Ecology and application of haloalkaliphilic anaerobic microbial communities

Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation

The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20 years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.

Synthetic biology of extremophiles: a new wave of biomanufacturing

Microbial biomanufacturing, powered by the advances of synthetic biology, has attracted growing interest for the production of diverse products. In contrast to conventional microbes, extremophiles have shown better performance for low-cost production owing to their outstanding growth and synthesis capacity under stress conditions, allowing unsterilized fermentation processes. We review increasing numbers of products already manufactured utilizing extremophiles in recent years. In addition, genetic parts, molecular tools, and manipulation approaches for extremophile engineering are also summarized, and challenges and opportunities are predicted for non-conventional chassis. Next-generation industrial biotechnology (NGIB) based on engineered extremophiles promises to simplify biomanufacturing processes and achieve open and continuous fermentation, without sterilization, and utilizing low-cost substrates, making NGIB an attractive green process for sustainable manufacturing.

Elevated inorganic carbon and salinity enhances photosynthesis and ATP synthesis in picoalga Picocystis salinarum as revealed by label free quantitative proteomics

Saline soda lakes are of immense ecological value as they niche some of the most exclusive haloalkaliphilic communities dominated by bacterial and archaeal domains, with few eukaryotic algal representatives. A handful reports describe Picocystis as a key primary producer with great production rates in extremely saline alkaline habitats. An extremely haloalkaliphilic picoalgal strain, Picocystis salinarum SLJS6 isolated from hypersaline soda lake Sambhar, Rajasthan, India, grew robustly in an enriched soda lake medium containing mainly Na₂CO₃, 50 g/l; NaHCO_3, 50 g/l, NaCl, 50 g/l (salinity ≈150‰) at pH 10. To elucidate the molecular basis of such adaptation to high inorganic carbon and NaCl concentrations, a high-throughput label-free quantitation based quantitative proteomics approach was applied. Out of the total 383 proteins identified in treated samples, 225 were differentially abundant proteins (DAPs), of which 150 were statistically significant (p < 0.05) including 70 upregulated and 64 downregulated proteins after 3 days of growth in highly saline-alkaline medium. Most DAPs were involved in photosynthesis, oxidative phosphorylation, glucose metabolism and ribosomal structural components envisaging that photosynthesis and ATP synthesis were central to the salinity-alkalinity response. Key components of photosynthetic machinery like photosystem reaction centres, adenosine triphosphate (ATP) synthase ATP, Rubisco, Fructose-1,6-bisphosphatase, Fructose-bisphosphate aldolase were highly upregulated. Enzymes peptidylprolyl isomerases (PPIase), important for correct protein folding showed remarkable marked-up regulation along with other chaperon proteins indicating their role in osmotic adaptation. Enhanced photosynthetic activity exhibited by P. salinarum in highly saline-alkaline condition is noteworthy as photosynthesis is suppressed under hyperosmotic conditions in most photosynthetic organisms. The study provided the first insights into the proteome of extremophilic alga P. salinarum exhibiting extraordinary osmotic adaptation and proliferation in polyextreme conditions prevailing in saline sodic ecosystems, potentially unraveling the basis of resilience in this not so known organism and paves the way for a promising future candidate for biotechnological applications and model organism for deciphering the molecular mechanisms of osmotic adaptation. The mass spectrometry proteomics data is available at the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD037170.

Polyhydroxyalkanoates from extremophiles: A review

Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.

Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions

Biological sulfate and thiosulfate reduction under haloalkaline conditions can be applied to treat waste streams from biodesulfurization systems. However, the lack of microbial aggregation under haloalkaline conditions limits the volumetric rates of sulfate and thiosulfate reducing bioreactors. As biomass retention in haloalkaline bioreactors has not been studied before, sand was chosen as a biomass carrier material to increase cell retention and consequently raise the volumetric rates. The results showed that ~10 fold higher biomass concentrations could be achieved with sand, compared to previous studies without carrier addition. The volumetric rates of sulfate/thiosulfate reduction increased approximately 4.5 times. Biomass attachment to the sand was restricted to cavities within the sand particles. Acetate produced by acetogenic bacteria from H₂ and CO₂ was used as carbon source for biomass growth, while formate that was also produced from H₂ and CO₂ enhanced sulfate reduction. The microbial community composition was analyzed by 16S rRNA gene amplicon sequencing, and Tindallia related bacteria were probably responsible for formate formation from hydrogen. The community attached to the sand particles was similar to the suspended fraction, but the relative abundance of sequences most closely related to Desulfohalobiaceae was much higher in the attached fraction compared to the suspended fraction (30% and 13%, respectively). The results indicated that even though the biomass attachment to sand was poor, it still increased the biomass concentration and consequently the sulfate and thiosulfate reduction volumetric rates.

Syngas as Electron Donor for Sulfate and Thiosulfate Reducing Haloalkaliphilic Microorganisms in a Gas-Lift Bioreactor

Biodesulfurization processes remove toxic and corrosive hydrogen sulfide from gas streams (e.g., natural gas, biogas, or syngas). To improve the efficiency of these processes under haloalkaline conditions, a sulfate and thiosulfate reduction step can be included. The use of H₂/CO mixtures (as in syngas) instead of pure H₂ was tested to investigate the potential cost reduction of the electron donor required. Syngas is produced in the gas-reforming process and consists mainly of H₂, carbon monoxide (CO), and carbon dioxide (CO₂). Purification of syngas to obtain pure H₂ implies higher costs because of additional post-treatment. Therefore, the use of syngas has merit in the biodesulfurization process. Initially, CO inhibited hydrogen-dependent sulfate reduction. However, after 30 days the biomass was adapted and both H₂ and CO were used as electron donors. First, formate was produced, followed by sulfate and thiosulfate reduction, and later in the reactor run acetate and methane were detected. Sulfide production rates with sulfate and thiosulfate after adaptation were comparable with previously described rates with only hydrogen. The addition of CO marginally affected the microbial community in which Tindallia sp. was dominant. Over time, acetate production increased and acetogenesis became the dominant process in the bioreactor. Around 50% of H₂/CO was converted to acetate. Acetate supported biomass growth and higher biomass concentrations were reached compared to bioreactors without CO feed. Finally, CO addition resulted in the formation of small, compact microbial aggregates. This suggests that CO or syngas can be used to stimulate aggregation in haloalkaline biodesulfurization systems.

Effect of pressure and temperature on anaerobic methanotrophic activities of a highly enriched ANME-2a community

This study investigated the effect of temperature and methane partial pressure on the anaerobic methane-oxidizing and sulfate-reducing (AOM-SR) activities by a highly enriched ANME-2a community. The ANME-2a-enriched biomass was incubated at different pressures, i.e., 2, 10, 20, and 30 MPa at 15 °C for 80 days. The response of the microbial community with temperature was investigated in incubations at 4, 15, and 25 °C at 10 MPa. Among all tested conditions, the incubation at 10 MPa pressure and 15 °C showed the highest AOM-SR activity of the studied ANME-2a phylotype, whereas activity at 2 MPa pressure and 15 °C was almost comparative to the response at 10 MPa pressure. The finding of the most favorable conditions for AOM-SR activity by the studied AOM-SR community comparable to the in situ pressure and temperature (15 °C at 10 MPa) suggests that the studied ANME-2a phylotype was well adapted to the conditions similar to its origin. The microbial community analysis showed that the bacterial community composition shifted upon changing the incubation temperature and pressure.

Inhibition of volatile fatty acids on methane production kinetics during dry co-digestion of food waste and pig manure

Compared with wet digestion, dry digestion of organic wastes reduces reactor volume and requires less energy for heating, but it is easily inhibited by high volatile fatty acid (VFA) or ammonia concentration. The inhibition on methane production kinetics during dry co-digestion of food waste and pig manure is rarely reported. The aim of this study was to explore the inhibition mechanisms and the microbial interactions in food waste and pig manure dry co-digestion systems at different inoculum rates (25% and 50% based on volatile solids) and food waste/pig manure ratios (0:100, 25:75, 50:50, 75:25 and 100:0 based on volatile solids). The results showed that the preferable operation conditions were obtained at the inoculum rate of 50% and food waste/pig manure ratio of 50:50, with a specific methane yield of 263 mL/g VS_added. High VFA concentration was the main inhibition factor on methane production, and the threshold VFA inhibition concentrations ranged 16.5-18.0 g/L. Syntrophic oxidation with hydrogenotrophic methanogenesis might be the main methane production pathway in dry co-digestion systems due to the dominance of hydrogenotrophic methanogens in the archaeal community. In conclusion, dry co-digestion of food waste and pig manure is feasible for methane production without pH adjustment and can be operated stably by choosing proper operation conditions.

The chemostat metabolite spectra of alkaline mixed culture fermentation under mesophilic, thermophilic, and extreme-thermophilic conditions

Alkaline mixed culture fermentation (MCF) is a promising technology for reducing organic waste and producing biochemicals. However, chemostat metabolite spectra that are necessary for constructing a model and analyzing factors are seldom reported. In the present study, the effects of pH on the metabolites distribution in mesophilic (35 °C), thermophilic (55 °C), and extreme-thermophilic (70 °C) alkaline MCF were demonstrated. A chemical oxygen demand balance above 80% was achieved, and the main metabolites included acetate, ethanol, propionate, lactate, and formate. The yields of ethanol and formate increased as pH was increased from 7.5 to higher pH under mesophilic and thermophilic conditions, while the yields of acetate, lactate, and/or propionate decreased. The yields of ethanol, acetate, and formate increased under extreme-thermophilic conditions as pH was increased from 7.5 to 9.0, whereas lactate and hydrogen yields decreased. Low biomass yield under thermophilic and extreme-thermophilic conditions benefited higher metabolite production and minimized the accumulation of sludge.

Selection and Application of Sulfide Oxidizing Microorganisms Able to Withstand Thiols in Gas Biodesulfurization Systems

After the first commercial applications of a new biological process for the removal of hydrogen sulfide (H₂S) from low pressure biogas, the need arose to broaden the operating window to also enable the removal of organosulfur compounds from high pressure sour gases. In this study we have selected microorganisms from a full-scale biodesulfurization system that are capable of withstanding the presence of thiols. This full-scale unit has been in stable operation for more than 10 years. We investigated the microbial community by using high-throughput sequencing of 16S rRNA gene amplicons which showed that methanethiol gave a competitive advantage to bacteria belonging to the genera Thioalkalibacter (Halothiobacillaceae family) and Alkalilimnicola (Ectothiorhosdospiraceae family). The sulfide-oxidizing potential of the acclimatized population was investigated under elevated thiol loading rates (4.5-9.1 mM d^-1), consisting of a mix of methanethiol, ethanethiol, and propanethiol. With this biomass, it was possible to achieve a stable bioreactor operation at which 80% of the supplied H₂S (61 mM d^-1) was biologically oxidized to elemental sulfur. The remainder was chemically produced thiosulfate. Moreover, we found that a conventionally applied method for controlling the oxygen supply to the bioreactor, that is, by maintaining a redox potential set-point value, appeared to be ineffective in the presence of thiols.