished with organic carbon from the Baltic Sea and are likely less than 20 years old (171.3 and 415.4 m below sea level) and an extremely oligotrophic “thoroughly mixed” water (448.8 m below sea level) of unknown age that is composed of very old saline and marine waters. Cells were captured either using a sampling device that rapidly fixed RNA under in situ conditions or by filtering flowing groundwater over an extended period before fixation. Comparison of metatranscriptomes between the methods showed statistically similar transcript profiles for the respective water types, and they were analyzed as biological replicates. Study of the small subunit (SSU) rRNA confirmed active populations from all three domains of life, with many potentially novel unclassified populations present. Statistically supported differences between communities included heterotrophic sulfate-reducing bacteria in the modern marine water at 171.3 m below sea level that has a higher organic carbon content than do largely autotrophic populations in the H2- and CO2-fed thoroughly mixed water. While this modern marine water had signatures of methanogenesis, syntrophic populations were predominantly in the thoroughly mixed water. The study provides a first statistical evaluation of differences in the active microbial communities in groundwaters differentially fed by organic carbon or “geogases.” IMPORTANCE Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth’s carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.
format	article
author	Margarita Lopez-Fernandez Elias Broman Domenico Simone Stefan Bertilsson Mark Dopson
author_facet	Margarita Lopez-Fernandez Elias Broman Domenico Simone Stefan Bertilsson Mark Dopson
author_sort	Margarita Lopez-Fernandez
title	Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
title_short	Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
title_full	Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
title_fullStr	Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
title_full_unstemmed	Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters
title_sort	statistical analysis of community rna transcripts between organic carbon and geogas-fed continental deep biosphere groundwaters
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/abc5f52717b346efbbd540ad540260f0
work_keys_str_mv	AT margaritalopezfernandez statisticalanalysisofcommunityrnatranscriptsbetweenorganiccarbonandgeogasfedcontinentaldeepbiospheregroundwaters AT eliasbroman statisticalanalysisofcommunityrnatranscriptsbetweenorganiccarbonandgeogasfedcontinentaldeepbiospheregroundwaters AT domenicosimone statisticalanalysisofcommunityrnatranscriptsbetweenorganiccarbonandgeogasfedcontinentaldeepbiospheregroundwaters AT stefanbertilsson statisticalanalysisofcommunityrnatranscriptsbetweenorganiccarbonandgeogasfedcontinentaldeepbiospheregroundwaters AT markdopson statisticalanalysisofcommunityrnatranscriptsbetweenorganiccarbonandgeogasfedcontinentaldeepbiospheregroundwaters
_version_	1718426924040060928

Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters

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