skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Comparison of Thaumarchaeotal populations from four deep sea basins

Abstract

The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.

Authors:
 [1];  [2];  [2];  [3];  [4];  [4];  [5]
  1. Michigan Technological Univ., Houghton, MI (United States). Department of Biological Sciences
  2. Univ. of Tennessee, Knoxville, TN (United States). Department of Civil and Environmental Engineering
  3. Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology and Bredesen Center
  4. Univ. of Tennessee, Knoxville, TN (United States). Department of Civil and Environmental Engineering and Center for Environmental Biotechnology
  5. Univ. of Tennessee, Knoxville, TN (United States). Department of Civil and Environmental Engineering, Center for Environmental Biotechnology, Bredesen Center, Department of Earth and Planetary Sciences, Department of Microbiology, and Institute for a Secure and Sustainable Environment; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1415207
Grant/Contract Number:
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
FEMS Microbiology Ecology (Online)
Additional Journal Information:
Journal Name: FEMS Microbiology Ecology (Online); Journal Volume: 93; Journal Issue: 11; Journal ID: ISSN 1574-6941
Publisher:
Federation of European Microbiological Societies
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; Thaumarchaeota; qPCR; minimum entropy decomposition; biogeography

Citation Formats

Techtman, Stephen M., Mahmoudi, Nagissa, Whitt, Kendall T., Campa, Maria Fernanda, Fortney, Julian L., Joyner, Dominique C., and Hazen, Terry C. Comparison of Thaumarchaeotal populations from four deep sea basins. United States: N. p., 2017. Web. doi:10.1093/femsec/fix128.
Techtman, Stephen M., Mahmoudi, Nagissa, Whitt, Kendall T., Campa, Maria Fernanda, Fortney, Julian L., Joyner, Dominique C., & Hazen, Terry C. Comparison of Thaumarchaeotal populations from four deep sea basins. United States. doi:10.1093/femsec/fix128.
Techtman, Stephen M., Mahmoudi, Nagissa, Whitt, Kendall T., Campa, Maria Fernanda, Fortney, Julian L., Joyner, Dominique C., and Hazen, Terry C. 2017. "Comparison of Thaumarchaeotal populations from four deep sea basins". United States. doi:10.1093/femsec/fix128. https://www.osti.gov/servlets/purl/1415207.
@article{osti_1415207,
title = {Comparison of Thaumarchaeotal populations from four deep sea basins},
author = {Techtman, Stephen M. and Mahmoudi, Nagissa and Whitt, Kendall T. and Campa, Maria Fernanda and Fortney, Julian L. and Joyner, Dominique C. and Hazen, Terry C.},
abstractNote = {The nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. In conclusion, these findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.},
doi = {10.1093/femsec/fix128},
journal = {FEMS Microbiology Ecology (Online)},
number = 11,
volume = 93,
place = {United States},
year = 2017,
month =
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:
  • Many studies have shown that microbes, which share nearly identical 16S rRNA genes, can have highly divergent genomes. Microbes from distinct parts of the ocean also exhibit biogeographic patterning. Here in this study we seek to better understand how certain microbes from the same species have adapted for growth under local conditions. The phenotypic and genomic heterogeneity of three strains of Colwellia psychrerythraea was investigated in order to understand adaptions to local environments. Colwellia are psychrophilic heterotrophic marine bacteria ubiquitous in cold marine ecosystems. We have recently isolated two Colwellia strains: ND2E from the Eastern Mediterranean and GAB14E from themore » Great Australian Bight. The 16S rRNA sequence of these two strains were greater than 98.2% identical to the well-characterized C. psychrerythraea 34H, which was isolated from arctic sediments. Salt tolerance, and carbon source utilization profiles for these strains were determined using Biolog Phenotype MicoArrays. These strains exhibited distinct salt tolerance, which was not associated with the salinity of sites of isolation. The carbon source utilization profiles were distinct with less than half of the tested carbon sources being metabolized by all three strains. Whole genome sequencing revealed that the genomes of these three strains were quite diverse with some genomes having up to 1600 strain-specific genes. Many genes involved in degrading strain-specific carbon sources were identified. Finally, there appears to be a link between carbon source utilization and location of isolation with distinctions observed between the Colwellia isolate recovered from sediment compared to water column isolates.« less
  • mtDNA sequence variation was examined in 60 Native Americans (Mixtecs from the Alta, Mixtecs from the Baja, Valley Zapotecs, and Highland Mixe) from southern Mexico by PCR amplification and high-resolution restriction endonuclease analysis. Four groups of mtDNA haplotypes (haplogroups A,B,C, and D) characterize Amerind populations. The comparison of their mtDNA variation with that observed in other populations from Mexico and Central America permits a clear distinction among the different Middle American tribes and raises questions about some of their linguistic affiliations. The males of these population samples were also analyzed for Y-chromosome RFLPs with the probes 49a, 49f, and 12f2.more » This analysis suggests that certain Y-chromosome haplotypes were brought from Asia during the colonization of the Americas, and a differential gene flow was introduced into Native American populations from European males and females. 31 refs., 4 figs., 5 tabs.« less
  • Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four locimore » in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. As a result, this study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality.« less
  • Surveys of radiation dose rate were made in two predominantly granite districts and in two districts of sedimentary rocks. Data are tabulated on the mean bonemarrow dose rates. (C.H.)
  • Lead content was determined in the skeletal tissue of 82 individuals representing two black and two white Colonial American populations: Catoctin Furnace, College Landing, Governor's Land, and Irene Mound. Group and individual differences in bone lead concentrations were used to assess behavioral, social and occupational characteristics. Variations in skeletal lead content suggested that the white owners of the Catoctin iron furnace shared little of their food and beverage with their black, male, industrial slaves, but that some of these workers women had access to the owners food sources--probably via domestic duty assignments. A broad range of lead concentrations in bonesmore » of the free blacks at College Landing implies a wide range of economic success among these tradesmen. Bone lead content of the white populations at Governor's Land and Irene Mound helped confirm family relationships that had been assigned on an archaeological and osteological basis, and also suggested that the social and functional status of the white tenant farmers white servants frequently differed little from that of black slaves. These findings suggest that, when applied in appropriate circumstances, lead studies of archaeological skeletal tissue may provide information supplemental to that derived from historical, archaeological, or other conventional sources.« less