Anoxic nitrification in marine sediments

Nitrate peaks are found in pore-water profiles in marine sediments at depths considerably below the conventional zone of oxic nitrification. These have been interpreted to represent nonsteady- state effects produced by the activity of nitrifying bacteria, and suggest that nitrification occurs throughout the anoxic sediment region. In this study, ΣNO3 peaks and molecular analysis of DNA and RNA extracted from anoxic sediments of Loch Duich, an organic-rich marine fjord, are consistent with nitrification occurring in the anoxic zone. Analysis of ammonia oxidiser 16S rRNA gene fragments amplified from sediment DNA indicated the abundance of autotrophic ammonia-oxidising bacteria throughout the sediment depth sampled (40 cm), while RT-PCR analysis indicated their potential activity throughout this region. A large non-steady-state pore-water ΣNO3 peak at ~21 cm correlated with discontinuities in this ammonia-oxidiser community. In addition, a subsurface nitrate peak at ~8 cm below the oxygen penetration depth, correlated with the depth of a peak in nitrification rate, assessed by transformation of 15N-labelled ammonia. The source of the oxidant required to support nitrification within the anoxic region is uncertain. It is suggested that rapid recycling of N is occurring, based on a coupled reaction involving Mn oxides (or possibly highly labile Fe oxides) buried during small-scale slumping events. However, to fully investigate this coupling, advances in the capability of high-resolution pore-water techniques are required

Схиигумен Сергий как маргинальная языковая личность в пространстве религиозно-политической коммуникации

SummaryThaumarchaeota are globally distributed and abundantmicroorganisms occurring in diverse habitats and thusrepresent a major source of archaeal lipids. The scopeof lipids as taxonomic markers in microbial ecologicalstudies is limited by the scarcity of comparative dataon the membrane lipid composition of cultivated representatives,including the phylum Thaumarchaeota.Here, we comprehensively describe the core and intactpolar lipid (IPL) inventory of ten ammonia-oxidisingthaumarchaeal cultures representing all four characterizedphylogenetic clades. IPLs of these thaumarchaealstrains are generally similar and consist of membranespanning,glycerol dibiphytanyl glycerol tetraetherswith monoglycosyl, diglycosyl, phosphohexose andhexose-phosphohexose headgroups. However, the relativeabundances of these IPLs and their core lipidcompositions differ systematically between the phylogeneticsubgroups, indicating high potential forchemotaxonomic distinction of thaumarchaeal clades.Comparative lipidomic analyses of 19 euryarchaeal andcrenarchaeal strains suggested that the lipid methoxyarchaeol is synthesized exclusively by Thaumarchaeotaand may thus represent a diagnostic lipidbiomarker for this phylum. The unprecedented diversityof the thaumarchaeal lipidome with 118 differentlipids suggests that membrane lipid composition andadaptation mechanisms in Thaumarchaeota are morecomplex than previously thought and include uniquelipids with as yet unresolved properties

Growth kinetics of Botrytis cinerea on organic acids and sugars in relation to colonization of grape berries

The relationship between hyphal growth and branching of the grape pathogen Botrytis cinerea was determined on solid media containing either glucose, fructose, sucrose, tartaric acid or malic acid. The concentration of the carbon source has little effect on specific growth rate or the specific rate of tip formation, but growth was inhibited at high concentration of tartaric and malic acids. Hyphal growth unit length and hyphal extension rate increased with increasing sugar concentration and were always significantly greater than values on tartaric or malic acids. The data provide an explanation for colonization patterns of grape berries. Growth will be poor during the period from setting to the onset of ripening, when organic acids are teh main carbon source produced by the berry. Following the onset of ripening, the production of sugars provides more favourable carbon sources for the fungus, enabling achievement of higher specific growth rates, greater hyphal extension rates and, hence, greater colonizing potential

Ecology and metagenomics of soil microorganisms.

no Abstrac

Analysis of ß-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing

A combination of denaturing gradient gel electrophoresis (DGGE) and oligonucleotide probing was used to investigate the influence of soil pH on the compositions of natural populations of autotrophic beta-subgromp proteobacterial ammonia oxidizers. PCR primers specific to this group were used to amplify 16S ribosomal DIVA (rDNA) from soils maintained for 36 years at a range of pH values, and PCR products were analyzed by DGGE, Genus- and cluster-specific probes were designed to bind to sequences within the region amplified by these primers, A sequence specific to all beta-subgroup ammonia oxidizers could not be identified, but probes specific for Nitrosospira clusters 1 to 4 and Nitrosomonas clusters 6 and 7 (J. R. Stephen, A. E. McCaig, Z. Smith, J. I. Presser, and T. M. Embley, Appl. Environ. Microbiol. 62:4147-4154, 1996) were designed. Elution profiles of probes against target sequences and closely related nontarget sequences indicated a requirement for high-stringency hybridization conditions to distinguish between different clusters, DGGE banding patterns suggested the presence of Nitrosomonas cluster 6a and Nitrosospira clusters 2, 3, and 4 in all soil plots, but results mere ambiguous because of overlapping banding patterns, Unambiguous hand identification of the same clusters was achieved by combined DGGE and probing of blots with the cluster-specific radiolabelled probes, The relative intensities of hybridization signals provided information on the apparent selection of different Nitrosospira genotypes in samples of soil of different pHs. The signal from the Nitrosospira cluster 3 probe decreased significantly, relative to an internal control probe, with decreasing soil pH in the range of 6.6 to 3.9, while Nitrosospira cluster 2 hybridization signals increased with increasing soil acidity. Signals from Nitrosospira cluster 4 were greatest at pH 5.5, decreasing at lower and higher values, while Nitrosomonas cluster 6a signals did not vary significantly with pH. These findings are in agreement with a previous molecular study (J, R Stephen, A. E. McCaig, Z. Smith, J. I, Presser, and T, M. Embley, Appl, Environ. Microbiol 62:4147-4154, 1996) of the same sites, which demonstrated the presence of the same four clusters of ammonia oxidizers and indicated that selection might be occurring for clusters 2 and 3 at acid and neutral pHs, respectively. The two studies used different sets of PCR primers for amplification of 16S rDNA sequences from soil, and the similar findings suggest that PCR bias was unlikely to be a significant factor, The present study demonstrates the value of DGGE and probing for rapid analysis of natural soil communities of beta-subgroup proteobacterial ammonia oxidizers, indicates significant pH-associated differences in Nitrosospira populations, and suggests that Nitrosospira cluster 2 may be of significance for ammonia- oxidizing activity in acid soils. [KEYWORDS: 16s ribosomal-rna; nitrifying bacteria; gene-sequences; low ph; autotrophic nitrification; purple bacteria; diversity; organization; subdivision; oxidation]

Variation in Biofilm Formation among Strains of Listeria monocytogenes

Contamination of food by Listeria monocytogenes is thought to occur most frequently in food-processing environments where cells persist due to their ability to attach to stainless steel and other surfaces. Once attached these cells may produce multicellular biofilms that are resistant to disinfection and from which cells can become detached and contaminate food products. Because there is a correlation between virulence and serotype (and thus phylogenetic division) of L. monocytogenes , it is important to determine if there is a link between biofilm formation and disease incidence for L. monocytogenes . Eighty L. monocytogenes isolates were screened for biofilm formation to determine if there is a robust relationship between biofilm formation, phylogenic division, and persistence in the environment. Statistically significant differences were detected between phylogenetic divisions. Increased biofilm formation was observed in Division II strains (serotypes 1/2a and 1/2c), which are not normally associated with food-borne outbreaks. Differences in biofilm formation were also detected between persistent and nonpersistent strains isolated from bulk milk samples, with persistent strains showing increased biofilm formation relative to nonpersistent strains. There were no significant differences detected among serotypes. Exopolysaccharide production correlated with cell adherence for high-biofilm-producing strains. Scanning electron microscopy showed that a high-biofilm-forming strain produced a dense, three-dimensional structure, whereas a low-biofilm-forming strain produced a thin, patchy biofilm. These data are consistent with data on persistent strains forming biofilms but do not support a consistent relationship between enhanced biofilm formation and disease incidence