Status of the Archaeal and Bacterial Census: an Update

ABSTRACT A census is typically carried out for people across a range of geographical levels; however, microbial ecologists have implemented a molecular census of bacteria and archaea by sequencing their 16S rRNA genes. We assessed how well the census of full-length 16S rRNA gene sequences is proceed...

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Autores principales:	Patrick D. Schloss, Rene A. Girard, Thomas Martin, Joshua Edwards, J. Cameron Thrash
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Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7d636cdd7e614947a88e60c311cad382
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spelling	oai:doaj.org-article:7d636cdd7e614947a88e60c311cad3822021-11-15T15:50:16ZStatus of the Archaeal and Bacterial Census: an Update10.1128/mBio.00201-162150-7511https://doaj.org/article/7d636cdd7e614947a88e60c311cad3822016-07-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00201-16https://doaj.org/toc/2150-7511ABSTRACT A census is typically carried out for people across a range of geographical levels; however, microbial ecologists have implemented a molecular census of bacteria and archaea by sequencing their 16S rRNA genes. We assessed how well the census of full-length 16S rRNA gene sequences is proceeding in the context of recent advances in high-throughput sequencing technologies because full-length sequences are typically used as references for classification of the short sequences generated by newer technologies. Among the 1,411,234 and 53,546 full-length bacterial and archaeal sequences, 94.5% and 95.1% of the bacterial and archaeal sequences, respectively, belonged to operational taxonomic units (OTUs) that have been observed more than once. Although these metrics suggest that the census is approaching completion, 29.2% of the bacterial and 38.5% of the archaeal OTUs have been observed more than once. Thus, there is still considerable diversity to be explored. Unfortunately, the rate of new full-length sequences has been declining, and new sequences are primarily being deposited by a small number of studies. Furthermore, sequences from soil and aquatic environments, which are known to be rich in bacterial diversity, represent only 7.8 and 16.5% of the census, while sequences associated with host-associated environments represent 55.0% of the census. Continued use of traditional approaches and new technologies such as single-cell genomics and short-read assembly are likely to improve our ability to sample rare OTUs if it is possible to overcome this sampling bias. The success of ongoing efforts to use short-read sequencing to characterize archaeal and bacterial communities requires that researchers strive to expand the depth and breadth of this census. IMPORTANCE The biodiversity contained within the bacterial and archaeal domains dwarfs that of the eukaryotes, and the services these organisms provide to the biosphere are critical. Surprisingly, we have done a relatively poor job of formally tracking the quality of the biodiversity as represented in full-length 16S rRNA genes. By understanding how this census is proceeding, it is possible to suggest the best allocation of resources for advancing the census. We found that the ongoing effort has done an excellent job of sampling the most abundant organisms but struggles to sample the rarer organisms. Through the use of new sequencing technologies, we should be able to obtain full-length sequences from these rare organisms. Furthermore, we suggest that by allocating more resources to sampling environments known to have the greatest biodiversity, we will be able to make significant advances in our characterization of archaeal and bacterial diversity.Patrick D. SchlossRene A. GirardThomas MartinJoshua EdwardsJ. Cameron ThrashAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 7, Iss 3 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Patrick D. Schloss Rene A. Girard Thomas Martin Joshua Edwards J. Cameron Thrash Status of the Archaeal and Bacterial Census: an Update
description	ABSTRACT A census is typically carried out for people across a range of geographical levels; however, microbial ecologists have implemented a molecular census of bacteria and archaea by sequencing their 16S rRNA genes. We assessed how well the census of full-length 16S rRNA gene sequences is proceeding in the context of recent advances in high-throughput sequencing technologies because full-length sequences are typically used as references for classification of the short sequences generated by newer technologies. Among the 1,411,234 and 53,546 full-length bacterial and archaeal sequences, 94.5% and 95.1% of the bacterial and archaeal sequences, respectively, belonged to operational taxonomic units (OTUs) that have been observed more than once. Although these metrics suggest that the census is approaching completion, 29.2% of the bacterial and 38.5% of the archaeal OTUs have been observed more than once. Thus, there is still considerable diversity to be explored. Unfortunately, the rate of new full-length sequences has been declining, and new sequences are primarily being deposited by a small number of studies. Furthermore, sequences from soil and aquatic environments, which are known to be rich in bacterial diversity, represent only 7.8 and 16.5% of the census, while sequences associated with host-associated environments represent 55.0% of the census. Continued use of traditional approaches and new technologies such as single-cell genomics and short-read assembly are likely to improve our ability to sample rare OTUs if it is possible to overcome this sampling bias. The success of ongoing efforts to use short-read sequencing to characterize archaeal and bacterial communities requires that researchers strive to expand the depth and breadth of this census. IMPORTANCE The biodiversity contained within the bacterial and archaeal domains dwarfs that of the eukaryotes, and the services these organisms provide to the biosphere are critical. Surprisingly, we have done a relatively poor job of formally tracking the quality of the biodiversity as represented in full-length 16S rRNA genes. By understanding how this census is proceeding, it is possible to suggest the best allocation of resources for advancing the census. We found that the ongoing effort has done an excellent job of sampling the most abundant organisms but struggles to sample the rarer organisms. Through the use of new sequencing technologies, we should be able to obtain full-length sequences from these rare organisms. Furthermore, we suggest that by allocating more resources to sampling environments known to have the greatest biodiversity, we will be able to make significant advances in our characterization of archaeal and bacterial diversity.
format	article
author	Patrick D. Schloss Rene A. Girard Thomas Martin Joshua Edwards J. Cameron Thrash
author_facet	Patrick D. Schloss Rene A. Girard Thomas Martin Joshua Edwards J. Cameron Thrash
author_sort	Patrick D. Schloss
title	Status of the Archaeal and Bacterial Census: an Update
title_short	Status of the Archaeal and Bacterial Census: an Update
title_full	Status of the Archaeal and Bacterial Census: an Update
title_fullStr	Status of the Archaeal and Bacterial Census: an Update
title_full_unstemmed	Status of the Archaeal and Bacterial Census: an Update
title_sort	status of the archaeal and bacterial census: an update
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/7d636cdd7e614947a88e60c311cad382
work_keys_str_mv	AT patrickdschloss statusofthearchaealandbacterialcensusanupdate AT reneagirard statusofthearchaealandbacterialcensusanupdate AT thomasmartin statusofthearchaealandbacterialcensusanupdate AT joshuaedwards statusofthearchaealandbacterialcensusanupdate AT jcameronthrash statusofthearchaealandbacterialcensusanupdate
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Status of the Archaeal and Bacterial Census: an Update

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