Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica

© Copyright © 2020 Karray, Gargouri, Chebaane, Mhiri, Mliki and Sayadi. Recent microbiome research has shown that soil fertility, plant-associated microbiome, and crop production can be affected by abiotic environmental parameters. The effect of aridity gradient on rhizosphere-soil (rhizosphere) and endosphere-root (endosphere) prokaryotic structure and diversity associated with cacti remain poorly investigated and understood. In the current study, next-generation sequencing approaches were used to characterize the diversity and composition of bacteria and archaea associated with the rhizosphere and endosphere of Opuntia ficus-indica spineless cacti in four bioclimatic zones (humid, semi-arid, upper-arid, and lower-arid) in Tunisia. Our findings showed that bacterial and archaeal cactus microbiomes changed in inside and outside roots and along the aridity gradient. Plant compartment and aridity gradient were the influencing factors on the differentiation of microbial communities in rhizosphere and endosphere samples. The co-occurrence correlations between increased and decreased OTUs in rhizosphere and endosphere samples and soil parameters were determined according to the aridity gradient. Blastococcus, Geodermatophilus, Pseudonocardia, Promicromonospora, and Sphingomonas were identified as prevailing hubs and were considered as specific biomarkers taxa, which could play a crucial role on the aridity stress. Overall, our findings highlighted the prominence of the climatic aridity gradient on the equilibrium and diversity of microbial community composition in the rhizosphere and endosphere of cactus.We thank the Tunisian authorities for the support in prickly pear tree sampling and also Dr. Fabrice Armougoum from the Mediterranean Institute of Oceanography (MIO, IRD, UM 110, 13288, Marseille, France) for his great help on microbiome analysis

Olive agroforestry shapes rhizosphere microbiome networks associated with annual crops and impacts the biomass production under low-rainfed conditions

Agroforestry (AF) is a promising land-use system to mitigate water deficiency, particularly in semi-arid areas. However, the belowground microbes associated with crops below trees remain seldom addressed. This study aimed at elucidating the effects of olive AF system intercropped with durum wheat (Dw), barely (Ba), chickpea (Cp), or faba bean (Fb) on crops biomass and their soil-rhizosphere microbial networks as compared to conventional full sun cropping (SC) under rainfed conditions. To test the hypothesis, we compared the prokaryotic and the fungal communities inhabiting the rhizosphere of two cereals and legumes grown either in AF or SC. We determined the most suitable annual crop species in AF under low-rainfed conditions. Moreover, to deepen our understanding of the rhizosphere network dynamics of annual crops under AF and SC systems, we characterized the microbial hubs that are most likely responsible for modifying the microbial community structure and the variability of crop biomass of each species. Herein, we found that cereals produced significantly more above-ground biomass than legumes following in descending order: Ba > Dw > Cp > Fb, suggesting that crop species play a significant role in improving soil water use and that cereals are well-suited to rainfed conditions within both types of agrosystems. The type of agrosystem shapes crop microbiomes with the only marginal influence of host selection. However, more relevant was to unveil those crops recruits specific bacterial and fungal taxa from the olive-belowground communities. Of the selected soil physicochemical properties, organic matter was the principal driver in shaping the soil microbial structure in the AF system. The co-occurrence network analyses indicated that the AF system generates higher ecological stability than the SC system under stressful climate conditions. Furthermore, legumes’ rhizosphere microbiome possessed a higher resilient capacity than cereals. We also identified different fungal keystones involved in litter decomposition and drought tolerance within AF systems facing the water-scarce condition and promoting crop production within the SC system. Overall, we showed that AF reduces cereal and legume rhizosphere microbial diversity, enhances network complexity, and leads to more stable beneficial microbial communities, especially in severe drought, thus providing more accurate predictions to preserve soil diversity under unfavorable environmental conditions.This research was carried out as part of the D4DECLIC Project, ARIMNet 2 Young Scientists Call 2017 (ERA-NET program), and Grant agreement no. 618127

Isolation and Characterization of Hydrocarbon-Degrading Yeast Strains from Petroleum Contaminated Industrial Wastewater

Two yeast strains are enriched and isolated from industrial refinery wastewater. These strains were observed for their ability to utilize several classes of petroleum hydrocarbons substrates, such as n-alkanes and aromatic hydrocarbons as a sole carbon source. Phylogenetic analysis based on the D1/D2 variable domain and the ITS-region sequences indicated that strains HC1 and HC4 were members of the genera Candida and Trichosporon, respectively. The mechanism of hydrocarbon uptaking by yeast, Candida, and Trichosporon has been studied by means of the kinetic analysis of hydrocarbons-degrading yeasts growth and substrate assimilation. Biodegradation capacity and biomass quantity were daily measured during twelve days by gravimetric analysis and gas chromatography coupled with mass spectrometry techniques. Removal of n-alkanes indicated a strong ability of hydrocarbon biodegradation by the isolated yeast strains. These two strains grew on long-chain n-alkane, diesel oil, and crude oil but failed to grow on short-chain n-alkane and aromatic hydrocarbons. Growth measurement attributes of the isolates, using n-hexadecane, diesel oil, and crude oil as substrates, showed that strain HC1 had better degradation for hydrocarbon substrates than strain HC4. In conclusion, these yeast strains can be useful for the bioremediation process and decreasing petroleum pollution in wastewater contaminated with petroleum hydrocarbons

Performance of UASB reactor treating waste activated sludge: Effect of electro-chemical disintegration on the anaerobic microbial population structure and abundance

The electro-Fenton (EF) disintegration using iron electrodes was performed for the pretreatment of waste activated sludge (WAS). The effect of this electro-chemical pretreatment on anaerobic digestion (AD) performance and microbial population structure was studied. An improvement of biodegradability and bioaccessibility of organic matter was demonstrated. AD of pretreated WAS in an up-flow anaerobic sludge blanket reactor (UASB) resulted to an increase of biogas production by 60 % compared to control reactor without disintegration. PCR-DGGE and real-time qPCR analyses showed that the high abundance of bacteria and the coexistence of Coprothermobacter in the UASB digestate fed with disintegrated sample established a stable bacterial association which is in line with the AD performance. Besides, the increased number of methanogens along the process allowed the improvement of methane production in comparison to control reactor

Isolation and characterization of a newly naphthalene degrading Halomonas pacifica, strain Cnaph3: biodegradation and biosurfactant production studies

A newly marine Halomonas pacifica strain Cnaph3 was isolated, as a naphthalene degrader and biosurfactant producer, from contaminated seawater collected in Ataya's fishing harbor, located in Kerkennah Islands, Tunisia. Chromatography flame ionization detector analysis revealed that 98.8% of naphthalene (200 mg/L) was degraded after 7 days of incubation, at 30 g/L NaCl and 37 C. Strain Cnaph3 showed also a noticeable capacity to grow on a wide range of aliphatic, aromatic, and complex hydrocarbons. Interestingly, strain Cnaph3 showed a significant potential to produce biosurfactants in the presence of all tested substrates, particularly on glycerol (1%, v/v). Electrospray ionization analysis of the biosurfactant, designated Bios-Cnaph3, suggested a lipopeptide composition. The critical micelle concentration of Bios-Cnaph3 was about 500 mg/L. At this concentration, the surface tension of the water was reduced to 27.6 mN/m. Furthermore, Bios-Cnaph3 displayed interesting stabilities over a wide range of temperatures (4-105 C), salinities (0-100 g/L NaCl), and pH (2.2-12.5). In addition, it showed promising capacities to remove used motor oil from contaminated soils. The biodegradation and biosurfactant-production potential of the Halomonas sp. strain Cnaph3 would present this strain as a favorite agent for bioremediation of hydrocarbon-contaminated sites under saline conditions

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities' analysis

This study evaluated firstly the performance of the Continuous Stirred Tank bioReactor system (CSTR) for the treatment of highly toxic petroleum refinery wastewaters at the pilot-scale. The reduction of the COD, BOD5, phenols, and the total petroleum hydrocarbon (TPH) reached 82.10%, 85.87%, 91.63%, and 81.11%, respectively at high hydraulic residence time (HRT = 10 days). Decreasing HRT to 5 and 2.5 days led to a decrease in the efficiency of the process and a decrease in biomass concentration was also observed (<1000 mg/l). We investigated to test Membrane Bioreactor (MBR) configuration inoculated with the same microbial consortium of CSTR. Therefore, the removal efficiency reached 89.14% of COD and biomass concentration increased to 2800 mg/l at HRT = 1 day. Microbial biomass showed high acclimatization to the toxic wastewater. Communities' abundance and composition in CSTR and MBR were then performed using culture-independents approaches (qPCR, Illumina Miseq sequencing, and DGGE) based on the 16S rRNA gene sequencing. Results showed that major genera affiliated with Betaproteobacteria and Gammaproteobacteria were commonly shared in both bioreactors. The MBR presented a higher bacterial abundance and diversity than the CSTR. Furthermore, dominant genera belonging to Alphaproteobacteria and Bacteroidetes were exclusively detected in CSTR and MBR, respectively. Six potential hydrocabonclastic bacteria were isolated from the CSTR. This study demonstrates the occurrence of specific acclimated bacterial communities in MBR different from those identified in CSTR, improving the petroleum hydrocarbon wastewater treatment. The results would be useful in developing an MBR system for treating toxic stripped wastewater at a larger scale

Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays

International audienceChott El Jerid is the largest hypersaline ephemeral lake in southern Tunisian Sahara desert and is one of the biggest depressions at the North of Africa. This study aimed to investigate the diversity and abundance of microbial communities inhabiting Chott El Jerid during wet season (when it was flooded), using molecular methods [Illumina Miseq sequencing, DGGE and qPCR (qPCR)]. 16S rRNA gene analyses revealed that bacterial community was dominated by Proteobacteria (especially Ralstonia species), followed by Firmicutes, Bacteroidetes, Cyanobacteria, Actinobacteria and Verrucomicrobia. The results obtained using prokaryotic universal primers showed low relative abundance of Archaea dominated by few OTUs related to Methanosarcinaceae and Methanomassiliicoccaceae families and the presence of sulfate-reducing Archaea affiliated with Archaeoglobus. However, the results obtained using Archaea-specific primers showed that archaeal community was mainly composed of aerobic Halobacteria (especially Halorubrum species) and anaerobic members of Methanomicrobia. These results also provided evidence for the presence of members of the genus Halohasta in this environment. qPCR results revealed that Archaea were more abundant in studied samples than Bacteria. The sulfate-reducing Bacteria were also found abundant (~ one-third of the bacterial community) and outnumbered methanogens, suggesting their potential important role in this sulfate-rich and hypersaline ecosystem

Desulfobulbus aggregans sp. nov., a Novel Sulfate Reducing Bacterium Isolated from Marine Sediment from the Gulf of Gabes

International audienc

Table1_Role of biochar in anaerobic microbiome enrichment and methane production enhancement during olive mill wastewater biomethanization.pdf

The current research work attempted to investigate, for the first time, the impact of biochar addition, on anaerobic digestion of olive mill wastewater with different initial chemical oxygen demand loads in batch cultures (10 g/L, 15 g/L, and 20 g/L). Methane yields were compared by applying one-way analysis of variance (ANOVA) followed by post-hoc Tukey’s analysis. The results demonstrated that adding at 5 g/L biochar to olive mill wastewater with an initial chemical oxygen demand load of 20 g/L increased methane yield by 97.8% and mitigated volatile fatty acid accumulation compared to the control batch. According to the results of microbial community succession revealed by the Illumina amplicon sequencing, biochar supplementation significantly increased diversity of the microbial community and improved the abundance of potential genera involved in direct interspecies electron transfer, including Methanothrix and Methanosarcina. Consequently, biochar can be a promising alternative in terms of the recovery of metabolic activity during anaerobic digestion of olive mill wastewater at a large scale.</p