Exploiting the diverse microbial ecology of marine sponges

Marine sponges (phylum Porifera) are the oldest extant metazoan animals on earth and host large populations of symbiotic microbes: Bacteria, Archaea and unicellular Eukaryota. Those microbes play ecological functions which are essential to the health of the host including carbon, nitrogen and sulfur cycling as well as host defence through the production of bioactive secondary metabolites which protect against infection and predation. The diversity of sponge-associated microbes is remarkable with thousands of OTUs reported from individual sponge species. Amongst those populations are sponge-specific microbes which may be specific to sponges or specific to sponge species. While marine natural product discovery concerns many animal phyla, Porifera account for the largest proportion of novel compounds. Evidence suggests that many of these compounds are the products of symbiotic microbes. Descriptions of sponge-associated microbial community structures have been advanced by the development of next-generation sequencing technologies while the discovery and exploitation of sponge derived bioactive compounds has increased due to developments in sequence-based and function-based metagenomics. Here, we use pyrosequencing to describe the bacterial communities associated with two shallow, temperate water sponges (Raspailia ramosa and Stelligera stuposa) from Irish coastal waters and to describe the bacterial and archaeal communities of a single sponge species (Inflatella pellicula) from two different depths in deep waters in the Atlantic Ocean, including at a depth of 2900m, a depth far greater than that of any previous sequence-based sponge-microbe investigation. We identified diverse microbial communities in all sponges and the presence of sponge-specific taxa recruiting to previously described and novel spongespecific clusters. We also identified archaeal communities which dominated sponge-microbe communities. We demonstrate that sponge-associated microbial communities differ from seawater communities indicating host selection processes. We used sequence-based metagenomic techniques to identify genes of potential industrial and pharmacological interest in the metagenomes of various sponge species and functionbased metagenomic screening in an attempt to identify lipolytic and antibacterial activities from metagenomic clones from the metagenome of the marine sponge Stelletta normani. In addition we have cultured diverse bacterial species from sponge tissues, many of which display antimicrobial activities against clinically relevant bacterial and yeast test strains. Other isolates represent novel species in the genus Maribacter and require emendments to the description of that genus.

Decomposing the mid-holocene Tsuga decline in eastern North America

The mid-Holocene decline of Tsuga canadensis (hereafter Tsuga) populations across eastern North America is widely perceived as a synchronous event, driven by pests/pathogens, rapid climate change, or both. Pattern identification and causal attribution are hampered by low stratigraphic density of pollen-sampling and radiometric dates at most sites, and by absence of highly resolved, paired pollen and paleoclimate records from single sediment cores, where chronological order of climatic and vegetational changes can be assessed. We present an intensely sampled (contiguous 1-cm intervals) record of pollen and water table depth (inferred from testate amoebae) from a single core spanning the Tsuga decline at Irwin Smith Bog in Lower Michigan, with high-precision chronology. We also present an intensively sampled pollen record from Tower Lake in Upper Michigan. Both sites show high-magnitude fluctuations in Tsuga pollen percentages during the pre-decline maximum. The terminal decline is dated at both sites ca. 5000 cal yr BP, some 400 years later than estimates from other sites and data compilations. The terminal Tsuga decline was evidently heterochronous across its range. A transient decline ca. 5350 cal yr BP at both sites may correspond to the terminal decline at other sites in eastern North America. At Irwin Smith Bog, the terminal Tsuga decline preceded an abrupt and persistent decline in water table depths by;200 years, suggesting the decline was not directly driven by abrupt climate change. The Tsuga decline may best be viewed as comprising at least three phases: a long-duration predecline maximum with high-magnitude and high-frequency fluctuations, followed by a terminal decline at individual sites, followed in turn by two millennia of persistently low Tsuga populations. These phases may not be causally linked, and may represent dynamics taking place at multiple temporal and spatial scales. Further progress toward understanding the phenomenon requires an expanded network of high-resolution pollen and paleoclimate chronologies.

Summary of the Snowmastodon Project Special Volume: A high-elevation, multi-proxy biotic and environmental record of MIS 6-4 from the Ziegler Reservoir fossil site, Snowmass Village, Colorado, USA

In North America, terrestrial records of biodiversity and climate change that span Marine Oxygen Isotope Stage (MIS) 5 are rare. Where found, they provide insight into how the coupling of the ocean-atmosphere system is manifested in biotic and environmental records and how the biosphere responds to climate change. In 2010-2011, construction at Ziegler Reservoir near Snowmass Village, Colorado (USA) revealed a nearly continuous, lacustrine/wetland sedimentary sequence that preserved evidence of past plant communities between similar to 140 and 55 lea, including all of MIS 5. At an elevation of 2705 m, the Ziegler Reservoir fossil site also contained thousands of well-preserved bones of late Pleistocene megafauna, including mastodons, mammoths, ground sloths, horses, camels, deer, bison, black bear, coyotes, and bighorn sheep. In addition, the site contained more than 26,000 bones from at least 30 species of small animals including salamanders, otters, muskrats, minks, rabbits, beavers, frogs, lizards, snakes, fish, and birds. The combination of macro- and micro-vertebrates, invertebrates, terrestrial and aquatic plant macrofossils, a detailed pollen record, and a robust, directly dated stratigraphic framework shows that high-elevation ecosystems in the Rocky Mountains of Colorado are climatically sensitive and varied dramatically throughout MIS 5 

Letter, to Colonel Calvin Spencer, Chesterfield, SC, 1786 October 12

This letter is from General Henry William Harrington to Colonel Calvin Spencer.

Registry of samples and environmental context from the Ocean Sampling Day 2014

The Ocean Sampling Day (OSD) is a simultaneous sampling campaign of the world's oceans which took place (for the first time) on the summer solstice (June 21st) in the year 2014. These cumulative samples, related in time, space and environmental parameters, provide insights into fundamental rules describing microbial diversity and function and contribute to the blue economy through the identification of novel, ocean-derived biotechnologies. We see OSD data as a reference data set for generations of experiments to follow in the coming decade. The present data set includes a description of each sample collected during the Ocean Sampling Day 2014 and provides contextual environmental data measured concurrently with the collection of water samples for genomic analyses.

Orientation of the transcription preinitiation complex in Archaea

The basal transcription machinery of Archaea corresponds to the minimal subset of factors required for RNA polymerase II transcription in eukaryotes. Using just two factors, Archaea recruit the RNA polymerase to promoters and define the direction of transcription. Notably, the principal determinant for the orientation of transcription is not the recognition of the TATA box by the TATA-box-binding protein. Instead, transcriptional polarity is governed by the interaction of the archaeal TFIIB homologue with a conserved motif immediately upstream of the TATA box. This interaction yields an archaeal preinitiation complex with the same orientation as the analogous eukaryal complex.

Late Quaternary extinction of a tree species in eastern North America

Widespread species- and genus-level extinctions of mammals in North America and Europe occurred during the last deglaciation [16,000–9,000 yr B.P. (by 14C)], a period of rapid and often abrupt climatic and vegetational change. These extinctions are variously ascribed to environmental change and overkill by human hunters. By contrast, plant extinctions since the Middle Pleistocene are undocumented, suggesting that plant species have been able to respond to environmental changes of the past several glacial/interglacial cycles by migration. We provide evidence from morphological studies of fossil cones and anatomical studies of fossil needles that a now-extinct species of spruce (Picea critchfieldii sp. nov.) was widespread in eastern North America during the Last Glacial Maximum. P. critchfieldii was dominant in vegetation of the Lower Mississippi Valley, and extended at least as far east as western Georgia. P. critchfieldii disappeared during the last deglaciation, and its extinction is not directly attributable to human activities. Similarly widespread plant species may be at risk of extinction in the face of future climate change.

Temperature, template topology, and factor requirements of archaeal transcription

Although Archaea are prokaryotic and resemble Bacteria morphologically, their transcription apparatus is remarkably similar to those of eukaryotic cell nuclei. Because some Archaea exist in environments with temperatures of around 100°C, they are likely to have evolved unique strategies for transcriptional control. Here, we investigate the effects of temperature and DNA template topology in a thermophilic archaeal transcription system. Significantly, and in marked contrast with characterized eucaryal systems, archaeal DNA template topology has negligible effect on transcription levels at physiological temperatures using highly purified polymerase and recombinant transcription factors. Furthermore, archaeal transcription does not require hydrolysis of the β-γ phosphoanhydride bond of ATP. However, at lower temperatures, negatively supercoiled templates are transcribed more highly than those that are positively supercoiled. Notably, the block to transcription on positively supercoiled templates at lowered temperatures is at the level of polymerase binding and promoter opening. These data imply that Archaea do not possess a functional homologue of transcription factor TFIIH, and that for the promoters studied, transcription is mediated by TATA box-binding protein, transcription factor TFB, and RNA polymerase alone. Furthermore, they suggest that the reduction of plasmid linking number by hyperthermophilic Archaea in vivo in response to cold shock is a mechanism to maintain gene expression under these adverse circumstances.

Feedback Control and Diurnal Regulation of Gibberellin 20-Oxidase Transcript Levels in Potato1

Tuber formation in potato (Solanum tuberosum) is promoted by short photoperiods and is inhibited by gibberellins (GAs). Endogenous levels of GA1 were shown to decrease in stolons and leaves of potato plants induced to tuberize, which suggests that photoperiodic regulation of GA biosynthesis may play a role in tuber induction. We report the isolation of three potato cDNA clones (StGA20ox1–3) encoding GA 20-oxidase, a key regulatory enzyme in the GA-biosynthetic pathway. Using northern analysis, we detected a differential pattern of tissue-specific expression of the mRNAs corresponding to these clones. StGA20ox mRNAs were also very abundant in leaves of the potato ga1 mutant, which is blocked in the 13-hydroxylation step, and were strongly down-regulated by gibberellic acid, suggesting a feedback regulation of these genes. In plants grown in short-day (inductive) conditions, levels of the StGA20ox transcripts in leaves fluctuated during a 24-h period, with a peak of accumulation observed about 4 h after the lights were turned off. Interruption of the night with a 30-min “night break” of light (noninductive conditions) did not have a marked effect on the levels of accumulation of the three GA 20-oxidase mRNAs during the day, but it induced a second peak of expression of StGA20ox1 and StGA20ox3 transcripts late in the night. This observation, together with the finding that StGA20ox1 mRNA is expressed at high levels in leaves, suggests that night-break induction of this gene might play a role in the control of tuberization by regulating endogenous levels of GAs in response to daylength conditions.

Phytochrome B Affects the Levels of a Graft-Transmissible Signal Involved in Tuberization1

Grafting experiments between phytochrome B antisense and wild-type potato (Solanum tuberosum L. subsp. andigena [line 7540]) plants provide evidence that phytochrome B is involved in the production of a graft-transmissible inhibitor of tuberization, the level of which is reduced in the antisense plants, allowing them to tuberize in noninducing photoperiods.