Recent advances in constructing artificial microbial consortia for the production of medium-chain-length polyhydroxyalkanoates.

Polyhydroxyalkanoates (PHAs) are a class of high-molecular-weight polyesters made from hydroxy fatty acid monomers. PHAs produced by microorganisms have diverse structures, variable physical properties, and good biodegradability. They exhibit similar physical properties to petroleum-based plastics but are much more environmentally friendly. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs), in particular, have attracted much interest because of their low crystallinity, low glass transition temperature, low tensile strength, high elongation at break, and customizable structure. Nevertheless, high production costs have hindered their practical application. The use of genetically modified organisms can reduce production costs by expanding the scope of substrate utilization, improving the conversion efficiency of substrate to product, and increasing the yield of mcl-PHAs. The yield of mcl-PHAs produced by a pure culture of an engineered microorganism was not high enough because of the limitations of the metabolic capacity of a single microorganism. The construction of artificial microbial consortia and the optimization of microbial co-cultivation have been studied. This type of approach avoids the addition of precursor substances and helps synthesize mcl-PHAs more efficiently. In this paper, we reviewed the design and construction principles and optimized control strategies for artificial microbial consortia that produce mcl-PHAs. We described the metabolic advantages of co-cultivating artificial microbial consortia using low-value substrates and discussed future perspectives on the production of mcl-PHAs using artificial microbial consortia.

Functional assembly of root-associated microbial consortia improves nutrient efficiency and yield in soybean.

Root-associated microbes are critical for plant growth and nutrient acquisition. However, scant information exists on optimizing communities of beneficial root-associated microbes or the mechanisms underlying their interactions with host plants. In this report, we demonstrate that root-associated microbes are critical influencers of host plant growth and nutrient acquisition. Three synthetic communities (SynComs) were constructed based on functional screening of 1,893 microbial strains isolated from root-associated compartments of soybean plants. Functional assemblage of SynComs promoted significant plant growth and nutrient acquisition under both N/P nutrient deficiency and sufficiency conditions. Field trials further revealed that application of SynComs stably and significantly promoted plant growth, facilitated N and P acquisition, and subsequently increased soybean yield. Among the tested communities, SynCom1 exhibited the greatest promotion effect, with yield increases of up to 36.1% observed in two field sites. Further RNA-seq implied that SynCom application systemically regulates N and P signaling networks at the transcriptional level, which leads to increased representation of important growth pathways, especially those related to auxin responses. Overall, this study details a promising strategy for constructing SynComs based on functional screening, which are capable of enhancing nutrient acquisition and crop yield through the activities of beneficial root-associated microbes.

Integration between bacterial consortium and magnetite (Fe3O4) nanoparticles for the treatment of oily industrial wastewater.

The study aimed to investigate the efficiency of exogenous bacterial consortium (Enterobacter cloacae and Pseudomonas otitidis) decorated (immobilized) with Fe3O4 Nanoparticles for the treatment of petroleum hydrocarbon-contaminated wastewater. Glycine coated magnetite Nanoparticles (Fe3O4 NPs) were prepared using reverse co-precipitation method and were characterized using X-ray diffraction, transmission and scanning electron microscopy and vibrating sample magnetometer. They were used to decorate exogenous bacterial consortium (Enterobacter cloacae and Pseudomonas otitidis) at 3 different Fe3O4/bacteria ratios (1:1, 1:3 and 3:1 w/w). Bioremediation of oil contaminated wastewater collected from one of the petroleum distribution companies, Alexandria was conducted for 168 h using Fe3O4/bacterial association at the best ratio (3:1) and compared with non-decorated consortium and the indigenous bacteria in the control. Analysis indicated crystalline structure of Fe3O4 NPs with spherical particles (size: 15-20 nm) and superparamagnetic properties. Glycine modified-Fe3O4 exhibited high ability to immobilize bacteria which acquired its magnetic properties. The highest coating efficiency (92%) was achieved at 3:1 Fe3O4/bacteria ratio after 1 h. This ratio positively affected bacterial growth reaching the highest growth rate (5.07 fold higher than the control) after 4 h. The highest removal efficiencies of the total suspended solids (TSS), chemical oxygen demands (COD), oil and grease (O&G) and total petroleum hydrocarbons (TPH) recording 96, 65.4, 83.9 and 85% reaching residual concentrations of 9.5, 598, 99 and 60 mg/l respectively were achieved after 4 h by the Fe3O4-bacteria assembly. Compared with the maximum permissible limits of the tested parameters, TSS residue was highly compiled with its limit (50 mg/l), while COD, O&G and TPH were 7.5, 9.9, and 120-folds higher than their limits (100, 15 and 0.5 mg/l respectively). To the best of our knowledge it is first time to use integrated Enterobacter cloacae and Pseudomonas otitidis consortium decorated with Fe3O4 NPs for the treatment of petroleum hydrocarbon-contaminated wastewater. The proposed system proved to be a very efficient, economical and applicable for the removal of the included contaminants in very short running time which increases its biotechnological added value.

Consumption of Wild Rice (Zizania latifolia) Prevents Metabolic Associated Fatty Liver Disease through the Modulation of the Gut Microbiota in Mice Model.

Metabolic associated fatty liver disease (MAFLD) due to excess weight and obesity threatens public health worldwide. Gut microbiota dysbiosis contributes to obesity and related diseases. The cholesterol-lowering, anti-inflammatory, and antioxidant effects of wild rice have been reported in several studies; however, whether it has beneficial effects on the gut microbiota is unknown. Here, we show that wild rice reduces body weight, liver steatosis, and low-grade inflammation, and improves insulin resistance in high-fat diet (HFD)-fed mice. High-throughput 16S rRNA pyrosequencing demonstrated that wild rice treatment significantly changed the gut microbiota composition in mice fed an HFD. The richness and diversity of the gut microbiota were notably decreased upon wild rice consumption. Compared with a normal chow diet (NCD), HFD feeding altered 117 operational taxonomic units (OTUs), and wild rice supplementation reversed 90 OTUs to the configuration in the NCD group. Overall, our results suggest that wild rice may be used as a probiotic agent to reverse HFD-induced MAFLD through the modulation of the gut microbiota.

Bioremediation of oil contaminated soil using agricultural wastes via microbial consortium.

Agricultural wastes, such as wheat bran and swine wastewater, were used for bioremediation of oil-contaminated soil. Two optimised strains that could degrade oil efficiently were selected. The result showed that the best ratio of strain A to strain B was 7:3. Swine wastewater could be a replacement for nitrogen source and process water for bioremediation. Next, the Box-Behnken design was used to optimise the culture medium, and the optimal medium was as follows: microbial dosage of 97 mL/kg, wheat bran of 158 g/kg and swine wastewater of 232 mL/kg. Under the optimal medium, the oil degradation rate reached 68.27 ± 0.71% after 40 d. The urease, catalase, and dehydrogenase activities in oil-contaminated soil all increased, and the microbe quantity increased significantly with manual composting. These investigations might lay a foundation for reducing the pollution of agricultural wastes, exploring a late model for bioremediation of oil-contaminated soil.

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.).

With the increase in iron/steel production, the higher volume of by-products (slag) generated necessitates its efficient recycling. Because the Linz-Donawitz (LD) slag is rich in silicon (Si) and other fertilizer components, we aim to evaluate the impact of the LD slag amendment on soil quality (by measuring soil physicochemical and biological properties), plant nutrient uptake, and strengthens correlations between nutrient uptake and soil bacterial communities. We used 16 S rRNA illumine sequencing to study soil bacterial community and APIZYM assay to study soil enzymes involved in C, N, and P cycling. The LD slag was applied at 2 Mg ha-1 to Japonica and Indica rice cultivated under flooded conditions. The LD slag amendment significantly improved soil pH, plant photosynthesis, soil nutrient availability, and the crop yield, irrespective of cultivars. It significantly increased N, P, and Si uptake of rice straw. The slag amendment enhanced soil microbial biomass, soil enzyme activities and enriched certain bacterial taxa featuring copiotrophic lifestyles and having the potential role for ecosystem services provided to the benefit of the plant. The study evidenced that the short-term LD slag amendment in rice cropping systems is useful to improve soil physicochemical and biological status, and the crop yield.

In vitro toxicological evaluation of domestic effluent treated by formulated synthetic autochthonous bacterial consortium.

Supplementation of consortium comprising of aboriginal bacterial species with high degradation capacity can significantly enhance the biodegradation process of the domestic wastewater. The present study examined the bioremediation of domestic wastewater using a novel bacterial consortium comprising of five autochthonous bacterial strains with high potential for reduction in BOD, COD and protein content to 89%, 55% and 86%, respectively after 24 h of incubation. HPLC and GC-MS analyses revealed that the chosen consortium had successfully degraded wide-ranging complex organic compounds, which is crucial in the decontamination of wastewater. Phytotoxicity assay of the effluent exhibited that the seeds of Vigna radiata showed better growth and germination when subjected to wastewater treated by novel bacterial consortium as compared to the seeds exposed to untreated wastewater. Further, raw and treated wastewater were assessed for their genotoxicity with comet assay which displayed the intensity of DNA damage in the Allium cepa root tip cells before and after exposure to treated effluent. It is evident from the demonstrated results that the formulated bacterial consortium can be used successfully in a small-scale wastewater treatment plant.

Technical approaches to evaluate the surfactant-enhanced biodegradation of biodiesel and vegetable oils.

This research compared the effects of biosurfactant on the biodegradation of biodiesel and vegetable oils while validating two conceptually diverging methodologies. The two experimental setups were successfully modeled towards the effects of biosurfactants during biodegradation. We established the equivalence of both methodologies from the data output. As expected, the biosurfactants caused an increased oil uptake, thus increasing biodegradation performance. Cooking oils were favored by the microbial consortium as a carbon source when compared with biodiesel fuel, especially after use in food preparation. However, we found that biodiesel substrate standout with the highest biodegradation rates. Our results might indicate that a rapid metabolic change from the original compound initially favored biodiesels during the assimilation of organic carbon for a set specialized microbial inoculum. The data output was successfully combined with mathematical models and statistical tools to describe and predict the actual environmental behavior of biodiesel and vegetable oils. The models confirmed and predicted the biodegradation effectiveness with biosurfactants and estimated the required timeframe to achieve satisfactory contaminant removal.

Biodegradation of crude oil using self-immobilized hydrocarbonoclastic deep sea bacterial consortium.

Hydrocarbonoclastic bacterial consortium that utilizes crude oil as carbon and energy source was isolated from marine sediment collected at a depth of 2100 m. Molecular characterization by 16S rRNA gene sequences confirmed that these isolates as Oceanobacillus sp., Nesiotobacter sp., Ruegeria sp., Photobacterium sp., Enterobacter sp., Haererehalobacter sp., Exiguobacterium sp., Acinetobacter sp. and Pseudoalteromonas sp. Self-immobilized consortium degraded more than 85% of total hydrocarbons after 10 days of incubation with 1% (v/v) of crude oil and 0.05% (v/v) of Tween 80 (non-ionic surfactant) at 28 ±â€¯2 °C. The addition of nitrogen and phosphorus sources separately i.e. 0.1% (v/v) of CO (NH2)2 or K2HPO4 enhanced the hydrocarbon utilization percentage. The pathways of microbial degradation of hydrocarbons were confirmed by FTIR, GC-MS, 1H and 13C NMR spectroscopy analyses. These results demonstrated a novel approach using hydrocarbonoclastic self-immobilized deep sea bacterial consortium for eco-friendly bioremediation.

Nitrogen Removal in Oligotrophic Reservoir Water by a Mixed Aerobic Denitrifying Consortium: Influencing Factors and Immobilization Effects.

Nitrogen pollution in reservoirs has received increasing attention in recent years. Although a number of aerobic denitrifying strains have been isolated to remove nitrogen from eutrophic waters, the situation in oligotrophic water environments has not received significant attention. In this study, a mixed aerobic denitrifying consortium screened from reservoir samples was used to remove nitrogen in an oligotrophic denitrification medium and actual oligotrophic source water. The results showed that the consortium removed 75.32% of nitrate (NO3--N) and 63.11% of the total nitrogen (TN) in oligotrophic reservoir water during a 24-h aerobic cultivation. More initial carbon source was helpful for simultaneous removal of carbon and nitrogen in the reservoir source water. NO3--N and TN were still reduced by 60.93% and 46.56% at a lower temperature (10 °C), respectively, though the rates were reduced. Moreover, adding phosphorus promoted bacterial growth and increased TN removal efficiency by around 20%. The performance of the immobilized consortium in source water was also explored. After 6 days of immobilization, approximately 25% of TN in the source water could be removed by the carriers, and the effects could last for at least 9 cycles of reuse. These results provide a good reference for the use of aerobic denitrifiers in oligotrophic reservoirs.

Microbial decomposition of biomass residues mitigated hydrogeochemical dynamics in strongly alkaline bauxite residues.

Effective neutralization of strongly alkaline conditions in bauxite residues (BR) is the fundamental step to initiate the process of eco-engineering BR into growth substrate (or soil-like medium) for direct phytostabilization with pioneer plant species. The present study aimed to evaluate the effectiveness of microbial decomposition of organic matter (OM) (i.e., biomass residues) in neutralizing the strong alkalinity of residues under saturated conditions, together with the regulatory role of calcium sulfate (CaSO4) addition. Admixing OM (i.e., sugarcane mulch, Lucerne hay) alone in the BR significantly lowered the porewater pH from 11.4 to around 9.0 by Day 7, which persisted until the end of incubation (Day 28). The pH reduction in the porewater of OM-amended BR coincided with the production of acidic organic compounds (mainly acetic acid). Diverse species of organotrophic bacteria (e.g., Enterobacteriales, Pasteurellales, Lactobacillales, and Streptophyta) were found to have colonized in the OM-amended BR, but which were dominated by haloalkaliphilic bacteria (e.g., Halomonas and Bacillaceae). The CaSO4 addition in the OM-amended BR further lowered pH to 8.3 in the porewater. Besides, the bioneutralization effects resulted in dramatic reduction (>90%) of soluble Al in the porewater, which is a prerequisite to lowering Al toxicity in plants. At the same time, the levels of major cations (i.e., K, Ca, Mg) in the porewater were elevated by the OM + CaSO4 amendment, which would facilitate subsequent leaching of these soluble salts to lower the salinity in the BR, and improve the diversity of organotrophic bacterial communities in the amended BR.

Bacteria associated with moon jellyfish during bloom and post-bloom periods in the Gulf of Trieste (northern Adriatic).

Jellyfish are a prominent component of the plankton community. They frequently form conspicuous blooms which may interfere with different human enterprises. Among the aspects that remain understudied are jellyfish associations with microorganisms having potentially important implications for organic matter cycling. To the best of our knowledge, this study is the first to investigate the bacterial community associated with live moon jellyfish (Aurelia solida, Scyohozoa) in the Adriatic Sea. Using 16S rRNA clone libraries and culture-based methods, we have analyzed the bacterial community composition of different body parts: the exumbrella surface, oral arms, and gastric cavity, and investigated possible differences in medusa-associated bacterial community structure at the time of the jellyfish population peak, and during the senescent phase at the end of bloom. Microbiota associated with moon jellyfish was different from ambient seawater bacterial assemblage and varied between different body parts. Betaproteobacteria (Burkholderia, Cupriavidus and Achromobacter) dominated community in the gastral cavity of medusa, while Alphaproteobacteria (Phaeobacter, Ruegeria) and Gammaproteobacteria (Stenotrophomonas, Alteromonas, Pseudoalteromonas and Vibrio) prevailed on 'outer' body parts. Bacterial community structure changed during senescent phase, at the end of the jellyfish bloom, showing an increased abundance of Gammaproteobacteria, exclusively Vibrio. The results of cultured bacterial isolates showed the dominance of Gammaproeteobacteria, especially Vibrio and Pseudoalteromonas in all body parts. Our results suggest that jellyfish associated bacterial community might have an important role for the host, and that anthropogenic pollution in the Gulf of Trieste might affect their community structure.

Multimicrobial Kombucha Culture Tolerates Mars-Like Conditions Simulated on Low-Earth Orbit.

A kombucha multimicrobial culture (KMC) was exposed to simulated Mars-like conditions in low-Earth orbit (LEO). The study was part of the Biology and Mars Experiment (BIOMEX), which was accommodated in the European Space Agency's EXPOSE-R2 facility, outside the International Space Station. The aim of the study was to investigate the capability of a KMC microecosystem to survive simulated Mars-like conditions in LEO. During the 18-month exposure period, desiccated KMC samples, represented by living cellulose-based films, were subjected to simulated anoxic Mars-like conditions and ultraviolet (UV) radiation, as prevalent at the surface of present-day Mars. Postexposure analysis demonstrated that growth of both the bacterial and yeast members of the KMC community was observed after 60 days of incubation; whereas growth was detected after 2 days in the initial KMC. The KMC that was exposed to extraterrestrial UV radiation showed degradation of DNA, alteration in the composition and structure of the cellular membranes, and an inhibition of cellulose synthesis. In the "space dark control" (exposed to LEO conditions without the UV radiation), the diversity of the microorganisms that survived in the biofilm was reduced compared with the ground-based controls. This was accompanied by structural dissimilarities in the extracellular membrane vesicles. After a series of subculturing, the revived communities restored partially their structure and associated activities.

Simulated reactive zone with emulsified vegetable oil for the long-term remediation of Cr(VI)-contaminated aquifer: dynamic evolution of geological parameters and groundwater microbial community.

Cr(VI), which is highly toxic and soluble, is one of the most challenging groundwater contaminants. Previous work has indicated that emulsified vegetable oil (EVO) is an effective in situ amendment for removing Cr(VI) from groundwater. However, the spatial and temporal changes in geological parameters and microbial community structures throughout the remediation period are poorly understood. In this study, a large laboratory-scale sand-packed chamber (reactive zone of 100 × 50 × 30 cm) was used to simulate the bioremediation of Cr(VI)-contaminated aquifer by EVO over a 512-day period. Various geological parameters and microbial communities were monitored during both the establishment and remediation stages. The results indicate that several biogeochemical reactions occurred in a specific sequence following the injection of EVO, creating an acidic and reducing environment. A shift in the community structure and a decrease in the community diversity were observed. The abundance of microbes involved in the degradation of EVO and reduction of electron acceptors significantly increased. Then, the EVO reactive zone was flushed with Cr(VI)-contaminated groundwater. Biogeochemical reactions were inhibited after the inflow of Cr(VI) and subsequently recovered a month later. The pH of the aquifer returned to the initial neutral condition (approximately 7.2). The EVO reactive zone could remediate Cr(VI)-contaminated groundwater at an efficiency exceeding 97% over 480 days. Biogeochemistry played a major role in the early period (0~75 days). In the later period (240~480 days), the remediation of Cr(VI) in the reactive zone depended mostly on bio-reduction by Cr(VI)-reducing bacteria.

Diversity and distribution of bacteria in a multistage surface flow constructed wetland to treat swine wastewater in sediments.

Managing waste produced from swine farming operations is a significant agricultural and environmental challenge. Confined animal feeding operations continually generate large amounts of animal waste, which necessitates adequate waste management systems. This study examines the use of multistage surface flow constructed wetlands (SFCWs) to treat pig farm sewage. The wastewater removal rate, sediment deposits, physicochemical properties, and microbial community compositions of each segment of a SFCW were examined. The results indicated that removal rates of chemical oxygen demand (COD), total nitrogen (TN), NH4+, NO3-, and total phosphorus (TP) were 89.8%, 97.9%, 98.2%, 87.6%, and 96.4%, respectively, in the multistage SFCW. The general trend showed increase in the dissolved oxygen (DO) concentrations and oxidation reduction potential (Eh) from the beginning of the SFCW to its end. Sediment concentrations of N and P in each segment of the SFCW generally decreased, suggesting their accumulation in each segment. High-throughput sequencing indicated that the bacterial diversity increased over time. Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were dominant in multistage SFCW bacterial communities at the phylum level. Results further indicate that DO and Eh are major environmental factors that influence the bacterial community distribution. Overall, our findings suggest that multistage SFCWs not only improve contaminant removal but also change the bacterial community composition and promote bacterial community diversity.

Gut Colonization with Methanogenic Archaea Lowers Plasma Trimethylamine N-oxide Concentrations in Apolipoprotein e-/- Mice.

A mechanistic link between trimethylamine N-oxide (TMAO) and atherogenesis has been reported. TMAO is generated enzymatically in the liver by the oxidation of trimethylamine (TMA), which is produced from dietary choline, carnitine and betaine by gut bacteria. It is known that certain members of methanogenic archaea (MA) could use methylated amines such as trimethylamine as growth substrates in culture. Therefore, we investigated the efficacy of gut colonization with MA on lowering plasma TMAO concentrations. Initially, we screened for the colonization potential and TMAO lowering efficacy of five MA species in C57BL/6 mice fed with high choline/TMA supplemented diet, and found out that all five species could colonize and lover plasma TMAO levels, although with different efficacies. The top performing MA, Methanobrevibacter smithii, Methanosarcina mazei, and Methanomicrococcus blatticola, were transplanted into Apoe-/- mice fed with high choline/TMA supplemented diet. Similar to C57BL/6 mice, following initial provision of the MA, there was progressive attrition of MA within fecal microbial communities post-transplantation during the initial 3 weeks of the study. In general, plasma TMAO concentrations decreased significantly in proportion to the level of MA colonization. In a subsequent experiment, use of antibiotics and repeated transplantation of Apoe-/- mice with M. smithii, led to high engraftment levels during the 9 weeks of the study, resulting in a sustained and significantly lower average plasma TMAO concentrations (18.2 ± 19.6 µM) compared to that in mock-transplanted control mice (120.8 ± 13.0 µM, p < 0.001). Compared to control Apoe-/- mice, M. smithii-colonized mice also had a 44% decrease in aortic plaque area (8,570 µm [95% CI 19587-151821] vs. 15,369 µm [95% CI [70058-237321], p = 0.34), and 52% reduction in the fat content in the atherosclerotic plaques (14,283 µm [95% CI 4,957-23,608] vs. 29,870 µm [95% CI 18,074-41,666], p = 0.10), although these differences did not reach significance. Gut colonization with M. smithii leads to a significant reduction in plasma TMAO levels, with a tendency for attenuation of atherosclerosis burden in Apoe-/- mice. The anti-atherogenic potential of MA should be further tested in adequately powered experiments.

Petroleum hydrocarbon and microbial community structure successions in marine oil-related aggregates associated with diatoms relevant for Arctic conditions.

Oil-related aggregates (ORAs) may contribute to the fate of oil spilled offshore. However, our understanding about the impact of diatoms and associated bacteria involved in the formation of ORAs and the fate of oil compounds in these aggregates is still limited. We investigated these processes in microcosm experiments with defined oil dispersions in seawater at 5 °C, employing the Arctic diatom Fragilariopsis cylindrus and its associated bacterial assemblage to promote ORA formation. Accumulation of oil compounds, as well as biodegradation of naphthalenes in ORAs and corresponding water phases, was enhanced in the presence of diatoms. Interestingly, the genus Nonlabens was predominating the bacterial communities in diatom-supplemented microcosms, while this genus was not abundant in other samples. This work elucidates the relevance of diatom biomass for the formation of ORAs, microbial community structures and biodegradation processes in chemically dispersed oil at low temperatures relevant for Arctic conditions.

Study on the bacterial and archaeal community structure and diversity of activated sludge from three wastewater treatment plants.

In this study, the bacterial and archaeal communities along with their functions of activated sludge from three wastewater treatment plants were investigated by Illumina MiSeq Platform. The treatment processes were modified A/A/O, DE oxidation ditch and pre-anaerobic carrousel oxidation ditch, respectively. The taxonomic analyses showed that Proteobacteria was the predominant bacterial phylum, and Nitrosospira was the dominant nitrification genus. Candidatus Accumulibacter was abundant in DE oxidation ditch process, and the main archaea communities were methanosaeta-like species which had the capability to anaerobic ammonia oxidation. The results illustrated that anaerobic ammonium oxidation played an important role in the nitrogen metabolism and there might be other unknown phosphate-accumulating organisms (PAOs) performing phosphorus removal in activated sludge. The predicted function analyses indicated that both bacteria and archaea were involved in nitrification, denitrification, ammonification and phosphorus removal processes, and their relative abundance varied metabolic modules differed from each other.

Genetic diversity and antimicrobial activity of lactic acid bacteria in the preparation of traditional fermented potato product 'tunta'.

Fermentation microorganisms, lactic acid bacteria (LAB) and yeast from 12 samples of tunta production chain were quantified, from the native potatoes used by the process fermentation of potatoes in the river up to the final product. During fermentation, the LAB population steadily increased from 3 to 4 to 8 log CFU/g during the first 8 days in the river and the yeast population increased from 2 to 3 to 3-4 log CFU/g. Overall, 115 LAB strains were isolated using a culture-dependent method. Molecular techniques and 16S rRNA gene sequencing enabled the identification of native species. In LAB isolates, members of the Lactobacillaceae (64%), Leuconostocaceae (9%) and Enterococcaceae (2%) families were identified. The most prevalent LAB species in the tunta production chain was Lactobacillus curvatus, followed by Leuconostoc mesenteroides and Lactobacillus sakei, Lactobacillus brevis and Enterococcus mundtii were also present. Only 13 LAB strains showed anti-listerial activity, and one of them, identified as En. mundtii DSM 4838T [MG031213], produced antimicrobial compounds that were determined to be proteins after treatment with proteolytic enzymes. Based on these results, we suggest that traditional fermented product-derived LAB strains from specific environments could be selected and used for technological application to control pathogenic bacteria and naturally protect food from post-harvest deleterious microbiota.

Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture.

Consecutive monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive monoculture. The results showed R. glutinosa monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive monoculture.