Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework.

We have developed a flexible undergraduate curriculum that leverages the place-based research of environmental microbiomes to increase the number of Indigenous researchers in microbiology, data science and scientific computing. Monitoring Environmental Microbiomes (MEM) provides a curriculum and research framework designed to integrate an Indigenous approach when conducting authentic scientific research and to build interest and confidence at the undergraduate level. MEM has been successfully implemented as a short summer workshop to introduce computing practices in microbiome analysis. Based on self-assessed student knowledge of topics and skills, increased scientific confidence and interest in genomics careers were observed. We propose MEM be incorporated in a scalable course-based research experience for undergraduate institutions, including tribal colleges and universities, community colleges and other minority serving institutions. This coupled curricular and research framework explicitly considers cultural perspectives, access and equity to train a diverse future workforce that is more informed to engage in microbiome research and to translate microbiome science to benefit community and environmental health.

Microbial antibiotic production aboard the International Space Station.

Previous studies examining metabolic characteristics of bacterial cultures have mostly suggested that reduced gravity is advantageous for microbial growth. As a consequence, the question of whether space flight would similarly enhance secondary metabolite production was raised. Results from three prior space shuttle experiments indicated that antibiotic production was stimulated in space for two different microbial systems, albeit under suboptimal growth conditions. The goal of this latest experiment was to determine whether the enhanced productivity would also occur with better growth conditions and over longer durations of weightlessness. Microbial antibiotic production was examined onboard the International Space Station during the 72-day 8A increment. Findings of increased productivity of actinomycin D by Streptomyces plicatus in space corroborated with previous findings for the early sample points (days 8 and 12); however, the flight production levels were lower than the matched ground control samples for the remainder of the mission. The overall goal of this research program is to elucidate the specific mechanisms responsible for the initial stimulation of productivity in space and translate this knowledge into methods for improving efficiency of commercial production facilities on Earth.

Antifungal activities of actinomycete strains associated with high-altitude sagebrush rhizosphere.

The antifungal-producing potential of actinomycete populations from the rhizosphere of low-altitude sagebrush, Artemisia tridentata, has been examined. In a continued investigation of new sources of antifungal-producing microorganisms, this study examined the antifungal-producing potential of actinomycetes from the rhizosphere of high-altitude A. tridentata. With high-altitude sagebrush, rhizosphere soil actinomycete numbers were one to four orders of magnitude higher than those found in nonrhizosphere bulk soils and different from those found with the low-altitude plants. A total of 122 actinomycete isolates was screened against nine fungal species and six bacterial species for the production of antimicrobial compounds. Four rhizosphere isolates, Streptomyces amakusaensis, S. coeruleorubidus, S. hawaiiensis and S. scabies, showed broad-spectrum antifungal activity against three or more fungal species in plate assays. In liquid antagonism assays, mycelium production by Aspergillus niger was reduced by up to 50% by two of the actinomycete isolates. These results demonstrate the potential of rhizosphere microbiology in the search for new antimicrobials.

Dual-bioaugmentation strategy to enhance remediation of cocontaminated soil.

Although metals are thought to inhibit the ability of microorganisms to degrade organic pollutants, several microbial mechanisms of resistance to metal are known to exist. This study examined the potential of cadmium-resistant microorganisms to reduce soluble cadmium levels to enhance degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) under conditions of cocontamination. Four cadmium-resistant soil microorganisms were examined in this study. Resistant up to a cadmium concentration of 275 microg ml(-1), these isolates represented the common soil genera Arthrobacter, Bacillus, and Pseudomonas. Isolates Pseudomonas sp. strain H1 and Bacillus sp. strain H9 had a plasmid-dependent intracellular mechanism of cadmium detoxification, reducing soluble cadmium levels by 36%. Isolates Arthrobacter strain D9 and Pseudomonas strain I1a both produced an extracellular polymer layer that bound and reduced soluble cadmium levels by 22 and 11%, respectively. Although none of the cadmium-resistant isolates could degrade 2,4-D, results of dual-bioaugmentation studies conducted with both pure culture and laboratory soil microcosms showed that each of four cadmium-resistant isolates supported the degradation of 500-microg ml(-1) 2,4-D by the cadmium-sensitive 2,4-D degrader Ralstonia eutropha JMP134. Degradation occurred in the presence of up to 24 microg of cadmium ml(-1) in pure culture and up to 60 microg of cadmium g(-1) in amended soil microcosms. In a pilot field study conducted with 5-gallon soil bioreactors, the dual-bioaugmentation strategy was again evaluated. Here, the cadmium-resistant isolate Pseudomonas strain H1 enhanced degradation of 2,4-D in reactors inoculated with R. eutropha JMP134 in the presence of 60 microg of cadmium g(-1). Overall, dual bioaugmentation appears to be a viable approach in the remediation of cocontaminated soils.

Characterization of bacterial communities in heavy metal contaminated soils.

Heavy metal pollution is a principle source of environmental contamination. We analyzed heavy metal impacted soil microbial communities and found that, in general, although lead adversely affected biomass, metabolic activity, and diversity, autochthonous lead- and cadmium-resistant isolates were found. In several metal-stressed soils, the microbial community consisted of two populations, either resistant or sensitive to lead. Additionally, a lead-resistant isolate was isolated from a control soil with no known previous exposure to lead, suggesting widespread lead resistance. Lead-resistant genera isolated included Pseudomonas, Bacillus, Corynebacterium, and Enterobacter species. Plasmids, ranging from 5 to 260 kb, were not detected through standard purifications from lead-resistant isolates. Positive correlations existed between antibiotic resistance and isolation habitat for lead-resistant strains, microbial metabolic activity and soil type, soluble lead concentration and microbial diversity, and arsenic concentration and total or viable cell concentrations.