Carbon Substrate Utilization Research Articles

Bacterial functional responses to environmental variability: a case study in three distinct mountain lakes within a single watershed

The utilization of carbon substrates (CSs) is crucial for the functioning of heterotrophic bacterial communities and aquatic ecosystems. This study used the Biolog EcoplateTM technique to explore spatial and temporal community-level physiological profiles (CLPPs) of bacteria in three eutrophic-dystrophic mountain lakes in Bulgaria. Bacterial metabolic activity varied among the lakes, being highest in the lake dominated by phytoplankton and lowest in the lake dominated by macrophyte primary producers. CLPP highlighted specific bacterial metabolic preferences to certain carbon guilds (CGs), showing a higher affinity for carbohydrates and polymers and lower preferences for amino acids and amines. The overall metabolic dissimilarity among the lakes was approximately 32%, primarily driven by the CGs of amino acids and amines. The most preferred CSs included the carbohydrates D-Mannitol and N-Acetyl-D-glucosamine, and the carboxylic acid D-Galacturonic acid. Bacterial functional diversity was high (H′: 3.18 − 3.33) due to the high evenness of CS utilization. Multidimensional analyses revealed significant influences of lake-specific characteristics, sampling month, and the interaction between these factors on CLPP patterns. Nutrients and water temperature were identified as the most influential environmental factors affecting bacterial communities. This study enhances our understanding of bacterial functional responses to changing environments, demonstrating the effectiveness of the Biolog EcoplateTM technique in providing insights into these changes.

Pile burns as a proxy for high severity wildfire impacts on soil microbiomes

Wildfires in the western US are increasing in frequency, size, and severity. These disturbances alter soil microbiome structure and function, with greater fire severity leading to more pronounced impacts to bacterial, archaeal, and fungal communities. These changes have implications for the provisioning of microbially-mediated ecosystem services (e.g., carbon sequestration, clean water supplies) typically associated with forested watersheds. Challenges in sampling wildfire-impacted areas immediately post-burn have limited our assessment of short-term (i.e., days to weeks) changes in the soil microbiome and understanding of how microbial populations may influence post-fire biogeochemistry and ecosystem recovery. The identification of potential high severity wildfire proxies may help address some of these knowledge gaps. One potential proxy is pile burns scars, which are produced from a set of common techniques for fuel disposal and site preparation in conifer forests throughout the western US and beyond. We sampled depth-resolved layers from fire-impacted soil and combusted litter and woody materials in a series of recent pile burn scars near West Yellowstone, Montana and nearby unburned mineral soil controls to assess whether the pile burn scars exhibited microbial signatures characteristic of forest soils impacted by recent high severity wildfire. Changes in soil carbon and nitrogen chemistry and patterns of microbial alpha and beta diversity broadly aligned with those observed following wildfire, particularly the enrichment of so-called ‘pyrophilous’ taxa. Furthermore, many of the taxa enriched in burned soils likely encoded putative traits that benefit microorganisms colonizing these environments, such as the potential for fast growth or utilization of pyrogenic carbon substrates. We suggest that pile burn scars may represent a useful proxy along the experimental gradient from muffle furnace or pyrocosm studies to largescale prescribed burns in the field to advance understanding of the soil (and related layers, like ash) microbiome following high severity wildfires, particularly when coupled with experimental manipulation. Finally, we discuss existing research gaps that experimentally manipulated pile burns could be utilized to address.

An inclusive study to elucidation the heavy metals-derived ecological risk nexus with antibiotic resistome functional shape of niche microbial community and their carbon substrate utilization ability in serpentine soil

Heavy metals (HMs) contained terrestrial ecosystems are often significantly display the antibiotic resistome in the pristine area due to increasing pressure from anthropogenic activity, is complex and emerging research interest. This study investigated that impact of chromium (Cr), nickel (Ni), cobalt (Co) concentrations in serpentine soil on the induction of antibiotic resistance genes and antimicrobial resistance within the native bacterial community as well as demonstrated their metabolic fingerprint. The full-length 16S-rRNA amplicon sequencing observed an increased abundance of Firmicutes, Actinobacteriota, and Acidobacteriota in serpentine soil. The microbial community in serpentine soil displayed varying preferences for different carbon sources, with some, such as carbohydrates and carboxylic acids, being consistently favored. Notably, 27 potential antibiotic resistance opportunistic bacterial genera have been identified in different serpentine soils. Among these, Lapillicoccus, Rubrobacter, Lacibacter, Chloroplast, Nitrospira, Rokubacteriales, Acinetobacter, Pseudomonas were significantly enriched in high and medium HMs concentrated serpentine soil samples. Functional profiling results illustrated that vancomycin resistance pathways were prevalent across all groups. Additionally, beta-lactamase, aminoglycoside, tetracycline, and vancomycin resistance involving specific bio-maker genes (ampC, penP, OXA, aacA, strB, hyg, aph, tet(A/B), otr(C), tet(M/O/Q), van(A/B/D), and vanJ) were the most abundant and enriched in the HMs-contaminated serpentine soil. Overall, this study highlighted that heavy-metal enriched serpentine soil is potential to support the proliferation of bacterial antibiotic resistance in native microbiome, and might able to spread antibiotic resistance to surrounding environment.

Uncovering the microbial community structure and physiological profiles of terrestrial mud volcanoes: A comprehensive metagenomic insight towards their trichloroethylene biodegradation potentiality

Mud volcanoes are dynamic geological features releasing methane (CH4), carbon dioxide (CO2), and hydrocarbons, harboring diverse methane and hydrocarbon-degrading microbes. However, the potential application of these microbial communities in chlorinated hydrocarbons bioremediation purposes such as trichloroethylene (TCE) has not yet been explored. Hence, this study investigated the mud volcano's microbial diversity functional potentiality in TCE degradation as well as their eco-physiological profiling using metabolic activity. Geochemical analysis of the mud volcano samples revealed variations in pH, temperature, and oxidation-reduction potential, indicating diverse environmental conditions. The Biolog Ecoplate™ carbon substrates utilization pattern showed that the Tween 80 was highly consumed by mud volcanic microbial community. Similarly, MicroResp® analysis results demonstrated that presence of additive C-substrates condition might enhanced the cellular respiration process within mud-volcanic microbial community. Full-length 16 S rRNA sequencing identified Proteobacteria as the dominant phylum, with genera like Pseudomonas and Hydrogenophaga associated with chloroalkane degradation, and methanotrophic bacteria such as Methylomicrobium and Methylophaga linked to methane oxidation. Functional analysis uncovered diverse metabolic functions, including sulfur and methane metabolism and hydrocarbon degradation, with specific genes involved in methane oxidation and sulfur metabolism. These findings provide insights into the microbial diversity and metabolic capabilities of mud volcano ecosystems, which could facilitate their effective application in the bioremediation of chlorinated compounds.

Submerged macrophyte restoration enhanced microbial carbon utilization in shallow lakes

Submerged macrophytes are integral to the functioning of shallow lakes through their interaction with microorganisms. However, we have a limited understanding of how microbial communities in shallow lakes respond when macrophytes are restored after being historically extirpated. Here, we explored the interactions between prokaryotic communities and carbon utilization in two lakes where submerged macrophytes were restored. We found restoration reduced total carbon in sediment by 8.9 %–27.9 % and total organic carbon by 16.7 %–36.9 % relative to control treatment, but had no effects on carbon content in the overlying water. Sediment microbial communities were more sensitive to restoration than planktonic microbes and showed enhanced utilization of simple carbon substrates, such as Tween 40, after restoration. The increase in carbon utilization was attributed to declines in the relative abundance of some genera, such as Saccharicenans and Desertimonas, which were found weakly associated with the utilization of different carbon substrates. These genera likely competed with microbes with high carbon utilization in restored areas, such as Lubomirskia. Our findings highlight how restoring submerged macrophytes can enhance microbial carbon utilization and provide guidance to improve the carbon sequestration capacity of restored shallow lakes.

Methylotrophic bacteria from rice paddy soils: mineral-nitrogen-utilizing isolates richness in bulk soil and rhizosphere.

Methanol, the second most abundant volatile organic compound, primarily released from plants, is a major culprit disturbing atmospheric chemistry. Interestingly, ubiquitously found methanol-utilizing bacteria, play a vital role in mitigating atmospheric methanol effects. Despite being extensively characterized, the effect of nitrogen sources on the richness of methanol-utilizers in the bulk soil and rhizosphere is largely unknown. Therefore, the current study was planned to isolate, characterize and explore the richness of cultivable methylotrophs from the bulk soil and rhizosphere of a paddy field using media with varying nitrogen sources. Our data revealed that more genera of methylotrophs, including Methylobacterium, Ancylobacter, Achromobacter, Xanthobacter, Moraxella, and Klebsiella were enriched with the nitrate-based medium compared to only two genera, Hyphomicrobium and Methylobacterium, enriched with the ammonium-based medium. The richness of methylotrophic bacteria also differed substantially in the bulk soil as compared to the rhizosphere. Growth characterization revealed that majority of the newly isolated methanol-utilizing strains in this study exhibited better growth at 37°C instead of 30 or 45°C. Moreover, Hyphomicrobium sp. FSA2 was the only strain capable of utilizing methanol even at elevated temperature 45°C, showing its adaptability to a wide range of temperatures. Differential carbon substrate utilization profiling revealed the facultative nature of all isolated methanol-utilizer strains with Xanthobacter sp. TS3, being an important methanol-utilizer capable of degrading toxic compounds such as acetone and ethylene glycol. Overall, our study suggests the role of nutrients and plant-microbial interaction in shaping the composition of methanol-utilizers in terrestrial environment.

Urea promoted soil microbial community and reduced the residual ciprofloxacin in soil and its uptake by Chinese flowering cabbage.

Antibiotics in agricultural soil can be accumulated in crops and might pose a potential risk to human health. Nevertheless, there is a lack of knowledge about the impact of nitrogen fertilizers on the dissipation and uptake of antibiotics in soils. Therefore, our aim in this study is to investigate the effects of urea fertilizer on the residues of ciprofloxacin and its uptake by Chinese flowering cabbage (Brassica parachinensis L.) as affected by the associated changes on the soil microbial community. A pot experiment has been conducted using spiked soil with 20 mg ciprofloxacin /kg soil and fertilized with urea at dosages equal to 0, 0.2, 0.4, 0.8 t/ha. Application urea especially at 0.4 t/ha decreased the residue of ciprofloxacin in the soil and its uptake by the roots and its translocation to the shoots of Chinese flowering cabbage. The translocation factors (TFs) for ciprofloxacin were significantly decreased (P < 0.05) only at the treatment of 0.4 t/ha, while no significant difference of bio-concentration factors (BCFs). The average well color development (AWCD) values, Shannon diversity, and richness index were higher in the fertilized than the un-fertilized soils, and all such indicators were greater at the treatment of 0.4 t/ha than at 0.2 and 0.8 t/ha. The carbon substrate utilization of phenolic acids at the treatments of 0.4 t/ha were greater than with other levels of urea fertilizer. In conclusion, moderate urea addition significantly increased soil microbial activity and abundance, which in turn promoted the ciprofloxacin dissipation in soil and plant tissue. The present study provides an economical and operational strategy for the remediation of ciprofloxacin contaminated soils.

Exploring the hidden treasures: Deep-sea bacterial community structure in the Bay of Bengal and their metabolic profile

Deep sea bacterial communities demonstrate remarkable adaptability to high-pressure environments coupled with low temperatures which has sparked curiosity about their diversity and exceptional metabolic pathways. Additionally, bacteria in the deep sea exert a substantial influence over various biogeochemical processes. To date, we have relatively very little information about the deep-sea bacterial communities and, they remain largely unexplored. We investigated the variability in the physicochemical conditions, heavy metals and their influence on deep-sea bacterial community structure across three different depths in the Bay of Bengal. The structural and metabolic diversity of deep-sea sediment microbial communities were examined through culture-based sequencing of 16S rRNA genes, ecto-enzymatic studies, and community-level physiological profiling. Bacillota was the most dominant phylum representing 61% of the cultured bacterial isolates, while the remaining belonged to Actinomycetota and Pseudomonodata. Five potential novel species belonging to the genera Fictibacillus, Lysinibacillus, Salinicola, Robertmurraya and Blastococcus were identified. The extracellular enzymatic activity was positive for &amp;gt;50% of the bacterial isolates, wherein the genera Bacillus and Micromonospora exhibited versatile profiles. High metabolic diversity was recorded through the carbon substrate utilization profiles indicating that microbial communities are active participants in biogeochemical cycles in the deep sea. The most prominently utilized carbon substrates were α-cyclodextrin, glucose-1-phosphate, D-xylose, glycogen, and 2-hydroxy benzoic acid which serve as organic substrates for microbial metabolism, facilitating the decomposition of organic matter and, recycling carbon in deep-sea ecosystems. Multivariate statistical analyses confirmed that the environmental variables had a profound influence on the bacterial community. The findings shed light on spatial variability in the bacterial community structure, enzyme activity and metabolic profiles, and enhance our understanding of Bay of Bengal deep-sea sedimentary microbial ecology.

Raman spectroscopy online monitoring of biomass production, intracellular metabolites and carbon substrates during submerged fermentation of oleaginous and carotenogenic microorganisms

BackgroundMonitoring and control of both growth media and microbial biomass is extremely important for the development of economical bioprocesses. Unfortunately, process monitoring is still dependent on a limited number of standard parameters (pH, temperature, gasses etc.), while the critical process parameters, such as biomass, product and substrate concentrations, are rarely assessable in-line. Bioprocess optimization and monitoring will greatly benefit from advanced spectroscopy-based sensors that enable real-time monitoring and control. Here, Fourier transform (FT) Raman spectroscopy measurement via flow cell in a recirculatory loop, in combination with predictive data modeling, was assessed as a fast, low-cost, and highly sensitive process analytical technology (PAT) system for online monitoring of critical process parameters. To show the general applicability of the method, submerged fermentation was monitored using two different oleaginous and carotenogenic microorganisms grown on two different carbon substrates: glucose fermentation by yeast Rhodotorula toruloides and glycerol fermentation by marine thraustochytrid Schizochytrium sp. Additionally, the online FT-Raman spectroscopy approach was compared with two at-line spectroscopic methods, namely FT-Raman and FT-infrared spectroscopies in high throughput screening (HTS) setups.ResultsThe system can provide real-time concentration data on carbon substrate (glucose and glycerol) utilization, and production of biomass, carotenoid pigments, and lipids (triglycerides and free fatty acids). Robust multivariate regression models were developed and showed high level of correlation between the online FT-Raman spectral data and reference measurements, with coefficients of determination (R2) in the 0.94–0.99 and 0.89–0.99 range for all concentration parameters of Rhodotorula and Schizochytrium fermentation, respectively. The online FT-Raman spectroscopy approach was superior to the at-line methods since the obtained information was more comprehensive, timely and provided more precise concentration profiles.ConclusionsThe FT-Raman spectroscopy system with a flow measurement cell in a recirculatory loop, in combination with prediction models, can simultaneously provide real-time concentration data on carbon substrate utilization, and production of biomass, carotenoid pigments, and lipids. This data enables monitoring of dynamic behaviour of oleaginous and carotenogenic microorganisms, and thus can provide critical process parameters for process optimization and control. Overall, this study demonstrated the feasibility of using FT-Raman spectroscopy for online monitoring of fermentation processes.

Quantifying the Respiratory Pattern of Rhizosphere Microbial Communities in Healthy and Diseased Tomato Plants Using Carbon Substrates

The sustainable production of tomatoes (Solanum lycopersicum) is important, and this can be achieved by determining the rate of respiration of microbes in the tomato plants' rhizosphere soil. This study aimed at the potential of microbes to utilize carbon substrates embedded in the rhizosphere soil thereby contributing to the healthy nature of the tomato plants. The potential soil physiochemical features and utilization of carbon substrate by soil microorganisms as a result of their respiration to reveal their functions in the ecosystem were evaluated. The soil samples were amassed from the healthy tomato plant rhizosphere, diseased tomatoes, and bulk soil in this study. The physiochemical features and carbon substrate utilization in the bulk soil samples, and rhizosphere samples of powdery diseased, and healthy tomato plants were assessed. The MicroRespTM procedure was used to determine the community-level physiological profiles (CLPP) employing fifteen (15) carbon (C) substrates selected based on their importance to microbial communities embedded in the soil samples. Our results revealed that various physiochemical properties, moisture content, water retention, and C substrates including sugar, amino acid, and carboxylic acid were greater in HR and the substrates were not significantly different (p < 0.05). The study reveals higher soil respiration in HR as a result of the microbial communities inhabiting HR utilizing more of the C-substrates. This investigation contributes to the tomato plant's healthy state as the microbial communities utilized carbon substrate compared to DR after employing the CLPP assays.

Vermicast Analysis with the Earthworm Species Pheretima losbanosensis (Crassiclitellata: Megascolecidae): Bacterial Profiles for Potential Applications in Agriculture

In the Philippines, the use of non-native earthworm species in vermicomposting is popular. Given that the country is a vital geographical resource for earthworm diversity, the study of earthworm species to establish the potential of their vermicasts in agricultural applications is essential. In this study, the bacteria associated with the vermicasts of the recently described indigenous species, Pheretima losbanosensis, were investigated using next-generation sequencing, community-level physiological profiling, and NPK activity screening. The results showed diverse bacterial species belonging to the phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Spirochaetes, Thermodesulfobacteria, and Verrucomicrobia. Higher diversity and carbon substrate utilization (p &lt; 0.05) of amines and amides, phenolic compounds, polymers, and carboxylic and acetic acids were exhibited by the bacterial communities of P. losbanosensis compared to those of Eudrilus eugeniae. Likewise, bacteria (n = 25) isolated from P. losbanosensis vermicasts had higher nitrogen fixation and phosphate and potassium solubilization activities (p &lt; 0.05) than the bacteria (n = 20) isolated from E. eugeniae vermicasts. Overall, our results indicate that the diverse bacterial communities inhabiting the vermicasts of P. losbanosensis have nutrient mineralization and carbon substrate utilization activities that may have applications in sustainable agriculture as a potential organic input to promote plant growth and improve soil substrate.

Effects of the Coculture Initiation Method on the Production of Secondary Metabolites in Bioreactor Cocultures of Penicillium rubens and Streptomyces rimosus.

Bioreactor cocultures involving Penicillium rubens and Streptomyces rimosus were investigated with regard to secondary metabolite production, morphological development, dissolved oxygen levels, and carbon substrate utilization. The production profiles of 22 secondary metabolites were analyzed, including penicillin G and oxytetracycline. Three inoculation approaches were tested, i.e., the simultaneous inoculation of P. rubens with S. rimosus and the inoculation of S. rimosus delayed by 24 or 48 h relative to P. rubens. The delayed inoculation of S. rimosus into the P. rubens culture did not prevent the actinomycete from proliferating and displaying its biosynthetic repertoire. Although a period of prolonged adaptation was needed, S. rimosus exhibited growth and the production of secondary metabolites regardless of the chosen delay period (24 or 48 h). This promising method of coculture initiation resulted in increased levels of metabolites tentatively identified as rimocidin B, 2-methylthio-cis-zeatin, chrysogine, benzylpenicilloic acid, and preaustinoid D relative to the values recorded for the monocultures. This study demonstrates the usefulness of the delayed inoculation approach in uncovering the metabolic landscape of filamentous microorganisms and altering the levels of secondary metabolites.

Responses of soil microbes and enzymes to long-term warming incubation in different depths of permafrost peatland soil

Soil microbes and enzymes mediate soil carbon–climate feedback, and their responses to increasing temperature partly affect soil carbon stability subjected to the effects of climate change. We performed a 50-month incubation experiment to determine the effect of long-term warming on soil microbes and enzymes involved in carbon cycling along permafrost peatland profile (0–150 cm) and investigated their response to water flooding in the active soil layer. Soil bacteria, fungi, and most enzymes were observed to be sensitive to changes in temperature and water in the permafrost peatland. Bacterial and fungal abundance decreased in the active layer soil but increased in the deepest permafrost layer under warming. The highest decrease in the ratio of soil bacteria to fungi was observed in the deepest permafrost layer under warming. These results indicated that long-term warming promotes recalcitrant carbon loss in permafrost because fungi are more efficient in decomposing high-molecular-weight compounds. Soil microbial catabolic activity measured using Biolog Ecoplates indicated a greater degree of average well color development at 15 °C than at 5 °C. The highest levels of microbial catabolic activity, functional diversity, and carbon substrate utilization were found in the permafrost boundary layer (60–80 cm). Soil polyphenol oxidase that degrades recalcitrant carbon was more sensitive to increases in temperature than β-glucosidase, N-acetyl-β-glucosaminidase, and acid phosphatase, which degrade labile carbon. Increasing temperature and water flooding exerted a synergistic effect on the bacterial and fungal abundance and β-glucosidase, acid phosphatase, and RubisCO activity in the topsoil. Structural equation modeling analysis indicated that soil enzyme activity significantly correlated with ratio of soil bacteria to fungi and microbial catabolic activity. Our results provide valuable insights into the linkage response of soil microorganisms, enzymes to climate change and their feedback to permafrost carbon loss.

Temperature-mediated microbial carbon utilization in China's lakes.

Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.

Microbial Biofilm Colonizing Plastic Substrates in the Ross Sea (Antarctica): First Overview of Community-Level Physiological Profiles

The microbial colonization of plastic substrates made of polyvinylchloride (PVC) and polyethylene (PE) was studied in Tethys and Road Bays (Ross Sea, Antarctica) in order to evaluate the metabolic profiles of the plastisphere community in comparison with those of the surrounding waters. PVC and PE panels, mounted on stainless steel structures, were deployed in the austral summer 2017 at 5 and 20 m and recovered one year later at four different stations (Amorphous Glacier-AG was potentially impacted by the ice-melting process, and its control site was within Tethys Bay-TB; Road Bay-RB, close to the wastewater plant of the Italian research station Mario Zucchelli and its control site Punta Stocchino-PTS). Additional panels were settled in Road Bay at 5 m and recovered after three months to follow time variability in the microbial colonization process. At the same times and depths as plastic substrates, water samples were also collected. Carbon substrates’ utilization rates were determined on scraped microbial biofilm and water samples, with a fluorimetric assay based on 96-well Biolog Ecoplates. Complex carbon sources, carbohydrate and amines were the organic substrates that mostly fuelled the community metabolism in the RB area, while in the TB area, in addition to carbohydrates, phosphate carbon compounds and amino acids were also actively utilized. Within Road Bay, small differences in the physiological profiles were found, with higher metabolic rates in the biofilm community after 3 months’ deployment (late austral summer period) compared to 12 months, suggesting that autumn to spring period conditions negatively affected foulers’ metabolism. Moreover, different metabolic profiles between the plastisphere and the pelagic microbial community were observed; this last utilized a higher number of carbon sources, while plastic substrates were colonized by a more specialized community. Higher carbon substrate utilization rates were recorded at RB and AG stations, receiving organic supply from anthropic activity or ice melting sources, respectively, compared to their control sites. These results highlighted the functional plasticity of the microbial community, with the adaptive ability to utilize a diversified range of organic substrates.

Porewater constituents inhibit microbially mediated greenhouse gas production (GHG) and regulate the response of soil organic matter decomposition to warming in anoxic peat from a Sphagnum-dominated bog.

Northern peatlands store approximately one-third of terrestrial soil carbon. Climate warming is expected to stimulate the microbially mediated degradation of peat soil organic matter (SOM), leading to increasing greenhouse gas (GHG; carbon dioxide, CO2; methane, CH4) production and emission. Porewater dissolved organic matter (DOM) plays a key role in SOM decomposition; however, the mechanisms controlling SOM decomposition and its response to warming remain unclear. The temperature dependence of GHG production and microbial community dynamics were investigated in anoxic peat from a Sphagnum-dominated peatland. In this study, peat decomposition, which was quantified by GHG production and carbon substrate utilization is limited by terminal electron acceptors (TEA) and DOM, and these controls of microbially mediated SOM degradation are temperature-dependent. Elevated temperature led to a slight decrease in microbial diversity, and stimulated the growth of specific methanotrophic and syntrophic taxa. These results confirm that DOM is a major driver of decomposition in peatland soils contains inhibitory compounds, but the inhibitory effect is alleviated by warming.

Physico-Chemical Quality and Physiological Profiles of Microbial Communities in Freshwater Systems of Mega Manila, Philippines

Studying the quality of freshwater systems and drinking water in highly urbanized megalopolises around the world remains a challenge. This article reports data on the quality of select freshwater systems in Mega Manila, Philippines. Water samples collected between 2020 and 2021 were analyzed for physico-chemical parameters and microbial community metabolic fingerprints, i.e., carbon substrate utilization patterns (CSUPs). The detection of arsenic, lead, cadmium, mercury, polyaromatic hydrocarbons (PAHs), and organochlorine pesticides (OCPs) was carried out using standard chromatography- and spectroscopy-based protocols. Physiological profiles were determined using the Biolog EcoPlate™ system. Eight samples were free of heavy metals, and none contained PAHs or OCPs. Fourteen samples had high microbial activity, as indicated by average well color development (AWCD) and community metabolic diversity (CMD) values. Community-level physiological profiling (CLPP) revealed that (1) samples clustered as groups according to shared CSUPs, and (2) microbial communities in non-drinking samples actively utilized all six substrate classes compared to drinking samples. The data reported here can provide a baseline or a comparator for prospective quality assessments of drinking water and freshwater sources in the region. Metabolic fingerprinting using CSUPs is a simple and cheap phenotypic analysis of microbial communities and their physiological activity in aquatic environments.

Functional characterization of the phosphotransferase system in Parageobacillus thermoglucosidasius

Parageobacillus thermoglucosidasius is a thermophilic bacterium characterized by rapid growth, low nutrient requirements, and amenability to genetic manipulation. These characteristics along with its ability to ferment a broad range of carbohydrates make P. thermoglucosidasius a potential workhorse in whole-cell biocatalysis. The phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) catalyzes the transport and phosphorylation of carbohydrates and sugar derivatives in bacteria, making it important for their physiological characterization. In this study, the role of PTS elements on the catabolism of PTS and non-PTS substrates was investigated for P. thermoglucosidasius DSM 2542. Knockout of the common enzyme I, part of all PTSs, showed that arbutin, cellobiose, fructose, glucose, glycerol, mannitol, mannose, N-acetylglucosamine, N-acetylmuramic acid, sorbitol, salicin, sucrose, and trehalose were PTS-dependent on translocation and coupled to phosphorylation. The role of each putative PTS was investigated and six PTS-deletion variants could not grow on arbutin, mannitol, N-acetylglucosamine, sorbitol, and trehalose as the main carbon source, or showed diminished growth on N-acetylmuramic acid. We concluded that PTS is a pivotal factor in the sugar metabolism of P. thermoglucosidasius and established six PTS variants important for the translocation of specific carbohydrates. This study lays the groundwork for engineering efforts with P. thermoglucosidasius towards efficient utilization of diverse carbon substrates for whole-cell biocatalysis.

Pseudomonas isolates from raw milk with high level proteolytic activity display reduced carbon substrate utilization and higher levels of antibiotic resistance

Milk is an ideal food but can be easily contaminated during milking, transportation and storage by Pseudomonas spp. That secrete proteases resulting in milk spoilage. However, genomic features and functional metabolic diversity of Pseudomonas with different protease activity have not been extensively studied. With this aim, the genomic features and functional metabolic diversity of Pseudomonas with differing proteolytic activity were evaluated using whole genome sequencing and metabolomic approaches, respectively as well as, the presence of genes encoding the aprX protease and antibiotic resistance were screened. Pseudomonas strains with higher protease activity possessed more carbohydrate transport and metabolism, signal transduction, secondary metabolite synthesis, polysaccharide lyase and carbohydrate esterase genes. These isolates were more efficient at carbon source utilization and this phenotype was positively related to incubation temperature. The high protease activity group also displayed a multidrug resistance index that was significantly higher than that for the low protease activity group. This is the first report comparing the gene function and metabolic diversity of Pseudomonas with differing levels of proteolytic activity in raw milk.

Screening potential polyhydroxyalkanoate-producing bacteria from wastewater sludge.

We applied fluorescence staining of Nile red, polymerase chain reaction (PCR), and carbon substrate utilization and pressure tolerance analysis to execute three-stage screening for potential polyhydroxyalkanoate (PHA) producers in the sludge samples of 21 large-scale wastewater treatment plants of city and industrial parks in Taiwan area. Total 35,429 colonies were grown on 196 plates, the screened 30 strains were subjected to 16S rRNA analysis, and 18 identified genera belonged to Proteobacteria (67%), Firmicutes (17%), and Actinomycetota (16%). The PHA accumulation results revealed that nine genera (50% of 18 screened) produced PHAs by limiting the nitrogen source and excess single carbon sources of glucose in an aerobic status. The PHA accumulation percentage was 1.44-58.77% at dry cell weight, and the theoretical yield from glucose was 0.52-58.76%. Our results indicate that our triple-screening method is promising for identifying a high biodiversity of PHA-accumulating bacteria from activated sludge for future industrial applications.