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

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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Community Dynamics and Metabolic Potential of Petroleum-Degrading Microbes in the North West Shelf, Western Australia

10.3997/2214-4609.201902758 ◽

2019 ◽

Author(s):

Darren Cheah ◽

Kliti Grice ◽

Cornelia Wuchter ◽

Alan G. Scarlett ◽

Marco J. L. Coolen

Keyword(s):

Western Australia ◽

Community Dynamics ◽

Metabolic Potential ◽

North West ◽

The North

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Viruses of Polar Aquatic Environments

Viruses ◽

10.3390/v11020189 ◽

2019 ◽

Vol 11 (2) ◽

pp. 189 ◽

Cited By ~ 5

Author(s):

Sheree Yau ◽

Mansha Seth-Pasricha

Keyword(s):

Community Dynamics ◽

Spatial Scales ◽

Extreme Environments ◽

Cold Climate ◽

Polar Regions ◽

Microbial Life ◽

The North ◽

Cellular Life ◽

Antarctic Continent ◽

Cycling Of Nutrients

The poles constitute 14% of the Earth’s biosphere: The aquatic Arctic surrounded by land in the north, and the frozen Antarctic continent surrounded by the Southern Ocean. In spite of an extremely cold climate in addition to varied topographies, the polar aquatic regions are teeming with microbial life. Even in sub-glacial regions, cellular life has adapted to these extreme environments where perhaps there are traces of early microbes on Earth. As grazing by macrofauna is limited in most of these polar regions, viruses are being recognized for their role as important agents of mortality, thereby influencing the biogeochemical cycling of nutrients that, in turn, impact community dynamics at seasonal and spatial scales. Here, we review the viral diversity in aquatic polar regions that has been discovered in the last decade, most of which has been revealed by advances in genomics-enabled technologies, and we reflect on the vast extent of the still-to-be explored polar microbial diversity and its “enigmatic virosphere”.

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Metagenomics meets time series analysis: unraveling microbial community dynamics

Current Opinion in Microbiology ◽

10.1016/j.mib.2015.04.004 ◽

2015 ◽

Vol 25 ◽

pp. 56-66 ◽

Cited By ~ 196

Author(s):

Karoline Faust ◽

Leo Lahti ◽

Didier Gonze ◽

Willem M de Vos ◽

Jeroen Raes

Keyword(s):

Time Series ◽

Microbial Community ◽

Time Series Analysis ◽

Community Dynamics ◽

Series Analysis ◽

Microbial Community Dynamics

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Manganese in the world ocean: a first global model

10.5194/bg-2016-282 ◽

2016 ◽

Cited By ~ 1

Author(s):

Marco van Hulten ◽

Jean-Claude Dutay ◽

Rob Middag ◽

Hein de Baar ◽

Matthieu Roy-Barman ◽

...

Keyword(s):

Hydrothermal Vents ◽

Manganese Oxides ◽

High Surface ◽

World Ocean ◽

Essential Element ◽

Circulation Model ◽

Deep Ocean ◽

Global Scale ◽

Background Concentration ◽

The North

Abstract. Dissolved manganese (Mn) is a biologically essential element. Moreover, its oxidised form is involved in the removal of itself and several other trace elements from ocean waters. Recently, a large number of highly accurate Mn measurements has been obtained in the Atlantic, Indian and Arctic Oceans as part of the GEOTRACES programme. The goal of this study is to combine these new observations with state-of-the-art modelling to give new insights into the main sources and redistribution of Mn throughout the ocean. To this end, we simulate the distribution of dissolved Mn using a global-scale circulation model. Our model reproduces observations accurately and provides the following insights: – The high surface concentrations of manganese are caused by the combination of photoreduction and sources to the upper ocean. The most important sources are dust, then sediments, and, more locally, rivers. – Results show that surface Mn in the Atlantic Ocean moves downwards into the North Atlantic Deep Water, but because of strong removal rates the Mn does not propagate southwards. – There is a mostly homogeneous background concentration of dissolved Mn of about 0.10 nM to 0.15 nM throughout most of the deep ocean. The model reproduces this by means of a threshold on particulate manganese oxides of 25 pM, suggesting that a minimal concentration of particulate Mn is needed before aggregation and removal become efficient. – The observed sharp hydrothermal signals are produced by assuming both a high source and a strong removal of Mn near hydrothermal vents.

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All-In-One: Microbial Response to Natural and Anthropogenic Forcings in a Coastal Mediterranean Ecosystem, the Syracuse Bay (Ionian Sea, Italy)

Journal of Marine Science and Engineering ◽

10.3390/jmse10010019 ◽

2021 ◽

Vol 10 (1) ◽

pp. 19

Author(s):

Gabriella Caruso ◽

Maria Grazia Giacobbe ◽

Filippo Azzaro ◽

Franco Decembrini ◽

Marcella Leonardi ◽

...

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Community Dynamics ◽

Heterotrophic Bacteria ◽

Nutrient Concentrations ◽

Mediterranean Ecosystem ◽

Organic Substrates ◽

Metabolic Potential ◽

Microbial Response ◽

Phytoplankton Communities

Bacterial and phytoplankton communities are known to be in close relationships, but how natural and anthropogenic stressors can affect their dynamics is not fully understood. To study the response of microbial communities to environmental and human-induced perturbations, phytoplankton and bacterial communities were seasonally monitored in a Mediterranean coastal ecosystem, Syracuse Bay, where multiple conflicts co-exist. Quali-quantitative, seasonal surveys of the phytoplankton communities (diatoms, dinoflagellates and other taxa), the potential microbial enzymatic activity rates (leucine aminopeptidase, beta-glucosidase and alkaline phosphatase) and heterotrophic culturable bacterial abundance, together with the thermohaline structure and trophic status in terms of nutrient concentrations, phytoplankton biomass (as Chlorophyll-a), and total suspended and particulate organic matter, were carried out. The aim was to integrate microbial community dynamics in the context of the environmental characterization and disentangle microbial patterns related to natural changes from those driven by the anthropic impact on this ecosystem. In spite of the complex relationships between the habitat characteristics, microbial community abundance and metabolic potential, in Syracuse Bay, the availability of organic substrates differently originated by the local conditions appeared to drive the distribution and activity of microbial assemblage. A seasonal pattern of microbial abundances was observed, with the highest concentrations of phytoplankton in spring and low values in winter, whereas heterotrophic bacteria were more abundant during the autumn period. The autumn peaks of the rates of enzymatic activities suggested that not only phytoplankton-derived but also allochthonous organic polymers strongly stimulated microbial metabolism. Increased microbial response in terms of abundance and metabolic activities was detected especially at the sites directly affected by organic matter inputs related to agriculture or aquaculture activities. Nitrogen salts such as nitrate, rather than orthophosphate, were primary drivers of phytoplankton growth. This study also provides insights on the different seasonal scenarios of water quality in Syracuse Bay, which could be helpful for management plans of this Mediterranean coastal environment.

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Constructing the Microbial Association Network from Large-Scale Time Series Data Using Granger Causality

Genes ◽

10.3390/genes10030216 ◽

2019 ◽

Vol 10 (3) ◽

pp. 216 ◽

Cited By ~ 3

Author(s):

Dongmei Ai ◽

Xiaoxin Li ◽

Gang Liu ◽

Xiaoyi Liang ◽

Li Xia

Keyword(s):

Time Series ◽

Microbial Community ◽

Granger Causality ◽

Large Scale ◽

Community Dynamics ◽

Time Series Data ◽

Series Data ◽

Association Network ◽

Causal Relationships ◽

Network Analyses

The increasing availability of large-scale time series data allows the inference of microbial community dynamics by association network analysis. However, correlation-based association network analyses are noninformative of causal, mediating and time-dependent relationships between microbial community functional factors. To address this insufficiency, we introduced the Granger causality model to the analysis of a recent marine microbial time series dataset. We systematically constructed a directed acyclic network, representing both internal and external causal relationships among the microbial and environmental factors. We further optimized the network by removing false causal associations using the conditional Granger causality. The final network was visualized as a Granger graph, which was analyzed to identify causal relationships driven by key functional operators in the environment, such as Gammaproteobacteria, which was Granger caused by total organic nitrogen and primary production (p < 0.05 and Q < 0.05).

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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

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;

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Deep Learning for Autonomous Extraction of Millimeter-scale Deformation in InSAR Time Series

10.5194/egusphere-egu21-3569 ◽

2021 ◽

Author(s):

Bertrand Rouet-Leduc ◽

Romain Jolivet ◽

Manon Dalaison ◽

Paul Johnson ◽

Claudia Hulbert

Keyword(s):

Time Series ◽

Ground Deformation ◽

A Priori ◽

Active Faults ◽

Global Scale ◽

Geothermal Field ◽

The North ◽

Atmospheric Propagation ◽

Propagation Delays ◽

Deformation Dynamics

Systematically characterizing slip behaviours on active faults is key to unraveling the physics of tectonic faulting and the interplay between slow and fast earthquakes. Interferometric Synthetic Aperture Radar (InSAR), by enabling measurement of ground deformation at a global scale every few days, may hold the key to those interactions.&#160; However, atmospheric propagation delays often exceed ground deformation of interest despite state-of-the art processing, and thus InSAR analysis requires expert interpretation and a priori knowledge of fault systems, precluding global investigations of deformation dynamics.&#160; We show that a deep auto-encoder architecture tailored to untangle ground deformation from noise in InSAR time series autonomously extracts deformation signals, without prior knowledge of a fault's location or slip behaviour. Applied to InSAR data over the North Anatolian Fault, our method reaches &#160;2 mm detection, revealing a slow earthquake twice as extensive as previously recognized. We further explore the generalization of our approach to inflation/deflation-induced deformation, applying the same methodology to the geothermal field of Coso, California.&#160;

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

10.1101/171934 ◽

2017 ◽

Cited By ~ 1

Author(s):

Benjamin Tully ◽

Charles Geoff Wheat ◽

Brian T Glazer ◽

Julie Huber

Keyword(s):

Microbial Community ◽

Community Dynamics ◽

Carbon Fixation ◽

Biogeochemical Cycles ◽

Functional Redundancy ◽

Microbial Life ◽

Crustal Fluid ◽

Mid Atlantic Ridge ◽

Taxonomic Groups ◽

A Site

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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