Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling.

Cyanobacterial life at low O(2): community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat.

Cyanobacteria are renowned as the mediators of Earth's oxygenation. However, little is known about the cyanobacterial communities that flourished under the low-O(2) conditions that characterized most of their evolutionary history. Microbial mats in the submerged Middle Island Sinkhole of Lake Huron provide opportunities to investigate cyanobacteria under such persistent low-O(2) conditions. Here, venting groundwater rich in sulfate and low in O(2) supports a unique benthic ecosystem of purple-colored cyanobacterial mats. Beneath the mat is a layer of carbonate that is enriched in calcite and to a lesser extent dolomite. In situ benthic metabolism chambers revealed that the mats are net sinks for O(2), suggesting primary production mechanisms other than oxygenic photosynthesis. Indeed, (14)C-bicarbonate uptake studies of autotrophic production show variable contributions from oxygenic and anoxygenic photosynthesis and chemosynthesis, presumably because of supply of sulfide. These results suggest the presence of either facultatively anoxygenic cyanobacteria or a mix of oxygenic/anoxygenic types of cyanobacteria. Shotgun metagenomic sequencing revealed a remarkably low-diversity mat community dominated by just one genotype most closely related to the cyanobacterium Phormidium autumnale, for which an essentially complete genome was reconstructed. Also recovered were partial genomes from a second genotype of Phormidium and several Oscillatoria. Despite the taxonomic simplicity, diverse cyanobacterial genes putatively involved in sulfur oxidation were identified, suggesting a diversity of sulfide physiologies. The dominant Phormidium genome reflects versatile metabolism and physiology that is specialized for a communal lifestyle under fluctuating redox conditions and light availability. Overall, this study provides genomic and physiologic insights into low-O(2) cyanobacterial mat ecosystems that played crucial geobiological roles over long stretches of Earth history.

Aurantimonas manganoxydans, sp. nov. and Aurantimonas litoralis, sp. nov.: Mn(II) oxidizing representatives of a globally distributed clade of alpha-Proteobacteria from the order Rhizobiales.

Several closely related Mn(II)-oxidizing alpha-Proteobacteria were isolated from very different marine environments: strain SI85-9A1 from the oxic/anoxic interface of a stratified Canadian fjord, strain HTCC 2156 from the surface waters off the Oregon coast, and strain AE01 from the dorsal surface of a hydrothermal vent tubeworm. 16S rRNA analysis reveals that these isolates are part of a tight phylogenetic cluster with previously characterized members of the genus Aurantimonas. Other organisms within this clade have been isolated from disparate environments such as surface waters of the Arctic and Mediterranean seas, a deep-sea hydrothermal plume, and a Caribbean coral. Further analysis of all these strains revealed that many of them are capable of oxidizing dissolved Mn(II) and producing particulate Mn(III/IV) oxides. Strains SI85-9A1 and HTCC 2156 were characterized further. Despite sharing nearly identical 16S rRNA gene sequences with the previously described Aurantimonas coralicida, whole genome DNA-DNA hybridization indicated that their overall genomic similarity is low. Polyphasic phenotype characterization further supported distinguishing characteristics among these bacteria. Thus SI85-9A1 and HTCC 2156 are described as two new species within the family 'Aurantimionadaceae': Aurantimonas manganoxydans sp. nov. and Aurantimonas litoralis sp. nov. This clade of bacteria is widely distributed around the globe and may be important contributors to Mn cycling in many environments. Our results highlight the difficulty in utilizing 16S rRNA-based approaches to investigate the microbial ecology of Mn(II) oxidation.

The astrobiology primer: an outline of general knowledge--version 1, 2006.

The Astrobiology Primer has been created as a reference tool for those who are interested in the interdisciplinary field of astrobiology. The field incorporates many diverse research endeavors, but it is our hope that this slim volume will present the reader with all he or she needs to know to become involved and to understand, at least at a fundamental level, the state of the art. Each section includes a brief overview of a topic and a short list of readable and important literature for those interested in deeper knowledge. Because of the great diversity of material, each section was written by a different author with a different expertise. Contributors, authors, and editors are listed at the beginning, along with a list of those chapters and sections for which they were responsible. We are deeply indebted to the NASA Astrobiology Institute (NAI), in particular to Estelle Dodson, David Morrison, Ed Goolish, Krisstina Wilmoth, and Rose Grymes for their continued enthusiasm and support. The Primer came about in large part because of NAI support for graduate student research, collaboration, and inclusion as well as direct funding. We have entitled the Primer version 1 in hope that it will be only the first in a series, whose future volumes will be produced every 3-5 years. This way we can insure that the Primer keeps up with the current state of research. We hope that it will be a great resource for anyone trying to stay abreast of an ever-changing field.

Stability and phase noise tests of two cryo-cooled sapphire oscillators.

A cryocooled compensated sapphire oscillator (CSO), developed for the Cassini Ka-band Radio Science experiment, and operating in the 7 K-10 K temperature range, was demonstrated to show ultra-high stability of sigma(y)=2.5x10(-15) for measuring times 200 seconds

Local oscillator limited frequency stability for passive atomic frequency standards using square wave frequency modulation.

Atomic frequency standards using square wave frequency modulation effectively interrogate the atomic line by switching back and forth between two frequencies with equal atomic absorption values. For a symmetric absorption line, the slope of the responses will also be equal. In the quasistatic limit, this would seem to be an ideal interrogation process: the sign reversal of frequency slope can be removed by detection electronics to give an essentially unvarying sensitivity to local oscillator frequency variations. Such an interrogation would seem to eliminate L.O. aliasing and relieve stringent requirements on L.O. phase noise. Nevertheless, sign changes in the interrogation and detection processes mean that the sensitivity is actually zero at some point in the cycle. We derive consequences of this fact by an analysis in terms of the sensitivity function g(t). For white phase noise, we derive an optimal form for g(t) and show that the aliased noise always diverges as g(t) approaches a constant. For flicker phase noise, we find a limiting form that could, in principle, eliminate the aliasing effect; in practice, however, the improvement is limited by a slow dependence on available bandwidth. Finally, we derive optimized forms for any phase noise spectrum.

Frequency stability degradation of an oscillator slaved to a periodically interrogated atomic resonator.

Atomic frequency standards using trapped ions or cold atoms work intrinsically in a pulsed mode. Theoretically and experimentally, this mode of operation has been shown to lead to a degradation of the frequency stability due to the frequency noise of the interrogation oscillator. In this paper a physical analysis of this effect has been made by evaluating the response of a two-level atom to the interrogation oscillator phase noise in Ramsey and multi-Rabi interrogation schemes using a standard quantum mechanical approach. This response is then used to calculate the degradation of the frequency stability of a pulsed atomic frequency standard such as an atomic fountain or an ion trap standard. Comparison is made to an experimental evaluation of this effect in the LPTF Cs fountain frequency standard, showing excellent agreement.

Measurement and analysis of a microwave oscillator stabilized by a sapphire dielectric ring resonator for ultra-low noise.

Phase-noise measurements are presented for a microwave oscillator whose frequency is stabilized by a whispering gallery mode sapphire ring resonator with Q of 2x10(5). The nature of the mode, which involves little metallic conduction, allows nearly full use of the very low dielectric loss in sapphire. Several mode families have been identified with good agreement with calculated frequency predictions. Waveguide coupling parameters have been characterized for the principal (lowest frequency) mode family, for n=5 to n =10 full waves around the perimeter. For a 5-cm wheel resonator in a 7.6-cm container, Q-values of above 10(5) were found at room temperature for all of the modes in this sequence. Coupling Q-values for the same modes ranged from 10(4) (n =5) to 10(5) (n=10) for a WR112 waveguide port at the center of the cylinder wall of the containing can. Phase noise measurements for a transistor oscillator locked to the n=10 (7.84-GHz) mode showed a 1/f(3) dependence for low offset frequencies, and a value of L(f)=-55 dB/Hz at an offset of 10 Hz from the carrier. The oscillator shows phase noise below the previously reported for any X-band source.

Linear ion trap for second-order Doppler shift reduction in frequency standard applications.

The authors have designed and are presently testing a novel linear ion trap that permits storage of a large number of ions with reduced susceptibility to the second-order Doppler effect caused by the RF confining fields. This new trap should store about 20 times the number of ions as a conventional RF trap with no corresponding increase in second-order Doppler shift from the confining field. In addition, the sensitivity of this shift to trapping parameters, i.e., RF voltage, RF frequency, and trap size, is greatly reduced. The authors have succeeded in trapping mercury ions and xenon ions in the presence of helium buffer gas. Trap times as long as 2x 10(3) s have been measured.