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Ian R. MacDonald

Bio: Ian R. MacDonald is an academic researcher from Florida State University. The author has contributed to research in topics: Clathrate hydrate & Methane. The author has an hindex of 44, co-authored 144 publications receiving 7067 citations. Previous affiliations of Ian R. MacDonald include Lanzhou University & Stennis Space Center.


Papers
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Journal ArticleDOI
30 Dec 2010-PLOS ONE
TL;DR: This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management.
Abstract: A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive functions of surface primary production and delivery of the particulate organic carbon (POC) flux to the seafloor. At a regional scale, the census maps illustrate that integrated biomass is highest at the poles, on continental margins associated with coastal upwelling and with broad zones associated with equatorial divergence. Lowest values are consistently encountered on the central abyssal plains of major ocean basins The shift of biomass dominance groups with depth is shown to be affected by the decrease in average body size rather than abundance, presumably due to decrease in quantity and quality of food supply. This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management.

394 citations

Journal ArticleDOI
01 Aug 1994-Geology
TL;DR: In this paper, the authors report observations that concern formation and dissociation of gas hydrate near the sea floor at depths of ∼540 m in the northern Gulf of Mexico and conclude that the effects of accumulating buoyant force and fluctuating water temperature cause shallow gas hydrates alternately to check and release gas venting.
Abstract: We report observations that concern formation and dissociation of gas hydrate near the sea floor at depths of ∼540 m in the northern Gulf of Mexico. In August 1992, three lobes of gas hydrate were partly exposed beneath a thin layer of sediment. By May 1993, the most prominent lobe had evidently broken free and floated away, leaving a patch of disturbed sediment and exposed hydrate. The underside of the gas hydrate was about 0.2 °C warmer than ambient sea water and had trapped a large volume of oil and free gas. An in situ monitoring device, deployed on a nearby bed of mussels, recorded sustained releases of gas during a 44 day monitoring period. Gas venting coincided with a temporary rise in water temperature of 1 °C, which is consistent with thermally induced dissociation of hydrate composed mainly of methane and water. We conclude that the effects of accumulating buoyant force and fluctuating water temperature cause shallow gas hydrate alternately to check and release gas venting.

305 citations

Journal ArticleDOI
TL;DR: Tube worms and mussels both occurred in dense clusters; however, the clusters of mussels had a more restricted distribution within the study site than did clusters of tube worms, which were most abundant in the vicinity of the subsurface fault.
Abstract: Sediment and water samples were collected by submersible in September 1986 at 16 locations on the carbonate cap overlying a conical diapir, which was formed by the upward migration of oil and gas through a subsurface fault on the continental slope off Louisiana, USA (27°47′N; 91°30.4′W). The biological community at the site was photographed quantitatively with still and video cameras. Rigorous spatial sampling indices were maintained so that variation in chemical parameters and in the abundance of photographed organisms could be estimated within the bounds of the study site. Concentrations of extractable organic material (EOM) ranged from 0.24 to 119.26‰ in the sediment samples, while methane concentrations in the water samples were from 0.037 to 66.474 μM. The visible biological community was predominantly composed of the chemosynthetic tube worms (Vestimentifera) Lamellibrachia sp. and Escarpia sp., and an undescribed, methane-oxidizing mussel (Mytilidae: Bathymodiolus-like), as well as diverse non-chemosynthetic organisms. The ranked abundance of tube worms was significantly correlated (p<0.05) with the concentration of EOM in the sediment samples, while the abundance of mussels was significantly correlated (p<0.05) with the concentration of methane in the water samples. Tube worms and mussels both occurred in dense clusters; however, the clusters of mussels had a more restricted distribution within the study site than did clusters of tube worms. Both organisms were most abundant in the vicinity of the subsurface fault.

291 citations

Journal ArticleDOI
TL;DR: The authors showed that the degree of gas hydrate alteration appears to be related to duration of exposure at the sea floor and that bacterial oxidation of a mixed pool of hydrocarbons yields a net production of CO2 depleted in 13C.

248 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI

6,278 citations

Journal ArticleDOI
TL;DR: The overall biomass composition of the biosphere is assembled, establishing a census of the ≈550 gigatons of carbon (Gt C) of biomass distributed among all of the kingdoms of life and shows that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of ≈6 Gt C of marine biota, doubling the previous estimated quantity.
Abstract: A census of the biomass on Earth is key for understanding the structure and dynamics of the biosphere. However, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. Here, we assemble the overall biomass composition of the biosphere, establishing a census of the ≈550 gigatons of carbon (Gt C) of biomass distributed among all of the kingdoms of life. We find that the kingdoms of life concentrate at different locations on the planet; plants (≈450 Gt C, the dominant kingdom) are primarily terrestrial, whereas animals (≈2 Gt C) are mainly marine, and bacteria (≈70 Gt C) and archaea (≈7 Gt C) are predominantly located in deep subsurface environments. We show that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of ≈6 Gt C of marine biota, doubling the previous estimated quantity. Our analysis reveals that the global marine biomass pyramid contains more consumers than producers, thus increasing the scope of previous observations on inverse food pyramids. Finally, we highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined and report the historical impact of humanity on the global biomass of prominent taxa, including mammals, fish, and plants.

1,714 citations

Journal ArticleDOI
TL;DR: In this paper, the authors show that bottom water temperature increased by more than 4°C during a brief time interval (<104 years) of the latest Paleocene (∼55.6 Ma) and there also was a coeval −2 to −3‰ excursion in the δ13C of the ocean/atmosphere inorganic carbon reservoir.
Abstract: Isotopic records across the “Latest Paleocene Thermal Maximum“ (LPTM) indicate that bottom water temperature increased by more than 4°C during a brief time interval (<104 years) of the latest Paleocene (∼55.6 Ma). There also was a coeval −2 to −3‰ excursion in the δ13C of the ocean/atmosphere inorganic carbon reservoir. Given the large mass of this reservoir, a rapid δ13C shift of this magnitude is difficult to explain within the context of conventional hypotheses for changing the mean carbon isotope composition of the ocean and atmosphere. However, a direct consequence of warming bottom water temperature from 11 to 15°C over 104 years would be a significant change in sediment thermal gradients and dissociation of oceanic CH4 hydrate at locations with intermediate water depths. In terms of the present-day oceanic CH4 hydrate reservoir, thermal dissociation of oceanic CH4 hydrate during the LPTM could have released greater than 1.1 to 2.1 × 1018 g of carbon with a δ13C of approximately −60‰. The release and subsequent oxidation of this amount of carbon is sufficient to explain a −2 to −3‰ excursion in δ13C across the LPTM. Fate of CH4 in oceanic hydrates must be considered in developing models of the climatic and paleoceanographic regimes that operated during the LPTM.

1,300 citations

Journal ArticleDOI
TL;DR: The specific role of microbes and the EPS matrix in various mineralization processes are reviewed and examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites are discussed.

1,219 citations