Signature Lipid Biomarkers Research Articles

Intact polar lipidome and membrane adaptations of microbial communities inhabiting serpentinite-hosted fluids.

The generation of hydrogen and reduced carbon compounds during serpentinization provides sustained energy for microorganisms on Earth, and possibly on other extraterrestrial bodies (e.g., Mars, icy satellites). However, the geochemical conditions that arise from water-rock reaction also challenge the known limits of microbial physiology, such as hyperalkaline pH, limited electron acceptors and inorganic carbon. Because cell membranes act as a primary barrier between a cell and its environment, lipids are a vital component in microbial acclimation to challenging physicochemical conditions. To probe the diversity of cell membrane lipids produced in serpentinizing settings and identify membrane adaptations to this environment, we conducted the first comprehensive intact polar lipid (IPL) biomarker survey of microbial communities inhabiting the subsurface at a terrestrial site of serpentinization. We used an expansive, custom environmental lipid database that expands the application of targeted and untargeted lipodomics in the study of microbial and biogeochemical processes. IPLs extracted from serpentinite-hosted fluid communities were comprised of >90% isoprenoidal and non-isoprenoidal diether glycolipids likely produced by archaeal methanogens and sulfate-reducing bacteria. Phospholipids only constituted ~1% of the intact polar lipidome. In addition to abundant diether glycolipids, betaine and trimethylated-ornithine aminolipids and glycosphingolipids were also detected, indicating pervasive membrane modifications in response to phosphate limitation. The carbon oxidation state of IPL backbones was positively correlated with the reduction potential of fluids, which may signify an energy conservation strategy for lipid synthesis. Together, these data suggest microorganisms inhabiting serpentinites possess a unique combination of membrane adaptations that allow for their survival in polyextreme environments. The persistence of IPLs in fluids beyond the presence of their source organisms, as indicated by 16S rRNA genes and transcripts, is promising for the detection of extinct life in serpentinizing settings through lipid biomarker signatures. These data contribute new insights into the complexity of lipid structures generated in actively serpentinizing environments and provide valuable context to aid in the reconstruction of past microbial activity from fossil lipid records of terrestrial serpentinites and the search for biosignatures elsewhere in our solar system.

Archaeal lipid diversity, alteration, and preservation at the Cathedral Hill deep sea hydrothermal vent, Guaymas Basin, Gulf of California, and its implications regarding the deep time preservation paradox

Archaea are among the earliest evolved organisms. Today, they exist in nearly every habitable environment and their highly recalcitrant membrane lipids are both abundant and easily detected in modern sediments. Yet, unlike bacteria and eukaryotes, the lipid biomarker signatures of archaea are almost entirely absent in the ancient rock record (>145 Ma). We present a comprehensive study of archaeal lipids from the Cathedral Hill hydrothermal vent complex in Guaymas Basin, Gulf of California. Here, porewaters reach 155 °C by 21 cm below the sea floor (cmbsf), which enables the near-complete tracking of sedimentary organic matter (SOM) accumulation, diagenetic alteration and thermochemical transformation into petroleum-like hydrocarbons within and beyond the habitable zone of life. Identified intact polar lipids (IPLs) of living archaea included mono- and di-glycosidic archaeols (1G-AR, 2G-AR) and glycerol dialkyl glycerol tetraethers (1G- and 2G-GDGTs). The 1G- and 2G-ARs, potentially derive from methane-oxidizing archaeal groups ANME-1 and ANME-2 and anaerobic thermophilic methanogens, reach sediment depths of ∼ 135 cm and 50 °C temperatures. The 1G-and 2G-GDGT lipids reach a depth of ~180 cm where vent fluid temperatures are ~145 ± 15 °C. Core lipids (CLs) include archaeols (AR) and isoprenoidal and branched GDGTs (iGDGTs, brGDGTs). The core GDGTs (cGDGTs) closest to the vent center have high rates of lipid loss. Up to 95% of all identified archaeal biomarkers, including lipids supplied from the upper water column, are degraded or recycled in the surface sediments and do not reach conditions of late diagenesis and catagenesis. Only ∼ 0.11%, proportional to the lipid bound component in the protokerogen, marks thermochemically cracked biphytane – a prominent archaeal hydrocarbon biomarker. This extreme reduction indicates archaeal lipids do not necessarily become incorporated into kerogen thereby helping to explain the deep time archaeal lipid preservation paradox.

Porewater geochemical and lipid biomarker signatures for anaerobic methane oxidation in the hydrate-bearing system from the Taixinan Basin, the South China Sea

Abstract Anaerobic oxidation of methane (AOM) is one of the most important biogeochemical processes associated with hydrate dissociation and carbon cycling. Though AOM has been extensively investigated, the variations of its microorganisms and lipid biomarkers are still not fully understood. In this study, the porewater geochemical and lipid biomarker evidence for AOM was systematically investigated in the hydrate-bearing system from the Taixinan Basin, the South China Sea, aiming to better expound the vertical variations of AOM-related biomarker signatures and causes of the weak lipid biomarker patterns. Accordingly, the sulfate-methane interface (SMI) depth of 1,000 cmbsf and onset of AOM were determined on the basis of the vertical profiles of porewater parameters. The occurrence of 13C-depleted 2,6,10,15,19-pentamethylicosane (PMI) with the δ13C ratios of −77.7‰ to −131.4‰ near the SMI are in accord with the porewater parameters, despite the absence of archaeol and sn2-hydroxyarchaeol and low abundances of PMI. Meanwhile, the strongly 13C-enriched iso-C15:0 and anteiso-C15:0 fatty acids suggest that non-methane hydrocarbons or oil derivatives are speculated as the probable carbon sources for sulfate-reducing bacteria due to the presence of unresolved complex mixtures (UCMs) and odd–even predominance (OEP) values (about 1.0). The weak in situ signal of AOM-related biomarkers may be attributed to the low-flux methane supply, and dilution effect from the high input of allochthonous and autochthonous organic matters. The great difference in biomarkers between the Taixinan Basin and previously reported sites should be further clarified on the basis of more extensive studies in various AOM-related settings.

Response of soil microbial communities to natural and managed vegetation restoration in a subtropical karst region

The soil microbial community is a key indicator to evaluate the effectiveness of vegetation restoration in degraded ecosystems. However, few studies have simultaneously compared the effects of managed and natural vegetation restoration strategies on the soil microbial community in the ecologically fragile karst region using signature lipid biomarker analysis to provide information on a variety of microbial properties. Here, phospholipid fatty acids (PLFAs) in the soil microbial community were measured following different restoration strategies in a karst region of southwest China. Managed vegetation restoration (including restoration with plantation forest, forage grass, and a combination of plantation forest and forage grass) and natural vegetation restoration (spontaneous regeneration to natural grassland) were compared, using cropland as a reference. The abundance of total PLFAs and the PLFAs of four microbial functional groups (bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi [AMF]) significantly increased in the topsoil (0–5 cm soil depth) following vegetation restoration. In the sub-topsoil layer (5–10 cm soil depth), the abundance of PLFAs was not significantly higher than that in the cropland, except in AMF in natural vegetation restoration. Principal component analysis indicated that the microbial PLFA composition differed between the restoration strategies, and the abundance of AMF PLFAs was significantly higher in natural than in managed vegetation restoration for both soil depths. The ratio of soil organic carbon to total nitrogen and dissolved organic carbon content were the primary factors affecting the abundance of soil microbial communities in the topsoil and sub-topsoil, respectively. In addition, soil pH served as another explanatory variable for the topsoil. Our findings suggest that vegetation restoration over a relatively short period (15 years) mainly improved topsoil fertility. Moreover, natural vegetation restoration may be superior to managed vegetation restoration for the maintenance of multiple ecosystem functions in the short term in the karst regions, owing to the potentially significant role of AMF.

Constraining the formation of authigenic carbonates in a seepage-affected cold-water coral mound by lipid biomarkers.

Cold-water coral (CWC) mounds are build-ups comprised of coral-dominated intervals alternating with a mixed carbonate-siliciclastic matrix. At some locations, CWC mounds are influenced by methane seepage, but the impact of methane on CWC mounds is poorly understood. To constrain the potential impact of methane on CWC mound growth, lipid biomarker investigations were combined with mineralogical and petrographic analyses to investigate the anaerobic oxidation of methane (AOM) and authigenic carbonate formation in sediment from a seep-affected CWC mound in the Gulf of Cadiz. The occurrence of AOM was confirmed by characteristic lipids found within a semi-lithified zone (SLZ) consisting of authigenic aragonite, high-magnesium calcite and calcium-excess dolomite. The formation of high-Mg calcite is attributed to AOM, acting as a lithifying agent. Aragonite is only a minor phase. Ca-excess dolomite in the SLZ and upper parts may be formed by organoclastic sulphate reduction, favouring precipitation by increased alkalinity. The AOM biomarkers in the SLZ include isoprenoid-based archaeal membrane lipids, such as abundant glycerol dibiphytanyl glycerol tetraethers (GDGTs) dominated by GDGT-2. The δ13 C values of GDGT-2, measured as ether-cleaved monocyclic biphytanes, are as low as -100‰ versus V-PDB. Further, bacterial dialkyl glycerol diethers with two anteiso-C15 alkyl chains and δ13 C values of -81‰ are interpreted as biomarkers of sulphate-reducing bacteria. The lipid biomarker signatures and mineralogical patterns suggest that anaerobic methane-oxidizing archaea of the ANME-1 group thrived in the subsurface at times of slow and diffusive methane seepage. Petrographic analyses revealed that the SLZ was exhumed at some point (e.g. signs of bioerosion of the semi-lithified sediment), providing a hard substrate for CWC larval settlement. In addition, this work reveals that AOM-induced semi-lithification likely played a role in mound stabilization. Lipid biomarker analysis proves to be a powerful tool to disentangle early diagenetic processes induced by microbial metabolisms.

Lipid biomarker signatures as tracers for harmful cyanobacterial blooms in the Baltic Sea.

The recent proliferation of harmful cyanobacterial blooms (cyanoHABs) in the Baltic and other marginal seas poses a severe threat for the health of infested ecosystems as e.g. the massive export and decay of cyanobacterial biomass facilitates the spread of bottom water hypoxia. There is evidence that cyanoHABs occurred repeatedly in the Baltic Sea but knowledge of their spatiotemporal distribution and the cyanobacteria that contributed to them is limited. In this study, we examined representatives of the major bloom-forming heterocystous cyanobacteria (i.e. Aphanizomenon, Dolichospermum (formerly Anabaena) and Nodularia) to establish lipid fingerprints that allow tracking these environmentally important diazotrophs in the modern and past Baltic Sea. The distribution of normal and mid-chain branched alkanes, fatty acid methyl esters, bacteriohopanepolyols and heterocyst glycolipids permitted a clear chemotaxonomic separation of the different heterocystous cyanobacteria but also indicated a close phylogenetic relationship between representatives of the genera Aphanizomenon and Dolichospermum. Compared to the discontinuous nature of phytoplankton surveys studies, the distinct lipid profiles reported here will allow obtaining detailed spatiotemporal information on the frequency and intensity of Baltic Sea cyanoHABs as well as their community composition using the time-integrated biomarker signatures recorded in surface and subsurface sediments. As heterocystous cyanobacteria of the genera Aphanizomenon, Dolichospermum and Nodularia are generally known to form massive blooms in many brackish as well as lacustrine systems worldwide, the chemotaxonomic markers introduced in this study may allow investigating cyanoHABs in a great variety of contemporary environments from polar to tropical latitudes.

Lipid biomarkers and their environmental significance in mine soils from Eastern Europe

ABSTRACTThe present study describes signature lipid biomarkers in reclaimed mine soils (RMSs), an unreclaimed spoil and a natural soil (Vertisol) for a major coal mine basin in Eastern Europe. Alkanes, fatty acids and fatty alcohols, as well as coal biomarkers were abundant in the mine soils and the unreclaimed spoil. The alkanes distribution in the RMSs was bimodal with maxima at C18 and C29/C31 and points at two origins for the alkanes, terrigenous plants, including soil borne and from the coal source. Fatty acid carbon preference indices (CPIeven/odd = 10.4 and 8.1 for the mine soils under pine and grass vegetation) reflect the increasing role of terrestrial vegetation in the formation of organic matter. The higher concentrations of the long-chain alkanes, fatty acids and alcohols are speculated as the reason for the severe and extreme water repellency observed with the Vertisol and the unreclaimed spoil. The presence of terrigenous steroid and triterpenoid markers in the RMSs is an indication of the ongoing soil formation processes. The analysis of lipid extracts allowed for the assessment of sensitive molecular indicators of biogenic terrigenous and coal origin and the degree of soil recovery following >20 years of spoils reclamation.

Allelochemical-mediated soil microbial community in long-term monospecific Chinese fir forest plantations

Productivity decline of monospecific forest plantations has remained a serious problem. Despite increasing knowledge of the problem involved in the build-up of soil-borne pathogens and allelopathy, relatively little is known about tree-derived allelochemicals and their impacts on the soil microbial community and root growth. Therefore, the objective of this study was to examine a novel allelochemical cyclic dipeptide in relation to the soil microbial community and phytotoxicity to tree roots in 25-year-old monospecific Chinese fir (Cunninghamia lanceolata) forest plantations. We sampled soils and fine roots in situ and quantified soil cyclic dipeptide, microbial and root characteristics along with their correlation analyses. When compared with soil from a plantation established following removal of natural forest vegetation, soil from a replanted plantation contained a greater amount of cyclic dipeptide. Furthermore, increased soil potentially pathogenic fungi and reduced root biomass, root surface area and root length density were observed in the replanted plantations. There were negative relationships among cyclic dipeptide concentration, microbial community composition and root biomass in given plantations. Phospholipid fatty acid profiling showed that the signature lipid biomarkers of soil bacteria and fungi, and soil microbial community structure were affected under cyclic dipeptide application. Soil degradation dynamics indicated that cyclic dipeptide declined rapidly. The results demonstrated that allelochemical cyclic dipeptide not only had direct phytotoxicity to tree roots but also indirectly altered soil microbial community compositions, suggesting that productivity decline of continuous Chinese fir monocultures may be a negative feedback interaction between allelochemical-mediated soil microbial community and root phytotoxicity.

Plasma lipid biomarker signatures in squamous carcinoma and adenocarcinoma lung cancer patients

There is a clinical need for reliable biomarkers for lung cancer that permit early diagnosis of the disease and provide prediction of histological phenotype. A prospective study design was used with a study population of patients with suspected lung cancer. Blood samples were collected from 17 patients with histologically confirmed squamous cell lung carcinoma, 17 individuals with adenocarcinoma, and 17 control individuals who did not subsequently have a diagnosis of lung cancer or any other cancer. Blood plasma samples were analysed for their lipid profiles using liquid chromatography coupled with high resolution mass spectrometry. Data were analysed using multivariate statistical methods. There was good separation between histological subtypes and control groups and also between individuals with a subsequent diagnosis of adenocarcinoma and squamous cell carcinoma (sensitivity 80 %, specificity 83 %, Q2 = 0.70). Alterations in the levels of different classes of lipids including triglycerides (TGs), phosphatidylinositols (PIs), phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), free fatty acids, lysophospholipids and sphingolipids were observed in squamous carcinoma and adenocarcinoma lung cancer patients when compared with control patients. In conclusion, this study has identified candidate lipid biomarkers of non-small cell lung cancer patients which may be helpful to indicate the tumour subtype and to differentiate them from patients who do not have lung cancer. Measuring these biomarkers has the potential to improve diagnosis in patients with suspected lung cancer and risk stratification in screening.

Microbial signature lipid biomarker analysis - an approach that is still preferred, even amid various method modifications.

The lipid composition of microbial communities can indicate their response to changes in the surrounding environment induced by anthropogenic practices, chemical contamination or climatic conditions. A considerable number of analytical techniques exist for the examination of microbial lipids. This article reviews a selection of methods available for environmental samples as applied for lipid extraction, fractionation, derivatization and quantification. The discussion focuses on the origin of the standard methods, the different modified versions developed for investigation of microbial lipids, as well as the advantages and limitations of each. Current modifications to standard methods show a number of improvements for each of the different steps associated with analysis. The advantages and disadvantages of lipid analysis compared to other popular techniques are clarified. Accordingly, the preferential utilization of signature lipid biomarker analysis in current research is considered. It is clear from recent literature that this technique stays relevant - mainly for the variety of microbial properties that can be determined in a single analysis.

Seeking a Unique Lipid Signature Predicting Cardiovascular Disease Risk

There is now overwhelming evidence that alterations in lipid metabolism underlie the pathogenesis of atherosclerotic cardiovascular disease (CVD). However, research in this area has focused primarily on abundant plasma lipids such as cholesterol, triglycerides, and oxidized phospholipids that are largely carried on circulating lipoproteins.1,2 Circulating levels of abundant lipids can provide valuable information for CVD risk stratification, yet the majority of CVD risk cannot be explained by traditional lipid risk factors.3 Over the last decade, there have been rapid advances in mass spectrometry–based methods to comprehensively annotate the entire “lipidome,” which includes a large variety of lipid molecular species such as non–lipoprotein-associated lipids and less abundant signaling lipids that affect disease. This new field of lipidomics provides a powerful platform for the identification of potential lipid biomarker signatures predicting disease risk but also provides clues into novel lipid metabolic pathways that may be directly involved in the pathogenesis of disease. At an amazingly rapid pace (Figure 1), lipidomic approaches have yielded valuable information linking specific lipid types with structural and signaling roles in the development of cancer,4 obesity,5 diabetes mellitus,6 hypertension,7 Alzheimer disease,8 infectious diseases,9 and CVD.10 Undoubtedly, lipidomic approaches provide a powerful discovery platform that has promise both to identify new biomarkers of chronic disease and to provide clues into unrecognized lipid metabolic pathways with potential mechanistic links to disease pathogenesis and untapped therapeutic potential. Figure 1. The growth of lipidomic technology over the last decade. The histogram represents the number of publications using lipidomics as a discovery platform. The numbers were obtained by using “lipidomics” as a search term in the PubMed database. Article see p 1821 In this issue of Circulation , Stegemann and colleagues11 apply a targeted lipidomic approach to population-based cohorts with documented CVD events. …

Lipid and DNA Evidence of Dominance of Planktonic Archaea Preserved in Sediments of the South China Sea: Insight for Application of the TEX86 Proxy in an Unstable Marine Sediment Environment

The marine planktonic archaea are dominated by Thaumarchaeotal Marine Group I, which is characterized by the lipid biomarker thaumarchaeol. The marine benthic archaea are characterized by greater diversity of currently unknown species whose lipid biomarker signatures are uncertain. In this study, a sediment core from the northwestern part of the South China Sea (SCS) (water depth 1474 m) was analyzed using molecular DNA and lipid biomarker approaches. While 16S rRNA gene analysis showed changing archaeal community structures with sediment depth, this change had little impact on the fossil record of archaeal lipids that are characteristic of the planktonic community. As a result, the fossil archaeal lipids recorded paleo sea surface temperature of the SCS since the last glacial maxima by the TEX86 proxy, which agreed generally with the winter temperature recorded by planktonic foraminiferas collected from the same area of the SCS that hosted mass-transported deposits. This suggests that this deep water deposit may have partially preserved paleoclimate record reflecting seasonal temperature variation in a near shore setting, which is in contrast to annual sea surface temperature or sub sea surface temperature variation recorded by TEX86 in the open ocean.

Temporal variation of soil friedelin and microbial community under different land uses in a long-term agroecosystem

Despite increasing knowledge of soil microbial community dynamics involved in various factors, relatively little is known about plant-derived allelochemicals and their impact on the development of soil microbial community either independently or synergistically with the other factors. Here we examined an allelochemical friedelin and its relation to microbial community in soils from a long-term agroecosystem under different land uses and seasons. Four land uses (paddy field, maize field, barren and fallow) in an eight-year old continuous establishment were selected to conduct the experiments. Soil samples were taken in spring, summer, autumn and winter at different depths. Friedelin was quantified by gas chromatography (GC) and microbial communities were characterized by phospholipid fatty acid (PLFA) analysis. Subsequently, friedelin was found in all soils but its concentration varied with land uses, seasons and soil depths. The largest observed concentrations always occurred in surface soils and winter samples of all four land uses. Compared with tillage fields, barren and fallow contained a greater amount of friedelin. Both soil microbial community and friedelin varied seasonally, and there were positive relationships between friedelin and microbial community. The signature lipid biomarkers of soil bacteria and fungi, and soil microbial community structure were affected under friedelin application. The results suggest that friedelin may be one of the factors involved in microbial community dynamics under different land-use scenarios and seasonal variations, and friedelin-specific influences in the corresponding microbial community composition result in changes in the microbial community structure in soils from a given agroecosystem.

Pendant bioconstructions cemented by microbial carbonate in submerged marine caves (Holocene, SE Sicily)

Unusual pendant bioconstructions occur within two submerged caves in the Plemmirio Marine Protected Area, south of Syracuse (SE Sicily). These cm- to dm-sized bioconstructions project downward from the cave roofs. The main framework builders are serpulids belonging to the genera Protula, Semivermilia and Josephella. Encrusting bryozoans, corals, hydrozoans and sponges are subordinately present, whereas bivalves and brachiopods are overall rare. These faunal associations are characteristic of the studied caves, but only in some places they form small bioconstructions that are cemented by microbial carbonates made up by autochthonous, peloidal to clotted peloidal and aphanitic micrite. The autochthonous micrite stabilizes the pendant bioconstructions, herein referred to as biostalactites. The microbial carbonate reveals high contents of bacterial lipid biomarkers. Among the most abundant compounds are mono-O-alkyl glycerol ethers (MAGEs) and branched fatty acids (10-Me-C16:0; iso- and anteiso-C15:0 and -C17:0), interpreted as biomarkers of sulfate-reducing bacteria. Other compounds preserved in the autochthonous carbonates include lipids derived from marine zoo- and phytoplankton (brassicasterol, dinosterol and monounsaturated short-chain fatty acids), unspecified marine bacteria (saturated and monounsaturated short-chain fatty acids) and land plants (long-chain fatty acids, long-chain alcohols, stigmasterol, sitosterol and campesterol). The observed lipid biomarker signatures are remarkably similar to those of post-glacial reefal microbialites, where microbialite formation in cavities of the coral framework was also mediated by sulfate-reducing bacteria. In the submerged caves of Plemmirio Marine Protected Area, serpulid colonies apparently occur preferentially where freshwater is seeping through crevices in the limestone. The consequent nutrification is believed to favor serpulid aggregation and the growth of other skeletal (i.e., bryozoans and corals) and soft-bodied organisms (i.e., sponges and ascidiae). The resultant accumulation of biomass and its taphonomy provide niches for sulfate-reducing bacteria, which induce carbonate precipitation cementing and stabilizing the biostalactites. The finding of pendant, cemented bioconstructions in the Mazzere and Granchi caves of the Plemmirio Marine Protected Area reveals that sulfate-reducing bacteria are involved in microbialite formation in various cryptic environments. The formation of such peloidal to clotted peloidal microcrystalline carbonates in cryptic ecosystems is a significant factor for the stabilization of different kinds of bioconstructions, spanning from small biostalactites to large reefs.

Crabgrass (Digitaria sanguinalis) Allelochemicals That Interfere with Crop Growth and the Soil Microbial Community

Three chemicals, veratric acid, maltol, and (−)-loliolide, were isolated from crabgrass and their structures were identified by spectroscopic analysis. The chemicals were detected in crabgrass root exudates and rhizosphere soils, and their concentrations ranged from 0.16 to 8.10 μg/g. At an approximate concentration determined in crabgrass root exudates, all chemicals significantly inhibited the growth of wheat, maize, and soybean and reduced soil microbial biomass carbon. Phospholipid fatty acid profiling showed that veratric acid, maltol, and (−)-loliolide affected the signature lipid biomarkers of soil bacteria, actinobacteria, and fungi, resulting in changes in soil microbial community structures. There were significant relationships between crop growth and soil microbes under the chemicals' application. Chemical-specific changes in the soil microbial community generated negative feedback on crop growth. The results suggest that veratric acid, maltol, and (−)-loliolide released from crabgrass may act as allelochemicals interfering with crop growth and the soil microbial community.

Thaumarchaeotal Signature Gene Distribution in Sediments of the Northern South China Sea: an Indicator of the Metabolic Intersection of the Marine Carbon, Nitrogen, and Phosphorus Cycles?

Thaumarchaeota are abundant and active in marine waters, where they contribute to aerobic ammonia oxidation and light-independent carbon fixation. The ecological function of thaumarchaeota in marine sediments, however, has rarely been investigated, even though marine sediments constitute the majority of the Earth's surface. Thaumarchaeota in the upper layer of sediments may contribute significantly to the reservoir of nitrogen oxides in ocean waters and thus to productivity, including the assimilation of carbon. We tested this hypothesis in the northern South China Sea (nSCS), a section of a large oligotrophic marginal sea with limited influx of nutrients, including nitrogen, by investigating the diversity, abundance, community structure, and spatial distribution of thaumarchaeotal signatures in surface sediments. Quantitative real-time PCR using primers designed to detect 16S rRNA and amoA genes in sediment community DNA revealed a significantly higher abundance of pertinent thaumarchaeotal than betaproteobacterial genes. This finding correlates with high levels of hcd genes, a signature of thaumarchaeotal autotrophic carbon fixation. Thaumarchaeol, a signature lipid biomarker for thaumarchaeota, constituted the majority of archaeal lipids in marine sediments. Sediment temperature and organic P and silt contents were identified as key environmental factors shaping the community structure and distribution of the monitored thaumarchaeotal amoA genes. When the pore water PO4(3-) concentration was controlled for via partial-correlation analysis, thaumarchaeotal amoA gene abundance significantly correlated with the sediment pore water NO2(-) concentration, suggesting that the amoA-bearing thaumarchaeota contribute to nitrite production. Statistical analyses also suggest that thaumarchaeotal metabolism could serve as a pivotal intersection of the carbon, nitrogen, and phosphorus cycles in marine sediments.

Reproduction allocation and potential mechanism of individual allelopathic rice plants in the presence of competing barnyardgrass

In spite of increasing knowledge of allelopathic rice as an efficient component involved in paddy weed management, relatively little is known about its reproduction in response to competing weeds. Reproduction allocation of individual allelopathic rice plants in relation to monoculture and mixed culture with competing barnyardgrass in a paddy field was studied, along with analyses of soil nutrients and microbial communities to understand the potential mechanism. At a 1:1 barnyardgrass and rice mixture proportion identified from a replacement series study, biomass, grain yield and major parameters of individual allelopathic rice plants at the mature stage were increased by competing barnyardgrass. There was no difference in allelopathic rice root-zone soil ammonium N and Olsen P between monoculture and mixed culture. However, mixed culture altered soil microbial biomass C and communities. When mixed with barnyardgrass, allelopathic rice root zone had an 87% increase in soil microbial biomass C. Phospholipid fatty acid (PLFA) profiling indicated that the signature lipid biomarkers of bacteria, actinobacteria and fungi were affected by mixed culture. Principal component analysis clearly identified differences in the composition of PLFA in different soil samples. Allelopathic rice specific changes in soil microbial communities may generate a positive feedback on its own growth and reproduction in the presence of competing barnyardgrass in a given paddy system.

Lipid biomarker signatures in a hypersaline lake on Isabel Island (Eastern Pacific) as a proxy for past rainfall anomaly (1942–2006 AD)

Isabel Lake is a hypersaline crater-lake on Isabel Island, Mexico, situated in the eastern tropical Pacific, an area highly sensitive to hydrological changes. Today, annual rainfall mostly occurs during the wet season, from June to October, when the northern edge of the Intertropical Convergence Zone (ITCZ) extends over the island. In order to evaluate the potential of sedimentary lipid biomarker signatures as a proxy of past hydroclimatic variability we have performed a calibration analysis comparing changes in biomarker distribution in the upper 16cm of the sediment core with a regional instrumental data set. Annual laminations present in the sediment sequence allow for precise chronological control (1942–2006). More than 80 different lipid compounds were identified in the sediment and could be assigned to three major groups of source organisms: (1) algal populations; (2) a mixed community of ciliates, bacteria and cyanobacteria; and (3) photosynthetic sulfur bacteria. We found that the observed changes in the relative contribution of the different lipid biomarkers to the sediment record were determined by the regional rainfall variability over the last 65years. The planktonic community of Isabel Lake was highly sensitive to salinity fluctuations related to rainfall variability; seasonal precipitation results in freshwater input into the lake, driving an annual algal bloom and a relative decrease in the abundance of the more halotolerant populations of (cyano)bacteria and ciliates. Consequently, the concentration ratio between the two most abundant biomarkers in the Isabel Lake sediments, n-alkyl diols and tetrahymanol (which we define as the DiTe index), representing algal and ciliate planktonic populations, respectively, was significantly correlated with the seasonal rainfall anomaly (r=0.68, p<0.01). We propose that the DiTe index is a proxy of changes in the aquatic ecosystem of Isabel Lake and, by extension, regional hydrological changes in a sensitive climatic area of the eastern tropical Pacific.

Rhizosphere isoflavones (daidzein and genistein) levels and their relation to the microbial community structure of mono-cropped soybean soil in field and controlled conditions

Despite an increase in the understanding of the soybean isoflavones involved in root-colonizing symbioses, relatively little is known about their levels in the rhizosphere and their interactions with the soil microbial community. Based on a 13-year experiment of continuous soybean monocultures, in the present study we quantified isoflavones in the soybean rhizosphere and analyzed the soil microbial community structure by examining its phospholipid fatty acid (PLFA) profile. Two isoflavones, daidzein (7, 4′-dihydroxyisoflavone) and genistein (5,7,4′- trihydroxyisoflavone), were detected in the rhizosphere soil of soybean plants, with the concentrations in the field varying with duration of mono-cropping. Genistein concentrations ranged from 0.4 to 1.2 μg g −1 dry soil over different years, while daidzein concentrations rarely exceeded 0.6 μg g −1 dry soil. PLFA profiling showed that the signature lipid biomarkers of bacteria and fungi varied throughout the years of the study, particularly in mono-cropping year 2, and mono-cropping years 6–8. Principal component analysis clearly identified differences in the composition of PLFA during different years under mono-cropping. There was a positive correlation between the daidzein concentrations and soil fungi, whereas the genistein concentration showed a correlation with the total PLFA, fungi, bacteria, Gram (+) bacteria and aerobic bacteria in the soil microbial community. Both isoflavones were easily degraded in soil, resulting in short half-lives. Concentrations as small as 1 μg g −1 dry soil were sufficient to elicit changes in microbial community structure. A discriminant analysis of PLFA patterns showed that changes in microbial community structures were induced by both the addition of daidzein or genistein and incubation time. We conclude that daidzein and genistein released into the soybean rhizosphere may act as allelochemicals in the interactions between root and soil microbial community in a long-term mono-cropped soybean field.

Matrix protected organic matter in a river dominated margin: A possible mechanism to sequester terrestrial organic matter?

The provenance of organic matter in surface sediments from the northern Gulf of Mexico was investigated by analyzing the compositions of lipid biomarkers ( n-alkanes, fatty acids, sterols) liberated after a series of chemical treatments designed to remove different organo-mineral matrix associations (i.e. freely extractable, base-hydrolyzable, unhydrolyzable). Bulk analyses of the organic matter (carbon content, carbon:nitrogen ratios, stable and radiocarbon isotopic analyses) were also performed on the intact sediments and their non-hydrolyzable, demineralized residue. We found recognizable lipids from distinct sources, including terrestrial vascular plants, bacteria and marine algae and zooplankton, within each of the isolated fractions. Based on the lipid signatures and bulk compositions, the organic matter within the unhydrolyzable fractions appeared to be the most diagenetically altered, was the oldest in age, and had the highest abundance of terrigenous lipids. In contrast, the base-hydrolyzable fraction was the most diagentically unaltered, had the youngest ages and was most enriched in N and marine lipids. Our results indicate that fresh, autochthonous organic matter is the most important contributor to base-hydrolyzable lipids, whereas highly altered allochthonous sources appear to be predominant source of unhydrolyzable lipids in the surface sediments from the Atchafalaya River shelf. Overall, the lipid biomarker signatures of intact sediments were biased towards the autochthonous source because many of the organic compounds indicative of degraded, terrigenous sources were protected from extraction and saponification by organo-mineral matrices. It is only after these protective matrices were removed by treatment with HCl and HF that these compounds became evident.