Metagenome tracking biogeographic agroecology: Phytobiota of tomatoes from Virginia, Maryland, North Carolina and California

Applied microbiology of the phyllosphere

The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System

Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.

Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum

The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.

Soil Bacterial Communities from Three Agricultural Production Systems in Rural Landscapes of Palmira, Colombia

Soils play important roles in the proper functioning of agroecosystems. Using molecular characterization methods such as metabarcoding, soils from eight farms (57 samples) belonging to three production system types-agroecological (two farms with twenty-two sampling points), organic (three farms with twenty-one sampling points), and conventional (three farms with fourteen sampling points)-were compared from the rural villages of El Arenillo and El Mesón in Palmira, Colombia. Amplification and sequencing of the hypervariable V4 region of the 16S rRNA gene was performed using next-generation sequencing (Illumina MiSeq) to estimate the bacterial composition and the alpha and beta diversity present. Across all soil samples, we found 2 domains (Archaea and Bacteria), 56 phylum, 190 classes, 386 orders, 632 families, and 1101 genera to be present. The most abundant phyla in the three systems were Proteobacteria, (agroecological 28%, organic 30%, and conventional 27%), Acidobacteria (agroecological 22%, organic 21%, and conventional 24%), and Verrucomicrobia (agroecological 10%, organic 6%, and conventional 13%). We found 41 nitrogen-fixing and phosphate-dissolving genera which promote growth and pathogens. Alpha and beta diversity indices were very similar across the three agricultural production systems, as reflected by shared amplicon sequence variants (ASVs) among them, likely due to the proximity of the sampling sites and recent management changes.

Comparison of the Peel-Associated Epiphytic Bacteria of Anthocyanin-Rich "Sun Black" and Wild-Type Tomatoes under Organic and Conventional Farming

Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. Proteobacteria was the dominant phylum (relative abundances 79-91%) in all experimental conditions. Enterobacteriaceae represented a large fraction (39.3-47.5%) of the communities, with Buttiauxella and Atlantibacter as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (Buttiauxella), OTU 2 (Enterobacteriales), and OTU 6 (Bacillales) were higher in red and purple tomatoes grown under organic farming. OTU 5 (Acinetobacter) had the highest abundance in red tomatoes subjected to organic farming. OTU 3 (Atlantibacter) was among the major OTUs in red tomatoes under both farming conditions. OTU 7 (Clavibacter) and OTU 8 (Enterobacteriaceae) had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture.

Food Safety Risks of Harvesting Dropped and Drooping Produce: A Review

ABSTRACT

The Produce Safety Rule of the Food Safety Modernization Act (FSMA) sets forth minimum standards for fruit and vegetable production in the United States. One provision states that growers must not harvest dropped produce because damage or ground contact may contaminate produce. In an unpublished survey of 2020 food safety inspections conducted by the Northeast Center to Advance Food Safety, handling of dropped produce covered by the FSMA was a common misunderstood and noncompliance issue among growers in the Northeast. In consideration of this provision's on-farm practicality, this review was conducted to evaluate the risks associated with dropped and drooping produce, to guide growers in making informed risk management decisions, and to answer the following questions: (i) what are the risk factors that influence transferability of pathogens from touching the ground to produce and (ii) what are the risks associated with harvesting dropped or drooping produce covered under the Produce Safety Rule? A search of online databases revealed 12 relevant publications, which highlighted moisture, contact time, and crop features as affecting contamination rates from a ground surface to a crop surface. Soil and mulch posed a differential risk, with bare soil generally presenting a lower risk than plastic mulch. The effects of other mulch types are unclear. Mulches may promote pathogen persistence in soil, although they may also protect produce from contaminated soils. These studies were limited in their scope and applicability and most did not directly address dropped produce. Research is needed to clarify the various effects of dropped and drooping produce, the impact of ground surface type on pathogen survivability and transfer, soil and crop features that facilitate contamination, and postharvest risks of harvesting dropped or drooping produce. A comprehensive understanding of these issues will guide growers in implementing preventive measures and better managing risk in a way practicable to each farm's unique conditions.

HIGHLIGHTS

Seasonality, shelf life and storage atmosphere are main drivers of the microbiome and E. coli O157:H7 colonization of post-harvest lettuce cultivated in a major production area in California

BACKGROUND

Lettuce is linked to recurrent outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections, the seasonality of which remains unresolved. Infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the microbiome and STEC O157:H7 (EcO157) colonization of fresh-cut lettuce of two cultivars with long and short shelf life harvested in the spring and fall in California and stored in modified atmosphere packaging (MAP) at cold and warm temperatures.

RESULTS

Inoculated EcO157 declined significantly less on the cold-stored cultivar with short shelf life, while multiplying rapidly at 24 °C independently of cultivar. Metagenomic sequencing of the lettuce microbiome revealed that the pre-storage bacterial community was variable but dominated by species in the Erwiniaceae and Pseudomonadaceae. After cold storage, the microbiome composition differed between cultivars, with a greater relative abundance (RA) of Erwiniaceae and Yersiniaceae on the cultivar with short shelf life. Storage at 24 °C shifted the microbiome to higher RAs of Erwiniaceae and Enterobacteriaceae and lower RA of Pseudomonadaceae compared with 6 °C. Fall harvest followed by lettuce deterioration were identified by recursive partitioning as important factors associated with high EcO157 survival at 6 °C, whereas elevated package CO₂ levels correlated with high EcO157 multiplication at 24 °C. EcO157 population change correlated with the lettuce microbiome during 6 °C storage, with fall microbiomes supporting the greatest EcO157 survival on both cultivars. Fall and spring microbiomes differed before and during storage at both temperatures. High representation of Pantoea agglomerans was a predictor of fall microbiomes, lettuce deterioration, and enhanced EcO157 survival at 6 °C. In contrast, higher RAs of Erwinia persicina, Rahnella aquatilis, and Serratia liquefaciens were biomarkers of spring microbiomes and lower EcO157 survival.

CONCLUSIONS

The microbiome of processed MAP lettuce evolves extensively during storage. Under temperature abuse, high CO₂ promotes a lettuce microbiome enriched in taxa with anaerobic capability and EcO157 multiplication. In cold storage, our results strongly support a role for season and lettuce deterioration in EcO157 survival and microbiome composition, suggesting that the physiology and microbiomes of fall- and spring-harvested lettuce may contribute to the seasonality of STEC outbreaks associated with lettuce grown in coastal California.

Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples

Purpose

Ready-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market.

Methods

The study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3.

Results

Bacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1).

Conclusion

The results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.

13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern

Chloromethane (CH₃ Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH₃ Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH₃ Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH₃ Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with ¹³ C-labelled CH₃ Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH₃ Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH₃ Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH₃ Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH₃ Cl degradation in the investigated tree ferns.

Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas

Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.

Microbiome convergence following sanitizer treatment and identification of sanitizer resistant species from spinach and lettuce rinse water

Fresh produce, as a known or suspected source of multiple foodborne outbreaks, harbors large populations of diverse microorganisms, which are partially released into wash water during processing. However, the dynamics of bacterial communities in wash water during produce processing is poorly understood. In this study, we investigated the effect of chlorine (FC) and peracetic acid (PAA) on the microbiome dynamics in spinach and romaine lettuce rinse water. Treatments with increasing concentrations of sanitizers resulted in convergence of distinct microbiomes. The resultant sanitizer resistant microbiome showed dominant presence by Bacillus sp., Arthrobacter psychrolactophilus, Cupriavidus sp., and Ralstonia sp. Most of the FC and PAA resistant bacteria isolated from spinach and lettuce rinse water after sanitation were gram positive spore forming species including Bacillus, Paenibacillus, and Brevibacillus spp., while several PAA resistant Pseudomonas spp. were also isolated from lettuce rinse water. Inoculation of foodborne pathogens altered the microbiome shift in spinach rinse water under PAA treatment, but not in lettuce rinse water or FC treated samples. These inoculated foodborne pathogens were not isolated among the sanitizer resistant strains.

An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples?

Apples are among the most consumed fruits world-wide. They represent a source of direct human exposure to bacterial communities, which is less studied. We analyzed the apple microbiome to detect differences between tissues and the impact of organic and conventional management by a combined approach of 16S rRNA gene amplicon analysis and qPCR, and visualization using fluorescence in situ hybridization and confocal laser scanning microscopy (FISH-CLSM). Each apple fruit harbors different tissues (stem, peel, fruit pulp, seeds, and calyx), which were colonized by distinct bacterial communities. Interestingly, fruit pulp and seeds were bacterial hot spots, while the peel was less colonized. In all, approximately 10⁸ 16S rRNA bacterial gene copy numbers were determined in each g apple. Abundances were not influenced by the management practice but we found a strong reduction in bacterial diversity and evenness in conventionally managed apples. In addition, despite the similar structure in general dominated by Proteobacteria (80%), Bacteroidetes (9%), Actinobacteria (5%), and Firmicutes (3%), significant shifts of almost 40% of bacterial genera and orders were monitored. Among them, especially bacterial signatures known for health-affecting potential were found to be enhanced in conventionally managed apples. Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples.

Dynamics of bacterial communities in alfalfa and mung bean sprouts during refrigerated conditions

Sprouts are considered a healthy ready-to-eat food and has gained popularity in recent years. The objective of the present study was to determine the dynamics of sprouts' microbiome during cold storage to the end of their shelf-life at home. The microbiological quality of fresh alfalfa (Medicago sativa) and mung bean (Vigna radiata) sprouts from two commercial brands was tested and the number of APC ranges from 5.0 to 8.7 log CFU/g in alfalfa and 6.7 to 9.3 log CFU/g in mung bean sprouts. In the case of alfalfa, but not mung beans, there were differences in the mean numbers of APC between the two brands. The number of coliform bacteria ranges from 4.3 to 7.7 log CFU/g in alfalfa and 4.1 to 8.1 log CFU/g in mung bean sprouts. Four independent batches of sprouts were used for DNA preparation and were sampled immediately after purchase and once a week during subsequent storage in refrigerator until the end of their shelf-life. Microbial population of the sprouts was determined using next generation sequencing of 16S rRNA amplicons. Alfalfa sprouts were dominated by Pseudomonas throughout the storage time with relative abundance of >60% at 3 weeks. Fresh mung bean sprouts were dominated by both Pseudomonas and Pantoea, but Pantoea became the dominant taxa after 2 weeks of storage, with >46% of relative abundance. The bacterial communities associated with sprouts were largely dependent on the sprout type, and less dependent on the brand. The species richness and diversity declined during storage and the development of spoilage. Among the 160 genera identified on sprouts, 23 were reported to contain known spoilage-associated species and 30 genera comprise potential human pathogenic species. This study provides new insight into the microbiome dynamics of alfalfa and mung bean sprouts during cold storage.

An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples?

Apples are among the most consumed fruits world-wide. They represent a source of direct human exposure to bacterial communities, which is less studied. We analyzed the apple microbiome to detect differences between tissues and the impact of organic and conventional management by a combined approach of 16S rRNA gene amplicon analysis and qPCR, and visualization using fluorescence in situ hybridization and confocal laser scanning microscopy (FISH-CLSM). Each apple fruit harbors different tissues (stem, peel, fruit pulp, seeds, and calyx), which were colonized by distinct bacterial communities. Interestingly, fruit pulp and seeds were bacterial hot spots, while the peel was less colonized. In all, approximately 10⁸ 16S rRNA bacterial gene copy numbers were determined in each g apple. Abundances were not influenced by the management practice but we found a strong reduction in bacterial diversity and evenness in conventionally managed apples. In addition, despite the similar structure in general dominated by Proteobacteria (80%), Bacteroidetes (9%), Actinobacteria (5%), and Firmicutes (3%), significant shifts of almost 40% of bacterial genera and orders were monitored. Among them, especially bacterial signatures known for health-affecting potential were found to be enhanced in conventionally managed apples. Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples.