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Western science has grown increasingly reductionistic and, in parallel, the undergraduate life sciences curriculum has become disciplinarily fragmented. While reductionistic approaches have led to landmark discoveries, many of the most exciting scientific advances in the late 20th century have occurred at disciplinary interfaces; work at these interfaces is necessary to manage the world's looming problems, particularly those that are rooted in cellular-level processes but have ecosystem- and even global-scale ramifications (e.g., nonsustainable agriculture, emerging infectious diseases). Managing such problems requires comprehending whole scenarios and their emergent properties as sums of their multiple facets and complex interrelationships, which usually integrate several disciplines across multiple scales (e.g., time, organization, space). This essay discusses bringing interdisciplinarity into undergraduate cellular biology courses through the use of multiscalar topics. Discussing how cellular-level processes impact large-scale phenomena makes them relevant to everyday life and unites diverse disciplines (e.g., sociology, cell biology, physics) as facets of a single system or problem, emphasizing their connections to core concepts in biology. I provide specific examples of multiscalar topics and discuss preliminary evidence that using such topics may increase students' understanding of the cell's position within an ecosystem and how cellular biology interfaces with other disciplines.

A single software platform, mothur, is used to trim, screen, and align sequences, calculate distances, assign sequences to operational taxonomic units and also to describe the [alpha] and [beta] diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. The analysis of the huge sequence is completed in less than 2 hours with a laptop computer.

With the growing number of antibiotic-resistant pathogens, there is a need for new antibiotics. Bacteria within the order Actinomycetales produce the majority of known antibiotic compounds but harbor cryptic secondary metabolic pathways that likely produce thousands more antibiotics awaiting discovery. This has recently renewed interests in bioprospecting for novel Actinomycetales in underexplored environments, such as the lower atmosphere, and activating cryptic secondary metabolic pathways in previously characterized members of this order. Many antibiotic-producing Actinomycetales have complex metabolic interactions with trace metals (such as iron, zinc, and manganese); adding these metals to bacterial growth media may trigger antibiotic production, which could lead to the discovery of novel drugs that may otherwise be overlooked during screening in the absence of such metals. To test this hypothesis, a collection of bacterial isolates, composed primarily of taxa within the order Actinomycetales, was obtained from the lower atmosphere. In support of our hypothesis, we found that several isolates produced antibiotics in the presence of trace metals, but not in their absence. Further investigation is required to identify the compounds being produced, but our results suggest that adding trace metals to growth media during high-throughput screening efforts may be a fruitful approach for identifying antibiotic-producing bacteria in large culture collections. [ABSTRACT FROM AUTHOR]

The simultaneous increase of atmospheric CO2 and nitrogen (N) deposition to terrestrial ecosystems is predicted to alter plant productivity and, consequently, to change the amount and quality of above- and belowground carbon entering forest soils. It is not known how such changes will impact the composition and function of soil fungal communities that play a key role in degrading complex carbon. We sequenced the fungal cellobiohydrolase I gene (cbhI) from soil DNA and cDNA to compare the richness and composition of resident and expressed cbhI genes at a U.S. Department of Energy free air-carbon dioxide enrichment (FACE) site (NC), which had been exposed to elevated atmospheric CO2 and/or N fertilization treatment for several years. Our results provide evidence that the richness and composition of the cellulolytic fungi surveyed in this study were distinct in the DNA- and cDNA-based gene surveys and were dominated by Basidiomycota that have low or no representation in public databases. The surveys did not detect differences in richness or phylum-level composition of cbhI-containing, cellulolytic fungi that correlated with elevated CO2 or N fertilization at the time of sampling. [ABSTRACT FROM AUTHOR]

B urkholderia is a physiologically and ecologically diverse genus that occurs commonly in assemblages of soil and rhizosphere bacteria. Although B urkholderia is known for its heterotrophic versatility, we demonstrate that 14 distinct environmental isolates oxidized carbon monoxide ( CO) and possessed the gene encoding the catalytic subunit of form I CO dehydrogenase ( coxL). DNA from a B urkholderia isolate obtained from a passalid beetle also contained coxL as do the genomic sequences of species H160 and Ch1-1. Isolates were able to consume CO at concentrations ranging from 100 ppm (vol/vol) to sub-ambient (< 60 ppb (vol/vol)). High concentrations of pyruvate inhibited CO uptake (> 2.5 mM), but mixotrophic consumption of CO and pyruvate occurred when initial pyruvate concentrations were lower ( c. 400 μ M). With the exception of an isolate most closely related to B urkholderia cepacia, all CO-oxidizing isolates examined were members of a nonpathogenic clade and were most closely related to B urkholderia species, B. caledonica, B. fungorum, B. oxiphila, B. mimosarum, B. nodosa, B. sacchari, B. bryophila, B. ferrariae, B. ginsengesoli, and B. unamae. However, none of these type strains oxidized CO or contained coxL based on results from PCR analyses. Collectively, these results demonstrate that the presence of CO oxidation within members of the B urkholderia genus is variable but it is most commonly found among rhizosphere inhabitants that are not closely related to B . cepacia. [ABSTRACT FROM AUTHOR]

Summary Elevated atmospheric CO2 generally increases plant productivity and subsequently increases the availability of cellulose in soil to microbial decomposers. As key cellulose degraders, soil fungi are likely to be one of the most impacted and responsive microbial groups to elevated atmospheric CO2. To investigate the impacts of ecosystem type and elevated atmospheric CO2 on cellulolytic fungal communities, we sequenced 10 677 cbhI gene fragments encoding the catalytic subunit of cellobiohydrolase I, across five distinct terrestrial ecosystem experiments after a decade of exposure to elevated CO2. The cbhI composition of each ecosystem was distinct, as supported by weighted Unifrac analyses (all P-values; < 0.001), with few operational taxonomic units (OTUs) being shared across ecosystems. Using a 114-member cbhI sequence database compiled from known fungi, less than 1% of the environmental sequences could be classified at the family level indicating that cellulolytic fungi in situ are likely dominated by novel fungi or known fungi that are not yet recognized as cellulose degraders. Shifts in fungal cbhI composition and richness that were correlated with elevated CO2 exposure varied across the ecosystems. In aspen plantation and desert creosote bush soils, cbhI gene richness was significantly higher after exposure to elevated CO2 (550 µmol mol−1) than under ambient CO2 (360 µmol mol−1 CO2). In contrast, while the richness was not altered, the relative abundance of dominant OTUs in desert soil crusts was significantly shifted. This suggests that responses are complex, vary across different ecosystems and, in at least one case, are OTU-specific. Collectively, our results document the complexity of cellulolytic fungal communities in multiple terrestrial ecosystems and the variability of their responses to long-term exposure to elevated atmospheric CO2. [ABSTRACT FROM AUTHOR]

Patterns of microbial colonization and interactions between microbial processes and vascular plants on volcanic deposits have received little attention. Previous reports have shown that atmospheric CO and hydrogen contribute significantly to microbial metabolism on Kilauea volcano (Hawaii) deposits with varied ages and successional development. Relationships between CO oxidation and plant communities were not clear, however, since deposit age and vegetation status covaried. To determine plant–microbe interactions in deposits of uniform ages, CO and hydrogen dynamics have been assayed for unvegetated tephra on a 1959 deposit at Pu’u Puai (PP-bare), at the edge of tree ‘islands’ within the PP deposit (PP-edge) and within PP tree islands (PP-canopy). Similar assays have been conducted for vegetated and unvegetated sites on a 1969 Mauna Ulu (MU) lava flow. Net in situ atmospheric CO uptake was highest at PP-edge and PP-bare sites (2.2±0.5 and 1.3±0.1 mg CO m−2 day−1, respectively), and least for PP-canopy (−3.2±0.9 mg CO m−2 day−1, net emission). Respiration rates, microbial biomass and maximum CO uptake potential showed an opposing pattern. Comparisons of atmospheric CO uptake and CO2 production rates indicate that CO contributes significantly to microbial metabolism in PP-bare and MU-unvegetated sites, but negligibly where vegetation is well developed. Nonetheless, maximum potential CO uptake rates indicate that CO oxidizer populations increase with increasing plant biomass and consume CO actively. Some of these CO oxidizers may contribute to elevated nitrogen fixation rates (acetylene reduction) measured within tree islands, and thus, support plant successional development.The ISME Journal (2008) 2, 195–203; doi:10.1038/ismej.2007.101; published online 29 November 2007 [ABSTRACT FROM AUTHOR]

The simultaneous increase of atmospheric CO(2) and nitrogen (N) deposition to terrestrial ecosystems is predicted to alter plant productivity and, consequently, to change the amount and quality of above- and belowground carbon entering forest soils. It is not known how such changes will impact the composition and function of soil fungal communities that play a key role in degrading complex carbon. We sequenced the fungal cellobiohydrolase I gene (cbhI) from soil DNA and cDNA to compare the richness and composition of resident and expressed cbhI genes at a U.S. Department of Energy free air-carbon dioxide enrichment (FACE) site (NC), which had been exposed to elevated atmospheric CO(2) and/or N fertilization treatment for several years. Our results provide evidence that the richness and composition of the cellulolytic fungi surveyed in this study were distinct in the DNA- and cDNA-based gene surveys and were dominated by Basidiomycota that have low or no representation in public databases. The surveys did not detect differences in richness or phylum-level composition of cbhI-containing, cellulolytic fungi that correlated with elevated CO(2) or N fertilization at the time of sampling.