Kai Finster

Biogeochemical and Molecular Signatures of Anaerobic Methane Oxidation in a Marine Sediment

ABSTRACT Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802–805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the generaDesulfonema, Desulfococcus, andDesulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.

A constant flux of diverse thermophilic bacteria into the cold Arctic seabed.

Monitoring Massive Microbial Dispersal Quantifying the relative influence of present-day environmental conditions and geological history on the spatial distribution of species represents a major challenge in microbial ecology. Ecological approaches to distinguish between these two biogeographic controls are limited by environmental variability both in space and through time (see the Perspective by Patterson). Using a 1.5-million-year fossil record of marine diatoms, Cermeño and Falkowski (p. 1539) show that, even at the largest (global) spatial scale, the dispersal of marine diatoms is not very limited. Environmental factors are the primary control shaping the global biogeography of marine diatom morphospecies. Thermophilic microorganisms are routinely detected in permanently cold environments from deep sea sediments to polar soils. Hubert et al. (p. 1541) provide a quantitative analysis of a potentially large-scale dispersion of thermophilic bacteria in the ocean. Approximately 108 thermophilic spores are deposited each year on every square meter of Arctic sediment. Spore-forming bacteria adapted to the hot subsurface biosphere are continually deposited in polar marine sediments. Microorganisms have been repeatedly discovered in environments that do not support their metabolic activity. Identifying and quantifying these misplaced organisms can reveal dispersal mechanisms that shape natural microbial diversity. Using endospore germination experiments, we estimated a stable supply of thermophilic bacteria into permanently cold Arctic marine sediment at a rate exceeding 108 spores per square meter per year. These metabolically and phylogenetically diverse Firmicutes show no detectable activity at cold in situ temperatures but rapidly mineralize organic matter by hydrolysis, fermentation, and sulfate reduction upon induction at 50°C. The closest relatives to these bacteria come from warm subsurface petroleum reservoir and ocean crust ecosystems, suggesting that seabed fluid flow from these environments is delivering thermophiles to the cold ocean. These transport pathways may broadly influence microbial community composition in the marine environment.

Variable sensitivity of fungi and bacteria to compounds produced by the metapleural glands of leaf-cutting ants

Summary: Ants are the only group of insects that have metapleural glands. Secretions of these exocrine glands are known to have antibiotic properties and have been hypothesised to function as a general defence against microbial and fungal infections. Such defences are likely to be particularly important in leaf-cutting ants that need to protect both themselves and their clonal mutualistic fungus against pathogens. The metapleural gland of the leaf-cutting ant Acromyrmex octospinosus produces an array of organic compounds (Ortius-Lechner et al., 2000), suggesting that different compounds may be effective against different kinds of infections. Here we provide a detailed analysis of the sensitivity of two species of bacteria and seven species of fungi (including the mutualistic fungus) to these metapleural gland compounds, grouped in seven classes: acetic acid, short chain acids, medium chain acids, long chain acids, indoleacetic acid, γ-lactones and γ-ketoacids. All classes of compounds inhibited the growth of at least some of the tested micro-organisms. Cluster analysis produced four groups of micro-organisms differing in their overall sensitivity. Among-cluster differences explained a major part of the total variation in sensitivity (MANOVA), although differences between micro-organisms within clusters were also significant. Fungal hyphae and fungal spores never clustered together, indicating that defence mechanisms against these fungal life stages are fundamentally different. The mutualistic fungus was sensitive to all classes of compounds, which suggests that defence via metapleural gland secretion is under constraint when the protection of the fungus garden is concerned.

Hailstones: A Window into the Microbial and Chemical Inventory of a Storm Cloud

Storm clouds frequently form in the summer period in temperate climate zones. Studies on these inaccessible and short-lived atmospheric habitats have been scarce. We report here on the first comprehensive biogeochemical investigation of a storm cloud using hailstones as a natural stochastic sampling tool. A detailed molecular analysis of the dissolved organic matter in individual hailstones via ultra-high resolution mass spectrometry revealed the molecular formulae of almost 3000 different compounds. Only a small fraction of these compounds were rapidly biodegradable carbohydrates and lipids, suitable for microbial consumption during the lifetime of cloud droplets. However, as the cloud environment was characterized by a low bacterial density (Me = 1973 cells/ml) as well as high concentrations of both dissolved organic carbon (Me = 179 µM) and total dissolved nitrogen (Me = 30 µM), already trace amounts of easily degradable organic compounds suffice to support bacterial growth. The molecular fingerprints revealed a mainly soil origin of dissolved organic matter and a minor contribution of plant-surface compounds. In contrast, both the total and the cultivable bacterial community were skewed by bacterial groups (γ-Proteobacteria, Sphingobacteriales and Methylobacterium) that indicated the dominance of plant-surface bacteria. The enrichment of plant-associated bacterial groups points at a selection process of microbial genera in the course of cloud formation, which could affect the long-distance transport and spatial distribution of bacteria on Earth. Based on our results we hypothesize that plant-associated bacteria were more likely than soil bacteria (i) to survive the airborne state due to adaptations to life in the phyllosphere, which in many respects matches the demands encountered in the atmosphere and (ii) to grow on the suitable fraction of dissolved organic matter in clouds due to their ecological strategy. We conclude that storm clouds are among the most extreme habitats on Earth, where microbial life exists.

Fermentation of methanethiol and dimethylsulfide by a newly isolated methanogenic bacterium

AbstractFrom dilution series in defined mineral medium, a marine iregular coccoid methanogenic bacterium (strain MTP4) was isolated that was able to grow on methanethiol as sole source of energy. The strain also grew on dimethylsulfide, mono-, di-, and trimethylamine, methanol and acetate. On formate the organism produced methane without significant growth. Optimal growth on MT, with doubling times of about 20 h, occurred at 30°C in marine medium. The isolate required p-aminobenzoate and a further not identified vitamin. Strain MTP4 had a high tolerance to hydrogen sulfide but was very sensitive to mechanical forces or addition of detergents such as Triton X-100 or sodium dodecylsulfate. Methanethiol was fermented by strain MTP4 according to the following equation: 1

Microbiological disproportionation of inorganic sulfur compounds

\begin{array}{*{20}c} {4CH_3 SH + 3H_2 O \to 3CH_4 + HCO_3^ - } \\ { + 4HS^ - + 5H^ + } \\ {(\Delta G^{{\rm O}{\rm I}} = - 36.9kJ/MT)} \\ \end{array}

Sulfurospirillum arcachonense sp. nov., a New Microaerophilic Sulfur-Reducing Bacterium

The growth yield was 3.06 g cell dry mass per mol of MT. During growth on MT the isolate released small amounts of DMS and, vice versa, degradation of DMS was accompanied by significant intermediate MT production.

A Comprehensive Investigation on Iron Cycling in a Freshwater Seep Including Microscopy, Cultivation and Molecular Community Analysis

Formation of gas and of methylated sulfur compounds was observed in anaerobic enrichment cultures with methoxylated aromatic compounds as substrates. Via direct dilution of mud samples in defined reduced media supplemented with trimethoxybenzoate or syringate two new strains of anaerobic homoacetogenic bacteria (strain TMBS4 and strain SA2) were obtained in pure culture. Both strains produced dimethylsulfide and methanethiol during growth on methoxylated aromatic compounds. Growth tests and determination of stoichiometries demonstrated that the volatile sulfur compounds were formed from the methyl group at the aromatic ring and the sulfide added as reducing agent to the medium (R = aromatic residue): 2 R - O - CH3 + H2 S → 2 R - OH + (CH3)2SDimethylsulfide was the major organic sulfur compound formed, whereas methanethiol appeared only as intermediate in small quantities. The isolates grew also with trihydroxybenzenes such as gallate, phloroglucinol, or pyrogallol without formation of methylated sulfur compounds. The aromatic compounds were degraded to acetate. The freshwater strain TMBS4 also fermented pyruvate. Other aliphatic or aromatic compounds were not utilized. External electron acceptors (sulfate, nitrate, fumarate) were not reduced. Both strains were mesophilic and formed rod-shaped, non-motile, Gram-negative cells. Spore formation was not observed. Tentatively, both isolates can be affiliated to the genus Pelobacter.