Prevalence of alkane monooxygenase genes in Arctic and Antarctic hydrocarbon-contaminated and pristine soils

The prevalence of four alkane monooxygenase genotypes (Pseudomonas putida GPo1, Pp alkB; Rhodococcus sp. strain Q15, Rh alkB1 and Rh alkB2; and Acinetobacter sp. strain ADP-1, Ac alkM) in hydrocarbon-contaminated and pristine soils from the Arctic and Antarctica were determined by both culture-independent (PCR hybridization analyses) and culture-dependent (colony hybridization analyses) molecular methods, using oligonucleotide primers and DNA probes specific for each of the alk genotypes. PCR hybridization of total soil community DNA detected the rhodococcal alkB genotypes in most of the contaminated (Rh alkB1, 18/20 soils; Rh alkB2, 13/20) and many pristine soils (Rh alkB1, 9/10 soils; Rh alkB2, 7/10), while Pp alkB was generally detected in the contaminated soils (15/20) but less often in pristine soils (5/10). Ac alkM was rarely detected in the soils (1/30). The colony hybridization technique was used to determine the prevalence of each of the alk genes and determine their relative abundance in culturable cold-adapted (5°C) and mesophilic populations (37°C) from eight of the polar soils. The cold-adapted populations, in general, possessed relatively higher percentages of the Rh alkB genotypes (Rh alkB1, 1.9% (0.55); Rh alkB2, 2.47% (0.89)), followed by the Pp alkB (1.13% (0.50)), and then the Ac alkM (0.53% (0.36)). The Rh alkB1 genotype was clearly more prevalent in culturable cold-adapted bacteria (1.9% (0.55)) than in culturable mesophiles (0.41 (0.55)), suggesting that cold-adapted bacteria are the predominant organisms possessing this genotype. Overall, these results indicated that (i) Acinetobacter spp. are not predominant members of polar alkane degradative microbial communities, (ii) Pseudomonas spp. may become enriched in polar soils following contamination events, and (iii) Rhodococcus spp. may be the predominant alkane-degradative bacteria in both pristine and contaminated polar soil

Adiabatic transfer of light in a double cavity and the optical Landau-Zener problem

We analyze the evolution of an electromagnetic field inside a double cavity when the difference in length between the two cavities is changed, e.g. by translating the common mirror. We find that this allows photons to be moved deterministically from one cavity to the other. We are able to obtain the conditions for adiabatic transfer by first mapping the Maxwell wave equation for the electric field onto a Schroedinger-like wave equation, and then using the Landau-Zener result for the transition probability at an avoided crossing. Our analysis reveals that this mapping only rigorously holds when the two cavities are weakly coupled (i.e. in the regime of a highly reflective common mirror), and that, generally speaking, care is required when attempting a hamiltonian description of cavity electrodynamics with time-dependent boundary conditions.Comment: 24 pages, 18 figures. Version 2 includes a new section (Sec. VIII) on the regimes of validity of the Schroedinger-like equations and also of the adiabatic approximation, together with a new figure (Fig. 10). The discussion section (Sec. XI) has also been enhance

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia.

The objective of this work was to evaluate the catabolic gene diversity for the bacterial degradation of aromatic hydrocarbons in anthropogenic dark earth of Amazonia (ADE) and their biochar (BC). Functional diversity analyses in ADE soils can provide information on how adaptive microorganisms may influence the fertility of soils and what is their involvement in biogeochemical cycles. For this, clone libraries containing the gene encoding for the alpha subunit of aromatic ring-hydroxylating dioxygenases (a-ARHD bacterial gene) were constructed, totaling 800 clones. These libraries were prepared from samples of an ADE soil under two different land uses, located at the Caldeirão Experimental Station - secondary forest (SF) and agriculture (AG) -, and the biochar (SF_BC and AG_BC, respectively). Heterogeneity estimates indicated greater diversity in BC libraries; and Venn diagrams showed more unique operational protein clusters (OPC) in the SF_BC library than the ADE soil, which indicates that specific metabolic processes may occur in biochar. Phylogenetic analysis showed unidentified dioxygenases in ADE soils. Libraries containing functional gene encoding for the alpha subunit of the aromatic ring-hydroxylating dioxygenases (ARHD) gene from biochar show higher diversity indices than those of ADE under secondary forest and agriculture

Expedition 376 summary

Volcanic arcs are the surface expression of magmatic systems that result from subduction of mostly oceanic lithosphere at convergent plate boundaries. Arcs with a submarine component include intraoceanic arcs and island arcs that span almost 22,000 km on Earth’s surface, and the vast majority of them are located in the Pacific region. Hydrothermal systems hosted by submarine arc volcanoes commonly contain a large component of magmatic fluid. This magmatic-hydrothermal signature, coupled with the shallow water depths of arc volcanoes and their high volatile contents, strongly influences the chemistry of the fluids and resulting mineralization and likely has important consequences for the biota associated with these systems. The high metal content and very acidic fluids in these hydrothermal systems are thought to be important analogs to numerous porphyry copper and epithermal gold deposits mined today on land. During International Ocean Discovery Program (IODP) Expedition 376 (5 May–5 July 2018), a series of five sites was drilled on Brothers volcano in the Kermadec arc. The expedition was designed to provide the missing link (i.e., the third dimension) in our understanding of hydrothermal activity and mineral deposit formation at submarine arc volcanoes and the relationship between the discharge of magmatic fluids and the deep biosphere. Brothers volcano hosts two active and distinct hydrothermal systems: one is seawater influenced and the other is affected by magmatic fluids (largely gases). In total, 222.4 m of volcaniclastics and lavas were recovered from the five sites drilled, which include Sites U1527 and U1530 in the Northwest (NW) Caldera seawater-influenced hydrothermal field; Sites U1528 and U1531 in the magmatic fluid-influenced hydrothermal fields of the Upper and Lower Cones, respectively; and Site U1529, located within an area of low crustal magnetization that marks the West (W) Caldera upflow zone on the caldera floor. Downhole logging and borehole fluid sampling were completed at two sites, and two tests of a prototype turbine-driven coring system (designed by the Center for Deep Earth Exploration [CDEX] at Japan Agency for Marine-Earth Science and Technology [JAMSTEC]) for drilling and coring hard rocks were conducted. Core recovered from all five sites consists of dacitic volcaniclastics and lava flows with only limited chemical variability relative to the overall range in composition of dacites in the Kermadec arc. Pervasive alteration with complex and variable mineral assemblages attest to a highly dynamic hydrothermal system. The upper parts of several drill holes at the NW Caldera hydrothermal field are characterized by secondary mineral assemblages of goethite + opal + zeolites that result from low-temperature (<150°C) reaction of rock with seawater. At depth, NW Caldera Site U1527 exhibits a higher temperature (~250°C) secondary mineral assemblage dominated by chlorite + quartz + illite + pyrite. An older mineral assemblage dominated by diaspore + quartz + pyrophyllite + rutile at the bottom of Hole U1530A is indicative of acidic fluids with temperatures of ~230°–320°C. In contrast, the alteration assemblage at Site U1528 on the Upper Cone is dominated by illite + natroalunite + pyrophyllite + quartz + opal + pyrite, which attests to high-temperature reaction of rocks with acid-sulfate fluids derived from degassed magmatic volatiles and the disproportionation of magmatic SO2. These intensely altered rocks exhibit extreme depletion of major cation oxides, such as MgO, K2O, CaO, MnO, and Na2O. Furthermore, very acidic (as low as pH 1.8), relatively hot (≤236°C) fluids collected at 160, 279, and 313 meters below seafloor in Hole U1528D have chemical compositions indicative of magmatic gas input. In addition, preliminary fluid inclusion data provide evidence for involvement of two distinct fluids: phase-separated (modified) seawater and a ~360°C hypersaline brine, which alters the volcanic rock and potentially transports metals in the system. The material and data recovered during Expedition 376 provide new stratigraphic, lithologic, and geochemical constraints on the development and evolution of Brothers volcano and its hydrothermal systems. Insights into the consequences of the different types of fluid–rock reactions for the microbiological ecosystem elucidated by drilling at Brothers volcano await shore-based studies