Endophyte Growth on Two Species of Conifers on the Shawangunk Ridge, Mid-Hudson Valley, New York

The Middle Silurian Shawangunk Formation is underlain by the Upper Ordovician Martinsburg Formation in the mid-Hudson Valley. The Shawangunk Ridge is composed of a very resistant quartz pebble conglomerate whereas the Martinsburg consists of less resistant shales and graywackes. Endophytes are fungi growing asymptomatically in plant tissues that are thought to act as a support system for the plant, protecting against desiccation and pathogens. We compared the diversity of endophytes colonizing two species of conifers, Pinus strobus and Tsuga canadensis, on two different substrates, conglomerate and shale. We hypothesized that there would be a marked difference in diversity between the two substrates, resulting in different microenvironments for the endophytes, since differences in diversity between species would occur if endophytes are host specific. We collected 7 individuals of each of the two conifer species along with pH readings of the soil at the base of the trees. Readings were taken at several sites on the Ridge last spring (2015). The needles of the specimens collected were surfaced sterilized and plated within 48 hours, then grown for 8 weeks on an agar plate. There was no difference in pH between the two substrates. To date, we have grown over 90 morphotypes of endophytes, including fungi from the genera Cladosporium, Chaetomium, Alternaria, Lophodermium, and Phoma. We expect to continue this project as we investigate endophyte growth on other genera such as Quercus, Hamamelis and Acer

Defining early steps in <i>Bacillus subtilis</i> biofilm biosynthesis

ABSTRACT The Bacillus subtilis extracellular biofilm matrix includes an exopolysaccharide (EPS) that is critical for the architecture and function of the community. To date, our understanding of the biosynthetic machinery and the molecular composition of the EPS of B. subtilis remains unclear and incomplete. This report presents synergistic biochemical and genetic studies built from a foundation of comparative sequence analyses targeted at elucidating the activities of the first two membrane-committed steps in the EPS biosynthetic pathway. By taking this approach, we determined the nucleotide sugar donor and lipid-linked acceptor substrates for the first two enzymes in the B. subtilis biofilm EPS biosynthetic pathway. EpsL catalyzes the first phosphoglycosyl transferase step using uridine diphosphate (UDP)-di-N-acetyl bacillosamine as phospho-sugar donor. EpsD is a predicted GT-B fold (GT4 family) retaining glycosyl transferase that catalyzes the second step in the pathway that utilizes the product of EpsL as an acceptor substrate and UDP-N-acetyl glucosamine as the sugar donor. Thus, the study defines the first two monosaccharides at the reducing end of the growing EPS unit. In doing so, we provide the first evidence of the presence of bacillosamine in an EPS synthesized by a Gram-positive bacterium. IMPORTANCE Biofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here, we identify the first two essential steps in the Bacillus subtilis biofilm matrix exopolysaccharide (EPS) synthesis pathway. Together, our studies and approaches provide the foundation for the sequential characterization of the steps in EPS biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenyl diphosphate-linked glycan substrates

Elevated methane alters dissolved organic matter composition in the Arctic Ocean cold seeps

Cold seeps release methane (CH4) from the seafloor to the water column, which fuels microbially mediated aerobic methane oxidation (MOx). Methane-oxidising bacteria (MOB) utilise excess methane, and the MOB biomass serves as a carbon source in the food web. Yet, it remains unclear if and how MOx modifies the composition of dissolved organic matter (DOM) in cold seeps. We investigated MOx rates, DOM compositions and the microbial community during ex-situ incubations of seawater collected from a cold seep site at Norskebanken (north of the Svalbard archipelago) in the Arctic Ocean. Samples were incubated with and without methane amendments. Samples amended with methane (∼1 µM final concentration) showed elevated rates of MOx in both seep and non-seep incubations. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analyses showed that the number of DOM formulas (i.e., molecular diversity) increased by up to 39% in these incubations. In contrast, the number of formulas decreased by 20% in samples not amended with methane, both from non-seep and seep locations. DOM composition was thus altered towards a more diverse and heterogeneous composition along with elevated methanotrophic activity in methane-amended conditions. In addition to microbial DOM production, abating microbial diversity indicates that elevated DOM diversity was potentially related to grazing pressure on bacteria. The diversity of DOM constituents, therefore, likely increased with the variety of decaying cells contributing to DOM production. Furthermore, based on a principal coordinate analysis, we show that the final DOM composition of non-seep samples amended with methane became more resemblant to that of seep samples. This suggests that methane intrusions will affect water column DOM dynamics similarly, irrespective of the water column’s methane history

Microbial Community Dynamics during a Harmful Chrysochromulina leadbeateri Bloom in Northern Norway

A harmful algal bloom occurred in late spring 2019 across multiple, interconnected fjords and bays in northern Norway. The event was caused by the haptophyte Chrysochromulina leadbeateri and led to severe fish mortality at several salmon aquaculture facilities. This study reports on the spatial and temporal succession dynamics of the holistic marine microbiome associated with this bloom by relating all detectable 18S and 16S rRNA gene amplicon sequence variants to the relative abundance of the C. leadbeateri focal taxon. A k-medoid clustering enabled inferences on how the causative focal taxon cobloomed with diverse groups of bacteria and microeukaryotes. These coblooming patterns showed high temporal variability and were distinct between two geographically separated time series stations during the regional harmful algal bloom. The distinct blooming patterns observed with respect to each station were poorly connected to environmental conditions, suggesting that other factors, such as biological interactions, may be at least as important in shaping the dynamics of this type of harmful algal bloom. A deeper understanding of microbiome succession patterns during these rare but destructive events will help guide future efforts to forecast deviations from the natural bloom cycles of the northern Norwegian coastal marine ecosystems that are home to intensive aquaculture activities

Structural and molecular interrogation of intact biological systems

Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease

Innovating carbon-capture biotechnologies through ecosystem-inspired solutions

Rising atmospheric carbon concentrations affect global health, the economy, and overall quality of life. We are fast approaching climate tipping points that must be addressed, not only by reducing emissions but also through new innovation and action toward carbon capture for sequestration and utilization (CCSU). In this perspective, we delineate next-generation biotechnologies for CCSU supported by engineering design principles derived from ecological processes inspired by three major biomes (plant-soil, deep biosphere, and marine). These are to interface with existing industrial infrastructure and, in some cases, tap into the carbon sink potential of nature. To develop ecosystem-inspired biotechnology, it is important to identify accessible control points of CO2 and CH4 within a given system as well as value-chain opportunities that drive innovation. In essence, we must supplement natural biogeochemical carbon sinks with new bioengineering solutions

Recommendations of the task force on public policy

This is the published version, reproduced here with permission from the publisher. This article is also available electronically from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741851/.The Task Force on Public Policy was established by the Association for Behavior Analysis to examine ways to encourage members to contribute to policymaking relevant to the public interest. Members discussed issues pertinent to this activity and summarized their discussion in a formal report.' Recommendations of the Task Force for conducting and disseminating policy research and for training, technical assistance, and other services supportive of behavior-analytic research in the public policy arena are presented here

Financial diversification strategies before World War I: Buy-and-hold versus naïve portfolio selection

This study contributes to a growing volume of scholarship that highlights the importance of financial diversification in business history. It shows that, pre-WWI, financial advice for equal portfolio weighting, the so-called naïve diversification, then called scientific investment or geographical distribution of risk, was a sophisticated strategy for Victorian investors and not suboptimal to Markowitz optimization. Drawing upon a unique dataset of 507 individual portfolios at death, this study shows that, although Victorian investors, in particular wealthy investors, did diversify investment risk across a number of securities, they did not hold equally weighted portfolios. It explores possible reasons for the unbalanced nature of investor portfolios and dismisses socio economic factors, illiquidity, passive ‘buy the market’ and market timing strategies as possible explanatory factors. The results rather point to a strategy of naïve diversification spread over time, a ‘buy as you go and hold strategy’, buying new securities as savings allowed and holding them until death