Symbiosis of methylotrophic bacteria and deep-sea mussels

Characterization of symbiont populations in life-history stages of mussels from chemosynthetic environments

The densities of chemoautotrophic and methanotrophic symbiont morphotypes were determined in life- history stages (post-larvae, juveniles, adults) of two species of mussels (Bathymodiolus azoricus and B. heckerae) from deep-sea chemosynthetic environments (the Lucky Strike hydrothermal vent and the Blake Ridge cold seep) in the Atlantic Ocean. Both symbiont morphotypes were observed in all specimens and in the same relative proportions, regardless of life-history stage. The relative abundance of symbiont morphotypes, determined by transmission electron microscopy, was different in the two species: chemoautotrophs were dominant (13:1-18:1) in B. azoricus from the vent site; methanotrophs were dominant (2:1-3:1) in B. heckerae from the seep site. The ratio of CH4:H2S is proposed as a determinant of the relative abundance of symbiont types: where CH4:H2S is less than 1, as at the Lucky Strike site, chemoautotrophic symbionts dominate; where CH4:H2S is greater than 2, as at the seep site, methanotrophs dominate. Organic carbon and nitrogen isotopic compositions of B. azoricus (delta 13C = -30 per thousand; delta 15N = -9 per thousand) and B. heckerae (delta 13C = -56 per thousand; delta 15N = -2 per thousand) varied little among life-history stages and provided no record of a larval diet of photosynthetically derived organic material in the post-larval and juvenile stages.

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath)

Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.

Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus bathymodiolus

Deep-sea Bathymodiolus mussels, depending on species and location, have the capacity to host sulfur-oxidizing (thiotrophic) and methanotrophic eubacteria in gill bacteriocytes, although little is known about the mussels' mode of symbiont acquisition. Previous studies of Bathymodiolus host and symbiont relationships have been based on collections of nonoverlapping species across wide-ranging geographic settings, creating an apparent model for vertical transmission. We present genetic and cytological evidence for the environmental acquisition of thiotrophic endosymbionts by vent mussels from the Mid-Atlantic Ridge. Open pit structures in cell membranes of the gill surface revealed likely sites for endocytosis of free-living bacteria. A population genetic analysis of the thiotrophic symbionts exploited a hybrid zone where two Bathymodiolus species intergrade. Northern Bathymodiolus azoricus and southern Bathymodiolus puteoserpentis possess species-specific DNA sequences that identify both their symbiont strains (internal transcribed spacer regions) and their mitochondria (ND4). However, the northern and southern symbiont-mitochondrial pairs were decoupled in the hybrid zone. Such decoupling of symbiont-mitochondrial pairs would not occur if the two elements were transmitted strictly vertically through the germ line. Taken together, these findings are consistent with an environmental source of thiotrophic symbionts in Bathymodiolus mussels, although an environmentally "leaky" system of vertical transmission could not be excluded.

Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria

Methanotrophic bacteria play a major role in the global carbon cycle, degrade xenobiotic pollutants, and have the potential for a variety of biotechnological applications. To facilitate ecological studies of these important organisms, we developed a suite of oligonucleotide probes for quantitative analysis of methanotroph-specific 16S rRNA from environmental samples. Two probes target methanotrophs in the family Methylocystaceae (type II methanotrophs) as a group. No oligonucleotide signatures that distinguish between the two genera in this family, Methylocystis and Methylosinus, were identified. Two other probes target, as a single group, a majority of the known methanotrophs belonging to the family Methylococcaceae (type I/X methanotrophs). The remaining probes target members of individual genera of the Methylococcaceae, including Methylobacter, Methylomonas, Methylomicrobium, Methylococcus, and Methylocaldum. One of the family-level probes also covers all methanotrophic endosymbionts of marine mollusks for which 16S rRNA sequences have been published. The two known species of the newly described genus Methylosarcina gen. nov. are covered by a probe that otherwise targets only members of the closely related genus Methylomicrobium. None of the probes covers strains of the newly proposed genera Methylocella and "Methylothermus," which are polyphyletic with respect to the recognized methanotrophic families. Empirically determined midpoint dissociation temperatures were 49 to 57 degrees C for all probes. In dot blot screening against RNA from positive- and negative-control strains, the probes were specific to their intended targets. The broad coverage and high degree of specificity of this new suite of probes will provide more detailed, quantitative information about the community structure of methanotrophs in environmental samples than was previously available.

Intracellular life

Intracellular parasites and endosymbionts are present in almost all forms of life, including bacteria. Some eukaryotic organelles are believed to be derived from ancestral endosymbionts. Parasites and symbionts show several adaptations to intracellular life. A comparative analysis of their biology suggests some general considerations involved in adapting to intracellular life and reveals a number of independently achieved strategies for the exploitation of an intracellular habitat. Symbioses mainly based on a form of syntrophy may have led to the establishment of unique physiological systems. Generally, a symbiont can be considered to be an attenuated pathogen. The combination of morphological studies, molecular phylogenetic analyses, and palaeobiological data has led to considerable improvement in the understanding of intracellular life evolution. Comparing host and symbiont phylogenies could lead to an explanation of the evolutionary history of symbiosis. These studies also provide strong evidences for the endosymbiogenesis of the eukaryotic cell. Indeed, an eubacterial origin for mitochondria and plastids is well accepted and is suggested for other organelles. The expansion of intracellular living associations is presented, with a particular emphasis on peculiar aspects and/or recent data, providing a global evaluation.

Something from almost nothing: carbon dioxide fixation in chemoautotrophs

The last decade has seen significant advances in our understanding of the physiology, ecology, and molecular biology of chemoautotrophic bacteria. Many ecosystems are dependent on CO2 fixation by either free-living or symbiotic chemoautotrophs. CO2 fixation in the chemoautotroph occurs via the Calvin-Benson-Bassham cycle. The cycle is characterized by three unique enzymatic activities: ribulose bisphosphate carboxylase/oxygenase, phosphoribulokinase, and sedoheptulose bisphosphatase. Ribulose bisphosphate carboxylase/oxygenase is commonly found in the cytoplasm, but a number of bacteria package much of the enzyme into polyhedral organelles, the carboxysomes. The carboxysome genes are located adjacent to cbb genes, which are often, but not always, clustered in large operons. The availability of carbon and reduced substrates control the expression of cbb genes in concert with the LysR-type transcriptional regulator, CbbR. Additional regulatory proteins may also be involved. All of these, as well as related topics, are discussed in detail in this review.

Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems

Mixing of hydrothermal fluids and seawater at the ocean floor, combined with slow reaction kinetics for oxidation/reduction reactions, provides a source of metabolic energy for chemolithotrophic microorganisms which are the primary biomass producers for an extensive submarine ecosystem that is essentially independent of photosynthesis. Thermodynamic models are used to explore geochemical constraints on the amount of metabolic energy potentially available from chemosynthetic reactions involving S, C, Fe, and Mn compounds during mixing of hydrothermal fluids with seawater. For the vent fluid used in the calculations (EPR 21 degrees N OBS), the model indicates that mixing environments are favorable for oxidation of H2S, CH4, Fe2+ and Mn2+ only below approximately 38 degrees C, with methanogenesis and reduction of sulfate or S degrees favored at higher temperatures, suggesting that environments dominated by mixing provide habitats for mesophilic (but not thermophilic) aerobes and thermophilic (but not mesophilic) anaerobes. A maximum of approximately 760 cal per kilogram vent fluid is available from sulfide oxidation while between 8 and 35 cal/kg vent fluid is available from methanotrophy, methanogenesis, oxidation of Fe or Mn, or sulfate reduction. The total potential for chemosynthetic primary production at deep-sea hydrothermal vents globally is estimated to be about 10(13) g biomass per year, which represents approximately 0.02% of the global primary production by photosynthesis in the oceans. Thermophilic methanogens and sulfate- and S degree-reducers are likely to be the predominant organisms in the walls of vent chimneys and in the diffuse mixing zones beneath warm vents, where biological processes may contribute to the high methane concentrations of vent fluids and heavy 34S/32S ratios of vent sulfide minerals. The metabolic processes taking place in these systems may be analogs of the first living systems to evolve on the Earth.

Filamentous sulfide-oxidizing bacteria at hydrocarbon seeps of the Gulf of Mexico

Mats consisting of the large sulfide-oxidizing bacterium, Beggiatoa, were collected from the sediment/water interface at several locations in the Gulf of Mexico. The collection sites were associated with the presence of petroleum hydrocarbons or the microbial breakdown products of the hydrocarbons. The morphologies of the mats varied with the nature of the underlying sediments, and some mats were pigmented either yellow or orange instead of the usual white. At one site, beggiatoas were found that had a diameter of nearly 200 mu m, making them the largest prokaryotic organism known. In filaments with a diameter of over approximately 10 mu m the cytoplasm was restricted to a thin layer immediately underlying the cell membrane, and the majority of the cell consisted of a vacuole with unknown contents. Beggiatoa filaments often rotated as they moved by gliding. Parallel rows of 15 nm diameter pores were found on the surface of the beggiatoas. The pores may have been wound in a spiral fashion around the cell. These pores may be involved in the gliding motility of the bacteria by the motion imparted by the excretion of slime through the pores. Several structures with the typical morphology of prokaryotic cells but lacking a cell wall were found within the vacuolar and cytoplasmic portions of the hollow beggiatoas. Some of these internal "symbionts" ultrastructurally resembled methanotrophic bacteria like those that have been seen in animals taken from vent areas. Other symbionts ultrastructurally resembled autotrophic bacteria with carboxysome-like structures. These internal symbionts may enable the Beggiatoa to grow in different environments on different carbon sources. They also provide important evidence for the endosymbiotic theory of the evolution of internal organelles of eukaryotic organisms.

Assimilation of Inorganic Nitrogen by Marine Invertebrates and Their Chemoautotrophic and Methanotrophic Symbionts

Symbioses between marine invertebrates and their chemoautotrophic and methanotrophic symbionts are now known to exist in a variety of habitats where reduced chemical species are present. The utilization of chemical energy and reliance on C 1 compounds by these symbioses are well documented. Much less is known about their metabolism of nitrogen. Earlier work has shown that the tissues of organisms in these associations are depleted of 15 N compared with those of other marine organisms, indicating that local sources of nitrogen are assimilated and that novel mechanisms of nitrogen metabolism may be involved. Although these symbioses have access to rich sources of ammonium (NH 4 + and NH 3 ) and/or nitrate, several investigators have proposed that N 2 fixation may account for some of these isotope values. Here we report that [ 15 N]ammonium and, to a lesser degree, [ 15 N]nitrate are assimilated into organic compounds by Solemya reidi , a gutless clam containing S-oxidizing bacteria, and seep mussel Ia, an undescribed mytilid containing methanotrophic bacteria. In contrast, Riftia pachyptila , the giant hydrothermal vent tube worm symbiotic with S-oxidizing bacteria, assimilated nitrate but not exogenous ammonium. The rates of assimilation of these sources are sufficient to at least partially support C 1 compound metabolism. N 2 assimilation was not exhibited by the symbionts tested.

High taurine levels in the Solemya velum symbiosis

1. To compare biochemical differences between bivalves with and without endosymbiotic chemoautotrophic bacteria, specimens of Solemya velum, a bivalve species known to contain bacterial endosymbionts, and the symbiont-free soft-shelled clam Mya arenaria, were collected from the same subtidal reducing sediments during October and November 1988. 2. Total and free amino acid compositions were determined for both species. Protein-bound amino acids were calculated as the difference between total and free amino acids. In addition, stable isotope ratios of the total and free amino acids of each species were measured to determine potential sources for these molecules. 3. Both species had similar total hydrolyzable- and protein-bound amino acid compositions; approximately 50% of the protein-bound amino acids were essential amino acids. In S. velum, the small size of the digestive system suggests that these amino acids are probably synthesized by the endosymbiotic bacteria and translocated to the animal tissue. The delta 13C and delta 15N ratios of the amino acids are very similar to the isotope ratios previously found in both the endosymbionts and whole tissues of S. velum. The relative and absolute amounts of free amino acids are very different in the two species. In S. velum, the absolute concentrations of taurine, a sulfur-containing amino acid, were greater than the total free amino acid concentrations found in other bivalves. 4. The delta 34S ratios of the free amino acids of S. velum, which were predominantly composed of taurine, were extremely negative (-17.2/1000) suggesting that taurine is synthesized using sulfur originally derived from external reduced sulfur sources, such as pore water sulfides. The possible roles for taurine in this animal-bacteria symbiosis are discussed.

Description of a Novel Symbiotic Bacterium from the Brittle Star, Amphipholis squamata

A gram-negative, marine, facultatively anaerobic bacterial isolate designated strain AS-1 was isolated from the subcuticular space of the brittle star, Amphipholis squamata. Its sensitivity to O/129 and novobiocin, overall morphology, and biochemical characteristics and the moles percent guanine-plus-cytosine composition of its DNA (42.9 to 44.4) suggest that this isolate should be placed in the genus Vibrio. Strain AS-1 was not isolated from ambient seawater and is distinct from described Vibrio species. This symbiotic bacterium may assist its host as one of several mechanisms of nutrient acquisition during the brooding of developing embryos.

Chemosynthetic Mussels at a Brine-Filled Pockmark in the Northern Gulf of Mexico

A large (540 square meters) bed of Bathymodiolus n. sp. (Mytilidae: Bivalvia) rings a pool of hypersaline (121.35 practical salinity units) brine at a water depth of 650 meters on the continental slope south of Louisiana. The anoxic brine (dissolved oxygen </=0.17 milliliters per liter) contains high concentrations of methane, which nourishes methanotrophic symbionts in the mussels. The brine, which originates from a salt-cored diapir that penetrates to within 500 meters ofthe sea floor, fills a depression that was evidently excavated by escaping gas. The spatial continuity of the mussel bed indicates that the brine level has remained fairly constant; however, demographic differences between the inner and outer parts of the bed record small fluctuations.

Particle density and protein composition of the peribacteroid membrane from soybean root nodules is affected by mutation in the microsymbiont Bradyrhizobium japonicum

Particle frequency of the peribacteroid membrane (PBM) from nodules of Glycine max (L.) Merr. cv. Maple Arrow infected with Bradyrhizobium japonicum 61-A-101 (wild-type strain) was determined by freeze-fracturing to be about 2200·μm(-2) in the protoplasmic fracture face and 700·μm(-2) in the exoplasmic fracture face. In membranes isolated from nodules infected with the mutant RH 31-Marburg of B. japonicum, the particle frequency was similar in both fracture faces with 1200-1300 particles·μm(-2). Analysis of particlesize distribution on peribacteroid membranes showed a loss, especially of particle sizes larger than 11 nm, in the mutant-infected nodules. Two-dimensional gel electrophoresis (isoelectric focussing and sodium dodecyl sulfate-polyacrylamide) showed 27 different polypeptides in the PBM from nodules infected with the wild-type strain, four of which were absent from the PBM of nodules infected with the mutant RH 31-Marburg, which also exhibited one extra small-molecular-weight polypeptide. At least 14 of the 27 polypeptides in the PBM from the wild-type-infected nodule were glycoproteins. In three of these glycoproteins, post-translational modifications were either lacking or different when the membrane was derived from mutant-infected nodules.

Isolation and characterization of marine methanotrophs

Four new methane-oxidizing bacteria have been isolated from marine samples taken at the Hyperion sewage outfall, near Los Angeles, CA. These bacteria require NaCl for growth. All exhibit characteristics typical of Type I methanotrophs, except they contain enzyme activities of both the ribulose monophosphate pathway and the serine cycle. All four strains are characterized by rapid growth in liquid culture and on agar plates, and all have temperature optima above 35 degrees C. One strain, chosen for further study, has been shown to maintain broadhost range cloning vectors and is currently being used for genetic studies.