Microbial Fatty Acids Research Articles

Alteration of organic matter during infaunal polychaete gut passage and links to sediment organic geochemistry. Part II: Fatty acids and aldoses

The activities of sediment-dwelling fauna are known to influence the rates of and pathways through which organic matter is cycled in marine sediments, and thus to influence eventual organic carbon burial or decay. However, due to methodological constraints, the role of faunal gut passage in determining the subsequent composition and thus degradability of organic matter is relatively little studied. Previous studies of organic matter digestion by benthic fauna have been unable to detect uptake and retention of specific biochemicals in faunal tissues, and have been of durations too short to fit digestion into the context of longer-term sedimentary degradation processes.Therefore this study aimed to investigate the aldose and fatty acid compositional alterations occurring to organic matter during gut passage by the abundant and ubiquitous polychaetes Hediste diversicolor and Arenicola marina, and to link these to longer-term changes typically observed during organic matter decay.This aim was approached through microcosm experiments in which selected polychaetes were fed with 13C-labelled algal detritus, and organisms, sediments, and faecal pellets were sampled at three timepoints over ∼6weeks. Samples were analysed for their 13C-labelled aldose and fatty acid contents using GC–MS and GC–IRMS.Compound-selective net accumulation of biochemicals in polychaete tissues was observed for both aldoses and fatty acids, and the patterns of this were taxon-specific. The dominant patterns included an overall loss of glucose and polyunsaturated fatty acids; and preferential preservation or production of arabinose, microbial compounds (rhamnose, fucose and microbial fatty acids), and animal-synthesised fatty acids. These patterns may have been driven by fatty acid essentiality, preferential metabolism of glucose, and A. marina grazing on bacteria.Fatty acid suites in sediments from faunated microcosms showed greater proportions of saturated fatty acids and bacterial markers than those from afaunal controls. Aldose suite alterations were similar in faunated microcosms and afaunal controls, however the impact of faunal gut passage on sedimentary aldose compositions may be observable over longer timescales. Therefore this study provides direct evidence that polychaete gut passage influences OM composition both through taxon-specific selective assimilation and retention in polychaete tissues, and also through interactions with the microbial community.

Fatty acid synthesis in Escherichia coli and its applications towards the production of fatty acid based biofuels

The idea of renewable and regenerative resources has inspired research for more than a hundred years. Ideally, the only spent energy will replenish itself, like plant material, sunlight, thermal energy or wind. Biodiesel or ethanol are examples, since their production relies mainly on plant material. However, it has become apparent that crop derived biofuels will not be sufficient to satisfy future energy demands. Thus, especially in the last decade a lot of research has focused on the production of next generation biofuels. A major subject of these investigations has been the microbial fatty acid biosynthesis with the aim to produce fatty acids or derivatives for substitution of diesel. As an industrially important organism and with the best studied microbial fatty acid biosynthesis, Escherichia coli has been chosen as producer in many of these studies and several reviews have been published in the fields of E. coli fatty acid biosynthesis or biofuels. However, most reviews discuss only one of these topics in detail, despite the fact, that a profound understanding of the involved enzymes and their regulation is necessary for efficient genetic engineering of the entire pathway. The first part of this review aims at summarizing the knowledge about fatty acid biosynthesis of E. coli and its regulation, and it provides the connection towards the production of fatty acids and related biofuels. The second part gives an overview about the achievements by genetic engineering of the fatty acid biosynthesis towards the production of next generation biofuels. Finally, the actual importance and potential of fatty acid-based biofuels will be discussed.

Occurrence and fate of fatty acyl biomarkers in an ancient whale bone (Oligocene, El Cien Formation, Mexico)

The taphonomic and diagenetic processes by which organic substances are preserved in animal remains are not completely known and the originality of putative metazoan biomolecules in fossil samples is a matter of scientific discussion. Here we report on biomarker information preserved in a fossil whale bone from an Oligocene phosphatic limestone (El Cien Fm., Mexico), with a focus on fatty acyl compounds. Extracts were quantitatively analysed using gas chromatography–mass spectrometry (GC–MS) and, to identify macromolecular-linked remains, demineralised extraction residues were subjected to catalytic hydropyrolysis (HyPy). To better recognise potential authentic (i.e. animal-derived) lipids, the data from the ancient bone were compared with those obtained from (i) the adjacent host sediment of the fossil and (ii) a recent whale (Phocoena phocoena) vertebra. In addition, the spatial distribution of organic and inorganic species was observed at the μm level by imaging MS (time-of-flight-secondary ion mass spectrometry, ToF-SIMS). Our results revealed a rather even distribution of hydrocarbon-, O- and N-containing ions in the trabecular network of the ancient bone. A different, more patchy arrangement of organic compounds was evident in the former marrow cavities that were partly cemented by clotted micrites of putative microbial origin. The concentration of fatty acids (FAs) in the ancient bone was in the permil range of the amount extracted from the recent whale vertebra. Endogenous compounds, including monoenoic n-C16 and n-C18 as well as branched FAs, were identified in the fossil bone by comparison with the host sediment. Ca. 80% of the prevalent n-C16 and n-C18 moieties in the ancient bone were extractable as FAs, whereas ca. 20% were covalently bound in the non-saponifiable kerogen fraction. Ample pyrite precipitates, distinctive 10-methyl branched FAs and microbial microborings (“tunneling”) indicate that sulfate reducers and collagen-degrading actinomycetes were central players in the microbial decomposition of the bone. Similarities with reported microbial FA patterns suggest that the FAs in the fossil bone were largely contributed by these microbial “last eaters”. The results highlight some of the degradation and preservation mechanisms during marine FA diagenesis in the “natural laboratory” of bones, and therefore the processes that lead to either degradation, preservation, or introduction of these widespread biomolecules in the fossils of ancient marine animals.

Distribution of microbial fatty acids and fatty alcohols in soils from an altitude transect of Mt. Jianfengling in Hainan, China: Implication for paleoaltimetry and paleotemperature reconstruction

The temperature gradient along the altitude transect of Mt. Jianfengling provides a good opportunity to establish and evaluate the microbial lipid-based environmental proxies. The soils collected from 14 different altitudes of Mt. Jianfengling contain abundant microbial fatty acids and fatty alcohols, including iso/anteiso fatty acids (i/aC12:0-i/aC19:0), 10-Me-C16:0 fatty acid, iso/anteiso fatty alcohols (i/aC13-iC26), 10-Me-C16:0 fatty alcohol and unsaturated fatty alcohols, which can indicate a strong microbial activity in the Jianfengling soils. The branched and unsaturated fatty alcohols can be only detected when saponification is performed, implying that these lipids are present as the constituents of bacterial wax esters in the soils. The ratio of aC15/iC15 fatty acids is positively correlated with altitude, suggesting that the decrease in temperature can induce the increase in the relative abundance of anteiso C15 fatty acid. In contrast, the ratio of aC15/iC15 fatty alcohols and of aC15/nC15 fatty alcohols both decrease with increased altitude or decreased temperature. Similarly, the ratio of nC18:1/nC18:0 fatty alcohols also decreases with decreased temperature, which is opposite to the previous observation that unsaturation of fatty acids in microorganism increases in response to decreased temperature. Besides, the average chain length (ACL) of long chain fatty alcohols (C22–C30) from leaf waxes and carbon preference index (CPI) of all n-fatty alcohols are also significantly correlated with altitude or mean annual temperature, demonstrating their potential for paleoclimate reconstruction. The correlation of microbial fatty acids and alcohols as well as ACL and CPI of plant wax-derived fatty alcohols with altitude may provide novel ways to reconstruct paleotemperature and paleoaltimetry.

Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions

Major efforts in bioenergy research have focused on producing fuels that can directly replace petroleum-derived gasoline and diesel fuel through metabolic engineering of microbial fatty acid biosynthetic pathways. Typically, growth and pathway induction are conducted under aerobic conditions, but for operational efficiency in an industrial context, anaerobic culture conditions would be preferred to obviate the need to maintain specific dissolved oxygen concentrations and to maximize the proportion of reducing equivalents directed to biofuel biosynthesis rather than ATP production. A major concern with fermentative growth conditions is elevated NADH levels, which can adversely affect cell physiology. The purpose of this study was to identify homologs of Escherichia coli FabG, an essential reductase involved in fatty acid biosynthesis, that display a higher preference for NADH than for NADPH as a cofactor. Four potential NADH-dependent FabG variants were identified through bioinformatic analyses supported by crystallographic structure determination (1.3- to 2.0-Å resolution). In vitro assays of cofactor (NADH/NADPH) preference in the four variants showed up to ≈ 35-fold preference for NADH, which was observed with the Cupriavidus taiwanensis FabG variant. In addition, FabG homologs were overexpressed in fatty acid- and methyl ketone-overproducing E. coli host strains under anaerobic conditions, and the C. taiwanensis variant led to a 60% higher free fatty acid titer and 75% higher methyl ketone titer relative to the titers of the control strains. With further engineering, this work could serve as a starting point for establishing a microbial host strain for production of fatty acid-derived biofuels (e.g., methyl ketones) under anaerobic conditions.

Continuous cultivation of photosynthetic bacteria for fatty acids production

In the present work, we introduced a novel approach for microbial fatty acids (FA) production. Photosynthetic bacteria, Rhodobacter sphaeroides KD131, were cultivated in a continuous-flow, stirred-tank reactor (CFSTR) at various substrate (lactate) concentrations. At hydraulic retention time (HRT) 4d, cell concentration continuously increased from 0.97 g dcw/L to 2.05 g dcw/L as lactate concentration increased from 30 mM to 60mM. At 70 mM, however, cell concentration fluctuated with incomplete substrate degradation. By installing a membrane unit to CFSTR, a stable performance was observed under much higher substrate loading (lactate 100mM and HRT 1.5d). A maximum cell concentration of 16.2g dcw/L, cell productivity of 1.9 g dcw/L/d, and FA productivity of 665 mg FA/L/d were attained, and these values were comparable with those achieved using microalgae. The FA content of R. sphaeroides was around 35% of dry cell weight, mainly composed of vaccenic acid (C18:1, omega-7).

Tailored fatty acid synthesis via dynamic control of fatty acid elongation

Medium-chain fatty acids (MCFAs, 4-12 carbons) are valuable as precursors to industrial chemicals and biofuels, but are not canonical products of microbial fatty acid synthesis. We engineered microbial production of the full range of even- and odd-chain-length MCFAs and found that MCFA production is limited by rapid, irreversible elongation of their acyl-ACP precursors. To address this limitation, we programmed an essential ketoacyl synthase to degrade in response to a chemical inducer, thereby slowing acyl-ACP elongation and redirecting flux from phospholipid synthesis to MCFA production. Our results show that induced protein degradation can be used to dynamically alter metabolic flux, and thereby increase the yield of a desired compound. The strategy reported herein should be widely useful in a range of metabolic engineering applications in which essential enzymes divert flux away from a desired product, as well as in the production of polyketides, bioplastics, and other recursively synthesized hydrocarbons for which chain-length control is desired.

Comparison of Whole-Cell Fatty Acid (MIDI) or Phospholipid Fatty Acid (PLFA) Extractants as Biomarkers to Profile Soil Microbial Communities

The whole-cell lipid extraction to profile microbial communities on soils using fatty acid (FA) biomarkers is commonly done with the two extractants associated with the phospholipid fatty acid (PLFA) or Microbial IDentification Inc. (MIDI) methods. These extractants have very different chemistry and lipid separation procedures, but often shown a similar ability to discriminate soils from various management and vegetation systems. However, the mechanism and the chemistry of the exact suite of FAs extracted by these two methods are poorly understood. Therefore, the objective was to qualitatively and quantitatively compare the MIDI and PLFA microbial profiling methods for detecting microbial community shifts due to soil type or management. Twenty-nine soil samples were collected from a wide range of soil types across Oregon and extracted FAs by each method were analyzed by gas chromatography (GC) and GC-mass spectrometry. Unlike PLFA profiles, which were highly related to microbial FAs, the overall MIDI-FA profiles were highly related to the plant-derived FAs. Plant-associated compounds were quantitatively related to particulate organic matter (POM) and qualitatively related to the standing vegetation at sampling. These FAs were negatively correlated to respiration rate normalized to POM (RespPOM), which increased in systems under more intensive management. A strong negative correlation was found between MIDI-FA to PLFA ratios and total organic carbon (TOC). When the reagents used in MIDI procedure were tested for the limited recovery of MIDI-FAs from soil with high organic matter, the recovery of MIDI-FA microbial signatures sharply decreased with increasing ratios of soil to extractant. Hence, the MIDI method should be used with great caution for interpreting changes in FA profiles due to shifts in microbial communities.

Vitamin B12 and homocysteine levels in blood of dairy cows during subacute ruminal acidosis

Abstract. The aim of this study was to investigate the variations of vitamin B12 and homocysteine in blood of dairy cows during subacute ruminal acidosis (SARA). On 228 subjects ruminal liquid was collected through rumenocentesis technique and rumen pH was immediately measured by a portable pH-meter. On the basis of pH values all cows were classified (bovine class) in Group A (animals with rumen pH>5.7), Group B (animals with rumen pH between 5.6 and 5.7) and Group C (animals with rumen pH<5.6). In relation to the acidosis risk depending on the rumen pH (herd class), the herds were classified in Group 1 (normal herds: less than 33 % cows with rumen pH<5.8), Group 2 (critical herds: more than 33 % cows with rumen pH between 5.5 and 5.8) and Group 3 (acidosis herds: more than 33 % cows with rumen pH<5.5). On blood samples, collected by jugular venipuncture, vitamin B12 and homocysteine were measured by chemiluminescent immunological tests. One-way analysis of variance (ANOVA), followed by Bonferroni test, showed significant differences (P<0.05) for vitamin B12 in bovine class and significant differences (P<0.05) for homocysteine in herd class. The influence of rumen pH values resulted in adequate vitamin B12 and homocysteine levels to meet microbial and cow requirements and fatty acids modifications in dairy cows affected by SARA. Moreover, the increase of vitamin B12 could be due to the presence of analogues which interfere with the transport of the vitamin. These findings provide more information on blood modifications during SARA.

인 결핍에 따른 하수배양 미세조류의 지방산 특성 분석 연구

하수에서 배양된 미세조류인 Chlorella vulgaris AG10032, Ankistrodesmus gracilis SAG278-2, Scenedesmus quadricauda AG10308은 오폐수에서 질소 및 인 제거가 우수하고 높은 지질을 함유하고 있어서, 오폐수에서 바이오연료나 기타 바이오 기반의 자원 회수에 유용한 생물자원이다. 오폐수 환경에는 다양한 인의 농도가 존재하는데, 인의 농도 특히 인 결핍조건에 따른 조류의 지방산 특성에 대한 정보가 매우 제한적이다. 이는 표준 분석방법이 정립되어 있지 않은데 일부 기인한다. 본 연구에서는 미생물의 지방산을 분석하는데 일반적으로 사용되는 무극성 컬럼법과 식물성 지질을 분석하는데 널리 사용되는 극성 WAX-type 컬럼 GC-FID 방법의 미세조류 지방산 분석 성능을 비교 분석하였고, 하수배양 조류에 적용이 보다 적절한 방법을 이용해서 인 결핍에 의한 조류 지방산 생성특성에 미치는 영향을 평가하였다. 그 결과 무극성 컬럼 방법에 비해 극성 WAX-type 컬럼 GC 방법이 <TEX>$C_{18:3}$</TEX> 지방산과 같은 고불포화지방산을 규명하는 분석능력이 우수하였고, 실제 하수배양에서 배양 분리된 미세조류의 지방산 분석에 보다 정확한 결과를 보이었다. 이 WAX-type 컬럼 방법으로 인 결핍 영향을 분석한 결과, 미세조류의 지방산 조성과 생성량은 인의 농도 변화에 크게 영향을 받지 않음을 밝히었다. Wastewater-adapted microalgae such as Chlorella vulgaris AG10032, Ankistrodesmus gracilis SAG278-2 and Scenedesmus quadricauda AG10308 are useful biological resources for recovering biofuel and other bio-based materials from wastewater because of their efficient removals of nitrogen and phosphorus from wastewater and their high fatty acid contents in biomass. Although the concentrations of phosphorus typically vary in wastewater environment, very little is known about the effect of phosphorus concentration, especially phosphorus starvation, on microalgal fatty acid synthesis. This is partially due to the lack of methodological establishment for algal fatty acid analysis. In this study, we compared the analysis performances of microalgal fatty acids by two different methods; one is a non-polar GC (gas chromatography) column based method, which is generally used for microbial fatty acids, and the other is a polar WAX-type GC column method, which is typically used for plant fatty acids. And then, we explored the effect of phosphorus concentration levels on fatty acid production in microalgae cultivated from wastewater. As results, the polar WAX-type column method has better ability to separate poly unsaturated fatty acids (PUFA) including <TEX>$C_{18:3}$</TEX> (linolenic acid), and was found to be more applicable in analyzing fatty acids from wastewater-cultivated microalgae than the non-polar column method. The fatty acid characterization by the WAX-type column method revealed little effect of phosphorus starvation on the quantity and composition of fatty acids from wastewater-cultivated microalgae.

Influence of Soil Acidification on Soil Microorganisms in Pear Orchards

To evaluate the influences of soil acidification on soil microorganisms and soil fertility, soil physicochemical and microbial properties were studied in pear orchards of Wendeng city where soil acidification is severe with soil pH value ranging from 4.06 to 6.59. Soil pH value was found to be significantly positively correlated with the amount of culturable bacteria (r = 0.935) and total extractable microbial fatty acids (r = 0.931) by correlation analysis and stepwise regression analysis, as well as amount of culturable actinomycetes (r = 0.865) and fluorescein diacetate hydrolysis activity (r = 0.780) by correlation analysis. Soil pH was determined to have a large influence on microbial community structure by principal component analysis of fatty acid methyl ester, which showed that microbial community structures were similar in soils with similar pH values. Being sensitive to environmental changes, soil microorganisms proved to be good indicators for the evaluation of soil health conditions and to monitor changes of soil quality.

Heterologous Co-expression of accA, fabD, and Thioesterase Genes for Improving Long-Chain Fatty Acid Production in Pseudomonas aeruginosa and Escherichia coli

The goal of the present study was to increase the content of intracellular long-chain fatty acids in two bacterial strains, Pseudomonas aeruginosa PA14 and Escherichia coli K-12 MG1655, by co-overexpressing essential enzymes that are involved in the fatty acid synthesis metabolic pathway. Recently, microbial fatty acids and their derivatives have been receiving increasing attention as an alternative source of fuel. By introducing two genes (accA and fabD) of P. aeruginosa into the two bacterial strains and by co-expressing with them the fatty acyl-acyl carrier protein thioesterase gene of Streptococcus pyogenes (strain MGAS10270), we have engineered recombinant strains that are efficient producers of long-chain fatty acids (C16 and C18). The recombinant strains exhibit a 1.3-1.7-fold increase in the production of long-chain fatty acids over the wild-type strains. To enhance the production of total long-chain fatty acids, we researched the carbon sources for optimized culture conditions and results were used for post-culture incubation period. E. coli SGJS17 (containing the accA, fabD, and thioesterase genes) produced the highest content of intracellular total fatty acids; in particular, the unsaturated fatty acid content was about 20-fold higher than that in the wild-type E. coli.

Microbial Communities of Alpine Meadow Soil in the Eastern Qinghai-Tibetan Plateau Subjected to Experimental Warming and Grazing*

oil microbes are important for many underground ecological processes and the change in their total biomass and community structure is regarded as a sensitive indicator for climate warming and human disturbances.Through open top chambers(OTCs) warming and clipping plus dung application,the effects of warming and grazing on soil microbial biomass and community structure were determined in an alpine meadow on the eastern Qinghai-Tibetan Plateau.The profiles of microbial phospholipid fatty acids(PLFAs) showed that soil microbial communities were dominated by bacteria in the growing seasons.An increase of 1.17 ℃ by OTCs warming soil at 10 cm depth resulted in a rise of 34.58% of total PLFAs,while the clipping plus dung application in spring caused a rise of 65.77%.Both experimental warming and grazing led to a significant change in soil microbial community structure.Compared to the control treatment,OTCs warming increased bacterial PLFAs by 8.80% and decresaed fungal PLFAs by 17.48%.The ratio of bacteria to fungi changed from 7.3 to 9.6.Grazing also markedly increased bacterial PLFAs by 8.40% and decreased fungal PLFAs by 14.04%.The ratio of bacteria to fungi increased to 9.2.The effects of OTCs warming and grazing on soil microbial biomass and community structure were found more notable than those of OTCs warming or grazing alone.Our results suggest that climatic warming and human disturbances might cause significant changes in soil microbial communities in a short period of time,which could have important effects on carbon budget and nutrient cycling in the alpine meadow ecosystem in the eastern Qinghai-Tibetan Plateau.

In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli

Microbial fatty acid derivatives are emerging as promising alternatives to fossil fuel derived transportation fuels. Among bacterial fatty acid synthases (FAS), the Escherichia coli FAS is perhaps the most well studied, but little is known about its steady-state kinetic behavior. Here we describe the reconstitution of E. coli FAS using purified protein components and report detailed kinetic analysis of this reconstituted system. When all ketosynthases are present at 1 μM, the maximum rate of free fatty acid synthesis of the FAS exceeded 100 μM/ min. The steady-state turnover frequency was not significantly inhibited at high concentrations of any substrate or cofactor. FAS activity was saturated with respect to most individual protein components when their concentrations exceeded 1 μM. The exceptions were FabI and FabZ, which increased FAS activity up to concentrations of 10 μM; FabH and FabF, which decreased FAS activity at concentrations higher than 1 μM; and holo-ACP and TesA, which gave maximum FAS activity at 30 μM concentrations. Analysis of the S36T mutant of the ACP revealed that the unusual dependence of FAS activity on holo-ACP concentration was due, at least in part, to the acyl-phosphopantetheine moiety. MALDI-TOF mass spectrometry analysis of the reaction mixture further revealed medium and long chain fatty acyl-ACP intermediates as predominant ACP species. We speculate that one or more of such intermediates are key allosteric regulators of FAS turnover. Our findings provide a new basis for assessing the scope and limitations of using E. coli as a biocatalyst for the production of diesel-like fuels.

Facile Determination of Double Bond Position in Unsaturated Fatty Acids and Esters by Low Temperature Plasma Ionization Mass Spectrometry

Unsaturated fatty acids and esters can be oxidized in situ during ionization using a low temperature plasma (LTP) probe. The discharge generates ozone from air that reacts with and cleaves olefins. The molecular ions of the resulting acid/ester oxidation products are present in the full scan mass spectra and are confirmed by exact mass measurements. The fragmentation information can be used to assign double bond positions. We have successfully applied this strategy to a range of mono-/polyunsaturated fatty acids and fatty acid methyl/ethyl esters to assign their double bond locations. The procedure allows rapid and direct identification of double bond positions in situ at atmospheric pressure without sample preparation prior to mass spectrometric analysis. Microbial fatty acid ethyl ester (FAEE) mixtures from complex bacterial samples were directly analyzed by this method. Structural confirmation of their diagnostic ions by using exact mass measurements and tandem mass spectrometry confirms double bond positions in unsaturated bacterial FAEEs.

Conversion of oil waste to valuable fatty acids using Oleaginous yeast

Oil waste poses a highly dangerous threat to the environment, mainly because it is considered a high energy demanding degradation process. Oleaginous yeast utilizing oil waste to produce microbial fatty acids is considered an innovative method for oil waste elimination. In the present study, fifteen yeast isolates were screened for their lipid content, three of which were chosen for their high lipid content as compared to the standard strain Phaffia rhodozyma NRRL-Y-10921. The three selected isolates were further screened for their fatty acid profile. Yeast isolate (NC-I), identified as Yarrowia lipolytica, was chosen because it exceeded the lipid production of the standard strain by 21%, it also produced the highest C 14:0 (myristic acid), C 18:1 (oleic acid) and C18:2 (linoleic acid), compared to the other two isolates. Growth on different oil wastes resulted in an increase in total lipid content which reached its maximum when oil waste of frying vegetables was added to the media (57.89%). A variation in the fatty acid profile was detected when different types of oil waste were used before and after fermentation. The addition of different glucose concentrations to the vegetable oil waste media resulted in the appearance of C 22:0 (behenic acid) which was not present when the basal medium was used. Scanning Electron Microscopy indicated morphologic changes when the yeast was grown in high glucose concentration as compared to those grown in oil waste media. The activity of malate dehydrogenase (MDH) enzyme exhibited a correlative relationship with the lipid content under various glucose concentrations. The obtained results indicate that vegetable oil waste is suitable for microbial fatty acid production and that the fatty acid profile could be maneuvered through the manipulation of the fermentation media.

Soil Microbial Community Diversity and Its Relationships with Geochemical Elements under different Farmlands in Shouguang, China

The aims of this study were to investigate soil microbial community characteristics and their interrelationships with soil geochemistry under different farmlands in Shouguang, China. The traditional dilution plate counts, BIOLOG system, and fatty acid methyl ester (FAME) analyses were used to assess microbial populations, substrate utilization, and fatty acid profiles. The number of aerobic heterotrophic bacteria varied significantly among untilled land, maize, and mungbean fields. The amounts of actinomycetes, fungal fatty acids, and Gram-positive/Gram-negative bacteria ratios varied greatly among celery, tomato, and aubergine fields. In the tomato field, the soil microbial community characteristics were significantly different from other fields. Principal component analysis of BIOLOG and FAME data revealed differences in the catabolic capability and fatty acid profiles of soil microbial communities among different farmlands. Spearman correlation analyses showed that in these sand clay soils of Shouguang, microbial communities in different farmlands were closely correlated with soil geochemical elements, moisture, and organic matter.

Forest floor properties across sharp compositional boundaries separating trembling aspen and jack pine stands in the southern boreal forest

Jack pine and trembling aspen are two early-seral boreal tree species with contrasting nutrient cycling strategies. Both species may form adjacent mono-specific stands separated by sharp compositional boundaries. We hypothesized that such boundaries result in wider functional ecotones. Spatial transitions in humus forms, forest floor chemistry and microbial communities were assessed across 32 m long transects set perpendicular to sharp compositional boundaries separating four jack pine and aspen stands. Split moving window analysis (SMWA) and moving window regression analysis (MWRA) were used to locate functional boundaries and ecotones. We found a gradual transition from moder (aspen) to mor (jack pine) humus spanning 16 m across the compositional boundary. An abrupt increase in forest floor water content at 3 m within jack pine stands was possibly due to aspen roots foraging for water beyond the boundary. The functional boundary and associated ecotone for forest floor pH, C:N ratio, Mg and ammonification were skewed toward jack pine stands, likely the result of aspen leaf dispersal. Low nitrification rates throughout jack pine stands and up to 11 m into aspen stands suggested that jack pine roots might extend far within aspen stands and produce metabolites that suppress nitrification. SMWA performed on the multivariate dataset of microbial fatty acids (FAs) revealed three distinct forest floor microbial communities that were skewed toward jack pine stands. Pine-type communities were associated to fungal FAs, pine-type and transition-type communities to non-fungal eukaryotic FAs, and aspen-type communities to bacterial FAs. Taken collectively, our data delimit a 24 m wide functional ecotone straddling sharp compositional boundaries separating trembling aspen and jack pine stands. We conclude that the functional diversity of boreal landscapes, where adjacent mono-specific stands are prevalent, is related to the patchiness of the landscape.

Study of human microecology by mass spectrometry of microbial markers

This review shows that mass spectrometry of microbial markers (MSMM) permits simultaneous in situ determination of more than one hundred microbial fatty acids in clinical, biotechnological or environmental samples, without precultivation and use of biochemical test materials and primers. Unprecedented information about the quantity of anaerobes and uncultivated aerobes, as well as actinobacteria, yeasts, viruses and microscopic fungi in one sample has provided a full understanding of microbial etiology in clinical conditions of patients. The study of intestine dysbiosis has confirmed the hypothesis about the nosological specificity of changes in the intestinal microbiota. It has been proven that infectious processes are polymicrobial. Measurements have shown that anaerobes dominate in number and functional activities in inflammation. The division of microbes into pathogenic and non- pathogenic is artificial. All microbes living in a human body simultaneously stay in both forms. Lactobacilli and bifidobacteria appear as agents of septic conditions and endocarditis. МSММ data confirm that anaerobes of Clostridium, Eubacterium, Propionibacterium, as well as actinobacteria of Streptomyces, Nocardia, Rhodococcus are mixed infection dominants. The data testify translocation of these microbes in inflammation loci from the intestine. Quantitative comparison of concentration of markers in the inflamed organ and blood proves reproduction of microorganisms in this locus. The current hypothesis is confirmed that the goal of translocation is not only infection, but also a biofilm formation similar to intestines, which stimulate local immunity, protection from local pathogens and restoration of the damaged tissues. Quantification using GC-MS revealed that the influence of antibiotics on the normal intestine's microbiota are not as dramatic as believed. Growth-promoting effects are the most important benefits of probiotic applications. The probiotic essence is not the microbial biomass itself, but growth factors, alarm molecules, and other factors of intestinal microbes. There are new possibilities in improving probiotics by using microbial 'consortia', modelling real gut microbiota.

Profiles of Microbial Fatty Acids in the Human Metabolome are Disease-Specific

The human gastrointestinal tract is inhabited by a diverse and dense symbiotic microbiota, the composition of which is the result of host–microbe co-evolution and co-adaptation. This tight integration creates intense cross-talk and signaling between the host and microbiota at the cellular and metabolic levels. In many genetic or infectious diseases the balance between host and microbiota may be compromised resulting in erroneous communication. Consequently, the composition of the human metabolome, which includes the gut metabolome, may be different in health and disease states in terms of microbial products and metabolites entering systemic circulation. To test this hypothesis, we measured the level of hydroxy, branched, cyclopropyl and unsaturated fatty acids, aldehydes, and phenyl derivatives in blood of patients with a hereditary autoinflammatory disorder, familial Mediterranean fever (FMF), and in patients with peptic ulceration (PU) resulting from Helicobacter pylori infection. Discriminant function analysis of a data matrix consisting of 94 cases as statistical units (37 FMF patients, 14 PU patients, and 43 healthy controls) and the concentration of 35 microbial products in the blood as statistical variables revealed a high accuracy of the proposed model (all cases were correctly classified). This suggests that the profile of microbial products and metabolites in the human metabolome is specific for a given disease and may potentially serve as a biomarker for disease.