Publications

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    ABSTRACT: During the past decade, the IODP (International Ocean Discovery Program) has fostered a significant increase in deep biosphere investigations in the marine sedimentary and crustal environments, and scientists are well-poised to continue this momentum into the next phase of the IODP. The goals of this workshop were to evaluate recent findings in a global context, synthesize available biogeochemical data to foster thermodynamic and metabolic activity modeling and measurements, identify regional targets for future targeted sampling and dedicated expeditions, foster collaborations, and highlight the accomplishments of deep biosphere research within IODP. Twenty-four scientists from around the world participated in this one-day workshop sponsored by IODP-MI and held in Florence, Italy, immediately prior to the Goldschmidt 2013 conference. A major topic of discussion at the workshop was the continued need for standard biological sampling and measurements across IODP platforms. Workshop participants renew the call to IODP operators to implement recommended protocols.
    03/2014;
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    ABSTRACT: Rising CO2 concentration in the atmosphere, global climate change, and the sustainability of the Earth's biosphere are great societal concerns for the 21st century. Global climate change has, in part, resulted in a higher frequency of flooding events, which allow for greater exchange between soil/plant litter and aquatic carbon pools. Here we demonstrate that the summer 2011 flood in the Mississippi River basin, caused by extreme precipitation events, resulted in a "flushing" of terrestrially derived dissolved organic carbon (TDOC) to the northern Gulf of Mexico. Data from the lower Atchafalaya and Mississippi rivers showed that the DOC flux to the northern Gulf of Mexico during this flood was significantly higher than in previous years. We also show that consumption of radiocarbon-modern TDOC by bacteria in floodwaters in the lower Atchafalaya River and along the adjacent shelf contributed to northern Gulf shelf waters changing from a net sink to a net source of CO2 to the atmosphere in June and August 2011. This work shows that enhanced flooding, which may or may not be caused by climate change, can result in rapid losses of stored carbon in soils to the atmosphere via processes in aquatic ecosystems.
    Geophysical Research Letters 01/2013; 40(1):116-122. · 3.98 Impact Factor
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    ABSTRACT: The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists-all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these "extreme" environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) "theme team" on microbial activity (www.darkenergybiosphere.org).
    Frontiers in Microbiology 01/2013; 4:189. · 3.90 Impact Factor
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    ABSTRACT: A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate-methane transition zone (SMTZ), which was observed approximately 20 m below the seafloor (mbsf). Small subunit ribosomal RNA were extracted, quantified, amplified, and sequenced using high-throughput 454 pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 m below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing techniques.
    Frontiers in Microbiology 01/2012; 3:113. · 3.90 Impact Factor
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    Heath J Mills, Brandi Kiel Reese, Cruz St Peter
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    ABSTRACT: The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.
    Frontiers in Microbiology 01/2012; 3:49. · 3.90 Impact Factor
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    ABSTRACT: Multiple environmental mechanisms have been proposed to control bottom water hypoxia (< 2 mg O2 L) in the northern Gulf of Mexico Louisiana shelf. Near-bottom hypoxia has been attributed to a direct consumption of oxygen through benthic microbial respiration and a secondary chemical reaction between oxygen and reduced metabolites (i.e. ferrous iron and total sulfide) from these populations. No studies to date have examined the metabolically active microbial community structure in conjunction with the geochemical profile in these sediments. Temporal and spatial differences in dissolved and solid phase geochemistry were investigated in the upper 20 cm of the sediment column. Pyrosequencing of reverse transcribed small subunit (SSU) ribosomal ribonucleic acid (rRNA) was used to determine population distribution. Results indicated that populations shallower than 10 cm below surface were temporally variable yet uniform between sites, while below this depth, populations were more site specific. This suggests a potential interaction between the water column and the benthic microbial population limited to a shallow depth. The presence of dissolved reduced iron in the upper sediment column was indicative of low oxygen concentration, yet sulfide was at or below detection limits. Putative sulfate and iron reducing and oxidizing populations were metabolically active at similar depths suggesting potential recycling of products. Results from this study indicate low carbon concentrations in the shallow sediments limit general metabolic activity, reducing the potential for microbial respiration. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the free supplemental file.
    Geomicrobiology 01/2012; · 1.61 Impact Factor
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    ABSTRACT: Microbial life in deep marine sediments is widespread, metabolically active and diverse. Evidence of prokaryotic communities in sediments as deep as 800 m below the seafloor (mbsf) have been found. By recycling carbon and nutrients through biological and geochemical processes, the deep subsurface has the potential to remain metabolically active over geologic time scales. While a vast majority of the subsurface biosphere remains under studied, recent advances in molecular techniques and an increased focus on microbiological sampling during IODP expeditions have provided the initial steps toward better characterizations of the microbial communities. Coupling of geochemistry and RNA-based molecular analysis is essential to the description of the active microbial populations within the subsurface biosphere. Studies based on DNA may describe the taxa and metabolic pathways from the total microbial community within the sediment, whether the cells sampled were metabolically active, quiescent or dead. Due to a short lifespan within a cell, only an RNA-based analysis can be used to identify linkages between active populations and observed geochemistry. This study will coalesce and compare RNA sequence and geochemical data from Expeditions 316 (Nankai Trough), 320 (Pacific Equatorial Age Transect), 325 (Great Barrier Reef) and 329 (South Pacific Gyre) to evaluate the biogeography of microbial lineages actively altering the deep subsurface. The grouping of sediments allows for a wide range of geochemical environments to be compared, including two environments limited in organic carbon. Significant to this study is the use of similar extraction, amplification and simultaneous 454 pyrosequencing on all sediment populations allowing for robust comparisons with similar protocol strengths and biases. Initial trends support previously described reduction of diversity with increasing depth. The co-localization of active reductive and oxidative lineages suggests a potential cryptic geochemical cycling of elements. The presence of cryptic cycles support a more biologically active subsurface than previously hypothesized. Similarities were observed between expeditions and will be presented using a novel combination of statistical correlations and dendrogram-based comparisons.
    AGU Fall Meeting Abstracts. 12/2011;
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    ABSTRACT: The accurate and precise measurement of total sulfide has been of major interest for well over a century. The most commonly used method involves the formation of a methylene blue–sulfide complex and spectrophotometric measurement of its concentration. The study presented herein compares the two most commonly used methods as outlined in Standard Methods for the Examination of Water and Wastewater (in APHA, Standard methods for the examination of water and wastewater, Washington, 1960) and by Cline (Limnol Oceanogr 14:454–458, 1969). In addition, this study clarifies the existing confusion of Cline’s reagent preparation procedure, as it is apparent that various interpretations exist among research groups regarding reagent preparation. After evaluating both methods with respect to precision and accuracy, detection limit, sample storage time, and ease of use, the method outlined in Cline was determined to be superior. Furthermore, we suggest that the reagent concentration has to be optimized depending on the range of sulfide concentrations to increase the accuracy and precision of the method. KeywordsSulfide–Methylene blue–Cline method–Diamine
    Aquatic Geochemistry 01/2011; 17(4):567-582. · 1.53 Impact Factor
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    ABSTRACT: The Salton Sea is a large shallow saline lake located in southern California that is noted for high sulfate concentrations, substantial algal productivity, and very warm water column temperatures. These conditions are well-suited for sulfide production, and sulfide has been implicated in summer fish kills, although no studies have been conducted to specifically understand hydrogen sulfide production and volatilization there. Despite polymictic mixing patterns and relatively short accumulation periods, the amount of sulfide produced is comparable to meromictic lakes. Sulfide levels in the Salton Sea reached concentrations of 1.2 mmol L(-1) of total free sulfide in the hypolimnion and 5.6 mmol L(-1) in the sediment pore water. Strong winds in late July mixed H2S into the surface water, where it depleted the entire water column of dissolved oxygen and reached a concentration of 0.1 mmol L(-1). Sulfide concentrations exceeded the toxicity threshold of tilapia (Oreochromis mossambicus) and combined with strong anoxia throughout the water column, resulted in a massive fish kill. The mixing of sulfide into the surface waters also increased atmospheric H2S concentrations, reaching 1.0 micromol m(-3). The flux of sulfide from the sediment into the water column was estimated to range from 2-3 mmol m(-2) day(-1) during the winter and up to 8 mmol m(-2) day(-1) during the summer. Application of the two-layer model for volatilization indicates that up to 19 mmol m(-2) day(-1) volatilized from the surface during the mixing event. We estimate that as much as 3400 Mg year(-1) or approximately 26% of sulfide that diffused into the water column from the deepest sediments may have been volatilized to the atmosphere.
    Science of The Total Environment 09/2008; 406(1-2):205-18. · 3.16 Impact Factor
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    Brandi Kiel Reese, Michael A. Anderson
    Geochmica et Cosmochimica Acta 07/2008; 72(12).
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    David R Parker, Angelia L Seyfferth, Brandi Kiel Reese
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    ABSTRACT: Perchlorate is widely used as an oxidant in solid rocket propellants and energetic applications, and it has frequently been detected in groundwaters at concentrations relevant to human health. The possibility of naturally occurring perchlorate has only recently received significant attention. Relying primarily on domestic, agricultural, and recreational wells, we utilized a network of volunteers to help collect 326 groundwater samples from across the coterminous United States. Care was taken to avoid known, USEPA-documented sites of perchlorate use or release, as well as perchlorate contamination due to disinfection using hypochlorite. Using IC-ESI-MS and a Cl18O4- internal standard, we achieved a method detection limit (MDL) of 40 ng/L perchlorate and a minimum reporting level (MRL) of 120 ng/L. Of the 326 samples, 147 (45%) were below the MDL, while 42 (13%) were between the MDL and the MRL. Of the 137 samples that could be quantified, most (109) contained < 1000 ng/L perchlorate; the remaining 28 samples contained from 1000 to 10400 ng/L. Our results support the notion that perchlorate occurs naturally in many groundwaters, but the unusually high concentrations (> 10000 ng/L) previously reported for the west-central Texas area appear to be anomalous. Perchlorate concentrations were positively correlated with nitrate levels (P < 0.001) but not with chloride concentrations. Opportunities exist for follow-up studies of perchlorate's origins using isotope forensics and for further elucidation of the role of atmospheric processes in the formation or transport of perchlorate.
    Environmental Science and Technology 04/2008; 42(5):1465-71. · 5.48 Impact Factor

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