Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico

Characterization by culture and molecular analysis of the microbial diversity of a deep subsurface gas storage aquifer

Research in Microbiology ◽

10.1016/j.resmic.2008.10.010 ◽

2009 ◽

Vol 160 (2) ◽

pp. 107-116 ◽

Cited By ~ 38

Author(s):

Odile Basso ◽

Jean-François Lascourreges ◽

François Le Borgne ◽

Cyril Le Goff ◽

Michel Magot

Keyword(s):

Microbial Diversity ◽

Molecular Analysis ◽

Gas Storage ◽

Deep Subsurface

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A global perspective on microbial diversity in the terrestrial deep subsurface

10.1101/602672 ◽

2019 ◽

Cited By ~ 1

Author(s):

A. Soares ◽

A. Edwards ◽

D. An ◽

A. Bagnoud ◽

M. Bomberg ◽

...

Keyword(s):

Microbial Diversity ◽

Meta Analysis ◽

Global Perspective ◽

Rrna Gene ◽

Sequencing Data ◽

Deep Subsurface ◽

Rock Types ◽

Marine Habitats ◽

Terrestrial Subsurface ◽

Metabolic Strategies

SummaryWhile recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12% to 20% of Earth’s bacterial and archaeal biomass is suggested to inhabit the terrestrial deep subsurface, compared to ∼1.8% in the deep subseafloor1–3. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities4–6. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Here, we show the diversity of bacterial communities in deep subsurface groundwater is controlled by aquifer lithology globally, by using 16S rRNA gene datasets collected across five countries on two continents and from fifteen rock types over the past decade. Furthermore, our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, likely as a function of the diverse metabolic strategies of these taxa. Despite this similarity, evidence was found not only for aquifer-specific microbial communities, but also for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacterial OTUs across the localities. This finding implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, that may play an important role in colonising and sustaining microbial habitats in the deep terrestrial subsurface. Anin-silicocontamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

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Microbial Diversity in Deep-Subsurface Hot Brines of Northwest Poland: from Community Structure to Isolate Characteristics

Applied and Environmental Microbiology ◽

10.1128/aem.00252-20 ◽

2020 ◽

Vol 86 (10) ◽

Author(s):

Agnieszka Kalwasińska ◽

Arkadiusz Krawiec ◽

Edyta Deja-Sikora ◽

Marcin Gołębiewski ◽

Przemysław Kosobucki ◽

...

Keyword(s):

Community Structure ◽

16S Rrna ◽

Microbial Diversity ◽

High Throughput Sequencing ◽

Rrna Gene ◽

Deep Subsurface ◽

Content Type ◽

Microbial Life ◽

Bacillus Paralicheniformis ◽

Low Diversity

ABSTRACT Deep-subsurface hot brines in northwest Poland, extracted through boreholes reaching 1.6 and 2.6 km below the ground surface, were microbiologically investigated using culture-independent and culture-dependent methods. The high-throughput sequencing of 16S rRNA gene amplicons showed a very low diversity of bacterial communities, which were dominated by phyla Proteobacteria and Firmicutes. Bacterial genera potentially involved in sulfur oxidation and nitrate reduction (Halothiobacillus and Methylobacterium) prevailed in both waters over the sulfate reducers (“Candidatus Desulforudis” and Desulfotomaculum). Only one archaeal taxon, affiliated with the order Thermoplasmatales, was detected in analyzed samples. Bacterial isolates obtained from these deep hot brines were closely related to Bacillus paralicheniformis based on the 16S rRNA sequence similarity. However, genomic and physiological analyses made for one of the isolates, Bacillus paralicheniformis strain TS6, revealed the existence of more diverse metabolic pathways than those of its moderate-temperature counterpart. These specific traits may be associated with the ecological adaptations to the extreme habitat, which suggest that some lineages of B. paralicheniformis are halothermophilic. IMPORTANCE Deep-subsurface aquifers, buried thousands of meters down the Earth’s crust, belong to the most underexplored microbial habitats. Although a few studies revealed the existence of microbial life at the depths, the knowledge about the microbial life in the deep hydrosphere is still scarce due to the limited access to such environments. Studying the subsurface microbiome provides unique information on microbial diversity, community structure, and geomicrobiological processes occurring under extreme conditions of the deep subsurface. Our study shows that low-diversity microbial assemblages in subsurface hot brines were dominated by the bacteria involved in biogeochemical cycles of sulfur and nitrogen. Based on genomic and physiological analyses, we found that the Bacillus paralicheniformis isolate obtained from the brine under study differed from the mesophilic species in the presence of specific adaptations to harsh environmental conditions. We indicate that some lineages of B. paralicheniformis are halothermophilic, which was not previously reported.

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