Phylogenetic diversity and community structure of sulfate-reducing bacteria in a salt marsh sediment

Phylogenetic diversity and community structure of sulfate-reducing bacteria (SRB) in a salt marsh sediment and rhizosphere of Spartina alterniflora were investigated. Uncultivated phylotypes were studied by selectively amplifying Desulfobacteriaceae 16S rRNA gene fragments from DNA extracted from salt marsh rhizosphere samples. An in vitro transcription technique was developed to synthesize reference RNAs containing sequences presumably identical to corresponding regions of the uncultivated organisms\u27 16S rRNAs. These reference RNAs were used in subsequent quantitative probing experiments. Oligonucleotide probes were designed to specifically target novel phylotypes and were tested for optimal hybridization wash conditions and target specificity. The newly designed probes were then applied together with eubacterial probes to determine the relative abundances of the novel phylotypes in the salt marsh sediment and rhizosphere. Lastly, 16S rRNA sequences of ten SRB isolates were analyzed and compared to sequences of other cultivated SRB and novel phylotypes retrieved directly from environmental samples. Two novel phylotypes were retrieved from rhizosphere samples, with A01 sharing 89.1% sequence identity with Desulfococcus multivorans and 4D19 sharing 96.3% sequence identity with Desulfosarcina variabilis. Additionally, six sequences were found that were extremely closely related to D. multivorans. Synthetic reference RNAs were successfully used in the optimization and application of probes A01-183 and 4D19-189, which specifically targeted A01 and 4D19, respectively. Mean relative abundances of A01-183 and 4D19-189 targets were 7.5% and 3.4%, respectively, suggesting that the target organisms of A01-183 and, to a lesser extent, 4D19-189 played a dominant role in the salt marsh sediment and rhizosphere. Phylogenetic analysis of SRB isolates placed all isolates within the Gram-negative mesophilic SRB group. Two isolates were members of the Desulfovibrionaceae family, with one a member of the genus Desulfovibrio and the other possibly representing a novel genus. The remaining eight isolates were members of the Desulfobacteriaceae family and were comprised of novel species within the genera Desulfobulbus, Desulfobacter, Desulfobacterium, and Desulfoarculus, as well as a novel genus most closely related to Desulfobotulus sapovorans. None of the SRB isolates appeared to be related to the phylotypes A01 or 4D19 at the species or genus level

Combining role-play with interactive simulation to motivate informed climate action: Evidence from the World Climate simulation

Climate change communication efforts grounded in the information deficit model have largely failed to close the gap between scientific and public understanding of the risks posed by climate change. In response, simulations have been proposed to enable people to learn for themselves about this complex and politically charged topic. Here we assess the impact of a widely-used simulation, World Climate, which combines a socially and emotionally engaging role-play with interactive exploration of climate change science through the C-ROADS climate simulation model. Participants take on the roles of delegates to the UN climate negotiations and are challenged to create an agreement that meets international climate goals. Their decisions are entered into C-ROADS, which provides immediate feedback about expected global climate impacts, enabling them to learn about climate change while experiencing the social dynamics of negotiations. We assess the impact of World Climate by analyzing pre- and post-survey results from >2,000 participants in 39 sessions in eight nations. We find statistically significant gains in three areas: (i) knowledge of climate change causes, dynamics and impacts; (ii) affective engagement including greater feelings of urgency and hope; and (iii) a desire to learn and do more about climate change. Contrary to the deficit model, gains in urgency were associated with gains in participants’ desire to learn more and intent to act, while gains in climate knowledge were not. Gains were just as strong among American participants who oppose government regulation of free markets–a political ideology that has been linked to climate change denial in the US–suggesting the simulation’s potential to reach across political divides. The results indicate that World Climate offers a climate change communication tool that enables people to learn and feel for themselves, which together have the potential to motivate action informed by science.National Science Foundation (U.S.) (grant DUE-124558)National Science Foundation (U.S.) (grant ICEER-1701062

Exploring the capacity for anaerobic biodegradation of polycyclic aromatic hydrocarbons and naphthenic acids by microbes from oil-sands-process-affected waters

Both polycyclic aromatic hydrocarbons (PAHs) and naphthenic acids (NAs) are natural components of fossil fuels, but they are also widespread toxic and environmentally persistent pollutants. They are the major cause of environmental toxicity in oil-sands-process waters (OSPW). This study aimed to investigate the anaerobic biodegradation of the PAHs pyrene and 2-methylnaphthalene, and the NAs adamantane-1-carboxylic acid and a "natural" NA mixture (i.e., acid-extractable NAs from OSPW) under sulfate-reducing and methanogenic conditions by a microbial community derived from an oil sands tailings pond. Using gas-chromatography mass spectrometry (GC-MS), the rate of biodegradation was measured in relation to changes in bacterial community composition. Only 2-methylnaphthalene was significantly degraded after 260 days, with significantly more degradation under sulfate-reducing (40%) than methanogenic conditions (25%). During 2-methylnaphthalene biodegradation, a major metabolite was produced and tentatively identified as 2-naphthoic acid. Denaturing gradient gel electrophoresis (DGGE) demonstrated an increase in intensity of bands during the anaerobic biodegradation of 2-methylnaphalene, which derived from species of the genera Fusibacter, Alkaliphilus, Desulfobacterium, Variovorax, Thaurea, and Hydrogenophaga. Despite the biodegradation of 2-methylnaphthalene, this study demonstrates that, under anaerobic conditions, NAs and high-molecular-weight PAHs are the predominant molecules likely to persist in OSPW. Therefore alternative remediation strategies are required

Genome-wide gene regulation of biosynthesis and energy generation by a novel transcriptional repressor in Geobacter species

Geobacter species play important roles in bioremediation of contaminated environments and in electricity production from waste organic matter in microbial fuel cells. To better understand physiology of Geobacter species, expression and function of citrate synthase, a key enzyme in the TCA cycle that is important for organic acid oxidation in Geobacter species, was investigated. Geobacter sulfurreducens did not require citrate synthase for growth with hydrogen as the electron donor and fumarate as the electron acceptor. Expression of the citrate synthase gene, gltA, was repressed by a transcription factor under this growth condition. Functional and comparative genomics approaches, coupled with genetic and biochemical assays, identified a novel transcription factor termed HgtR that acts as a repressor for gltA. Further analysis revealed that HgtR is a global regulator for genes involved in biosynthesis and energy generation in Geobacter species. The hgtR gene was essential for growth with hydrogen, during which hgtR expression was induced. These findings provide important new insights into the mechanisms by which Geobacter species regulate their central metabolism under different environmental conditions

Functional differences in the allometry of the water, carbon and nitrogen content of gelatinous organisms

We have supplemented available, concurrent measurements of fresh weight (W, g) and body carbon (C, g) (46 individuals, 14 species) and of body nitrogen (N, g) and C (11individuals, 9 species) of marine gelatinous animals with data obtained during the global ocean expedition MALASPINA 2010 (totalling 267 individuals and 33 species for the W vs. C data; totalling 232 individuals and 31 species for the N vs. C data). We then used those data to test the allometric properties of the W vs. C and N vs. C relationships. Overall, gelatinous organisms contain 1.13±1.57% of C (by weight, mean±SD) in their bodies and show a C:N of 4.56±2.46, respectively, although estimations can be improved by using separate conversion coefficients for the carnivores and the filter feeders. Reduced Major Axis Regression (RMA) indicates that W grows isometrically with C in the carnivores (cnidarians and ctenophores), implying that their water content can be described by a single conversion coefficient of 173.78 gW[gC]-1, or a C content of 1.17±1.90% by weight, although there is much variability due to the existence of carbon-dense species. In contrast, W grows faster than C in the filter feeders (salps and doliolids), according to the power relationship W=446.68)C1.54. This exponent is not significantly different from 1.2, which is consistent with the idea that the watery bodies of gelatinous animals represent an evolutionary response towards increasing food capture surfaces, i.e. a bottom up rather than a top down mechanism. Thus, the available evidence negates a bottom up mechanism in the carnivores, but supports it in the filter feeders. Last, N grows isometrically with C in both carnivores and herbivores, with C:N ratios of 3.89±1.34 and 4.38±1.21, respectively. These values are similar to those of compact, non-gelatinous organisms and reflect a predominantly herbivorous diet in the filter feeders, what is confirmed by a difference of one trophic level between filter feeders and carnivores, according to stable N isotope enrichment data.MALASPINA (CSD2008-00077)Versión del editor1,749

Planktonic Microbes in the Gulf of Maine Area

In the Gulf of Maine area (GoMA), as elsewhere in the ocean, the organisms of greatest numerical abundance are microbes. Viruses in GoMA are largely cyanophages and bacteriophages, including podoviruses which lack tails. There is also evidence of Mimivirus and Chlorovirus in the metagenome. Bacteria in GoMA comprise the dominant SAR11 phylotype cluster, and other abundant phylotypes such as SAR86-like cluster, SAR116-like cluster, Roseobacter, Rhodospirillaceae, Acidomicrobidae, Flavobacteriales, Cytophaga, and unclassified Alphaproteobacteria and Gammaproteobacteria clusters. Bacterial epibionts of the dinoflagellate Alexandrium fundyense include Rhodobacteraceae, Flavobacteriaceae, Cytophaga spp., Sulfitobacter spp., Sphingomonas spp., and unclassified Bacteroidetes. Phototrophic prokaryotes in GoMA include cyanobacteria that contain chlorophyll (mainly Synechococcus), aerobic anoxygenic phototrophs that contain bacteriochlorophyll, and bacteria that contain proteorhodopsin. Eukaryotic microalgae in GoMA include Bacillariophyceae, Dinophyceae, Prymnesiophyceae, Prasinophyceae, Trebouxiophyceae, Cryptophyceae, Dictyochophyceae, Chrysophyceae, Eustigmatophyceae, Pelagophyceae, Synurophyceae, and Xanthophyceae. There are no records of Bolidophyceae, Aurearenophyceae, Raphidophyceae, and Synchromophyceae in GoMA. In total, there are records for 665 names and 229 genera of microalgae. Heterotrophic eukaryotic protists in GoMA include Dinophyceae, Alveolata, Apicomplexa, amoeboid organisms, Labrynthulida, and heterotrophic marine stramenopiles (MAST). Ciliates include Strombidium, Lohmaniella, Tontonia, Strobilidium, Strombidinopsis and the mixotrophs Laboea strobila and Myrionecta rubrum (ex Mesodinium rubra). An inventory of selected microbial groups in each of 14 physiographic regions in GoMA is made by combining information on the depth-dependent variation of cell density and the depth-dependent variation of water volume. Across the entire GoMA, an estimate for the minimum abundance of cell-based microbes is 1.7×1025 organisms. By one account, this number of microbes implies a richness of 105 to 106 taxa in the entire water volume of GoMA. Morphological diversity in microplankton is well-described but the true extent of taxonomic diversity, especially in the femtoplankton, picoplankton and nanoplankton – whether autotrophic, heterotrophic, or mixotrophic, is unknown

Novel regulatory cascades controlling expression of nitrogen-fixation genes in Geobacter sulfurreducens

Geobacter species often play an important role in bioremediation of environments contaminated with metals or organics and show promise for harvesting electricity from waste organic matter in microbial fuel cells. The ability of Geobacter species to fix atmospheric nitrogen is an important metabolic feature for these applications. We identified novel regulatory cascades controlling nitrogen-fixation gene expression in Geobacter sulfurreducens. Unlike the regulatory mechanisms known in other nitrogen-fixing microorganisms, nitrogen-fixation gene regulation in G. sulfurreducens is controlled by two two-component His–Asp phosphorelay systems. One of these systems appears to be the master regulatory system that activates transcription of the majority of nitrogen-fixation genes and represses a gene encoding glutamate dehydrogenase during nitrogen fixation. The other system whose expression is directly activated by the master regulatory system appears to control by antitermination the expression of a subset of the nitrogen-fixation genes whose transcription is activated by the master regulatory system and whose promoter contains transcription termination signals. This study provides a new paradigm for nitrogen-fixation gene regulation

Stellar mass as a galaxy cluster mass proxy: application to the Dark Energy Survey redMaPPer clusters

We introduce a galaxy cluster mass observable, μ⋆, based on the stellar masses of cluster members, and we present results for the Dark Energy Survey (DES) Year 1 (Y1) observations. Stellar masses are computed using a Bayesian model averaging method, and are validated for DES data using simulations and COSMOS data. We show that μ⋆ works as a promising mass proxy by comparing our predictions to X-ray measurements. We measure the X-ray temperature–μ_{⋆} relation for a total of 129 clusters matched between the wide-field DES Y1 redMaPPer catalogue and Chandra and XMM archival observations, spanning the redshift range 0.1 < z < 0.7. For a scaling relation that is linear in logarithmic space, we find a slope of α = 0.488 ± 0.043 and a scatter in the X-ray temperature at fixed μ_{*} of σ1nT_{x}|μ_{*} = 0.266_{-0.020}^{+0.019} for the joint sample. By using the halo mass scaling relations of the X-ray temperature from the Weighing the Giants program, we further derive the μ⋆-conditioned scatter in mass, finding σ1nM|μ_{*} = 0.26_{-0.10}^{+0.15}. These results are competitive with well-established cluster mass proxies used for cosmological analyses, showing that μ_{⋆} can be used as a reliable and physically motivated mass proxy to derive cosmological constraints

Rock weathering creates oases of life in a high Artic desert.

During primary colonization of rock substrates by plants, mineral weathering is strongly accelerated under plant roots, but little is known on how it affects soil ecosystem development before plant establishment. Here we show that rock mineral weathering mediated by chemolithoautotrophic bacteria is associated to plant community formation in sites recently released by permanent glacier ice cover in the Midtre Lovénbreen glacier moraine (78°53_N), Svalbard. Increased soil fertility fosters growth of prokaryotes and plants at the boundary between sites of intense bacterial mediated chemolithotrophic iron-sulfur oxidation and pH decrease, and the common moraine substrate where carbon and nitrogen are fixed by cyanobacteria. Microbial iron oxidizing activity determines acidity and corresponding fertility gradients, where water retention, cation exchange capacity and nutrient availability are increased. This fertilization is enabled by abundant mineral nutrients and reduced forms of iron and sulfur in pyrite minerals within a conglomerate type of moraine rock. Such an interaction between microorganisms and moraine minerals determines a peculiar, not yet described model for soil genesis and plant ecosystem formation with potential past and present analogues in other harsh environments with similar geochemical settings