Ronald Benner

Bio: Ronald Benner is an academic researcher from University of South Carolina. The author has contributed to research in topics: Dissolved organic carbon & Organic matter. The author has an hindex of 94, co-authored 218 publications receiving 28299 citations. Previous affiliations of Ronald Benner include University of Georgia & University of Washington.

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean.

Abstract: The biological pump is a process whereby CO(2) in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO(2), which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter. The processes and mechanisms involved in the generation of this large carbon reservoir are poorly understood. Here, we propose the microbial carbon pump as a conceptual framework to address this important, multifaceted biogeochemical problem.

Bacterial utilization of different size classes of dissolved organic matter

Abstract: Bacterial utilization of high-molecular-weight (HMW; > 1 kDa) and low-molecular-weight (LMW; < 1 kDa) dissolved organic C (DOC) was investigated in freshwater and marine systems by measuring dissolved oxygen consumption, bacterial abundance, and bacterial production in size-fractionated samples. Tangentialflow ultrafiltration was used to separate HMW and LMW DOC. More than 80% of the DOC in Amazon River samples was recovered in the HMW fraction, whereas most marine DOC (up to 70%) was of LMW. Bacterial growth efficiencies were consistently higher in the LMW fractions (16-66%) than in the HMW fractions (8-39%), indicating compositional differences in the two size fractions. In all experiments, measured rates of bacterial growth and respiration in HMW incubations were higher than those in LMW incubations. Carbon-normalized bacterial DOC utilization rates were ‘1.4-4-fold greater in the HMW fractions than in the LMW fractions, and a greater proportion (0.7-22.5%) of HMW DOC was utilized per day than LMW DOC (0.5-6.6%). All bacterial growth and respiration measurements indicated that HMW DOC was utilized to a greater extent than LMW DOC in all environments investigated. The traditional model of DOM degradation, stating that LMW compounds are most bioreactive, does not appear to apply to the bulk of natural DOM. Rather, the data and results from independent studies suggest a new conceptual model whereby the bioreactivity of organic matter decreases along a continuum of size (from large to small) and diagenetic state (from fresh to old). This size-reactivity continuum model suggests that the bulk of HMW DOM is more bioreactive and less diagenetically altered than the bulk of LMW DOM.

Depletion of 13 C in lignin and its implications for stable carbon isotope studies

Abstract: Stable carbon isotope compositions of organic matter are now widely used to trace carbon flow in ecosystems, and have been instrumental in shaping current perceptions of the importance of terrestrial vegetation to estuarine and coastal marine environments. A general assumption in these and other studies relying on carbon isotope compositions for source identification of organic matter has been that the major biochemical components of plant tissues are isotopically invariant. We report here large differences between the carbon isotope compositions of the polysaccharide and lignin components of a variety of vascular plants, including the salt-marsh grass Spartina alterniflora, and demonstrate that the carbon isotope composition of Spartina detritus gradually changes during biogeochemical processing as polysaccharides are preferentially removed, leaving a material that is relatively enriched in lignin-derived carbon and depleted in 13C.

Bulk chemical characteristics of dissolved organic matter in the ocean

Abstract: Dissolved organic matter (DOM) is the largest reservoir of reduced carbon in the oceans. The nature of DOM is poorly understood, in part, because it has been difficult to isolate sufficient amounts of representative material for analysis. Tangential-flow ultrafiltration was shown to recover milligram amounts of >1000 daltons of DOM from seawater collected at three depths in the North Pacific Ocean. These isolates represented 22 to 33 percent of the total DOM and included essentially all colloidal material. The elemental, carbohydrate, and carbon-type (by 13C nuclear magnetic resonance) compositions of the isolates indicated that the relative abundance of polysaccharides was high (∼50 percent) in surface water and decreased to ∼25 percent in deeper samples. Polysaccharides thus appear to be more abundant and reactive components of seawater DOM than has been recognized.

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

Abstract: We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a one-step method for inactivation of chromosomal genes and primers designed to create in-frame deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in high-throughput studies, two independent mutants were saved for every deleted gene. These mutants-the 'Keio collection'-provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome-wide testing of mutational effects in a common strain background, E. coli K-12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase (http://ecoli.aist-nara.ac.jp/).

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Abstract: We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.

Persistence of soil organic matter as an ecosystem property

Abstract: Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

Ecology of Coarse Woody Debris in Temperate Ecosystems

Abstract: Publisher Summary This chapter reviews the rates at which Coarse Woody Debris (CWD) is added and removed from ecosystems, the biomass found in streams and forests, and many functions that CWD serves. CWD is an important component of temperate stream and forest ecosystems and is added to the ecosystem by numerous mechanisms, including wind, fire, insect attack, pathogens, competition, and geomorphic processes. Many factors control the rate at which CWD decomposes, including temperature, moisture, the internal gas composition of CWD, substrate quality, the size of the CWD, and the types of organisms involved. The mass of CWD in an ecosystem ideally represents the balance between addition and loss. In reality, slow decomposition rates and erratic variations in input of CWD cause the CWD mass to deviate markedly from steady-state projections. Many differences correspond to forest type, with deciduous-dominated systems having generally lower biomass than conifer-dominated systems. Stream size also influences CWD mass in lotic ecosystems, while successional stage dramatically influences CWD mass in boat aquatic and terrestrial settings. This chapter reviews many of these functions and concludes that CWD is an important functional component of stream and forest ecosystems. Better scientific understanding of these functions and the natural factors influencing CWD dynamics should lead to more enlightened management practices.