Carbon Utilization Patterns Research Articles

Detection of Changes in Soil Microbial Community Physiological Profiles in Relation to Forest Types and Presence of Antibiotics Using BIOLOG EcoPlate.

Soil is home to microbiota with diverse metabolic activities. These microorganisms play vital roles in many ecological processes. Thus, the assessment of microbial functional diversity is an important quality indicator of soil ecosystems. In this study, we collected soil samples from three distinct forest habitats, i.e., an agroforest, a primary forest (PF), and a secondary forest, within the Angat Watershed Reservation in Bulacan, Northern Philippines. Community-level physiological profiling (CLPP) was done with the BIOLOG EcoPlate™ to analyze the responses of the soil microbial communities from the three forest habitats in the absence or presence of antibiotics. The BIOLOG EcoPlate represents 31 utilizable carbon sources. Based on the CLPP analysis, soil samples from the PF showed significantly higher utilization of most carbon sources than the other forest types (p < 0.05). Thus, less disturbed forest types constitute more functionally diverse microbial communities. The presence of antibiotics significantly decreased the carbon utilization patterns of the soil microbial communities (p < 0.05), indicating the possible use of CLPP in monitoring contamination in soil.

Fictibacillus fluitans sp. nov., isolated from freshwater pond.

A Gram-positive, aerobic, rod-shaped, spore-forming bacterium, designated NE201T, was isolated from a freshwater pond in Village Nerur, India. Growth was observed in the range of 15-45°C temperature with optimum at 30°C, pH range of 5-9 (optimum at 7.0), and at concentrations of NaCl ranging between 0 and 14% (optimum 0%, w/v). The 16S rRNA gene sequence showed the highest similarity with Fictibacillus enclensis NIO-1003T (JF893461) at 99.01% followed by F. rigui WPCB074T (EU939689) at 98.9% and F. solisalsi CGMCC 1.6854T (EU046268) at 98.66%. The digital DNA-DNA hybridization (dDDH) and orthoANI values for strain NE201T against F. enclensis NIO-1003T (GCA_900094955.1) were 33.7% and 87.68%, respectively. The phylogenetic analysis based on the 16S rRNA gene, 92 core genes derived from the genome, and 20 proteins involving over 20,236 amino acid positions revealed the distinct phylogenetic position of strain NE201T and the formation of a clearly defined monophyletic clade with F. enclensis. The strain NE201T showed a unique carbon utilization and assimilation pattern that differentiated it from F. enclensis NIO-1003T. The major fatty acids were anteiso -C15:0 (51.42%) and iso-C15:0 (18.88%). The major polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE, and diphosphatidylglycerol (DPG). The antiSMASH analyzed genome of NE201T highlighted its diverse biosynthetic potential, unveiling regions associated with terpene, non-ribosomal peptide synthetases (NRPS), lassopeptides, NI-siderophores, lanthipeptides (LAP), and Type 3 Polyketide Synthases (T3PKS). The overall phenotypic, genotypic, and chemotaxonomic characters strongly suggested that the strain NE201T represents a novel species of genus Fictibacillus for which the name Fictibacillus fluitans sp. nov. is proposed. The type strain is NE201T(= MCC 5285 = JCM 36474).

The relationship between soil bacteria carbon utilization and soil physicochemical properties

This study aimed to explore the relationship between carbon utilization pattern of soil bacterial communities and the soil physicochemical properties in temperate forest of Poland under two different climatic conditions. Ten different forest soils from three forest types (deciduous, mixed, and coniferous forest) were incubated in laboratory conditions in two temperatures: 10°C and 30 °C, through 8 months. The soil bacteria carbon utilization was investigated using Biolog® Eco plates. The number of carbon substrate decayed on Biolog® Eco plates declined after the incubation in all studied forest soils. The soil samples originating from deciduous forest which were highly distinct performance with others correlated to their soil properties which were also highly different. Several soil properties e.g. pH, C/N ratio, SOM and the relation with vegetation types were found affecting the carbon utilization by bacterial communities. However, in this study, the relation between soil bacterial communities carbon utilization with soil physicochemical properties is limited, as soil bacteria are characterized by the high ability to adapt.

Root exudates from weedy ryegrass hybrid type and selected crop plants affect soil microbial communities in two soil types of the Western Cape, South Africa

&lt;p&gt;All growing plant roots have the ability to produce root exudates to which soil microbes are attracted. The objective of this study was to utilise the Biolog EcoPlate™ system to indicate the impact of soil type on soil microbial communities in the rhizosphere following treatment with pot leachates that contain various plant root exudates. A greenhouse experiment was conducted in 2021 and repeated in 2022 from May until July (southern hemisphere) in this winter rainfall area with Mediterranean climatic conditions. This ensured that natural daylight hours in the greenhouse coincided with those experienced in the field by winter-growing crops, from seeding until maturity (May to October). Pot leachate that contained various plant root exudates from six donor plant species (wheat, barley, two lupine cultivars, ryegrass pasture type, and weedy ryegrass hybrid type) was utilised as treatment for respective recipient pots, in which wheat (&lt;em&gt;Triticum aestivum&lt;/em&gt; v. SST 027) was grown as a test plant. Recipient plants were grown in two sets of pots, each with two different soil types. Soil samples from recipient pots were used to inoculate the Biolog EcoPlate™ system, and the carbon utilisation patterns obtained in this process were compared to the soil microbial populations present in the soil samples collected prior to treatments. Pot leachate treatment effects on the two soil types differed. Similarly, the treatments had differential effects on the measured soil microbial populations of the recipient wheat plants. Results indicate that the pattern of substrate utilisation by the Biolog EcoPlate™ methodology indicates changes in the number of colony forming units in the soil. In this regard, it was clear that ryegrass pasture variety and weedy ryegrass hybrid type caused similar effects on the soil bacteria communities in the rhizosphere. It is concluded that the primary impact of soil type is distinct microbial communities as an important factor regulating plant and plant-microbe synergy. Secondly, due to the strong selective forces root exudates have on the soil microbiome, conspicuous microbial communities in the rhizosphere of each plant species will continue to develop over time.&lt;/p&gt;

Utilization of Low Molecular Weight Carbon Sources by Fungi and Saprolegniales: Implications for Their Ecology and Taxonomy

Contributions of fungal and oomycete communities to freshwater carbon cycling have received increasing attention in the past years. It has been shown that fungi and oomycetes constitute key players in the organic matter cycling of freshwater ecosystems. Therefore, studying their interactions with dissolved organic matter is crucial for understanding the aquatic carbon cycle. Therefore, we studied the consumption rates of various carbon sources using 17 fungal and 8 oomycete strains recovered from various freshwater ecosystems using EcoPlate™ and FF MicroPlate™ approaches. Furthermore, phylogenetic relationships between strains were determined via single and multigene phylogenetic analyses of the internal transcribed spacer regions. Our results indicated that the studied fungal and oomycete strains could be distinguished based on their carbon utilization patterns, as indicated by their phylogenetic distance. Thereby, some carbon sources had a higher discriminative strength to categorize the studied strains and thus were applied in a polyphasic approach. We concluded that studying the catabolic potential enables a better understanding of taxonomic relationships and ecological roles of fungal vs. oomycete strains.

Characterization of fungi isolated from cattle dung with potential lignocellulolytic activities

Agricultural wastes not only serve as sources of environmental pollutions, but also serve as magnificent source of plant nutrients and natural repositories of bio-tools especially fungi of industrial interest for lignocellulolytic enzymes production. However, residues management particularly in rice–wheat system is a tedious phenomenon due to narrow gap between harvesting and sowing of these two crops. Hence, microbial intervention is one of the key options that may use successfully for their management. Thus, cellulolytic fungi were isolated from the cattle dung collected from various locations for cellulose manufacturing. The cellulolytic property of fungal isolates was confirmed by plate screening assay based on yellow zone formation surrounding of fungal culture on Congo red agar medium plate owing to production of cellulase enzyme. The colony diameter, clear zone diameter and cellulolytic index showing in descending order of CRD3, CRD5, CRD6 and CRD10 isolates, but –glucosidase activity was greater in CRD3 and CRD5 while, the lowest was in CRD9. However, isolates CRD7, CRD8 and CRD10 exhibited greater biochemical and enzymatic activity than rest of the promising fungal isolates. Similarly, isolates CRD1 and CRD2 utilized most of carbon sources as carbon substrate, but CRD7, CRD8 and CRD10 could not utilized mannitol and cellulose as carbon substrate. Overall, isolate CRD10 showed as a promising isolate in respect of biochemical, carbon utilization pattern and enzymatic activity than rest of the promising isolates.

Effects of nutrients on the utilization pattern of photosynthetic inorganic carbon of the tropical &amp;lt;italic&amp;gt;Thalassia hemprichii&amp;lt;/italic&amp;gt;

<p indent="0mm">Studies on the utilization strategy of photosynthetic inorganic carbon of seagrass can reveal its ecological adaptation mechanism. <italic>Thalassia hemprichii</italic>, a widely distributed seagrass species in the Indo-Pacific and Atlantic coastal seas, needs to evolve several utilization patterns of inorganic carbon to adapt different environments and meet its growth, development and reproduction. However, the effect of nutrient on the photosynthetic inorganic carbon utilization strategy in seagrass is still unknown and further research is urgently needed. Therefore, using oxygen electrode technology, chlorophyll fluorescence technology, and non-invasive micro-test technology, this study examined the similarity and difference in the utilization patterns of photosynthetic inorganic carbon of <italic>T</italic>.<italic> hemprichii </italic>from two typical tropical seagrass beds (Tanmen, Hainan Island, and Yongxing Island, Xisha), that were affected by varying degrees of human activity. Experiments showed that the photosynthetic oxygen release rate, maximum relative electron transfer rate, and half-saturated light intensity of <italic>T</italic>.<italic> hemprichii</italic> in Yongxing Island waters were 24.95%, 24.54%, and 28.73% higher than the corresponding in Tanmen, Hainan Island. This indicated that the growth status of <italic>T</italic>.<italic> hemprichii</italic> in the waters of Yongxing Island was better with higher photosynthetic efficiency. The addition of acetazolamide (AZ) and ethoxyzolamide (EZ) significantly reduced the photosynthetic oxygen release rate of <italic>T</italic>.<italic> hemprichii</italic>, with an insignificant difference in the inhibition between AZ and EZ. This indicated that it mainly absorbed HCO₃⁻ via extracellular carbonic anhydrase catalysis. Meanwhile, hydroxymethyl (Tris) inhibited the photosynthetic oxygen release of <italic>T</italic>.<italic> hemprichii</italic> in Tanmen by up to 100% and decreased the maximum relative electron transfer rate and the H⁺ inward flow rate, implying a synergistic H⁺/HCO₃⁻ transport mode. On the other hand, the rate of photosynthetic oxygen release and the maximum electron transfer rate of <italic>T</italic>.<italic> hemprichii</italic> in Xisha did not change significantly with the addition of AZ and EZ, while Tris buffer inhibited photosynthetic oxygen release by up to 100% and significantly reduced the maximum electron transfer rate. This suggested <italic>T</italic>.<italic> hemprichii </italic>in Xisha mainly relied on the H⁺/HCO₃⁻ synergistic transport. Therefore, <italic>T</italic>.<italic> hemprichii </italic>could uptake inorganic carbon in an environment with greater anthropogenic activity, larger nutrient load and lower light availability on Hainan Island by catalyzing HCO₃⁻ into CO₂ with extracellular carbonic anhydrase and the H⁺/HCO₃⁻ synergistic transport. In contrast, <italic>T</italic>.<italic> hemprichii</italic> in an environment with less anthropogenic activity, lower nutrient loading, and greater light availability, relied chiefly on H⁺/HCO₃⁻ synergistic transport. Facing a relatively unfavorable high-nutrient and low-light growth environment, <italic>T</italic>.<italic> hemprichii</italic> could increase the photosynthetic inorganic carbon utilization strategy (such as the activity of extracellular carbonic anhydrase) to improve its utilization ability of inorganic carbon to overcome stress and growth limitation. This suggested that <italic>T</italic>.<italic> hemprichii</italic> could adjust its inorganic carbon utilization patterns according to its geographical environment. With the continuous development of technology, it is urgent to study the utilization mechanism of inorganic carbon of seagrass by applying seagrass omics technology and stable isotope tracing to deepen the understanding of the carbon sink function of seagrass.

Microcystin-LR exposure enhances toxin-degrading capacity and reduces metabolic diversity of sediment microbial communities

Substantial outbreaks of cyanobacterial harmful algal blooms (cyanoHABs) are accompanied by the prevalent existence of microcystins (MCs) in eutrophic freshwater worldwide, which can compromise the safety of aquatic ecosystems and public health. However, the response of the sediment microbial community to MCs exposure remains unclear. In this study, the sediment microbial communities of Lake Taihu were continuously exposed to environmentally relevant concentration (10 μg/L) of microcystin-LR (MC-LR) in microcosms for three months to mimic MCs contamination during cyanoHABs. Meanwhile, the MC-LR degradation characteristics, metabolic profiles, functional genes, and structures of microbial communities were analyzed periodically. The results showed that the MC-LR degradation capacities of microbial communities significantly increased with prolonged toxin exposure time. The enhanced MC-LR degradation rate was positively correlated with the increase in the abundance of mlr genes, which corresponds to the MC-degrading bacterial community. However, the MC-LR degradation pathway was maintained, and one new biodegradation intermediate (Adda-Glu) was first identified. Moreover, the metabolic profiles of the microbial communities indicated that overall carbon metabolic activity displayed a stimulation-suppression trend, and the exposure led to different carbon utilization patterns. Furthermore, microbial community structure analysis showed that long-term MC-LR exposure enriched microbes associated with MC degradation (Pseudomonas, Stenotrophomonas, Sphingopyxis and Sphingomonas) but inhibited MC-sensitive bacterial genera. This study clearly elucidates that MC-LR exposure alters the function, metabolism, and structure of the sediment microbial community to adapt to polluted environments.

Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup.

Two aerobic, Gram-stain variable, catalase-positive and oxidase-negative rods named strain UniB2T and UniB3T, were isolated from digestive syrup containing fungal diastase (10mg/ml), pepsin (2mg/ml) and sugar base containing polyethylene glycol. Based on 16S rRNA gene sequence analysis, strain UniB2T has the highest sequence similarity with Paenibacillus humicus NBRC 102415T (98.3%) and strain UniB3T showed the highest sequence similarity with Niallia circulans DSM 11T (98.9%). The DNA G + C content of UniB2T was 63.7mol %. The dDDH and ANI values between the strain UniB2T and its phylogenetically close relative were < 38.3% and < 89.5%, respectively. The major fatty acids of the strain UniB2T were C16:0 (13.9%), C15:0 anteiso (39.7%), C17:0 anteiso (15.5%). The DNA G + C content of UniB3T was 35.6mol %. The dDDH and ANI values between the strain UniB3T and its close relatives were < 29.1% and 84.6%, respectively. The major fatty acids of strain UniB3T were C16:0 (13.5%), C15:0 anteiso (40.1%) and C17:0 anteiso (16.0%). Major polar lipids for both strains were Diphosphatidylglycerol and phosphatidylethanolamine. Both strains showed unique carbon utilization and assimilation pattern that differentiated them from their phylogenetically related neighbours. These phenotypic, genotypic and chemotaxonomic characters indicated the strains UniB2T and UniB3T represent two novel species for which the names Paenibacillus albicereus sp. nov. (Type strain UniB2T = MCC 3997T = KCTC 43095T = JCM34513T) and Niallia alba sp. nov. (Type strain UniB3T = MCC 3998T = KCTC 43235T = JCM 34492T) are proposed.

Carbon sources supporting macrobenthic crustaceans in tropical eastern pacific mangroves

In tropical mangroves, crustaceans are one of the most relevant components in terms of abundance, occurrence, biomass, function, and human welfare. Since these organisms are involved in the trophic dynamics of mangroves and also, are important fishery resources, the study of carbon used by crustaceans in mangrove ecosystems is important to understand the food web functioning of mangroves and estuaries, and how energy and matter flow through these organisms, via their participation in different trophic pathways. We compared the isotopic composition (δ13C/δ15N) of carbon sources and macrobenthic crustacean species of three macrotidal (fringe, internal and external riverine) mangroves, located in the central Colombian Pacific, and used a Bayesian aproached to evaluate if geomorphology induces differences in the isotopic composition and in the relative contribution of primary producers to different species of macrobenthic crustaceans. Differences were found in the isotopic composition between the three systems, with 13C values generally enriched for the external riverine mangrove, indicating a marine influence. The relative contribution of microphytobenthos with respect to other primary sources was highest in the three mangrove systems, followed by mangrove and seston in the internal and external riverine respectively, and macroalgae in fringe system. However, differences were found in the contribution of all sources depending on the species and type of mangrove but trophic pathways of the systems are the same. Our results confirm part of the hypothesis of this research, showing that geomorphological configuration of the habitat induces significative differences in the isotopic composition of primary sources and macrobenthic crustaceans but, the carbon utilization patterns of macrobenthic crustaceans show the same main trophic pathways (mangroves and microphytobenthos) in all three systems, due to the similar availability of carbon sources despite geomorphological differences.

Mechanisms underlying interactions between two abundant oral commensal bacteria

Complex polymicrobial biofilm communities are abundant in nature particularly in the human oral cavity where their composition and fitness can affect health. While the study of these communities during disease is essential and prevalent, little is known about interactions within the healthy plaque community. Here we describe interactions between two of the most abundant species in this healthy microbiome, Haemophilus parainfluenzae and Streptococcus mitis. We discovered that H. parainfluenzae typically exists adjacent to mitis group streptococci in vivo with which it is also positively correlated based on microbiome data. By comparing in vitro coculture data to ex vivo microscopy we revealed that this co-occurrence is density dependent and further influenced by H2O2 production. We discovered that H. parainfluenzae utilizes a more redundant, multifactorial response to H2O2 than related microorganisms and that this system’s integrity enhances streptococcal fitness. Our results indicate that mitis group streptococci are likely the in vivo source of NAD for H. parainfluenzae and also evoke patterns of carbon utilization in vitro for H. parainfluenzae similar to those observed in vivo. Our findings describe mechanistic interactions between two of the most abundant and prevalent members of healthy supragingival plaque that contribute to their in vivo survival.

Optimized Tube Dilution Technique and Sole Carbon Utilization Assay for Anti-leptospiral In Vitro Screening of Plant Extracts

Introduction: Leptospirosis is one of the neglected reemerging zoonoses that is of public health concern globally. The need to discover novel therapeutic alternatives for leptospirosis through screening for and elucidating the mechanism/s of the anti-leptospiral activity of plant extracts is therefore necessary. This study analyzes the optimized tube dilution technique and the BiologTM sole carbon utilization phenotype microarray as screening tool for anti-leptospiral activity of plant extracts. Methods: The suitability of the optimized tube dilution technique was evaluated by determining the minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and motility inhibition property of a plant extract and an antimicrobial control (pen G) against 4 dominantly circulating Leptospira serovars/serogroup in the Philippines. Likewise, the suitability of the BiologTM sole carbon utilization assay was evaluated using a plant extract and selected antimicrobials against L. interrogans serovar Manilae strain K64 and L. interrogans serovar Losbanos strain K37. Results: The MIC, MBC, and motility inhibition property of a plant extract and the antibiotic controls as well as its effect on the carbon utilization phenome of the Leptospira serovars gave consistent results, within and between several runs. With standard deviation = 0 for all serovars. The MIC and MBC of the antimicrobial control (pen G), the positive control, was 10 ug/ml. The growth control (leptospires without treatment), the negative control, showed presence of motile leptospires. The MIC and the MBC of the test plant extract was 250 ug/ml – 500 ug/ml. Results of the carbon utilization phenome or pattern of carbon utilization were consistent within the 3 replicates and between two runs. Conclusion: The optimized tube dilution technique and the BiologTM sole carbon utilization assay is a potential in vitro screening tool for determining anti-leptospiral activity of plant extracts.

Carbon Catabolite Repression of Methyl Parathion Degradation in a Bacterial Isolate Characterized as a Cupriavidus sp. LMGR1

Among the mixture of carbon compounds, bacteria have the ability to select energetically efficient substrate as a preferred carbon source. This specific behavior often limits the use of pollutants as a secondary carbon source by bacteria grown with preferred carbon source and the pollutants. Therefore, to develop an efficient bioremediation technology for removal/degradation of organophosphorus pesticide methyl parathion (MP) from agricultural soils, a soil bacterial strain (LMGR1) capable of degrading MP and p-nitrophenol was isolated and identified as a Cupriavidus oxalaticus based on biochemical (carbon utilization pattern) and molecular analysis (16S rRNA gene sequence), but the phylogenetic analysis revealed a distinct position, and the name was designated as Cupriavidus sp. LMGR1. The effect of preferred carbon source on degradation was also investigated. The bacterium assimilated the pesticide as a sole source of carbon and consumes about 100 mg L−1 of MP within 6 to 7 h of incubation. Furthermore, the methyl parathion hydrolase (MPH) enzyme (localized in the periplasm of bacterium) activity was induced by the carbon deficiency instead of substrate. Determination of kinetic parameters, i.e., Vmax and Km for MPH enzyme in the extracted periplasmic protein indicated significant higher affinity towards the substrate. The reduced MPH activity in the bacterium grown in presence of preferred carbon source indicated the role of carbon catabolite repression in regulation of pesticide degradation. Thus, the bacterium has prodigious capability to be used as a bioremediation agent, but the availability of preferred carbon source may affect its potential in field application.

Illuminating microbial species-specific effects on organic matter remineralization in marine sediments.

Marine microorganisms play a fundamental role in the global carbon cycle by mediating the sequestration of organic matter in ocean waters and sediments. A better understanding of how biological factors, such as microbial community composition, influence the lability and fate of organic matter is needed. Here, we explored the extent to which organic matter remineralization is influenced by species-specific metabolic capabilities. We carried out aerobic time-series incubations of Guaymas Basin sediments to quantify the dynamics of carbon utilization by two different heterotrophic marine isolates (Vibrio splendidus 1A01; Pseudoalteromonas sp. 3D05). Continuous measurement of respiratory CO2 production and its carbon isotopic compositions (13 C and 14 C) shows species-specific differences in the rate, quantity and type of organic matter remineralized. Each species was incubated with hydrothermally-influenced versus unimpacted sediments, resulting in a ~2-fold difference in respiratory CO2 yield across the experiments. Genomic analysis indicated that the observed carbon utilization patterns may be attributed in part to the number of gene copies encoding for extracellular hydrolytic enzymes. Our results demonstrate that the lability and remineralization of organic matter in marine environments is not only a function of chemical composition and/or environmental conditions, but also a function of the microorganisms that are present and active.

Biochemical and molecular identification of Solanum lycopersicum L. temperature tolerant bacterial endophytes

Abstract Endophytes are non-pathogenic microorganisms and potential natural bio-inoculant that reside within internal tissues of plant, without causing any apparent symptoms of infection and improve the plant health through acquisition of nutrients. The endophytic bacteria were isolated from the roots of Solanum lycopersicum L. surviving at 45–47 °C in the month of June 2013. On the basis of morphological, biochemical, carbon utilization pattern by Biolog and 16S rRNA gene sequence analysis, the isolates were identified as Rhizobium pusense (MS-1), Bacillus flexus (MS-2), B. cereus (MS-3), Methylophilus flavus (MS-4) and Pseudomonas aeruginosa (MS-5). Most of the endophytic bacterial strains showed plant growth promoting traits activities such as phosphate solubilization, production of IAA, siderophore, ammonia, and nitrate reductase. Carbon sources and other chemicals utilization pattern observed with GEN III microplate of Biolog exhibited strains specific responses. Ten antibiotics discs and 96 wells PM 11C plates were used for their antibiotic sensitivity assay. All the strains were sensitive to chloramphenical, erythromycin, rifampicin, piperacillin, imipenam and gentamycin, while P. aeruginosa (MS-5) was resistant to penicillin, linezolid, and clotrimazole discs. This is first report of M. flavus, a facultative methylotroph as an endophyte of tomato plant.

Investigation of carbon substrate utilization patterns of three ureolytic bacteria

Abstract Bacteria have developed specific substrate utilization profiles which allow them to grow only under specific conditions. They assimilate different organic substrates as carbon and energy sources for their growth and biomass production. In this study the carbon substrate utilization patterns of three bacteria [Bacillus paramycoides (Isolate-3), Citrobacter sedlakii (Isolate-7), and Enterobacter bugadensis (Isolate-11)] were investigated using BIOLOG Gen III microPlate and API strip techniques. These techniques employ various carbon substrates to determine bacterial carbon utilization patterns more quickly, economically, and effectively. Subsequently, biochemical analysis using API 20NE test showed that the three bacterial species were positive for Nitrate reduction, Glucose fermentation, Urease activity, hydrolysis of Esculine, assimilation of N-acetyl-glucosamine, d -maltose and Potassium Gluconate. In addition, the three bacteria assimilated 19 carbon substrates ( d -Glucose, D-Sorbitol, Methyl Pyruvate, Dextrin, d -Maltose, d -Fructose, l -Alanine, l -lactic Acid, d -Gluconic Acid, d -Trehalose, d -Cellobiose, Glycerol, Glucuronamide, l -Glutamic Acid, N-Acetyl- d -Glucosamine, b-Gentiobiose, Acetic Acid, l -Serine, and Inosine) of BIOLOG Gen III MicroPlates. On the other hand, they were all unable to assimilate Tween-40, D-Arabitol, d -Lactic Acid, Methyl Ester, d -Fucose, Quinic Acid, and d -Aspartic Acid. Similarly, API 50CH carbohydrate fermentation analysis showed that the three bacteria intensively metabolized d -Ribose, d -Glucose, d -Fructose, N-Acetyl-Glucosamine, Arbutine, Esculine Citrate, d -Maltose, and d -Trehalose. It was also determined that none of the three bacteria could assimilate Erythritol, l -Xylose, D-Adonitol, Methyl-β- d -Xylopyranoside, l -Sorbose, Methyl-α- d -mannopyranoside, Amygdaline, Inuline, d -Melezitose, Amidon, Glycogene, Xylitol, d -turanose, d -Tagatose, d -Fucose, D-Arabitol, L-Arabitol, and Potassium 5-Ceto-Gluconate. The study revealed that Enterobacter bugadensis and Citrobacter sedlakii exhibited an intensive metabolic activity and strong metabolic correlation than Bacillus paramycoides.

Insight into a highly polymorphic endophyte isolated from the roots of the halophytic seepweed Suaeda salsa: Laburnicola rhizohalophila sp. nov. (Didymosphaeriaceae, Pleosporales)

We surveyed root endophytic fungi of the coastal halophyte Suaeda salsa and detected a population of a novel species that we described here as Laburnicola rhizohalophila sp. nov. No sexual sporulating structure was observed. Instead, it produced a large amount of thalloconidia, 0–1 transverse septa, hyaline to darkly pigmented, often peanut-shaped and sometimes dumbbell-shaped, both ends enlarged with numerous oil droplets inside the hyphal cells. Surprisingly, a high degree of phenotypic and physiological intraspecific variation (e.g., salinity tolerance, growth under different carbon:nitrogen ratios, and carbon utilization pattern) was recorded. The inoculation test indicated that the isolates could successfully infect host roots and form microsclerotia-like structures in cortical cells, a typical trait of dark septate endophytes (DSEs). Furthermore, most isolates were shown to promote host seedling growth. To evaluate conspecificity and infer its phylogenetic affinity, multiloci data including nuclear rRNA loci (ITS1 and 2, partial 28S), partial RNA Polymerase II second-largest subunit (rpb2), and partial translation elongation factor-1α (tef1) were characterized. Genealogical concordance phylogenetic species recognition (GCPSR) detected a genetically isolated clade of L. rhizohalophila within the Pleosporales in the Didymosphaeriaceae. Maximum likelihood phylogenetic reconstruction revealed that the endophytic fungus was genetically close to Laburnicoladactylidis but separated by a relatively long genetic distance. Our work highlights that the pleosporalean taxa might represent an underexplored reservoir of root DSEs.

A Clonal Shiga Toxin-Producing Escherichia coli O121:H19 Population Exhibits Diverse Carbon Utilization Patterns.

Shiga toxin-producing Escherichia coli (STEC) serotype O121:H19 is one of the major non-O157:H7 serotypes associated with severe human disease. Here we examined population structure, virulence potential, and metabolic profile of environmental STEC O121 strains recovered from a major produce production region in California and performed comparative analyses with STEC O121 clinical isolates. Multilocus sequence typing revealed that sequence type (ST)-655, a common ST in clinical strains, was the predominant genotype among the environmental strains. Phylotyping placed all STEC O121 strains in B1 group, a lineage containing other major non-O157 serogroups of STEC. Genes encoding different subtypes of Shiga toxin 1 and 2 were detected in O121, including stx1a, stx1d, stx2a, and stx2e. Furthermore, genes encoding intimin (eae) and enterohemolysin (ehxA) were detected in a majority of environmental strains (83.3%), suggesting that the majority of environmental STEC O121 strains are enterohemorrhagic E. coli. The STEC O121 strains with the same genotype were clustered together based on the carbon utilization pattern. Among the 122 carbon substrates that supported the growth of STEC O121 strains, 44 and 35 exhibited lineage (ST) and strain-specific metabolic profiles, respectively. Although clinical ST-655 strains displayed higher metabolic activity than environmental ST-655 strains for several carbon substrates, including l-alaninamide, 5-keto-d-gluconic acid, 3-O-β-d-galactopyranosyl-d-arabinose, α-ketoglutaric acid, and lactulose, a few environmental strains with the enhanced metabolic potential for the above substrates were detected. Variations in curli biogenesis and swimming motility were also observed in ST-655 strains, suggesting that phenotypic variants are widespread in STEC. Considering the ecological niches that STEC colonizes, increased metabolic potential for plant-derived carbohydrates, mucus-derived substrates, or secondary metabolites produced by the indigenous microorganisms might have been selected. Such traits would confer STEC competitive advantages and facilitate survival and adaptation of STEC population to a given niche, including infected humans.

Effects of di-n-butyl phthalate on rhizosphere and non-rhizosphere soil microbial communities at different growing stages of wheat

The potential effects of dibutyl phthalate (DBP) on soil ecosystems and biological processes have recently aroused great concern because of the ubiquitous nature of this pollutant. However, the effects of DBP-associated disturbance on rhizosphere and non-rhizosphere soil microbial communities remain poorly understood. In the present study, we investigated the effects of DBP contamination on microbial function and soil enzyme activities in rhizosphere and non-rhizosphere soils throughout the growing season of wheat. We conducted pot experiments under glasshouse conditions and used different concentrations of DBP: 10, 20, and 40 mg kg–1. We found that the average well color development value and McIntosh index in rhizosphere and non-rhizosphere soils increased in the 10 and 20 mg kg–1 DBP treatments, but declined in the 40 mg kg–1 DBP treatment at the seedling and tillering stages, particularly, in the non-rhizosphere soil. DBP addition enhanced the Shannon-Wiener and Simpson indexes in rhizosphere and non-rhizosphere soils throughout the growing period of wheat. A principal component analysis clearly differentiated the treatments from the control, indicating that DBP led to different patterns of potential carbon utilization in rhizosphere and non-rhizosphere soils. The microbial use of amino acids was significantly increased in rhizosphere and non-rhizosphere soils after DBP addition, while the use of carbohydrates was significantly declined (p < 0.05). The dehydrogenase, urease, and acid phosphatase activities were significantly stimulated (p < 0.05) at the seedling stage, while the phenol oxidase and β-glucosidase activities were inhibited. The 40 mg kg–1 DBP treatment significantly decreased the phenol oxidase and β-glucosidase activities in rhizosphere and non-rhizosphere soils at the seedling stage, particularly in non-rhizosphere soil (p < 0.05). The microbial function and soil enzymatic activities were gradually restored following the wheat growing stage. These results offer a better understanding of the effects of DBP on the activities and functional diversity of microbial communities in farmland soils.

Interstitial water microbial communities as an indicator of microbial denitrifying capacity in wood-chip bioreactors

The discharge from food production greenhouses (greenhouse effluent) contains high nutrient and salt concentrations, which, if directly released, can have adverse effects on the environment. Wood-chip bioreactors are increasingly popular passive water treatment systems favoured for their economical denitrification in treating agricultural field tile drainage. Microbial communities are central to denitrification; however little is known about the maturation of microbial communities in wood-chip bioreactors treating greenhouse effluents. In this study, multiple subsurface flow wood-chip bioreactors, each vegetated with a different plant species, together with an unplanted unit, received synthetic greenhouse effluent with elevated nitrate concentrations. The hybrid bioreactors were operated for over 2 years, during which time water samples were collected from the inlet, outlet and within the reactors. The increasing denitrification rate in the bioreactor planted with Typha angustifolia (narrowleaf cattail) correlated with increasing microbial activity and metabolic richness, measured by the carbon utilization patterns in Biolog® EcoPlates. Increased denitrifying gene (nirS) copies (determined by quantitative polymerase chain reaction, qPCR), and near-complete nitrate removal were observed in the T. angustifolia and unplanted reactors after 16 and 23 months of operation respectively. The findings suggested that an acclimation period of at least one year can be expected in unseeded bioreactors planted with T. angustifolia, while bioreactors without vegetation may require a longer time to maximize their denitrification capacity. These results are important for the design and operation of wood-chip bioreactors, which are expected to be more commonly applied in the future.