A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized genomic reconstruction of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement. Twenty-one samples were collected during a two-year period at three different depths and two locations with the basaltic aquifer to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the two years, yet a dynamic microbial community was present in the crustal fluids that underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the dataset and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in a diverse group of microorganisms. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes and alternative electron acceptors. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles.

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A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

Scientific Reports ◽

10.1038/srep22541 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 31

Author(s):

Julie L. Meyer ◽

Ulrike Jaekel ◽

Benjamin J. Tully ◽

Brian T. Glazer ◽

C. Geoffrey Wheat ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Elevated Temperatures ◽

Geochemical Composition ◽

Crustal Fluid ◽

Functional Potential ◽

Mid Atlantic Ridge ◽

Bacterial Groups ◽

Insight Into

Abstract The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.

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Biogeochemical cycles and microbial community dynamics in replicate woodchip bioreactors

10.31274/etd-20210609-166 ◽

2021 ◽

Author(s):

Abby Elizabeth Schaefer

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Biogeochemical Cycles ◽

Microbial Community Dynamics

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The effect of stream microbial inoculation on in-stream carbon processing

10.5194/egusphere-egu2020-20555 ◽

2020 ◽

Author(s):

Jakob Schelker ◽

Florian Caillon ◽

Katharina Besemer ◽

Peter Peduzzi ◽

Astrid Harjung

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Soil Microbes ◽

Microbial Community Composition ◽

Microbial Life ◽

Soil Microbial ◽

Microbial Inoculation ◽

Microbial Community Dynamics ◽

Small Streams ◽

Carbon Processing

<p>Hydrological events mobilize chemically diverse dissolved organic matter (DOM) from soils to streams. Further, such events can also cause an influx of soil microbial life into fluvial systems. Here we present results from the HYDRO-DIVERSITY project, which aims to investigate the dynamic transfer of DOM and microbial life from catchment soils to streams, as well as their downstream fate. We studied the microbial community composition and DOM quality using 16S Illumina sequencing and fluorescence and absorbance spectroscopy. Data from small streams showed strong changes in DOM composition and in the microbial community delivered from soils during hydrological events. Moreover, we performed a flume experiment, in which soil microbial inoculation and the processing of DOM across different biofilm ages were evaluated. As such, biofilm age did not directly affect the establishment of soil microbes in the stream ecosystem. However, in-stream processing of soil DOM appeared to be affected by the inoculation event. This poses the fundamental question, if the processing of DOM in streams and rivers depends on the transient presence of specific soil microbes in stream ecosystems. Overall our results show that soils provide a dynamic and relevant influx of microbes and DOM to first order streams and that this dynamic influx likely affects microbial community dynamics of downstream fluvial networks as well as in-stream DOM processing.&#160;</p>

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Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

10.1101/2020.08.03.235341 ◽

2020 ◽

Author(s):

L.M. Seyler ◽

E. Trembath-Reichert ◽

B.J. Tully ◽

J.A. Huber

Keyword(s):

Time Series ◽

Microbial Community ◽

Community Dynamics ◽

Deep Ocean ◽

Transcript Abundance ◽

Global Scale ◽

Low Oxygen ◽

Metabolic Potential ◽

Microbial Life ◽

The North

AbstractThe rock-hosted oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment that is representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. The data suggest that the microbial community in this subseafloor habitat is motile, chiefly heterotrophic or mixotrophic, and capable of using alternative electron acceptors such as nitrate and thiosulfate, in addition to oxygen. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. Together, our results indicate the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust, and is also metabolically flexible, with the ability to switch from autotrophy to heterotrophy, as well as function under low oxygen conditions. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.

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Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community

The ISME Journal ◽

10.1038/s41396-020-00843-4 ◽

2020 ◽

Author(s):

Lauren M. Seyler ◽

Elizabeth Trembath-Reichert ◽

Benjamin J. Tully ◽

Julie A. Huber

Keyword(s):

Time Series ◽

Microbial Community ◽

Community Dynamics ◽

Deep Ocean ◽

Transcript Abundance ◽

Global Scale ◽

Low Oxygen ◽

Metabolic Potential ◽

Microbial Life ◽

The North

AbstractThe oceanic crustal aquifer is one of the largest habitable volumes on Earth, and it harbors a reservoir of microbial life that influences global-scale biogeochemical cycles. Here, we use time series metagenomic and metatranscriptomic data from a low-temperature, ridge flank environment representative of the majority of global hydrothermal fluid circulation in the ocean to reconstruct microbial metabolic potential, transcript abundance, and community dynamics. We also present metagenome-assembled genomes from recently collected fluids that are furthest removed from drilling disturbances. Our results suggest that the microbial community in the North Pond aquifer plays an important role in the oxidation of organic carbon within the crust. This community is motile and metabolically flexible, with the ability to use both autotrophic and organotrophic pathways, as well as function under low oxygen conditions by using alternative electron acceptors such as nitrate and thiosulfate. Anaerobic processes are most abundant in subseafloor horizons deepest in the aquifer, furthest from connectivity with the deep ocean, and there was little overlap in the active microbial populations between sampling horizons. This work highlights the heterogeneity of microbial life in the subseafloor aquifer and provides new insights into biogeochemical cycling in ocean crust.

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Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

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