Abundance Of Gram-negative Bacteria Research Articles

Proactive Monitoring of Changes in the Microbial Community Structure in Wastewater Treatment Bioreactors using Phospholipid Fatty Acid Analysis

Diverse microbial community structures (MCS) in wastewater treatment plants (WWTPs) are vital for effectively removing nutrients and chemicals from wastewater. However, the regular monitoring of MCS in WWTP bioreactors remains unattractive owing to the skill and cost required for deploying modern microbial molecular techniques in the routine assessment of engineered systems. In contrast, low-resolution methods for assessing broad changes in the MCS, such as phospholipid fatty acid (PLFA) analysis, have been used effectively in soil studies for decades. Despite using PLFA analysis in soil remediation studies to capture the long-term effects of environmental changes on MCS, its application in WWTPs, where the microbial mass is dynamic and operational conditions are more fluid, remains limited. In this study, microbial communities in a controlled pilot plant and 12 full-scale activated sludge plants (ASPs) were surveyed over a two-year period using PLFA analysis. This study revealed that changes in the MCS in wastewater bioreactors could be detected using PLFA analysis. The MCS comprised 59% Gram-negative and 9% Gram-positive bacteria, 31% fungi, and 1% actinomycetes. The abundances of Gram-negative bacteria and fungi were strongly inversely correlated, with an R2 = 0.93, while the fatty acids cy17:0 and 16:1ω7c positively correlated (R2 = 0.869). Variations in temperature, solid retention time, and WWTP configuration significantly influenced the MCS in activated sludge reactors. This study showed that WWTP bioreactors can be routinely monitored using PLFA analysis, and changes in the bioreactor profile that may indicate imminent bioreactor failure can be identified.

Inhaled polystyrene microplastics impaired lung function through pulmonary flora/TLR4-mediated iron homeostasis imbalance

Microplastics (MPs) have been found in the air, human nasal cavity, and lung, suggesting that the respiratory tract is one of the important exposure routes for MPs. The lung is a direct target organ for injury from inhaled MPs, but data on lung injury from longer-term exposure to environmental doses of MPs are limited, and the mechanisms remain unclear. Here, C57BL/6 J mice were treated with 5 μm polystyrene (PS)-MPs by intratracheal instillation (0.6, 3, and 15 mg/kg) for 60 days to establish MPs exposure model. We found that PS-MPs lead to increased collagen fibers and decreased lung barrier permeability and lung function in lung tissue. Mechanistically, the abundance of gram-negative bacteria in the pulmonary flora increased after inhalation of PS-MPs, causing lipopolysaccharide (LPS) release. The expression of Toll-like receptor 4 (TLR4), the key receptor of LPS, was increased, and ferroptosis occurred in lung tissue cells. Further in vitro intervention experiments were performed, pulmonary flora/TLR4-induced imbalance of lung iron homeostasis is an important mechanism of PS-MPs-induced lung injury. Our study provides new evidence for lung injury caused by environmental doses of MPs and strategies to prevent it through longer-term dynamic observation.

Differential responses of soil community to reclamation with legumes versus grasses after an application of blended amendments in mining-disturbed soils

Alkaline and organic amendment are effective options to ensure successful phytostabilization in mining-disturbed soil ecosystems. However, the different effects of a blended amendment composed of coal fly ash, compost, and biochar (BCC) on soil microorganisms in mining-disturbed soil ecosystems restored with legumes versus grasses remain unknown. Therefore, we conducted a field experiment to measure the influences of amendment blends on soil physicochemical properties, plant growth parameters, and soil microbial community in mining-disturbed soils after vegetation restoration with legumes versus grasses. We found soil organic matter (SOM), nutrient availability (e.g., available potassium), and soil pH, regulated by the amendment blends, were the dominant edaphic predictors explaining the soil community changes. Specifically, the abundance of gram-negative bacteria and arbuscular mycorrhizal fungi in the field plots restored with legumes increased greater than those in the field plots restored with grasses (P < 0.05). Application of the amendment blends further increased the relative abundances of the total bacteria and total fungi, and decreased the fungal: bacterial ratio in the field plots restored with legumes (P < 0.05), while no significant changes were found for those in the field plots restored with grasses. Moreover, our structural equation model suggests that the shifts in the microbial community after incorporation of the amendment blends were driven by the increased SOM and soil nutrient availability (e.g., potassium), and enhanced soil pH. We thus suggest that legume-based vegetation restoration combined with a blend amendment holding the comprehensive functions of acidic amelioration and nutrient-building would be a preferable option for ecological restoration in the mining-disturbed regions.

Carbon and Nitrogen Availability Drives Seasonal Variation in Soil Microbial Communities along an Elevation Gradient

Changes in soil abiotic and biotic properties can be powerful drivers of feedback between plants and soil microbial communities. However, the specific mechanisms by which seasonal changes in environmental factors shape soil microbial communities are not well understood. Here, we collected soil samples from three sites along an elevational gradient (200–1200 m) in subtropical forests with unvarying canopy vegetation. We used an elevation gradient with similar annual precipitation but a clear temperature gradient, and phospholipid fatty acids (PLFAs) were measured to determine the seasonal variations in the composition of soil microbial communities in response to rising temperatures. Our results showed that the abundance of Gram-negative bacteria and total PLFAs were the lowest at low elevations in winter, and the ratio of Gram-positive to Gram-negative bacteria decreased with increasing elevation. However, the biomass of other microbial groups was the highest at medium elevations in summer, with the exception of actinomycetes species and fungi. Regardless of seasonal changes, soil fungal biomass tended to increase with increasing elevation. Moreover, in summer, microbial carbon use efficiency (CUE) increased with increasing elevation, whereas an opposite trend was observed in winter. Redundancy analysis and structural equation modeling showed that the dissolved organic carbon in soil was the main factor affecting the microbial communities along the elevation gradient in winter, whereas in summer, the microbial community structure was driven by shifting nitrogen availability, with both being associated with changing microbial CUE. As such, this study demonstrates distinct seasonal changes in the soil microbial community composition across an elevation gradient that are driven by carbon and nitrogen resource availability and shifts in microbial CUE. Furthermore, our results suggest that the interaction of underground plant roots and microbes drives changes in resource availability, thereby resulting in seasonal variation in soil microbial community composition across an elevation gradient.

The Role of Probiotic Bacillus Spores and Amino Acids with Immunoglobulins on a Rat Enteropathy Model.

Non-steroidal anti-inflammatory drugs (NSAIDs) are some of the most widely used drugs due to their anti-inflammatory, analgesic and antipyretic pharmacological effects. Gastrointestinal side effects are some of the most severe and frequent side effects of NSAIDs. These depend on the balance of the gut microbiome, the abundance of Gram-negative bacteria, and the amount of lipopolysaccharide released. Therefore, restoring or improving gut bacteria balance with probiotic supplements could prove to be an adjuvant therapy against mild NSAID-induced enteropathy. Twenty-five Wistar albino male rats were divided into five groups. The negative control group was administered carboxymethylcellulose and the positive control group diclofenac (DIC), 8 mg/kg for 7 days, which represented the enteropathy model. Treatment groups consisted of a combination of pro-biotic spores (MSB), amino acids and immunoglobulins supplement (MM), which were also administered for 7 days. We analyzed hepatic injury markers (AST, ALT) and creatinine, and inflammatory markers, IL-6, TNF-α, PGE2, iNOS, as well as total antioxidant capacity. The results obtained in the present study suggest that the modulation of the intestinal microbiota by administration of probiotics (Bacillus spores), alone or in combination with immunoglobulins and amino acids, represents an attractive therapy for the prevention of NSAID-induced enteropathy.

Arctic soil respiration and microbial community structure driven by silicon and calcium

Global warming is most pronounced in the Arctic region. Greenhouse gas (GHG) release from Arctic soils increase due to global warming. By this, the Arctic may change from currently being a carbon sink to a future source. To improve accurate predictions of future GHG release from Arctic soils, it is important to unravel factors controlling both the microbial community structure and activity. Soil microbial activity is important for Arctic greenhouse gas production, but depends on soil conditions such as salinity being increased by calcium (Ca) and decreased by amorphous silica (Si) potentially enhancing water availability. In the Arctic, climate changes may alter salinity by changing Si and Ca concentrations upon permafrost thaw as a result of global warming with Si potentially decreasing and Ca potentially increasing salinity. Here, we show that higher Si concentration increased and higher Ca concentrations decreased the microbial CO2 production for both a salt-poor and a salt-rich soil from Greenland. In the salt-rich soil, Si amendment increased CO2 production and the abundance of gram-negative bacteria. However, the bacterial community became dominated by spore-forming gram-positive Firmicutes and Actinobacteria. The CO2 release from soils was directly affected by the abundance of bacteria and fungi, and their community structure. Our results highlight the importance of the soil Si and Ca concentration on organic carbon turnover by strongly changing microbial abundance and community structure, with consequences for CO2 release in the Arctic. Consequently, Ca and Si and their relation to Arctic soil microbial community structure has to be considered when estimating pan-Arctic carbon budgets.

Cynanchum atratum Alleviates Non-Alcoholic Fatty Liver by Balancing Lipogenesis and Fatty Acid Oxidation in a High-Fat, High-Fructose Diet Mice Model.

Cynanchum atratum, a medicinal herb, is traditionally used as an antidote, diuretic, and antipyretic in eastern Asia. The current study aimed to investigate the anti-fatty liver capacity of the ethanol extract of Cynanchum atratum (CAE) using a 10-week high-fat, high-fructose diet mouse model. A six-week treatment of CAE (from the fifth week) significantly attenuated the weights of the body, liver, and mesenteric fat without a change in diet intake. CAE also considerably restored the alterations of serum aminotransferases and free fatty acid, fasting blood glucose, serum and hepatic triglyceride, and total cholesterol, as well as platelet and leukocyte counts. Meanwhile, CAE ameliorated hepatic injury and lipid accumulation, as evidenced by histopathological and immunofluorescence observations. Additionally, CAE significantly lowered the elevation of hepatic TNF-α, the TNF-α/IL-10 ratio, fecal endotoxins, and the abundance of Gram-negative bacteria. Hepatic lipogenesis and β-oxidation-related proteins and gene expression, including PPAR-α, SREBP-1, SIRT1, FAS, CTP1, etc., were normalized markedly by CAE. In particular, the AMPK, a central regulator of energy metabolism, was phosphorylated by CAE at an even higher rate than metformin. Overall, CAE exerts anti-hepatic steatosis effects by reducing lipogenesis and enhancing fatty acid oxidation. Consequently, Cynanchum atratum is expected to be a promising candidate for treating chronic metabolic diseases.

Localized plant-soil-microbe interactions regulate spatial variations of soil oxidase activities within afforested systems in a subtropical area

Soil oxidases play a vital role in soil organic carbon decomposition. However, the question how biotic and abiotic factors interactively affect spatial variations of soil oxidase activities within ecosystems remains unresolved. Here, we identified soil oxidase (peroxidase (PER) and polyphenol oxidase (PPO)) activities at different locations within two afforested systems (coniferous woodland and leguminous shrubland), and investigated the associated variables of vegetation, soil environments, microbial communities and spatial structure to explore their relative importance in regulating oxidase activities. Our results showed that 32.5%–46.9% of variations in oxidase activities could be explained by the localized effects of vegetation, soil environments and microbial communities. Plant-soil-microbe interactions explained more variations of oxidases compared to the sole fraction of each group. High oxidase activities were closely associated with high pH and low present litter biomass. Meanwhile, the abundance of gram-negative bacteria was the key microbial factor on oxidase activities in the woodland, while the abundance of gram-positive bacteria was the key factor on PER activity in the shrubland. Taken together, our results provide novel experimental insight into spatial variability of soil oxidases, and reveal a profound impact of key vegetation, soil and microbial factors and their localized interactions on spatial patterns of soil oxidases at ecosystem-level.

Effects of Thinning on Microbial Community Structure in the Organic Horizon of Chinese Pine Plantations in Badaling, Beijing, China

Research Highlights: Moderate thinning can effectively improve forestry production and change the microenvironment of understory vegetation. Background and Objectives: Microbial communities control the decomposition and transformation of forest organic matter; however, the influence of thinning on microbes in the organic horizon remains unclear. Materials and Methods: In this study, we subjected four plots of Chinese pine plantations in Badaling, Beijing to different thinning intensities, including no thinning (T0), low-intensity thinning (T10), medium-intensity thinning (T20), and high-intensity thinning (T50). The changes in chemical properties and microbial community compositions observed in the organic horizon, which comprised undecomposed litter (L layer) and half-decomposed litter (F layer), were analyzed after thinning. Microbial community compositions were evaluated using phospholipid fatty acid (PLFA) methods. Results: The results showed that the abundances of gram-negative bacteria (GN) and total bacteria (B) under the T10 thinning condition were the highest among the four thinning intensities, and the abundance of arbuscular mycorrhizal fungi (AMF) in T20 was higher than under other thinning intensities. The abundance of gram-positive bacteria (GP) and actinobacteria (ACT) in T10 was lower than in both T0 and T50. The abundance of total PLFAs and fungi (FU) was higher in the L layer, whereas the abundance of GP, GN, B, ACT, and AMF was higher in the F layer. Conclusions: Our results demonstrated that the L layer better reflects the influence of thinning on litter. Redundancy analysis (RDA) results indicated that the organic carbon (LOC) , dissolved organic carbon (DOC), and ammonium nitrogen (NH4+-N)contents of litter were primarily responsible for the observed changes in microbial community structure, with LOC alone explaining 62.6% of the total variance among the litter substrate factors selected. Overall, moderate-intensity thinning of Pinus tabulaeformis Carr. plantations created more favorable conditions for microbial communities in the organic horizon.

Obligate anaerobes are abundant in human necrotizing soft tissue infection samples - a metagenomics analysis.

Necrotizing soft tissue infections (NSTIs) are associated with high morbidity and mortality and are increasing in incidence. Proper identification of the microbial causes of NSTIs is a crucial step in diagnosis and treatment, but the majority of data collected are culture based, which is biased against fastidious organisms, including obligate anaerobes. The goal of this study was to address this gap in knowledge by characterizing NSTI microbial communities through molecular diagnostics. We performed 16S rRNA sequencing on human NSTI samples and identified five genera most commonly found in NSTIs (Prevotella, Bacteroides, Peptoniphilus, Porphyromonas, and Enterococcus). We found that a >70% contribution of obligate anaerobes to the bacterial population distribution was associated with NSTI mortality, and that NSTI samples, from both survivors and non‐survivors, had an increased relative abundance of gram negative bacteria compared to those of abscess patients. Based on our data, we conclude that obligate anaerobes are abundant in NSTIs and a high relative abundance of anaerobes is associated with a worse outcome. We recommend increasing anaerobe antibiotic coverage during the treatment of NSTIs even when anaerobes are not found by traditional clinical microbiology methods, and especially when there is a clinical suspicion for anaerobe involvement.

Microbial inoculation of seeds characteristically shapes the rhizosphere microbiome in desi and kabuli chickpea types

Chickpea is generally cultivated after seed treatment with host-specific Mesorhizobium ciceri, the nitrogen-fixing bacterium forming root nodules. Some species of free-living cyanobacteria are capable of nitrogen fixation. We examined the rhizosphere microbiota changes and the potential for plant growth promotion by applying a free-living, nitrogen-fixing cyanobacterium and the biofilm formulation of cyanobacterium with M. ciceri, relative to M. ciceri applied singly, to two each of desi and kabuli varieties of chickpea. Denaturing gradient gel electrophoresis (DGGE) profiles of archaeal, bacterial and cyanobacterial communities and those of phospholipid fatty acids (PLFAs) were obtained to evaluate the changes of the microbial communities in the chickpea rhizosphere. Plant growth attributes, including the pod yields and the availabilities of soil macronutrients and micronutrients, were monitored. The DGGE profiles showed distinct and characteristic changes due to the microbial inoculation; varietal differences exerted a marked influence on the archaeal and cyanobacterial communities. However, bacterial communities were modulated more by the type of microbial inoculants. Abundance of Gram-negative bacteria (in terms of notional PLFAs) differed between the desi and the kabuli varieties inoculated with M. ciceri alone, and the principal component analysis of PLFA profiles confirmed the characteristic effect of microbial inoculants tested. Microbial inoculation led to increases in the 100-seed weight and differential effects on the concentrations of available nitrogen and phosphorus, and those of iron, zinc and copper, suggesting their increased cycling in the rhizosphere. Microbial inoculation of chickpea brought out the characteristic changes in rhizosphere microbiota. Consequently, the growth promotion of chickpea and nutrient cycling in its rhizosphere distinctively differed. Further studies are needed to analyse the association and dynamic changes in the microbial communities to define the subset of microorganisms selected by chickpea in its rhizosphere and the influence of microbial inoculation.

Shift in soil microbial communities with shrub encroachment in Inner Mongolia grasslands, China

The ongoing expansion of shrub encroachment into grasslands represents a unique form of land cover change. How this process affects soil microbial communities is poorly understood. In this study, we aim to assess the effects of shrub encroachment on soil microbial biomass, abundance and composition by comparing data between shrub patches and neighboring herb patches in shrub-encroached grasslands (SEGs) in Inner Mongolia, China. Fourteen SEG sites from two ecosystem types (typical and desert grasslands) were investigated. The phospholipid fatty acid (PLFA) method was used to analyze the composition and biomass of the soil microbial community. Our results showed that the top-soil microbial biomass and abundances of gram-negative bacteria, arbuscular mycorrhizal fungi, and actinomycetes were significantly higher in shrub patches than in herb patches in both typical and desert grasslands (P < 0.05). The fungi to bacteria ratio was significantly higher in shrub patches than in herb patches in desert grassland (P < 0.05). The microbial biomass was positively associated with mean annual precipitation, total nitrogen and available phosphorus, and negatively associated with mean annual temperature. Our results also indicated that the variation in microbial composition was largely explained by edaphic factors, followed by climate factors. In conclusion, shrub encroachment in Inner Mongolia grasslands has significantly influenced the structure and abundance of soil microbial communities, which makes the microbial communities toward a fresh organic carbon-based structure. This study highlights the importance of edaphic and climate factors in microbial community shifts in SEGs.

Primary effects of extracellular enzyme activity and microbial community on carbon and nitrogen mineralization in estuarine and tidal wetlands.

Estuarine and tidal wetlands with high primary productivity and biological activity play a crucial role in coastal nutrient dynamics. Here, to better reveal the effects of extracellular enzymes and microbial community on carbon (C) and nitrogen (N) mineralization, the incubation experiments with different C and N addition patterns to the tidal sediments of the Yangtze Estuary (China) were conducted. The results suggested a significant increase in cumulative CO2 effluxes in the C and CN treatment experiments, while no significant difference in cumulative CO2 effluxes between the N treatment and control (CK) experiments was observed. In addition, the nutrient addition patterns had a great influence on dissolve organic C and N levels, but a small effect on microbial biomass C and N. Microbial community composition and microbial activity were found to be positively correlated with organic C (OC) and the molar ratio of C to N (C/N). Partial correlation analysis, controlling for C/N, supported direct effects of OC on the activity of carbon-cycling extracellular enzymes (cellulase and polyphenol oxidase), while C/N exhibited negatively correlations with urease and Gram-positive bacteria to Gram-negative bacteria (G+/G-). Strong relationships were found between CO2 efflux and mineral nitrogen with the activity of specific enzymes (sucrase, cellulase, and polyphenol oxidase) and abundances of Gram-negative bacteria, arbuscular mycorrhizal fungi, and fungi, suggesting the significant influences of microbial community and enzyme activity on C and N mineralization in the estuarine and tidal wetlands. Furthermore, this study could highlight the need to explore effects of nutrient supply on microbial communities and enzyme activity changes associated with the C and N mineralization in these wetlands induced by the climate change.

Endotoxemia unrequired in the pathogenesis of pediatric nonalcoholic steatohepatitis

Nonalcoholic steatohepatitis (NASH), the severe form of nonalcoholic fatty liver disease, is a serious liver complication associated with obesity. Several studies suggest that endotoxemia is associated with nonalcoholic fatty liver disease and NASH. We aimed to study the correlation of gut microbiome composition and the incidence of endotoxemia in obese patients and NASH patients in comparison with normal controls. The abundance of Gram-negative bacteria in the gut microbiomes of normal controls, obese patients with normal liver, and biopsy-proven NASH patients were assessed using 16S rRNA pyrosequencing data. Serum endotoxin was determined by endpoint limulus amebocyte lysate assay. Higher abundance of Gram-negative bacteria in gut microbiome was observed in obese and NASH patients in comparison with normal controls, but no difference was detected between obese and NASH patients. Serum endotoxin is higher in the NASH group than the normal controls. In addition, the obese and NASH patients had a higher incidence of endotoxemia compared with normal controls. However, Spearman's test found no correlation between the abundance of Gram-negative bacteria and serum endotoxin levels. The majority of the NASH patients and the obese patients had low serum endotoxin level. Among NASH patients, serum endotoxin is not correlated with disease severity. Our data suggest that the gut microbiome composition does not contribute to the incidence of endotoxemia in NASH, and endotoxemia is not required in the pathogenesis of NASH. Our observations highlight the current concept that multiple factors contribute to the development of NASH.

Biotransformation of atrazine and metolachlor within soil profile and changes in microbial communities

Biotransformation studies of atrazine, metolachlor and evolution of their metabolites were carried out in soils and subsoils of Northern Greece. Trace atrazine, its metabolites and metolachlor residues were detected in field soil samples 1year after their application. The biotransformation rates of atrazine were higher in soils and subsoils of field previously exposed to atrazine (maize field sites) than in respective layers of the field margin. The DT50 values of atrazine ranged from 5 to 18d in the surface layers of the adapted soils. DT50 values of atrazine increased as the soil depth increased reaching the value of 43d in the 80–110cm depth layer of adapted soils. Metolachlor degraded at slower rates than atrazine in surface soils, subsoils of field and field margins with the respective DT50 values ranging from 56 to 72d in surface soils and from 165 to 186d in subsoils. Hydroxyatrazine was the most frequently detected metabolite of atrazine. The maximum concentrations of metolachlor-OXA and metolachlor-ESA were detected in the soil layers of 20–40cm depth after 90d of incubation. Principal Component Analysis (PCA) of soil Phospholipid Fatty Acids (PLFAs), fungal/bacterial and Gram-negative/Gram-positive ratios of the PLFA profiles revealed that the higher biotransformation rates of atrazine were simultaneously observed with the abundance of Gram-negative bacteria while the respective rates of metolachlor were observed in soil samples with abundance of fungi.

Organic matter in sediments of an acidic mining lake as assessed by lipid analysis. Part I: Fatty acids

Fatty acid (FA) patterns of sediments collected from the bottom of an acidic mine pit lake (AML) at different depths (surface sediment: 0 to 1cm; deep sediment: 4 to 5cm) were studied to characterize microbial communities and the sources of sedimentary organic matter (SOM). Studies were performed on the molecular level utilizing source-specific, diagnostic FA biomarkers. The biomarker-based approach has been used widely in marine sediment studies, but has not been applied for sediments from AMLs so far.Combined FA concentrations in the surface sediment were higher compared to those in the deep sediment (497 vs. 127μgg−1d.w., respectively). This was related to deposition of autochthonous biomass and higher terrestrial plants onto the surface sediment, as well as – to lesser extent – with higher bacterial activity on the sediment-water interface. The FA distribution in both sediments was characterized by a strong even-over-odd preference and was bimodal in nature: there was a cluster at nC14–nC18 characteristic of chiefly autochthonous (algal and bacterial) SOM production, and another cluster at nC22–28 related to input from higher plants. The FA distribution in the surface sediment pointed to higher terrestrial input compared to autochthonous contribution to SOM (67%:33%) as an estimate. Fingerprinting of viable bacteria was accomplished through signature FA markers including branched C15 and C17 surrogates, cyclopropanoic acids, 3-hydroxy (OH) acids and monounsaturated surrogates with unusual double bond localization. The abundance of Gram-negative bacteria was higher in the surface sediment as evidenced by total diagnostic 3-OH-fatty acids (37μgg−1 versus 25μgg−1). Potential source taxa in both sediment layers included acidophilic iron- and sulfur-oxidizing bacteria including Acidithiobacillus ferrooxidans. High abundances of terminally branched C15 and C17 surrogates in both sediments pointed to sulfate- and iron-reducing bacteria. Signature FAs characteristic of methanotrophs were virtually lacking in both sediments.

Sources of organic matter and microbial community structure in the sediments of the Visakhapatnam harbour, east coast of India

Organic matter in the coastal sediments originates from various terrestrial and marine sources. Within the sampling sites, relative inputs from these sources may vary and can influence the microbial community structure. In order to identify the sources of organic matter, and its influence on microbial community structure in coastal environment, 19 surface sediment samples were collected from various stations in the Visakhapatnam harbour, east coast of India. These samples were analyzed for organic carbon (OC) content, bulk ∂ 13C signatures, and the concentration and composition of phospholipid fatty acids (PLFAs). Contents of OC, ∂ 13C oc values, and PLFA concentrations varied spatially and ranged from 0.6 to 7.6%, − 29.32 to − 23.75‰, and 0.30 to 33.30 μg g − 1 dw sediment, respectively. The bulk ∂ 13C oc of sediments reflected mixed carbon sources from marine and terrestrial end members with dominance of the latter at most of the stations. The PLFA community was not influenced by concentration and source of OC. Saturated PLFAs were the most abundant followed by monounsaturated fatty acids (MUFAs), branched PLFAs, and polyunsaturated fatty acids (PUFAs). MUFAs indicate the abundance of Gram negative bacteria, cynobacteria and microalgae. The Branched PLFAs (iso and anteiso) suggest the presence of Gram positive bacteria, Gram negative anaerobes and sulfate reducing bacteria. Similarly, PUFAs indicate the presence of eukaryotes. Moreover, the presence of trans-monounsaturated PLFAs in the harbour sediments imply that PLFA community was under stress due to contamination of the sampling sites by sewage and industrial waste, sulfur and petroleum products. Principal component analysis (PCA) based on concentrations of PLFAs established three factors that accounted for 81% of the total variance. The first factor contributed 57% of variance, and was mostly influenced by MUFAs and branched PLFAs. The second factor was controlled by PUFAs such as C20:3n6, C18:3n3, C20:4n6, C20:5n3 and C22:6n3, whereas the third factor was influenced by C20:3n3, C22:2 and C22:1n9. PLFA community in the Visakhapatnam harbour sediments was mostly dominated by bacteria along with some contribution from eukaryotes.

Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient

Abstract. Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; Caricetum gracilis at the wet depression and Arrhenatheretum elatioris at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.

Microbial community structure in biofilms and water of a drinking water distribution system determined by lipid biomarkers

The development of microbial communities in biofilms of a drinking water distribution system was monitored, and compared to the microbial communities in water. The microbial communities were studied by phospholipid fatty acid (PLFA) profiles. In drinking water samples the most common PLFAs, with the proportion of 60.9%, were monoenoic fatty acids, such as 16:1omega7c and 18:1omega7c, indicating high abundance of gram-negative bacteria. Instead, in biofilm samples saturated fatty acids, such as 16:0 and 18:0, indicating general biomass, accounted for 54.9-78.4% of the total PLFAs. The proportions of monoenoic fatty acids in biofilm increased from 11.5% to 31.2% with water aging from 22 h to 62 h in the distribution system. In conclusion, water aging affected the structure of microbial communities in biofilms, and the microbes in water differed from those in biofilms. These differences might also reflect the differences in the physiological state of the microbes, which is influenced by water chemistry and by the growth environment, i.e. water or biofilm.

Variations in microbial community composition through two soil depth profiles

Soil profiles are often many meters deep, but with the majority of studies in soil microbiology focusing exclusively on the soil surface, we know very little about the nature of the microbial communities inhabiting the deeper soil horizons. We used phospholipid fatty acid (PLFA) analysis to examine the vertical distribution of specific microbial groups and to identify the patterns of microbial abundance and community-level diversity within the soil profile. Samples were collected from the soil surface down to 2 m in depth from two unsaturated Mollisol profiles located near Santa Barbara, CA, USA. While the densities of microorganisms were generally one to two orders of magnitude lower in the deeper horizons of both profiles than at the soil surface, approximately 35% of the total quantity of microbial biomass found in the top 2 m of soil is found below a depth of 25 cm. Principal components analysis of the PLFA signatures indicates that the composition of the soil microbial communities changes significantly with soil depth. The differentiation of microbial communities within the two profiles coincides with an overall decline in microbial diversity. The number of individual PLFAs detected in soil samples decreased by about a third from the soil surface down to 2 m. The ratios of cyclopropyl/monoenoic precursors and total saturated/total monounsaturated fatty acids increased with soil depth, suggesting that the microbes inhabiting the deeper soil horizons are more carbon limited than surface-dwelling microbes. Using PLFAs as biomarkers, we show that Gram-positive bacteria and actinomycetes tended to increase in proportional abundance with increasing soil depth, while the abundances of Gram-negative bacteria, fungi, and protozoa were highest at the soil surface and substantially lower in the subsurface. The vertical distribution of these specific microbial groups can largely be attributed to the decline in carbon availability with soil depth.