mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the ␣ and ␤ diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Numerous studies indicate that carbon monoxide (CO) participates in a broader range of processes than any other single molecule, ranging from subcellular to planetary scales. Despite its toxicity to many organisms, a diverse group of bacteria that span multiple phylogenetic lineages metabolize CO. These bacteria are globally distributed and include pathogens, plant symbionts and biogeochemically important lineages in soils and the oceans. New molecular and isolation techniques, as well as genome sequencing, have greatly expanded our knowledge of the diversity of CO oxidizers. Here, we present a newly emerging picture of the distribution, diversity and ecology of aerobic CO-oxidizing bacteria.

Increasing levels of atmospheric carbon dioxide (CO2) and rates of nitrogen (N)-deposition to forest ecosystems are predicted to alter the structure and function of soil fungal communities, but the spatially heterogeneous distribution of soil fungi has hampered investigations aimed at understanding such impacts. We hypothesized that soil physical and chemical properties and fungal community composition would be differentially impacted by elevated atmospheric CO2 (eCO2) and N-fertilization in spatially separated field samples, in the forest floor, 0–2, 2–5, and 5–10 cm depth intervals in a loblolly pine Free-Air Carbon Dioxide Enrichment (FACE) experiment. In all soils, quantitative PCR-based estimates of fungal biomass were highest in the forest floor. Fungal richness, based on pyrosequencing of the fungal ribosomal large subunit gene, increased in response to N-fertilization in 0–2 cm and forest floor intervals. Composition shifted in forest floor, 0–2 and 2–5 cm intervals in response to N-fertilization, but the shift was most distinct in the 0–2 cm interval, in which the largest number of statistically significant changes in soil chemical parameters (i.e., phosphorus, organic matter, calcium, pH) was also observed. In the 0–2 cm interval, increased recovery of sequences from the Thelephoraceae, Tricholomataceae, Hypocreaceae, Clavicipitaceae, and Herpotrichiellaceae families and decreased recovery of sequences from the Amanitaceae correlated with N-fertilization. In this same depth interval, Amanitaceae, Tricholomataceae, and Herpotriciellaceae sequences were recovered less frequently from soils exposed to eCO2 relative to ambient conditions. These results demonstrated that vertical stratification should be taken into consideration in future efforts to elucidate environmental impacts on fungal communities and their feedbacks on ecosystem processes.

Relatively little is known about the distribution and diversity of CO-oxidizing bacteria during succession on volcanic deposits even though they are among the primary colonists. We surveyed CO-oxidizing communities across a vegetation gradient on a 1959 cinder deposit using coxL (large subunit gene of carbon monoxide dehydrogenase) sequences. Sequences most closely related to a coxL sequence from Ktedonobacter racemifer, dominated unvegetated cinders, while Proteobacteria-like sequences dominated vegetated sites. The number of coxL operational taxonomic units (OTUs) increased threefold with increased vegetation, and correlated most strongly with the increased beta-Proteobacteria richness (r = 0.987). These compositional shifts were also reflected in overall bacterial community compositions as determined by 16S rRNA gene analysis. Notably, coxL OTU:16S rRNA OTU ratios increased with increased vegetation, indicating that CO oxidizers became a larger fraction of total bacterial richness during succession. Results from most probable number estimates and maximum potential CO uptake activity assays indicate that increased richness is paralleled by increased CO oxidizer abundance, which likely results from increased vegetation and organic carbon content. Collectively, results suggest that in contrast to patterns observed for plant succession, a versatile bacterial functional group that is important during early colonization and succession can remain important in later stages of succession, irrespective of dramatic environmental changes.

Current malnourishment statistics are high and are exacerbated by contemporary agricultural practices that damage the very environments on which the production of nutritious food depends. As the World’s population grows at an unprecedented rate, food systems must be revised to provide adequate nutrition while minimizing environmental impacts. One specific nutritional problem that needs attention is mineral (e.g., Fe and Zn) malnutrition, which impacts over two-thirds of the World’s people living in countries of every economic status. Microgreens, the edible cotyledons of many vegetables, herbs, and flowers, is a newly emerging crop that may be a dense source of nutrition and has the potential to be produced in just about any locale. This study examined the mineral concentration of broccoli microgreens produced using compost-based and hydroponic growing methods that are easily implemented in one’s own home. The nutritional value of the resulting microgreens was quantitatively compared to published nutritional data for the mature vegetable. Nutritional data were also considered in the context of the resource demands (i.e., water, fertilizer, and energy) of producing microgreens in order to gain insights into the potential for local microgreen production to diversify food systems, particularly for urban areas, while minimizing the overall environmental impacts of broccoli farming. Regardless of how they were grown, microgreens had larger quantities of Mg, Mn, Cu, and Zn than the vegetable. However, compost-grown (C) microgreens had higher P, K, Mg, Mn, Zn, Fe, Ca, Na, and Cu concentrations than the vegetable. For eight nutritionally important minerals (P, K, Ca, Mg, Mn, Fe, Zn, and Na), the average C microgreen:vegetable nutrient ratio was 1.73. Extrapolation from experimental data presented here indicates that broccoli microgreens would require 158–236 times less water than it does to grow a nutritionally equivalent amount of mature vegetable in the fields of California’s Central Valley in 93–95% less time and without the need for fertilizer, pesticides, or energy-demanding transport from farm to table. The results of this study suggest that broccoli microgreens have the potential to be a rich source of minerals that can be produced by individuals, even in urban settings, providing better access to adequate nutrition.