Characterization of an anaerobic marine microbial community exposed to combined fluxes of perchlorate and salinity.

The recent recognition of the environmental prevalence of perchlorate and its discovery on Mars, Earth's moon, and in meteorites, in addition to its novel application to controlling oil reservoir sulfidogenesis, has resulted in a renewed interest in this exotic ion and its associated microbiology. However, while plentiful data exists on freshwater perchlorate respiring organisms, information on their halophilic counterparts and microbial communities is scarce. Here, we investigated the temporal evolving structure of perchlorate respiring communities under a range of NaCl concentrations (1, 3, 5, 7, and 10 % wt/vol) using marine sediment amended with acetate and perchlorate. In general, perchlorate consumption rates were inversely proportional to NaCl concentration with the most rapid rate observed at 1 % NaCl. At 10 % NaCl, no perchlorate removal was observed. Transcriptional analysis of the 16S rRNA gene indicated that salinity impacted microbial community structure and the most active members were in families Rhodocyclaceae (1 and 3 % NaCl), Pseudomonadaceae (1 NaCl), Campylobacteraceae (1, 5, and 7 % NaCl), Sedimenticolaceae (3 % NaCl), Desulfuromonadaceae (5 and 7 % NaCl), Pelobacteraceae (5 % NaCl), Helicobacteraceae (5 and 7 % NaCl), and V1B07b93 (7 %). Novel isolates of genera Sedimenticola, Marinobacter, Denitromonas, Azoarcus, and Pseudomonas were obtained and their perchlorate respiring capacity confirmed. Although the obligate anaerobic, sulfur-reducing Desulfuromonadaceae species were dominant at 5 and 7 % NaCl, their enrichment may result from biological sulfur cycling, ensuing from the innate ability of DPRB to oxidize sulfide. Additionally, our results demonstrated enrichment of an archaeon of phylum Parvarchaeota at 5 % NaCl. To date, this phylum has only been described in metagenomic experiments of acid mine drainage and is unexpected in a marine community. These studies identify the intrinsic capacity of marine systems to respire perchlorate and significantly expand the known diversity of organisms capable of this novel metabolism.

Air Pollution in China: Mapping of Concentrations and Sources.

China has recently made available hourly air pollution data from over 1500 sites, including airborne particulate matter (PM), SO2, NO2, and O3. We apply Kriging interpolation to four months of data to derive pollution maps for eastern China. Consistent with prior findings, the greatest pollution occurs in the east, but significant levels are widespread across northern and central China and are not limited to major cities or geologic basins. Sources of pollution are widespread, but are particularly intense in a northeast corridor that extends from near Shanghai to north of Beijing. During our analysis period, 92% of the population of China experienced >120 hours of unhealthy air (US EPA standard), and 38% experienced average concentrations that were unhealthy. China's population-weighted average exposure to PM2.5 was 52 µg/m3. The observed air pollution is calculated to contribute to 1.6 million deaths/year in China [0.7-2.2 million deaths/year at 95% confidence], roughly 17% of all deaths in China.

(Per)chlorate-reducing bacteria can utilize aerobic and anaerobic pathways of aromatic degradation with (per)chlorate as an electron acceptor.

UNLABELLED: The pathways involved in aromatic compound oxidation under perchlorate and chlorate [collectively known as (per)chlorate]-reducing conditions are poorly understood. Previous studies suggest that these are oxygenase-dependent pathways involving O2 biogenically produced during (per)chlorate respiration. Recently, we described Sedimenticola selenatireducens CUZ and Dechloromarinus chlorophilus NSS, which oxidized phenylacetate and benzoate, two key intermediates in aromatic compound catabolism, coupled to the reduction of perchlorate or chlorate, respectively, and nitrate. While strain CUZ also oxidized benzoate and phenylacetate with oxygen as an electron acceptor, strain NSS oxidized only the latter, even at a very low oxygen concentration (1%, vol/vol). Strains CUZ and NSS contain similar genes for both the anaerobic and aerobic-hybrid pathways of benzoate and phenylacetate degradation; however, the key genes (paaABCD) encoding the epoxidase of the aerobic-hybrid phenylacetate pathway were not found in either genome. By using transcriptomics and proteomics, as well as by monitoring metabolic intermediates, we investigated the utilization of the anaerobic and aerobic-hybrid pathways on different electron acceptors. For strain CUZ, the results indicated utilization of the anaerobic pathways with perchlorate and nitrate as electron acceptors and of the aerobic-hybrid pathways in the presence of oxygen. In contrast, proteomic results suggest that strain NSS may use a combination of the anaerobic and aerobic-hybrid pathways when growing on phenylacetate with chlorate. Though microbial (per)chlorate reduction produces molecular oxygen through the dismutation of chlorite (ClO2(-)), this study demonstrates that anaerobic pathways for the degradation of aromatics can still be utilized by these novel organisms. IMPORTANCE: S. selenatireducens CUZ and D. chlorophilus NSS are (per)chlorate- and chlorate-reducing bacteria, respectively, whose genomes encode both anaerobic and aerobic-hybrid pathways for the degradation of phenylacetate and benzoate. Previous studies have shown that (per)chlorate-reducing bacteria and chlorate-reducing bacteria (CRB) can use aerobic pathways to oxidize aromatic compounds in otherwise anoxic environments by capturing the oxygen produced from chlorite dismutation. In contrast, we demonstrate that S. selenatireducens CUZ is the first perchlorate reducer known to utilize anaerobic aromatic degradation pathways with perchlorate as an electron acceptor and that it does so in preference over the aerobic-hybrid pathways, regardless of any oxygen produced from chlorite dismutation. D. chlorophilus NSS, on the other hand, may be carrying out anaerobic and aerobic-hybrid processes simultaneously. Concurrent use of anaerobic and aerobic pathways has not been previously reported for other CRB or any microorganisms that encode similar pathways of phenylacetate or benzoate degradation and may be advantageous in low-oxygen environments.

In situ microbial metabolism as a cause of gas anomalies in ice.

Isolated spikes of anomalously high concentrations of N(2)O have been reported at depths in Greenland and Antarctic ice cores corresponding to narrow time intervals over the past approximately 10(5) years. Now, using a calibrated spectrofluorimeter to map protein-bound Trp, a proxy for microbes, versus depth in the 3,053-m GISP2 ice core, we find six depths at which localized spikes of high cell concentrations coincide with N(2)O spikes. We show that the excess gases are consistent with accumulation of in situ metabolic wastes during residence times of the excess microbes in the ice. Because of sparseness of N(2)O measurements and our spectrofluorimetry versus depth, the total number of microbially produced N(2)O spikes in GISP2 is probably much larger than six. Spikes of excess methanogens coincident with CH(4) spikes are found at three depths in the bottom 3% of GISP2, most likely because of methanogenic metabolism in the underlying silty ice, followed by turbulent flow of the lowest approximately 90 m of ice. The apparent rates of in situ production of N(2)O and CH(4) spikes by metabolism are observed to be consistent with a single activation energy, U, and maintain proportionality to exp(-U/RT) over the entire temperature range down to -40 degrees C. Fluorescence of nonmicrobial aerosols in GISP2 ice is distinguishable from microbial fluorescence by its different emission spectra. Our spectrofluorimetric scans throughout the GISP2 ice core lead us to conclude that both microbes and nonmicrobial aerosols are deposited in discontinuous bursts, which may provide a tool for studying wind storms in the distant past.

Diffusion-controlled metabolism for long-term survival of single isolated microorganisms trapped within ice crystals.

Two known habitats for microbial metabolism in ice are surfaces of mineral grains and liquid veins along three-grain boundaries. We propose a third, more general, habitat in which a microbe frozen in ice can metabolize by redox reactions with dissolved small molecules such as CO(2), O(2), N(2), CO, and CH(4) diffusing through the ice lattice. We show that there is an adequate supply of diffusing molecules throughout deep glacial ice to sustain metabolism for >10(5) yr. Using scanning fluorimetry to map proteins (a proxy for cells) and F420 (a proxy for methanogens) in ice cores, we find isolated spikes of fluorescence with intensity consistent with as few as one microbial cell in a volume of 0.16 microl with the protein mapper and in 1.9 microl with the methanogen mapper. With such precise localization, it should be possible to extract single cells for molecular identification.

Cycles in fossil diversity.

It is well known that the diversity of life appears to fluctuate during the course of the Phanerozoic, the eon during which hard shells and skeletons left abundant fossils (0-542 million years ago). Here we show, using Sepkoski's compendium of the first and last stratigraphic appearances of 36,380 marine genera, a strong 62 +/- 3-million-year cycle, which is particularly evident in the shorter-lived genera. The five great extinctions enumerated by Raup and Sepkoski may be an aspect of this cycle. Because of the high statistical significance we also consider the contributions of environmental factors, and possible causes.