Utilization Of Different Carbon Sources Research Articles

Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™

The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years.Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H′), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H′ and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity.The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.

The Identification of a Strain for the Biological Purification of Soy Molasses to Produce Functional Soy Oligosaccharides and Optimize Purification Conditions.

Soy molasses is rich in oligosaccharides like sucrose, stachyose, and raffinose, with stachyose and raffinose being functional oligosaccharides. Harnessing soy molasses for the production of functional soy oligosaccharides (FSO) can significantly elevate its value. Biological purification, a method leveraging the selective utilization of different carbon sources by microorganisms, allows for the specific removal of sucrose from soy molasses while preserving stachyose and raffinose, thereby increasing the FSO content. This research identified a yeast named YT312 with strong purification capabilities for soy molasses and optimized the purification conditions. The study revealed that yeast YT312 was Wickerhamomyces anomalus, exhibiting a broad range of growth temperatures and pH levels alongside a high tolerance to glucose, sucrose, and NaCl. Through single-factor and orthogonal experiments, it was established that under specific conditions-0.375% inoculum size, 30 °C fermentation temperature, 150 rpm shaking speed, 10-fold dilution ratio, pH of 7, and 12 h of fermentation-sucrose was completely removed from soy molasses, while functional raffinose and stachyose were retained at rates of 96.1% and 90.2%, respectively. Consequently, W. anomalus YT312 displayed exceptional characteristics for the biological purification of soy molasses and the production of FSO.

Screening Bacterial Strains Capable of Producing 2,3-Butanediol: Process Optimization and High Diol Production by Klebsiella oxytoca FMCC-197

In the present investigation, the potential of various newly isolated strains which belong to the Enterobacteriaceae family to produce 2,3-butanediol (BDO), an important bio-based compound, was studied. The most interesting strain, namely Klebsiella oxytoca FMCC-197, was selected for further investigation. Commercial (raw) sucrose or molasses, which are important agro-industrial surpluses, were employed as carbon sources for most of the trials performed. Different fermentation parameters (viz. incubation te4mperature, utilization of different carbon sources, substrate inhibition, aeration) were tested to optimize the process. Fermentations under non-aseptic conditions were also conducted to investigate the potential of growth of the strain K. oxytoca FMCC-197 to surpass the growth of other microorganisms in the culture medium and produce BDO. Besides BDO production, in trials in which molasses was employed as the sole carbon source, significant color removal was observed simultaneously with the production of microbial metabolites. The very high BDO concentration ≈115 g L−1 was reported in approximately 64 h during a fed-batch bioreactor experiment, using sucrose and molasses as carbon sources at 30 °C, reaching a conversion yield (YBDO) of 0.40 g g−1 and a productivity rate (PBDO) of 1.80 g L−1 h−1, while similar results were also obtained at 37 °C. The strain demonstrated remarkable results in non-previously sterilized media, as it produced 58.0 g L−1 in 62 h during a fed-batch bioreactor experiment, while the potential to decolorize molasses-based substrates over 40% was also recorded. From the results obtained it is shown that this wild-type strain can be used in large-scale microbial BDO production using various raw materials as fermentative substrates. The wastewater derived after BDO fermentation by K. oxytoca FMCC-197 can be disposed relatively safely into the environment.

Pathogenicity analysis and comparative genomics reveal the different infection strategies between the generalist Metarhizium anisopliae and the specialist Metarhizium acridum.

The fungal genera Metarhizium contain many important multiple species that are used as biocontrol agents and as model organisms for exploring insect-fungal interactions. Metarhizium spp. exhibit different traits of pathogenicity, suggesting that the pathogenesis can be quite distinctive. However, the underlying differences in their pathogenesis remain poorly understood. Pathogenicity analysis showed that Metarhizium anisopliae (strain CQMa421) displayed higher virulence against oriental migratory locusts, Locusta migratoria manilensis (Meyen), than the acridid-specific specie Metarhizium acridum (strain CQMa102). Relative to M. acridum, M. anisopliae possessed a higher conidial hydrophobicity, increased ability to penetrate the host, accelerated growth under hypoxia and enhanced ability for the utilization of different carbon sources. Different distributions of carbohydrate epitopes at cell wall surface of M. anisopliae might also contribute to successful evasion of host immune defenses. Comparative genomics showed that M. anisopliae has 98 more virulence-related secreted proteins (133) than M. acridum (35), which can be functionally classified as hydrolases, virulence effectors, cell wall degradation and stress tolerance-related proteins, and helpful to the cuticle penetration and host internal environment adaption. In addition, differences in genomic clusters specifically related to secondary metabolites, including the clusters of Indole-NRPS hybrid, T1PKS-NRPS like hybrid, Betalactone, Fungal-Ripp and NRPS-Terpene hybrid, may lead to differences in core virulence-related secondary metabolite genes in M. acridum (18) and M. anisopliae (36). The comparative study provided new insights into the different infection strategies between M. anisopliae and M. acridum, and further facilitate the identification of virulence-related genes for the improvement of mycoinsecticides. © 2023 Society of Chemical Industry.

Streptococcus thermophilus JM905-Strain Carbon Source Utilization and Its Fermented Milk Metabolic Profile at Different Fermentation Stages.

The metabolic utilization of different carbon sources by Streptococcus thermophilus JM905(S. thermophilus JM905) was determined using a high-throughput microbial phenotyping system, and changes in fermentation characteristics of S. thermophilus JM905 fermented milk were investigated at different fermentation periods, with changes in pH, water-holding capacity, viscosity, nuisance odor, and viable bacteria count being used to define the fermentation characteristics of the strain. Changes in the key metabolites, 2-hydroxybutyric acid, folic acid, L-lactic acid, D-glycerol-D-galactose-heptanol, (R)-leucine, L-aspartic acid, L-proline, D-arginine, L-isoleucine, hydra starch, L-lysine, L-tryptophan, and D-galactose, were clarified. Correspondingly, the fermented milk protein, amino acid, and fermented milk fat quality nutrient contents were determined to be 3.78 ± 0.054 g per 100 g, 3.405 ± 0.0234 g per 100 mL, and 0.161 ± 0.0030 g per 100 g, respectively. This study addressed strain carbon source utilization, changes in fermentation characteristics and metabolites during fermentation, with the aim of investigating the link between fermentation characteristics and metabolite quality components of Streptococcus thermophilus JM905 and its fermented milk with fermentation potential and to provide a useful reference for the screening of superior fermentation strains.

A New Mechanism of Carbon Metabolism and Acetic Acid Balance Regulated by CcpA.

Catabolite control protein A (CcpA) is a critical regulator in Gram-positive bacteria that orchestrates carbon metabolism by coordinating the utilization of different carbon sources. Although it has been widely proved that CcpA helps prioritize the utilization of glucose over other carbon sources, this global regulator's precise mechanism of action remains unclear. In this study, a mutant Bacillus licheniformis deleted for CcpA was constructed. Cell growth, carbon utilization, metabolites and the transcription of key enzymes of the mutant strain were compared with that of the wild-type one. It was found that CcpA is involved in the regulation of glucose concentration metabolism in Bacillus. At the same time, CcpA regulates glucose metabolism by inhibiting acetic acid synthesis and pentose phosphate pathway key gene zwF. The conversion rate of acetic acid is increased by about 3.5 times after ccpA is deleted. The present study provides a new mechanism of carbon metabolism and acetic acid balance regulated by CcpA. On the one hand, this work deepens the understanding of the regulatory function of CcpA and provides a new view on the regulation of glucose metabolism. On the other hand, it is helpful to the transformation of B. licheniformis chassis microorganisms.

Transcriptomic analysis of biofilm formation by Bacillus cereus under different carbon source conditions

Abstract Background Previous studies found differences in the utilization of different carbon sources during biofilm formation by Bacillus cereus. Illumina HiSeq high-throughput sequencing technology was used to investigate the changes in gene transcript levels in Bacillus cereus biofilm bacteria under different carbon source conditions. Results Compared with the control group, the number of differentially expressed genes in the glucose, maltose, lactose, and skim milk-supplemented groups was 351, 1136, 133, and 487, respectively. The results showed that the pathways involved in the differentially expressed genes were mainly distributed in glycolysis and pentose phosphate pathway, tricarboxylic acid cycle, amino acid metabolism, and fatty acid metabolism. The gene expression of enzymes related to acetoin synthesis from pyruvate was mostly upregulated in the glucose-supplemented group. The gene expression of enzymes related to pyruvate synthesis of branched-chain amino acids in the maltose-supplemented group was mostly upregulated. In the lactose-supplemented group, the gene expression of acetoin biosynthesis from pyruvate was upregulated. Pyruvate production through glycolysis pathway increased in the skim milk-supplemented group, but the metabolic capacity of the tricarboxylic acid cycle did not change significantly. Conclusion The content of pyruvate stored by Bacillus cereus biofilm bacteria through glycolysis or pentose phosphate pathway increased, but the carbon flux into the tricarboxylic acid cycle did not increase, which suggested that carbon fluxes in the extracellular polysaccharide synthesis pathway of the biofilm may be increased, resulting in increased biofilm biomass formation.

[Effects of the Transformation from Natural Alpine Grassland to Mixed Artificial Grassland on the Characteristics of Soil Microbial Community].

This study aimed to analyze the effects of the transformation from natural alpine grassland (NAG) to mixed artificial grassland (MAG) on the characteristics of soil microbial community. We used Illumina Miseq high-throughput sequencing technology to investigate the soil microbial community of natural grassland and mixed artificial grassland. The results showed that plant diversity and the content of soil organic matter decreased significantly from NAG to MAG. In total, 29 and 11 phyla bacteria and fungi were detected, respectively. Compared with that in NAG, the Shannon indexes of the bacterial community increased significantly in MAG (from 9.51 to 9.89), whereas these differences were not significant between the NAG and MAG fungal community. The structure and composition of the soil microbial community showed significant differences between NAG and MAG. In addition, Mantel test results suggested that soil total organic matter, total nitrogen, and soil moisture were significantly correlated with variations in the bacterial community, and soil total organic matter and soil moisture were significantly correlated with variations in fungal community. The results of linear discriminant analysis (LEfSe) indicated that Atribacteria and Ascomycota microorganisms could be considered as the indicator groups for NAG, whereas Gemmata and Trichocomaceae microorganisms could be considered as the indicator groups for MAG. Tax4Fun2 results showed that the transition from NAG to MAG affected the utilization of different carbon sources by bacteria.

Optimization of medium composition of Lactobacillus plantarum Y44 using Plackett–Burman and Box–Behnken designs

The biomass of Lactobacillus strains depends on the culture media and culture conditions. The purpose of this study was to optimize the culture medium composition and culture conditions of Lactobacillus plantarum Y44 to improve its biomass. The utilization of different carbon sources and nitrogen sources by L. plantarum Y44 was assessed by single factor experiment to screen out the economical carbon and nitrogen sources for L. plantarum Y44 growth. Through optimization experiments, the optimized culture medium for L. plantarum Y44 growth consists of soybean peptone 44.1 g/L, yeast extract 22.1 g/L, sucrose 35.6 g/L, hydrogen diamine citrate 2 g/L, anhydrous sodium acetate 8.5 g/L, dipotassium hydrogen phosphate 4 g/L, Tween-80 2 mL/L, manganese sulfate 0.25 g/L, and magnesium sulfate 0.58 g/L, and the initial pH 6.7. The concentration of viable bacteria cells of L. plantarum Y44 culturing in the optimized medium at 37 °C for 16 h was up to 3.363 × 1010 CFU/mL, as 6.11 times higher than that in the MRS medium.

Carbon Source Utilisation as a Basis of Variability among Different Ramularia Isolates Collected from Cotton Belt of Odisha, India

The impact of various carbon sources on the growth and sporulation of six different Ramularia isolates was investigated by testing eight different sources of carbon in liquid Richard's medium. The mycelial growth was assessed by determining the dry biomass weight, and there were three replicate flasks for each combination of isolates and carbon source. The study showed that the extent of utilization of different carbon sources varied among the isolates, and the highest mean dry biomass weight was recorded by RGKN1 followed by RGGNPR1. Maltose and sucrose were found to be the best source of carbon supporting highest mycelial growth and sporulation. Starch and lactose supported the least mycelial growth and sporulation. The results clearly established the essentiality of carbon source for metabolic activities of the fungus. The study proved the existence of cultural variability among the Ramularia isolates basing on their carbon utilisation.

Utilization of Different Carbon Sources by Nordic Microalgae Grown Under Mixotrophic Conditions

Microalgae are promising candidates for sustainable wastewater treatment coupled to the production of biofuel, bioplastic and/or bio-fertilizers. In Nordic countries, however, light is a limiting factor for photosynthesis and biomass production during the winter season. Compared to municipal wastewater, industrial wastewater streams from the pulp and paper industry contain lower amounts of nitrogen, but high concentrations of carbon sources, which could be utilized by microalgae to enhance biomass production in limiting light. This study focused on the utilization of methanol, glycerol and xylose by five different Nordic microalgae [Chlorella vulgaris (13–1), Coelastrella sp. (3–4), Desmodesmus sp. (2–6), Chlorococcum sp. (MC1) and Scotiellopsis reticulata (UFA-2)] grown under mixotrophic conditions. Two of these strains, i.e., Chlorococcum sp. (MC1) and Scotiellopsis reticulata (UFA-2) were able to grow in the presence of xylose or methanol at concentrations of 6 g L–1, or 3%, respectively, in a 12/12 h day/night cycle. HPLC analysis confirmed the consumption of those substrates. Glycerol (2.3 g L–1) was tolerated by all strains and increased growth for Chlorella vulgaris (13–1), while higher concentrations (20 g L–1) were only tolerated by Chlorococcum sp. (MC-1). Fourier-transform infrared spectroscopy, performed after growth in presence of the dedicated carbon source, indicated an increase in the fingerprint region of the carbohydrate fraction. This was particularly the case for Chlorococcum sp. (MC1), when grown in presence of glycerol, and Scotiellopsis reticulata (UFA-2), when grown in presence of xylose. Therefore, these strains could be potential candidates for the production of biofuels, e.g., bioethanol or biogas. We could show that Nordic microalgae are able to grow on various carbon sources; the actual uptake rates are low during a 12/12 h day/night cycle requesting additional optimization of the cultivation conditions. Nonetheless, their potential to use pulp and paper waste-streams for cheap and sustainable biomass production is high and will support the development of new technologies, turning waste-streams into resources in a circular economy concept.

Repurposing brewery contaminant yeast as production strains for low-alcohol beer fermentation.

A number of fungal isolates were recently obtained from a survey of the microbiota of multiple breweries and brewery products. Here, we sought to explore whether any of these brewery contaminants could be repurposed for beneficial use in beer fermentations, with particular focus on low-alcohol beer. There were 56 yeast strains first screened for the utilization of different carbon sources, ability to ferment brewer's wort, and formation of desirable aroma compounds. A number of strains appeared maltose-negative and produced desirable aromas without obvious off-flavours. These were selected for further scaled-up wort fermentations. The selected strains efficiently reduced wort aldehydes during fermentation, thus eliminating undesirable wort-like off-flavours, and produced a diverse volatile aroma profile. Two strains, Trigonopsis cantarellii and Candida sojae, together with a commercial Saccharomycodes ludwigii reference strain, were selected for 30-L-scale wort fermentations based on aroma profile and similarity to a commercial reference beer during sensory analysis using projective mapping. Both strains performed comparably to the commercial reference, and the T.cantarellii strain in particular, produced low amounts of off-flavours and a significantly higher amount of the desirable monoterpene alcohol trans-geraniol. The strain was also sensitive to common food preservatives and antifungal compounds and unable to grow at 37°C, suggesting it is relatively easily controllable in the brewery, and appears to have low risk of pathogenicity. This study shows how the natural brewery microbiota can be exploited as a source of non-conventional yeasts for low-alcohol beer production.

Rewiring the microbial metabolic network for efficient utilization of mixed carbon sources.

Carbon sources represent the most dominant cost factor in the industrial biomanufacturing of products. Thus, it has attracted much attention to seek cheap and renewable feedstocks, such as lignocellulose, crude glycerol, methanol, and carbon dioxide, for biosynthesis of value-added compounds. Co-utilization of these carbon sources by microorganisms not only can reduce the production cost but also serves as a promising approach to improve the carbon yield. However, co-utilization of mixed carbon sources usually suffers from a low utilization rate. In the past few years, the development of metabolic engineering strategies to enhance carbon source co-utilization efficiency by inactivation of carbon catabolite repression has made significant progress. In this article, we provide informative and comprehensive insights into the co-utilization of two or more carbon sources including glucose, xylose, arabinose, glycerol, and C1 compounds, and we put our focus on parallel utilization, synergetic utilization, and complementary utilization of different carbon sources. Our goal is not only to summarize strategies of co-utilization of carbon sources, but also to discuss how to improve the carbon yield and the titer of target products.

Diversity of Bacteria in Ants (Hymenoptera: Formicidae) from Canopy and Understory of Selected Trees at Mount Makiling Forest Reserve, Laguna, Philippines

The Mount Makiling Forest Reserve (MMFR) is a biodiversity hotspot and listed as one of the 170 conservation priority areas established by the Philippine government. Its flora and fauna diversity has been reported, but knowledge gap has been identified concerning the bacterial communities associated with the flora and fauna. This study focused on ants (Hymenoptera: Formicidae), which are dominant in forest canopy and play essential roles in the ecosystem functionality. A metagenomic sequencing approach based on amplified V3–V4 regions of the 16S rRNA was employed to investigate the bacterial communities associated with five arboreal ant species collected from MMFR. The collected ants were identified as Dolichoderus thoracicus, Myrmicaria sp., Colobopsis leonardi, Polyrhachis mindanaensis, and Polyrhachis semiinermis. The sequence analyses revealed that Proteobacteria, Spirochaetes, Firmicutes, Bacteroides, and Actinobacteria were the most abundant phyla. Individual analysis of the bacterial genera associated with the five ant species showed that unclassified members of Rhizobiaceae, Orbaceae, and Burkholderiaceae were dominant in D. thoracicus. Unclassified members of Rhizobiaceae, Spirochaetaceae, and Ruminococcaceae were dominant in Myrmicaria sp. On the other hand, Candidatus Blochmannia, and Wolbachia were abundant in Camponotini ants C. leonardi, P. mindanaensis, and P. semiinermis. Bray-Curtis distance and UPGMA cluster analyses showed that the microbiomes of the Camponotini group clustered together, while D. thoracicus and Myrmicaria sp. exhibited unique bacterial profiles. Predictive gene profile analysis showed that the most functional categories were those associated with metabolism and biosynthesis of amino acids, pathways for metabolism of nucleotide, amino sugars and nitrogen, and utilization of different carbon sources.

Two Homologues of the Global Regulator Csr/Rsm Redundantly Control Phaseolotoxin Biosynthesis and Virulence in the Plant Pathogen Pseudomonas amygdali pv. phaseolicola 1448A.

The widely conserved Csr/Rsm (carbon storage regulator/repressor of stationary-phase metabolites) post-transcriptional regulatory system controls diverse phenotypes involved in bacterial pathogenicity and virulence. Here we show that Pseudomonas amygdali pv. phaseolicola 1448A contains seven rsm genes, four of which are chromosomal. In RNAseq analyses, only rsmE was thermoregulated, with increased expression at 18 °C, whereas the antagonistic sRNAs rsmX1, rsmX4, rsmX5 and rsmZ showed increased levels at 28 °C. Only double rsmA-rsmE mutants showed significantly altered phenotypes in functional analyses, being impaired for symptom elicitation in bean, including in planta growth, and for induction of the hypersensitive response in tobacco. Double mutants were also non-motile and were compromised for the utilization of different carbon sources. These phenotypes were accompanied by reduced mRNA levels of the type III secretion system regulatory genes hrpL and hrpA, and the flagellin gene, fliC. Biosynthesis of the phytotoxin phaseolotoxin by mutants in rsmA and rsmE was delayed, occurring only in older cultures, indicating that these rsm homologues act as inductors of toxin synthesis. Therefore, genes rsmA and rsmE act redundantly, although with a degree of specialization, to positively regulate diverse phenotypes involved in niche colonization. Additionally, our results suggest the existence of a regulatory molecule different from the Rsm proteins and dependent on the GacS/GacA (global activator of antibiotic and cyanide production) system, which causes the repression of phaseolotoxin biosynthesis at high temperatures.

The High Osmolarity Glycerol Mitogen-Activated Protein Kinase regulates glucose catabolite repression in filamentous fungi.

The utilization of different carbon sources in filamentous fungi underlies a complex regulatory network governed by signaling events of different protein kinase pathways, including the high osmolarity glycerol (HOG) and protein kinase A (PKA) pathways. This work unraveled cross-talk events between these pathways in governing the utilization of preferred (glucose) and non-preferred (xylan, xylose) carbon sources in the reference fungus Aspergillus nidulans. An initial screening of a library of 103 non-essential protein kinase (NPK) deletion strains identified several mitogen-activated protein kinases (MAPKs) to be important for carbon catabolite repression (CCR). We selected the MAPKs Ste7, MpkB, and PbsA for further characterization and show that they are pivotal for HOG pathway activation, PKA activity, CCR via regulation of CreA cellular localization and protein accumulation, as well as for hydrolytic enzyme secretion. Protein-protein interaction studies show that Ste7, MpkB, and PbsA are part of the same protein complex that regulates CreA cellular localization in the presence of xylan and that this complex dissociates upon the addition of glucose, thus allowing CCR to proceed. Glycogen synthase kinase (GSK) A was also identified as part of this protein complex and shown to potentially phosphorylate two serine residues of the HOG MAPKK PbsA. This work shows that carbon source utilization is subject to cross-talk regulation by protein kinases of different signaling pathways. Furthermore, this study provides a model where the correct integration of PKA, HOG, and GSK signaling events are required for the utilization of different carbon sources.

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

BackgroundThe genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus.ResultsIn this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains.ConclusionsGenome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.

Fungicide azoxystrobin induced changes on the soil microbiome

Azoxystrobin is a widely used systemic fungicide in the Northeast of China, but it is unclear how azoxystrobin impacts the soil microbiome. Thus, we studied the impact of azoxystrobin on the microbial community structure and function in Chinese Spodosols. Field soil that had never been exposed to azoxystrobin was amended in laboratory batch experiments with 0 mg kg-1, 2 mg kg-1, 25 mg kg-1 and 50 mg kg-1 of azoxystrobin. Four soil enzymes (urease, invertase, phosphatase and catalase) were monitored to assess the impact of azoxystrobin on carbon, nitrogen and phosphorus cycling as well as the microbial activity. The results show that the urease, invertase, and phosphatase (hydrolytic enzymes) activities was inhibited by as little as 2 mg kg−1 of azoxystrobin after 35 days, whereas the catalase (oxidoreductase enzyme) activity was promoted by the same concentration in most cases. Biolog Ecoplate analysis indicated that the utilization of different carbon sources was inhibited by azoxystrobin. 16S rRNA sequencing showed the bacterial operational taxonomic unit richness and the Shannon index decreased with increasing azoxystrobin concentration. Relative abundances of Sphingomonas decreased while Amycolatopsis and Sphingomonas increased by addition of increasing levels of azoxystrobin. In conclusion, azoxystrobin application to Spodosols leads to reduced urease, invertase, and phosphatase activities, which can impact nutrient cycling and carbon utilization. Furthermore, azoxystrobin application changed the microbiome community structure.

Resistance to pentamidine is mediated by AdeAB, regulated by AdeRS, and influenced by growth conditions in Acinetobacter baumannii ATCC 17978.

In recent years, effective treatment of infections caused by Acinetobacter baumannii has become challenging due to the ability of the bacterium to acquire or up-regulate antimicrobial resistance determinants. Two component signal transduction systems are known to regulate expression of virulence factors including multidrug efflux pumps. Here, we investigated the role of the AdeRS two component signal transduction system in regulating the AdeAB efflux system, determined whether AdeA and/or AdeB can individually confer antimicrobial resistance, and explored the interplay between pentamidine resistance and growth conditions in A. baumannii ATCC 17978. Results identified that deletion of adeRS affected resistance towards chlorhexidine and 4’,6-diamidino-2-phenylindole dihydrochloride, two previously defined AdeABC substrates, and also identified an 8-fold decrease in resistance to pentamidine. Examination of ΔadeA, ΔadeB and ΔadeAB cells augmented results seen for ΔadeRS and identified a set of dicationic AdeAB substrates. RNA-sequencing of ΔadeRS revealed transcription of 290 genes were ≥2-fold altered compared to the wildtype. Pentamidine shock significantly increased adeA expression in the wildtype, but decreased it in ΔadeRS, implying that AdeRS activates adeAB transcription in ATCC 17978. Investigation under multiple growth conditions, including the use of Biolog phenotypic microarrays, revealed resistance to pentamidine in ATCC 17978 and mutants could be altered by bioavailability of iron or utilization of different carbon sources. In conclusion, the results of this study provide evidence that AdeAB in ATCC 17978 can confer intrinsic resistance to a subset of dicationic compounds and in particular, resistance to pentamidine can be significantly altered depending on the growth conditions.

Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages

Abstract. Isotopes of dissolved inorganic carbon (DIC) are used to indicate both transit times and biogeochemical evolution of groundwaters. These signals can be complicated in carbonate aquifers, as both abiotic (i.e., carbonate equilibria) and biotic factors influence the δ13C and 14C of DIC. We applied a novel graphical method for tracking changes in the δ13C and 14C of DIC in two distinct aquifer complexes identified in the Hainich Critical Zone Exploratory (CZE), a platform to study how water transport links surface and shallow groundwaters in limestone and marlstone rocks in central Germany. For more quantitative estimates of contributions of different biotic and abiotic carbon sources to the DIC pool, we used the NETPATH geochemical modeling program, which accounts for changes in dissolved ions in addition to C isotopes. Although water residence times in the Hainich CZE aquifers based on hydrogeology are relatively short (years or less), DIC isotopes in the shallow, mostly anoxic, aquifer assemblage (HTU) were depleted in 14C compared to a deeper, oxic, aquifer complex (HTL). Carbon isotopes and chemical changes in the deeper HTL wells could be explained by interaction of recharge waters equilibrated with post-bomb 14C sources with carbonates. However, oxygen depletion and δ13C and 14C values of DIC below those expected from the processes of carbonate equilibrium alone indicate considerably different biogeochemical evolution of waters in the upper aquifer assemblage (HTU wells). Changes in 14C and 13C in the upper aquifer complexes result from a number of biotic and abiotic processes, including oxidation of 14C-depleted OM derived from recycled microbial carbon and sedimentary organic matter as well as water–rock interactions. The microbial pathways inferred from DIC isotope shifts and changes in water chemistry in the HTU wells were supported by comparison with in situ microbial community structure based on 16S rRNA analyses. Our findings demonstrate the large variation in the importance of biotic as well as abiotic controls on 13C and 14C of DIC in closely related aquifer assemblages. Further, they support the importance of subsurface-derived carbon sources like DIC for chemolithoautotrophic microorganisms as well as rock-derived organic matter for supporting heterotrophic groundwater microbial communities and indicate that even shallow aquifers have microbial communities that use a variety of subsurface-derived carbon sources.