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Bacterial community diversity and variation in spray water sources and the tomato fruit surface.

Telias A, White JR, Pahl DM, Ottesen AR, Walsh CS - BMC Microbiol. (2011)

Bottom Line: The two water sources tested had a significantly different bacterial composition.Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia.Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Science and Landscape Architecture Department, University of Maryland, College Park, MD 21201, USA. atelias@umd.edu

ABSTRACT

Background: Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production.

Results: The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant.

Conclusions: Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.

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Related in: MedlinePlus

Phylum level abundance profiles using 16S rRNA sequence classifications. Columns reflect the percentage of 16S rRNA sequences assigned to each phylum using the RDP classifier. All ws samples show a more even representation of Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia, as well as a higher representation of sequences that could not be assigned to any phylum (with a confidence threshold of 80%). We also observe a spike in Firmicutes abundance in a surface water-treated phyllosphere sample 4 (ps4). In all other samples, Proteobacteria 16S rRNA sequences tend to dominate the profiles.
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Figure 1: Phylum level abundance profiles using 16S rRNA sequence classifications. Columns reflect the percentage of 16S rRNA sequences assigned to each phylum using the RDP classifier. All ws samples show a more even representation of Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia, as well as a higher representation of sequences that could not be assigned to any phylum (with a confidence threshold of 80%). We also observe a spike in Firmicutes abundance in a surface water-treated phyllosphere sample 4 (ps4). In all other samples, Proteobacteria 16S rRNA sequences tend to dominate the profiles.

Mentions: We taxonomically classified all sequences (from phylum to genus) using the RDP Bayesian classifier with a confidence threshold of 80%. Examining the phylum level distributions across samples, we found that nearly all fruit surface samples appeared to have very similar 16S rRNA profiles. In these, Proteobacteria dominated the observed sequences, with smaller representations of Firmicutes and Actinobacteria. One surface water treated sample (ps4) was dominated by Firmicutes sequences, most likely as a result of contamination with internal fruit material. While the wg samples displayed similar 16S rRNA profiles dominated by Proteobacteria, the ws samples had a more even representation among four dominant phyla. In addition, ws samples contained a large number of sequences that could not be classified even at the phylum level (Figure 1).


Bacterial community diversity and variation in spray water sources and the tomato fruit surface.

Telias A, White JR, Pahl DM, Ottesen AR, Walsh CS - BMC Microbiol. (2011)

Phylum level abundance profiles using 16S rRNA sequence classifications. Columns reflect the percentage of 16S rRNA sequences assigned to each phylum using the RDP classifier. All ws samples show a more even representation of Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia, as well as a higher representation of sequences that could not be assigned to any phylum (with a confidence threshold of 80%). We also observe a spike in Firmicutes abundance in a surface water-treated phyllosphere sample 4 (ps4). In all other samples, Proteobacteria 16S rRNA sequences tend to dominate the profiles.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108269&req=5

Figure 1: Phylum level abundance profiles using 16S rRNA sequence classifications. Columns reflect the percentage of 16S rRNA sequences assigned to each phylum using the RDP classifier. All ws samples show a more even representation of Proteobacteria, Firmicutes, Actinobacteria, and Verrucomicrobia, as well as a higher representation of sequences that could not be assigned to any phylum (with a confidence threshold of 80%). We also observe a spike in Firmicutes abundance in a surface water-treated phyllosphere sample 4 (ps4). In all other samples, Proteobacteria 16S rRNA sequences tend to dominate the profiles.
Mentions: We taxonomically classified all sequences (from phylum to genus) using the RDP Bayesian classifier with a confidence threshold of 80%. Examining the phylum level distributions across samples, we found that nearly all fruit surface samples appeared to have very similar 16S rRNA profiles. In these, Proteobacteria dominated the observed sequences, with smaller representations of Firmicutes and Actinobacteria. One surface water treated sample (ps4) was dominated by Firmicutes sequences, most likely as a result of contamination with internal fruit material. While the wg samples displayed similar 16S rRNA profiles dominated by Proteobacteria, the ws samples had a more even representation among four dominant phyla. In addition, ws samples contained a large number of sequences that could not be classified even at the phylum level (Figure 1).

Bottom Line: The two water sources tested had a significantly different bacterial composition.Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia.Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Science and Landscape Architecture Department, University of Maryland, College Park, MD 21201, USA. atelias@umd.edu

ABSTRACT

Background: Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production.

Results: The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant.

Conclusions: Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.

Show MeSH
Related in: MedlinePlus