1,720,994 research outputs found
Data Associated with publication "Vertical transport of sediment-associated metals and cyanobacteria by ebullition in a stratified lake"
No full textThe purpose of this collection is to make available to the public the material necessary to validate the research findings for the article listed in "Related Publications." Bubbles adsorb and transport particulate matter both in industrial and marine systems. While methane-containing bubbles emitted from anoxic sediments are found extensively in aquatic ecosystems, relatively little attention has been paid to the possibility that such bubbles transport particle-associated chemical or biological material from sediments to surface waters of freshwater lakes. We quantified transport of particulate material from sediments to the surface by bubbles in Upper Mystic Lake, MA and in a 15 m tall experimental column. Vertical particle transport was positively correlated with the volume of gas bubbles released from the sediment. Particles transported by bubbles originated almost entirely in the sediment, rather than being scavenged from the water column. Concentrations of arsenic, chromium, lead, and cyanobacterial cells in bubble-transported particulate material were similar to those of bulk sediment, and particles were transported from depths exceeding 15 m, resulting in daily fluxes as large as 0.18 µg of arsenic m-2 and 2 x 104 cyanobacterial cells m-2 in the strongly stratified Upper Mystic Lake. While bubble-facilitated arsenic transport currently appears to be a modest component of total arsenic cycling in this lake, bubble-facilitated cyanobacterial transport could comprise as much as 17% of recruitment in this lake and may thus be of particular importance in large, deep, stratified lakes
Data associated with the publication: Influence of simplified microbial community biofilms on bacterial retention in porous media under conditions of stormwater biofiltration
No full textPorous media filters are used widely to remove bacteria from contaminated water, such as stormwater run-off. Biofilms that colonize filter media during normal function can significantly alter performance, but it is not clear how characteristics of individual populations colonizing porous media combine to affect bacterial retention. We assess how four bacterial strains isolated from stormwater and a laboratory strain, Pseudomonas aeruginosa PAO1, alter Escherichia coli retention in experimental sand columns under conditions of stormwater filtration relative to a clean-bed control. Our results demonstrate that these strains differentially affect E. coli retention, as was previously shown for a model colloid. To determine whether E. coli retention could be influenced by changes in relative abundance of strains within a microbial community, we selected two pairs of biofilm strains with the largest observed differences in E. coli retention and tested how changes in relative abundance of strain pairs in the biofilm affected E. coli retention. The results demonstrate that E. coli retention efficiency is influenced by the retention characteristics of the strains within biofilm microbial community, but individual strain characteristics influence retention in a manner that cannot be determined from changes in their relative abundance alone. This study demonstrates that changes in the relative abundance of specific members of a biofilm community can significantly alter filter performance, but these changes are not a simple function of strain-specific retention and the relative abundance. Our results suggest that the microbial community composition of biofilms should be considered when evaluating factors that influence filter performance
Data associated with the publication: Abundant and Persistent Sulfide-oxidizing Microbial Populations are Responsive to Hypoxia in the Chesapeake Bay
No full textThe number, size and severity of aquatic low oxygen dead-zones are increasing worldwide. Microbial processes in low oxygen environments have important ecosystem-level consequences, such as denitrification, greenhouse gas production and acidification. To identify key microbial processes occurring in low oxygen bottom waters of the Chesapeake Bay, we sequenced both 16S rRNA genes and shotgun metagenomic libraries to determine the identity, functional potential and spatiotemporal distribution of microbial populations in the water column. Unsupervised clustering algorithms grouped samples into three clusters using water chemistry or microbial communities, with extensive overlap of cluster composition between methods. Clusters were strongly differentiated by temperature, salinity, and oxygen. Sulfide-oxidizing microorganisms were found to be enriched in the low-oxygen bottom water and predictive of hypoxic conditions. Metagenome assembled genomes demonstrate that some of these sulfide-oxidizing populations are capable of partial denitrification, and transcriptionally active in a prior study. These results establish the importance of sulfide-oxidizing microorganisms in the microbial response to low oxygen in the Chesapeake Bay and suggest ties between the sulfur, nitrogen and oxygen cycles that could be important to capture when predicting the ecosystem response to remediation efforts or climate change
Data associated with the publication: Genes involved in carbon, nitrogen, and sulfur cycling in an important estuarine ecosystem show coherent shifts in response to changes in environmental conditions
No full textThis dataset is associated with two publications: "Spatiotemporal shifts in the distribution of genes in Chesapeake Bay: Part I- Major trends, gene-gene relationships, and environmental correlates" and "Spatiotemporal shifts in the distribution of genes in Chesapeake Bay: Part II- Relationship between genes and associated modeled rates."
Metagenomics can provide insight into microbial community metabolic potential, but understanding factors that influence gene abundance could maximize the information gained from this analysis. Gene abundances are influenced by chemical or physical conditions along with other factors, such as copy number variation between taxa or methodological issues associated with identification and classification. Here, we identify major drivers of spatiotemporal shifts in microbial gene relative abundance from multiple months, sites, and depths within Chesapeake Bay in 2017 using shotgun metagenomics. We compared changes in relative abundance of bacterial photosynthesis and nitrogen and sulfur metabolism genes with other genes and measured environmental variables. Major drivers of differences in key metabolic gene abundances are associated with environmental variables that largely change with depth and season (e.g. temperature, oxygen, phosphate). For sulfur oxidation, bacterial photosynthesis, and denitrification, genes within each process are generally significantly correlated with each other and with several environmental variables. For other processes, such as nitrification, nitrogen fixation, and dissimilatory nitrate reduction to ammonium, genes that encode enzymes within the same pathway are not well correlated. The lack of correlation typically results from differences in identified taxa carrying these genes, suggesting methodological errors or discrepancies in gene copy number between taxonomic groups. Genes or pathways strongly correlated with environmental variables and specific to and inclusive of all taxa mediating the associated process may be the most suitable as indicators of biogeochemical processes, and we compare gene abundances to model predictions in our companion paper
Polyphyly of non-bioluminescent Vibrio fischeri sharing a lux-locus deletion
Full text linkavailable in PMC 2013 May 16This study reports the first description and molecular characterization of naturally occurring, non-bioluminescent strains of Vibrio fischeri. These ‘dark’V. fischeri strains remained non-bioluminescent even after treatment with both autoinducer and aldehyde, substrate additions that typically maximize light production in dim strains of luminous bacteria. Surprisingly, the entire lux locus (eight genes) was absent in over 97% of these dark V. fischeri strains. Although these strains were all collected from a Massachusetts (USA) estuary in 2007, phylogenetic reconstructions allowed us to reject the hypothesis that these newly described non-bioluminescent strains exhibit monophyly within the V. fischeri clade. These dark strains exhibited a competitive disadvantage against native bioluminescent strains when colonizing the light organ of the model V. fischeri host, the Hawaiian bobtail squid Euprymna scolopes. Significantly, we believe that the data collected in this study may suggest the first observation of a functional, parallel locus-deletion event among independent lineages of a non-pathogenic bacterial species.National Institutes of Health (U.S.) (NIH Molecular Biosciences (5T32GM007215-35))National Institutes of Health (U.S.) (NIH Microbes in Health and Disease, training grant (2T32AI055397-07))Gordon and Betty Moore FoundationBroad Institute of MIT and Harvard (SPARC programme)National Science Foundation (U.S.) (NSF IOS 0841507)National Institutes of Health (U.S.) (NIH R01 RR12294)National Science Foundation (U.S.) (NSF Microbial Systems in the Biosphere programme)Woods Hole Center for Oceans & Human Healt
O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates
No full textThe O-antigen is a highly diverse structure expressed on the outer surface of Gram-negative bacteria. The products responsible for O-antigen synthesis are encoded in the wbe region, which exhibits extensive genetic diversity. While heterogeneous O-antigens are observed within Vibrio species, characterization of these structures has been devoted almost exclusively to pathogens. Here, we investigate O-antigen diversity among coastal marine Vibrio splendidus-like isolates. The wbe region was first identified and characterized using the sequenced genomes of strains LGP32, 12B01 and Med222. These regions were genetically diverse, reflective of their expressed O-antigen. Additional isolates from physically distinct habitats in Plum Island Estuary (MA, USA), including within animal hosts and on suspended particles, were further characterized based on multilocus sequence analysis (MLSA) and O-antigen profiles. Results showed serotype diversity within an ecological setting. Among 48 isolates which were identical in three MLSA genes, 41 showed gpm genetic diversity, a gene closely linked to the wbe locus, and at least 12 expressed different O-antigen profiles further suggesting wbe genetic diversity. Our results demonstrate O-antigen hyper-variability among these environmental strains and suggest that frequent lateral gene transfer generates wbe extensive diversity among V. splendidus and its close relatives.National Institute of General Medical Sciences (U.S.) (F32GM084640)United States. Dept. of Energy (Grant no. DE-FG09-93ER-20097)Woods Hole Center for Oceans and Human HealthGordon and Betty Moore Foundatio
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
REMOVAL OF BACTERIA FROM STORMWATER DURING BIOFILTRATION: THE ROLE OF ACTIVATED CARBON AND BIOFILM-FORMING STRAINS
No full textWith rapid population growth and industrial water use, the Earth is facing an unprecedented water crisis, with global freshwater demand predicted to exceed supply by more than 40% in 2030. Consequently, sustaining water resources by exploring alternative sources has become a priority in most countries. Rainwater collection represents an alternative source of water for many purposes. However, surface runoff after rainfall results in the microbial contamination of the rainwater. Therefore, calls for effective filtration of rainwater to remove microbial contaminants and safeguard human health during subsequent use are needed.
Presently, stormwater filtration is commonly carried out through sand filters, but their effectiveness on bacterial retention is low relative to other media, such as activated carbon. However, the presence of biofilms from naturally occurring bacteria in stormwater on the media can change the filter performance. This research investigated the capacities of sand filters modified with activated carbon and biofilms to remove a model bacterial species, Escherichia coli, from stormwater. We found a statistically significant improvement of E. coli retention on the columns with increasing amounts of activated carbon within the sand filter. This improvement may be due to the greater surface area and improved porosity offered by activated carbon, which gives more attachment points for the bacteria. Next, sand filters modified with 20% activated carbon were pre-inoculated with microorganisms capable of forming biofilms, which simulates the process of naturally occurring bacterial biofilm formation on the filtration media. We found that sand filters with activated carbon maintained a significant increase over sand columns in the bacterial retention capacity even in the presence of a biofilm-forming stormwater isolate. However, neither the sand nor the activated carbon breakthrough curves reached a steady-state in the presence of the biofilm-forming isolate, suggesting an extension of the experimental period is necessary to determine long term removal. These results demonstrate the potential benefit of using sand filters modified with activated carbon to further advance the treatment of stormwater for reuse, although more research is needed to determine whether it would make a sustainable long-term approach to stormwater management
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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