The Succession of Bacterial Community Structure in Groundwater from a 250-m Gallery in the Horonobe Underground Research Laboratory

Ise, Kotaro; Sasaki, Yoshito; Amano, Yuki; Iwatsuki, Teruki; Nanjo, Isao; Asano, Takeshi; Yoshikawa, Hiroyuki

doi:10.1080/01490451.2016.1152329

Cited by 7 publications

(3 citation statements)

References 53 publications

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“…In this study, OTU004 exhibited a negative correlation with pH, which is consistent with a circumneutral optimal growth pH. It has been detected in sewage treatment facilities ( Auguet et al, 2015 ; Yan et al, 2015 ) and coal bed methane environments ( Guo et al, 2012 ), as well as in the deep subsurface ( Ise et al, 2016 ; Jangir et al, 2016 ). In QV1.2A, Group 1 [NiFe]-hydrogenase gene hyaB and the rbcL gene of RuBisCo were detected on contigs identified as Azonexus hydrophilus (Supplementary Dataset S1 ), suggesting that these Betaproteobacteria are involved in H 2 -oxidation and carbon fixation in the moderate wells.…”

Section: Discussionsupporting

confidence: 84%

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

et al. 2017

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Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

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Section: Discussionsupporting

confidence: 84%

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

et al. 2017

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“…In terms of VSB249, the gammaproteobacterial proportion mainly comprised the genera Ferribacterium , Rheinheimera , and Pseudomonas increased (Figure 3 ). The genus Rheinheimera has been reported from the deep terrestrial subsurface, including VSB249 (Ise et al, 2017 ). Since the genus Rheinheimera is aerobic (Brettar et al, 2002 ), its presence in VSB249 might be from drilling disturbance introducing O 2 .…”

Section: Resultsmentioning

confidence: 99%

Anaerobic methane‐oxidizing activity in a deep underground borehole dominantly colonized by Ca. Methanoperedenaceae

Nishimura

Kouduka

Fukuda

et al. 2023

Environ Microbiol Rep

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The family Ca. Methanoperedenaceae archaea mediates the anaerobic oxidation of methane (AOM) in different terrestrial environments. Using a newly developed high-pressure laboratory incubation system, we investigated 214-and 249-m deep groundwater samples at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Ca. Methanoperedenaceae archaea have been shown by genome-resolved metagenomics, respectively. The groundwater samples amended with 13 Clabelled methane and amorphous Fe(III) were incubated at a pressure of 1.6 MPa. After 3-7 days of incubation, the AOM rate was 45.8 ± 19.8 nM/day in 214-m groundwater. However, almost no activity was detected from 249-m groundwater. Based on the results from 16S rRNA gene analysis, the abundance of Ca. Methanoperedenaceae archaea was high in the 214-m deep groundwater sample, whereas Ca. Methanoperedenaceae archaea was undetected in the 249-m deep groundwater sample. These results support the in situ AOM activity of Ca. Methanoperedenaceae archaea in the 214-m deep subsurface borehole interval. Although the presence of Fe-bearing phyllosilicates was demonstrated in the 214-m deep groundwater, it needs to be determined whether Ca. Methanoperedenaceae archaea use the Fe-bearing phyllosilicates as in situ electron acceptors by high-pressure incubation amended with the Fe-bearing phyllosilicates.

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“…Several novel bacterial lineages in this ecosystem, including taxa with unusual chemoautotrophic pathways, appear to be unique to groundwater environments [13] and therefore may have potential utility in various areas of bio-technology. Microbial communities in these low-nutrient environments are extremely vulnerable to environmental change [9,10], hence these communities can be used to predict and assess the effect of various stressors on groundwater ecosystem health and services [14][15][16]. This is particularly important for island communities which are isolated by the sea and have limited capacity, hence more vulnerable to impacts from human activity and climate change.…”

Section: Introductionmentioning

confidence: 99%

Distinct bacterial communities in tropical island aquifers

et al. 2020

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The groundwater biome is a poorly characterized habitat hypothesized to harbor uniquely diverse bacterial communities; the degree to which these communities differ from associated soils is a central question in environmental microbiology. We characterized the Bacterial community composition in 37 aquifer and 32 surface soil samples across the island of O'ahu, Hawai'i. Several bacterial phyla (Acetothermia, Omnitrophica, Parcubacteria, Peregrinibacteria) relatively abundant in the aquifer samples were rare to absent in the soils. Immense bacterial diversity detected in the deep aquifers indicates that these environments are not as homogenous as expected, but provide various niches and energy sources for wide variety of bacteria. A small proportion of OTUs were widespread in all the basal (0.63%) and all the dike aquifer (0.31%) samples. However, these core bacteria comprised an average of 31.8% (ranging 16.2%-62.0%) and 15.4% (0.1%-31.5%) of all sequences isolated from the basal and dike aquifers respectively. Bacterial community composition correlated significantly with the sodium, sulfate, potassium, total dissolved solids, nitrate, conductivity, and pH in the basal aquifers, while phosphate and bicarbonate levels were also highly important when dike water samples were included in the analyses. This was consistent with high relative abundance of putative chemolithoautoroph taxa in the aquifer communities relative to soils. Targeted molecular and culture-based fecal indicator microbial analyses indicated good water quality of aquifers. The dominance of unique, deeply branching lineages in tropical aquifers emphasizes a large adaptive potential in O'ahu's aquifers; variability among groundwater samples suggests that aquifer habitats are surprisingly variable potentially harboring a variety of chemolithotrophic energy sources. Although parallel analyses of conventional and alternative indicators indicated good groundwater quality, this study calls for groundwater monitoring programs which would consider public as well as ecosystem health.

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The Succession of Bacterial Community Structure in Groundwater from a 250-m Gallery in the Horonobe Underground Research Laboratory

Cited by 7 publications

References 53 publications

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

Anaerobic methane‐oxidizing activity in a deep underground borehole dominantly colonized by Ca. Methanoperedenaceae

Distinct bacterial communities in tropical island aquifers

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