Bacterial Carbon Metabolism Research Articles

Fertilization shapes microbial life strategies, carbon and nitrogen metabolic functions in Camellia oleifera soil

Mineral, organic and microbial fertilizers are crucial for maintaining and improving soil quality, ecosystem functions, and fruit yield in Camellia oleifera plantations. However, how the application of these fertilizers shapes the life strategies and functions of soil microbial communities is unclear. Here, we conducted a one-year field experiment with three types of fertilizers: mineral (NPK), manure (Man), and microbial (MicrF), and analyzed soil properties, bacterial and fungal communities to assess microbial life strategies, functional traits and their determinants. The application of MicrF strongly increased the diversity of both soil bacterial (by 6.4%) and fungal communities (by 23%). Organic matter inputs from Man and MicrF had greater effects on the life strategies of bacteria than fungi: the dominant r-strategy bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased with Man and MicrF, but K-strategists (Acidobacteria) decreased. Conversely, the abundance of r-strategy fungi (Ascomycota) decreased, but that of K-fungi (Basidiomycota) increased. Predictions of the functions indicated that microbial fertilization accelerated the bacterial carbohydrates, carbon and nitrogen metabolism, while also increasing the prevalence of wood saprotrophic fungi. The changes in the taxonomic and functional characteristics of the microbial communities induced co-metabolism priming effects, which were mainly regulated by soil organic carbon, available phosphorus, ammonium nitrogen contents, and carbon-nitrogen ratio. The application of MicrF is an effective approach to increase the diversity and multifunctionality of soil microbial communities in Camellia oleifera plantations, including organic matter decomposition, carbon and nitrogen metabolism. These findings provide valuable insights into the fertilizer regimes based on microbial ecological strategies and functional profiles in Camellia oleifera plantations.

Stable isotope labeling and functional gene prediction elucidate the carbon metabolism in fermentative bacteria and microalgae coupling system

The application of the fermentative bacteria and microalgae coupling system in the wastewater treatment has been studied, but there remains few knowledge regarding the organic and inorganic carbon metabolism within this system. In this study, the carbon metabolism of microalgae and fermentative bacteria was elucidated by 13C stable isotope labeling and functional gene prediction, respectively. The 13C glucose and 13C NaHCO3 were used as stable isotope tracers to clarify the organic and inorganic carbon metabolism of microalgae, indicating that approximately 71.5 % of the Acetyl-CoA in microalgae was synthesized from organic carbon sources, while 26.8 % was synthesized through the utilization of inorganic carbon sources. Inorganic carbon sources can enhance the activity of photosynthetic system and facilitate the Calvin cycle. Considering the adequate organic carbon sources and insufficient inorganic carbon sources in the fermentative bacteria and microalgae coupling system, NaHCO3 was added to improve carbon utilization of microalgae. The maximum microalgal lipid yield reached 1130.37 mg/L with 1000 mg/L NaHCO3 supplementation. Functional gene prediction was used to analysis the effect of various carbon composition on the bacterial carbon metabolism. Notably, the additional inorganic carbon sources increased the abundance of bacterial functional genes associated with the fermentation and acetic acids synthesis, which was advantageous for VFAs production and further promoted microalgae growth. This study can gain a deeper understanding of microbial metabolic mechanisms during the operation of fermentative bacteria and microalgae system, and improve its sustained operational stability.

Antibacterial Activities of the Algal Bromophenol Methylrhodomelol Against Pseudomonas aeruginosa.

Methylrhodomelol (1: ) is a bromophenol from the red alga Vertebrata lanosa that has been associated with antimicrobial properties. The aim of the current study was, therefore, to assess the antimicrobial potential of this compound in more detail against the gram-negative pathogen Pseudomonas aeruginosa. 1: exerted weak bacteriostatic activity against different strains when grown in minimal medium, whereas other phenolics were inactive. In addition, 1: (35 and 10 µg/mL) markedly enhanced the susceptibility of multidrug-resistant P. aeruginosa toward the aminoglycoside gentamicin, while it did not affect the viability of Vero kidney cells up to 100 µM. Finally, pyoverdine release was reduced in bacteria treated at sub-inhibitory concentration, but no effect on other virulence factors was observed. Transcriptome analysis of treated versus untreated P. aeruginosa indicated an interference of 1: with bacterial carbon and energy metabolism, which was corroborated by RT-qPCR and decreased ATP-levels in treated bacteria. In summary, the current study characterized the antibacterial properties of methylrhodomelol, revealed its potential as an adjuvant to standard antibiotics, and generated a hypothesis on its mode of action.

Changes in bacterial community structure and carbon metabolism in sandy soil under the long-term application of chitin-rich organic material and attapulgite

Continuous expansion of sandy soil deeply threatens crop security and has become one of the main challenges facing modern society. Chitin-rich organic material and attapulgite have been considered efficient materials to improve degraded soil based on their rich nutrient contents and unique structures. However, their potential effects on microbial community and functions in sandy soil are poorly understood. Therefore, we conducted a 4-year field experiment featuring amendment with chitin-rich organic material and attapulgite and investigated the effect of amendments on microbial community diversity, structure and function using amplicons (16S and ITS) and metagenomic sequencing. The four treatments were as follows: (1) CK: no soil amendment; (2) SA: CK + attapulgite amendment; (3) SC: CK + chitin-rich organic material; and (4) SCA: CK + chitin-rich organic material + attapulgite amendment. The results indicated that the concentrations of soil organic carbon (SOC), total nitrogen, available phosphate (AP), available potassium, and enzyme activities increased while pH decreased in the treatments with chitin-rich organic material application (SC and SCA). Microorganisms have different responses to different soil amendments. Bacteria are the main components of microorganisms and their community structure was altered under chitin-rich organic material treatments (SC and SCA). Furthermore, 14 OTUs belonging to five phyla (Proteobacteria, Actinobacteriota, Firmicutes, Gemmatimonadota, and Patescibacteria) related to the decomposition of organic matter were enriched in SC, while 22 OTUs belonging to six phyla (Proteobacteria, Actinobacteriota, Firmicutes, Gemmatimonadota, Patescibacteria, and Cyanobacteria) were enriched significantly in SCA, suggesting that the combination of the two amendments had the potential to further alter the bacterial community compared with a single amendment. The metagenomic analysis revealed a decrease in the relative abundance of genes involved in carbon metabolism in SCA, with soil pH, AP, enzyme activity, SOC, and bacterial community structure identified as primary influencing factors. In conclusion, we conducted a comprehensive analysis of the effects of chitin-rich organic material and attapulgite on microorganisms in sandy soil and found a robust link between soil properties, bacterial community structure, and microbial carbon metabolism function.

Microbial degradation mechanisms of surface petroleum contaminated seawater in a typical oil trading port

Petroleum hydrocarbons are significant new persistent organic pollutants for marine oil spill risk areas. Oil trading ports, in turn, have become major bearers of the risk of offshore oil pollution. However, studies on the molecular mechanisms of microbial degradation of petroleum pollutants by natural seawater are limited. Here, an in situ microcosm study was conducted. Combined with metagenomics, differences in metabolic pathways and in the gene abundances of total petroleum hydrocarbons (TPH) are revealed under different conditions. About 88% degradation of TPH was shown after 3 weeks of treatment. The positive responders to TPH were concentrated in the genera Cycloclasticus, Marivita and Sulfitobacter of the orders Rhodobacterales and Thiotrichales. The genera Marivita, Roseobacter, Lentibacter and Glaciecola were key degradation species when mixing dispersants with oil, and all of the above are from the Proteobacteria phylum. The analysis showed that the biodegradability of aromatic compounds, polycyclic aromatic hydrocarbon and dioxin were enhanced after the oil spill, and genes with higher abundances of bphAa, bsdC, nahB, doxE and mhpD were found, but the photosynthesis-related mechanism was inhibited. The dispersant treatment effectively stimulated the microbial degradation of TPH and then accelerated the succession of microbial communities. Meanwhile, functions such as bacterial chemotaxis and carbon metabolism (cheA, fadeJ and fadE) were better developed, but the degradation of persistent organic pollutants such as polycyclic aromatic hydrocarbons was weakened. Our study provides insights into the metabolic pathways and specific functional genes for oil degradation by marine microorganisms and will help improve the application and practice of bioremediation.

Differential Effects of Viruses on the Growth Efficiency of Freshwater Bacterioplankton in Eutrophic Relative to Non-Eutrophic Lakes

In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10-60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters.

Effect of biochar application rate on changes in soil labile organic carbon fractions and the association between bacterial community assembly and carbon metabolism with time

Biochar aging affects the stability of soil carbon. Analyzing the effect of biochar on soil organic carbon (SOC) forms and their relations with microbial community assembly and carbon metabolism with time is helpful for soil carbon sequestration (by adapting the farm management approach). Four treatments with no, low, medium, and high biochar application rates (0 %, 1 %, 2 %, and 4 % of the total dry weight of topsoil before winter wheat planting, abbreviated as control, LB, MB, and HB, respectively) were conducted in the field. The SOC and particulate organic carbon positively correlated with the biochar application rate. Biochar decreased readily oxidizable carbon (P < 0.05) after 8 months of application compared to the control; however, the difference disappeared with time. Biochar increased dissolved organic carbon (DOC) but had no effect on water- soluble organic carbon (WSOC); DOC and WSOC decreased with time. Furthermore, LB and HB stabilized the bacterial alpha diversities with time. Based on high-throughput sequencing, HB reduced the relative abundance of Actinobacteriota but increased that of Acidobacteria (P < 0.05) after 12 months of biochar application. Time-wise, the bacterial community assembly was determined by deterministic processes that were significantly affected by the available nitrogen, DOC, or WSOC. Compared with the control, biochar decreased bacterial links and improved bacterial metabolism of phenolic acids and polymers with time, as evidenced by Biolog EcoPlates. Structural equation modeling revealed that the contribution of bacterial assembly processes to carbon metabolism changed with time. Microbial carbon metabolism was most positively influenced by differences in the composition of bacterial specialists. These findings reinforced that changes in soil labile organic carbon were time-dependent but not necessarilty affected by the biochar application rate.

Bacterial functional redundancy and carbon metabolism potentials in soil, sediment, and water of thermokarst landscapes across the Qinghai-Tibet Plateau: Implications for the fate of permafrost carbon

Permafrost thaw create widespread thermokarst landscapes. As a result, distinct habitats are provided to harbor different bacterial communities in degraded permafrost soil (PBCs), thermokarst lake sediment (SBCs), and lake water (WBCs), driving carbon metabolism differentially. In this study, we investigated functional diversity and redundancy, and carbon metabolism potentials of PBCs, SBCs, and WBCs in thermokarst landscapes across the Qinghai-Tibet Plateau. The results showed that PBCs and SBCs had higher taxonomic and functional alpha diversity than WBCs, while WBCs had lower functional redundancy. WBCs had the highest beta diversity followed by SBCs and PBCs, suggesting strong determination of taxonomic variations on functional differences. Community assembly processes also had significant influences on beta diversity, especially for SBCs. Metabolism pathways of carbohydrate metabolism, methane metabolism, and carbon fixation were enriched differentially in PBCs, SBCs, and WBCs, suggesting different C fate in distinct habitats. Carbohydrate metabolism data suggested that PBCs might have stronger potentials to mineralize a greater diversity of organic carbon substrate than SBCs and WBCs, promoting degradation of organic carbon stocks in degraded permafrost soils. Methane metabolism data showed that SBCs had a stronger methanogenesis potential followed by PBCs and WBCs, while PBCs had a stronger methane oxidation potential. High abundance of genes involving in formaldehyde assimilation might suggested that a large proportion of produced methane might be assimilated by methanotrophs in the thermokarst landscapes. Both aerobic and anaerobic carbon fixation pathways were enriched in PBCs. The results added our understanding of functional properties and biogeochemical carbon cycles in thermokarst landscapes, improving our abilities in accurate modeling of carbon dynamics and the ultimate fate of permafrost carbon in a warming world.

Understanding the contribution of metabolism to Mycobacterium tuberculosis drug tolerance.

Treatment of Mycobacterium tuberculosis (Mtb) infections is particularly arduous. One challenge to effectively treating tuberculosis is that drug efficacy in vivo often fails to match drug efficacy in vitro. This is due to multiple reasons, including inadequate drug concentrations reaching Mtb at the site of infection and physiological changes of Mtb in response to host derived stresses that render the bacteria more tolerant to antibiotics. To more effectively and efficiently treat tuberculosis, it is necessary to better understand the physiologic state of Mtb that promotes drug tolerance in the host. Towards this end, multiple studies have converged on bacterial central carbon metabolism as a critical contributor to Mtb drug tolerance. In this review, we present the evidence that changes in central carbon metabolism can promote drug tolerance, depending on the environment surrounding Mtb. We posit that these metabolic pathways could be potential drug targets to stymie the development of drug tolerance and enhance the efficacy of current antimicrobial therapy.

Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water.

Methylmercury (MeHg) is a potent neurotoxin commonly found in aquatic environments and primarily formed by microbial methylation of inorganic divalent mercury (Hg(II)) under anoxic conditions. Recent evidence, however, points to the production of MeHg also in oxic pelagic waters, but the magnitude and the drivers for this process remain unclear. Here, we performed a controlled experiment testing the hypothesis that inputs of terrestrial dissolved organic matter (tDOM) to coastal waters enhance MeHg formation via increased bacterial activity. Natural brackish seawater from a coastal area of the Baltic Sea was exposed to environmentally relevant levels of Hg(II) and additions of tDOM according to climate change scenarios. MeHg formation was observed to be coupled to elevated bacterial production rates, which, in turn, was linked to input levels of tDOM. The increased MeHg formation was, however, not coupled to any specific change in bacterial taxonomic composition nor to an increased abundance of known Hg(II) methylation genes. Instead, we found that the abundance of genes for the overall bacterial carbon metabolism was higher under increased tDOM additions. The findings of this study may have important ecological implications in a changing global climate by pointing to the risk of increased exposure of MeHg to pelagic biota.

Long‐term ground cover affects soil bacterial community and carbon metabolism in the Loess Plateau, China

AbstractFarmland mulching can maintain soil nutrients, which plays a positive role in agricultural planting in the arid area. However, the composition of the soil microbial community and the C cycle involved is unclear under farmland mulching. Based on the Changwu Agro‐Ecological Experiment Station, this study set up a long‐term positioning experiment to explore the effect on soil bacterial community structure and C metabolism capacity. In this study, we include five treatments: control uncovered (CK), plastic film mulching (PF), high amount of straw mulching carried out in July, August, and September every year (St90), low amount of straw mulch throughout the growth period (S45), and high amount of straw cover throughout the growth period (S90). We combined Illumina MiSeq sequencing and Biolog‐ECO technology to analyze the functional characterization of soil bacterial community composition in terms of C source metabolism. The results indicated that the soil bacteria showed a high degree of epistatic clustering, and the operational taxonomic unit numbers of soil bacteria decrease as St90, S45, PF, CK, and S90. Redundancy analysis showed that soil available P, NH4+–N, soil moisture content were the main environmental factors affecting bacterial community composition. Proteobacteria, Acidobacteria, and Actinobacteria are the main dominant flora in this area. Soil bacterial C metabolism was highest under PF treatment. Structural equation modeling (SEM) shows that surface cover has direct and indirect effects on bacterial C metabolism capacity and diversity through soil physicochemical properties. Reasonable mulching methods have a positive effect on the sustainable development of agro‐ecosystems in arid areas.

Top-Down Controls of Bacterial Metabolism: A Case Study from a Temperate Freshwater Lake Ecosystem.

In freshwater environments, limited data exist on the impact of mortality forces (viruses and heterotrophic nanoflagellates) on bacterial growth efficiency (BGE, index of bacterial carbon metabolism) compared to resource availability. An investigation to determine the relative influence of viral lysis and flagellate predation (top-down forces) on BGE was conducted in a mesotrophic freshwater system (Lake Goule, France) with time and space. Viral abundance was significantly (p < 0.001) related to bacterial abundance by a power law function with an exponent less than 1, emphasizing that the increases in host population (bacteria) together with viruses were not proportionate. A lytic viral strategy was evident throughout the study period, with high lysis of the bacterial population (up to 60%) supported by viral production rates. Viral processes (lysis and production) that were influenced by bacterial production and heterotrophic nanoflagellate abundance had a positive impact on BGE. Estimates of BGE were variable (9.9–45.5%) due to uncoupling between two metabolic parameters—namely bacterial production and respiration. The existence of a synergistic relationship between viruses and flagellates with bacteria in Lake Goule highlighted the decisive impact of top-down agents in sustaining the bacterial carbon metabolism of non-infected population through the nature of vital resources released via mortality processes.

Coordinated bacterial and plant sulfur metabolism in Enterobacter sp. SA187–induced plant salt stress tolerance

Enterobacter sp. SA187 is a root endophytic bacterium that maintains growth and yield of plants under abiotic stress conditions. In this work, we compared the metabolic wirings of Arabidopsis and SA187 in the free-living and endophytic interaction states. The interaction of SA187 with Arabidopsis induced massive changes in bacterial gene expression for chemotaxis, flagellar biosynthesis, quorum sensing, and biofilm formation. Besides modification of the bacterial carbon and energy metabolism, various nutrient and metabolite transporters and the entire sulfur pathway were up-regulated. Under salt stress, Arabidopsis resembled plants under sulfate starvation but not when colonized by SA187, which reprogramed the sulfur regulon of Arabidopsis. In accordance, salt hypersensitivity of multiple Arabidopsis sulfur metabolism mutants was partially or completely rescued by SA187 as much as by the addition of sulfate, L-cysteine, or L-methionine. Many components of the sulfur metabolism that are localized in the chloroplast were partially rescued by SA187. Finally, salt-induced accumulation of reactive oxygen species as well as the hypersensitivity of LSU mutants were suppressed by SA187. LSUs encode a central regulator linking sulfur metabolism to chloroplast superoxide dismutase activity. The coordinated regulation of the sulfur metabolic pathways in both the beneficial microorganism and the host plant is required for salt stress tolerance in Arabidopsis and might be a common mechanism utilized by different beneficial microbes to mitigate the harmful effects of different abiotic stresses on plants.

Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems

Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.

Biomineralization of Cd2+ and inhibition on rhizobacterial Cd mobilization function by Bacillus Cereus to improve safety of maize grains

Reducing cadmium (Cd) bioavailability and rhizobacterial Cd mobilization functions in the rhizosphere via the inoculation of screened microbial inoculum is an environmental-friendly strategy to improve safety of crop grains. In this study, Bacillus Cereus, a model Cd resistant strain, was selected to explore its effects on Cd bioavailability and uptake, bacterial metabolic functions related to Cd mobilization. Results indicated that inoculation of Bacillus Cereus in maize roots of sand pot with water-soluble Cd (0.06–0.15 mg/kg) and soil pot with high Cd-contaminated soil (total Cd: 2.33 mg/kg; Cd extracted by NH4NO3: 38.6 μg/kg) could decrease water-soluble Cd ion concentration by 7.7–30.1% and Cd extracted with NH4NO3 solution by 7.8–22.5%, inducing Cd concentrations in maize grains reduced by 10.6–39.9% and 17.4–38.6%, respectively. Even for a single inoculation in soil, Cd concentration in maize grains still satisfy food safety requirements (Cd content: 0.1 mg/kg dry weight) due to its successful colonization on root surface of maize. Bacillus Cereus could enrich more plant growth promotion bacteria (PGPB) and down-regulate the expression of genes related to bacterial motility, membrane transports, carbon and nitrogen metabolism in the rhizosphere soil, decreasing Cd bioavailability in soil. Approximately 80% Cd2+ in media was transferred into intracellular, meanwhile Cd salts (sulfide and/or phosphate) were produced in Bacillus Cereus through biomineralization process. Overall, this study could provide a feasible method for improving safety of maize grains via the inoculation of Bacillus Cereus under Cd pollution.

Tracking the changes of wetland soil bacterial community and metabolic potentials under drought and flooding conditions in experimental microcosms

Wetland soils may face more severe water stress under future climate change. Our aim was to assess the change characteristics of wetland soil bacterial community and metabolic potentials under drought and flood conditions. Wetland soil was incubated under five different water environments (including constant moisture at 30%, natural air-dried, and 3 types of flooding depths) by conducting experimental microcosms. After 1, 21, and 132 days of incubation, the soil bacterial community structure and metabolic potential were examined by the 16S rRNA gene sequencing and Biolog-Ecoplates method, respectively. The results showed that Actinobacteria and Firmicutes were significantly enriched under drought and flooding treatments, respectively. Compared to flooding, drought decreased soil microbial biomass and carbon metabolism more severely. However, the depth of flooding did not significantly change bacterial community composition and carbon metabolism. In addition, the responses of soil metabolic functions to drought were more sensitive than the change of bacterial community composition. When the wetland soil faced water stress (drought and flooding), its metabolic functions showed close correlations with bacterial community composition and were negatively affected by most of environmental factors (such as pH, NO3-N, and NH4-N). The results indicate that the drying condition is more severe and rapid than flooding in threatening soil microbial metabolic activity. In addition, the depth of flooding does not significantly change bacterial community composition and carbon metabolism.

Difference and interplay of microbial communities, metabolic functions, trophic modes and influence factors between sludge and bulking agent in a composting matrix

The difference and interplay of microbial communities, metabolic functions and influence factors between sewage sludge and bulking agent were evaluated in 60 days composting. Results showed that fungal communities were mainly affected by pH (42.4%) and ORP (35.9%) of sludge but by VS (41.1%) and temperature (34.7%) of sawdust in a composting system. Bacterial communities were primarily affected by VS (43.5%) and C/N (34.8%) of sludge but by ORP (44.5%) and temperature (31.0%) of sawdust. Tepidimicrobium dominated in the sludge at thermophilic period, while Alcaligenes prevailed in the sawdust. Bacterial carbon metabolism was significantly higher in the sludge than that in the sawdust except carbohydrate metabolism. Saprophytic fungi were the main trophic mode both in the sludge and sawdust. Water transfer facilitated Aspergillus and Trichosporon moving from sludge to sawdust to decompose lignocellulose. Ammonia transfer promoted the migration of Alcaligenes and Pseudomonas from sludge to sawdust and facilitated ammonia assimilating.

Global control of bacterial nitrogen and carbon metabolism by a PTSNtr-regulated switch

The nitrogen-related phosphotransferase system (PTSNtr) of Rhizobium leguminosarum bv. viciae 3841 transfers phosphate from PEP via PtsP and NPr to two output regulators, ManX and PtsN. ManX controls central carbon metabolism via the tricarboxylic acid (TCA) cycle, while PtsN controls nitrogen uptake, exopolysaccharide production, and potassium homeostasis, each of which is critical for cellular adaptation and survival. Cellular nitrogen status modulates phosphorylation when glutamine, an abundant amino acid when nitrogen is available, binds to the GAF sensory domain of PtsP, preventing PtsP phosphorylation and subsequent modification of ManX and PtsN. Under nitrogen-rich, carbon-limiting conditions, unphosphorylated ManX stimulates the TCA cycle and carbon oxidation, while unphosphorylated PtsN stimulates potassium uptake. The effects are reversed with the phosphorylation of ManX and PtsN, occurring under nitrogen-limiting, carbon-rich conditions; phosphorylated PtsN triggers uptake and nitrogen metabolism, the TCA cycle and carbon oxidation are decreased, while carbon-storage polymers such as surface polysaccharide are increased. Deleting the GAF domain from PtsP makes cells "blind" to the cellular nitrogen status. PTSNtr constitutes a switch through which carbon and nitrogen metabolism are rapidly, and reversibly, regulated by protein:protein interactions. PTSNtr is widely conserved in proteobacteria, highlighting its global importance.

Physicochemical and carbon quantity–quality gradients equally influence bacterial carbon metabolism across an arid riverscape

Although freshwater systems comprise a small portion of land surface, they play a pivotal role in landscape carbon (C) cycling. Carbon processing by heterotrophic bacteria is critical, contributing to ecosystem production and dissolved organic carbon (DOC) processing. Riverine bacterial C metabolism is related to a diversity of factors, including (1) physiochemical conditions and inorganic nutrient concentrations and (2) DOC quality and quantity; however, the relative importance of these factors in influencing C metabolism across arid fluvial networks remains equivocal. This study examined C metabolism by heterotrophic bacterioplankton in the Rio Grande drainage, an arid river network in Texas, USA. We examined spatial variation in physicochemical and inorganic nutrient conditions, bacterial C metabolism, and DOC lability across the drainage and assessed whether variation in bacterial C metabolism was more related to physicochemical–inorganic nutrient conditions or DOC quantity and lability. Across the drainage, hydrology and landscape position influenced physicochemical conditions, bacterial abundance, phytoplankton biomass, and bacterial C metabolism and the proportion of variation in bacterial C metabolism explained by physicochemical/inorganic nutrient and DOC quality–quantity gradients was approximately equal. Bacterial abundance and production were associated with greater NH4+ and DOC concentrations and phytoplankton biomass, whereas bacterial respiration and growth efficiency were driven by DOC color and suspended particulate concentrations. Results indicate that aspects of bacterial C metabolism are influenced by different environmental factors related to autochthonous and allochthonous inputs to riverine systems, which has implications for C transformation, sequestration, and transport to the ocean.

Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria.

The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on 'strictly' heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any 'known' light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green-red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This 'metabolic switching' was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in 'green-colored' chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in 'blue-colored' oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.