Substrate-specific clades of active marine methylotrophs associated with a phytoplankton bloom in a temperate coastal environment

Marine microorganisms that consume one-carbon (C1) compounds are poorly described, despite their impact on global climate via an influence on aquatic and atmospheric chemistry. This study investigated marine bacterial communities involved in the metabolism of C1 compounds. These communities were of relevance to surface seawater and atmospheric chemistry in the context of a bloom that was dominated by phytoplankton known to produce dimethylsulfoniopropionate. In addition to using 16S rRNA gene fingerprinting and clone libraries to characterize samples taken from a bloom transect in July 2006, seawater samples from the phytoplankton bloom were incubated with 13C-labeled methanol, monomethylamine, dimethylamine, methyl bromide, and dimethyl sulfide to identify microbial populations involved in the turnover of C1 compounds, using DNA stable isotope probing. The [13C]DNA samples from a single time point were characterized and compared using denaturing gradient gel electrophoresis (DGGE), fingerprint cluster analysis, and 16S rRNA gene clone library analysis. Bacterial community DGGE fingerprints from 13C-labeled DNA were distinct from those obtained with the DNA of the nonlabeled community DNA and suggested some overlap in substrate utilization between active methylotroph populations growing on different C1 substrates. Active methylotrophs were affiliated with Methylophaga spp. and several clades of undescribed Gammaproteobacteria that utilized methanol, methylamines (both monomethylamine and dimethylamine), and dimethyl sulfide. rRNA gene sequences corresponding to populations assimilating 13C-labeled methyl bromide and other substrates were associated with members of the Alphaproteobacteria (e.g., the family Rhodobacteraceae), the Cytophaga-Flexibacter-Bacteroides group, and unknown taxa. This study expands the known diversity of marine methylotrophs in surface seawater and provides a comprehensive data set for focused cultivation and metagenomic analyses in the future

LaSER oceanography: Data report number 1, R/V Pelican cruise, July 21-August 1, 1987, CTD and hydrographic data

The LaSER oceanography program is a five year multi-institutional and multi-investigator program titled "Oceanographic Processes on Continental Shelves Influenced by Large Rivers." Funding for this program began in January, 1987. The scientific goals of this program are: a) investigations on a large spatial scale, from the Mississippi River delta to some far field (down-plume) location, to examine biological responses to riverine inputs of dissolved nutrients, suspended sediments, and fresh water; b) investigations on small spatial scales, both horizontally and vertically, in a cross plume direction to examine the role of oceanographic fronts, convergences, and discontinuities in biological production; and c) investigations on small temporal scales, particularly to examine the biological responses to the passage of winter storms. This report summarizes the CTD and hydrographic (bottle) data from the first LaSER oceanography cruise

Comparison of bacterioneuston and bacterioplankton dynamics during a phytoplankton bloom in a fjord mesocosm

The bacterioneuston is the community of Bacteria present in surface microlayers, the thin surface film that forms the interface between aquatic environments and the atmosphere. In this study we compared bacterial cell abundance and bacterial community structure of the bacterioneuston and the bacterioplankton (from the subsurface water column) during a phytoplankton bloom mesocosm experiment. Bacterial cell abundance, determined by flow cytometry, followed a typical bacterioplankton response to a phytoplankton bloom, with Synechococcus and high nucleic acid (HNA) bacterial cell numbers initially falling, probably due to selective protist grazing. Subsequently HNA and low nucleic acid (LNA) bacterial cells increased in abundance but Synechococcus did not. There was no significant difference between bacterioneuston and bacterioplankton cell abundances during the experiment. Conversely, distinct and consistent differences between the bacterioneuston and the bacterioplankton community structure were observed. This was monitored simultaneously by Bacteria 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). The conserved patterns of community structure observed in all of the mesocosms indicate that the bacterioneuston is distinctive and non-random

Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog

The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, Minnesota, USA. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing, expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14-17 μmol CH4 g dry wt soil-1 d-1. Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25-36% after 8 -14 days. Phylogenetic analysis of the 13C-enriched DNA fractions revealed the active methanotrophs were dominated by the genera Methylocystis (Type II; Alphaproteobacteria), Methylomonas, and Methylovulum (Type I; Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers which attenuated rapidly with depth, indicating the highest methane consumption was associated with the 0-10 cm depth interval. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed the dominant active methanotrophs were Methylocystis and Methylomonas. Although Type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate members of the genera Methylomonas and Methylovulum (Type I) can significantly contribute to aerobic methane oxidation in these ecosystems

Multivariate geometric anisotropic Cox processes

This paper introduces a new modeling and inference framework for multivariate and anisotropic point processes. Building on recent innovations in multivariate spatial statistics, we propose a new family of multivariate anisotropic random fields, and from them a family of anisotropic point processes. We give conditions that make the proposed models valid. We also propose a Palm likelihood-based inference method for this type of point process, circumventing issues of likelihood tractability. Finally we illustrate the utility of the proposed modeling framework by analyzing spatial ecological observations of plants and trees in the Barro Colorado Island data

Feasibility and systems definition study for Microwave Multi-Application Payload (MMAP)

Work completed on three Shuttle/Spacelab experiments is examined: the Adaptive Multibeam Phased Array Antenna (AMPA) Experiment, Electromagnetic Environment Experiment (EEE) and Millimeter Wave Communications Experiment (MWCE). Results included the definition of operating modes, sequence of operation, radii of operation about several ground stations, signal format, foot prints of typical orbits and preliminary definition of ground and user terminals. Conceptual hardware designs, Spacelab interfaces, data handling methods, experiment testing and verification studies were included. The MWCE-MOD I was defined conceptually for a steerable high gain antenna

Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle

Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound

Civil War Almanac: The Best Civil War Books of All Time

For our latest newsstand-only special issue, The Civil War Almanac, we asked a panel of Civil War historians—J. Matthew Gallman, Matthew C. Hulbert, James Marten, and Amy Murrell Taylor—for their opinions on a variety of popular topics, including the war\u27s most overrated and underratred commanders, top turning points, most influential women, and best depictions on film. Space constraints prevented us from including their answers to one of the questions we posed: What are the 10 best Civil War books ever published (nonfiction or fiction)? Below are their responses