Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades

Lee, Michael D.; Walworth, Nathan G.; Sylvan, Jason B.; Edwards, Katrina J.; Orcutt, Beth N.

doi:10.3389/fmicb.2015.01470

Cited by 49 publications

(70 citation statements)

References 66 publications

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“…This difference was stark, but not unexpected due to the intrinsic variability between the chemistry, mineralogy and porosity of the respective environments. Major differences between free‐floating and surface‐adhered in microbial community structures have also been observed in soil and groundwater environments (Bougon et al ., ), seafloor and pelagic environments (Lozupone and Knight, ; Lee et al ., ) and biofilms within industrial water systems (Hong et al ., ).…”

Section: Resultsmentioning

confidence: 99%

“…In ocean drilling investigations, it has become relatively routine to extract genomic DNA from deep biosphere sediment core samples and corresponding pore fluids (e.g., Jungbluth et al, 2012;Lee et al, 2015). However, in the terrestrial realm, this is the first high-throughput 16S rRNA sequencing study of deep subsurface fluid and corresponding host rock.…”

Section: Discussionmentioning

confidence: 99%

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Major phylum‐level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface

Momper

Reese

Zinke

et al. 2017

Environ Microbiol Rep

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Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines and sampling of deeply sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply circulating groundwater and corresponding host rock (at a depth of 1.45 km below ground surface). Pyrotag DNA sequencing of the 16S rRNA gene revealed diverse communities of putative chemolithoautotrophs, aerobic and anaerobic heterotrophs, numerous candidate phyla and unique rock-associated microbial assemblage. There was a clear and near-total separation of communities between SURF deeply circulating fracture fluids and SURF host-rocks. Sequencing data from SURF compared against five similarly sequenced terrestrial subsurface sites in Europe and North America revealed classes Clostridia and Betaproteobacteria were dominant in terrestrial fluids. This study presents a unique analysis showing differences in terrestrial subsurface microbial communities between fracture fluids and host rock through which those fluids permeate.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Major phylum‐level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface

Momper

Reese

Zinke

et al. 2017

Environ Microbiol Rep

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“…Because of its coarse nature as a community-level summary, diversity analyses are especially relevant to studies of novel ecological communities. Lee et al (2015) collected and analyzed microbial communities living on seafloor rocks on the Dorado Outcrop, an area of exposed basalt on the East Pacific Rise. Hydrothermal vents such as the Dorado Outcrop inform our understanding of microbe-mineral interactions in the subsurface.…”

Section: Estimation Error Is Stable Across Large Communitiesmentioning

confidence: 99%

“…Samples were collected from the seafloor rock, including lithified carbonate ("carbonate," n = 1), glassy, altered basalts ("glassy," n = 4), and highly altered basalts ("altered," n = 8). Analysis of the microbial communities on these rocks revealed 1490 distinct microbial taxa after filtering for low quality sequences (see Lee et al (2015) and Lee (2018) for details surrounding sequencing and construction of the abundance table). Here we investigate if the community-level structure differs between the different rock types.…”

Section: Estimation Error Is Stable Across Large Communitiesmentioning

confidence: 99%

“…Fig 6. The log-ratio model described in Section 3 can only be fit to data with a minimum abundance greater than zero. Abundance data for microbiome studies is generally sparse, and 46% of the observed abundances of the Lee et al (2015) dataset are zero. For this reason, it is common to add a perturbation offset p to the observed abundance table before fitting the log-ratio model.…”

Section: Estimation Error Is Stable Across Large Communitiesmentioning

confidence: 99%

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DivNet: Estimating diversity in networked communities

Willis¹,

Bd²

2018

Preprint

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Diversity is a marker of ecosystem health in ecology, microbiology and immunology, with implications for disease diagnosis and infection resistance. However, accurately comparing diversity across environmental gradients is challenging, especially when number of different taxonomic groups in the community is large. Furthermore, existing approaches to estimating diversity do not perform well when the taxonomic groups in the community interact via an ecological network, such as by competing within their niche, or with mutualistic relationships. To address this, we propose DivNet, a method for estimating within-and between-community diversity in ecosystems where taxa interact via an ecological network. In particular, accounting for network structure permits more accurate estimates of alphaand beta-diversity, even in settings with a large number of taxa and a small number of samples. DivNet is fast, accurate, precise, performs well with large numbers of taxa, and is robust to both weakly and strongly networked communities. We show that the advantages of incorporating taxon interactions into diversity estimation are especially clear in analyzing microbiomes and other high-diversity, strongly networked ecosystems. Therefore, to illustrate the method, we analyze the microbiome of seafloor basalts based on a 16S amplicon sequencing dataset with 1490 taxa and 13 samples.

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Impacts of deep‐sea mining on microbial ecosystem services

Orcutt

Bradley

Brazelton

et al. 2020

Limnology & Oceanography

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Interest in extracting mineral resources from the seafloor through deep-sea mining has accelerated in the past decade, driven by consumer demand for various metals like zinc, cobalt, and rare earth elements. While there are ongoing studies evaluating potential environmental impacts of deep-sea mining activities, these focus primarily on impacts to animal biodiversity. The microscopic spectrum of seafloor life and the services that this life provides in the deep sea are rarely considered explicitly. In April 2018, scientists met to define the microbial ecosystem services that should be considered when assessing potential impacts of deep-sea mining, and to provide recommendations for how to evaluate and safeguard these services. Here, we indicate that the potential impacts of mining on microbial ecosystem services in the deep sea vary substantially, from minimal expected impact to loss of services that cannot be remedied by protected area offsets. For example, we (1) describe potential major losses of microbial ecosystem services at active hydrothermal vent habitats impacted by mining, (2) speculate that there could be major ecosystem service degradation at inactive massive sulfide deposits without extensive mitigation efforts, (3) suggest minor impacts to carbon sequestration within manganese nodule fields coupled with potentially important impacts to primary production capacity, and (4) surmise that assessment of impacts to microbial ecosystem services at seamounts with ferromanganese crusts is too poorly understood to be definitive. We conclude by recommending that baseline assessments of microbial diversity, biomass, and, importantly, biogeochemical function need to be considered in environmental impact assessments of deep-sea mining.With increasing demand for rare and critical metals-such as cobalt, copper, manganese, tellurium, and zinc-there is increasing interest in mining these resources from the seafloor (Hein et al. 2013; Wedding et al. 2015;Thompson et al. 2018). The primary mineral resources in the deep sea that attract attention fall into four categories (Figs. 1, 2): (1) massive sulfide deposits created at active high-temperature hydrothermal vent systems along mid-ocean ridges, back-arc spreading centers, and volcanic arcs, from the mixing of mineral-rich, advecting hydrothermal fluids with bottom seawater; (2) similar deposits at inactive hydrothermal vent sites, where fluid advection has ceased but mineral deposits remain; (3) polymetallic nodules that form on the seafloor of the open ocean

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Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades

Cited by 49 publications

References 66 publications

Major phylum‐level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface

Major phylum‐level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface

DivNet: Estimating diversity in networked communities

Impacts of deep‐sea mining on microbial ecosystem services

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