Endophytic Bacterial Community Structure and Function of Herbaceous Plants From Petroleum Hydrocarbon Contaminated and Non-contaminated Sites

Bacterial endophytes (BEs) are non-pathogenic residents of healthy plant tissues that can confer benefits to plants. Many Bacterial endophytes have been shown to contribute to plant growth and health, alleviation of plant stress and to in-planta contaminant-degradation. This study examined the endophytic bacterial communities of plants growing abundantly in a heavily hydrocarbon contaminated site, and compared them to those found in the same species at a non-contaminated. We used culture- dependent and independent methods to characterize the community structure, hydrocarbon degrading capabilities, and plant growth promoting traits of cultivable endophytes isolated from Achillea millefolium, Solidago Canadensis, and Daucus carota plants from these two sites. Culture- dependent and independent analyses revealed class Gammaproteobacteria predominated in all the plants regardless of the presence of petroleum hydrocarbon, with Pantoea spp. as largely dominant. It was interesting to note a >50% taxonomic overlap (genus level) of 16s rRNA high throughput amplicon sequences with cultivable endophytes. PERMANOVA analysis of TRFLP fragments revealed significant structural differences between endophytic bacterial communities from hydrocarbon-contaminated and non-contaminated soils—however, there was no marked difference in their functional capabilities. Pantoea spp. demonstrated plant beneficial characteristics, such as P solubilization, indole-3-acetic acid production and presence of 1-aminocyclopropane-1-carboxylate deaminase. Our findings reveal that functional capabilities of bacterial isolates being examined were not influenced by the presence of contamination; and that the stem endosphere supports ubiquitous BEs that were consistent throughout plant hosts and sites

Survival and Activity of a 3-Chlorobenzoate-Catabolic Genotype in a Natural System

A chlorobenzoate-degrading Alcaligenes strain, BR60, was introduced to flowthrough lake microcosms and exposed to 3-chlorobenzoate (3Cba) concentrations from 0 to 25 μM. A DNA probe specific for BR60 chlorobenzoate catabolic genes was used with the most probable number (MPN) technique to enumerate bacteria harboring this genetic information. This MPN-DNA hybridization method combined with [U-(14)C]3Cba uptake rate measurements allowed the correlation of the size and activity of a specific catabolic population in a natural mixed community for the first time. An experiment involving the release of a streptomycin-resistant strain of BR60 indicated that estimates of bacteria carrying the introduced catabolic genotype often outnumbered plate count estimates of viable BR60 by as much as 3 orders of magnitude, particularly when 3Cba inputs were high. The MPN-DNA hybridization method provided catabolic population estimates highly correlated to 3Cba exposure levels and the [U-(14)C]3Cba uptake rates in the microcosms. Plate counts of BR60 were poorly correlated with both 3Cba exposure levels and uptake rates. In the absence of chlorobenzoate selection, the catabolic genotype declined to very low levels by the MPN-DNA hybridization technique after 8 weeks in the microcosms

Draft genome sequence of Bacillus sp. strain UFRGS-B20, a hydrocarbon degrader

Bacillus sp. strain UFRGS-B20 was isolated in 2012 from Brazilian landfarming soil contaminated with petrochemical oily sludge. This strain was subjected to hydrocarbon biodegradation tests, showing degradation rates of up to 60%. Here, we present the 6.82-Mb draft genome sequence of the strain, which contains 2,178 proteins with functional assignments

Molecular analysis of bacterial isolates and total community DNA from kraft pulp mill effluent treatment systems

NRC publication: Ye

Bacterial community dynamics in the hyporheic zone of an intermittent stream

The dynamics of in situ bacterial communities in the hyporheic zone of an intermittent stream were described in high spatiotemporal detail. We assessed community dynamics in stream sediments and interstitial pore water over a two-year period using terminal-restriction fragment length polymorphism. Here, we show that sediments remained saturated despite months of drought and limited hydrologic connectivity. The intermittency of stream surface water affected interstitial pore water communities more than hyporheic sediment communities. Seasonal changes in bacterial community composition was significantly associated with water intermittency, phosphate concentrations, temperature, nitrate and dissolved organic carbon (DOC) concentrations. During periods of low- to no-surface water, communities changed from being rich in operational taxonomic units (OTUs) in isolated surface pools, to a few OTUs overall, including an overall decline in both common and rare taxa. Individual OTUs were compared between porewater and sediments. A total of 19% of identified OTUs existed in both porewater and sediment samples, suggesting that bacteria use hyporheic sediments as a type of refuge from dessication, transported through hydrologically connected pore spaces. Stream intermittency impacted bacterial diversity on rapid timescales (that is, within days), below-ground and in the hyporheic zone. Owing to the coupling of intermittent streams to the surrounding watershed, we stress the importance of understanding connectivity at the pore scale, consequences for below-ground and above-ground biodiversity and nutrient processing, and across both short- and long-time periods (that is, days to months to years). © 2012 International Society for Microbial Ecology All rights reserved

Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour

Aquatic viruses have been extensively studied over the past decade, yet fundamental aspects of freshwater virus communities remain poorly described. Our goal was to characterize virus communities captured in the >0.22 µm size-fraction seasonally and spatially in a freshwater harbour. Community DNA was extracted from water samples and sequenced on an Illumina HiSeq platform. Assembled contigs were annotated as belonging to the virus groups (i.e., order or family) Caudovirales, Mimiviridae, Phycodnaviridae, and virophages (Lavidaviridae), or to other groups of undefined viruses. Virophages were often the most abundant group, and discrete virophage taxa were remarkably stable across sites and dates despite fluctuations in Mimiviridae community composition. Diverse Mimiviridae contigs were detected in the samples and the two sites contained distinct Mimiviridae communities, suggesting that Mimiviridae are important algal viruses in this system. Caudovirales and Phycodnaviridae were present at low abundances in most samples. Of the 18 environmental parameters tested, only chlorophyll a explained the variation in the data at the order or family level of classification. Overall, our findings provide insight into freshwater virus community assemblages by expanding the documented diversity of freshwater virus communities, highlighting the potential ecological importance of virophages, and revealing distinct communities over small spatial scales