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"Dubinsky, Eric A."
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The beautiful brain : the drawings of Santiago Ramâon y Cajal /
Santiago Ramâon y Cajal (1852-1934) was the father of modern neuroscience and an exceptional artist. He devoted his life to the anatomy of the brain, the body's most complex and mysterious organ. His superhuman feats of visualization, based on fanatically precise techniques and countless hours at the microscope, resulted in some of the most remarkable illustrations in the history of science. Beautiful Brain presents a selection of his exquisite drawings of brain cells, brain regions, and neural circuits with accessible descriptive commentary.
Book
Tropical forest soil microbial communities couple iron and carbon biogeochemistry
We report that iron-reducing bacteria are primary mediators of anaerobic carbon oxidation in upland tropical soils spanning a rainfall gradient (3500-5000 mm/yr) in northeast Puerto Rico. The abundant rainfall and high net primary productivity of these tropical forests provide optimal soil habitat for iron-reducing and iron-oxidizing bacteria. Spatially and temporally dynamic redox conditions make iron-transforming microbial communities central to the belowground carbon cycle in these wet tropical forests. The exceedingly high abundance of iron-reducing bacteria (up to 1.2 × 10
9
cells per gram soil) indicated that they possess extensive metabolic capacity to catalyze the reduction of iron minerals. In soils from the higher rainfall sites, measured rates of ferric iron reduction could account for up to 44% of organic carbon oxidation. Iron reducers appeared to compete with methanogens when labile carbon availability was limited. We found large numbers of bacteria that oxidize reduced iron at sites with high rates of iron reduction and large numbers of iron reducers. The coexistence of large populations of iron-reducing and iron-oxidizing bacteria is evidence for rapid iron cycling between its reduced and oxidized states and suggests that mutualistic interactions among these bacteria ultimately fuel organic carbon oxidation and inhibit CH
4
production in these upland tropical forests.
Journal Article
Bacterial community structure transformed after thermophilically composting human waste in Haiti
Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98-99%), Lachnospiraceae (83-94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.
Journal Article
Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the
Oceanospirillales
was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the
Oceanospirillales
and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two
Oceanospirillales
single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the
Oceanospirillales
single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the
Oceanospirillales
to aliphatic hydrocarbons in the deep sea.
Journal Article
Iron Reduction and Soil Phosphorus Solubilization in Humid Tropical Forests Soils: The Roles of Labile Carbon Pools and an Electron Shuttle Compound
The affinity of iron oxides and hydroxides for phosphorus is thought to contribute to phosphorus limitation to net primary productivity in humid tropical forests on acidic, highly weathered soils. Perennially warm, humid conditions and high biological activity in these soils can result in fluctuating redox potential that in turn leads to considerable iron reduction in the presence of labile carbon and humic substances. We investigated the effects of reducing conditions in combination with the addition of labile carbon substrates (glucose and acetate) and an electron shuttle compound on iron reduction and phosphorus release in a humid tropical forest soil. Glucose or acetate was added to soils as a single dose at the beginning of the experiment, and as pulsed inputs over time, which more closely mimics patterns in labile carbon availability. Iron reduction and phosphorus mobilization were weakly stimulated by a single low level addition of carbon, and the addition of the electron shuttle compound with or without added carbon. Pulsed labile carbon additions produced a significant increase in soil pH, soluble iron, and phosphorus concentrations. Pulsed labile carbon inputs also promoted the precipitation of ferrous hydroxide complexes which could increase the capacity for P sorption, although our results suggest that rates of P solubilization exceeded re-adsorption. Plant and microbial P demand are also likely to serve as an important sinks for released P, limiting the role of P re-adsorption. Our results suggest that reducing conditions coupled with periodic carbon inputs can stimulate iron reduction and a corresponding increase in soil phosphorus mobilization, which may provide a source of phosphorus to plants and microorganisms previously undocumented in these ecosystems.
Journal Article
Intestinal Microbiota as Novel Biomarkers of Prior Radiation Exposure
There is an urgent need for rapid, accurate, and sensitive diagnostic platforms to confirm exposure to radiation and estimate the dose absorbed by individuals subjected to acts of radiological terrorism, nuclear power plant accidents, or nuclear warfare. Clinical symptoms and physical dosimeters, even when available, do not provide adequate diagnostic information to triage and treat life-threatening radiation injuries. We hypothesized that intestinal microbiota act as novel biomarkers of prior radiation exposure. Adult male Wistar rats (n = 5/group) received single or multiple fraction total-body irradiation of 10.0 Gy and 18.0 Gy, respectively. Fresh fecal pellets were obtained from each rat prior to (day 0) and at days 4, 11, and 21 post-irradiation. Fecal microbiota composition was determined using microarray and quantitative PCR (polymerase chain reaction) analyses. The radiation exposure biomarkers consisted of increased 16S rRNA levels of 12 members of the Bacteroidales, Lactobacillaceae, and Streptococcaceae after radiation exposure, unchanged levels of 98 Clostridiaceae and Peptostreptococcaceae, and decreased levels of 47 separate Clostridiaceae members; these biomarkers are present in human and rat feces. As a result of the ubiquity of these biomarkers, this biomarker technique is non-invasive; microbiota provide a sustained level of reporting signals that are increased several-fold following exposure to radiation, and intestinal microbiota that are unaffected by radiation serve as internal controls. We conclude that intestinal microbiota serve as novel biomarkers of prior radiation exposure, and may be able to complement conventional chromosome aberrational analysis to significantly enhance biological dose assessments.
Journal Article
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders
The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 1010 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment and succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia, Cycloclasticus, and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.
Journal Article
Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume
The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared with outside the plume, indicating a great potential for
intrinsic
bioremediation or natural attenuation in the deep sea. Various other microbial functional genes that are relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments.
Journal Article
Integrating microbial ecology into ecosystem models: challenges and priorities
Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment.
Journal Article
REPLY TO DELMONT AND EREN
A laboratory simulation revealed the succession patterns of oil degradation and microbial community changes during the Deepwater Horizon oil spill, one of the largest environmental catastrophes in human history. Hu et al. successfully recovered genomes of several oil-degrading bacteria, including one of “Candidatus Bermanella macondoprimitus,” with high identity to the dominant Oceanospirillales 16S rRNA gene sequences recovered from the deep-ocean hydrocarbon plumes. Delmont and Eren (3) reanalyzed metagenomic data generated from these plumes to argue that this Bermanella was not present.
Journal Article