Molecular Analysis of Carbon Monoxide-Oxidizing Bacteria Associated with Recent Hawaiian Volcanic Deposits

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity

Analysis of the distribution and diversity in recent Hawaiian volcanic deposits of a putative carbon monoxide dehydrogenase large subunit gene

A putative carbon monoxide dehydrogenase large subunit gene (BMS putative coxL) was amplified from genomic DNA extracts of four recent (42-300 year old) Hawaiian volcanic deposits by polymerase chain reaction (PCR). Sequence databases derived from clone libraries constructed using PCR products were analysed phylogenetically and statistically. These analyses indicated that each of the deposits supported distinct BMS putative coxL gene assemblages. Statistical analyses also showed that the youngest deposit (42 years old) contained the least diverse sequences (P \u3c 0.05), but that diversity did not vary significantly among three older deposits with ages from about 108-300 years. Although diversity indices did not vary among the older deposits, mismatch analyses suggested population structures increased in complexity with increasing deposit age. At each of the sites, most of the clone sequences appeared to originate from Proteobacteria not currently represented in culture or recognized as CO oxidizers. © 2005 Society for Applied Microbiology and Blackwell Publishing Ltd

Data from: Temporal dynamics of plant-soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant

1. Pathogens can accumulate on invasive plants over time, which could lead to population declines. The time required for these dynamics to occur is unknown and seldom addressed. Furthermore, no study has assessed plant-soil feedback while characterising plant pathogen and mutualist root fungal communities in the context of invasion time. 2. We used a plant-soil feedback study and 454 pyrosequencing to investigate pathogen accumulation over 100 years on a highly invasive plant in eastern North America that shows localised declines, Vincetoxicum rossicum (Apocynaceae). 3. We collected soil from five sites representing each of four invasion periods of V. rossicum across Ontario, Canada (old, ~100 years; intermediate, 50-60 years; young, <12 years; and uninvaded), and grew V. rossicum in these soils in a glasshouse study. Our hypothesis was that plants grown in soils invaded for longer periods of time would experience less positive feedbacks compared to those grown in more recently invaded or uninvaded soils. We collected roots of V. rossicum from the invasion periods and performed 454 pyrosequencing targeting fungi. We hypothesised that the abundance and richness of fungi that are known plant pathogens would be higher in roots from older invasions compared to more recent invasions. 4. Contrasting with our hypothesis, V. rossicum experienced overall growth promotion due to soil biota, regardless of invasion period. Vincetoxicum rossicum roots were colonised by a large number of fungal taxa, including many known plant pathogens or mutualistic arbuscular mycorrhizal fungi. However, we found no evidence of pathogen accumulation in older invaded sites in terms of species composition, richness or abundance. 5. Synthesis: Our consistent results in the glasshouse and the field highlight the strength of combining high-throughput sequencing data with plant-soil feedback experiments. We showed that the roots of Vincetoxicum rossicum (Apocynaceae) were colonised by many fungal taxa, but found no evidence for changes in plant growth or accumulation of fungal pathogens with longer invasion time. High pathogen loads may not lead to concurrent declines in invasive plants. Plant invasions, as demonstrated by V. rossicum, may be unpredictable in their ability to accumulate pathogens capable of leading to population declines

Site by species matrix from 454 pyrosequencing

This file contains the site by species matrix of the Genome Quebec pyrosequencing data. Metadata provided

Plant dry weights

This file contains the dry weights of roots, shoots, and pods. These data were used in the models to assess V. rossicum biomass growing in soils from different invasion periods. Metadata included

Plant dry weights

This file contains the dry weights of roots, shoots, and pods. These data were used in the models to assess V. rossicum biomass growing in soils from different invasion periods. Metadata included