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

Multidisciplinary Scientific Cruises for Environmental Characterization in the Santos Basin – Methods and Sampling Design

The Santos Basin (SB) is the main petroliferous basin in the Brazilian continental margin and one of the most studied marine areas in Brazil. However, historical data suggest that new efforts should be carried out to acquire quantitative biological data, especially in the deep sea, to establish the baseline of essential ocean variables in different ecosystems for future monitoring programs. The Brazilian energy company Petrobras planned and executed 24 oceanographic cruises over a period of 2 years to assess the benthic (SANSED cruise) and pelagic (SANAGU cruise) systems of the SB (356 days at sea in 2019 and 2021/2022). These efforts were part of the Santos Project, which comprised a comprehensive environmental study aimed at investigating benthic and pelagic variables to characterize ecology, biogeochemistry, thermohaline properties of water masses, and ocean circulation patterns, geomorphology, and sedimentology, as well as organic and inorganic chemistry. Here we present the detailed sampling designs and the field methods employed on board, during the SB scientific cruises. All sampling protocols were based on standardized approaches. For the benthos analyses, triplicate sediment samples were performed using a GOMEX-type box corer (0.25 m²) or a large modified Van Veen grab (0.75 m²) at 100 stations ranging from 25 to 2400 m depth. At each station, 25 geochemical and physico-chemical parameters were analyzed in addition to micro-, meio-, and macrofauna and living foraminifera samples. For the pelagic system, 60 stations were selected to investigate the plankton community, ranging in size from pico- to macroplankton, through vertical, horizontal, and oblique net hauls (20, 200, and 500 μm mesh size), as well as 25 biogeochemical parameters collected with an aid of a CTD-rosette sampler. Part of this scientific information also serves the Regional Environmental Characterization Project (PCR-BS) in support of Petrobras’ Santos Basin drilling licensing process led by the Brazilian Environmental Agency – IBAMA. This project contributes to the sustainable development of the SB, in line with the guidelines of the United Nations Decade of Ocean Science for Sustainable Development