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Different Nutritional Regimes in a Tomato Soilless System Affect the Bacterial Communities with Consequences on the Crop Quality
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Different Nutritional Regimes in a Tomato Soilless System Affect the Bacterial Communities with Consequences on the Crop Quality
by Luciano Beneduce 1,*ORCID,Federica Piergiacomo 1,2ORCID andKalina Sikorska-Zimny 3ORCID
1
Department of Agriculture, Food, Natural Resources and Engineering (DAFNE), University of Foggia, Via Napoli 25, 71122 Foggia, Italy
2
Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano-Bozen, Piazza Università 1, 39100 Bolzano-Bozen, Italy
3
Fruit and Vegetables Storage and Processing Department, Division of Fruit and Vegetable Storage and Postharvest Physiology, The Institute of Horticulture—National Research Institute, Konstytucji 3 Maja 1/3 Str., 96-100 Skierniewice, Poland
*
Author to whom correspondence should be addressed.
Agriculture 2024, 14(12), 2254; https://doi.org/10.3390/agriculture14122254
Submission received: 7 October 2024 / Revised: 5 December 2024 / Accepted: 6 December 2024 / Published: 10 December 2024
(This article belongs to the Section Crop Production)
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Abstract
This study investigates the impact of different nutritional regimes on the bacterial communities within the root-growing substrate of a soilless tomato production system and the effects on crop quality. The experiment was conducted with two tomato varieties, Conchita and Sweetelle, under three nutritional treatments: standard, nutrient solution with 20% increased salts and nitrogen and supplementation with the biostimulant Bio-algeen S-90. Bacterial communities in the root substrate were influenced by both the tomato variety and the nutritional regime. Sweetelle exhibited more pronounced shifts in bacterial communities compared to Conchita. An overall increase in bacterial populations with time was observed (+0.38 Log). Specifically, the 20% enhanced nutrient solution had varying effects on bacterial counts in the two tomato varieties, while the biostimulant promoted an increase in ammonia-oxidizing bacteria (+0.4 Log). Microbial community analysis highlighted the distinct impact of each nutritional regime on nitrogen-cycling bacteria, which correlated with differences in quality parameters such as the L-ascorbic acid and lycopene contents. In the first case, a decrease (25–30%) was observed, while the lycopene content decreased after harvest (−51% in Conchita variety) but was more stable in the postharvest phase (66–70% lycopene retained, only 44% in the control). This study highlights how increased sources of nutrients and the differential responses of microbial communities to nutritional regimes do not necessarily increase the crop quality and that tailored approaches are required for different tomato varieties
The metabolism of glucosinolates by gut microbiota
No full textGlucosinolates (GLS) and their derivatives are secondary plant metabolites abundant in Brassicaceae. Due to the enzymatic reaction between GLS and myrosinase enzyme, characteristic compounds with a pungent taste are formed, used by plants to defend themselves against insect herbivores. These GLS derivatives have an important impact on human health, including anti-in-flammation and anti-cancer effects. However, GLS derivatives’ formation needs previous enzymatic reactions catalyzed by myrosinase enzyme. Many of the brassica-based foods are processed at a high temperature that inactivates enzymes, hindering its bioavailability. In the last decade, several studies showed that the human gut microbiome can provide myrosinase activity that potentially can raise the beneficial effects of consumption of vegetables rich in GLS. The variability of the human gut microbiome (HGM) in human populations and the diverse intake of GLS through the diet may lead to greater variability of the real dose of pro-healthy compounds absorbed by the human body. The exploitation of the genetic and biochemical potential of HGM and correct ecological studies of both isolated strains and mixed population are of great interest. This review focuses on the most recent advances in this field
Does physical fractionation of SOM pools preserve information about microbial taxa distribution and ecological functions?
No full textIn a previous study (Zaccone et al., Appl. Soil Ecol., 2018), a preliminary evaluation of potential ecological partition of total, bacterial and plant DNA across soil organic matter (SOM) fractions linked to conceptual stabilization mechanisms was provided. Here, we investigated if different ecologically meaningful SOM fractions share the same microbial communities. To test this hypothesis, DNA was recovered from SOM pools that differ in quality and level of physical and chemical protection from decomposition: free SOM located between aggregates (FR), SOM occluded within macro (MA) and microagreggates (MI), and mineral-associated SOM (MIN) (Plaza et al., Soil Biol. Biochem., 2013). Bacterial communities were then assessed by amplification of V3-V4 region of 16S rDNA while fungal communities by amplification of ITS region. NGS was performed by Illumina Miseq platform and the sequences analysis carried out using QIIME2 v2018.6.0. Bacterial communities showed a clear separation among the different SOM fractions, independently from the kind of the amendment applied to the soil (i.e., biochar, municipal compost). In particular, FR and MIN fractions were dominated by Firmicutes (65-75%), followed by Actinobacteria (~13%). On the opposite, MA and MI had a lower level of Firmicutes (~50%) and higher level of Actinobacteria (20-30%). Interestingly, among Bacillales, Bacillus and Brevibacillus spp. (aerobic) were largely dominant in FR and MIN, whereas the facultative anaerobic Limnochordaceae were more represented in MA and MI, and the anaerobic sporeforming Clostridium spp. Mainly in MI. These data clearly depose for a ‘selection’ of the microbial taxa according to the level of physical and chemical protection of SOM, with O2 availability as one of the main drivers. Although at a less extent, also fungal population was related to the SOM pools rather than to the amendment, with MIN and FR differing from MA and MI. In particular, Sordariomycetes are a fungal class that can represent a proxy of SOM evolution. In conclusion, (i) the physical fractionation method caused no mixing over of bacterial DNA through all SOM pools, and (ii) different microbial taxa seem to be specifically associated to SOM fractions linked to conceptual stabilization mechanisms
Microbial taxa distribution in soil organic matter fractions with ecologically different functions
No full textIn a previous study (Zaccone et al., 2018), a preliminary evaluation of potential ecological partition of total, bacterial and plant DNA across soil organic matter (SOM) fractions linked to conceptual stabilization mechanisms was provided. Here, we investigated if different ecologically meaningful SOM fractions share the same microbial communities. To test this hypothesis, DNA was recovered from SOM pools that differ in quality and level of physical and chemical protection from decomposition: free SOM located between aggregates (FR), SOM occluded within macro (MA) and microagreggates (MI), and mineral-associated SOM (MIN) (Plaza et al., 2012). Bacterial communities were then assessed by amplification of V3-V4 region of 16S rDNA while fungal communities by amplification of ITS region. NGS was performed by Illumina Miseq platform and the sequences analysis carried out using QIIME2 v2018.6.0. Bacterial communities show a clear separation among the different SOM fractions, independently from the soil amendment (i.e., biochar, municipal compost). In particular, FR fractions were dominated by Firmicutes (70-80%), followed by Actinobacteria (10-20%) and Proteobacteria (5%). On the opposite, MA had a lower level of Firmicutes (ca. 40%) and higher level of Actinobacteria (30%) and Proteobacteria (20%). The dominance of spore forming taxa in all fractions is of interest and might be due to the better preservation of microbial DNA in the spore structure. Interestingly, the anaerobic spore-forming Clostridium spp. were mainly found in MA and MI and less in the MIN, whereas the most abundant taxa in FR were aerobic spore-formers (Bacillus spp., Brevibacillus spp.). These data clearly depose for a selection of the microbial taxa according to the level of physical and chemical protection of SOM, with O2 availability as one of the main possible drivers. Although at a less extent, also fungal population was related to the SOM pool, with MIN and FR differing from MA and MI. In conclusion, different microbial taxa (mostly bacterial) seem to be specifically associated to SOM fractions linked to conceptual stabilization mechanisms
Characterization of Lactobacillus plantarum from wine must by PCR species-specific and RAPD-PCR
No full textAims: Physiological and molecular analysis such as PCR species-specific and randomly
amplified polymorphic PCR (RAPD-PCR) have been used for typing of Lactobacillus plantarum
strains from typical wine must.
Methods and Results: Phenotypic tests such as API 50CH and evaluation of D-L-lactate
production from glucose were used to perform a preliminary characterization of lactobacilli.
Furthermore, 18 strains of lactobacilli were analyzed by PCR species-specific oligonucleotides
based on short sequences of the recA gene.
Conclusions: Four strains were identified as belonging to the L. plantarum species and were
further analysed by RAPD-PCR. The RAPD-PCR profiles were similar in all strains that had
positive results for species-specific PCR, suggesting that the four L. plantarum strains were
closely related.
Significance and Impact of the study: Using PCR species-specific as a preliminary
screening test and then RAPD-PCR can be as considered the most reliable method of
performing a rapid and correct typing of L. plantarum from wine must
The effect of substituting energy crop with agricultural waste on the dynamics of bacterial communities in a two-stage anaerobic digester
No full textThe replacement of energy crops with agricultural waste in biogas production through anaerobic digestion (AD) is both an environmentally sustainable and economically profitable strategy. However, the change of feeding mix in AD might result in nutrient imbalance or increase of the ammonium concentration, negatively affecting the activity of the microbes responsible for the process. In the present study the structure and dynamics of the bacterial communities of a full-scale two-stage AD plant, composed of a hydrolysis/acidogenesis (H) and an acetogenesis/methanogenesis (M) tanks, was monitored during feedstock substitution. Energy crop (triticale) was replaced by poultry manure litter and olive mill pomace. The increase percentage of poultry manure litter (up to 8.6%) and olive mill pomace (up to 30.5%) in the recipe incremented the total solids (up to 21% in H) and, consequently, the nitrogen content in the digestate (6.7 g N/kg in the solid fraction in H and 4–5 g NH4+-N/L in the liquid fraction). This favored the growth of Lactococcus sp. with consequent increment of lactate production (∼ 1 mg L−1 last two days of the survey) and the establishment of Weissella and Lactobacillus spp. Syntrophic acetate-oxidizers, including Syntrophaceticus (6% ± 1.7%), were detected manly in M but were negatively affected by the addition of the poultry manure litter, while the sulfate-reducing bacteria correlated with the variations of the volatile fatty acids. Planctomycetes putatively capable of anammox process were also found in the H during the first two days of the survey and accounted for 0.3 ± 0.01% of the total bacterial community. The stability of the process during feedstock change is the result of the shift of bacterial populations of different functional groups that showed peculiar adaptation patterns in the two stages of the plant
A new, multidisciplinary approach to monitor the health status of free-living fin (Balaenoptera physalus) and sperm (Physeter macrocephalus) whales in the Pelagos Sanctuary, Corsican-Ligurian-Provençal basin
No full textFin and sperm whale Mediterranean populations are classified respectively as vulnerable and endangered in the International Union for Conservation of Nature Red List and potentially threatened by both infectious diseases and anthropogenic factors. Parasites, bacteria, as well as organic and inorganic pollutants, are considered among the main causes of whale’s death or factors predisposing them to other pathologies. To date, most of the investigations on these species have been carried out on stranded and dead whales and performed by necropsy, occasionally providing information on the death causes. Nowadays, data on health status in free-living whales are limited, mainly due to both the difficulty and the high costs of sampling. In order to get information on the health status of fin and sperm whales living in the Pelagos Sanctuary, a preliminary, multidisciplinary study was carried out analysing three faecal samples (2 samples from fin whales and 1 sample from sperm whale) collected with a non-invasive sampling method in the framework of a 30-years long research project on the ecology of these two populations. Each faecal sample underwent parasitological, microbiological and chemical analysis. Results revealed that fin and sperm whales harbour Blastocystis sp., a protozoan parasite with an anthropozoonotic potential, which was never recorded before in these species. Furthermore, a more diverse bacterial community and a higher concentration of heavy metals ( i.e., As, Co, Hg) were found in the sperm whale sample compared to fin whale ones, while the concentration of 16 EPA PAHs and 21 PCBs was <2 ppb in all tested samples. This preliminary study represents the first report of a multidisciplinary approach in live whales investigation, and may provide a baseline for both future monitoring studies on the relationships between health status and anthropogenic pressure, and the development of effective conservation plan for these species in the Mediterranean Sea
Wild whale faecal samples as a proxy of anthropogenic impact
No full textThe occurrence of protozoan parasite, bacterial communities, organic pollutants and heavy metals was investigated in free-ranging species of fin (Balaenoptera physalus, n. 2) and sperm (Physeter macrocephalus, n. 2) whales from the Pelagos Sanctuary, Corsican-Ligurian Provencal Basin (Northern-Western Mediterranean Sea). Out of four faecal samples investigated, two from fin whales and one from sperm whale were found positive to Blastocystis sp. A higher number of sequences related to Synergistetes and Spirochaetae were found in sperm whales if compared with fin whales. Moreover, As, Co and Hg were found exclusively in sperm whale faecal samples, while Pb was found only in fin whale faecal samples. The concentration of both PAH and PCB was always below the limit of detection. This is the first report in which the presence of these opportunistic pathogens, bacteria and chemical pollutants have been investigated in faecal samples of free-ranging whale species and the first record of Blastocystis in fin and sperm whales. Thus, this study may provide baseline data on new anthropozoonotic parasite, bacterial records and heavy metals in free-ranging fin and sperm whales, probably as a result of an increasing anthropogenic activity. This survey calls for more integrated research to perform regular monitoring programs supported by national and/or international authorities responsible for preservation of these still vulnerable and threatened whale species in the Mediterranean Sea
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