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.
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.
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.
•The maximum biogas production obtained was 114mLg−1 VSadded with 75% of methane after anaerobic digestion.•Bacterial and archaeal community changed obviously during the anaerobic digestion of green ...macroalgae.
Ulva rigida is a green macroalgae, abundantly available in the Mediterranean which offers a promising source for the production of valuable biomaterials, including methane. In this study, anaerobic digestion assays in a batch mode was performed to investigate the effects of various inocula as a mixture of fresh algae, bacteria, fungi and sediment collected from the coast of Sfax, on biogas production from Ulva rigida. The results revealed that the best inoculum to produce biogas and feed an anaerobic reactor is obtained through mixing decomposed macroalgae with anaerobic sludge and water, yielding into 408mL of biogas. The process was then investigated in a sequencing batch reactor (SBR) which led to an overall biogas production of 375mL with 40% of methane. Further co-digestion studies were performed in an anaerobic up-flow bioreactor using sugar wastewater as a co-substrate. A high biogas production yield of 114mL g−1 VSadded was obtained with 75% of methane. The co-digestion proposed in this work allowed the recovery of natural methane, providing a promising alternative to conventional anaerobic microbial fermentation using Tunisian green macroalgae. Finally, in order to identify the microbial diversity present in the reactor during anaerobic digestion of Ulva rigida, the prokaryotic diversity was investigated in this bioreactor by the denaturing gradient gel electrophoresis (DGGE) method targeting the 16S rRNA gene.
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.
A continuously stirred tank bioreactor (CSTR) was used to optimize feasible and reliable bioprocess system in order to treat hydrocarbon-rich industrial wastewaters. A successful bioremediation was ...developed by an efficient acclimatized microbial consortium. After an experimental period of 225 days, the process was shown to be highly efficient in decontaminating the wastewater. The performance of the bioaugmented reactor was demonstrated by the reduction of COD rates up to 95%. The residual total petroleum hydrocarbon (TPH) decreased from 320
mg
TPH
l
−1 to 8
mg
TPH
l
−1. Analysis using gas chromatography–mass spectrometry (GC–MS) identified 26 hydrocarbons. The use of the mixed cultures demonstrated high degradation performance for hydrocarbons range n-alkanes (C10–C35). Six microbial isolates from the CSTR were characterized and species identification was confirmed by sequencing the 16S rRNA genes. The partial 16S rRNA gene sequences demonstrated that 5 strains were closely related to
Aeromonas punctata (
Aeromonas caviae),
Bacillus cereus,
Ochrobactrum intermedium,
Stenotrophomonas maltophilia and
Rhodococcus sp. The 6th isolate was affiliated to genera
Achromobacter. Besides, the treated wastewater could be considered as non toxic according to the phytotoxicity test since the germination index of
Lepidium sativum ranged between 57 and 95%. The treatment provided satisfactory results and presents a feasible technology for the treatment of hydrocarbon-rich wastewater from petrochemical industries and petroleum refineries.
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•Petroleum refinery wastewater is poorly treated in CSTR.•Higher performance treatment was achieved in MBR inoculated with the same consortium than CSTR.•Biomass concentration ...increased rapidly in MBR but declined in the CSTR due to high toxicity.•The MBR presented a higher bacterial abundance and diversity than the CSTR.•Identification of major acclimated bacterial genera in the MBR could explain its high performance treatment.
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.
The effects of aridity on soil and water-use efficient (WUE) crop species are relatively well known. However, the understanding of its impacts on the dynamics of below-ground microorganisms ...associated with plant roots is less well understood.
To investigate the influence of increasing aridity on the dynamics of the fungal communities, samples from the root endosphere and rhizosphere associated with the prickly pear cactus trees (Opuntia ficus-indica) growing along the aridity gradient were collected and the internal transcribed spacer (ITS) were sequenced. The diversity and network analyses of fungal taxa were determined along with standard measurements of soil parameters.
We found that (i) the fungal community exhibited similar alpha diversity and shared a set of core taxa within the rhizosphere and endosphere, but there was significant beta diversity differences; (ii) the relative abundance of major phyla was higher in the rhizosphere than in the endosphere; (iii) arbuscular endomycorrhizal colonization was highest in the humid climate and decreased under lower-arid, and was negatively correlated with increased concentration of Ca2+ in the soil; (iv) increased aridity correlated with increased connectivity of the soil microbial-root fungal networks in the arid soils, producing a highly cohesive network in the upper-arid area; and (v) distinct fungal hubs sculpt the fungal microbiome network structure in the rhizosphere and endosphere within each bioclimatic zone.
Our findings highlight the importance of gradient analysis-based correlation network as a powerful approach to understand changes in the diversity, the dynamics, and the structure of fungal communities associated with the rhizosphere-endosphere interaction and led to the identification of microbes at each bioclimatic zone that are potentially involved in promoting the survival, protection, and growth of Opuntia trees. The variability of fungal hubs composition depending on plant compartment and bioclimatic zone will give key implications for the application of rhizospheric fungi and endophytes as microbial inoculants in agriculture, as well as in the conservation and restoration of cacti plants in arid and semi-arid lands against the backdrop of climate change. Overall, this study will enhance our understanding of the microbiomes'dynamic of CAM plants in nature.
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•Prickly pear cactus species threatened in the future by climate change.•Dynamics of the fungal rhizosphere and endosphere along increased aridity gradient.•Analysis of soil properties, fungal community composition and correlation based-networks•Significant beta diversity, identification of fungal composition and hubs of each zone•Increasing aridity correlates with an increase of fungal connectivity networks.
We investigated the efficiency of a benthic diatom-associated bacteria in removing benzo(a)pyrene (BaP) and fluoranthene (Flt). The diatom, isolated from a PAH-contaminated sediment of the Bizerte ...Lagoon (Tunisia), was exposed in axenic and non-axenic cultures to PAHs over 7 days. The diversity of the associated bacteria, both attached (AB) and free-living bacteria (FB), was analyzed by the 16S rRNA amplicon sequencing. The diatom, which maintained continuous growth under PAH treatments, was able to accumulate BaP and Flt, with different efficiencies between axenic and non-axenic cultures. Biodegradation, which constituted the main process for PAH elimination, was enhanced in the presence of bacteria, indicating the co-metabolic synergy of microalgae and associated bacteria in removing BaP and Flt. Diatom and bacteria showed different capacities in the degradation of BaP and Flt. Nitzschia sp. harbored bacterial communities with a distinct composition between attached and free-living bacteria. The AB fraction exhibited higher diversity and abundance relative to FB, while the FB fraction contained genera with the known ability of PAH degradation, such as Marivita, Erythrobacter, and Alcaligenes. Moreover, strains of Staphylococcus and Micrococcus, isolated from the FB community, showed the capacity to grow in the presence of crude oil. These results suggest that a “benthic Nitzschia sp.-associated hydrocarbon-degrading bacteria” consortium can be applied in the bioremediation of PAH-contaminated sites.
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•An indigenous benthic diatom accumulated BaP and Flt, but biodegradation played the main role in the removal of PAH.•The biodegradation was enhanced by the presence of the diatom and its associated bacteria.•The diatom harbored bacterial genera identified as potential PAH degraders.•Strains isolated from the associated bacteria were able to grow in the presence of crude oil.
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