Carbon and nitrogen assimilation in deep subseafloor microbial cells

Morono, Yuki; Terada, T.; Nishizawa, Manabu; Ito, Motoo; Hillion, F.; Takahata, Naoto; Sano, Yuji; Inagaki, Fumio

doi:10.1073/pnas.1107763108

Cited by 190 publications

(195 citation statements)

References 38 publications

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“…Interestingly, the majority of the cDNA transcripts were of bacterial origin, with fungal and archaeal transcripts formally minor components. What this study, and others, does confirm is that deep subsurface microbial communities are indeed active [55,57,59,60] and that metabolic activity and growth is apparently limited by energy and not the availability of carbon and nitrogen compounds [59]. It remains unclear, however, which archaea or bacteria mediate key trophic functions.…”

Section: Deep Subterranean Habitatssupporting

confidence: 62%

Metagenomics of extreme environments

Cowan¹,

Ramond²,

Makhalanyane³

et al. 2015

Current Opinion in Microbiology

112

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Whether they are exposed to extremes of heat, cold, or buried deep beneath the Earth"s surface, microorganisms have an uncanny ability to survive under these conditions. This ability to survive has fascinated scientists for nearly a century, but the recent development of metagenomics and "omics tools has allowed us to make huge leaps in understanding the remarkable complexity and versatility of extremophile communities. Here, in the context of the recently developed metagenomic tools, we discuss recent research on the community composition, adaptive strategies and biological functions of extremophiles.

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Section: Deep Subterranean Habitatssupporting

confidence: 62%

Metagenomics of extreme environments

Cowan¹,

Ramond²,

Makhalanyane³

et al. 2015

Current Opinion in Microbiology

112

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“…It was shown that genes carried by prophages affect host metabolism by providing metabolic facilities (Jiang and Paul, 1998) and might increase host cell fitness and survivability. For example, the integration of prophages in bacterial genomes can shut down host genes (Brussow et al, 2004) and might help to save energy, which appears to be of critical importance for survival in subsurface sediments (Morono et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

“…Their abundance was shown to be high in various marine sediments below the world's oceans (Parkes et al, 1994). Even though the organisms within deep-sea sediments have to cope with severe substrate and nutrient depletion (Jørgensen and D'Hondt, 2006), a large proportion of the microbial inhabitants were shown to be alive (Schippers et al, 2005;Morono et al, 2011). Furthermore, geochemical characteristics of deeper sediments indicate microbial activity as several chemical transformations are linked to microbial processes (Parkes et al, 2000;D'Hondt et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments

et al. 2012

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Bacteriophages might be the main 'predators' in the marine deep subsurface and probably have a major impact on indigenous microbial communities. To identify their function within this habitat, we have determined their abundance and distribution along the sediment columns of two continental margin and two open ocean sites that were recovered during Leg 201 of the Ocean Drilling Program. For all investigated sites, viral abundance followed the total cell numbers with a virus-to-cell ratio between 1 and 10 in the upper 100 mbsf (meters below seafloor). An increasing ratio of about 20 in deeper layers indicated an ongoing viral production in up to 11 Ma old sediments. We have used Rhizobium radiobacter as the most frequently isolated organism from the deep subsurface with a high in situ abundance to identify the frequency of associated rhizobiophages. In this study, 16S rRNA gene copies of R. radiobacter accounted for up to 5.6% of total bacterial 16S rRNA genes (average: 0.75%) as detected by quantitative PCR. A distinctive distribution was identified for R. radiobacter as indicated by a site-specific arrangement of genetically similar populations. Whole genome information of rhizobiophage RR1-A was used to generate a primer system for quantitative PCR specifically targeting the prophage antirepressor gene, indicative for temperate phages. The quantification of this gene within various sediment horizons showed a contribution of temperate phages of up to 14.3% to the total viral abundance. Thus, the high amount of temperate phages within the sediments and among all investigated isolates indicates that lysogeny is the main viral proliferation mode in deep subsurface populations.

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“…The organisms within deep-sea sediments have to cope with severe substrate and nutrient limitation (Jørgensen and D'Hondt, 2006) due to an increasing recalcitrance of organic matter with depth (Wellsbury et al, 1997). Even though prokaryotes are prone to starvation (Jørgensen and D'Hondt, 2006), the majority of the cells were shown to be alive and metabolically active (Schippers et al, 2005;Morono et al, 2011). The available energy per cell was estimated to be close to the minimum requirement for cell maintenance.…”

Section: Introductionmentioning

confidence: 99%

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments

et al. 2014

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Marine sediments cover two-thirds of our planet and harbor huge numbers of living prokaryotes. Long-term survival of indigenous microorganisms within the deep subsurface is still enigmatic, as sources of organic carbon are vanishingly small. To better understand controlling factors of microbial life, we have analyzed viral abundance within a comprehensive set of globally distributed subsurface sediments. Phages were detected by electron microscopy in deep (320 m below seafloor), ancient (B14 Ma old) and the most oligotrophic subsurface sediments of the world's oceans (South Pacific Gyre (SPG)). The numbers of viruses (10 4 -10 9 cm À 3 , counted by epifluorescence microscopy) generally decreased with sediment depth, but always exceeded the total cell counts. The enormous numbers of viruses indicate their impact as a controlling factor for prokaryotic mortality in the marine deep biosphere. The virus-to-cell ratios increased in deeper and more oligotrophic layers, exhibiting values of up to 225 in the deep subsurface of the SPG. High numbers of phages might be due to absorption onto the sediment matrix and a diminished degradation by exoenzymes. However, even in the oldest sediments, microbial communities are capable of maintaining viral populations, indicating an ongoing viral production and thus, viruses provide an independent indicator for microbial life in the marine deep biosphere.

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Carbon and nitrogen assimilation in deep subseafloor microbial cells

Cited by 190 publications

References 38 publications

Metagenomics of extreme environments

Metagenomics of extreme environments

Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments

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