Breier John A.

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Breier

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John A.

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0000-0002-3591-5548

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Mineral phase analysis of deep-sea hydrothermal particulates by a Raman spectroscopy expert algorithm : toward autonomous in situ experimentation and exploration

(American Geophysical Union, 2009-05-14) Breier, John A. ; German, Christopher R. ; White, Sheri N.

This paper demonstrates that a Raman spectroscopy, point-counting technique can be used for phase analysis of minerals commonly found in deep-sea hydrothermal plumes, even for minerals with similar chemical compositions. It also presents our robust autonomous identification algorithm and spectral database, both of which were developed specifically for deep-sea hydrothermal studies. The Raman spectroscopy expert algorithm was developed and tested against multicomponent mixtures of minerals relevant to the deep-sea hydrothermal environment. It is intended for autonomous classification where many spectra must be examined with little or no human involvement to increase analytic precision, accuracy, and data volume or to enable in situ measurements and experimentation.
Biogeochemical processes at hydrothermal vents : microbes and minerals, bioenergetics, and carbon fluxes

(The Oceanography Society, 2012-03) Holden, James F. ; Breier, John A. ; Rogers, Karyn L. ; Schulte, Mitchell D. ; Toner, Brandy M.

Hydrothermal vents are among the most biologically active regions of the deep ocean. However, our understanding of the limits of life in this extreme environment, the extent of biogeochemical transformation that occurs in the crust and overlying ocean, and the impact of vent life on regional and global ocean chemistry is in its infancy. Recently, scientific studies have expanded our view of how vent microbes gain metabolic energy at vents through their use of dissolved chemicals and minerals contained in ocean basalts, seafloor sulfide deposits, and hydrothermal plumes and, in turn, how they catalyze chemical and mineral transformations. The scale of vent environments and the difficulties inherent in the study of life above, on, and below the deep seafloor have led to the development of geochemical and bioenergetic models. These models predict habitability and biological activity based on the chemical composition of hydrothermal fluids, seawater, and the surrounding rock, balanced by the physiological energy demand of cells. This modeling, coupled with field sampling for ground truth and discovery, has led to a better understanding of how hydrothermal vents affect the ocean and global geochemical cycles, and how they influence our views of life on the early Earth and the search for life beyond our own planet.
Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea sulfur-oxidizing bacteria

( 2012-11-08) Anantharaman, Karthik ; Breier, John A. ; Sheik, Cody S. ; Dick, Gregory J.

Hydrothermal vents are a well-known source of energy that powers chemosynthesis in the deep sea. Recent work suggests that microbial chemosynthesis is also surprisingly pervasive throughout the dark oceans, serving as a significant CO2 sink even at sites far-removed from vents. Ammonia and sulfur have been identified as potential electron donors for this chemosynthesis, but they do not fully account for measured rates of dark primary production in the pelagic water column. Here we use metagenomic and metatranscriptomic analyses to show that deep-sea populations of the SUP05 group of uncultured sulfur oxidizing Gammaproteobacteria, which are abundant in widespread and diverse marine environments, contain and highly express genes encoding group 1 Ni-Fe hydrogenase enzymes for H2 oxidation. Reconstruction of near-complete genomes of two co-occurring SUP05 populations in hydrothermal plumes and deep waters of the Gulf of California enabled detailed population-specific metatranscriptomic analyses, revealing dynamic patterns of gene content and transcript abundance. SUP05 transcripts for genes involved in H2 and sulfur oxidation are most abundant in hydrothermal plumes where these electron donors are enriched. In contrast, a second hydrogenase has more abundant transcripts in background deep sea samples. Coupled with results from a bioenergetic model that suggest that H2 oxidation can contribute significantly to the SUP05 energy budget, these findings reveal the potential importance of H2 as a key energy source in the deep ocean. This study also highlights the genomic plasticity of SUP05, which enables this widely distributed group to optimize its energy metabolism (electron donor and acceptor) to local geochemical conditions.
Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea

(Nature Publishing Group, 2015-11-17) Li, Meng ; Baker, Brett J. ; Anantharaman, Karthik ; Jain, Sunit ; Breier, John A. ; Dick, Gregory J.

Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.
Using carbon isotope fractionation to constrain the extent of methane dissolution into the water column surrounding a natural hydrocarbon gas seep in the northern Gulf of Mexico

(American Geophysical Union, 2018-10-20) Leonte, Mihai ; Wang, Binbin ; Socolofsky, Scott A. ; Mau, Susan ; Breier, John A. ; Kessler, John D.

A gas bubble seep located in the northern Gulf of Mexico was investigated over several days to determine whether changes in the stable carbon isotopic ratio of methane can be used as a tracer for methane dissolution through the water column. Gas bubble and water samples were collected at the seafloor and throughout the water column for isotopic ratio analysis of methane. Our results show that changes in methane isotopic ratios are consistent with laboratory experiments that measured the isotopic fractionation from methane dissolution. A Rayleigh isotope model was applied to the isotope data to determine the fraction of methane dissolved at each depth. On average, the fraction of methane dissolved surpasses 90% past an altitude of 400 m above the seafloor. Methane dissolution was also investigated using a modified version of the Texas A&M Oil spill (Outfall) Calculator (TAMOC) where changes in methane isotopic ratios could be calculated. The TAMOC model results show that dissolution depends on depth and bubble size, explaining the spread in measured isotopic ratios during our investigations. Both the Rayleigh and TAMOC models show that methane bubbles quickly dissolve following emission from the seafloor. Together, these results show that it is possible to use measurements of natural methane isotopes to constrain the extent of methane dissolution following seafloor emission.
Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems

(Public Library of Science, 2015-03-11) Scott, Jarrod J. ; Breier, John A. ; Luther, George W. ; Emerson, David

Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.
Sulfur oxidation genes in diverse deep-sea viruses

( 2014-04) Anantharaman, Karthik ; Duhaime, Melissa B. ; Breier, John A. ; Wendt, Kathleen A. ; Toner, Brandy M. ; Dick, Gregory J.

Viruses are the most abundant biological entities in the oceans and a pervasive cause of mortality of microorganisms that drive biogeochemical cycles. Although the ecological and evolutionary impacts of viruses on marine phototrophs are well-recognized, little is known about their impact on ubiquitous marine lithotrophs. Here we report 18 genome sequences of double-stranded DNA viruses that putatively infect widespread sulfur-oxidizing bacteria. Fifteen of these viral genomes contain auxiliary metabolic genes for the alpha and gamma subunits of reverse dissimilatory sulfite reductase (rdsr). This enzyme oxidizes elemental sulfur, which is abundant in the hydrothermal plumes studied here. Our findings implicate viruses as a key agent in the sulfur cycle and as a reservoir of genetic diversity for bacterial enzymes that underpin chemosynthesis in the deep oceans.
Particle dynamics in the rising plume at Piccard Hydrothermal Field, Mid-Cayman Rise

(John Wiley & Sons, 2015-08-25) Estapa, Margaret L. ; Breier, John A. ; German, Christopher R.

Processes active in rising hydrothermal plumes, such as precipitation, particle aggregation, and biological growth, affect particle size distributions and can exert important influences on the biogeochemical impact of submarine venting of iron to the oceans and their sediments. However, observations to date of particle size distribution within these systems are both limited and conflicting. In a novel buoyant hydrothermal plume study at the recently discovered high-temperature (398°C) Piccard Hydrothermal Field, Mid-Cayman Rise, we report optical measurements of particle size distributions (PSDs). We describe the plume PSD in terms of a simple, power-law model commonly used in studies of upper and coastal ocean particle dynamics. Observed PSD slopes, derived from spectral beam attenuation and laser diffraction measurements, are among the highest found to date anywhere in the ocean and ranged from 2.9 to 8.5. Beam attenuation at 650 nm ranged from near zero to a rarely observed maximum of 192 m−1 at 3.5 m above the vent. We did not find large (>100 μm) particles that would settle rapidly to the sediments. Instead, beam attenuation was well-correlated to total iron, suggesting the first-order importance of particle dilution, rather than precipitation or dissolution, in the rising plume at Piccard. Our observations at Piccard caution against the assumption of rapid deposition of hydrothermal, particulate metal fluxes, and illustrate the need for more particle size and composition measurements across a broader range of sites, globally.
Observations of bubbles in natural seep flares at MC 118 and GC 600 using in situ quantitative imaging

(John Wiley & Sons, 2016-04-02) Wang, Binbin ; Socolofsky, Scott ; Breier, John A. ; Seewald, Jeffrey S.

This paper reports the results of quantitative imaging using a stereoscopic, high-speed camera system at two natural gas seep sites in the northern Gulf of Mexico during the Gulf Integrated Spill Research G07 cruise in July 2014. The cruise was conducted on the E/V Nautilus using the ROV Hercules for in situ observation of the seeps as surrogates for the behavior of hydrocarbon bubbles in subsea blowouts. The seeps originated between 890 and 1190 m depth in Mississippi Canyon block 118 and Green Canyon block 600. The imaging system provided qualitative assessment of bubble behavior (e.g., breakup and coalescence) and verified the formation of clathrate hydrate skins on all bubbles above 1.3 m altitude. Quantitative image analysis yielded the bubble size distributions, rise velocity, total gas flux, and void fraction, with most measurements conducted from the seafloor to an altitude of 200 m. Bubble size distributions fit well to lognormal distributions, with median bubble sizes between 3 and 4.5 mm. Measurements of rise velocity fluctuated between two ranges: fast-rising bubbles following helical-type trajectories and bubbles rising about 40% slower following a zig-zag pattern. Rise speed was uncorrelated with hydrate formation, and bubbles following both speeds were observed at both sites. Ship-mounted multibeam sonar provided the flare rise heights, which corresponded closely with the boundary of the hydrate stability zone for the measured gas compositions. The evolution of bubble size with height agreed well with mass transfer rates predicted by equations for dirty bubbles.
Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes

(Springer Nature, 2023-05-13) Zhou, Zhichao ; Tran, Patricia Q. ; Adams, Alyssa M. ; Kieft, Kristopher ; Breier, John A. ; Fortunato, Caroline S. ; Sheik, Cody S. ; Huber, Julie A. ; Li, Meng ; Dick, Gregory J. ; Anantharaman, Karthik

In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients, and trace metals. However, the impacts of plume biogeochemistry on the oceans are poorly constrained due to a lack of integrated understanding of microbiomes, population genetics, and geochemistry. Here, we use microbial genomes to understand links between biogeography, evolution, and metabolic connectivity, and elucidate their impacts on biogeochemical cycling in the deep sea. Using data from 36 diverse plume samples from seven ocean basins, we show that sulfur metabolism defines the core microbiome of plumes and drives metabolic connectivity in the microbial community. Sulfur-dominated geochemistry influences energy landscapes and promotes microbial growth, while other energy sources influence local energy landscapes. We further demonstrated the consistency of links among geochemistry, function, and taxonomy. Amongst all microbial metabolisms, sulfur transformations had the highest MW-score, a measure of metabolic connectivity in microbial communities. Additionally, plume microbial populations have low diversity, short migration history, and gene-specific sweep patterns after migrating from background seawater. Selected functions include nutrient uptake, aerobic oxidation, sulfur oxidation for higher energy yields, and stress responses for adaptation. Our findings provide the ecological and evolutionary bases of change in sulfur-driven microbial communities and their population genetics in adaptation to changing geochemical gradients in the oceans.
Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents

( 2014-01) Li, Meng ; Toner, Brandy M. ; Baker, Brett J. ; Breier, John A. ; Sheik, Cody S. ; Dick, Gregory J.

Deep-sea hydrothermal vents are a significant source of oceanic iron. Although hydrothermal iron rapidly precipitates as inorganic minerals upon mixing with seawater, it can be stabilized by organic matter and dispersed more widely than previously recognized. The nature and source of this organic matter is unknown. Here we show that microbial genes involved in cellular iron uptake are highly expressed in the Guaymas Basin deep-sea hydrothermal plume. The nature of these microbial iron transporters, taken together with the low concentration of dissolved iron and abundance of particulate iron in the plume, indicates that iron minerals are the target for this microbial scavenging and uptake. Our findings indicate that cellular iron uptake is a major process in plume microbial communities and suggest new mechanisms for generating Fe-C complexes. This “microbial iron pump” could represent an important mode of converting hydrothermal iron into bioavailable forms that can be dispersed through the oceans.

Breier John A.

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