Bacterial and Archaeal 16S rRNA Genes in Late Pleistocene to Holocene Muddy Sediments from the Kanto Plain of Japan

Takeuchi, Mio; Komai, Takeshi; Hanada, Satoshi; Tamaki, Hideyuki; Tanabe, Susumu; Miyachi, Yoshinori; Uchiyama, Masanori; Nakazawa, Tsutomu; Kimura, Katsumi; Kamagata, Yoichi

doi:10.1080/01490450802662355

Cited by 20 publications

(19 citation statements)

References 52 publications

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“…Uncultivated lineages within the bacterial phylum Chloroflexi were detected in surface sediment samples in relatively high abundance (Table T2); specifically, the vadinBA26 lineage was the most common group detected. Similar to the other groups mentioned above, highly related gene clones were detected in other samples described herein, as well as in marine sediment worldwide (e.g., Takeuchi et al, 2009;Durbin and Teske, 2011) (Fig. F5).…”

Section: Resultssupporting

confidence: 60%

“…Similar to the samples described above, candidate bacterial phyla BHI80-139 and JS1 and lineages within the phylum Chloroflexi (i.e., Napoli-4B-65, Sh765B-AG-111, and vadinBA26) were shared between these samples, and all groups were phylogenetically related to gene clones that have previously been identified from marine sediment (e.g., Li et al, 1999;Reed et al, 2002;Newberry et al, 2004;Inagaki et al, 2006;Takeuchi et al, 2009;Briggs et al, 2011;Durbin and Teske, 2011;Hoshino et al, 2011). Candidate bacterial phylum JS1 formed the most abundant group detected (3 of 17 clones) in the near-surface squeeze cake sample from Hole U1363G (Fig.…”

Section: Resultsmentioning

confidence: 84%

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Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

Jungbluth¹,

Johnson²,

Cowen³

et al. 2013

Proceedings of the IODP

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Microorganisms inhabiting sediment in close proximity to recharging basement outcrops are of interest because of the enhanced advective fluid flow in these locations, which is expected to exert unique selective pressures on the resident microbial communities. Here, Integrated Ocean Drilling Program (IODP) boreholes were used to access sediment microbial communities near Grizzly Bare recharge seamount on the Juan de Fuca Ridge eastern flank. The two locations examined in this study, Holes U1363G and U1363B, are 50 and 177 m away from the center of the outcrop, respectively. In general, small subunit ribosomal RNA gene clones from all three domains of life were detected; these groups were predominantly related to microorganisms known to reside in marine sediment. A large fraction of environmental gene clones recovered from Hole U1363B and U1363G sediment were related to uncultivated, candidate phyla of Bacteria such as BHI80-139, BRC1, JS1, OPB41, and TA06. Hole U1363B and U1363G sediment clone libraries were generally dominated by the domain Bacteria and particularly the phylum Chloroflexi, which comprised approximately one-quarter of the total gene clones identified. However, borehole sediment also contained several archaeal lineages that were phylogenetically affiliated with the Miscellanenous Crenarchaeotal Group. Eukaryotic fungi were only detected within the interstitial water sample from Hole U1363B. Finally, a minor portion of clones recovered from sediment in this study were also recovered from basement fluid samples previously characterized from Baby Bare discharge seamount and Ocean Drilling Program and IODP borehole Circulation Obviation Retrofit Kit Observatories (CORKs) in Holes 1026B and U1301A, which are ~50 km to the north-northeast.

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Section: Resultssupporting

confidence: 60%

Section: Resultsmentioning

confidence: 84%

Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

Jungbluth¹,

Johnson²,

Cowen³

et al. 2013

Proceedings of the IODP

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“…Among the modules, we observed intriguing cases where all or the majority of lineages have not been characterized before. An example is shown in Figure 3 (data from Heijs et al 2005;Inagaki et al 2006;Ley et al 2006;Lloyd et al 2006;Isenbarger et al 2008;Zhang et al 2008;Harrison et al 2009;Takeuchi et al 2009;Ghosh et al 2010)-five lineages that are co-occurring very specifically in certain marine sediments; they are from three distinct phyla, and each lineage is entirely uncharacterized. (A closer phylogenetic analysis revealed that the two Planctomycetes OTUs are related to each other, to the exclusion of other Planctomycetes lineages; they have been found also in other marine and freshwater environments, and our cooccurrence thus defines a more restricted home context for this lineage.)…”

Section: à9mentioning

confidence: 99%

A global network of coexisting microbes from environmental and whole-genome sequence data

Chaffron¹,

Rehrauer²,

Pernthaler³

et al. 2010

Genome Res.

440

322

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Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic organisms, their environmental preferences and ecological interdependencies remain difficult to assess, requiring laborious molecular surveys at diverse sampling sites. Here, we present a global meta-analysis of previously sampled microbial lineages in the environment. We grouped publicly available 16S ribosomal RNA sequences into operational taxonomic units at various levels of resolution and systematically searched these for co-occurrence across environments. Naturally occurring microbes, indeed, exhibited numerous, significant interlineage associations. These ranged from relatively specific groupings encompassing only a few lineages, to larger assemblages of microbes with shared habitat preferences. Many of the coexisting lineages were phylogenetically closely related, but a significant number of distant associations were observed as well. The increased availability of completely sequenced genomes allowed us, for the first time, to search for genomic correlates of such ecological associations. Genomes from coexisting microbes tended to be more similar than expected by chance, both with respect to pathway content and genome size, and outliers from these trends are discussed. We hypothesize that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.

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“…DNAs were extracted from 10 g of sediment sample using a PowerSoil DNA Isolation Kit (MOBIO) according to the manufacture's recommended protocol. The bacterial 16S rRNA genes were amplified from DNA, cloned, and sequenced as previously described [21]. Partial sequences (>420 bp) were analyzed by using the ARB program package, as described previously [21].…”

Section: Bacterial Community Analysismentioning

confidence: 99%

Characterization of humic acids in sediments from dam reservoirs by pyrolysis-gas chromatography/mass spectrometry using tetramethylammonium hydroxide: Influence of the structural features of humic acids on iron(II) binding capacity

Fukushima

Furubayashi

Fujisawa

et al. 2011

Journal of Analytical and Applied Pyrolysis

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Bacterial and Archaeal 16S rRNA Genes in Late Pleistocene to Holocene Muddy Sediments from the Kanto Plain of Japan

Cited by 20 publications

References 52 publications

Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

Data report: microbial diversity in sediment near Grizzly Bare Seamount in Holes U1363B and U1363G

A global network of coexisting microbes from environmental and whole-genome sequence data

Characterization of humic acids in sediments from dam reservoirs by pyrolysis-gas chromatography/mass spectrometry using tetramethylammonium hydroxide: Influence of the structural features of humic acids on iron(II) binding capacity

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