Alternative Carbon Sources Research Articles

Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches.

The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.

Elucidating the Role of O2 Uncoupling for the Adaptation of Bacterial Biodegradation Reactions Catalyzed by Rieske Oxygenases.

Oxygenation of aromatic and aliphatic hydrocarbons by Rieske oxygenases is the initial step of various biodegradation pathways for environmental organic contaminants. Microorganisms carrying Rieske oxygenases are able to quickly adapt their substrate spectra to alternative carbon and energy sources that are structurally related to the original target substrate, yet the molecular events responsible for this rapid adaptation are not well understood. Here, we evaluated the hypothesis that reactive oxygen species (ROS) generated by unproductive activation of O2, the so-called O2 uncoupling, in the presence of the alternative substrate exert a selective pressure on the bacterium for increasing the oxygenation efficiency of Rieske oxygenases. To that end, we studied wild-type 2-nitrotoluene dioxygenase from Acidovorax sp. strain JS42 and five enzyme variants that have evolved from adaptive laboratory evolution experiments with 3- and 4-nitrotoluene as alternative growth substrates. The enzyme variants showed a substantially increased oxygenation efficiency toward the new target substrates concomitant with a reduction of ROS production, while mechanisms and kinetics of enzymatic O2 activation remained unchanged. Structural analyses and docking studies suggest that amino acid substitutions in enzyme variants occurred at residues lining both substrate and O2 transport tunnels, enabling tighter binding of the target substrates in the active site. Increased oxygenation efficiencies measured in vitro for the various enzyme (variant)-substrate combinations correlated linearly with in vivo changes in growth rates for evolved Acidovorax strains expressing the variants. Our data suggest that the selective pressure from oxidative stress toward more efficient oxygenation by Rieske oxygenases was most notable when O2 uncoupling exceeded 60%.

Natural Polyhydroxyalkanoates—An Overview of Bacterial Production Methods

Polyhydroxyalkanoates (PHAs) are intracellular biopolymers that microorganisms use for energy and carbon storage. They are mechanically similar to petrochemical plastics when chemically extracted, but are completely biodegradable. While they have potential as a replacement for petrochemical plastics, their high production cost using traditional carbon sources remains a significant challenge. One potential solution is to modify heterotrophic PHA-producing strains to utilize alternative carbon sources. An alternative approach is to utilize methylotrophic or autotrophic strains. This article provides an overview of bacterial strains employed for PHA production, with a particular focus on those exhibiting the highest PHA content in dry cell mass. The strains are organized according to their carbon source utilization, encompassing autotrophy (utilizing CO2, CO) and methylotrophy (utilizing reduced single-carbon substrates) to heterotrophy (utilizing more traditional and alternative substrates).

Biodegradation of flavonoids – Influences of structural features

Flavonoids, a class of natural products with a variety of applications in nutrition, pharmacy and as biopesticides, could substitute more harmful synthetic chemicals that persist in the environment. To gain a better understanding of the biodegradability of flavonoids and the influence of structural features, firstly, the ultimate biodegradation of 19 flavonoids was investigated with the Closed Bottle Test according to the OECD guideline 301 D. Secondly, regarding the fast abiotic degradation reported for several flavonoids with severe concentration decrease within hours and its possible impacts on the processes behind the ultimate biodegradation, primary degradation of 4 selected flavonoids was compared at conditions representing biodegradation, abiotic degradation, and mixed substrates by monitoring the flavonoids' concentrations with HPLC-UV/vis. Our results showed that 17 out of the 19 tested flavonoids were readily biodegradable. Structural features like a hydroxy group at C3, the C2–C3 bond order, a methoxy group in the B ring, and the position of the B ring in regard to the chromene core did not affect biodegradation of the tested flavonoids. Only flavone without any hydroxy groups and morin with an uncommon 2′,4′ pattern of hydroxy groups were non-readily biodegradable. Monitoring the concentration of 4 selected flavonoids by HPLC-UV/vis revealed that biodegradation occurred faster than abiotic degradation at CBT conditions with no other carbon sources present. The presence of an alternative carbon source tends to increase lag phases and decrease biodegradation rates. At this condition, abiotic degradation contributed to the degradation of unstable flavonoids. Overall, as a first tier to assess the environmental fate, our results indicate low risks for persistence of most flavonoids. Thus, flavonoids could represent benign substitutes for persistent synthetic chemicals.

Valorization of black carrot pomace and pea powder for co-production of polygalacturonase and pectin lyase

AbstractPectic enzyme groups, particularly polygalacturonase and pectin lyase, are vital components of a high-value microbial enzyme category widely employed in applications within the fruit juice and wine industries. The exploration of alternative carbon and nitrogen sources remains crucial for enhancing enzyme production while reducing costs. This study evaluates the impact of carbon (black carrot pomace) and nitrogen (pea protein) loading on fermentable sugar content, protein content, and enzyme activities during both batch and fed-batch cultivation. Additionally, three distinct valorization techniques—thermal (steam), thermochemical (steam assisted with dilute acid), and microwave-assisted with dilute acid pretreatments—were assessed for their effectiveness in hydrolyzing black carrot pomace as a carbon source. The findings indicate that microwave-assisted dilute acid, coupled with enzymatic saccharification, resulted in the highest fermentable sugar production (0.493 g/g), achieving an 87.3% conversion yield. Pea protein demonstrated more favorable outcomes with the highest polygalacturonase activity (20.50 ± 0.52 U/L) and pectin lyase activity (46.44 ± 3.45 U/L) compared to whey protein and yeast extract used as nitrogen sources. Meanwhile, the highest polygalacturonase and pectin lyase activity, along with the highest total protein content (52.25 ± 0.06 mg/L), was recorded under the same culture conditions, reaching 164.34 ± 2.26 and 188.22 ± 1.72 U/L, respectively, after 72 h, representing approximately 1.18- and 1.34-fold increases from the batch system. Consequently, these results prove that fed-batch cultivation, utilizing black carrot pomace hydrolyzate as a feeding substrate and pea protein as a nitrogen source, significantly increases polygalacturonase and pectin lyase activity compared to batch cultivation.

Intestinal carbapenem-resistant Klebsiella pneumoniae undergoes complex transcriptional reprogramming following immune activation

ABSTRACT Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) is a significant threat to public health worldwide. The primary reservoir for CR-Kp is the intestinal tract. There, the bacterium is usually present at low density but can bloom following antibiotic treatment, mostly in hospital settings. The impact of disturbances in the intestinal environment on the fitness, survival, expansion, and drug susceptibility of this pathogen is not well-understood, yet it may be relevant to devise strategies to tackle CR-Kp colonization and infection. Here, we adopted an in vivo model to examine the transcriptional adaptation of a CR-Kp clinical isolate to immune activation in the intestine. We report that as early as 6 hours following host treatment with anti-CD3 antibody, CR-Kp underwent rapid transcriptional changes including downregulation of genes involved in sugar utilization and amino acid biosynthesis and upregulation of genes involved in amino acid uptake and catabolism, antibiotic resistance, and stress response. In agreement with these findings, treatment increased the concentration of oxidative species and amino acids in the mouse intestine. Genes encoding for proteins containing the domain of unknown function (DUF) 1471 were strongly upregulated, however their deletion did not impair CR-Kp fitness in vivo upon immune activation. Transcription factor enrichment analysis identified the global regulator cAMP-Receptor Protein, CRP, as a potential orchestrator of the observed transcriptional signature. In keeping with the recognized role of CRP in regulating utilization of alternative carbon sources, crp deletion in CR-Kp resulted in strongly impaired gut colonization, although this effect was not amplified by immune activation. Thus, following intestinal colonization, which occurs in a CRP-dependent manner, CR-Kp can rapidly respond to immune cues by implementing a well-defined and complex transcriptional program whose direct relevance toward bacterial fitness warrants further investigation. Additional analyses utilizing this model may identify key factors to tackle CR-Kp colonization of the intestine.

Fructose-induced metabolic reprogramming of cancer cells.

Excess dietary fructose consumption has been long proposed as a culprit for the world-wide increase of incidence in metabolic disorders and cancer within the past decades. Understanding that cancer cells can gradually accumulate metabolic mutations in the tumor microenvironment, where glucose is often depleted, this raises the possibility that fructose can be utilized by cancer cells as an alternative source of carbon. Indeed, recent research has increasingly identified various mechanisms that show how cancer cells can metabolize fructose to support their proliferating and migrating needs. In light of this growing interest, this review will summarize the recent advances in understanding how fructose can metabolically reprogram different types of cancer cells, as well as how these metabolic adaptations can positively support cancer cells development and malignancy.

Advances in the Production of Sustainable Bacterial Nanocellulose from Banana Leaves.

Interest in bacterial nanocellulose (BNC) has grown due to its purity, mechanical properties, and biological compatibility. To address the need for alternative carbon sources in the industrial production of BNC, this study focuses on banana leaves, discarded during harvesting, as a valuable source. Banana midrib juice, rich in nutrients and reducing sugars, is identified as a potential carbon source. An optimal culture medium was designed using a simplex-centroid mixing design and evaluated in a 10 L bioreactor. Techniques such as Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffraction (XRD), and thermogravimetric analysis (TGA) were used to characterize the structural, thermal, and morphological properties of BNC. Banana midrib juice exhibited specific properties, such as pH (5.64), reducing sugars (15.97 g/L), Trolox (45.07 µM), °Brix (4.00), and antioxidant activity (71% DPPH). The model achieved a 99.97% R-adjusted yield of 6.82 g BNC/L. Physicochemical analyses revealed distinctive attributes associated with BNC. This approach optimizes BNC production and emphasizes the banana midrib as a circular solution for BNC production, promoting sustainability in banana farming and contributing to the sustainable development goals.

Coupling use of stable isotopes and functional genes as indicators for the impacts of artificial restoration on the carbon storage of a coastal wetland invaded by Spartina alterniflora, southeastern China

Coastal wetlands are characterized by high production and thus play an important role in global climate change. In past decades, the invasion of Spartina alterniflora has caused many problems of coastal wetlands in southeastern China, and the restoration of such areas was mainly conducted by replacing Spartina alterniflora with mangrove plants. This may impact the carbon storage dynamics in such areas. In this study, stable isotopes (δ13C and δ15N) and molecular analysis were used to reveal the impact of artificial restoration on the carbon storage of Quanzhou Bay Estuary Wetland Natural Reserve. The major results are as follows: (1) the change in dominant plants results in a changing major source of soil organic matter, from external sources to mangrove plants; (2) the decrease in soil organic matter following the removal of Spartina alterniflora may be primarily caused by the loss of external organic matter, while the production of mangroves may offset such loss and enhance the content and stability of carbon storage over the long term; (3) microbial CO2 assimilation may serve as an alternative source of bioavailable carbon and thus support the activity of benthic community. Our results revealed the long-term benefits of such restoration on the carbon storage function of wetlands invaded by Spartina alterniflora. Furthermore, the integrating of isotopic tracers and molecular technology may provide new insights in understanding the response of the carbon storage in coastal areas to human activity.

Poly(3-hydroxybutyrate) production from cassava processing wastes by Paracoccus sp. through high cell density cultivation: Effects of substrates limitation and kinetic analysis

Polyhydroxybutyrate (PHB) is bioplastic that has been recognized as a viable alternative to petroleum-based ones, owing to its biodegradability and biocompatibility. However, its use has long been hampered by its high selling price, caused mainly by using costly fermentation feedstock. In the present study, cassava pulp (CP) was investigated as an alternative low-cost carbon source for a high cell density cultivation of Paracoccus sp. KKU01 for PHB production. CP was hydrolyzed enzymatically, and the resulting hydrolysate was used as the base medium to optimize the bacterial growth conditions, i.e., medium compositions and dissolved oxygen setpoints, attaining as high as 40.9 ± 0.0 g/L of biomass. The optimum growth conditions were subsequently used in 4 fed-batch fermentation regimes, and Regime 2, where complete medium (CP hydrolysate supplemented with other nutrients) was fed twice followed by twice feedings of concentrated CP hydrolysate (CPH), was found to give highest biomass and PHB production of 114.5 ± 1.3 and 47.8 ± 3.9 g/L, respectively, with 41.8 ± 2.9% PHB content and yield of 0.12 kg/kg-CP. PHB productivity was 0.80 ± 0.06 g/(L·h). Logistic and Luedeking-Piret models were used successfully to describe the profiles of bacterial growth and PHB production, respectively. Curve fitting using the Luedeking-Piret model revealed that PHB synthesis and PHB turnover occurred simultaneously during the process. Overall, the results demonstrated that cassava processing wastes are feasible feedstock for PHB production by Paracoccus sp. KKU01.

Comparing methanol and glycerol as carbon sources for mainstream partial denitrification/anammox in an IFAS process.

This study explored the implementation of mainstream partial denitrification with anammox (PdNA) in the second anoxic zone of a wastewater treatment process in an integrated fixed film activated sludge (IFAS) configuration. A pilot study was conducted to compare the use of methanol and glycerol as external carbon sources for an IFAS PdNA startup, with a goal to optimize nitrogen removal while minimizing carbon usage. The study also investigated the establishment of anammox bacteria on virgin carriers in IFAS reactors without the use of seeding, and it is the first IFAS PdNA startup to use methanol as an external carbon source. The establishment of anammox bacteria was confirmed in both reactors 102 days after startup. Although the glycerol-fed reactor achieved a higher steady-state maximum ammonia removal rate because of anammox bacteria (1.6 ±0.3g/m2/day) in comparison with the methanol-fed reactor (1.2±0.2g/m2/day), both the glycerol- and methanol-fed reactors achieved similar average in situ ammonia removal rates of 0.39 ±0.2g/m2/day and 0.40 ±0.2g/m2/day, respectively. Additionally, when the upstream ammonia versus NOx (AvN) control system maintained an ideal ratio of 0.40-0.50 g/g, the methanol-fed reactor attained a lower average effluent TIN concentration (3.50 ±1.2mg/L) than the glycerol-fed reactor (4.43 ±1.6mg/L), which was prone to elevated nitrite concentrations in the effluent. Overall, this research highlights the potential for PdNA in IFAS configurations as an efficient and cost-saving method for wastewater treatment, with methanol as a viable carbon source for the establishment of anammox bacteria. PRACTITIONER POINTS: Methanol is an effective external carbon source for an anammox startup that avoids the need for costly alternative carbon sources. The methanol-fed reactor demonstrated higher TIN removal compared with the glycerol-fed reactor because of less overproduction of nitrite. Anammox bacteria was established in an IFAS reactor without seeding and used internally stored carbon to reduce external carbon addition. Controlling the influent ammonia versus NOx (AvN) ratio between 0.40 and 0.50 g/g allowed for low and stable TIN effluent conditions.

Abstract 1801: Rewiring of cortical glucose metabolism fuels human brain cancer growth

Abstract The brain avidly consumes glucose to fuel neurophysiology. Cancers of the brain, such as glioblastoma (GBM), lose aspects of normal biology and gain the ability to proliferate and invade healthy tissue. How brain cancers rewire glucose utilization to fuel these processes is poorly understood. Here we perform infusions of 13C-labeled glucose into patients and mice with brain cancer to define the metabolic fates of glucose-derived carbon in tumor and cortex. By combining these measurements with quantitative metabolic flux analysis, we find that human cortex funnels glucose-derived carbons towards physiologic processes including TCA cycle oxidation and neurotransmitter synthesis. In contrast, brain cancers downregulate these physiologic processes, scavenge alternative carbon sources from the environment, and instead use glucose-derived carbons to produce molecules needed for proliferation and invasion. Targeting this metabolic rewiring in mice through dietary modulation selectively alters GBM metabolism and slows tumor growth. Citation Format: Andrew J. Scott, Anjali Mittal, Baharan Meghdadi, Sravya Palavalasa, Abhinav Achreja, Alexandra O'Brien, Ayesha Kothari, Weihua Zhou, Jie Xu, Angelica Lin, Kari Wilder-Romans, Donna M. Edwards, Vijay Tarnal, Nathan Qi, Theodore S. Lawrence, Sriram Venneti, Nathalie Y. Agar, Costas A. Lyssiotis, Wajd N. Al-Holou, Deepak Nagrath, Daniel R. Wahl. Rewiring of cortical glucose metabolism fuels human brain cancer growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1801.

Evaluation of aircraft deicing fluid as an external carbon source for denitrification

Water resource recovery facilities (WRRFs) performing biological nitrogen removal (BNR) often require external carbon sources for meeting nitrogen discharge permit limits. This brings an additional financial burden to the facilities considering the continuous need of these external carbon sources. This paper evaluates the utilization of airport stormwater, which in the winter season is rich in aircraft deicing fluid (ADF) as an alternative external carbon source. Denitrification and nitrification bench scale experiments were performed to assess the efficacy of external carbon sources to remove nitrogen in WRRFs. Experimental results showed that ADFs achieve denitrification rates of 0.064–0.066 d−1, higher than what achieved by a commercial carbon source, MicroC 2000A, with corresponding value of 0.058 d−1 at low temperatures, as low as 13 °C, which is considered a worst-case scenario for nitrogen removal efficiency. Furthermore, no inhibition to nitrification associated with the ADFs was observed. Subsequently a dynamic modeling study was conducted to assess the performance of ADFs as external carbon sources for denitrification and compared them to the conventional source that was being used in a full-scale BNR process. Results from the dynamic modeling study revealed that if 40 % of the spent-ADF at LaGuardia airport, New York City, could be collected with the stormwater and conveyed to a WRRF via the sewer collection system, an approximate reduction of 30 % of the commercial external carbon source could be accomplished by repurposing a waste product. This study contributes to the potential of ADF as a denitrification aid and an alternative for commercially available carbon sources with comparable nitrogen removal efficiencies.

Insight into performance of nitrogen removal enhanced by adding lactic acid-rich food waste fermentation liquid as carbon source in municipal wastewater treatment

Lactic acid-rich fermentation liquid (LAFL) of food waste is found to act as a promising alternative carbon source for nitrogen removal in wastewater treatment. Here, LAFL was employed to investigate its impacts on nitrogen removal during raw municipal wastewater treatment with a comparison to sodium acetate (NaAc). Results indicated that nitrogen removals were comparable when incorporated with LAFL and NaAc (92.89 % v.s. 91.23 %). Unlike the utilization of NaAc, using LAFL could avoid suppressing the relative abundance of the nitrification genes and thus pose a negative risk to nitrogen removal during prolonged operation. The introduction of LAFL increased the stability and robustness of the functional microbial community and effectively reduced excess activated sludge (AS) generation by 109 % compared to NaAc addition, consequently enhancing nitrogen removal but diminishing the treatment cost. In general, LAFL exhibits prospective engineering application potentials and economic advantages in improving nitrogen removal by AS process.

Lactic Acid Production by Enterococcus durans Is Improved by Cell Recycling and pH Control

Lactic acid bacteria are widely used because they produce lactic acid naturally, are resistant to acidic pH and a wide temperature range, and frequently produce lactic acid as a primary metabolite. In this study, Enterococcus durans isolated from buffalo milk was employed in lactic acid fermentation with the primary goal of obtaining fermentation parameters for an effective process enabling the use of lactose as an alternative carbon source. Fermentative parameters such as initial concentration of carbon source, dissolved oxygen concentration, cell recycling, and batch with pulse operation mode were studied to find the best conditions for L-(+)-lactic acid production. The association of 20 g·L−1 of lactose with 10 g·L−1 of glucose enabled the best bioconversion to lactic acid. Anaerobiosis did not contribute to increasing lactic acid production. Batch fermentation with cell recycling was the strategy that enhanced lactic acid production and lactose consumption, reaching 26.07 g·L−1, 0.36 g·L−1·h−1 of productivity and yielding about 0.86 g·g−1. It is fundamental to evaluate the parameters of lactic acid fermentation and provide efficient and sustainable production methods.

DoE-based medium optimization for improved biosurfactant production with Aureobasidium pullulans.

Polyol lipids (a.k.a. liamocins) produced by the polyextremotolerant, yeast-like fungus Aureobasidium pullulans are amphiphilic molecules with high potential to serve as biosurfactants. So far, cultivations of A. pullulans have been performed in media with complex components, which complicates further process optimization due to their undefined composition. In this study, we developed and optimized a minimal medium, focusing on biosurfactant production. Firstly, we replaced yeast extract and peptone in the best-performing polyol lipid production medium to date with a vitamin solution, a trace-element solution, and a nitrogen source. We employed a design of experiments approach with a factor screening using a two-level-factorial design, followed by a central composite design. The polyol lipid titer was increased by 56% to 48gL-1, and the space-time yield from 0.13 to 0.20gL-1h-1 in microtiter plate cultivations. This was followed by a successful transfer to a 1L bioreactor, reaching a polyol lipid concentration of 41gL-1. The final minimal medium allows the investigation of alternative carbon sources and the metabolic pathways involved, to pinpoint targets for genetic modifications. The results are discussed in the context of the industrial applicability of this robust and versatile fungus.

Substrate Matters: Ionic Silver Alters Lettuce Growth, Nutrient Uptake, and Root Microbiome in a Hydroponics System.

Ionic silver (Ag+) is being investigated as a residual biocide for use in NASA spacecraft potable water systems on future crewed missions. This water will be used to irrigate future spaceflight crop production systems. We have evaluated the impact of three concentrations (31 ppb, 125 ppb, and 500 ppb) of ionic silver biocide solutions on lettuce in an arcillite (calcinated clay particle substrate) and hydroponic (substrate-less) growth setup after 28 days. Lettuce plant growth was reduced in the hydroponic samples treated with 31 ppb silver and severely stunted for samples treated at 125 ppb and 500 ppb silver. No growth defects were observed in arcillite-grown lettuce. Silver was detectable in the hydroponic-grown lettuce leaves at each concentration but was not detected in the arcillite-grown lettuce leaves. Specifically, when 125 ppb silver water was applied to a hydroponics tray, Ag+ was detected at an average amount of 7 μg/g (dry weight) in lettuce leaves. The increase in Ag+ corresponded with a decrease in several essential elements in the lettuce tissue (Ca, K, P, S). In the arcillite growth setup, silver did not impact the plant root zone microbiome in terms of alpha diversity and relative abundance between treatments and control. However, with increasing silver concentration, the alpha diversity increased in lettuce root samples and in the water from the hydroponics tray samples. The genera in the hydroponic root and water samples were similar across the silver concentrations but displayed different relative abundances. This suggests that ionic silver was acting as a selective pressure for the microbes that colonize the hydroponic water. The surviving microbes likely utilized exudates from the stunted plant roots as a carbon source. Analysis of the root-associated microbiomes in response to silver showed enrichment of metagenomic pathways associated with alternate carbon source utilization, fatty-acid synthesis, and the ppGpp (guanosine 3'-diphosphate 5'-diphosphate) stringent response global regulatory system that operates under conditions of environmental stress. Nutrient solutions containing Ag+ in concentrations greater than 31 ppb in hydroponic systems lacking cation-exchange capacity can severely impact crop production due to stunting of plant growth.

Abstract 1211 Determination of efficient alternative carbon sources for wastewater denitrification

Abstract 1211 Determination of efficient alternative carbon sources for wastewater denitrification

Response of Bacillus velezensis 83 to interaction with Colletotrichum gloeosporioides resembles a Greek phalanx-style formation: a stress resistant phenotype with antibiosis capacity

Plant growth-promoting rhizobacteria, such as Bacillus spp., establish beneficial associations with plants and may inhibit the growth of phytopathogenic fungi. However, these bacteria are subject to multiple biotic stimuli from their competitors, causing stress and modifying their development. This work is a study of an in vitro interaction between two model microorganisms of socioeconomic relevance, using population dynamics and transcriptomic approaches. Co-cultures of Bacillus velezensis 83 with the phytopathogenic fungus Colletotrichum gloeosporioides 09 were performed to evaluate the metabolic response of the bacteria under conditions of non-nutritional limitation. The bacterial response was associated with the induction of a stress-resistant phenotype, characterized by a lower specific growth rate, but with antimicrobial production capacity. About 12% of co-cultured B. velezensis 83 coding sequences were differentially expressed, including the up-regulation of the general stress response (sigB regulon), and the down-regulation of alternative carbon sources catabolism (glucose preference). Defense strategies in B. velezensis are a determining factor in order to preserve the long-term viability of its population. Mostly, the presence of the fungus does not affect the expression of antibiosis genes, except for those corresponding to surfactin/bacillomycin D production. Indeed, the up-regulation of antibiosis genes expression is associated with bacterial growth, regardless of the presence of the fungus. This behavior in B. velezensis 83 resembles the strategy used by the classical Greek phalanx formation: by sacrificing growth rate and metabolic versatility, resources can be redistributed to defense (stress resistant phenotype) while maintaining the attack (antibiosis capacity). The presented results are the first characterization of the molecular phenotype at the transcriptome level of a biological control agent under biotic stress caused by a phytopathogen without nutrient limitation.

Bioleaching for metals removal from mine tailings flotation fractions

This study investigated two bioleaching strategies for removing heavy metals from three mine tailings fractions generated by flotation processes. On the one hand, bioleaching with microbial consortia of acidophilic mesophiles and moderate thermophiles efficiently extracted Co, Cu, Zn, and As, while the leaching of Pb was facilitated through the use of organic acids produced by a heterotrophic bacterium and a fungus. Approximately 100% Co, 68% Zn, 63% As, and 31% Cu were bioleached with acidophilic mesophiles from the barite tailings (BT) sample after 14 days, whereas for the barite concentrate (BC) sample the results showed about 100% Co, 70% Zn and As, and 45% Cu removal at the same period. The sulfide concentrate (SC) sample underwent bioleaching with both consortia, acidophilic mesophiles and moderate thermophiles over 28 days. Approximately, 67% of Co, 28% of Zn, 56% of As, 28% of Cu, and 6% of Mn were extracted from the sample using mesophiles, whereas the leaching efficiency with the moderate thermophiles was about 72% of Co, 50% of Zn, 28% of As, 36% of Cu, and 5% of Mn in 20 L bioreactors. On the other hand, bioleaching of Pb was explored using the bacterium Gluconobacter oxydans and the fungus Penicillium simplicissimum for the production of gluconic acid and citric acid, respectively. Additionally, besides glucose-based media, glycerol and crystal sugar were tested as alternative and cheaper carbon sources. The metabolic activity of P. simplicissimum allowed a maximum Pb leaching of 39–43% from the BT sample in 28 days in glycerol-based medium, while for the BC sample, the maximum Pb extraction was around 60% in glucose-based medium. A lower extraction of Pb was achieved with G. oxydans for both samples. The maximum extraction of 34% and 39% of Pb was reached within 7 days when glucose was used as the carbon source. Further optimization should address both the enhancement of metals removal and – especially for the organic acid bioleaching – the reduction of costs related to media formulation and fungal biomass production on a larger scale.