Publications

2009
Girguis PR, Robidart J, Nyholm S. Coupling metabolite flux to proteomics: Insights into the molecular mechanisms underlying primary productivity by tubeworm symbionts. Geochimica Et Cosmochimica Acta. 2009;73 :A439-A439.
Dilly GF, Girguis PR. Exploring the Boundaries of Metazoan Thermotolerance at Hydrothermal Vents: Respiration and Protein Expression of Paralvinellid Worms. Integrative and Comparative Biology. 2009;49 :E222-E222.
Girguis PR, Nyholm SV, Robidart JA, Girguis. From metabolite flux to gene expression and proteomics: insights into the molecular mechanisms underlying primary productivity in hydrothermal vent tubeworms. Integrative and Comparative Biology. 2009;49 :E63-E63.
Nielsen ME, Wu DM, Girguis PR, Reimers CE. Influence of Substrate on Electron Transfer Mechanisms in Chambered Benthic Microbial Fuel Cells. Environmental Science & Technology. 2009;43 :8671-8677.Abstract

This research investigated whether the addition of an exogenous electron donor would affect power production in laboratory-scale benthic microbial fuel cells (BMFC) by differentially influencing microbially mediated electron transfer processes. Six BMFCs were operated for over one year in a temperature-controlled laboratory. Three BMFCs relied on endogenous electron donors, and three were supplemented with lactate. The supplemented BMFCs generated more cumulative charge, but did not generate higher average current between periods of lactate enrichment Coulombic efficiencies during the lactate treatments ranged from 25 to 65% suggesting that lactate utilization was variably coupled to power production. Cumulative electron flux resulting from lactate additions and chemical changes within the anode chamber, as well as a difference in the anode-hosted microbial communities indicated that lactate supplementation promoted sulfate reduction. After the addition of molybdate to suppress sulfate reduction and sulfur disproportionation, all BMFCs continued to produce current but no longer responded to lactate additions. Chemical data support a two-step cycle in which endogenous organic carbon and/or supplemented lactate fuel sulfate reduction resulting in sulfide and simple organic molecules (such as acetate) that can act as the electron donors for the BMFC.

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Bradley AS, Song P, Summons RE, Girguis PR. Methane cycling at Lost City: A biological view of geochemistry. Geochimica Et Cosmochimica Acta. 2009;73 :A154-A154.
White HK, Reimers CE, Cordes EE, Dilly GF, Girguis PR. Quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells. Isme Journal. 2009;3 :635-646.Abstract

This study examines changes in diversity and abundance of bacteria recovered from the anodes of microbial fuel cells (MFCs) in relation to anode potential, power production and geochemistry. MFCs were batch-fed with plankton, and two systems were maintained at different potentials whereas one was at open circuit for 56.8 days. Bacterial phylogenetic diversity during peak power was assessed from 16S rDNA clone libraries. Throughout the experiment, microbial community structure was examined using terminal restriction fragment length polymorphism. Changes in cell density of key phylotypes, including representatives of delta-, epsilon-, gamma-proteobacteria and Flavobacterium-Cytophaga-Bacteroides, were enumerated by quantitative PCR. Marked differences in phylogenetic diversity were observed during peak power versus the final time point, and changes in microbial community structure were strongly correlated to dissolved organic carbon and ammonium concentrations within the anode chambers. Community structure was notably different between the MFCs at different anode potentials during the onset of peak power. At the final time point, however, the anode-hosted communities in all MFCs were similar. These data demonstrate that differences in growth, succession and population dynamics of key phylotypes were due to anode potential, which may relate to their ability to exploit the anode as an electron acceptor. The geochemical milieu, however, governs overall community diversity and structure. These differences reflect the physiological capacity of specific phylotypes to catabolize plankton-derived organic matter and exploit the anode of an MFC for their metabolism directly or indirectly through syntrophy. The ISME Journal (2009) 3, 635-646; doi: 10.1038/ismej.2009.12; published online 26 February 2009

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Wankel SD, Lilley MD, Olson E, Girguis PR. Real-time in situ volatile characterization and methane carbon stable isotopic composition in the deep sea. Geochimica Et Cosmochimica Acta. 2009;73 :A1418-A1418.
Yancey PH, Ishikawa J, Meyer B, Girguis PR, Lee RW. Thiotaurine and Hypotaurine Contents in Hydrothermal-Vent Polychaetes Without Thiotrophic Endosymbionts: Correlation With Sulfide Exposure. Journal of Experimental Zoology Part a-Ecological Genetics and Physiology. 2009;311A :439-447.Abstract

Invertebrates at hydrothermal vents and cold seeps must cope with toxic H(2)S. One proposed protection mechanism involves taurine derivatives: At vents and seeps, many animals have high levels of hypotaurine and thiotaurine (a product of hypotaurine and HS), originally found in animals with thiotrophic endosymbionts. To further test the role of these compounds, we analyzed them in vent polychaetes without endosymbionts: Paralvinella sulfincola, P. palmiformis and P. pandorae (paralvinellids) and Nicomache venticola (maldanid). P. sulfincola were collected from a high temperature (42-68 degrees C) and a warm site (21-35 degrees C). P. plamiformis and pandorae were from cool sites (12-18 degrees C) and N. venticola were from a cold site (4 degrees C). H(2)S concentrations in vent effluent largely correlate with temperature. Some specimens were frozen; other ones were kept alive in laboratory chambers, with and without sulfide. Tissues were analyzed for taurine derivatives and other solutes that serve as organic osmolytes. The major osmolyte of all species was glycine. Thiotaurine contents were significantly different among all species, in the order P. sulfincola hot > P. sulfincola warm > P. pandorae > P. palmiformis > N. venticola. P. sulfincola also had high levels of sarcosine; others species had none. Sarcosine and hypotaurine contents of P. sulfincola's branchiae were higher, while glycine contents were lower, than in main body. In P. palmiformis kept in pressure chambers with sulfide, thiotaurine contents were higher and hypotaurine lower than in those. kept without sulfide. These results support the hypothesis that conversion of hypotaurine to thiotaurine detoxifies sulfide in vent animals without endosymbionts. J. Exp. Zool. 311A:439-447, 2009, (C) 2009 Wiley-Liss, Inc.

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Seibel BA, Girguis PR, Childress JJ. Variation in evolved limits to life preclude universal tolerance indices: a critque of the Respiration Index. Science e-Letters. 2009. (pdf)
2008
Newton ILG, Girguis PR, Cavanaugh CM. Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts. Bmc Genomics. 2008;9.Abstract

Background: The Vesicomyidae (Bivalvia: Mollusca) are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genome-wide evolutionary analyses possible.Results: To examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. These four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents.Conclusion: The results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts. The fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments.

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Nyholm SV, Robidart J, Girguis PR. Coupling metabolite flux to transcriptomics: Insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae. Biological Bulletin. 2008;214 :255-265.Abstract

Deep-sea hydrothermal vents host highly productive ecosystems. Many of these communities are dominated by vestimentiferan tubeworms that house endosymbiotic chemoautotrophic bacteria that provide the hosts with their primary nutritional needs. Rates of carbon fixation by these symbioses are also among the highest recorded. Despite the breadth of physiological and biochemical research on these associations, the underlying molecular mechanisms that regulate host and symbiont metabolite flux and carbon fixation are largely unknown. Here we present metabolite flux and transcriptomics data from shipboard high-pressure respirometry experiments in which we maintained Ridgeia piscesae tubeworms at conditions comparable to those in situ. Host trophosome was used for cDNA library construction and sequencing. Of the 19,132 clones sequenced, 10,684 represented unique expressed sequence tags (ESTs). The highest proportions of genes are involved with translation, ribosomal structure and biogenesis, cellular processing, and signal transduction. There was moderate representation of genes involved in metabolite exchange and acid-base regulation. These data represent the first concomitant surveys of metabolite flux rates and gene expression for a chemoautotrophic symbiosis during net autotrophy, and they suggest that-in the case of Riageia piscesae-host-symbiont interactions such as cell cycle regulation may play a significant role in maintaining physiological poise during high productivity.

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Nielsen ME, Reimers CE, White HK, Sharma S, Girguis PR. Sustainable energy from deep ocean cold seeps. Energy & Environmental Science. 2008;1 :584-593.Abstract

Two designs of benthic microbial fuel cell (BMFC) were deployed at cold seeps in Monterey Canyon, CA, unattended for between 68 and 162 days. One design had a cylindrical solid graphite anode buried vertically in sediment, and the other had a carbon fiber brush anode semi-enclosed in a chamber above the sediment-water interface. Each chamber included two check valves to allow fluid flow from the sediment into the chamber. On average, power outputs were 0.2 mW (32 mW m(-2) normalized to cross sectional area) from the solid anode BMFC and from 11 to 56 mW (27-140 mW m(-2)) during three deployments of the chambered design. The range in power produced with the chambered BMFC was due to different valve styles, which appear to have permitted different rates of chemical seepage from the sediments into the anode chamber. Valves with the lowest breaking pressure led to the highest power production and presumably the highest inputs of electron donors. The increase in power coincided with a significant change in the microbial community associated with the anode from being dominated by epsilonproteobacteria to a more diverse community with representatives from deltaproteobacteria, epsilonproteobacteria, firmicutes, and flavobacterium/cytophaga/bacterioides (FCB). The highest levels of power delivered by the chambered BMFC would meet the energy requirements of many oceanographic sensors marketed today. In addition, these BMFCs did not exhibit signs of electrochemical passivation or progressive substrate depletion as is often observed with buried anodes.

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2007
Fisher CR, Girguis P. Microbiology. A proteomic snapshot of life at a vent. Science. 2007;315 :198-9. (pdf)
Reimers CE, Stecher HA, Westall JC, Alleau Y, Howell KA, Soule L, White HK, Girguis PR. Substrate degradation kinetics, microbial diversity, and current efficiency of microbial fuel cells supplied with marine plankton. Applied and Environmental Microbiology. 2007;73 (21) :7029-7040.Abstract

The decomposition of marine plankton in two-chamber, seawater-filled microbial fuel cells (MFCs) has been investigated and related to resulting chemical changes, electrode potentials, current efficiencies, and microbial diversity. Six experiments were run at various discharge potentials, and a seventh served as an open-circuit control. The plankton consisted of a mixture of freshly captured phytoplankton and zooplankton (0.21 to 1 mm) added at an initial batch concentration of 27.5 mmol liter(-1) particulate organic carbon (OC). After 56.7 days, between 19.6 and 22.2% of the initial OC remained, sulfate reduction coupled to OC oxidation accounted for the majority of the OC that was degraded, and current efficiencies (of the active MFCs) were between 11.3 and 15.5%. In the open-circuit control cell, anaerobic plankton decomposition (as quantified by the decrease in total OQ could be modeled by three terms: two first-order reaction rate expressions (0.79 day(-1) and 0.037 day(-1), at 15 degrees C) and one constant, no-reaction term (representing 10.6% of the initial 0Q. However, in each active MFC, decomposition rates increased during the third week, lagging just behind periods of peak electricity generation. We interpret these decomposition rate changes to have been due primarily to the metabolic activity of sulfur-reducing microorganisms at the anode, a finding consistent with the electrochemical oxidization of sulfide to elemental sulfur and the elimination of inhibitory effects of dissolved sulfide. Representative phylotypes, found to be associated with anodes, were allied with Delta-, Epsilon-, and Gamma-proteobacteria as well as the Flavobacterium-Cytophaga-Bacteroides and Fusobacteria. Based upon these results, we posit that higher current efficiencies can be achieved by optimizing plankton-fed MFCs for direct electron transfer from organic matter to electrodes, including microbial precolonization of high-surface-area electrodes and pulsed flowthrough additions of biomass.

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2006
McBride LR, Girguis PR, Reimers CE. Power Storage and Conversion from an Ocean Microbial Energy Source. Proceedings of the Marine Technology Society / Institute of Electrical and Electronics Engineers. 2006. (pdf)
Girguis PR, Childress JJ. Metabolite uptake, stoichiometry and chemoautotrophic function of the hydrothermal vent tubeworm Riftia pachyptila: responses to environmental variations in substrate concentrations and temperature. Journal of Experimental Biology. 2006;209 :3516-3528.Abstract

The hydrothermal vent tubeworm Riftia pachyptila is a dominant member of many hydrothermal vent communities along the East Pacific rise and is one of the fastest growing metazoans known. Riftia flourish in diffuse hydrothermal fluid flows, an environment with high spatial and temporal heterogeneity in physical and chemical conditions. To date, physiological and biochemical studies of Riftia have focused on Riftia's adaptations to its chemoautotrophic bacterial symbionts. However the relation between in situ physico-chemical heterogeneity and Riftia host and symbiont metabolism, in particular symbiont chemoautotrophic function, remain poorly understood. Accordingly, we conducted experiments using shipboard high-pressure respirometers to ascertain the effect of varying substrate concentrations and temperature on Riftia metabolite uptake and symbiont carbon fixation. Our results show that substrate concentrations can strongly govern Riftia oxygen and sulfide uptake rates, as well as net carbon uptake (which is a proxy for chemoautotrophic primary production). However, after sufficient exposure to sulfide and oxygen, Riftia were capable of sustaining symbiont autotrophic function for several hours in seawater devoid of sulfide or oxygen, enabling the association to support symbiont metabolism through brief periods of substrate deficiency. Overall, temperature had the largest influence on Riftia metabolite uptake and symbiont autotrophic metabolism. In sum, while Riftia requires sufficient availability of substrates to support symbiont chemoautotrophic function, it is extremely well poised to buffer the temporal and spatial heterogeneity in environmental substrate concentrations, alleviating the influence of environmental heterogeneity on symbiont chemoautotrophic function.

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Reimers CE, Girguis PR, Stecher HA, Tender LM, Ryckelynck N, Whaling P. Microbial fuel cell energy from an ocean cold seep. Geobiology. 2006;4 :123-136. (pdf)
Girguis PR, Lee RW. Thermal preference and tolerance of alvinellids. Science. 2006;312 :231. (pdf)
2005
Girguis PR, Cozen AE, Delong EF. Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor. Applied and Environmental Microbiology. 2005;71 (7) :3725-3733.Abstract

The consumption of methane in anoxic marine sediments is a biogeochemical phenomenon mediated by two archaeal groups (ANME-1 and ANME-2) that exist syntrophically with sulfate-reducing bacteria. These anaerobic methanotrophs have yet to be recovered in pure culture, and key aspects of their ecology and physiology remain poorly understood. To characterize the growth and physiology of these anaerobic methanotrophs and the syntrophic sulfate-reducing bacteria, we incubated marine sediments using an anoxic, continuous-How bioreactor during two experiments at different advective porewater flow rates. We examined the growth kinetics of anaerobic methanotrophs and Desulfosarcina-like sulfate-reducing bacteria using quantitative PCR as a proxy for cell counts, and measured methane oxidation rates using membrane-inlet mass spectrometry. Our data show that the specific growth rates of ANME-1 and ANME-2 archaea differed in response to porewater How rates. ANME-2 methanotrophs had the highest rates in lower-flow regimes (mu(ANME-2) 0.167 center dot week(-1)), whereas ANME-1 methanotrophs had the highest rates in higher-flow regimes (mu(ANME-1) = 0.218 center dot week(-1)). In both incubations, Desulfosarcina-like sulfate-reducing bacterial growth rates were approximately 0.3 center dot week(-1), and their growth dynamics suggested that sulfate-reducing bacterial growth might be facilitated by, but not dependent upon, an established anaerobic methanotrophic population. ANME-1 growth rates corroborate field observations that ANME-1 archaea flourish in higher-flow regimes. Our growth and methane oxidation rates jointly demonstrate that anaerobic methanotrophs are capable of attaining substantial growth over a range of environmental conditions used in these experiments, including relatively low methane partial pressures.

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2003
Girguis PR, Orphan VJ, Hallam SJ, Delong EF. Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor. Applied and Environmental Microbiology. 2003;69 (9) :5472-5482.Abstract

Anaerobic methanotrophic archaea have recently been identified in anoxic marine sediments, but have not yet been recovered in pure culture. Physiological studies on freshly collected samples containing archaea and their sulfate-reducing syntrophic partners have been conducted, but sample availability and viability can limit the scope of these experiments. To better study microbial anaerobic methane oxidation, we developed a novel continuous-flow anaerobic methane incubation system (AMIS) that simulates the majority of in situ conditions and supports the metabolism and growth of anaerobic methanotrophic archaea. We incubated sediments collected from within and outside a methane cold seep in Monterey Canyon, Calif., for 24 weeks on the AMIS system. Anaerobic methane oxidation was measured in all sediments after incubation on AMIS, and quantitative molecular techniques verified the increases in methane-oxidizing archaeal populations in both seep and nonseep sediments. Our results demonstrate that the AMIS system stimulated the maintenance and growth of anaerobic methanotrophic archaea, and possibly their syntrophic, sulfate-reducing partners. Our data demonstrate the utility of combining physiological and molecular techniques to quantify the growth and metabolic activity of anaerobic microbial consortia. Further experiments with the AMIS system should provide a better understanding of the biological mechanisms of methane oxidation in anoxic marine environments. The AMIS may also enable the enrichment, purification, and isolation of methanotrophic archaea as pure cultures or defined syntrophic consortia.

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