Holger W. Jannasch

Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments.

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments was used to explore the genetic diversity of hydrothermal vent microbial communities, specifically to determine the importance of sulfur-oxidizing bacteria therein. DGGE analysis of two different hydrothermal vent samples revealed one PCR band for one sample and three PCR bands for the other sample, which probably correspond to the dominant bacterial populations in these communities. Three of the four 16S rDNA fragments were sequenced. By comparison with 16S rRNA sequences of the Ribosomal Database Project, two of the DGGE-separated fragments were assigned to the genusThiomicrospira. To identify these ‘phylotypes’ in more detail, a phylogenetic framework was created by determining the nearly complete 16S rRNA gene sequence (approx. 1500 nucleotides) from three describedThiomicrospira species, viz.,Tms. crunogena, Tms. pelophila, Tms. denitrificans, and from a new isolate,Thiomicrospira sp. strain MA2-6. AllThiomicrospira species exceptTms. denitrificans formed a monophyletic group within the gamma subdivision of the Proteobacteria.Tms. denitrificans was assigned as a member of the epsilon subdivision and was distantly affiliated withThiovulum, another sulfur-oxidizing bacterium. Sequences of two dominant 16S rDNA fragments obtained by DGGE analysis fell into the gamma subdivisionThiomicrospira. The sequence of one fragment was in all comparable positions identical to the 16S rRNA sequence ofTms. crunogena. Identifying a dominant molecular isolate asTms. crunogena indicates that this species is a dominant community member of hydrothermal vent sites. Another ‘phylotype’ represented a newThiomicrospira species, phylogenetically in an intermediate position betweenTms. crunogena andTms. pelophila. The third ‘phylotype’ was identified as aDesulfovibrio, indicating that sulfate-reducing bacteria, as sources of sulfide, may complement sulfur- and sulfide-oxidizing bacteria ecologically in these sulfide-producing hydrothermal vents.

Microbial Diversity of Hydrothermal Sediments in the Guaymas Basin: Evidence for Anaerobic Methanotrophic Communities

ABSTRACT Microbial communities in hydrothermally active sediments of the Guaymas Basin (Gulf of California, Mexico) were studied by using 16S rRNA sequencing and carbon isotopic analysis of archaeal and bacterial lipids. The Guaymas sediments harbored uncultured euryarchaeota of two distinct phylogenetic lineages within the anaerobic methane oxidation 1 (ANME-1) group, ANME-1a and ANME-1b, and of the ANME-2c lineage within the Methanosarcinales, both previously assigned to the methanotrophic archaea. The archaeal lipids in the Guaymas Basin sediments included archaeol, diagnostic for nonthermophilic euryarchaeota, and sn-2-hydroxyarchaeol, with the latter compound being particularly abundant in cultured members of the Methanosarcinales. The concentrations of these compounds were among the highest observed so far in studies of methane seep environments. The δ-13C values of these lipids (δ-13C = −89 to −58‰) indicate an origin from anaerobic methanotrophic archaea. This molecular-isotopic signature was found not only in samples that yielded predominantly ANME-2 clones but also in samples that yielded exclusively ANME-1 clones. ANME-1 archaea therefore remain strong candidates for mediation of the anaerobic oxidation of methane. Based on 16S rRNA data, the Guaymas sediments harbor phylogenetically diverse bacterial populations, which show considerable overlap with bacterial populations of geothermal habitats and natural or anthropogenic hydrocarbon-rich sites. Consistent with earlier observations, our combined evidence from bacterial phylogeny and molecular-isotopic data indicates an important role of some novel deeply branching bacteria in anaerobic methanotrophy. Anaerobic methane oxidation likely represents a significant and widely occurring process in the trophic ecology of methane-rich hydrothermal vents. This study stresses a high diversity among communities capable of anaerobic oxidation of methane.

Geomicrobiology of Deep-Sea Hydrothermal Vents

During the cycling of seawater through the earths crust along the mid-ocean ridge system, geothermal energy is transferred into chemical energy in the form of reduced inorganic compounds. These compounds are derived from the reaction of seawater with crustal rocks at high temperatures and are emitted from warm (≤25�C) and hot (∼350�C) submarine vents at depths of 2000 to 3000 meters. Chemolithotrophic bacteria use these reduced chemical species as sources of energy for the reduction of carbon dioxide (assimilation) to organic carbon. These bacteria form the base of the food chain, which permits copious populations of certain specifically adapted invertebrates to grow in the immediate vicinity of the vents. Such highly prolific, although narrowly localized, deep-sea communities are thus maintained primarily by terrestrial rather than by solar energy. Reduced sulfur compounds appear to represent the major electron donors for aerobic microbial metabolism, but methane-, hydrogen-, iron-, and manganese-oxidizing bacteria have also been found. Methanogenic, sulfur-respiring, and extremely thermophilic isolates carry out anaerobic chemosynthesis. Bacteria grow most abundantly in the shallow crust where upwelling hot, reducing hydrothermal fluid mixes with downwelling cold, oxygenated seawater. The predominant production of biomass, however, is the result of symbiotic associations between chemolithotrophic bacteria and certain invertebrates, which have also been found as fossils in Cretaceous sulfide ores of ophiolite deposits.

Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110°C

A novel group of hyperthermophilic rod-shaped motile methanogens was isolated from a hydrothermally heated deep sea sediment (Guaymas Basin, Gulf of California) and from a shallow marine hydrothermal system (Kolbeinsey ridge, Iceland). The grew between 84 and 110°C (opt: 98°C) and from 0.2% to 4% NaCl (opt. 2%) and pH 5.5 to 7 (opt: 6.5). The isolates were obligate chemolithoautotrophes using H2/CO2 as energy and carbon sources. In the presence of sulfur, H2S was formed and cells tended to lyse. The cell wall consisted of a new type of pseudomurein containing ornithin in addition to lysine and no N-acetylglucosamine. The pseudomurein layer was covered by a detergent-sensitive protein surface layer. The core lipid consisted exclusively of phytanyl diether. The GC content of the DNA was 60 mol%. By 16S rRNA comparisons the new organisms were not related to any of the three methanogenic lineages. Based on the physiological and molecular properties of the new isolates, we describe here a new genus, which we name Methanopyrus (the “methane fire”). The type species is Methanopyrus kandleri (type strain: AV19; DSM 6324).

Deep-Sea Primary Production at the Galapagos Hydrothermal Vents

Dense animal populations surrounding recently discovered hydrothermal vents at the Galapagos Rift sea-floor spreading center, 2550 meters deep, are probably sustained by microbial primary production. Energy in the form of geothermically reduced sulfur compounds emitted from the vents is liberated during oxidation and used for the reduction of carbon dioxide to organic matter by chemosynthetic bacteria.

Anaerobic Magnetite Production by a Marine, Magnetotactic Bacterium

Bacterial production of magnetite represents a significant contribution to the natural remanent magnetism of deep-sea and other sediments1–5. Because cells of the freshwater magnetotactic bacterium Aquaspirillum magnetotacticum require molecular oxygen for growth and magnetite synthesis6, production of magnetite by magnetotactic bacteria has been considered to occur only in surficial aerobic sediments7. Moreover, it has been suggested that deposits of single-domain magnetite crystals are palaeooxygen indicators presumably having been formed under predominantly microaerobic conditions5–8. In contrast, some nonmagnetotactic, dissimilatory iron-reducing bacteria, such as the recently described strain GS-15 by Lovley et al.7, synthesize extracellular magnetite from hydrous ferric oxide under anaerobic conditions. We now report the first isolation and axenic culture of a marine, magnetotactic bacterium, designated MV-1, that can synthesize intracellular, single-domain magnetite crystals under strictly anaerobic conditions. We conclude that magnetotactic bacteria do not necessarily require molecular oxygen for magnetite synthesis and suggest that they, as well as dissimilatory iron-reducing bacteria, can contribute to the natural remanent magnetism of even long-term anaerobic sediments.

Bacterial Sulfate Reduction Above 100°C in Deep-Sea Hydrothermal Vent Sediments

The currently known upper temperature limit for growth of organisms, shared by a number of archaebacteria, is 110�C. However, among the sulfate-reducing bacteria, growth temperatures of greater than 100�C have not been found. A search for high-temperature activity of sulfate-reducing bacteria was done in hot deep-sea sediments at the hydrothermal vents of the Guaymas Basin tectonic spreading center in the Gulf of California. Radiotracer studies revealed that sulfate reduction can occur at temperatures up to 110�C, with an optimum rate at 103� to 106�C. This observation expands the upper temperature limit of this process in deep-ocean sediments by 20�C and indicates the existence of an unknown group of hyperthermophilic bacteria with a potential importance for the biogeochemistry of sulfur above 100�C.

Stable isotope studies of the carbon, nitrogen and sulfur cycles in the Black Sea and the Cariaco Trench

Abstract Samples for stable isotope studies of possible chemosynthesis in anoxic basins were collected in 1986 in the Cariaco Trench and May 1988 in the Black Sea. POM (particulate organic matter) collected at oxic/anoxic interfaces in the water column showed no distinctive carbon or nitrogen isotopic compositions that could be associated with chemosynthetic bacteria. Carbon and nitrogen isotopic compositions at POM concentration maxima near the top of the sulfide zone were −23%o and 4.5%o, respectively, in both the Black Sea and the Cariaco Trench. Measurements of dissolved inorganic carbon (DIC) in the Black Sea indicated that carbon respired during decomposition at depth had an isotopic composition of −23%o and was isotopically similar to phytoplankton, with no distinctive component that could be attributed to chemosynthetic carbon. These results indicate that either the biomass of chemosynthetic bacteria in the oxic/anoxic interface zones is low relative to sinking phytoplankton or that chemoautotrophic bacteria have isotopic compositions similar to those of phytoplankton. In the uppermost 50 m of sulfidic waters in the Black Sea, sulfide isotopic compositions changed significantly in a region of sulfide consumption, increasing up to 5%o vs deep-water background values of −40.5%o. These increases in sulfide isotopic compositions may be due to sulfide oxidation mediated by MnO 2 or oxygen, but are not consistent with sulfide oxidation by photosynthetic bacteria. Growth experiments with sulfate-reducing bacteria suggested that part of the increase in sulfide isotopic compositions could be due to rapid rates of sulfate reduction in the oxic/anoxic interface regions.

Sulfide oxidation in the anoxic Black Sea chemocline

The depth distributions of O2 and H2S and of the activity of chemical or bacterial sulfide oxidation were studied in the chemocline of the central Black Sea. Relative to measurements from earlier studies, the sulfide zone had moved upwards by 20–50 m and was now (May 1988) situated at a depth of 81–99 m. Oxygen in the water column immediately overlying the sulfide zone was depleted to undetectable levels resulting in a 20–30-m deep intermediate layer of O2 - and H2S-free water. Radiotracer studies with 35S-labelled H2S showed that high rates of sulfide oxidation, up to a few micromoles per liter per day, occurred in anoxic water at the top of the sulfide zone concurrent with the highest rates of dark CO2 assimilation. The main soluble oxidized products of sulfide were thiosulfate (68–82%) and sulfate. Indirect evidence was presented for the formation of elemental sulfur which accumulated to a maximum of 200 nmol l−1 at the top of the sulfide zone. Sulfide oxidation was stimulated by particles suspended at the chemocline, probably by bacteria. Green phototrophic sulfur bacteria were abundant in the chemocline, suggesting that photosynthetic H2S oxidation took place. Flux calculations showed that the measured H2S oxidation rates were 4-fold higher than could be explained by the downward flux of organic carbon and too high to balance the availability of electron acceptors such as oxidized iron or manganese. A nitrate maximum at the lower boundary of the O2 zone did not extend down to the sulfide zone.

Thermococcus litoralis sp. nov.: A new species of extremely thermophilic marine archaebacteria

We describe a new species, Thermococcus litoralis, which is different from the type species Thermococcus celer in molecular, morphological and physiological characteristics.