Accumulation Of Microbial Biomass Research Articles

The Influence of Physical Characteristics of Wet Wipe Fabrics on the Microbial Biomass Accumulation

The physicochemical properties of nonwoven wet wipe fabrics have a strong influence on the ability of microorganisms to attach and multiply, until a biofilm is formed. Cellulose-based fabrics, being biodegradable, represent a major contamination risk. In addition, having a hydrophilic nature, they provide a good platform for microorganisms attachment. To optimize biodegradable wet wipes antimicrobial quality, it is crucial to assess the impact of physicochemical properties, e.g., density, pore size, fiber diameter, contact angle and surface charge. Here, we investigated the physical characteristics of commonly used nonwoven fabrics from both synthetic (Polyethylene terephthalate, PET) and natural components (wood pulp and viscose), to evaluate their effect on microbial contamination. We found that the hydrophobicity of the fabric had varying influence on attachment, depending on the microbial strain. However, the geometry, as well as the fabric pore size greatly affected attachment regardless of the microbial strain, in which a larger pore size resulted in lower accumulation of microbial biomass. Our study gives insight into the characteristics of wet wipes that can affect the preservation efficacy and microbial contamination risk, in one of the biggest segments in the personal care industry.

Prospects for the use of probiotic microorganisms in the production of fermented buckwheat-based products

Relevance. The market segment for products based on plant-based ingredients continues to gain momentum. Protecting health and reducing the environmental burden are the most important driving forces for consumers to buy plant-based products. About 1% of the world’s population suffers from diagnosed celiac disease. Around 13% of the population exhibits symptoms of non-celiac gluten sensitivity. Thus, the production of gluten-free food products, including fermented ones, is becoming increasingly important.Methods. The technological parameters for producing buckwheat dispersion and its quality indicators were assessed. The analysis of the process of acid accumulation during fermentation by microorganisms Lactobacillus, Bifidobacterium, Propionibacterium, and Streptococcus was carried out. Data on the dynamics of microbial biomass accumulation during fermentation were obtained, and the influence of selected starter cultures on the antioxidant properties of fermented dispersions during storage was studied. The impact of chosen strains on organoleptic characteristics was determined, and the dependence of the viscosity of fermented samples on the shear rate was studied.Results. Buckwheat dispersion is a suitable medium for the production of fermented drinks. The duration of fermentation ranged from 5 to 9 hours. The most intense acid accumulation process is observed when S. thermophilus is used for 5 hours. The maximum increase in biomass is achieved with L. bulgaricus, L. acidophilus AT-41, and B. bifidum. Probiotic microorganisms provide stable levels of antioxidant activity during storage. The samples fermented with S. thermophilus, B. bifidum, P. shermanii KM-186, and L. bulgaricus were the most viscous. The most outstanding organoleptic preference was given to samples with L. acidophilus 57S, S. thermophilus, and L. bulgaricus.

Intensification of the production of a plant-based probiotic drink

The quality of the finished probiotic drink is closely related to the completeness and intensity of the fermentation process of lactic acid bacteria in the plant environment of the drink. As part of our research, ways to intensify the fermentation process are proposed due to the additional introduction of vegetable protein and curcumin into the oat drink. The activity of the fermentation process was assessed by the accumulation of biomass, the results of the titrated acidity assessment, the antioxidant properties of probiotic drinks, and the number of probiotic microorganisms. The research results showed that the introduction of additional vegetable protein and curcumin activates the accumulation of microbial biomass by an average of 15-85%, lactic acid – by 40-69% and 5.9 – 12%, respectively, increases antioxidant activity by an average of 2.2 – 6.7%, the increase in protozoan Paramecium Caudatum is when introduced into protein samples – 71.8-74.4%, curcumin – 3.1-22.8%. Thus, it was found that an additional increase in the protein component of the nutrient medium of a vegetable drink and the introduction of curcumin have a stimulating effect on biotechnological processes and are promising in the production of probiotic drinks.

Nutrient availability and stoichiometry mediate microbial effects on soil carbon sequestration in tropical forests

The persistence of soil organic carbon (SOC) is primarily driven by microbial metabolic activities; however, how microbial effects on SOC sequestration are affected by soil nutrient status remains unclear. Here, we conducted a one-year-long in situ soil incubation experiment using mesh bags (with a mesh size of 38 μm, allowing bacterial colonization and fungal hyphal penetration while preventing root penetration). This experiment involved incubating fertile sugarcane soil and infertile sand across an elevational gradient, characterized by diverse climatic and biotic conditions within a tropical forest. Biomarkers, such as phospholipid fatty acids, carbon-, nitrogen-, and phosphorus-acquiring hydrolases, glomalin-related proteins, and amino sugars, were measured to characterize the production and accumulation of microbial biomass, exo-enzymes, extracellular glycoproteins, and microbial necromass. These measurements aimed to elucidate their respective contribution to the sequestration of SOC. We found that Gram-negative bacteria dominated the microbial community composition in fertile soil, and the higher nutrient availability was related to the production and accumulation of microbial necromass via promoting microbial biomass turnover, thus enhancing the accumulation of SOC in fertile soil. This process was negatively associated with phosphorus availability and carbon- and phosphorus-acquiring enzyme activities in fertile soil. In contrast, the SOC accumulation was positively correlated with nitrogen availability and stoichiometry (including C:N and C:P), as well as moisture content in infertile sand. However, more resources were preferentially allocated to stress-tolerant fungi and Gram-positive bacteria under nutrient deficiency in infertile sand used for microbial biomass maintenance, nutrient acquisition, and environmental adaption which further aggravated the consumption of SOC, resulting in SOC loss after one year of field incubation. Our results suggest that microbial effects on SOC persistence are highly context-dependent and nutrient availability-induced changes in microbial communities and microbial resource-allocation strategies are key processes for understanding and predicting the fate of carbon in tropical forest soils.

Respiratory Activity and Biodiversity of Microbiomes in Podzolic Soils of Post-Pyrogenic Spruce Forests in the Krasnoyarsk Territory and the Komi Republic

Data on the microbiological properties of podzolic soils (Retisols) of old-growth spruce forests in the middle taiga of the Krasnoyarsk Krai and the Komi Republic are presented. It is shown that, despite the geographical distance, the soils of the regions are characterized by similar morphological and physicochemical properties. It was noted that in the soils of the spruce forests of the European North (R. Komi) and middle Siberia (Krasnoyarsk Krai), no significant difference in the accumulation of microbial biomass and the rate of microbial respiration was found. However, the content of carbon and nitrogen in soils, as well as microbial biomass, had significant differences in the qualitative composition of microbiomes in pyrogenic and non-pyrogenic soil horizons. A significant effect of the pyrogenic factor on the α-diversity of bacteria and fungi was noted. It was shown that representatives of the dominant phyla of bacteria (Proteobacteria, Actinobacteria and Planctomycetes) and fungi (Ascomycota, Basidiomycota and Mucoromycota) actively participate in the assimilation of organic matter with the presence of pyrogenic carbon. The microbiomes of the upper pyrogenic subhorizons include groups of carbotrophic bacteria (Thermomonosporaceae, Isosphaeraceae, Bacillaceae, Xanthobacteraceae) and fungi from the classes Dothideomycetes (Cenococcum), Eurotiomycetes (Penicillium), Sordariomycetes (Trichoderma), Leotiomycetes (Oidiodendron), Umbelopsidomycetes (Umbelopsis), which are capable of converting pyrolysis products into accessible and non-toxic substrates for other organisms.

Organic carbon accumulation and microbial activities in arable soils after abandonment: A chronosequence study

Increased plant carbon (C) input into the soils after cropland abandonment results in not only C accumulation, but also higher microbial activities and consequently faster organic matter decomposition. We investigated the link between soil C accumulation and microbial properties in a chronosequence (0–65 years) of post-agricultural self-restoration of Luvisols - the dominating soil type worldwide. Microbial biomass carbon (MBC) and enzyme activities increased in the top soil (0–20 cm) during the 37-year period of self-restoration. Accumulation of microbial biomass was faster than of soil organic C at earlier stages of self-restoration (0–22 years) because of the fast microbial growth induced by labile litter components. The response of microbial activity was more sensitive to land use changes compared to that of soil organic C. Activities of enzymes responsible for C cycle increased more than that of nitrogen (N) and phosphorus (P) cycles at least up to 37 years after abandonment, indicating microbial adaptations to high input of litter with wide C/N and C/P ratios. Similarly, β-xylosidase was the solely enzyme which reached the activity similar to secondary forest soils after 65 years, due to the accumulation of recalcitrant C in litter with cropland abandonment age. The increased C demand was caused by the higher bacterial portion in soil microbial community (based on PLFA composition), which in turn, resulted in a lower microbial biomass C/N ratio. Enzyme stoichiometry revealed that microorganisms were limited by C and N in the topsoil during the self-restoration up to 37 years. Overall, the quantity and quality of plant C inputs, which changed with post-agricultural land restoration, regulated the microbial activity and enzyme production, offering a profound comprehension of ecosystem succession.

Deep-injected straw incorporation improves subsoil fertility and crop productivity in a wheat-maize rotation system in the North China Plain

Deep-injected straw incorporation (DI-SI) is a novel soil tillage and straw management, which allowed for the formation of maize straw layer structure in the subsoil (20–38 cm) in wheat-maize rotation systems. However, little is known about how DI-SI affects soil physicochemical and enzymatic processes, as well as crop productivity. Therefore, we conducted a field experiment during 2018–2020 in the North China Plain to determine whether DI-SI would improve soil structure, nutrients, enzyme activities, and crop yield. Three treatments were included: straw removal (SR), conventional straw incorporation (SI), and DI-SI. The results showed that DI-SI improved soil structure and water retention through decreasing the bulk density and penetration resistance in 20–40 cm soil layer. DI-SI significantly increased soil organic C (67.5%), total N (61.3%), and available nutrients (i.e. NO 3 - , NH 4 + , dissolved organic C) compared with SI in the subsoil (20–40 cm), while no differences were detected among straw managements in the topsoil (0–20 cm). This was mainly attributed to the accumulation of microbial biomass C and C-, N-acquisition enzymes in the straw layers, which promoted the straw decomposition and nutrient release. Finally, with the combined effects of soil ecological processes, DI-SI significantly increased the grain yields of wheat and maize by 12.0% and 11.8% compared with SI in the second year, respectively. Our study suggested that deep placement of straw would better promote the utilization of crop residue for farming, and deep-injected straw incorporation represents a viable strategy to improve subsoil physical, chemical, and biological processes, and subsequently crop productivity in wheat-maize rotation systems. • DI-SI improves soil structure and water retention through decreasing the bulk density. • DI-SI considerably increases the SOC, TN, and available nutrients in the subsoil. • DI-SI stimulates microbial and C-, N-acquisition enzymes activities in the straw layers. • Wheat and maize yields were increased under DI-SI, especially in the second year.

Enhanced suppression of saprotrophs by ectomycorrhizal fungi under high level of nitrogen fertilization

Ectomycorrhizal fungi (EMF) are widespread in northern conifer forests. By competing with the free-living saprotrophic fungal and bacterial communities for limited soil nitrogen, EMF are expected to suppress litter decomposition and thus drive soil carbon accumulation. The EMF may also stimulate rhizosphere microbial growth through inputs of labile plant carbon, and subsequently contribute to the soil carbon pool via microbial necromass. Here we examined the relative strength of these two potential EMF effects in a northern conifer plantation of the Saihanba Forest, the largest plantation in China. The soil fungal and bacterial biomass, as well as their respiration, were quantified within the two types of soil cores that either allow or exclude the ingrowth of EMF. We also set up a nitrogen fertilization gradient (0, 5, 10, 15 g N m–2 y–1) in this plantation to quantify the influence of external inorganic nitrogen on the EMF effects. We found evidence that EMF inhibit the overall fungal and bacteria biomass, confirming the suppression of saprotrophs by EMF. In addition, high levels of external nitrogen fertilization (15 g N m–2 y–1) might further enhance the suppression by EMF. In contrast, the presence of EMF consistently increased soil microbial respiration across all nitrogen fertilization levels, indicating that the carbon allocated to EMF could have been largely consumed by microbial respiration and contributed minimally to the accumulation of microbial biomass. Our results also indicated that the suppression of saprotrophs by EMF may play a critical role in driving continuous soil carbon accumulation in this northern pine plantation under atmospheric nitrogen deposition.

Assessment of potential biotoxicity induced by biochar-derived dissolved organic matters to biological fermentative H2 production

Biochar is a widely used antecedent for improving bio‑hydrogen production. However, little is known about the impact of biochar-derived dissolved organic matter (DOM) on the performance of fermentative bio-H2 production. Herein, we evaluated the impact of biochar-derived DOM on the fermentation performance of hydrogen-producing microflora. The pyrolysis temperature of biochar affected the DOM composition, with lower pyrolysis temperatures showing more serious inhibition on H2 accumulation. When biochar was pyrolyzed at 500 °C, DOM prolonged the fermentation period and decreased H2 production from 1330.41 mL L−1 to 1177.05 mL L−1 compared to the control group. The xylose utilization in mixed substrate decreased from 29.72% to 26.41%, which is not favorable for practical applications where lignocellulosic biomass is used as a substrate. Otherwise, DOM caused a 6% reduction in microbial biomass accumulation and less soluble metabolites formation. The potential mechanism of DOM inhibiting bio‑hydrogen production was verified by identifying an increase in reactive oxygen species (ROS) level (178.2%) and the microbial community shifted to containing fewer hydrogen-producing strains. The finding prompts a more precise design of biochar applications in fermentation systems to alleviate the potential hazards and maximum the fermentation performance, not limited to fermentative hydrogen production system.

Reducing Nutrient Loss Caused by Thinning: Effects of Four Composts of Forest Thinning Shreds on Soil Nutrients and Tree Growth in Semimature Pinus tabuliformis Carr., Beijing, China

Traditional methods to deal with thinning shreds (twigs, bark, etc.) include using them as fuelwood (artificially taken out of the forest) and stacking in situ natural decompositions (slow decomposition and nutrient return to the field). These methods will cause the loss of nutrients in the forest, and composting with additives can effectively promote nutrient circulation effectively. The purpose of our study was to explore the effects of composts of forest thinning shreds with different additives on soil and tree growth in semimature Pinus tabuliformis Carr. We selected four composts of forest thinning shreds (T1 adjustment of C/N and C/P + 0.2% priming; T2: adjustment of C/N and C/P + 0.2% common compost; T3: adjustment of C/N and C/P only; T4: raw material grinding of thinning shreds) and applied them in the volume of 900 g·m−2, which were made in the early stage. The soil nutrient content, microbial characteristics, and growing volume of Pinus tabuliformis were measured at 0.5, 1, and 1.5 years after fertilization. The soil became acid after one year of fertilization, having a great impact on the 0–20 cm soil layer. At 0.5 years of fertilization, the total nitrogen (TN) content of the soil with priming compost (T1) was 1.5 times higher than that of the control group (T5); the soil organic matter (SOM) was increased by 4.93–6.41 mg·kg−1. After one year of fertilization, the difference in the soil microbial carbon and nitrogen (MBC and MBN) content of each treatment decreased gradually. Soil sucrase activity was the highest after fertilization, and different composts had the greatest impact on urease activity in the 0–20 cm layer; the alkaline phosphatase (AKPase) activity of soil with common compost (T2) changed the most, and after 0.5 years of fertilization, the acid phosphatase (APase) activity of T1 in the two layers increased by 0.31 mg·g−1 and 0.1 mg·g−1, and the increase in of T2 was slightly lower than that of T1. There were significant differences in the number of bacteria, fungi, and actinomycetes compared to T1 and T2 with other treatments. T1 promoted the height growth (H) of trees three times higher than T5 and T2 promoted the growth of diameter at breast height (DBH) by 2.5 cm. The results showed that T1 and T2 had obvious effects on promoting soil nutrient content, microbial biomass accumulation, and forest growth, and the application of compost had no significant effect on promoting understory regeneration. The findings of this study show that using compost with priming can effectively increase the soil nutrient content, microbial activity, and quantity of Pinus tabuliformis effectively in terms of promoting the growth of trees and reducing the nutrient loss caused by thinning.

Biomass of microbial communities in catenas of virgin and arable chernozems and gray forest soils

The biomass of microbial communities was studied in catenas of virgin chernozems and dark-gray forest soils within the “Belogor’e” natural reserve and vicinal arable soils developed in the same geomorphological and lithological conditions. Living and active microbial biomass was estimated from the point of the phospholipid content and respiratory responses of cells to glucose amendment respectively. In catena of virgin chernozem of the northern exposure, the biomass of microbial community changed slightly, while in catena of the southern exposure, a decrease of biomass was observed in soil on the lower part of the slope. The opposite trend of accumulation of microbial biomass towards the lower part of the slope was observed in catena of arable chernozems. In virgin gray forest soils, the biomass of microbial community did not differ on the watershed and the lower part, but distinctly decreased in the middle part of the catena. In agro-gray forest soils, the biomass tended to increase towards the lower part of the slope. In both soils plowing has led to a decrease in living and active microbial biomass.

Relationship Between Microbial Growth and Hydraulic Properties at the Sub-Pore Scale

Accumulation of microbial biomass and its influence on porous media flow were investigated under saturated flow conditions. Microfluidic experiments were performed with model organisms, and their accumulation was observed in the pore space and on the sub-pore scale. Time-lapse optical imaging revealed different modes of biomass accumulation through primary colonization, secondary growth, and filtration events, showing the formation of preferential flow pathways in the flooding domain as result of the increasing interstitial velocity. Navier–Stokes–Brinkmann flow simulations were performed on the segmented images—a digital-twin approach—considering locally accumulated biomass as impermeable or permeable based on optical biomass density. By comparing simulation results and the experimental responses, it was shown that accumulated biomass can be considered as a permeable medium. The average intra-biomass permeability was determined to be 500 ± 200 mD, which is more than a factor of 10 larger than previously assumed in modeling studies. These findings have substantial consequences: (1) a remaining interstitial permeability, as a result of the observed channel formation and the intra-biomass permeability, and (2) a potential advective nutrient supply, which can be considered more efficient than a purely diffusive supply. The second point may lead to higher metabolic activity and substrate conversion rates which is of particular interest for geobiotechnological applications.

Microbial Resource Limitation in Aggregates in Karst and Non-Karst Soils

Karst is a widespread ecosystem with properties that affect the microbial activity and storage and cycling of soil organic carbon. The mechanisms underlying microbial resource availability in karst, which limit the microbial growth and activity in soil aggregates, remain largely unknown. We assessed the microbial resource limitations using exoenzymatic stoichiometry and key extracellular enzyme activities in bulk soil and aggregates in karst and non-karst forest soils. Soil organic carbon, total nitrogen, and microbial biomass carbon and nitrogen were significantly higher in bulk soil and the aggregate fractions in karst forests. However, the microbial biomass accumulation was higher in finer aggregates than in macroaggregate fractions. This may be attributed to the surface area of finer aggregates that increase the microbial C accumulation. In karst forests, the activity of extracellular enzymes β-d-glucosidase, β-N-acetylglucosaminidase, α-glucosidase, and α-d-1,4-cellobiosidase was two to three times higher in microaggregates (0.053–0.25 mm) and mineral fractions (<0.053 mm) than in macroaggregates. This coincided with the distribution of microbial biomass carbon and phosphorus in finer aggregate fractions. The microorganisms in bulk soil and aggregates in karst forests were largely co-limited by carbon and phosphorus and rarely by nitrogen and only by phosphorus in non-karst soils. The microbial phosphorus limitation in non-karst soils was alleviated in finer soil aggregates, while these fractions reflected slightly higher. microbial C limitations than bulk and other aggregates in karst forests. The patterns of microbial resource limitations in the bulk and aggregate fractions in karst ecosystems reflected the regulation of enzyme activity and soil organic carbon accumulation in finer aggregate fractions but not in other aggregates.

Amino acid and amino sugar compositional changes during in vitro degradation of algal organic matter indicate rapid bacterial re-synthesis

Amino acids (AA) and, more recently, amino sugars (AS) in marine or lacustrine sediments have been increasingly used as paleoproxies. In order to assess AA and AS compositional changes during simulated microbial degradation, as well as to understand the importance of amino-compound re-synthesis by microbes during early diagenesis, decomposition experiments (300 days) were performed with algal (Fragilaria crotonensis) organic matter (OM)/quartz-sand mixtures under controlled redox conditions. Despite expected greater overall degradability under oxic conditions, decomposition kinetics of the bulk algal OM, as well as the total particulate AA and AS were similar under oxic and anoxic conditions, following exponential decay kinetics consistent with the observed mobilization and transfer of large parts of the particulate organic carbon (C) and nitrogen (N) into the dissolved inorganic and organic C and N pools. Carbon-normalized AA and AS yields suggest relative enrichment of amino compounds during partial decomposition, indicating the production and accumulation of microbial biomass during early diagenesis, independent of the redox environment. Moreover, AA and AS compositional changes, such as the relative enrichment of the AA glycine and the AS muramic acid (MurA), and the decrease in the molar ratio of glucosamine and galactosamine (GlcN:GalN) during degradation in both redox systems, were consistent with significant bacterial re-synthesis and the preferential preservation of bacterial biomaterial with increasing diagenesis. Large disparities between different bacterial amino-sugar based estimates of bacterial contribution indicate that bacterial end-member compositions are not currently known well enough to make these bacterial-biomarker constraints quantitative. However, the overall trends are consistent, indicating substantial turnover of eukaryotic into bacterial OM on short time scales of weeks to months. Together these results suggest that the influence of bacterial reworking in conserving sedimentary OM via its transfer into more refractory OM pools may be substantially greater than previously appreciated. We also investigated established amino-compound based indicators of OM degradation, bacterial synthesis, and sediment reactivity. Despite discrepancies, which we attribute to different susceptibilities of the respective indicators towards degradational changes on different time-scales, the tested indices were overall consistent with past data. These results therefore confirm their value as universal indicators of OM diagenesis. Together, our data highlight the vital role of bacterial reworking on the composition of sedimentary OM, with important implications for the alteration of primary geochemical signatures during early sedimentary diagenesis and their use as proxies in paleoenvironmental studies.

Land rehabilitation improves edaphic conditions and increases soil microbial biomass and abundance

Rehabilitation of farmland improves the local eco-environmental conditions. But to what extent this transformation influences soil microbial properties is less known. In our study we compared variations in soil microbial attributes following changes in land-use types to understand the influence of altered soil properties on microbial biomass and their community structure using chloroform fumigation extraction method and phospholipid fatty acid (PLFA) analysis. For this purpose, 3 agricultural (AL) (farmland, apple orchard and 2 years abandoned land) and 4 rehabilitated lands (RL) of various vegetations grassland, shrubland, mixed forest (Amorpha fruticosa and Pinus tabuliformis Carr.) and forest (Robinia pseudoacacia) were selected. Our results showed higher soil organic carbon (SOC) contents in RL soils (forest >mixed forest >grassland>shrub land) than that in AL soils. In RL soils, soil microbial biomass and abundance of group specific PLFA were significantly higher than those in AL soils. Under different land-use types, microbial community was bacteria dominated over fungi. The microbial physiological indices (G+/G–, cyc/prec and S/M) indicated decreased environmental stress in RL soils in comparison with AL soils. In loess soils, SOC and total N correlated positively (p < 0.05) with microbial biomass C, N and P and also with fungal and bacterial PLFA, indicating a positive microbial mediation in improving soil fertility. Taking together, our findings suggest that land rehabilitation, especially Robinia pseudoacacia planation, improves overall edaphic conditions and accelerates soil microbial biomass accumulation in local regions.

Effect of Long Term Manuring on Carbon Sequestration Potential and Dynamics of Soil Organic Carbon Labile Pool Under Tropical Rice-Rice Agro-ecosystem

ABSTRACTSoil carbon sequestration is a complex process influenced by agricultural practices, climate and soil conditions. Labile organic carbon is sensitive to soil management practices and thus provides better management of carbon dynamics than total carbon alone. Thus, an attempt is made here to investigate the Carbon sequestration potential and labile pool of soil organic carbon (SOC) in post kharif-2014 in flooded tropical rice (Oryza sativa L.) under long-term fertilizer experiment started in the year 2005–06 in the central farm of Odisha University of Agriculture and Technology (OUAT) under All India Coordinated Research Project (AICRP) taking rice as a test crop. The experiment was laid out in a Randomized Block Design with quadruplicated treatments. The treatments include no fertilization, 100% N, 100% NP, 100% NPK, 150% NPK and 100% NPK+FYM. The results revealed that cultivation over the years caused a 14% decrease in SOC in unfertilized control over uncultivated soil. The carbon sequestration potential (1.77 Mg ha−1) was highest in 100%NPK +FYM treatment. The greater accumulation of microbial biomass C, water and extractable carbon (WEO-C), potassium permanganate oxidizable C (KMnO4-C) was recorded in 100%NPK + FYM treatment. The highest carbon management index (CMI) was computed in 100%NPK with FYM. CMI can be used as a more sensitive indicator of the rate of change of SOC in response to soil management changes. Results suggested that 100% NPK+ FYM are adequate for maintaining SOC stock and this practice may help in maintaining the sustainability of rice-rice cropping system.

Effects of vegetation type on the microbial characteristics of the fissure soil-plant systems in karst rocky desertification regions of SW China

In karst regions, shallow karst fissure (SKF) soil has proven to be an important plant habitat and soil resource. However, how plants affect the microbial abundance and community composition of SKF soil remains poorly studied. We explored the soil microbial community structure differences in fractured soil-plant systems by determining phospholipid fatty acid (PLFA) profiles under three vegetation types (herbs, shrubs and trees) in SKF and used a bare SKF without vegetation as the control in a karst rocky desertification area. The total microbial biomass and microbial community composition differed between surface soil and SKF soil. The total microbial biomass in surface soil was higher than that in SKF soil. In addition, in contrast to surface soil, the microbial communities in SKF soil were more vulnerable to the effects of environmental variables. Furthermore, plants had a significant positive effect on the accumulation of microbial biomass in surface and SKF soil: shrubs had the strongest effect, followed by trees. Vegetation types significantly affected the ratios of saturated PLFAs to monounsaturated PLFAs (SAT/MONO ratio) and cyclopropyl PLFAs to precursors (cy/pre ratio). In contrast to the SKF without vegetation, the SAT/MONO ratio and cy/pre ratio under grasslands, shrublands and trees were low. Herbs and shrubs had the greatest capacity to enhance the ability of soil to respond to environmental stress compared to trees. Our results suggest that, as an important plant habitat in karst regions, the condition of SKF soil should be urgently improved. The stereoscopic collocation of shrub-grass vegetation may be the preferred measure for vegetation restoration. Deep-rooted shrubs and grasses are best at improving soil and plant growth. Our study can be useful for developing strategies for vegetation rehabilitation in karst regions.

Predicting the Longitudinally and Radially Varying Gut Microbiota Composition using Multi-Scale Microbial Metabolic Modeling

Background: The gut microbiota is a heterogeneous group of microbes that is spatially distributed along various sections of the intestines and across the mucosa and lumen in each section. Understanding the dynamics between the spatially differential microbial populations and the driving forces for the observed spatial organization will provide valuable insights into important questions such as the nature of colonization of the infant gut and different types of inflammatory bowel disease localized in different regions of the intestines. However, in most studies, the microbiota is sampled only at a single site (often feces) or from a particular anatomical site of the intestines. Differential oxygen availability is putatively a key factor shaping the spatial organization. Results: To test this hypothesis, we constructed a community genome-scale metabolic model consisting of representative organisms for the major phyla present in the human gut microbiome. By solving step-wise optimization problems embedded in a dynamic framework to predict community metabolism and integrate the mucosally-adherent with the luminal microbiome between consecutive sections along the intestines, we were able to capture (i) the essential features of the spatially differential composition of obligate anaerobes vs. facultative anaerobes and aerobes determined experimentally, and (ii) the accumulation of microbial biomass in the lumen. Sensitivity analysis suggests that the spatial organization depends primarily on the oxygen-per-microbe availability in each region. Oxygen availability is reduced relative to the ~100-fold increase in mucosal microbial density along the intestines, causing the switch between aerobes and anaerobes. Conclusion: The proposed integrated dynamic framework is able to predict spatially differential gut microbiota composition using microbial genome-scale metabolic models and test hypotheses regarding the dynamics of the gut microbiota. It can potentially become a valuable tool for exploring therapeutic strategies for site-specific perturbation of the gut microbiota and the associated metabolic activities.

Rare taxa of alkaline phosphomonoesterase-harboring microorganisms mediate soil phosphorus mineralization

As a homologous gene encoding microbial alkaline phosphomonoesterase, the expression of phoD is critically controlled by P availability and thus contributes to the mineralization of soil organic P under P-depleted condition. However, its role in the regulation of soil P turnover is largely unknown due to the complex coupling of physiochemical and biological processes in the P cycle, especially in paddy field. We hypothesized that 1) P fertilization would decrease the abundance of phoD gene and change the composition of phoD-harboring microbial community and 2) the high abundance of phoD-harboring microorganisms in P-poor soil would stimulate the synthesis of alkaline phosphomonoesterase, thus mitigating P limitation via the mineralization of organic P. After 42 days of rice growth, the phoD abundance negatively correlated with soil P availability, and it was significantly higher in non-fertilized treatments than in P-fertilized treatments for both rhizosphere and bulk soils. A stronger competition among phoD-harboring microorganisms was detected in non-fertilized soil than in P-fertilized soil, with Bradyrhizobium, Methylobacterium, and Methylomonas being the dominant taxa in all samples. However, the high phoD gene abundance under P-poor condition was mainly due to the growth of rare operational taxonomic units (OTUs) affiliated to Actinobacteria and Cyanobacteria (relative abundance < 3%). Consistent with our hypothesis, the growth of phoD-harboring microorganisms stimulated the hydrolysis of organic P in non-fertilized soil. However, in the P-fertilized treatments, the increase in OTU abundance was accompanied by the depletion of exchangeable P and accumulation of microbial biomass P. Our findings suggest that phoD-harboring microorganisms have the potential to immobilize P in biomass when the supply is sufficient while mineralize organic P under P-poor condition, during which the rare taxa play an important role.

Impact of biological clogging on the barrier performance of landfill liners

The durability of landfill mainly relies on the anti-seepage characteristic of liner system. The accumulation of microbial biomass is effective in reducing the hydraulic conductivity of soils. This study aimed at evaluating the impact of the microorganism on the barrier performance of landfill liners. According to the results, Escherichia coli. produced huge amounts of extracellular polymeric substances and coalesced to form a confluent plugging biofilm. This microorganism eventually resulted in the decrease of soil permeability by 81%–95%. Meanwhile, the increase of surface roughness inside the internal pores improved the adhesion between microorganism colonization and particle surface. Subsequently, an extensive parametric sensitivity analysis was undertaken for evaluating the contaminant transport in landfill liners. Decreasing the hydraulic conductivity from 1 × 10−8 m/s to 1 × 10−10 m/s resulted in the increase of the breakthrough time by 345.2%. This indicates that a low hydraulic conductivity was essential for the liner systems to achieve desirable barrier performance.