Jens Harder

Sulfate reduction and methanogenesis in a Thioploca-dominated sediment off the coast of Chile

Continental shelf sediments of the central Chile upwelling area are dominated by the presence of dense mats of the filamentous, sulfur-depositing bacterium Thioploca spp. We examined rates and pathways of S and methane cycling in these sediments along a transect from the Bay of Concepcion to the continental slope. Sulfate reduction rates (170–4670 nmol cm−3 d−1) were equal to or exceeded rates reported for other subtidal marine sediments. Elemental S and pyrite were the dominant end-products of sulfate reduction in Thioploca mats on the continental shelf, whereas, in the highly-reducing, Beggiatoa-dominated sediments of the nearby Bay of Concepcion, acid-volatile S was the principal end-product. Dissolved organic C values were lowest at the stations with the highest sulfate reduction rates and increased offshore. Sediment porewater methane concentrations in all surface sediments were low (<12 nmol cm−3), and methane production rates at the station most dominated by Thioploca were extremely low ( <0.5 nmol cm−3 d−1). Low methane production rates and concentrations were matched by low methane oxidation rates (<0.1 nmol cm−3 d−1). Radio-tracer studies showed that methane production was almost exclusively from methylamines, substrates which are noncompetitive with sulfate reduction, rather than from acetate or CO2/H2. Bacterial MPN (most probable number) counts also indicated the presence of a methylotrophic population of methanogens. Surprisingly, high numbers of autotrophic acetogenic bacteria were found, suggesting that the bacterial population involved in anaerobic DOC degradation is more complex than expected. In spite of the high sulfate reduction rates, sulfide concentrations in the shelf and slope were low or undetectable (<0.5 μM), and sulfate concentrations were never depleted below bottom water levels down to depths of 25–30 cm. Calculations suggest that Thioploca were oxidizing a maximum of 35% of sulfide production—not enough to prevent sulfate depletion. Either other sulfide oxidizers were also present or transient hydrodynamic conditions coupled with bioturbation resulted in oxidation of the sediments.

Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean

Microbial biogeographic patterns in the deep sea depend on the ability of microorganisms to disperse. One possible limitation to microbial dispersal may be the Walvis Ridge that separates the Antarctic Lower Circumpolar Deep Water from the North Atlantic Deep Water. We examined bacterial communities in three basins of the eastern South Atlantic Ocean to determine diversity and biogeography of bacterial communities in deep-sea surface sediments. The analysis of 16S ribosomal RNA (rRNA) gene clone libraries in each basin revealed a high diversity, representing 521 phylotypes with 98% identity in 1051 sequences. Phylotypes affiliated with Gammaproteobacteria, Deltaproteobacteria and Acidobacteria were present in all three basins. The distribution of these shared phylotypes seemed to be influenced neither by the Walvis Ridge nor by different deep water masses, suggesting a high dispersal capability, as also indicated by low distance–decay relationships. However, the total bacterial diversity showed significant differences between the basins, based on 16S rRNA gene sequences as well as on terminal restriction fragment length polymorphism fingerprints. Noticeably, both geographic distance and environmental heterogeneity influenced bacterial diversity at intermediate (10–3000 km) and large scales (>3000 km), indicating a complex interplay of local contemporary environmental effects and dispersal limitation.

Anaerobic oxidation of alkanes by newly isolated denitrifying bacteria

Abstract The capacity of denitrifying bacteria for anaerobic utilization of saturated hydrocarbons (alkanes) was investigated with n-alkanes of various chain lengths and with crude oil in enrichment cultures containing nitrate as electron acceptor. Three distinct types of denitrifying bacteria were isolated in pure culture. A strain (HxN1) with oval-shaped, nonmotile cells originated from a denitrifying enrichment culture with crude oil and was isolated with n-hexane (C6H14). Another strain (OcN1) with slender, rod-shaped, motile cells was isolated from an enrichment culture with n-octane (C8H18). A third strain (HdN1) with oval, somewhat pleomorphic, partly motile cells originated from an enrichment culture with aliphatic mineral oil and was isolated with n-hexadecane (C16H34). Cells of hexane-utilizing strain HxN1 grew homogeneously in the growth medium and did not adhere to the alkane phase, in contrast to the two other strains. Quantification of substrate consumption and cell growth revealed the capacity for complete oxidation of alkanes under strictly anoxic conditions, with nitrate being reduced to dinitrogen.

New trends in marine chemical ecology

This essay is the outcome of a colloquium convened in November 2005 at the Benthos Laboratory of the Stazione Zoologica Anton Dohrn in Ischia, Italy, on chemical ecology and the role of secondary metabolites in the structuring and functioning of marine biodiversity. The participants of the workshop are part of the European Network of Excellence MarBEF (Marine Biodiversity and Ecosystem Function), a consortium of 56 European marine institutes to integrate and disseminate knowledge and expertise on marine biodiversity. Here we review some of the new trends and emerging topics in marine chemical ecology. The first section deals with microbial chemical interactions. Microbes communicate with each other using diffusible molecules such as N-acylhomoserine lactones (AHL). These are regulators in cell-density-dependent gene regulation (quorum sensing) controlling microbial processes. In chemical interactions with higher organisms, microbes can act either as harmful pathogens that are repelled by the host’s chemical defense or as beneficial symbionts. These symbionts are sometimes the true producers of the host’s secondary metabolites that have defensive and protective functions for their hosts. We also describe how allelochemicals can shape phytoplankton communities by regulating competition for available resources, and also interactions among individuals of the same species. Compounds such as the diatom-derived unsaturated aldehydes have been demonstrated to act as info chemicals, and they possibly function as a diffusible bloom-termination signal that triggers an active cell death and bloom termination at sea. The same molecules have also been shown to interfere with the reproductive capacity of grazing animals deterring future generations of potential predators. Such compounds differ from those that act as feeding deterrents since they do not target the predator but its offspring. Many of the neurotoxins produced by dinoflagellates act as feeding deterrents, and laboratory experiments have shown that ingestion of these algae by some microzooplankton and macrozooplankton can cause acute, responses such as death, incapacitation, altered swimming behavior, and reduced fecundity and egg-hatching success. These effects may rarely occur in nature because of low individual grazing rates on dinoflagellate cells and grazing on other food sources such as microflagellates and diatoms. We also consider the nutritional component of marine plant-herbivore interactions, especially in the plankton, and the information available on the effects of growing conditions of algae on the production of toxic metabolites. Species producing saxitoxins seem to consistently produce the highest amounts of toxins (on a per cell basis) in the exponential phase of growth, and there is a decrease in their production under nitrogen, but not under phosphorus stress, where the production actually increases. We try to explain the circumstances under which organisms defend themselves chemically and argue that the most likely explanatory model for the production of secondary metabolites used for defense in planktonic organisms is the carbon nutrient balance hypothesis, which predicts that most algae produce their toxins mainly under conditions where carbon is in excess and nitrogen (or other nutrients) is limiting. We also discuss chemically mediated macroalgal-herbivore interactions in the benthos and the large variation in concentration of seaweed defense metabolites at different spatial and temporal scales. Seaweeds have been shown to produce a large variety of secondary metabolites with highly variable chemical structures such as terpenoids, acetogenins, amino acid derivates, and polyphenols. Many of these compounds probably have multiple simultaneous functions for the seaweeds and can act as allelopathic, antimicrobial, and antifouling or ultraviolet-screening agents, as well as herbivore deterrents. We also provide examples of interactions between marine benthic invertebrates, especially sponges, molluscs, and cnidarians, that are mediated by specific secondary metabolites and discuss the role of these in shaping benthic communities.

The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides.

ABSTRACT In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901T), an isolate from the green alga Acrosiphonia sonderi. F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and κ-carrageenans.

Effects of Deletion of Genes Encoding Fe-Only Hydrogenase of Desulfovibrio vulgaris Hildenborough on Hydrogen and Lactate Metabolism

The physiological properties of a hyd mutant of Desulfovibrio vulgaris Hildenborough, lacking periplasmic Fe-only hydrogenase, have been compared with those of the wild-type strain. Fe-only hydrogenase is the main hydrogenase of D. vulgaris Hildenborough, which also has periplasmic NiFe- and NiFeSe-hydrogenases. The hyd mutant grew less well than the wild-type strain in media with sulfate as the electron acceptor and H(2) as the sole electron donor, especially at a high sulfate concentration. Although the hyd mutation had little effect on growth with lactate as the electron donor for sulfate reduction when H(2) was also present, growth in lactate- and sulfate-containing media lacking H(2) was less efficient. The hyd mutant produced, transiently, significant amounts of H(2) under these conditions, which were eventually all used for sulfate reduction. The results do not confirm the essential role proposed elsewhere for Fe-only hydrogenase as a hydrogen-producing enzyme in lactate metabolism (W. A. M. van den Berg, W. M. A. M. van Dongen, and C. Veeger, J. Bacteriol. 173:3688-3694, 1991). This role is more likely played by a membrane-bound, cytoplasmic Ech-hydrogenase homolog, which is indicated by the D. vulgaris genome sequence. The physiological role of periplasmic Fe-only hydrogenase is hydrogen uptake, both when hydrogen is and when lactate is the electron donor for sulfate reduction.

Anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on pivalic acid (2,2-dimethylpropionic acid).

ABSTRACT The degradability of pivalic acid was established by the isolation of several facultative denitrifying strains belonging to Zoogloea resiniphila, to Thauera and Herbaspirillum, and to Comamonadaceae, related to [Aquaspirillum] and Acidovorax, and of a nitrate-reducing bacterium affiliated with Moraxella osloensis. Pivalic acid was completely mineralized to carbon dioxide. The catabolic pathways may involve an oxidation to dimethylmalonate or a carbon skeleton rearrangement, a putative 2,2-dimethylpropionyl coenzyme A mutase.

Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes

Roseobacter clade bacteria (RCB) are abundant in marine bacterioplankton worldwide and central to pelagic sulfur cycling. Very little is known about their abundance and function in marine sediments. We investigated the abundance, diversity and sulfur oxidation potential of RCB in surface sediments of two tidal flats. Here, RCB accounted for up to 9.6% of all cells and exceeded abundances commonly known for pelagic RCB by 1000-fold as revealed by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA and sulfate thiohydrolase (SoxB) genes indicated diverse, possibly sulfur-oxidizing RCB related to sequences known from bacterioplankton and marine biofilms. To investigate the sulfur oxidation potential of RCB in sediments in more detail, we analyzed a metagenomic fragment from a RCB. This fragment encoded the reverse dissimilatory sulfite reductase (rDSR) pathway, which was not yet found in RCB, a novel type of sulfite dehydrogenase (SoeABC) and the Sox multi-enzyme complex including the SoxCD subunits. This was unexpected as soxCD and dsr genes were presumed to be mutually exclusive in sulfur-oxidizing prokaryotes. This unique gene arrangement would allow a metabolic flexibility beyond known sulfur-oxidizing pathways. We confirmed the presence of dsrA by geneFISH in closely related RCB from an enrichment culture. Our results show that RCB are an integral part of the microbial community in marine sediments, where they possibly oxidize inorganic and organic sulfur compounds in oxic and suboxic sediment layers.

Alcaligenes defragrans sp. nov., Description of Four Strains Isolated on Alkenoic Monoterpenes ((+)-menthene, α-pinene, 2-carene, and α-phellandrene) and Nitrate

Four pseudomonad strains 51Men, 54Pin, 62Car and 65Phen were recently isolated on the monoterpenes (+)-menthene, alpha-pinene, 2-carene and alpha-phellandrene as sole carbon source and nitrate as electron acceptor. These bacteria were characterised. The motile, mesophilic, Gram-negative rods had a strictly respiratory metabolism. Monoterpenes as carbon sources were completely mineralised to carbon dioxide. The physiology of all strains was very similar, but displayed an individual utilisation preference for the isolation substrate. The fatty acid composition of whole cells showed a high degree of similarity to that of Alcaligenes faecalis. Comparative 16S rDNA data analysis placed the isolates into the beta-subclass of Proteobacteria in a common offshoot together with Alcaligenes and Bordetella species. On the basis of these characteristics, the strains are described as a new species belonging to the genus Alcaligenes, A. defragrans sp. nov., with strain 54Pin (DSM 12141T) as type strain.

ANAEROBIC METHANE OXIDATION BY BACTERIA EMPLOYING 14C-METHANE UNCONTAMINATED WITH 14C-CARBON MONOXIDE

14C-labelled methane, biologically prepared by Methanobacterium thermoautotrophicum, is widely used to determine methane oxidation rates. However, M. thermoautotrophicum synthesizes carbon monoxide as a by-product during methanogenesis. In this study, sulfate-reducing bacteria utilizing the acetyl-CoA/carbon monoxide-dehydrogenase pathway were able to form 14CO2 from 14CH4 containing 14CO. 14C-labelled carbon monoxide was removed from 14CH4 by oxidation over hopcalite to carbon dioxide and fixation in sodium hydroxide solution. Measurable formation of 14CO2 from purified 14C-labelled methane by sulfate-reducing bacteria was not observed. Therefore, reported anaerobic methane oxidation rates in marine habitats measured with 14CH4 from M. thermoautotrophicum are inclined to include carbon monoxide oxidation rates. Anaerobic oxidation of 14CH4 by sulfate-reducing and acetogenic bacteria and methanogenic archaebacteria was tested. Only methanogenic species produced up to 900 ppm 14CO2 from 14CH4 applied. This observation and the absence of methane oxidation by sulfate-reducing bacteria sustain the hypothesis that methanogenic archaebacteria in a syntrophic community might be responsible for the oxidation of methane in anaerobic habitats.