Hallam SJ, Girguis PR, Preston CM, Richardson PM, Delong EF. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Applied and Environmental Microbiology. 2003;69 :5483-5491.Abstract

Phylogenetic and stable-isotope analyses implicated two methanogen-like archaeal groups, ANME-1 and ANME-2, as key participants in the process of anaerobic methane oxidation. Although nothing is known about anaerobic methane oxidation at the molecular level, the evolutionary relationship between methane-oxidizing archaea (MOA) and methanogenic archaea raises the possibility that MOA have co-opted key elements of the methanogenic pathway, reversing many of its steps to oxidize methane anaerobically. In order to explore this hypothesis, the existence and genomic conservation of methyl coenzyme M reductase (MCR), the enzyme catalyzing the terminal step in methanogenesis, was studied in ANME-1 and ANME-2 archaea isolated from various marine environments. Clone libraries targeting a conserved region of the alpha subunit of MCR (mcrA) were generated and compared from environmental samples, laboratory-incubated microcosms, and fosmid libraries. Four out of five novel mcrA types identified from these sources were associated with ANME-1 or ANME-2 group members. Assignment of mcrA types to specific phylogenetic groups was based on environmental clone recoveries, selective enrichment of specific MOA and mcrA types in a microcosm, phylogenetic congruence between mcrA and small-subunit rRNA tree topologies, and genomic context derived from fosmid sequences. Analysis of the ANME-1 and ANME-2 mcrA sequences suggested the potential for catalytic activity based on conservation of active-site amino acids. These results provide a basis for identifying methanotrophic archaea with mcrA sequences and define a functional genomic link between methanogenic and methanotrophic archaea.

Girguis PR, Childress JJ, Freytag JK, Klose K, Stuber R. Effects of metabolite uptake on proton-equivalent elimination by two species of deep-sea vestimentiferan tubeworm, Riftia pachyptila and Lamellibrachia cf luymesi: proton elimination is a necessary adaptation to sulfide-oxidizing chemoautotrophic symbiont. Journal of Experimental Biology. 2002;205 :3055-3066.Abstract

Intracellular symbiosis requires that the host satisfy the symbiont's metabolic requirements, including the elimination of waste products. The hydrothermal vent tubeworm Riftia pachyptila and the hydrocarbon seep worm Lamellibrachia cf luymesi are symbiotic with chemolithoautotrophic bacteria that produce sulfate and protons as end-products. In this report, we examine the relationship between symbiont metabolism and host proton equivalent elimination in R. pachyptila and L cf luymesi, and the effects of sulfide exposure on proton-equivalent elimination by Urechis caupo, an echiuran worm that lacks intracellular symbionts (for brevity, we will hereafter refer to proton-equivalent elimination as 'proton elimination'). Proton elimination by R. pachyptila and L. cf luymesi constitutes the worms' largest mass-specific metabolite flux, and R. pachyptila proton elimination is, to our knowledge, the most rapid reported for any metazoan. Proton elimination rates by R. pachyptila and L. cf luymesi correlated primarily with the rate of sulfide oxidation. Prolonged exposure to low environmental oxygen concentrations completely inhibited the majority of proton elimination by R. pachyptila, demonstrating that proton elimination does not result primarily from anaerobic metabolism. Large and rapid increases in environmental inorganic carbon concentrations led to short-lived proton elimination by R. pachyptila, as a result of the equilibration between internal and external inorganic carbon pools. U. caupo consistently exhibited proton elimination rates 5-20 times lower than those, of L cf luymesi and R. pachyptila upon exposure to sulfide. Treatment with specific ATPase inhibitors completely inhibited a fraction of proton elimination and sulfide and inorganic carbon uptake by R. pachyptila, suggesting that proton elimination occurs in large part via K+/H+-ATPases and Na+/H+-ATPases. In the light of these results, we suggest that protons are the primary waste product of the symbioses of R. pachyptila and L cf luymesi, and that proton elimination is driven by symbiont metabolism, and may be the largest energetic cost incurred by the worms.

Freytag JK, Girguis PR, Bergquist DC, Andras JP, Childress JJ, Fisher CR. A paradox resolved: Sulfide acquisition by roots of seep tubeworms sustains net chemoautotrophy. Proceedings of the National Academy of Sciences of the United States of America. 2001;98 (23) :13408-13413.Abstract

Vestimentiferan tubeworms, symbiotic with sulfur-oxidizing chemoautotrophic bacteria, dominate many cold-seep sites in the Gulf of Mexico. The most abundant vestimentiferan species at these sites, Lamellibrachia cf. luymesi, grows quite slowly to lengths exceeding 2 meters and lives in excess of 170-250 years. L. cf. luymesi can grow a posterior extension of its tube and tissue, termed a "root," down into sulfidic sediments below its point of original attachment. This extension can be longer than the anterior portion of the animal. Here we show, using methods optimized for detection of hydrogen sulfide down to 0.1 muM in seawater, that hydrogen sulfide was never detected around the plumes of large cold-seep vestimentiferans and rarely detectable only around the bases of mature aggregations. Respiration experiments, which exposed the root portions of L. cf. luymesi to sulfide concentrations between 51-561 muM, demonstrate that L. cf. luymesi use their roots as a respiratory surface to acquire sulfide at an average rate of 4.1 mu mol.g(-1).h(-1). Net dissolved inorganic carbon uptake across the plume of the tubeworms was shown to occur in response to exposure of the posterior (root) portion of the worms to sulfide, demonstrating that sulfide acquisition by roots of the seep vestimentiferan L. cf. luymesi can be sufficient to fuel net autotrophic total dissolved inorganic carbon uptake.

Girguis PR, Lee RW, Desaulniers N, Childress JJ, Pospesel M, Felbeck H, Zal F. Fate of nitrate acquired by the tubeworm Riftia pachyptila. Applied and Environmental Microbiology. 2000;66 (7) :2783-2790.Abstract

The hydrothermal vent tubeworm Riftia pachyptila lacks a mouth and gut and lives in association with intracellular, sulfide-oxidizing chemoautotrophic bacteria. Growth of this tubeworm requires an exogenous source of nitrogen for biosynthesis, and, as determined in previous studies, environmental ammonia and free amino acids appear to be unlikely sources of nitrogen. Nitrate, however, is present in situ (K, Johnson, J. Childress, R. Hessler, C. Sakamoto-Arnold, and C. Beehler, Deep-Sea Res. 35:1723-1744, 1988), is taken up by the host, and can be chemically reduced by the symbionts (U. Hentschel and H. Felbeck, Nature 366:338-340, 1993), Here we report that at an in situ concentration of 40 mu M, nitrate is acquired by R, pachyptila at a rate of 3.54 mu mol g(-1) h(-1), while elimination of nitrite and elimination of ammonia occur at much lower rates (0.017 and 0.21 mu mol g(-1) h(-1), respectively), We also observed reduction of nitrite (and accordingly nitrate) to ammonia in the trophosome tissue. When R. pachyptila tubeworms are exposed to constant in situ conditions for 60 h, there is a difference between the amount of nitrogen acquired via nitrate uptake and the amount of nitrogen lost via nitrite and ammonia elimination, which indicates that there is a nitrogen "sink" Our results demonstrate that storage of nitrate does not account for the observed stoichiometric differences in the amounts of nitrogen, Nitrate uptake was not correlated with sulfide or inorganic carbon flux, suggesting that nitrate is probably not an important oxidant in metabolism of the symbionts, Accordingly, we describe a nitrogen flux model for this association, in which the product of symbiont nitrate reduction, ammonia, is the primary source of nitrogen for the host and the symbionts and fulfills the association's nitrogen needs via incorporation of ammonia into amino acids.

Goffredi SK, Girguis PR, Childress JJ, Desaulniers NT. Physiological functioning of carbonic anhydrase in the hydrothermal vent tubeworm Riftia pachyptila. Biological Bulletin. 1999;196 :257-264.Abstract

On the basis of our experiments, it is clear that carbonic anhydrase (CA) plays an important role in the CO2-concentrating mechanisms in Riftia pachyptila. Plume tissue from freshly collected animals had the highest CA activity, 253.7 +/- 36.0 mu mol CO2 min(-1) g(-1) wet wt, and trophosome activity averaged 109.4 +/- 17.9 mu mol CO2 min(-1) g(-1) wet wt. Exposure of living worms to ethoxyzolamide, a carbonic anhydrase inhibitor, resulted in a 99% decrease in CA activity (from 103.9 +/- 38.6 to 0.7 +/- 0.2 mu mol CO2 min(-1) g(-1) wet wt in the plume tissue and 57.6 +/- 17.9 to 0.03 +/- 0,11 mu mol CO2 min(-1) g(-1) wet wt in the trophosome) and essentially a complete cessation of Sigma CO2, uptake. High concentrations of CA appear to facilitate the equilibration between inorganic carbon (Ci) in the external and internal environments, greatly enhancing the diffusion of CO2 into the animal. In summary, R. pachyptila demonstrates very effective acquisition of inorganic carbon from the environment, thereby providing the symbionts with large amounts of CO2. This effective acquisition is made possible by three factors: extremely effective pH regulation, a large external pool of CO2, and, described in this paper, high levels of carbonic anhydrase.

Girguis PR, Childress JJ. H+ equivalent elimination by the tube-worm Riftia pachyptila. Cahiers de Biologie Marine. 1998;39 :295-296. (pdf)