Influence of 16S rRNA Hypervariable Region on Estimates of Bacterial Diversity and Community Composition in Seawater and Marine Sediment

To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results

Microbial Selection and Survival in Subseafloor Sediment

Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial

Microbial Selection and Survival in Subseafloor Sediment

Many studies have examined relationships of microorganisms to geochemical zones in subseafloor sediment. However, responses to selective pressure and patterns of community succession with sediment depth have rarely been examined. Here we use 16S rDNA sequencing to examine the succession of microbial communities at sites in the Indian Ocean and the Bering Sea. The sediment ranges in depth from 0.16 to 332 m below seafloor and in age from 660 to 1,300,000 years. The majority of subseafloor taxonomic diversity is present in the shallowest depth sampled. The best predictor of sequence presence or absence in the oldest sediment is relative abundance in the near-seafloor sediment. This relationship suggests that perseverance of specific taxa into deep, old sediment is primarily controlled by the taxonomic abundance that existed when the sediment was near the seafloor. The operational taxonomic units that dominate at depth comprise a subset of the local seafloor community at each site, rather than a grown-in group of geographically widespread subseafloor specialists. At both sites, most taxa classified as abundant decrease in relative frequency with increasing sediment depth and age. Comparison of community composition to cell counts at the Bering Sea site indicates that the rise of the few dominant taxa in the deep subseafloor community does not require net replication, but might simply result from lower mortality relative to competing taxa on the long timescale of community burial

Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales

DNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given \u3e150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y

Substellar Companions to Main Sequence Stars: No Brown Dwarf Desert at Wide Separations

We use three field L and T dwarfs which were discovered to be wide companions to known stars by the Two Micron All-Sky Survey (2MASS) to derive a preliminary brown dwarf companion frequency. Observed L and T dwarfs indicate that brown dwarfs are not unusually rare as wide (Delta >1000 A.U.) systems to F-M0 main-sequence stars (M>0.5M_sun, M_V<9.5), even though they are rare at close separation (Delta <3 A.U.), the ``brown dwarf desert.'' Stellar companions in these separation ranges are equally frequent, but brown dwarfs are >~ 10 times as frequent for wide than close separations. A brown dwarf wide-companion frequency as low as the 0.5% seen in the brown dwarf desert is ruled out by currently-available observations.Comment: ApJL, in pres

A search for L dwarf binary systems

We present analysis of HST Planetary Camera images of twenty L dwarfs identified in the course of the Two Micron All-Sky Survey. Four of the targets have faint, red companions at separations between 0.07 and 0.29 arcseconds (1.6 to 7.6 AU). In three cases, the bolometric magnitudes of the components differ by less than 0.3 magnitudes. Since the cooling rate for brown dwarfs is a strong function of mass, similarity in luminosities implies comparable masses. The faint component in the 2M0850 system, however, is over 1.3 magnitudes fainter than the primary in the I-band, and ~0.8 magnitudes fainter in M(bol). Indeed, 2M0850B is ~0.8 magnitudes fainter in I than the lowest luminosity L dwarf currently known, while the absolute magnitude we deduce at J is almost identical with M_J for Gl 229B. Theoretical models indicate a mass ratio of \~0.75. The mean separation of the L dwarf binaries in the current sample is smaller by a factor of two than amongst M dwarfs. We discuss the implications of these results for the temperature scale in the L/T transition region and for the binary frequency amongst L dwarfs.Comment: 38 pages, 11 figures; accepted for A

Relationship of bacterial richness to organic degradation rate and sediment age in subseafloor sediment

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 4994-4999, doi:10.1128/AEM.00809-16.Subseafloor sediment hosts a large, taxonomically rich and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates to abundance-weighted community composition, but does not drive the vertical decrease in richness. Vertical patterns of richness at the open-ocean sites closely match organic degradation rates; both properties are highest near the seafloor and decline together as sediment depth increases. This relationship suggests that (i) total catabolic activity and/or electron donor diversity exerts a primary influence on bacterial richness in marine sediment, and (ii) many bacterial taxa that are poorly adapted for subseafloor sedimentary conditions are degraded in the geologically young sediment where respiration rates are high. Richness consistently takes a few hundred thousand years to decline from near-seafloor values to much lower values in deep anoxic subseafloor sediment, regardless of sedimentation rate, predominant terminal electron acceptor, or oceanographic context.This work, including the efforts of Mitchell L. Sogin and Steven D’Hondt, was funded by Sloan Foundation (Census of Deep Life). This work, including the efforts of Steven D’Hondt, was funded by U.S. Science Support Program for IODP. This work, including the efforts of Steven D’Hondt, was funded by National Science Foundation (NSF) (OCE- 0752336 and OCE-0939564). The work of E. A. Walsh, J. B. Kirkpatrick, R. Pockalny, and J. Sauvage was funded by the grants to S. D’Hondt

Moderate Resolution Spitzer Infrared Spectrograph (IRS) Observations of M, L, and T Dwarfs

We present 10 - 19 um moderate resolution spectra of ten M dwarfs, one L dwarf, and two T dwarf systems obtained with the Infrared Spectrograph (IRS) onboard the Spitzer Space Telescope. The IRS allows us to examine molecular spectroscopic features/lines at moderate spectral resolution in a heretofore untapped wavelength regime. These R~600 spectra allow for a more detailed examination of clouds, non-equilibrium chemistry, as well as the molecular features of H2O, NH3, and other trace molecular species that are the hallmarks of these objects. A cloud-free model best fits our mid-infrared spectrum of the T1 dwarf epsilon Indi Ba, and we find that the NH3 feature in epsilon Indi Bb is best explained by a non-equilibrium abundance due to vertical transport in its atmosphere. We examined a set of objects (mostly M dwarfs) in multiple systems to look for evidence of emission features, which might indicate an atmospheric temperature inversion, as well as trace molecular species; however, we found no evidence of either.Comment: 19 pages, 7 figures, accepted ApJ 1/12/0