16S ribosomal DNA analysis of marine ammonia-oxidising bacteria

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Oceanic detachment faults focus very large volumes of black smoker fluids

It is generally assumed that the seawater-derived fluids that feed black smoker vent fields on the seafloor are discharged vertically from depths of ~1–3 km. We present new oxygen and strontium isotope data that show that fluids at black smoker temperatures of 300–400 °C were focused along a low-angle detachment fault at 15°45'N near the Mid-Atlantic Ridge. Isotopic alteration is the most extreme ever reported from oceanic rocks altered at similar temperatures, indicating intensely focused fluid flow both in recharge and discharge parts of the hydrothermal system. Rare earth element mobility in the fault rocks demonstrates isotopic alteration by evolved hydrothermal fluids, not conductively heated seawater. The fault zone protolith was predominantly ultramafic, but also included mafic rocks, with metasomatic alteration to talc-tremolite-chlorite schists resulting mainly from chemical exchange between these lithologies during fluid flow. Fluids in equilibrium with this assemblage would be similar to ultramafic-hosted black smoker fluids. We present a new model in which hydrothermal circulation around detachment faults evolves from basalt hosted (TAG type), to footwall ultramafic hosted (Rainbow type), to low-temperature ultramafic hosted (Lost City type). Key features of our model are the intrusion of gabbro bodies immediately below the detachment to provide a heat source for circulation, and focusing of fluid flow into the detachment fault to allow venting away from the neovolcanic axis

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]

Taxa-area relationships for microbes: the unsampled and the unseen

The recent observation of a power–law relationship, S ∝ A<sup>z</sup>, between number of taxa, S, and area, A, for microbial eukaryotes and bacteria suggests that this is one of the few generic relationships in ecology, applicable to plants, animals and microbes. However, the rate of increase in the number of species with area varies from approximately the fourth (z = 0.26) to as little as the 50th root (z = 0.0019) in microbes. This is an enormous range for which no quantitative explanation has been proffered. We show by sampling from synthetic populations that the disparity between sample and community sizes in microbial community surveys means z can be considerably underestimated and accrual of rare taxa with increasing area will not be detectable. Significant microbial taxa–area relationships will only be observed when changes in community structure within samples correlate with area. Thus, the very low z values observed recently cannot be used as the sole evidence in support of any particular community theory of community assembly. More generally, this suggests that our search for patterns and laws in the microbial world will be profoundly influenced and, potentially distorted by the sample sizes that are typical of microbial community surveys