Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient.

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

Links between geographic location, environmental factors, and microbial community composition in sediments of the Eastern Mediterranean Sea.

The bacterial community composition of marine surface sediments originating from various regions of the Eastern Mediterranean Sea (12 sampling sites) was compared by parallel use of three fingerprinting methods: analysis of 16S rRNA gene fragment heterogeneity by denaturing gradient electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), and analysis of phospholipid-linked fatty acid composition (PLFA). Sampling sites were located at variable depths (30-2860 m; water column depth above the sediments) and the sediments differed greatly also in their degree of petroleum contamination (0.4-18 microg g(-1)), organic carbon (0.38-1.5%), and chlorophyll a content (0.01-7.7 microg g(-1)). Despite a high degree of correlation between the three different community fingerprint methods, some major differences were observed. DGGE banding patterns showed a significant separation of sediment communities from the northern, more productive waters of the Thermaikos Gulf and the oligotrophic waters of the Cretan, S. Ionian, and Levantine Sea. T-RFLP analysis clearly separated the communities of deep sediments (>1494 m depth) from their shallow (<617 m) counterparts. PLFA analysis grouped a shallow station from the productive waters of the north with the deep oligotrophic sediments from the Ionian and Levantine Sea, with low concentrations of PLFAs, and hence low microbial biomass, as the common denominator. The degree of petroleum contamination was not significantly correlated to the apparent composition of the microbial communities for any of the three methods, whereas organic carbon content and sediment chlorophyll a were important in this regard.

Reactions of hydroxyl radical with humic substances: bleaching, mineralization, and production of bioavailable carbon substrates.

In this study, we examine the role of the hydroxyl (OH*) radical as a mechanism for the photodecomposition of chromophoric dissolved organic matter (CDOM) in sunlit surface waters. Using gamma-radiolysis of water, OH* was generated in solutions of standard humic substances in quantities comparable to those produced on time scales of days in sunlit surface waters. The second-order rate coefficients of OH* reaction with Suwannee River fulvic (SRFA; 2.7 x 10(4) s(-1) (mg of C/L)(-1)) and humic acids (SRHA; 1.9 x 10(4) s(-1) (mg of C/L)(-1)) are comparable to those observed for DOM in natural water samples and DOM isolates from other sources but decrease slightly with increasing OH* doses. OH* reactions with humic substances produced dissolved inorganic carbon (DIC) with a high efficiency of approximately 0.3 mol of CO2/mol of OH*. This efficiency stayed approximately constant from early phases of oxidation until complete mineralization of the DOM. Production rates of low molecular weight (LMW) acids including acetic, formic, malonic, and oxalic acids by reaction of SRFA and SRHA with OH* were measured using HPLC. Ratios of production rates of these acids to rates of DIC production for SRHA and for SRFA were similar to those observed upon photolysis of natural water samples. Bioassays indicated that OH* reactions with humic substances do not result in measurable formation of bioavailable carbon substrates other than the LMW acids. Bleaching of humic chromophores by OH* was relatively slow. Our results indicate that OH* reactions with humic substances are not likely to contribute significantly to observed rates of DOM photomineralization and LMW acid production in sunlit waters. They are also not likely to be a significant mechanism of photobleaching except in waters with very high OH* photoformation rates.

An inhibitor-based method to measure initial decomposition of naturally occurring polysaccharides in sediments.

A method that can be used to measure the initial decomposition rates of polysaccharides in sediment samples was developed. It uses toluene to specifically inhibit microbial uptake of carbohydrates without affecting extracellular hydrolysis of polysaccharides. Accumulating carbohydrates were determined by high-performance liquid chromatography. Field-sampled litter from the common reed (Phragmites australis), which contains cellulose and arabinoxylan as its main polysaccharides, was used as a model system. Toluene concentrations of between 1 and 10% resulted in the accumulation of similar amounts of monomeric carbohydrates, which was linear over time for most neutral sugars. Toluene (3%) did not have an effect on extracellular enzyme activities, and microbial sugar uptake was completely inhibited, as demonstrated with (sup14)C-labelled xylose and glucose. Experiments with enhancement cultures and fixed reed litter suggested that enzymatic hydrolysis of polysaccharides in reed litter was the main source of glucose, xylose, arabinose, and galactose accumulation. In contrast, the accumulation of high amounts of the alditols mannitol and glucitol was probably caused by lysis of the microbial population in toluene-treated reed litter. Glucose accumulated at rates of 1.3 and 0.10 (mu)mol (middot) g of dry matter content(sup-1) (middot) h(sup-1) under aerobic and anaerobic conditions, respectively, whereas xylose accumulation rates were only 10% of the glucose accumulation rates.